Activity Report LNLS 2008

Editor Angelo Malachias

Production cubo multimidia

Management Adriana Lima

Proofreaders Beatrice Allain

The editors express their gratitude to the LNLS users and staff for their contributions, advice and patience Disclaimer This document was prepared as an account of work done

by LNLS users and staff. Whilst the document is believed to contain correct information, neither LNLS nor any of its employees make any warranty, expresses, implies or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed within. As well, the use of this material does not infringe any privately owned copyrights.

2008 LNLS Brazilian Synchrotron Light Laboratory Director General José A. Brum 2009 LNLS Brazilian Synchrotron Light Laboratory Director Antonio José Roque da Silva

CeBiME

Center for Structural Molecular Biology Director Kleber Gomes Franchini CTBE Bioethanol Science and Technology Center Director Marco Aurélio Pinheiro Lima ABTLuS Brazilian Association for Synchrotron Light Technology Director General Michal Gartenkraut The Brazilian Association for Synchrotron Light Technology (ABTLuS) is a non-profit organization created to operate the Brazilian Synchrotron Light Laboratory for the Brazilian Ministry of Science and Technology and the National Council for Scientific and Technological Development (CNPq).

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Activity Report/Brazilian Synchrotron Light Laboratory (1998/99) - Campinas - SP: Brazilian Association for Synchrotron Light Technology, 1999.

Annual ISSN 1518-0204 1. Synchrotron light. I. National Synchrotron Light Laboratory

Activity Report 2008

MinistĂŠrio da CiĂŞncia e Tecnologia

Brazilian Synchrotron Light Laboratory

Operated by ABTLuS for the Ministry of Science and Technology | CNPq

06 Introduction 09 Science Highlights 87 Facility Report 135 Scientific Reports in the CD-Rom

Welcome The year 2008 marks the beginning of the work for the

laboratories. ABTLuS was one of the first institutions

construction of a new synchrotron light source in Brazil,

in Brazil to carry a program dedicated to nanoscience

initially known as LNLS-2. Since LNLS inauguration in

and nanotechnology, in place since 1999 and focused on

1997, it was clear that, with the development of the scientific

producing high level fundamental research as well to

work associated with new organic and inorganic materials,

develop a strong interaction with the industrial sector. The

it would be necessary to offer the community, in the future,

increasing importance of this branch of research led to the

a state-of-art third generation storage ring and associate

creation of Cesar Lattes Nanoscience and Nanotechnology

beamlines. The necessity to start to move in the direction

Center – C2Nano, inaugurated in March 2008, by the president

of planning the new synchrotron light source was clearly

Luiz Inácio Lula da Silva in the presence of the Minister of

stated in ABTLuS four years planning 2006-2009 and it was

Science and Technology, Sergio Machado Rezende. A special

permanently emphasized by LNLS Scientific Committee in

chapter in this report will detail the aims of this new Center

its several reports. Despite the permanent struggle against

as well as the specifics of the new building.

the shortage of personal and fundings, the laboratory

With all these new and exciting novelties, the laboratory

started an effort to develop the first ideas and concepts for

continued its work along the year 2008, producing high quality

the new machine and the scientific case which would lead

science and continuously improving its installations. This

these efforts. A preliminary report for the construction of

Report gathers the ensemble of the works produced in the

LNLS-2, was delivered to the president of Brazil, Luis Inacio

facilities in 2008 and highlights some of its scientific results

Lula da Silva in March 2008, with a request of R$ 15 million

where it is possible to witness the high quality achieved as

for the preparation of the Conceptual Design Report – CDR

well the broad range of scientific areas investigated. An

for the new machine. By the end of the year, the Ministry of

important development in the research activities is the

Science and Technology agreed in funding the CDR and sent

increase participation of industry laboratories in the use of

the first R$ 2 million to initiate the work. This new phase in

LNLS installations. This effort started with a new concept

the life of the laboratory opens a bright new perspective for

of interaction with the industry, defined in 2001, which

the scientific community and culminates the eleven years of

surpassed its initial goal achieving near 10% of the total

operation of the laboratory when it reached its main goals:

activities developed in the campus. To accomplish all these

to become a truly national facility and a scientific laboratory

scientific and technological goals, it is necessary to carry a

on its own.

permanent effort in renewing and increasing the laboratory

In June, ABTLuS hired a new Associate Director, to act

installations. Here, we report an overview of the main

as a Scientific Director and, later on, also responsible for

developments and up-grades in the laboratory scientific

the Cesar Lattes Nanoscience and Nanotechnology Center,

instrumentation.

prof. Caio Lewenkopf. This position had been vacant for

The year 2008 also presented another novelty which would

many years. With more than one thousand users per year

finally lead to a turning point in the life of the Brazilian

from all parts of Brazil and abroad, particularly from Latin

Synchrotron Light Laboratory – LNLS as well as the social

America, it was urgent to have a scientific leadership in the

organization, the Brazilian Association for Synchrotron

campus to strengthen the ultimate goal of the laboratory, to

Light Technology – ABTLuS, responsible for its operation.

produce science and technology at the highest international

In December 2007, for occasion of the Administration Board

level and to lead the efforts in building the scientific case

last meeting of the year, following a request by the Ministry

for the new machine.

of Science and Technology, ABTLuS agreed to incubate the

Another milestone of the year was the completion of the

Bioethanol Science and Technology Center – CTBE. For

new building to host the nanoscience and nanotechnology

its characteristics as an incubation, it was decided that the

6

| Activity Report 2008

Center development would remain under direct supervision

LNLS achievements during this period. In particular, I

of the Administration Board.

would like to thank Dr. Pedro Tavares, who as ABTLuS

By the end of the year, the Ministry of Science and

Associate Director during almost all this period, shared

Technology and ABTLuS Administration Board decided that

with me the permanent struggle to continuously develop

the best way to proceed with the installation of CTBE would

the laboratory aiming to reach the highest goals established

be to aggregate it to the complex of laboratories managed

by the scientific needs of the country. In the last months,

by ABTLuS, until then identified by LNLS. In November

these efforts had the inspiring contribution of the Associate

2008, ABTLuS Administration Board issued new regulations

Director Dr. Caio Lewenkopf. Together with the Associate

that give a new structure for the laboratories and initiated

Directors who leave ABTLuS with me, I wish to welcome the

the process for appointing an entire new direction for the

new ABTLuS Director General and the new coming Directors

Association.

of Associate Centers, in their double task: to put in place a

Along the almost eight years acting as ABTLuS Director-

new operational structure for the laboratories and research

General, I had the honor to work with a great team of

centers and to develop the new exciting perspectives for

scientists, engineers, technicians, and administration staff

the laboratory, symbolized by the construction of the new

who were ultimately the ones responsible for the numerous

synchrotron light source.

JosĂŠ A. Brum* Director General ABTLuS *ABTLuS Director-General from July 2001 to May 2009; invited to address the Wellcome for LNLS Activity Report 2009.

Activity Report 2008 |

7

10 Vapor-solid-solid growth mechanism driven by an epitaxial match between solid AuZn alloy catalyst particle and ZnO nanowire at low temperature 22 A dynamic polyphasic model for the ferritin iron core 26 X-ray structural low-resolution features and functional insights to human Ki-1/57: an intrinsically unstructured protein that localizes to nuclear bodies related with RNA metabolism 28 Carbon nanotubes as R-bars of high aspect ratio composite nanotools 30 Evolution of Ge-Si:Si(001) open and closed nanocrystalline systems towards equilibrium 36 Insights into the mechanism of progressive RNA degradation by the archaeal exosome 44 Effect of alkaline treatment on the ultrastructure of starch granules 48 Magnetic resonant X-ray diffraction applied to the study of EuTe films and EuTe/PbTe multilayers 54 Evolution of the spectral weight in the Mott-Hubbard series SrVO3–CaVO3–LaVO3–YVO3 62 First crystal structure and catalytic mechanism of a bacterial glucuronosyltransferase 68 Coherent X-ray beam with a compact X-ray pathway 74 Calculation of the mixed iron valence (Fe+3/Fe+2) ratio in hexacyanoferrates (Prussian blue materials) using synchrotron X-ray powder diffraction 80 Structural properties of novel Ce-Zr mixed oxide nanotubes

1

Vapor-solid-solid growth mechanism driven by an epitaxial match between solid AuZn alloy catalyst particle and ZnO nanowire at low temperature Leonardo C. Campos1, Matteo Tonezzer1, Andre S. Ferlauto1, Vincenzo Grillo2, Rogério Magalhães-Paniago1, Sergio Oliveira1, Luiz O. Ladeira1 and Rodrigo G. Lacerda1

Departamento de Física, Laboratório de Nanomateriais, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil 2 TASC-INFM-CNR National Laboratory, Area Science Park – BasoVizza, Building MM, Trieste, Italy 1

Nowadays, the growth of nanomaterials, like nanowires and nanotubes, is one of the key research areas of nanotechnology. However, a full picture of the growth mechanism of these quasi-one dimensional systems still needs to be achieved if these materials are to be applied electronics, biology and medicinal fields. Nevertheless, in spite of considerable advances on the growth of numerous nanowires, a clear understanding of the growth mechanism is still controversial and highly discussed. The present work provides a comprehensive picture of the precise mechanism of ZnO vapor-solid-solid (VSS) nanowire growth at low temperatures and gives the fundamental reasons responsible. We demonstrate by using a combination of synchrotron XRD and high resolution TEM that the growth dynamics at low temperatures is not governed by the well-known vapor-liquid solid (VLS) mechanisms. A critical new insight on the driving factor of VSS growth is proposed in which the VSS process occurs by a solid diffusion mechanism that is driven by a preferential oxidation process of the Zn inside the alloy catalyst induced by an epitaxial match between the ZnO(10-10) plane and the γ-AuZn(222) plane.

We believe that these results are not only important for the understanding of ZnO nanowire growth but could also have significant impact on the understanding of growth mechanisms of other nanowire systems.

Facility: LME, XRD1 Publication: Advanced Materials, 20: 1499-1504 (2008) Funding: Fapemig, Instituto do Milenio/CNPq-MCT

Science Highlights

The controlled synthesis of quasi one-

Zn foil, or using a ZnO film as a nucleation center

dimensional materials such as nanowires and

for the Zn atoms. These methods are usually

nanotubes is one of the key research areas of

described as governed by the vapor-solid (VS)

nanotechnology. If these materials are to be useful

deposition process. Furthermore, ZnO nanowires

in electronics, biology and medical applications,

have also been grown by vapor deposition

full control of their structure and properties is

methods using metal nanoparticles (usually

needed through precise control of their growth

gold) as catalysts at high and low temperatures.

processes

. To achieve this, a full picture of

The VLS model has been used to explain the

the growth kinetics is fundamental, especially

growth mechanism at high temperatures, but

for nanomaterials grown via catalyst-assisted

a clear understanding of the growth process at

methods. Nevertheless, despite the considerable

low temperatures is still lacking. The growth

advances in the control of numerous nanowires,

regime of ZnO nanowires is more difficult to

1,2,3

a clear understanding of the growth mechanism is still controversial and highly discussed4. In the 1970s, Wagner proposed a model to explain

interpret in those cases due to the complexity of the Au-Zn phase diagram compared to that

the growth of catalyst-assisted silicon whiskers based on a vapor-liquid-solid (VLS) mechanism5.

This mechanism implies a growth temperature above the eutectic point of the seed catalyst particle and the nanowire material. The VLS model is acceptable for classical systems such as silicon (Si) and germanium (Ge) nanowires deposited at temperatures above the eutectic point6,7. Recently, the generality of the VLS model has been questioned for the growth of hybrid III-V and II-VI nanowires (GaAs, InP) and also for Ge and Si nanowires in certain growth conditions. For these cases, the growth mechanism based on a vapor-solid-solid (VSS)

1 Mm

regime has been proposed. In this context, another important nanowire system whose growth mechanism is yet to be fully understood is ZnO. Zinc oxide (ZnO) has been shown to be quite a complex and interesting material, with a variety of different structures such as nanowires, nanobelts, and tetrapods. Each of

10 nm

these structures can be formed by different growth mechanisms in a wide range of different thermodynamic conditions2,3,8,9. For instance, ZnO nanostructures have been grown directly (without catalyst) from a solid source, such as a

Figure 1

1 Mm

(a) SEM and (b) TEM images of the materials formed at T = 350 °C. a) High density of nanowires with diameters ranging from 20 to 100 nm (scale bar: 1 ¾m). b) The catalyst particle has an irregular shape, indicating that it was not liquid during the growth process (scale bar: 10 nm). c) Polycrystalline ZnO film formed without the use of a gold thin film (scale bar: 1 ¾m) Activity Report 2008 |

11

Vapor-solid-solid growth mechanism driven by an epitaxial match between solid AuZn alloy catalyst particle...

of the Au-Si or the Au-Ge phase diagrams,

the Zn source was obtained by the well known

where there is only a small temperature range

carbothermal reaction with a mixture of ZnO

in which the VLS mechanism is possible.

(99.99%) and graphite (99%) powders (1:1 weight

Additionally, intricate aspects of the growth

ratio) and the substrates were Si (100) wafers

mechanism such as the nature of the catalyst

covered with a thick (1 µm) oxide layer, and

particles during growth (solid or liquid) and,

a thin (~ 4 nm) Au layer. Scanning (SEM) and

also important, the role of oxygen (including

transmission electron microscopy (TEM) and

the oxidation process itself) necessary for ZnO

x-ray diffraction analysis (XRD) were used to

nanowire formation, remain unresolved.

characterize the morphological and structural

The present paper provides a comprehensive

properties of the nanowires and the catalyst

picture of the precise mechanism of ZnO

particles. The TEM was a JEOL 2010 equipped

vapor-solid-solid (VSS) nanowire growth at

with a FEG emitter working at 200KeV and a

low temperatures and gives the fundamental

Cs = 0.5 mm. The XRD was performed at the

reasons responsible for this mechanism10. Using

Brazilian National Synchrotron Laboratory,

a combination of synchrotron x-ray diffraction

using photons with λ = 0.15426 nm. Figure 1

and high resolution transmission electron

shows typical (a) SEM and (a) TEM results of

microscopy, we demonstrate that the growth

the material obtained at T = 350 ºC. Figure 1(a)

dynamics at low temperatures is not governed

shows a high density of nanowires with mean

by the well-known VLS mechanisms . Based

diameters of about 20 nm. Structures with similar

on the Au-Zn phase diagram, temperature

morphologies were formed at temperatures as

measurement and temperature size effects, we

low as 300 °C, whereas polycrystalline ZnO

show that growth occurs via VSS. The precise

films were formed at T > 450 °C. In order to

composition of the Au-Zn catalyst nanoparticle

determine the role of the gold catalyst in the

has been determined to be γ-AuZn. Furthermore,

formation of the ZnO nanowires, we performed

we experimentally observe that there is an

deposition runs using Si/SiO2 substrates

indication of an epitaxial relationship between

without the Au layer. In this case, instead of

the ZnO nanowires and the γ-AuZn seed particle.

ZnO nanowires, a polycrystalline ZnO film

A critical new insight on the driving factor of

was observed (Figure 1c). A typical catalytic

VSS growth is proposed, in which the VSS

particle is clearly visible in the TEM image of

process occurs by a solid diffusion mechanism

Figure 1b. Interestingly, the particle presented an

driven by a preferential oxidation process of the

irregular shape rather than the spherical shape

Zn inside the alloy catalyst, which is induced

commonly observed in catalytically-assisted

by an epitaxial match between the ZnO (10-10)

nanowire growth via VLS.

2,3

12

| Activity Report 2008

plane and the γ-AuZn(222) plane. We believe

A synchrotron X-ray diffraction analysis was

that these results are not only important for

performed to verify the crystalline structure

the understanding of ZnO nanowire growth

of the ZnO nanowires and to investigate the

but could also have a significant impact on the

nature of the catalyst particle at their tips.

understanding of growth mechanisms of other

Figure 2 shows a typical XRD pattern of a

nanowire systems.

sample grown at T = 350 °C. The majority of

ZnO nanowires were synthesized by well-

the peaks correspond to the ZnO structure,

known vapor deposition methods2,3. Specifically,

and their relative intensities are consistent

Science Highlights

with a reference powder diffraction pattern,

the lattice fringes of both the ZnO nanowire and

which indicates that there is no preferential

the Au-Zn particle. Thus, no conclusion could

alignment of the ZnO wires. There is also a

be drawn from these measurements. Figure 3

broad peak (2θ = 47.8°) which originates from

offers an example of the direct correlation that

the Si substrate (100). There is a clear peak at

was found. Selected regions of the HRTEM

2θ = 41.3° (corresponding to an interplanar

image in Figure 3a were Fourier-transformed

spacing of 0.217 nm) that cannot be assigned to

and the results are shown in Figure 3b and c.

ZnO or to Si. This peak must therefore originate

The features observed in the FFT image of the

from the catalyst particles. However, it does

nanowire region (Figure 3b) can be clearly

not match any of the possible reflections of the

assigned to ZnO, corresponding to the (10-10)

Au face-centered cubic structure, nor of the Zn

planes (dmeas = 0.28 nm, d10-10 = 0.281 nm),

hexagonal close-packed structure. To identify

and to the (0001) planes (dmeas = 0.52 nm,

the origin of this peak, the diffraction patterns

d0001 = 0.521 nm). The latter plane corresponds

of several Au-Zn alloys were analyzed. The

to the growth direction, which is often observed

inset in Figure 2 shows an enlarged view of

in ZnO nanowires. Likewise, the features

the unknown catalyst peak, which indicates

observed in the FFT of the catalytic particle

that the peak is formed by two overlapping

(Figure 3c) can be assigned to the (222) planes

contributions: a major one centered at ~41.5°

(dmeas = 0.27 nm, d2,2,2 = 0.266 nm) of the γ-AuZn

that can be attributed to the (330) and (411)

phase. Most importantly, it is clear from

reflections of the cubic gamma brass structure,

the comparison of the FFT images that the

γ-AuZn (lattice parameter, a = 0.922 nm), and a

ZnO (10-10) planes have the same direction

smaller shoulder at ~40.8° that can be attributed to the (110) reflection of the base-centered cubic beta structure, β’-AuZn (a = 0.314 nm). Both

G

B’

reflections are associated with the strongest

AuZn

patterns.

The structural identification of the catalyst particles was confirmed using high resolution TEM analysis of several particles found at

Intensity (a.u.)

lines in the corresponding powder diffraction 39

40

41

42

43

44

the nanowire tips. Although there are several possible assignments for some of the periodicities found in the images, all the measured values of interplanar spacing can be attributed to the γ-AuZn phase.

30

ZnO nanowire and the Au-Zn particle. The other two nanowires did not simultaneously show

60

ZnO

to high resolution TEM analyses. Three of a correlation between the lattice fringes of the

50

70

80

90

2Q (degrees)

Five different ZnO nanowires were subjected these five nanowires simultaneously showed

40

Figure 2

Si (subst.)

XRD pattern of the ZnO nanowire samples grown at T = 350 °C. All the observed peaks correspond to either ZnO (*) or Si (o), except the peak at 2θ = 41.3° (shown in detail in the inset).

This peak can be attributed to the (330) planes of the γ-brass Au-Zn alloy Activity ActivityReport Report 2009 2008 |

13

Vapor-solid-solid growth mechanism driven by an epitaxial match between solid AuZn alloy catalyst particle...

and almost the same spacing (6% strain) as

particles is particularly important at the initial

the γ-AuZn (222). Another (indirect) example

growth stages over the Si/SiO2 substrates to

showed evidence of an epitaxial relationship

provide nucleation sites for the Zn vapor.

between the ZnO nanowire and the Au-Zn

Assuming that, at the beginning of the growth,

particle. It is important to stress that in all the

the Si/SiO2 substrate is covered with Au islands,

cases where the crystalline structure of the

such islands will be the preferential sites for

nanowire and the AuZn particle were visible

Zn incorporation since the SiO2 surface has a

together, the epitaxial relationship was found.

relatively lower reactivity. This mechanism

These findings suggest that the ZnO nanowires

is evidenced by the fact that continuous ZnO

grow epitaxially from the solid catalytic

films are formed when the Au layer is absent

particles. In the present experiments, one can

(see insert of Figure 1a).

understand the low temperature growth of

In this situation, it seems worthwhile to

ZnO nanowires from solid Au-Zn catalysts as

consider the oxidation process as a critical

being an intermediate between the VLS and VS

step in ZnO nanowire formation. Wang and

processes. The presence of solid Au-Zn catalyst

colleagues have shown that the oxygen partial pressure strongly influences the growth yield and morphology of ZnO nanowires. However, they claim that the observed effects are a result of changes in the carbothermal reactions responsible for Zn vapor supply11. On the other hand, Heo et al. have proposed that ZnO nanowire formation can occur via the oxidation of Zn through a reaction with Ag2O inside Ag islands. Nevertheless, details of the Zn oxidation reactions that result in nanowire growth have never yet been presented. In the present case, it is likely that ZnO wires

10 nm

originate from the oxidation of Zn atoms within the solid Au-Zn alloy particle, since it is well known that the activity of metals

1010

can be increased upon alloying. Moreover, it has also been observed that the internal

0001

oxidation of alloys such as Zn-Ag and Zn-Cu results in the formation of ZnO crystalline precipitates that present preferential orientation

ZnO [1120] Figure 3

14

G - AuZn

(a) HRTEM image of the junction between ZnO nanowire and the γ-AuZn catalyst recorded along the ZnO[1,1,-2,0] zone axis. (b) and (c) show the FFT analysis of the ZnO nanowire and the γ-AuZn catalyst particle. The orientation relationship is evidenced by the coincidence of the two marked periodicities (see arrow)

| Activity Report 2008

relations with respect to the crystals of the remaining matrix metal.12 Similarly, it can be expected that, during the growth process, the oxidation of Au-Zn particles will generate ZnO precipitates (i.e., nanowires) having a fixed orientation with respect to the particle

Science Highlights

crystallographic orientation. In this sense, ZnO

oxidation mechanisms are outside the scope of

nanowire formation will occur preferentially

this work, it is reasonable to assume that the

at the (1,1,-2) or (1,-1,0) surfaces of the γ-AuZn

presence of a low-energy epitaxial interface

particles, as observed experimentally. According

between the solid catalyst particle and the

to Figure 4, these are two possible low-index

nanowire will favor nanowire growth.

surfaces that could form the interface with the

In summary, low temperature (T < 400 ºC)

ZnO nanowire. Such a preferential oxidation

growth of ZnO nanowires was demonstrated.

mechanism might explain why most of the

We presented clear evidence that the ZnO

observed catalyst particles have the γ-AuZn

nanowires originate from solid γ-AuZn particles

phase, since this phase provides a suitable surface

and proposed a model to describe such growth.

from which ZnO wires can grow epitaxially,

An original feature of this model is that the

enabling the ZnO(10-10) planes to match the

formation of nanowire occurs via preferential

γ-AuZn(222) planes. Although calculations

oxidation of specific γ-AuZn surfaces, induced

of the thermodynamics and kinetics of such

by an epitaxial-like growth mechanism.

RefeRences 1. Lieber, C. M.; Wang, Z. L. Functional nanowires. MRS Bulletin, v. 32, n. 2, p. 99107, 2007 2. Huang, M. H. et al. Catalytic growth of zinc oxide nanowires by vapor transport.

Advanced Materials, v. 13, n. 2, p. 113-116, 2001.

3. Yang, P. et al. Controlled growth of ZnO nanowires and their optical properties.

Advanced Functional Materials, v. 12, n. 5, p. 323-331, 2002.

4. Kodambaka, S. et al. Germanium nanowire growth below the Eutectic temperature.

Science, v. 316, n. 5825, p. 729-732, 2007.

5. Wagner, R. S.; Ellis, W. C. Vapor-liquidsolid mechanism of single crystal growth.

Applied Physics Letters, v. 4, n. 5, p. 89-90, 1964.

6. Morales, A. M.; Lieber, C. M. A laser ablation method for the synthesis of crystalline semiconductor nanowires. Science, v. 279, n. 5348, p. 208-211, 1998.

7. Lu, W.; Lieber, C. M. Semiconductor nanowires. Journal of Physics D: Applied Physics, v. 39, n. 21, p. R387-R406, 2006.

8. Wang, X.; Song, J.; Wang, Z. L. Nanowire and nanobelt arrays of zinc oxide from synthesis to properties and to novel devices.

Journal of Materials Chemistry, v.17, n. 8, p. 711-720, 2007.

9. Fan, H. J. et al. Template-assisted large-scale ordered arrays of ZnO pillars for optical and piezoelectric applications, Small, v. 2, n. 4, p. 561-568, 2006.

10. Campos, L. C. et al. Vapor-solid-solid growth mechanism driven by epitaxial match between solid AuZn alloy catalyst particles and ZnO nanowires at low temperatures.

Advanced Materials, v. 20, n. 8, p. 14991504, 2008.

11. Song, J. H. et al. Systematic study on experimental conditions for large-scale growth of aligned ZnO nanowires on nitrides. Journal of Physical Chemistry B, v. 109, n. 20, p. 9869-9872, 2005.

12. Vellinga, W. P.; DeHosson, J. T. M. Atomic structure and orientation relations of interfaces between Ag and ZnO. Acta Materialia, v. 45, n. 3, p. 933-950, 1997.

Activity ActivityReport Report 2009 2008 |

15

2

A dynamic polyphasic model for the ferritin iron core

José M. Domínguez-Vera1, Natividad Gálvez1, Belén Fernández1, Purificación Sánchez,1 Rafael Cuesta,2 José J. Calvino3 and Marcelo Ceolín4 1

Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada,Granada, Spain 2 Departamento de Química Inorgánica y Orgánica, EPS Linares, Universidad de Jaén, Linares, Spain, 3 Departamento Ciencia de Materiales y Química Inorgánica, Universidad de Cádiz, Cádiz, Spain, 4 Instituto de Investigaciones Físico-Químicas Teóricas y Aplicadas, UNLP-CONICET, Argentina.

Ferritin is one of the most complete paradigms for bioinorganic chemistry because of the way by which Fe is stored as an iron mineral inside the apoprotein. The structure of the ferritin iron core is directly related to the proper operation of iron storage and removal; therefore, understanding its structure may help elucidate the alteration or dysfunction of ferritin and its role in the development of several diseases related to radical processes as a consequence of free Fe. The present study demonstrated that the structure of the ferritin Fe core is composed of several Fe oxide phases (mainly ferrihydrite and magnetite), which are modified in percentage terms as iron is removed gradually through a biomimetic process. Specifically, when Fe is removed from ferritin by a reductive process, there is an increase in the magnetite phase with a corresponding decrease in the ferrihydrite phase.

The presence of magnetite in Alzheimer’s patients could be produced through the uncontrolled removal of reductive ferritin Fe.

Facility: XAFS1, SAXS1 Publication: Journal of the American Chemical Society, 130: 8062-8068 (2008) Funding: MEC (Spain), CONICET (Argentina)

Science Highlights

Iron is an essential element for living

In this study, we demonstrated that the

organisms but its excess is highly toxic. Free

structure of ferritin iron core is composed of

intracellular Fe(II) catalyzes the production of

several Fe oxide phases (mainly ferrihydrite and

hydroxyl radical OH• via Fenton reaction, an

magnetite), which are modified in percentage

extremely powerful oxidizing agent capable of

terms as iron is gradually removed by a

causing extensive cell damage1,2. Therefore, Fe

biomimetic process.

that is not required for immediate metabolic

A batch of horse spleen ferritins was

needs is stored for later use, thereby avoiding

prepared, containing 2200, 1200, 500 and 200

the toxic effects caused by its excess. The main storage form of Fe is ferritin, a spherical hollow protein (apoferritin) composed of 24 subunits surrounding a cavity, which can accommodate thousands of Fe atoms as a mineral traditionally described as ferrihydrite3-6.

The management of iron in cells could be the key to the origin and development of several diseases, especially those of free radical nature. However, the role of iron and ferritin in numerous diseases was ignored for many

Fe atoms, from which iron was gradually removed by reduction and iron(II) chelation.

These samples (Ft2200, Ft1200, Ft500 and Ft200) served as a biomimetic model to study the relationship between natural Fe removal and Fe core structure in brain ferritin10.

X-ray Absorption Near Edge Spectroscopy (XANES) was performed (D04B-XAFS1 beamline) on Ft200, Ft500, Ft1200 and Ft2200 as well as on the reference compounds ferrihydrite, magnetite, and hematite. After linear combination fits (using the procedure implemented in the ATHENA

years. In recent years, oxidative damage by

program of the IFFEFIT package), the fraction

OH• radicals in neurons has been found to be a

of each iron oxide phase in every ferritin sample

primary cause of degenerative diseases such as

was obtained. Figure 1 shows the fraction

Alzheimer’s disease (AD). Furthermore, it has been clearly evidenced that iron is accumulated in brain in several neurodegenerative diseases.

A surprising fact that has been demonstrated

0.8

is that the mineral core composition differs pathological (particularly Alzheimer’s) brain ferritins. Specifically, mixed Fe2+-Fe3+ iron oxide (e.g., magnetite) appears to be the main phase in brain ferritin of patients with AD .

7-9

This evidence suggests that ferritin dysfunction

Phase fraction

significantly between physiological and 0.6

0.4

0.2

increases toxic brain ferrous content, contributing to produce free radicals and inducing cellular oxidative stress associated to cognitive decline

0.0 500

and AD. Understanding the chemical structure

development of degenerative diseases.

1500

2000

Iron content

of the ferritin core may help to elucidate the alteration of ferritin and its role in the

1000

Figure 1

Phase distribution for ferritin samples with different iron content (200-2200 atoms) obtained from XANES experiments (see text).

Purple (hematite), red (magnetite), and orange (ferrihydrite) Activity Report 2008 |

17

A dynamic polyphasic model for the ferritin iron core

Ferrihydrite Figure 2

18

distribution in each sample with different

Ft1200, and Ft2200 and bead-count histograms

degrees of iron removal. As Fe was removed,

extracted from low resolution shape models

the relative amount of magnetite increased

of iron depleted ferritins obtained with the

while that of ferrihydrite decreased.

DAMMIN program.

We conclude that magnetite is formed

Chemical reduction induced changes in the

simultaneously with the reductive removal of

PDF corresponding to the Fe release process.

Fe. The presence of excess reducer removes a

Initially, little change was observed in the

large amount of Fe(II), part of which would

position of the first maximum at R~40 Å and

produce toxic OH• radicals while the other part

no definite tendency was visible. However,

would re-enter the ferritin cavity, producing

a systematic reduction in the amplitude of

magnetite by reaction with the remaining native

the curve at R~40 Å was accompanied by

ferrihydrite. With this mechanism in mind,

a simultaneous increase in the intensity at

magnetite should be located preferentially at the

R~90 Å. This behavior was also reflected in a

surface of the Fe core, so that the full process of

shift in the mean R value from 44.3 Å in Ft2200

ferritin iron elimination in reductive conditions

to 54.1 Å in Ft500. It should be noted that the

would consist of Fe removal from the labile

PDF signal around 40 Å was dominated by the

ferrihydrite core, leading to the formation of

excess electronic density of the inorganic core,

a magnetite shell (Figure 2).

whereas the intensity of the PDF curve around

Therefore, as a result of the reductive process,

90 Å was dominated by the excess electronic

Fe is removed from the center of the ferritin core,

density of the protein shell. The increase of the

hollowing it out rather than reducing its size

signal at 90 Å reflects the fact that a reduction of

from the surface. In fact, mean diameters found

the core should be accompanied by the relative

by Transmission Electron Microscopy were 6.0,

increase of the otherwise low shell signal. Our

5.9, 5.7 and 5.1 nm for Ft2200, Ft1200, Ft500, and Ft200

results demonstrate that, in agreement with

respectively, supporting our conclusions10.

previous observations, Fe atoms are extracted

SAXS experiments (D11A-SAXS1 beamline)

from the internal cavity, as expected for defective

also confirmed the model obtained from

particles and, in fact, depletion of occluded Fe

XANES and TEM experiments. Figure 3

reduces the excess electron density of the core,

shows the PDFs (Pair Distribution Functions)

keeping its size almost unchanged.

obtained after normalized Fourier Transform

To gain a better understanding of the

of the scattering patterns obtained for Ft500,

structural aspects of the Fe release mechanism,

Magnetite

Scheme of the dynamic process leading to a ferrihydrite-magnetite coreshell structure

| Activity Report 2008

Science Highlights

1.5 1.2 0.9 0.6 0.3 0.0

0.02 P (R)

Normalized bead count

1.5 1.2

0.01

0.9 0.6 0.00

0.3 0.0

0

25

50

75

100

125

R (Å)

1.5 1.2

Holo-ferritin Holo-ferritin 2200 Apo-ferritin

0.9 0.6

Holo-ferritin 1200 Holo-ferritin 500

0.3 0.0

0

10

20

30

40

50

60

70

R (Å) Figure 3

Bead-count histogram (left) and pair distribution function (top) obtained from SAXS experiments on holo-ferritin samples with different iron contents

a low-resolution bead model and bead-count

from the core surface but from the interior of

histograms of Ft2200, Ft1200 and Ft500 were

the particle. Further release of iron from Ft1200

produced using the simulated annealing method

to Ft500 proceeds in a similar fashion.

implemented in the DAMMIN program.

In conclusion, the formation of magnetite in

Figure 3 shows the normalized bead count

AD patients in native ferritin could be related

histograms for Ft2200, Ft1200 and Ft500, respectively.

to the Fe removal process. This finding opens

The vertical line indicates the (nominal) position

the door to a new approach in the search for

of the inner (R~40 Å) radius of the apoferritin

new biomarkers in Alzheimer’s disease.

shell. The red bars in the histogram represent the bead count for the inorganic oxide core (R < 40 Å) while the green bars correspond to

Acknowledgments

the bead count for the protein shell (R > 40 Å).

The authors are grateful for being given

A close inspection of the histograms in figure 3

access to the facilities of the XAFS and SAXS

suggests the existence of holes inside the inorganic

beamlines at the LNLS. This research was

core. The release of Fe from Ft2200 to Ft1200 mostly

supported by MEC (project CTQ2006-02840),

induces a reduction of core density. The external

Junta de Andalucía (Proyecto Excelencia

core radius remains unchanged and the “internal

FQM-02525) and CONICET, Argentina (partial).

core hole” increases slightly, suggesting that

N. G. thanks the MEC for a research contract

reductive demineralization does not proceed

(Ramón y Cajal program).

Activity ActivityReport Report 2009 2008 |

19

A dynamic polyphasic model for the ferritin iron core

RefeRences 1. Markesbery, W. R. Oxidative stress hypothesis in Alzheimer’s disease. Free Radical Biology and Medicine, v. 23, n. 1, p. 134-147, 1997.

2. George, G.; Cash, A. D.; Smith, M. A. Alzheimer Disease and Oxidative Stress.

Journal of Biomedicine and Biotechnology, v. 2, n. 3, p. 120-123, 2002.

7. Quintana, C.; Cowley, J. M.; Marhic, C. Electron nanodiffraction and high-resolution electron microscopy studies of the structure and composition of physiological and pathological ferritin. Journal of Structural Biology, v. 147, n. 2, p. 166-178, 2004.

3. Chasteen, N. D.; Harrison, P. M. Mineralization in ferritin: an efficient means of iron storage.

Journal of Structural Biology, v. 126, n. 3, p. 182-194, 1999.

8. Dobson, J. Magnetic iron compounds in neurological disorders. Annals of the New York Academy of Sciences, v. 1012, p. 183-192, 2004.

4. Harrison, P. M.; Arosio, P. Ferritins: molecular properties, iron storage function and cellular regulation. Biochimica et Biophysica Acta – Bioenergetics, v. 1275, n. 3, p. 161203, 1996.

9. Smith, M. A. et al. Iron accumulation in Alzheimer disease is a source of redoxgenerated free radicals. Proceedings of the National Academy of Sciences, v. 94, n. 18, p. 9866-9868,1997.

5. Theil, E. C. et al. The ferritin iron entry and exit problem. Inorganica Chimica Acta, v. 297, n. 1-2, p. 242-251, 2000.

10. Gálvez, N. et al. Comparative structural and chemical studies of ferritin cores with gradual removal of their iron contents.

Journal of the American Chemical Society, v. 130, n. 25, p. 8062-8068, 2008.

6. Liu, X.; Theil, E. C. Ferritins: dynamic management of biological iron and oxygen

20

| Activity Report 2008

chemistry. Accounts of Chemical Research, v. 38, n. 3, p. 167-175, 2005.

Science Highlights

Activity ActivityReport Report 2009 2008 |

21

3

X-ray structural low-resolution features and functional insights to human Ki-1/57: an intrinsically unstructured protein that localizes to nuclear bodies related with RNA metabolism Gustavo Costa Bressan1,2, Júlio César Silva1,3, Júlio César Borges4, Dario Oliveira dos Passos 1,2, Carlos Henrique Inacio Ramos5, Alexandre Jose Cristino Quaresma1,2, Eduardo Cruz Moraes1,2, Adriana O. Manfiolli6, Marcelo Damario Gomes6, Iris Concepcion Linares de Torriani1,3, Jörg Kobarg1,2 1

Laboratório Nacional de Luz Síncrotron, 2 Instituto de Biologia/UNICAMP, 3 Instituto de Física “Gleb Wataghin”/UNICAMP, 4 Instituto de Química de São Carlos/USP, 5 Instituto de Química/UNICAMP, 6 Departamento de Bioquímica e Imunologia/FMRP-USP,

SP, SP, SP, SP, SP, SP,

Brazil Brazil Brazil Brazil Brazil Brazil

The human protein Ki-1/57 was first identified through the cross reactivity of Ki-1 monoclonal antibody in Hodgkin lymphoma cells. Further studies have demonstrated that Ki-1/57 interacts with several regulatory proteins involved in cellular signaling, transcriptional regulation and RNA metabolism. Small Angle X-Ray Scattering (SAXS) of the protein in solution provided information on the dimensional and overall shape parameters. Additional measurements of circular dichroism, analytical ultracentrifugation and proteolytic susceptibility assays, among other techniques, proved that Ki-1/57 belongs to the class of intrinsically unstructured proteins. In further functional analyses, we found that Ki-1/57 has a splicing regulatory activity in mammalian cells and that it can localize to several nuclear dot-like domains involved in pre-mRNA splicing control and other events associated with RNA metabolism. We have found the first functional signatures for Ki-1/57 and characterized it as a highly unstructured and flexible protein. The latter property may be crucial to explain the wide array of protein partners with which Ki-1/57 is able to interact.

Facility:

SAXS2 e CEBIME

Publication:

Journal of Proteome Research. 2008; 7:4465-4474.

Funding:

FAPESP and CNPq

Science Highlights

Analyses of malignant cells of Hodgkin

as the most adequate technique to obtain a

lymphoma have shown that the monoclonal

real space description at the molecular level.

antibody Ki-1 not only reacted with a

Analysis of SAXS experimental data obtained

transmembrane protein of 120 kDa, but

for a C-terminal construct of Ki-1/57 spanning

also with an intracellular of 57 kDa protein.

the amino acid residues 122-413 [(122-413)

Isolation and cloning of the cDNA sequence

Ki-1/57 construct] provided parameters typical

corresponding to the 57 kDa antigen revealed

of a highly flexible and elongated molecule,

a novel, functionally uncharacterized protein,

which on average does not adopt a globular

which was named Ki-1/57. Aiming to obtain

structure in solution. We obtained several ab-

further clues about the function of Ki-1/57,

initio low-resolution models that may describe

we investigated the yeast-two hybrid system

this type of disordered molecule in solution,

and found several proteins with which it is

and performed several independent runs of

able to interact1,2. Although the exact cellular

calculations. In this paper, we present a typical

role of Ki-1/57 remains to be determined, its

model obtained (Figure 1), which is composed

protein-protein interaction profile has indicated

of spherical beads (dummy-atoms). In parallel

that it may be involved in gene expression

with these SAXS results, we also acquired

regulation either at the transcriptional level or

additional data confirming the unstructured

via its influence on RNA metabolism.

nature of (122-413)Ki-1/57 construct. These

In previous spectroscopic analyses, we observed a low content of secondary structure in Ki-1/57, suggesting it may belong to the class of intrinsically unstructured proteins. This rapidly growing list of proteins has recently gained

Unstructured Ki - 1/57: flexibility for binding to multiple functional partners

much attention, since many of its members

Post-translational modifications

are involved in regulatory mechanisms, signal

Splicing proteins

transduction, and noncatalytic interaction with DNA/RNA and other proteins. It is believed that the inherent flexibility of these proteins may be crucial to their functions, which commonly require plasticity and the combination of high

Amino acids composition Small angle X- ray scattering Analytical ultracentrifugation Analytical gel filtration Proteolytic susceptibility Circular dichroism

Transcriptional regulatory proteins Translational regulatory proteins

specificity and low affinity during interaction

Nuclear bodies

with their molecular partners .

3

Through theoretical computational predictions

U-rich region

we found, first, that Ki-1/57 has an amino acid

RNA binding

sequence typical of intrinsically unstructured proteins, with a high content of net charged amino acids along with low frequency of hydrophobic residues4. This characteristic precluded any possibility of crystallization to obtain a high resolution atomic structure.

Solution X-ray scattering was then adopted

Figure 1

Unstructured Ki-1/57 and its implications. At the center of the figure: an ab initio model of Ki-1/57 generated by processing SAXS data with the GASBOR software. The model is displayed using the program PyMOL and is representative of a set of different models obtained after multiple independent calculations based on the lowest NSD values. Left: the different approaches used to characterize Ki-1/57 as an intrinsically unstructured protein. Right: Ki-1/57â&#x20AC;&#x2122;s pleiotropic functions, which are supported by its flexible and elongated shape Activity ActivityReport Report 2009 2008 |

23

X-ray structural low-resolution features and functional insights to human Ki-1/57...

results included hydrodynamic parameters

as belonging to the intrinsically unstructured

from analytical gel filtration and analytical

group of proteins4.

ultracentrifugation techniques, and results of

Furthermore, we carried out experiments

circular dichroism and proteolytic susceptibility

aiming to obtain additional information about the

analyses (Figure 1). Taken together, all these

function of Ki-1/57. We found that Ki-1/57 binds

approaches support the notion that Ki-1/57

to a U-rich RNA probe and interacts in vitro and in

is a novel intrinsically unstructured protein.

vivo with splicing regulatory proteins. Moreover,

This finding is highly consistent with the

we verified that Ki-1/57 alters the splicing

characterization of Ki-1/57 as a hub protein

pattern of an adenoviral pre-mRNA, leading to

that interacts with many protein partners,

the formation of specific mRNA isoforms5. These

since several hub proteins have been described

findings suggest that the participation of Ki-1/57

GFP-Ki-1/57 Splicing speckles

Cytoplasm

RNA

Nucleus ?

Met Ki-1/57 ? Met Ki-1/57

Ki-1/57

24

pre-mRNA Splicing

Ki-1/57 Met Met Ki-1/57 ?

RNA

Met Ki-1/57

Cajal

AAAAA

?Translation?

Figure 2

Arginine methylation

Nuclear bodies Cajal Splicing speckles GEMS Nucleous

Met

Ki-1/57

?

Ki-1/57 Met Ki-1/57

Met

DNA

Met Ki-1/57 AAAAA

Schematic representation of the sub-cellular localization and dynamics of Ki-1/57. Top: representative confocal microscopic image obtained from a human HEK-293 cell treated with the methylation inhibitor Adox. Under this metabolic condition, GFP-Ki-1/57 (green) no longer co-localizes to the splicing speckles (red), but instead shows a close juxtaposition to the nucleolus, Cajal bodies and GEMS. All of these are nuclear sub-structures involved in the assembly, maturation or storage of RNA/pre-mRNA processing complexes. In untreated cells, we observed that Ki-1/57 co-localizes with splicing speckles (not shown). This suggests that Ki-1/57â&#x20AC;&#x2122;s dynamic localization to sub-nuclear structures depends on its arginine methylation status. Ki-1/57â&#x20AC;&#x2122;s functional activities in the context of RNA binding and pre-mRNA splicing are also represented

| Activity Report 2008

Science Highlights

in RNA metabolism may be related to regulatory

Additionally, we obtained evidence of the

events of pre-mRNA splicing.

importance of arginine methylation for the

Finally, we also performed sub-cellular

localization of Ki-1/57 to different nuclear

localization studies using a fluorescent-

bodies. This adds a new level of complexity

tagged construct of Ki-1/57 and observed

to the way Ki-1/57 may perform its functions

its co-localization to several dot-like regions

in the cell (Figure 1 and 2). Its flexible

called nuclear bodies (Figure 2). A number

structure and conformational plasticity

of these substructures are known to be

may be important both for its binding to

occupied by several RNA binding proteins

multiple partners, including RNA and several

and to orchestrate many regulatory events

regulatory proteins, and to allow for multiple

in RNA metabolism, including assembly,

post-translational modifications, including

maturation or storage of RNA or pre-mRNA

Serine/threonine phosphorylation and arginine

processing complexes . Therefore, these

methylation. Future studies should address

findings corroborate the functional data

the role of flexibility and post- translational

described above regarding the involvement

modifications of the function of Ki-1/57 in

of Ki-1/57 in pre-mRNA splicing events.

pre-mRNA splicing.

6

RefeRences 1. Nery, F. C. et al. Ki-1/57 Interacts with RACK1 and is a substrate for the phosphorylation by phorbol 12-myristate 13-acetate-activated protein kinase C. Journal of Biological Chemistry, v. 279, n. 12, p. 11444-11455, 2004.

4. Bressan, G. C. et al. Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein. Journal of Proteome Research, v. 7, n. 10, p. 44654474, 2008.

2. Nery, F. C. et al. A spectroscopic analysis of the interaction between the human regulatory proteins RACK1 and Ki-1/57.

Biological Chemistry, vol. 387, n. 5, p. 577582, 2006.

5. Bressan, G. C. et al. Functional association of human Ki-1/57 with pre-mRNA splicing events. FEBS Journal, v. 276, n. 14, p. 37703783. 2009.

3. Dyson, H. J.; Wright, P. E. Intrinsically unstructured proteins and their functions.

Nature Reviews Molecular Cell Biology, v. 6, n. 3, p. 197-208, 2005.

6. Handwerger, K. E.; Gall, J. G.. Subnuclear organelles: new insights into form and function. Trends of Cell Biology, v. 16, n. 1, p. 19-26, 2006.

Activity ActivityReport Report 2009 2008 |

25

4

Carbon nanotubes as R-bars of high aspect ratio composite nanotools

D. Nakabayashi1,2, A.L.D. Moreau2, V.R. Coluci2, D.S. Galvão2, M.A. Cotta2, D. Ugarte1,2* 1

Laboratório Nacional de Luz Síncrotron, Campinas SP, Brazil Instituto de Física “Gleb Wataghin”, Universidade Estadual de Campinas, Campinas SP, Brazil 2

Nanotechnology requires the development of nanoscale tools to manipulate nanosystems. From the point of view of materials science, this represents a serious challenge, because nanotools must meet a series of stringent requirements of shape (size, aspect ratio), mechanical, magnetic and electrical properties. We have developed long and narrow carbon-carbon composite nanotips using carbon nanotubes covered by an amorphous carbon shell; the very small nanotube tip remained uncoated to preserve apex size. This configuration renders the system stiffer and allows for the control of flexibility and vibrations. In addition, we have maintained the important nanotube properties of size, strength and resilience. Nanomanipulation experiments in situ in a high resolution scanning electron microscope were used to optimize the tips behavior and molecular dynamics simulations were used to study the mechanical response. Finally, we performed a practical application in atomic force microscopy. Composite tips yielded excellent image resolution and showed remarkable wear resistance (no degradation of image quality after acquiring several hundred images).

Facility: LME Publication: Nano Letters, 8: 842-847 (2008) Funding: FAPESP and CNPq

Science Highlights

Keen interest in nanoscience and tech-

CNTs were deposited on support tips

nology has stimulated the development of

(tungsten or silicon tips), where they adhered

nanomanipulators, including nanoscale tools to

by Van der Waals forces. The contact region and

interact with specific regions of nanodevices1-3.

subsequently the CNT itself were then covered

Nanometric probes for mechanical and

with an a-C layer generated by spontaneous

electrical studies should be conductive and mechanically robust. The first attribute can be achieved easily (e.g., metal tips); however, few materials show mechanical characteristics (tensile strength in the GPa range) that support the bending efforts associated with nN forces when shaped into a high aspect ratio beam of nanometric diameter. Multiwall carbon

Probe tips

nanotubes (CNTs)4 seem to be the best match from the standpoint of mechanical properties (tensile strength and elastic modulus) and morphology (length ~microns; diameter Sample

1-20 nm). Moreover, they can be bent easily without breaking, displaying a unique and surprising resilience. However, their huge aspect ratio renders them very flexible and even vibration modes are excited at room temperature5, making them difficult to use in high spatial resolution applications.

Modern technology routinely produces targeted materials by combining several constituents in composites. High aspect ratio composite structures (beams) are extensively used in construction, and reinforced concrete naturally arises as the typical example; briefly, steel reinforcement bars (rebars) withstand stress and concrete bear compression. Extrapolating this idea, we can generate nanobeams by

1 Mm

forming a C-C composite using CNT as rebars and diamond-like carbon as hard matrix. In this work, we used a home-built nanomanipulator6,7 operating in situ in a scanning electron microscope (JSM-6330F) to fabricate composite carbon tools and test their mechanical response (Figure 1a).

Figure 1

a) Home-built nanomanipulator including two probe tips. The system is based on a parallel-guiding plate-spring mechanism driven by commercial picomotors; precision movements are performed by piezoelectric elements6,7. b, c) progressive mechanical deformation of a high aspect ratio composite tip when a ~1 Âľm a-C shell is deposited on the CNT. Note that the upper section of the tip is not deformed, and the induced curvature is only generated on the protruding CNT region Activity ActivityReport Report 2009 2008 |

27

Carbon nanotubes as R-bars of high aspect ratio composite nanotools

When the tip is released, the CNT recovers its straight shape, indicating that its resilience property has been conserved.

Further insight into the reinforcement of CNT nanocomposite tips can be derived from computer simulations based on reactive empirical bond-order potential8. The effect of a diamond-like layer covering part of the length of a CNT has been thoroughly analyzed. In particular, we have analyzed the tip response when a rigid obstacle is dragged across the tip position (Figure 2). The results indicate that the presence of diamond-like shell not only increases the oscillation frequency (increase of tip stiffness), but also serves as a vibration Figure 2

Photographs extracted from the theoretical simulation of the mechanical deformation of the composite tip. Lateral view of a double-walled carbon CNT covered with a diamond-like shell; the rigid obstacle inducing the deformation travels along the x-direction

damper, which is in excellent agreement with experimental observations.

Finally, we tested the practical application of C-C composite nanotools as an Atomic Force Microscope (AFM) tip (Figure 3a).

28

| Activity Report 2008

carbon contamination (EBD, electron beam

Commercial high resolution Si tips yield

deposited carbon1). Figure 1b, c shows a CNT

images of equivalent quality9, but image

bundle with an apparently ~1.3 Âľm long section

resolution degrades after a mere 10-20 images;

hanging from a tungsten tip; the lower part

in contrast, composite tips showed no reduction

of the SEM image shows the second tip of the

of imaging capabilities after recording

manipulator. By approaching this second tip, one

400 images (Figures 3b, c).

can make mechanical contact with the protruding

Summarizing, reinforced nanotools can be

CNT. To reduce the nanotube vibrations and

generated easily by associating the extreme

keep the needle shape, we deposited a thin

mechanical properties of CNTs with hard

(50 nm) amorphous carbon (a-C) EBD layer

amorphous carbon; properties such as flexibility

generated along the CNT, creating a coaxial

and vibration can be controlled without

shell (~1 Âľm long see, Figures 1b, c). In this

deteriorating the excellent CNT characteristics of

way, the CNT apex size was preserved and the

size, aspect ratio, strength and resilience. These

a-C layer on the tube base had a strengthened

composite tips showed excellent wear resistance

region, maintaining the high aspect ratio.

and high resolution imaging capabilities when

The resistance of the composite tip is clearly

used as AFM probes. Further work is in progress

illustrated in Figures 1b and c, which show

to improve the mechanical properties of the

progressive deformation by the application of

nanocomposite tip through careful control of

a lateral load with the other manipulator tip.

the amorphous carbon layer and also to test

Bending occurs only in the free CNT region.

them as tools for nanomanipulation.

Science Highlights

1 Mm

Figure 3

Application of a CNT composite tool as an AFM tip. a) General view of the high aspect ratio composite tip ready for AFM imaging. b, c) AFM images of quantum dots (InAs, average dot size is 26 ± 6 nm in diameter and 6 ± 1 nm and in height) grown on InP substrate10 and acquired in tapping mode (1 µm × 1 µm scan area).

Image acquired just after initial use of the composite tip b) and; image of the same region of the sample after performing 400 scan (c). No degradation of the image’s lateral or vertical resolution was detected

RefeRences 1. Yu, M. F. et al. Strength and breaking mechanism of multiwalled carbon nanotubes under tensile load. Science, v. 287, n. 5453, p. 637-640, 2000.

6. Nakabayashi, D. et al. Low-cost nanomanipulator for in situ experiments in a SEM . Microscopy and Microanalysis, v. 12, n. 4, p. 311-316, 2006.

2. Kim, K. S. et al. In situ manipulation and characterizations using nanomanipulators inside a field emission-scanning electron microscope. Review of Scientific Instruments, v. 74, n. 9, p. 4021-4025, 2003.

7. Nakabayashi, D.; Silva, P.C.; Ugarte, D. Inexpensive two-tip nanomanipulator for a SEM . Applied Surface Science, v. 254, n. 1, p. 405-411, 2007.

3. Fahlbusch, St. et al. Nanomanipulation in a scanning electron microscope. Journal of Materials Processing Technology, v. 167, n. 2-3, p. 371-382, 2005.

8. Brenner, D.W. Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Physical Review B, v. 42, n. 15, p. 9458-9471, 1990.

4. Ijima, S. Helical microtubules of graphitic carbon. Nature, v. 354, n. 6348, p.56-58, 1991.

9. Gutiérrez, H.R. et al. Carbon nanotube probe resolution: a quantitative analysis using fourier transform. Physica Status Solidi A, v. 201, n. 5, p. 888-893, 2004.

5. Treacy, M. M. J.; Ebbesen, T. W.; Gibson, J. M. Exceptionally high young’s modulus observed for individual carbon nanotubes.

Nature, v. 381, n. 6584, p.678-680, 1996.

10. Bortoleto, J. R. R. Mechanism of lateral ordering of InP dots grown on InGaP layers. Applied Physics Letters, v. 87, n. 1, p.013105, 2005.

Activity ActivityReport Report 2009 2008 |

29

5

Evolution of Ge-Si:Si(001) open and closed nanocrystalline systems towards equilibrium

Marina S. Leite1,2, A. Malachias1, S. Kycia3, Ted I. Kamins4, R. Stanley Williams4, G. Medeiros-Ribeiro1,4 1 Laboratório Nacional de Luz Síncrotron Instituto de Física ‘Gleb Wataghin’ – UNICAMP 3 Department of Physics, MacNaughton Building, University of Guelph, Guelph, Ontario, Canada

2

4

Hewlett-Packard Laboratories, California – USA

The diffusion mechanisms for Si on Ge:Si were selectively tuned by annealing Si-Ge:Si(001) epitaxially grown islands in different environments in order to produce an open (or closed) system, in which matter is (or is not) exchanged through surface diffusion. The islands’ strain and composition were inferred by Anomalous X-Ray Synchrotron measurements, allowing for the evaluation of the driving forces for intermixing while both systems approached equilibrium.

In the open system, intermixing due to the Si inflow from the wetting layer (reservoir) caused a decrease in the Ge content, lowering the elastic energy and increasing the mixing entropy. In contrast, in the closed system, while the average Ge composition remained constant, atom rearrangements within the islands led to an increase in both elastic and entropic contributions. Gibbs free energy decreased in both cases, despite the different evolution paths for the composition profiles.

Facility: XRD 1-2, MTA Publication: Phys. Rev. Lett. 2008; 100:226101 Funding: FAPESP, HP Brazil, Rede SPMBrasil, CNPq

Science Highlights

Introduction

of 14.3 ± 2.3 nm were produced. The open and

Si-Ge is an extensively studied system

closed systems were implemented by growing

because of its direct impact on the semiconductor

two samples under the same experimental

industry. Moreover, strained epitaxial growth

conditions as R, but subsequently annealing

can lead to crystalline islands, a phenomenon that can be mapped onto other materials 15

systems. These nanostructures can be grown

R

areas, allowing for the assessment of statistically meaningful data. Thus, Si-Ge represents an attractive system to investigate alloying on

Height (nm)

with a high degree of uniformity over large

the nanoscale, and the equilibrium structures

10

5

that prevail in that regime . At relatively low 1

growth temperatures, elastic energy was found to model the islands’ final average composition,

15

shape and size2-4. Moreover, for islands with

O

be scaled with (strain)2. At ~ 600 ºC, intermixing takes place between the substrate atoms and the growing film, producing islands with

Height (nm)

uniform composition, the volume was found to

nonuniform composition caused by different

10

5

alloying mechanisms . Recently, simulations 5-7

were made of the evolution of alloyed islands, assuming only surface diffusion effects8 and the

15

dependence of equilibrium composition on island

C

potentials, which depend upon the system’s constraints, can provide a better understanding of the evolution of the island composition profile towards equilibrium9,10.

Height (nm)

shape and size9. However, the thermodynamic 10

5

–30

Experimental

–20

–10

0

10

20

30

Position (nm)

The samples were grown by chemical vapor deposition in order to control the

Ge content (fraction)

surface diffusion kinetics during annealing.

A reference sample (R) was grown under

0

conditions favoring a graded composition profile, by depositing 12 eq-ML of Ge for 240 s at 600 ºC onto a Si(001) substrate. Uniform ensembles of dome-shaped islands with heights

Figure 1

0.50

1.0

Ge concentration (fraction) in samples R (reference), O (open), and C (closed). The black solid lines correspond to 0.50 Ge content. Insets: AFM images of 1 × 1 µm2, showing islands of uniform size and shape in all the samples Activity ActivityReport Report 2009 2008 |

31

Evolution of Ge-Si:Si(001) open and closed nanocrystalline systems towards equilibrium

them for 10 minutes at the growth temperature

Figure 1). Measuring Anomalous Grazing

in different environments. The open system

Incidence X-Ray Diffraction (GIXRD) at the

was produced by annealing the islands under

XRD1 beam line of LNLS yielded the lattice

a H2 flux (10 Torr), allowing both Ge and Si

spacing distribution and the Ge content,

adatom surface diffusion (sample O). Sample

allowing for calculation of the thermodynamic

C was annealed in a PH3-H2 atmosphere

quantities.

(1.4 × 10 Torr), which strongly inhibited Si 5

surface diffusion due to the P-Si bond formed with the Si atoms from the WL’s surface11. As

Results and discussion Figure 1 shows the average composition

over the surface (closed system) . In both

profile for each island ensemble assuming

cases, the overall dome shape of the islands

cylindrical symmetry, measured by GIXRD5.

was preserved upon annealing (see inset of

Sample R exhibits 1.0 Ge fraction at the island

Height (nm)

7

15

R

10 5 –30

–15

0

15

Height (nm)

a result, only the Ge species could diffuse

15

R

10 5

30

–30

15

O

10 5 –30

–15

0

15

O

5 –30

15

Height (nm)

Height (nm)

5 0

32

| Activity Report 2008

15

30

10 5 –30

30

–15

0

15

30

Position (nm) 

Figure 2

0

C

 (GPa) –1.5

–15

15

Position (nm)

1.0

30

Position (nm)

10

–15

15

10

30

C

–30

0

15

Position (nm) 15

–15

Position (nm) Height (nm)

Height (nm)

Position (nm)

–4.0

0

 (meV/Å) 7.5

15.0

a) Stress σ (GPa), with positive (negative) values for tensile (compressed) material, and b) chemical potential gradient ∇µ (meV/Å) maps for R (reference), O (open), and C (closed) samples (systems)

Science Highlights

shell, and a less than 0.50 fraction below

significantly to 0.45 ± 0.02 because of Si surface

6 nm from the substrate surface, indicating

diffusion, although the island volume was

a high concentration gradient. The annealed

also found to increase (35 × 103 nm3). govern the intermixing processes are the

displaying a pure Ge-rich shell, and the

stress [σ = ε// (C112 + C11C12 – C122)/ C11]

0.50 iso-composition lines (black solid line)

and the chemical potential gradient

for O and C occurred at higher and lower

[∇µ = (r ∂/∂r + k ∂/∂z) (kT ln c)]12. As Figure

heights, respectively. The average Ge content

2a indicates, sample R showed a significant

in the closed system remained constant upon

amount of stress at the perimeter of the

annealing (0.75 ± 0.04 for R and 0.69 ± 0.03

island, but negligible σ at the core and base.

for C), despite a volume increase (19 × 10

3

Upon annealing, while σ decreased in the

nm3 for R and 38 × 103 nm3 for C). In sample

open system, the closed system displayed an

O, the average Ge concentration decreased

increase in internal stress. Simultaneously,

5

15 10 5 –15 0 15 Position (nm)

15 10 5 –15 0 15 Position (nm)

5 –30

30

10 5 –30

Figure 3

30

–15 0 15 Position (nm)

15 10 5 –15 0 15 Position (nm)

30

R

10 5 –30

0

30

30

O

10 5 –30

–15 0 15 Position (nm)

15

30

C

10 5 –30

TSM (meV/atom) 60

–15 0 15 Position (nm)

15

30

C

–30

15

30

O

H (meV/atom) 0

–15 0 15 Position (nm)

15

30

C

–30

10

30

O

–30

Height (nm)

–15 0 15 Position (nm)

Height (nm)

Height (nm)

–30

R

Height (nm)

10

15

Height (nm)

R

Height (nm)

15

Height (nm)

of intermixing when compared to R, no longer

Height (nm)

The generalized driving forces that

Height (nm)

samples (O and C) exhibited a higher degree

–15 0 15 Position (nm)

30

G (meV/atom) 60

–60

–20

20

a) Enthalpy H, b) Mixing entropy contribution TSM, and c) Gibbs free energy G (meV/atom) maps evaluated for samples R (reference), O (open), and C (closed). Volume averaged values for the corresponding thermodynamic potentials are also shown Activity ActivityReport Report 2009 2008 |

33

Evolution of Ge-Si:Si(001) open and closed nanocrystalline systems towards equilibrium

∇µ was higher in sample R than in O and C;

compensates the increase in H at the island

although the top of the islands in all the

core, as shown by the overall decrease in G. G

samples showed a very small gradient, since

is even lower in the open system (sample O),

the composition was constant, as shown in

as a direct consequence of the decrease in H

Figure 2b. R exhibited a considerable variation

(due to enhanced intermixing with Si during

of stress inside the island, which triggered

annealing) and the increase in TSM, since it is

the compositional change in the annealed

more likely for an open system to achieve a

samples. As a consequence, both open and

minimum energy configuration. A comparison

closed systems showed a more uniform

of samples O and C revealed volumes differing

distribution of σ, with C becoming more

by less than 10%, as mentioned earlier, although

stressed. In conclusion, depending upon the

the Ge composition is 1.5 times higher in the

constraints imposed on the system, chemical

closed system. Noting that the island volume

and mechanical forces have a distinct yet direct

should scale with c–6 for islands of uniform

impact on atom redistribution.

composition2, the expected volume increase

The Gibbs Free Energy (GFE) gives us a

would have been 20-fold. This unexpected

complete picture of the islands’ evolution

result demonstrates the determining factor of

towards equilibrium. The description given

the composition profile on island size during

by this thermodynamic potential encompasses

growth and annealing.

the enthalpy of formation H and the mixing entropy SM, both composition-dependent.

Here, GFE can be calculated as G = H – TSM, with H = Echem + Eel + Esurf + Elin, where the most

34

| Activity Report 2008

Conclusions In summary, closed and open systems were

important contributions to the enthalpic term

produced by controlling the surface diffusion

are the chemical energy or mixing enthalpy

kinetics. The evolution of the composition profile

Echem = Ωc(c-1), and Eel1, both inferred from

of the Si-Ge islands towards equilibrium were

the GIXRD measurements of strain and

monitored by evaluating the thermodynamic

composition. The entropic contribution related

potentials in both systems, which were inferred

to the mixture formation can be approximated

by GIXRD measurements of composition and

by TSM ≈ – kT[cln(c) + (1-c)ln(1-c)]13. Figure 3a

strain fields. The open system showed an

shows the enthalpy maps for all the samples.

overall decrease in the GFE due to the Si surface

As expected, H is higher for sample C, as a

diffusion process, leading to a decrease in the

direct consequence of σ. For the open and

Ge content. In the closed system, minimizing

closed systems, TSM increases dramatically,

the chemical potential gradient caused a

especially at the top of the island (Figure 3b).

decrease in the GFE, despite the unexpected

As indicated in Figure 3c, G is always negative

increase in elastic energy. In both cases, entropy

in both situations, unlike the reference sample

was found to play a very important role in

R, which displays positive values at the

alloying. Finally, atom rearrangement within

island shell. This result underscores the fact

the islands producing particular composition

that grown islands are not in a state of local

profiles can be a determining factor of island

equilibrium, even at low supersaturation.

size. We acknowledge LNLS for the use of the

In the closed system (C), the increase in TSM

XRD1 beamline.

Science Highlights

RefeRences 1. Tsao, J. Y. Materials fundamentals of molecular beam epitaxy. New York: Academic Press, 1993. 301 p.

2. Rastelli, A. et al. Reversible shape evolution of Ge Islands on Si(001). Physical Review Letters, v. 87, n. 25, p. 256101, 2001.

3. Medeiros-Ribeiro, G. et al. Shape transition of germanium nanocrystals on a silicon (001) surface from pyramids to domes.

Science, v. 279, n. 5349, p. 353-355, 1998.

4. Ross, F. M. et al. Coarsening of selfassembled Ge quantum dots on Si(001).

Physical Review Letters, v. 80, n. 5, p.

984-987, 1998.

5. Malachias, A. et al. 3D composition of epitaxial nanocrystals by anomalous X-ray diffraction: observation of a Si-rich core in Ge domes on Si(100). Physical Review Letters, v. 91, n. 17, p. 176101, 2003.

6. Katsaros, G. et al. Kinetic origin of island intermixing during the growth of Ge on Si(001). Physical Review B, v. 72, n. 19, p.

195320, 2005.

7. Leite, M. S. et al. Alloying mechanisms for epitaxial nanocrystals. Physical Review Letters, v. 98, n. 16, p. 165901, 2007.

8. Tu, Y. et al. Coarsening, mixing, and motion: the complex evolution of epitaxial islands.

Physical Review Letters, v. 98, n. 9, p.

096103, 2007.

9. Medhekar, N. V.; Hegadekatte, V.; Shenoy, V. B. Composition maps in self-assembled alloy quantum dots. Physical Review Letters, v. 100, n. 10, p. 106104, 2008.

10. Leite, M. S. et al. Evolution of thermodynamic potentials in closed and open nanocrystalline systems: Ge-Si:Si(001) islands. Physical Review Letters, v. 100, n. 22, p. 226101, 2008.

11. Kamins, T. I. et al. Influence of phosphine on Ge/Si (001) island growth by chemical vapor deposition. Journal of Applied Physics, v. 94, n. 6, p. 4215-4224, 2003.

12. Where Îľ// is the in-plane strain as measured

by GIXRD, C11 and C12 are the composition dependent elastic constants of the Si-Ge alloy, r and k are the unit vectors for the radial and growth directions, k is the Boltzmann constant, T is the growth and annealing temperatures, and c is the Ge concentration.

13. Medeiros-Ribeiro, G.; Williams, S. Thermodynamics of coherently-strained GexSi1-x nanocrystals on Si(001): alloy composition and island formation. Nano Letters, v. 7, n. 2, p. 223-227, 2007.

Activity ActivityReport Report 2009 2008 |

35

6

Insights into the mechanism of progressive RNA degradation by the archaeal exosome

Marcos V. A. S. Navarro1, Carla C. Oliveira2, Nilson I. T. Zanchin1, and Beatriz G. Guimar達es1 1

Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil.

2 Department of Biochemistry, Chemistry Institute, University of S達o Paulo, S達o Paulo, SP, Brazil.

Almost all RNA species produced by a cell undergo several post-transcriptional processing reactions to produce functional RNA molecules. The exosome complex is a central component of the RNA maturation and degradation machinery both in archaea and in eukaryotes. In this work, a series of crystallographic structures of the RNase PH ring from Pyrococcus abyssi exosome in combination with RNA degradation assays performed with mutants of key amino acid residues, allowed us to propose a model of exosome-mediated RNA degradation which integrates the events involving catalytic cleavage, product elimination and RNA translocation.

Facility: MX1 Publication: Journal of Biological Chemistry, 283: 14120-14131 (2008) Funding: FAPESP

Science Highlights

Introduction

are processed to remove introns and external spacer sequences and undergo extensive

In eukaryotes, nearly all ribonucleic acid

covalent modifications. The RNAs that play

(RNA) molecules are synthesized as precursors

both a structural and catalytic role include

that undergo extensive processing and covalent

the ribosomal RNA (rRNA), the small nuclear

modification until they acquire their final

RNAs (snRNA) and the small nucleolar RNAs

conformation that renders them suitable to

(snRNA). The ribosomal RNA is a major structural

play a biological function in the cell. The RNA molecules that play a role in decoding

component of ribosomes but is also involved

genetic information, namely the messenger

in ribosome function during protein synthesis.

RNAs (mRNA), are modified at the 5’ end to

The pre-rRNA is a large molecule containing

receive a 7-methyl-GTP also known as the cap

four spacer sequences that need to be removed

structure, the non-coding sequences known

to give rise to the three mature ribosomes of

as introns are removed by a process termed

18S 5.8S and 28S. During rRNA maturation, a

splicing and a poly-adenylate is added to

number of uridine residues are converted into

the 3’ end. The RNA molecules that play an

pseudouridine and the bases and riboses are

adapter role, the transporter RNAs (tRNA),

methylated. The small nucleolar RNAs play an

K91(2)

R89(2) N5

N1 V86(1) E87(1)

R115(1)

E87(1)

37

A134(1) G135(1)

D133(1)

T136(1) A134(1) G135(1)

Water Phosphate Figure 1

) 4 (1 A13 de) i (am

D133(1)

K45(3)

(1)

T136 (1)

A132(1) T136(1)

e)

D186 (1) R137(1) R1

K45(3)

N181 (1)

D180 (1)

R97(1)

V86(1)

A132(1)

2)

R97 (1)

E116 (1)

m id

R112 (1) N1

R137(1)

R115 (1)

R108 (1)

Rrp42

R97(1)

R96 (1)

(a

F71(1)

D111 (1)

G1 3 (am 5 (1 ide ) )

D180(1) D204(1) N3 N4

9(

1(

D186(1)

Rrp41

)

F71 (1

2)

R96(1)

R8

K45(3)

R137(1) R97(1) R108(1) N1 R112(1) N2

K9

T136(1)

K4

5(

3)

Hydrogen bond Pi-stacking

P. abyssi exosome RNA recognition cleft. Rrp41 and Rrp42 subunits are colored in blue and light brown

respectively. Heterodimers forming the hexameric ring are assigned 1 to 3 and numbers in parenthesis identify residues from the same dimer. a) Cartoon representation of the N1 to N5 binding sites. Residues involved in RNA interaction are labeled and shown in sticks. Residues mutated in this work are indicated with a colored star. b) Schematic representation showing the RNA-exosome interactions in detail. c) Stereo view of the N1 nucleotide binding site. The |Fo| – |Fc| electron density map contoured at 4 σ is superposed on the solvent atoms Activity ActivityReport Report 2009 2008 |

37

Insights into the mechanism of progressive RNA degradation by the archaeal exosome

essential role in the catalysis of these covalent

the human exosome PNPase-like core revealed

modifications. Depending on the physiological

an architecture very similar to the archaeal

conditions, the RNA must be degraded and the

complex9.

nucleotides recycled, especially the mRNAs,

This work was motivated by the fact that

which usually have time-restricted functions.

some key questions on the exosome catalytic

All these events must be highly coordinated

mechanism remained to be addressed, particularly

and a key player in the maturation of ribosomal

with regard to how the RNA is progressively

RNA and degradation of mRNA is the exosome

processed, how the free nucleoside diphosphate

complex, an RNA degradation machine that

is released, and the relevance of the archaeal

removes nucleotides, one by one, from the

exosome quaternary organization. New insights

3’ to the 5’ orientation of the RNA molecule

into these questions are reported in this work,

(reviewed in Figure 1). Scientists have made use

which is based on a set of high resolution crystal

of many model systems to gather information

structures of Pyrococcus abyssi Rrp41-Rrp42

on the exosome function. Yeast, the organism

complexes: two “native” structures at 2.14 and

providing the first evidence of the existence of

2.40 Å resolution, which revealed non-specific

exosomes, has been exploited from the genetic

nucleotides bound to the RNA cleft; a 10-mer

point of view, revealing all the components of

poly(A) RNA complex at 1.94 Å resolution and

the exosome complex. Structural analyses took

a CDP complex at 2.30 Å resolution.

advantage of the stable archaeal exosomes, which are more amenable to crystallization than exosome complexes from eukaryotes.

Previous studies have shown that the

The subunits Rrp41 and Rrp42 of the P. abyssi

archaeal exosome consists of two RNase PH

exosome were co-expressed in E. coli and

subunits (Rrp41 and Rrp42) and two proteins

the purified complex was crystallized. X-ray

containing the RNA-binding domains S1/KH

diffraction data were collected at the D03B-MX1

(Rrp4) or S1/zinc-ribbon (Csl4) RNA-binding

beam line of the Brazilian Synchrotron Light

domains . The exosome shows a PNPase-like

Laboratory. The structure was solved by molecular

fold5, composed of alternating RNase PH

replacement using the atomic coordinates of

subunits assembled into a hexameric ring

the A. fulgidus Rrp41-Rrp42 heterodimer as

capped by a trimer of RNA-binding proteins,

the search model (PDB code 2BA0).

2-4

which can be formed by either Rrp4 or Csl4

PH ring structure in complex with RNA8, the

architecture encloses the exoribonucleolytic

contacts found in the RNA recognition cleft of

active sites at the bottom of the RNase PH ring

the P. abyssi exosome ring described here are

catalytic chamber and restricts the entry to only

dominated by ionic interactions between the

unstructured RNA through the S1 pore, formed

phosphate backbone of the four nucleotides of

by the RNA-binding subunits of the exosome

the RNA 3’ end and a ladder of arginine side

cap placed at the top of the ring4,6-8. Compared

chains from both Rrp41(1) and Rrp42(1) subunits

to archaeal exosomes, the eukaryotic exosome

(Figure 1) (for clarity, the three heterodimers

displays a more diverse subunit composition .

which form the quaternary structure of the

Nevertheless, the recently reported structure of

archaeal exosome core are designated 1, 2 or

4,6,7

1

| Activity Report 2008

As in the case of the S. solfataricus RNase

. Such an

or possibly by a mixture of both

38

Results and discussion

Science Highlights

3 throughout the text and the residues and

These amino acid substitutions, as well as

subunits belonging to them will be distinguished

other mutations performed in this work, did

by these numbers in parenthesis). However,

not affect the RNase PH ring assembly and

the 10-mer poly(A) RNA-bound structure

stability. Substitution of R89 and K91 from

solved in this work showed a fifth nucleotide

Rrp41 by glutamic acids completely blocked

(N5) at the specific RNA recognition cleft.

RNA degradation, similarly to mutation of

Furthermore, the high resolution obtained

the catalytic residue D180 in the complex

for this complex revealed a more intricate

Rrp41D180A-Rrp42, whereas the exosome variant

network of RNA-exosome contacts, showing

bearing the point mutation Rrp42K45A displayed

that subunits from the three heterodimers

a slower catalytic rate. Thus, additionally to

participate in RNA recognition (Figure 1a,b).

the central heterodimer Rrp41(1)-Rrp42(1),

The phosphorolytic site of the P. abyssi exosome

conserved archaeal residues from both flanking

on the Rrp41(1) subunit, is formed by two

heterodimers (K45 from subunit Rrp42(3) and

conserved arginines (R97 and R137) and by

R89/K91 from subunit Rrp41(2)) (Figure 1b)

the catalytic residue D180, which interacts

are involved in the formation of the specific

with the phosphate moiety of nucleotide N1.

RNA recognition cleft and are essential for

The ribose 3’ OH of N1 is hydrogen-bonded to

efficient RNA degradation. These findings

the main chain of the conserved A134 and the

provide the first direct evidence of the role

inorganic phosphate binding site, comprised by

of archaeal exosome quaternary structure in

the conserved residues G135, T136 and R137, is

RNA processing.

occupied by three water molecules (Figure 1c).

Besides the nucleotides N1-N5 found at the

All the structures solved in this work showed

RNA recognition cleft, the electron density maps

a water-mediated interaction between the

of the RNA-bound structure allowed for the

ribose 2’ OH of N1 and the conserved lysine

modelling of two additional nucleotides, which

K45 from the Rrp42(3) subunit, which is part

were unambiguously assigned to positions N7

of the neighbor heterodimer (Figure 1c). On

and N10 (Figure 2a). Following the path from

the other extreme of the exosome specific RNA

the exosome phosphorolytic site towards the

recognition cleft, the nucleotide N5 found in

top entry of the RNase PH ring channel, the

the P. abyssi RNase PH core structure breaks the

nucleotides N7 and N10 were respectively

pattern of base stacking interaction observed for

found in a midway channel groove and in the

the four inner-most 3’ end nucleotides pointing

neck structure formed at the top of the ring

the RNA strand to the exosome central chamber

(Figure 2b). While the groove at N7 is formed by

and, most importantly, the phosphate moiety

conserved loops from the Rrp42(1) and Rrp41(2)

of N5 interacts with the conserved residues

subunits at the interface of two heterodimers,

R89 and K91 of the Rrp41(2) subunit from the

the neck at N10 is formed in the interface of the

adjacent heterodimer (Figure 1a).

three adjacent Rrp41. This finding reinforces

To verify the relevance of the Rrp42 K45

the requirement of a quaternary structure for

and Rrp41 R89 and K91 residues to catalysis,

the exosome function on RNA degradation,

RNA degradation assays were carried out

since residues from neighboring heterodimers

with reconstituted Rrp41-Rrp42

and

participate in nucleotide binding. Interestingly,

Rrp41 R89E-K91E-Rrp42 mutant complexes.

nucleotides N7 and N10 interact with the

K45A

Activity ActivityReport Report 2009 2008 |

39

Insights into the mechanism of progressive RNA degradation by the archaeal exosome

5’ N10

N10

N10 neck

N9

N8

1

N7 groove

N7 2

N7

2

1

N6 3’ Rrp41 N1

Figure 2

40

N2

N3

N4

N5

Rrp42

10-mer poly(A) RNA bound to the P. abyssi exosome catalytic chamber. a) |Fo| – |Fc| electron density map contoured at 2.5 σ superposed on the final 10-mer RNA model. Modeling of N7 and N10 bases is highlighted. b) Side cut of the exosome core structure showing the accommodation of the 10-mer poly(A) RNA. N7 and N10 binding sites are highlighted. Rrp41 and Rrp42 subunits are respectively colored in blue and light brown and subunits from the same heterodimer are labeled with the same number (1 or 2)

| Activity Report 2008

exosome mostly via their purine moieties,

similar structural conformation, but presents a

in contrast with the salt-bridge interactions

more extensive network of interactions with the

observed between the N1-N5 phosphate

exosome and lower normalized B-factor. This

backbone and the exosome RNA recognition

apparent structural stabilization of the catalysis

cleft. Nonetheless, the unspecific nature of the

product is inconsistent with the elimination of

interaction is preserved, given that N10 and

the 3’ end RNA cleaved nucleotide by simple

N7 binding are mediated by hydrophobic and

diffusion, especially if one takes into account the

π-stacking interactions which are not specific

high processive capacity of archaeal exosomes

to a particular base. Based on the position

towards RNA degradation. Unexpectedly, the

of nucleotides N1-N5, N7 and N10, it was

electron density maps of the second native P.

possible to model the entire 10-mer poly(A)

abyssi exosome structure solved in this work

RNA strand within the exosome catalytic

showed clearly a nucleoside diphosphate

chamber (Figure 2b).

bound to the N1 site (modelled as an ADP)

The CDP-bound structure solved in this work

with two possible conformations regarding

suggests that, following phosphorolytic cleavage,

the phosphates (Figure 3), suggesting a NDP

the newly formed nucleoside diphosphate (NDP)

structural rearrangement prior to diffusion. In

undergoes stabilization within the exosome

Figure 3, position A corresponds to the expected

active site prior to release. In comparison

conformation of the cleavage product after

with the N1 nucleotide modeled in the 10-mer

phosphorolytic attack, as shown by Lorentzen

poly(A) RNA-bound structure, CDP displays a

and Conti8 and also observed in our CDP-bound

Science Highlights

structure. The ADP alternative conformation places the phosphate PB moiety in position to interact with three conserved acidic residues from Rrp41 subunit: D186, D204 and catalytic

B D180(1) D204(1)

D180 (position B in Figure 3). Although phosphate binding sites are not expected to

D186(1)

be composed of acidic residues, the quality of the electron density maps clearly indicated the conformational change of phosphate PB. Such

K45(3)

a structural rearrangement could take place by a simple rotation along the PA—O4 bond, which is compatible with previous findings

A R137(1)

describing a displacement of about 4 Å of the newly formed 3’ end of the RNA molecule (N2) after phosphorolytic cleavage (8). To verify the effect of Rrp41 D186A and D204A mutations on the catalytic activity, RNA degradation

Figure 3

T136(1)

Structural rearrangement of the diphosphate nucleoside after cleavage. The |Fo| – |Fc| electron density map contoured at 3σ shows two possible positions for ADP phosphate PB moiety (labeled A and B). The residues involved in nucleotide-exosome interactions are indicated

assays were carried out with the reconstituted Rrp41D186A-Rrp42 and Rrp41D204A-Rrp42 complexes.

the cleavage product at the N1 site seems to be

Substitution of residue D186 in Rrp41 completely

compatible with such requirements. Firstly, given

eliminated RNA degradation, similarly to the

the negative charge of phosphate PB moiety,

results observed for the mutant Rrp41D180A-Rrp42,

interaction with the new site (position B in

whereas the variant Rrp41D204A-Rrp42 displayed

Figure 3) would require protonation of the aspartic

a slower activity.

acid residues, including the catalytic residue

These new structural and functional data

D180 of Rrp41. Additionally, the conformational

allow the proposition of a rationale for the

change of the nucleoside diphosphate creates

release of the excised nucleoside diphosphate,

space for the binding of an incoming inorganic

connecting the exosome mechanisms of RNA

phosphate. These observations suggest that after

catalytic cleavage to progressive processing. It

catalysis, the product undergoes a structural

was previously proposed that the phosphorolytic

rearrangement induced by protonation of

RNA attack proceeds via a SN2 mechanism, with

residues D204, D186 and catalytic D180 of

a conserved acidic residue performing the role

Rrp41. The pKa value for the conserved D186

of the general proton donor to the 3’ oxygen of

residue calculated according to Li et al. (10)

the cleaved RNA N2 ribose8. Following catalysis,

is approximately 11 and is in agreement with

several events must occur to promote continuous

the pKa observed for the equivalent residue

RNA processing, including: elimination of the

in S. solfataricus exosome8. This pKa value,

nucleoside diphosphate product, re-protonation

unusual for an aspartate, together with the close

of the catalytic acidic amino acid residue,

proximity of D186 to D180 and D204, suggests

re-positioning of the inorganic phosphate at

that this residue may serve as a proton donor

the phosphorolytic site and RNA translocation

to the aspartic acids involved in the alternative

to the N1 site. The structural rearrangement of

PB site. RNA degradation assays corroborate Activity ActivityReport Report 2009 2008 |

41

Insights into the mechanism of progressive RNA degradation by the archaeal exosome

Nucleotide rearrangement

Phosphorolytic attack O

O

D186

O

D180

O

P

O

OH O H2N +

NH

OH R137 T136

5’ O

O O

O P

O

P

O OH

O

O

3’ HO

H N G135

H N A134

H

OH O H2N

K45

H2N

O H H

D180

P

5’

O

O

O

O HO

O

K45

OH

O

P NH2 O O O O P O H2N O OH OH 3’ HO H O H H R137 N N H T136 A134 G135 +

OH

–

OH

D204

O

O

O

H

O NH2

D186

O

OH HO

D204

O

O

O

NH

Nucleotide elimination O

D186

D204

O

O

OH

OH

OH New round of catalysis

O

O

O H2N

O

R137 T136

P

5’

O O

O

HO

O

OH

O O

3’ HO

H N G135

K45

H N A134

OH

H2N

O H H

Schematic representation of the archaeal exosome RNA processing mechanism. Inorganic phosphate and PB moiety of the nucleoside diphosphate are represented in red. Green arrows indicate structural rearrangements putatively involved in the mechanism

this model, since the inactivity of variant

change would release the product from the

Rrp41D186A-Rrp42 towards the RNA substrate

base-stacked position assisted by binding of

indicates that residue Rrp41 D186 directly participates in catalysis. Furthermore, the low activity showed by the mutant Rrp41D204A-Rrp42 is in agreement with the role of D204 side chain in stabilizing the NDP PB moiety in its new

42

P

O

P P O NH2 + O O NH O OH

Figure 4

O

D180

O

| Activity Report 2008

a new inorganic phosphate at its specific site.

Thus, the newly formed RNA 3’ end, which has been shown to remain bound to the exosome after N1 cleavage8, may move to the exosome

conformation, prior to the product elimination.

catalytic site already prepared for the next

The nucleoside diphosphate conformational

round of 3’ end RNA cleavage (Figure 4).

Science Highlights

Finally, the new features of the archaeal

that the complex has exclusively assumed

phosphorolytic RNA degradation mechanism

the function of scaffold for the exosome

identified in this work allows us to propose

activating complexes. Structure determination

an explanation for the lack of such activity

of hydrolytic subunit-containing eukaryotic

in the eukaryotic complexes. Additionally, it

exosomes will help to confirm or refute this

has been speculated that the RNA substrate

hypothesis.

could reach the eukaryotic active subunits, specially the yeast Rrp44, either through the exosome PNPase-core central channel or by

Financial Support

direct access11. The lack of conservation of some

This work was supported by FAPESP grants

nucleotide binding sites within the eukaryotic

05/56493-9 (to CCO), CEPID/CBME 98/14138-2,

PNPase-core may indicate that this route is

SMolBNet 00/10266-8 (to NZ and BGG) and

not used by the RNA substrates, suggesting

06/02083-7 (to NZ).

RefeRences

1. Houseley, J.; LaCava, J.; Tollervey, D. RNAquality control by the exosome. Nature Reviews. Molecular Cell Biology, v. 7, n. 7, p. 529-530, 2006.

2. Evguenieva-Hackenberg, E. et al. An exosome-like complex in Sulfolobus solfataricus. EMBO Reports, v. 4, n. 9, p.889-893, 2003.

3. Ramos, C. R. R. et al. The Pyrococcus exosome complex: structural and functional characterization. Journal of Biological Chemistry, v. 281, n. 10, p. 6751-6759.

2006.

4. Büttner, K.; Wenig, K.; Hopfner, K.P. Structural framework for the mechanism of archaeal exosomes in RNA processing. Molecular Cell, v. 20, n. 3, p. 461-471, 2005.

5. Symmons, M. F.; Jones, G. H.; Luisi, B. F. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.

Structure, v. 8, n.11, p.1215-1226, 2000.

6. Lorentzen, E.et al. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nature Structural

& Molecular Biology, v. 12, n. 7, p. 575581, 2005.

7. Lorentzen, E. et al. RNA channelling by the archaeal exosome. EMBO Reports, v. 8, n. 5, p. 470-476, 2007.

8. Lorentzen, E.; Conti, E. Structural basis of 3’ end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core.

Molecular Cell, v. 20, n. 3, p. 473-481, 2005.

9. Liu, Q.; Greimann, J. C.; Lima, C. D. Reconstitution, activities, and structure of the Eukaryotic RNA exosome. Cell, v. 127, n. 6, p. 1223-1237, 2006.

10. Li, H.; Robertson, A. D.; Jensen, J. H. Very fast empirical prediction and rationalization of protein pKa values. Proteins, v. 61, n. 4, p. 704-721, 2005.

11. Wang, H.-W. et al. Architecture of the yeast Rrp44–exosome complex suggests routes of RNA recruitment for 3′ end processing.

Proceedings of the National Academy of Sciences, v. 104, n. 43, p. 16844-16849, 2007.

Activity ActivityReport Report 2009 2008 |

43

7

Effect of alkaline treatment on the ultrastructure of starch granules

Roberta C. S. Thys1, Harry Westfahl Jr2, Caciano P. Z. Noreña3, Lígia D. F. Marczak1, Nádya P. Silveira4, Mateus B. Cardoso2 1 Postgraduate Program in Chemical Engineering, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil 2

LNLS – Laboratório Nacional de Luz Síncrotron, Campinas, SP, Brazil 3

Instituto de Ciência e Tecnologia dos Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil 4

Instituto de Química, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil

Starch is a plant polysaccharide that occurs as discrete and partially crystalline microscopic granules. The development of different extraction methods to isolate granules with high purity and well-defined physical properties has increased due to the wide utilization of starch as an ingredient in the food industry.

Alternatives to the pattern alkaline extraction protocol have been investigated in order to improve the extraction yield while maintaining the functional properties of the starch granules. In this work, we focused our efforts on the evaluation of the effect of alkaline treatments on the ultrastructure of Araucaria angustifolia (pinhão) starch granules during their extraction.

Facility: FAC, SAXS2, GAR (Rotating Anode), LME and AFM/MTA.

Publication: Biomacromolecules. 2008; 9:1894-1901.

Funding: LNLS

Science Highlights

Starch is a plant polysaccharide that occurs

extracted through successive water washes

in the form of discrete and partially crystalline

are isolated granules with a typical starch

microscopic granules. The development of

morphology, while atomic force microscopy

different extraction methods to isolate high

(AFM) (Figure 1b) reveals the characteristic

purity granules with well-defined physical

spaced protuberances usually observed on

properties has increased due to the wide use

the surface of native starch1. SEM analysis

of starch as an ingredient in the food industry.

indicates that alkaline treatment allows for

Alternatives to the standard alkaline extraction

the formation of a continuous film in which

protocol have been investigated aiming to

the granular starch morphology is partially

improve the extraction yield while maintaining

damaged (Figure 1c). In parallel, the AFM image

the functional properties of starch granules.

in Figure 1d indicates a substantial alteration of

This work involved an evaluation of the effect

the granule surface, with the nodules presenting

of alkaline treatments on the ultrastructure

a significant reduction in height.

of starch granules of Parana pine (Araucaria

Figure 2 shows wide-angle X-ray scattering

angustifolia) seeds (popularly known as “pinhão”

(WAXS) diagrams representing the preferential

in Brazil) during their extraction.

organization of crystallites in pinhão starch

Starch presents an onion-like ultrastructure

granules5. The green profile shown in Figure 2a

composed of concentric semicrystalline

corresponds to granules obtained through

and soft amorphous growth rings1. These

successive water washes, whose crystallinity

semicrystalline growth rings are characterized by alternating crystalline and amorphous lamellae presenting a repetition period of 9-10 nm2. On the molecular scale, the crystalline lamellae of native starch are attributed to the short-chain fraction of amylopectin branches arranged as double helices packed in small crystallites3, 4. Starch can be extracted from different botanical species by a variety of purification techniques. However, some of

10 Mm

200 nm

10 Mm

200 nm

these methods cause irreversible changes in the ultrastructural organization of starch, impairing its use in several industrial applications.

Evaluating the extent of these modifications on the granules and their correlation to the extraction procedure is therefore crucial. In this work, we investigated the efficiency of the alkaline extraction method and compared it with starch granules extracted through successive washes in water.

The scanning electron microscopy (SEM) image in Figure 1a shows that pinhão starches

Figure 1

Scanning electron microscopy (a and c) and atomic force microscopy (b and d) images of pinhão starches obtained by water (a and b) and alkaline (c and d) extraction procedures Activity ActivityReport Report 2009 2008 |

45

Effect of alkaline treatment on the ultrastructure of starch granules

index was calculated as 23.3 ± 0.3%. After

crystalline and amorphous lamellae. Significant

alkaline treatment (blue profile in Figure 2a),

differences were visible, since the intensity of

the intensities at 5.6, 17.0, 22.0 and 24.0° were

the peak was slightly reduced when starch

significantly decreased, although the same

granules were alkali-extracted6. In this work,

diffraction pattern profile was still recognizable.

we used the paracrystalline lattice theory7 to

Therefore, the alkaline treatment reduced the

determine the structural characteristics of different

crystallinity index to 19.1 ± 0.4%. The small-angle

starches. The results of the paracrystalline fits

X ray scattering (SAXS) profiles in Figure 2b

are depicted in Figure 2b as solid red lines. The

show a typical peak at q ~ 0.6 nm–1, which is

main results obtained by WAXS and SAXS

believed to result from the granules’ alternating

are summarized in the schematic drawing presented in Figure 3.

Figures 3a and b represent a starch granule extracted with water, while Figures 3c and d show a granule affected by the alkaline solutions.

Intensity (a.u.)

The schematic difference between the two sectioned starch granules (Figures 3a and c) is represented by the swelling of the amorphous growth ring (pale gray zone) in the presence of NaOH through the expansion of this area.

As a consequence, the semicrystalline region (dark gray zone) is gradually compressed by the expansion of the amorphous growth 5

10

15

20

25

30

35

40

rings. Moreover, the swelling effect can be

2Q (°)

well correlated to the reduction of the lamellar periodicity (d). This change in d is portrayed

4

in Figures 3b and d, where the crystalline lamellae are represented by the blue helices Intensity (a.u.)

3

area while the amorphous ones are displayed in the intermediate green region between helices with no organization. Thus, the main effect

2

observed in the semicrystalline growth rings is attributed to the reduction of free volume of

1

soft amorphous lamellae (Figures 3b and d).

Finally, the results clearly indicate that alkaline extraction produces significant changes in the

0 0.4

0.5

0.6

0.7

0.8

0.9

1.0

q (nm ) –1

Figure 2

46

a) Wide-angle X-ray scattering profiles of starch granules extracted through water (green) and alkaline (blue) procedures. b) Small-angle X-ray scattering profiles of starches extracted through water () and alkaline () procedures. Full red lines represent the results of paracrystalline model fits

| Activity Report 2008

ultrastructure of starch granules.

The authors acknowledge ABTLuS for the use of X-ray facilities – SAXS-2 beamline and rotating anode GAR (Rotating Anode), and for the use of its SEM and AFM microscopy equipment.

Science Highlights

Figure 3

Ultrastructural schematic representation of pinh찾o starches obtained by water (a and b) and alkaline (c and d) extraction procedures. The sectioned spheres (a and c) represent a general view of starch growth rings. Pale gray: amorphous growth rings and dark gray: semicrystalline growth rings. The internal region of the boxes (b and d) corresponds to an amplification of lamellar starch organization. Crystalline lamellae are represented by the blue helices, while amorphous lamellae are visible as a green intermediate region between helices without any organization

RefeRences 1. Gallant, D. G.; Bouchet, B.; Baldwin, P. M. Microscopy of starch: evidence of a new level of granule organization. Carbohydrate Polymers, v. 32, n. 3-4, p. 177-191, 1997.

starch. Biopolymers, v. 27, n. 8, p. 12051221, 1988.

5. Cardoso, M. B.; Samios, D.; Silveira,

2. Calvert, P. Biopolymers: the structure of starch. Nature, v. 389, n. 6649, p. 338-339, 1997.

N. P. Study of protein detection and

3. Anne Imbertyet al. The double-helical nature of the crystalline part of A-starch.

Journal of Molecular Biology, v. 201, n. 2, p. 365-378, 1988.

v. 58, n. 7, p. 345-352, 2006.

4. Imberty, A. and Perez, S. A revisit to the three-dimensional structure of B-type

ultrastructure of brazilian rice starch during alkaline extraction. Starch-St채rke, 6. Cameron, R. E.; Donald, A. M. A small-angle X-ray scattering study of the annealing and gelatinization of starch. Polymer, v. 33, n. 12, p. 2628-2636, 1992.

Activity ActivityReport Report 2009 2008 |

47

8

Magnetic resonant X-ray diffraction applied to the study of EuTe films and EuTe/PbTe multilayers

B. Díaz1, E. Abramof, P.H.O. Rappl, E. Granado,2 V. A. Chitta, A. B. Henriques3 1

Laboratório Associado de Sensores e Materiais, Instituto Nacional de Pesquisas Espaciais, São José dos Campos, SP, Brazil

2 Instituto de Física “Gleb Wataghin”, UNICAMP, Campinas, SP, Brazil, Laboratório Nacional de Luz Síncrotron, Campinas, SP, Brazil 3 Instituto de Física, Universidade de São Paulo, São Paulo, SP, Brazil*

Magnetic resonant X-ray diffraction was used to study the magnetic order in thin EuTe films and EuTe/PbTe multilayers. The measurements were taken at the Eu LII absorption edge, taking advantage of more than two orders of magnitude enhancement in resonant intensity.

A graphite analyzer was used to separate magnetic and charge scattering, thus lowering background noise to ~1 cps. The finely tuned experimental setup, together with the high surface sensitivity of X-rays, allowed for the detection of the magnetic signal from a EuTe film of only 40 monolayers. Magnetic interlayer correlations were detected among the EuTe layers across the nonmagnetic PbTe spacers of a EuTe/PbTe superlattice. The temperature dependence of the superlattice magnetic satellite intensities indicated that the magnetization decreased preferentially in the outer monolayers of the individual EuTe layers when the Néel temperature was approached.

Facility: XRD-2 Publication: Applied Physics Letters, 92: 242511-1-3 (2008) Funding: CNPq and FAPESP

Science Highlights

Introduction

material.5 In type-II AFMs, the spins align

Magnetic resonant X-ray diffraction (MRXRD) is a relatively new technique, which appears as an interesting alternative to neutron diffraction in the study of magnetic structures.1 The main

parallel within (111) planes and antiparallel with spins in adjacent (111) planes. As a result, the magnetic unit cell along the [111] direction is twice the size of the structural cell. Hence,

drawback of MRXRD is the weak intensity

in the ordered state, magnetic peaks arise at

of the magnetic peaks compared with the

half order hkl (½ ½ ½), (1½ 1½ 1½),…

structural ones. However, this problem has been

The magnetic order of EuTe thin films

overcome partially by the increasing availability

and EuTe/PbTe multilayers has already

of synchrotron sources with high intensity

been investigated using neutron diffraction.6

beams. Furthermore, in resonant diffraction, an

However, neutron surface sensitivity is very

incident energy close to an absorption edge of

limited compared to X-rays. Working at the

the magnetic element is chosen, usually L and M

resonance condition at the Eu LII edge, and using

edges for rare earths and transition metals.

1-4

a polarimeter to separate the magnetic signal,

At these particular energies, an enhancement

we were able to measure the magnetic peak

of the magnetic diffracted intensity of up to six

from a EuTe layer of only 40 monolayers. We

orders of magnitude has been observed.

also studied the resonant magnetic diffraction

The high degree of polarization of synchrotron radiation is also advantageous for MRXRD because the polarization of the magnetically scattered radiation is rotated by 90o relative to the polarization of the incident radiation, while the polarization remains unchanged for charge

of a EuTe/PbTe superlattice, which evidenced EuTe intra- and inter-layer magnetic ordering, and provided information on the temperature dependence of the magnetic profiles within the individual EuTe layers.

scattering. An analyzer crystal placed behind the sample allows one to separate horizontally3.5

1.6 K

polarized σ´ charge-scattered radiation from

angle 2θ of the analyzer crystal must be 90 .

o 1

Because the background noise in X-ray experiments originates mainly from charge scattering, the measurements in the σ → π´ scattering channel are almost noise-free, thus favoring the observation

3.0

104

2.5 103 2.0

Fluorescence (a.u.)

radiation. For a perfect separation, the scattering

Integrated intensity (a.u.)

vertically-polarized π´ magnetically-scattered

of weak magnetic peaks.

In this work we use MRXRD to study the

1.5

Eu LII

102

magnetic order of a 1.5 µm EuTe film and of EuTe/PbTe multilayers. Both EuTe and PbTe are

7500

EuTe is a type-II antiferromagnet (AFM) below the Néel temperature, TN, of 9.6 K for the bulk

7600

7650

7700

Energy (eV)

semiconductors with NaCl structure, and a lattice mismatch of 2%. While PbTe is non-magnetic,

7550

Figure 1

Integrated intensity of the magnetic peak at (1½ 1½ 1½) as a function of the incident energy near the Eu LII edge (circles).

Fluorescence intensity around the same edge, with the detector placed outside the Bragg position (solid line) Activity ActivityReport Report 2009 2008 |

49

Magnetic resonant X-ray diffraction applied to the study of EuTe films and EuTe/PbTe multilayers

Experimental

EuTe layer and the EuTe/PbTe SL were found

The samples were grown on top of (111) BaF2 substrates by molecular beam epitaxy (MBE), in a Riber 32P MBE system containing solid sources of PbTe, Eu, Te and BaF2. Prior to the growth, freshly cleaved (111) BaF2 substrates were preheated to 400 ºC in the growth chamber for 15 min to remove impurities. Three samples were grown for this study: (1) a bulk-like 1.5 µm EuTe film grown directly on the BaF2 substrate, covered with a thin BaF2 cap layer to protect it from oxidation; (2) a 40 monolayer (ML) EuTe layer embedded between a 3 µm PbTe buffer layer and a 40 ML PbTe cap layer; and (3) a EuTe/PbTe superlattice (SL) grown on top of a 3 µm PbTe buffer layer and

by fitting the triple-axis θ/2θ scans around the (222) structural Bragg reflection, using Takagi-Taupin dynamic diffraction theory.

MRXRD experiments were carried out at the XRD2 beamline at LNLS.7 This beamline is located behind a bending magnet, followed by a vertically focusing Rh-coated mirror, and a double-bounce (111) Si monochromator. At the end-station is a six-circle Huber diffractometer with vertical scattering plane.

To measure the magnetic peaks, the samples must be cooled below TN. To this end, a closed cycle ARS Displex DE-202 cryostat with a Joule-Thomson circuit in the last stage was mounted on the χ-circle of the diffractometer.

composed of 50 repetitions of 7 and 14 ML of

The cryostat reaches a base temperature of 1.6 K.

EuTe and PbTe, respectively. An X´Pert MRD

Three beryllium domes separate the sample

high-resolution X-ray diffractometer was

from the atmosphere. A Cyberstar scintillation

used for the structural characterization of the

detector was used for all the measurements.

samples. The full-width at half-maximum of

To measure the magnetic peaks of the

the (222) rocking curve of the 1.5 µm EuTe film

40 ML EuTe layer and the EuTe/PbTe SL, a

was 300”, indicating a high structural quality.

polarimeter was placed at the Huber 2θ arm.

The individual layer thicknesses of the 40 ML

The polarimeter allows for rotation of the analyzer crystal and the detector around the Huber 2θ arm, so as to choose σ → σ´

101

(structural) or σ → π´ (magnetic) scattered

(1/2 1/2 1/2)  – ’

radiation. A graphite analyzer was used,

Intensity (cps)

whose (003) reflection had a 2θ of 93.3o for the Eu LII energy. The 2θ close to 90o assures a good separation of the σ → σ´ and σ → π´ radiation scattered at the sample.

Results and discussion 100

We started by investigating the bulk-like 0.70

0.75

0.80

0.85

0.90

0.95

QZ (Å–1) Figure 2

50

(½ ½ ½) magnetic reflection of the 40 ML EuTe layer measured in the σ → π´ channel of the polarimeter at a temperature of 1.6 K

| Activity Report 2008

1.5 µm EuTe film. As expected for a type-II AFM, magnetic peaks were observed below TN at half order hkl positions in the reciprocal space. The intensity of these peaks increased by more than two orders of magnitude when

Science Highlights

the energy was swept around the Eu LII and LIII

The kinematic model 6 was used to fit the

absorption edges (Figure 1). We also measured

magnetic scattering of the SL (solid line in

the fluorescence intensity as a function of the

Figure 3a). This model yields a parameter p,

incident energy, with the detector placed away

whose signal indicates if two adjacent EuTe

from any Bragg position. The Eu absorption edges

layers have the same (p > 0) or opposite (p < 0)

LII and LIII, determined as the maximum of the

magnetic sequence. The modulus of p is the

first derivative fluorescence, were identified at

probability of two adjacent EuTe layers being

7609.5 and 6970.9 eV, respectively. The maximum resonances of the magnetic peaks occurred

a

(1/2 1/2 1/2)  – ’

within 3 eV above the absorption edges. The at half order hkl further supported the magnetic nature of these reflections.8 Figure 2 shows the (½ ½ ½) magnetic peak measured in the σ → π´ channel, at 1.6 K, for

Intensity (cps)

polarization analysis of the radiation scattered 101

the 40 ML EuTe layer. The magnetic peak is clearly defined above a background of only

100

1 cps, demonstrating the feasibility of detecting 0.5

magnetic signals from very thin magnetic

0.6

0.7

0.8

peak was fitted using a kinematic model

b

5

obtained considering a EuTe thickness of 40 ML 60

peaks or satellites denotes the existence of

Intensity (cps)

characterization.

magnetic channel. The presence of several

Area ratio

S0

(Figure 2), supporting the previous structural

around the (½ ½ ½) position in the σ → π’

40

with 10 s counting time per point.

10

8.2 K

S1

0 0.70

0.75

0.80

0.85

0.90

0.95

QZ (Å–1)

with 300 to 400 repetitions were used due to

measurement shown in Figure 3a took 1.4 h,

5 T (K)

10.1 K

neutron diffraction experiments, superlattices

satellites for a SL with only 50 repetitions. The

S0/S–1

3

1.5 K

S–1

20

using neutron diffraction.6 However, in the

MRXRD, we were able to detect the magnetic

4

0

across the PbTe non-magnetic spacers. These

the low surface sensitivity of neutrons. Using

S0/S1

2

magnetic correlations among the EuTe layers correlations have been observed previously,

1.1

80

described by Kepa et al.6 The best match was

EuTe (7ML)/PbTe (14ML) SL measured

1.0

QZ (Å–1)

layers in the XRD2 line at LNLS. The magnetic

Figure 3a displays a θ/2θ scan of the

0.9

Figure 3

(½ ½ ½) magnetic reflection, measured in the σ → π´ channel of the polarimeter, for a 50 repetition EuTe (7ML)/PbTe (14ML) SL (a). The solid line is a kinematic fit to the measurement, while the dashed line represents the expected magnetic diffraction curve if there were no magnetic correlations. The magnetic satellites measured at different temperatures are shown in (b).

The inset shows the integral intensity ratio between central and outer satellites as a function of temperature Activity ActivityReport Report 2009 2008 |

51

Magnetic resonant X-ray diffraction applied to the study of EuTe films and EuTe/PbTe multilayers

correlated. The fit in Figure 3a yielded p = 0.7,

layer. Figure 4 illustrates the dependence of

indicating that adjacent EuTe layers in the SL

the envelope function on the magnetization

have a reversed magnetic order.

intensity and profile of the EuTe layer. Figure 4a

The magnetic satellites of the SL were

demonstrates that if the magnetization decreases

measured at different temperatures (Figure 3b).

homogeneously in the entire EuTe layer, the

A decrease in the intensity was observed when

envelope function decreases by a factor of

TN was approached, as expected for increasing

one, while its width remains constant. If this

magnetic disorder. The widths of the satellites remained fairly constant almost up to TN, indicating that the extent of the correlations was also constant. We also observed that the intensity of the outer satellites declined more slowly than the intensity of the central satellite (Figure 3b). This result can be explained by the fact that the satellites’ intensity is determined by the envelope function, which is shown

is the case, the satellites’ integral intensity ratio should remain constant at increasing temperatures. On the other hand, if the magnetization decreases preferentially in the outer monolayers of the EuTe layer, the envelope function both weakens and broadens, as depicted in Figure 4b. In this case, the intensity of the central satellite is expected to

as a dashed line in Figure 3a. This envelope

fall faster than that of the outer satellites, as

function is the expected magnetic peak shape

was in fact observed. Hence, we can conclude

for an individual EuTe layer.

that as the temperature increases toward TN,

The envelope function, which is equivalent

the magnetization within the EuTe layers in

to the structure factor in charge diffraction,

the SL not only weakens but also decreases

can be expressed as the Fourier transform of

preferentially in the outer monolayers of each

the squared magnetization profile of a EuTe

EuTe layer.

MLs 1

a 2

3

4

5

6

1

7

2

3

4

5

6

b

7 2

2

3

4

5

6

102

102

101

101

100 10–1 10–2

52

| Activity Report 2008

5

6 7

100 10–1 10–2

0.4

Figure 4

4

1

7

Intensity (a.u.)

Intensity (a.u.)

1

3

0.6

0.8 QZ (Å–1)

1.0

1.2

0.4

0.6

0.8 QZ (Å–1)

1.0

1.2

Dependence of the envelope function on the magnetic profile of a 7 ML EuTe layer. In (a) the magnetic profile decreases homogeneously across the layer, while in (b) it decreases preferentially in the outer monolayers

Science Highlights

Conclusions We have used magnetic resonant X-ray diffraction to study the magnetic order in EuTe films and EuTe/PbTe multilayers.

Magnetic peaks were observed below TN at half order hkl, resulting from the AFM order along the [111] direction. The magnetic scattered intensity increased by more than two orders of magnitude near the Eu LII and LIII absorption edges. The magnetic and charge

demonstrated by the clear detection of the magnetic peak from a 40 ML EuTe layer.

The observation of magnetic satellites near (½ ½ ½) in the EuTe/PbTe SL demonstrated the existence of magnetic correlations among the EuTe layers. The temperature dependence of the satellite intensities provided an insight on the variation of the magnetization profile within the EuTe layers with nearly monolayer resolution.

scattered intensities were separated using a polarimeter with a graphite analyzer, pushing

Acknowledgments

the charge noise down to 1 cps during the

We thank G. Kellerman and C. Azimonte

measurements of the magnetic peaks. This

for their technical assistance and the LNLS for

resulted in very high surface sensitivity, as

the use of the XRD2 beamline.

RefeRences 1. Lovesey, S. W.; Collins, S. P. X-ray scattering and absorption by magnetic materials.

New York: Oxford University Press, 1996.

377p.

5. Oliveira, N. F. et al. EuTe. I. Magnetic behavior of insulating and conducting single crystals. Physical Review B, v. 5, n. 7, p. 2634-2646, 1972.

2. Granado, E. et al. Magnetic structure and fluctuations of Gd2IrIn8: A resonant x-ray diffraction study. Physical Review B, v. 69, n. 14, p. 144411, 2004.

6. Kepa, H. et al. Magnetic interactions in EuTe epitaxial layers and EuTe/PbTe superlattices. Physical Review B, v. 68, n. 2, p. 024419, 2003.

3. Tonnerre, J. M. et al. X-ray resonant magnetic scattering at ledges of 3d transition metals in multilayers. Nuclear Instruments and Methods in Physics Research B, v. 97, n. 1-4, p. 444-448, 1995.

7. Giles, C. et al. High-resolution X-ray diffraction beamline at the LNLS for the study of charge, orbital and magnetic structures. Journal of Synchrotron Radiation, v. 10, n. 6, p. 430-434, 2003.

4. Langridge, S. et al. Resonant magnetic x-ray-scattering studies of NpAs. I. Magnetic and lattice structure. Physical Review B, v. 49, n. 17, p. 12010-12021, 1994.

8. Diaz, B. et al. Magnetic resonant x-ray diffraction study of europium telluride.

Physical Review B, v. 78, n. 13, p. 134423, 2008.

Activity ActivityReport Report 2009 2008 |

53

9

Evolution of the spectral weight in the Mott-Hubbard series SrVO3–CaVO3–LaVO3–YVO3

R.J.O. Mossanek1, M. Abbate1*, A. Fujimori2, H. Eisaki3, S. Kohno4, F.C. Vicentin5 1

2

Departamento de Física, Universidade Federal do Paraná, Curitiba PR, Brazil Department of Complexity Science and Engineering, University of Tokyo, Kashiwa, Japan 3 Nanoelectronics Research Institute, AIST, 1-1-1 Central 2, Umezono, Tsukuba, Japan 4 Department of Applied Electronics, Tokyo University of Science, Noda, Japan 5 Laboratório Nacional de Luz Síncrotron, Campinas SP, Brazil *Corresponding autor: Miguel Abbate, e-mail: miguel@fisica.ufpr.br

The Mott-Hubbard series SrVO3–CaVO3–LaVO3–YVO3 present a distinct metal-insulator transition. The microscopic origin of this transition can be related to the correlation effects in the electronic structure. The valence band photoemission results show very interesting trends across these Mott-Hubbard series. These results suggest that the O 2p states play an important role in the Mott-Hubbard transition. Some of the changes in the spectra are unexpected and cannot be explained by the current Mott-Hubbard theories.

Facility: SXS Publication: Physical Review B, 78, 075103 (2008) Funding: CNPq and CAPES

Science Highlights

Introduction

electronic structure. One of the main experimental

Substitution produces interesting changes in the electrical and magnetic properties of transition metal oxides. For example, it is related to the high-TC superconductivity in La2-xSrxCuO4, and the colossal magnetoresistance in La1-xSrxMnO3. Substitution also generates Mott-Hubbard transitions in early

techniques used to study these transitions is photoemission spectroscopy (PES). The V 3d band of SrVO3 showed a coherent peak at the Fermi level, and a broader incoherent structure at higher binding energies2,3. Recent works suggested that the differences in the surface vs. bulk correlation might affect the PES spectra4,5. This prompted the development of

transition metal oxides like La1-xSrxVO3. These

hard x-ray photoemission (HXPES), because

metal-insulator transitions (MIT) are usually

the greater probing depth would enhance the

classified according to the main controlling

bulk contribution.

mechanism. In bandwidth control, substitution

In this work, we study the electronic

induces a lattice distortion, leading to changes

structure of the Mott-Hubbard series SrVO3-

in 3d dispersion1. In band-filling control, doping

CaVO3-LaVO3-YVO3. The main experimental

produces changes in the chemical potential and

technique used in the study was valence band

thus in the 3d occupation .

photoemission. The different features in the

1

The microscopic origin of this transition

experimental spectra were analyzed using cluster

can be related to the correlation effects in the

model calculations. These series include both

Structural properties

Electrical properties

106

Magnetic properties

"Insulating"

TN~114K

4

"Antiferromagnetic"

YVO3

104

103 LaVO3 102 CaVO3 10–3

Distorted

10–4

"Metallic"

3

YVO3

TN~142K

2

LaVO3

1 "Paramagnetic"

SrVO3

SrVO3

CaVO3

0 0

100

200

Temperature (K) Figure 1

Susceptibility (10–3 emu/mol)

Cubic

Resistivity (cm)

105

300

0

100

200

300

Temperature (K)

Structural, electrical and magnetic properties of SrVO3, CaVO3, LaVO3, and YVO3. Cubic SrVO3 and distorted CaVO3 are paramagnetic metals, whereas distorted LaVO3 and YVO3 are antiferromagnetic insulators Activity ActivityReport Report 2009 2008 |

55

Evolution of the spectral weight in the Mott-Hubbard series SrVO 3 –CaVO 3 –LaVO 3 –YVO 3

bandwidth and band filling control, whereas

change affects the V 3d dispersion and, hence,

previous studies were concerned with either

the effective V 3d one-electron bandwidth.

bandwidth or band filling control. Figure 1

LaVO3 and YVO3 materials are antiferromagnetic

shows the main structural, electrical and magnetic properties of the compounds in these series. The SrVO3 and CaVO3 compounds are paramagnetic metals with a nominal occupation

insulators with a nominal valence of 3d2 (V3+).

The larger band-filling inhibits coherent charge fluctuations and induces a metal-insulator

of 3d1 (V4+). The different ionic radius causes

transition. The V–O–V angle decreases from

a decrease in the V–O–V angle from 180° in

158° in LaVO3 to 144° in YVO3, again affecting

cubic SrVO3 to 160° in distorted CaVO3. This

the one-electron bandwidth.

Removal spectra

Photoemission spectra a

SrVO3

b

SrVO3 3d0

incoherent

3d1L

coherent CaVO3

Normalized intensity

Normalized intensity

CaVO3

LaVO3

YVO3

LaVO3

YVO3 3d1

10

8

6

4

Binding energy (eV)

Figure 2

56

3d1C

2

0

10

8

3d2D

6

4

3d2L

2

0

Binding energy (eV)

(a) Valence band spectra of SrVO3, CaVO3, LaVO3 and YVO3 taken at 1840 eV. The bars indicate the position and evolution of the main structures in the spectra. The V 3d band of SrVO3 and CaVO3 shows the coherent and incoherent features. (b) Calculated removal spectra of SrVO3, CaVO3, LaVO3, and YVO3. The labels correspond to the main configuration in each final state, see text

| Activity Report 2008

Science Highlights

Experimental Details

a pair of InSb(111) single crystals. The electron

The SrVO3, CaVO3, LaVO3, and YVO3 samples were single crystals grown by the floating zone method. The samples presented a single phase

energy analyzer was a Perkin-Elmer and the base pressure was in the 1-2 10â&#x20AC;&#x201C;9 mbar range.

The photon energy was set to 1840 eV and the combined energy resolution was approximately

structure, which was confirmed by powder X-ray

0.4 eV. The spectra were normalized to the

diffraction (XRD). The photoemission spectra

maximum and the Fermi level was determined

were measured at room temperature at the SXS

using a clean gold foil. The samples were scoured

beamline at LNLS (Brazil) . The beamline has a

repeatedly with a diamond file to remove

double-crystal monochromator equipped with

surface contamination. The surface quality of

6

V 3d band spectra

Removal spectra a

SrVO3 3d L 1

b

SrVO3

3d1C

3d1L

3d1C

CaVO3 CaVO3

Incoherent

Incoherent

LaVO3

Coherent Normalized intensity

Normalized intensity

Coherent

Incoherent

LaVO3

Incoherent

YVO3 3d2L

4

3

2 Biding energy (eV)

Figure 3

3d2L

YVO3

1

0

4

3

2

1

0

Binding energy (eV)

(a) V 3d band spectra of SrVO3, CaVO3, LaVO3 and YVO3 in greater detail. (b) Calculated removal spectra of SrVO3, CaVO3, LaVO3, and YVO3 in greater detail (solid line). The cluster model calculation (dashed line) is outlined on the background (dotted line). The spectra of SrVO3 and CaVO3 show the coherent (3d1C) and incoherent (3d1L) features, whereas the spectra of LaVO3 and YVO3 show only the incoherent (3d2L) structure Activity ActivityReport Report 2009 2008 |

57

Evolution of the spectral weight in the Mott-Hubbard series SrVO 3 –CaVO 3 –LaVO 3 –YVO 3

the samples was confirmed by the absence of

final spectral weight is found within the sudden

a shoulder in the O 1s core level spectra.

approximation.

Figure 2b shows the calculated valence band

Results and Discussion

| Activity Report 2008

YVO3. The discrete transitions were convoluted

Figure 2 (a) shows the valence band

with a 0.5 eV Gaussian to simulate the dispersion

photoemission spectra of SrVO3, CaVO3,

and broadening. For the metallic SrVO3 and

LaVO3, and YVO3. The vertical bars in the figure

CaVO3 compounds, the calculated V 3d band

indicate the position and evolution of the main

reproduces both the coherent and incoherent

structures in the spectra. The spectra are formed

peaks. The coherent peak is given mainly by

by the O 2p band, from 9.0 to 3.0 eV, and the

the well-screened final state 3d1C configuration.

V 3d band, from 3.0 to 0.0 eV. The O 2p band

The incoherent peak is mostly due to the

presents a prominent feature around 6.7 eV

well-screened final state 3d1L configuration.

for SrVO3, which shifts to 6.9 eV for CaVO3,

Finally, there is a weaker V 3d contribution

to 7.0 eV for LaVO3 and to 7.5 eV for YVO3.

mixed in the much more intense O 2p band.

The V 3d band of metallic SrVO3 and CaVO3

This structure is related to the poorly-screened

presents two distinct components: the coherent

final state 3d0 configuration.

structure around 0.5 eV and the incoherent

For the insulating LaVO3 and YVO3 materials,

feature around 1.7 eV. The coherent structure

the coherent fluctuation (3d2C) is replaced by a

of insulating LaVO3 and YVO3 is substituted

Mott-Hubbard screening (3d2D). The transfer of

by a new feature emerging at about 5.1 eV. The

spectral weight from the 3d2C to the 3d2D final

disappearance of the coherent structure opens

states opens the corresponding band gap. The

the band gap, whereas the remaining incoherent

incoherent peak is mainly due to the well-screened

feature shifts slightly to 1.8 eV.

final state 3d2L configuration. The Mott-Hubbard

The interpretation of the experimental spectra

peak is mostly formed by the final state 3d2D

is given by extended cluster model calculations.

configuration. Finally, the poorly-screened final

The cluster consists of a VO6 regular octahedron

state 3d1 configuration contributes to the higher

which is embedded in an effective medium7. The

energy removal state.

cluster model is solved by exact diagonalization

The aforementioned calculated V 3d removal

using the configuration interaction method.

states coincide with the main features in the

The ground (N) state is expanded in terms of

experimental spectra. The DMFT attributes the

charge transfer configurations from the O 2p

coherent structure to the quasi-particle peak,

states (3d L ). The model also includes charge

and the incoherent feature to the remnant of

transfer configuration from the coherent states

the lower Hubbard band4,5. The present cluster

in the metallic phase (3d n+cCc), as well as Mott-

model ascribes the coherent feature to the 3dnC

Hubbard charge transfer configuration in the

final state, in the same spirit as the quasi-particle

insulating phase (3d n+dDd). The main parameters

peak in DMFT, but the incoherent structure is

are the d-d repulsion U, the p-d charge-transfer

attributed here to the 3dnL configuration. The

energy ∆, and the p-d hybridization T. The

3dn-1 final state configuration appears mostly

removal (N–1) state is obtained by removing

mixed with the O 2p band at higher energies.

a 3d electron from the ground state, and the

Indeed, resonant photoemission experiments

n+l

58

removal spectra of SrVO3, CaVO3, LaVO3, and

1

Science Highlights

in YVO3 and CaVO3 show a considerable V 3d

CaVO3, the increased distortion decreases the

character around 7.0 eV8 (although some of

effective one-electron bandwidth. This reduction,

this V 3d character is also partially due to the

in turn, results in the transfer of spectral weight

covalent hybridization with the O 2p states).

from the coherent to the incoherent structures.

Figure 3a presents the V 3d band photoemission

From metallic CaVO3 (3d1) to insulating LaVO3

of SrVO3, CaVO3, LaVO3 and YVO3 in more

(3d2), the increased band-filling inhibits the

detail. The V 3d spectral weight follows a very

metallic charge fluctuations. The replacement

interesting trend as a function of the bandwidth

of the coherent fluctuation (3d2C) by the

and band-filling control. In metallic SrVO3 and

Mott-Hubbard screening (3d2D) opens the band

LaVO3 photoemission spectra

CaVO3 photoemission spectra a

b

h = 1840 eV Incoherent Coherent

1840 eV

Exp.

Al K

Non-bonding Bonding

He II

Normalized intensity

Normalized intensity

3d1L 3d1C

Cal.

h = 60 eV Incoherent

V 3d band Coherent

He I

Exp.

3d1L 3d1C Cal.

10

8

6

4

Binding energy (eV) Figure 4

2

0

Cal.

3

2

1

0

Binding energy (eV)

(a) Valence band spectra of LaVO3 obtained with different photon energies. The spectra can be divided into the bonding O 2p – V 3d band, the non-bonding O 2p part, and the V 3d region. (b) Calculated removal spectra of CaVO3 compared to the photoemission spectra taken at high energy (1840 eV) and low energy (60 eV). The photon energy dependence of the spectra is related to the relative O 2p character in the incoherent structure and the corresponding V 3d/O 2p cross-section Activity ActivityReport Report 2009 2008 |

59

Evolution of the spectral weight in the Mott-Hubbard series SrVO 3 –CaVO 3 –LaVO 3 –YVO 3

gap. Finally, the increase of the distortion in

low energy spectra (He II), where the relative

the insulating phase produces an additional

V 3d/O 2p cross section is about 1/1.

effect. The bandwidth of the incoherent feature

Figure 4b compares the V 3d band photo-

decreases from around 1.4 eV in LaVO3 to about

emission spectra of CaVO3 taken at 60 eV and

1.2 eV in YVO3.

at 1840 eV. The spectra present the coherent

Figure 3b presents the calculated V 3d removal

and incoherent peaks in both cases, but the

spectra of SrVO3, CaVO3, LaVO3 and YVO3 in

intensity of the incoherent feature decreases

greater detail. The calculated spectrum was

at higher energies. This is usually attributed

mounted on the corresponding background

to an increase in the mean free path of the

and was convoluted with Gaussian functions.

photoelectrons, and the ensuing decrease of

The calculation reproduces the coherent (3d1C)

the incoherent feature, which would be mainly

and incoherent (3d1L) peaks in metallic SrVO3

concentrated at the surface4,5. The present

and CaVO3, as well as the remaining incoherent

calculation explains the changes in the spectra

structure (3d2L) in the insulating LaVO3 and

in terms of relative V 3d/O 2p cross sections.

YVO3 compounds. The transfer of spectral

The V 3d and O 2p cross sections decrease at

weight from the coherent to the incoherent

higher photon energies, but the cross section

feature, in the metallic systems, is related to

of the O 2p level decreases more rapidly. The

the reduction of the V–O–V angle. Finally, the

incoherent peak diminishes because it contains

band gap in the insulating systems is due to

a much larger contribution from the O 2p states.

the replacement of the coherent (3d C) by the

The calculated spectra, weighted with the

Mott-Hubbard fluctuation (3d2D).

relative cross sections, are in good agreement

2

Figure 4a presents the photoemission spectra

with the experiment.

of LaVO3 obtained with different photon energies. The valence band of this compound can be divided into three main features: a

60

| Activity Report 2008

Summary and Conclusion

bonding O 2p – V 3d band (from 8.0 to 6.0 eV),

In conclusion, we studied the Mott-Hubbard

an almost pure non-bonding O 2p part (from

series SrVO3-CaVO3-LaVO3-YVO3 using high

6.0 to 4.0 eV), and a V 3d region (from 3.0 to

energy spectroscopy. The different features in

0.0 eV). The photoemission spectra exhibit a

the experimental spectra were analyzed using

considerable and continuous variation as a

cluster model calculations. The V 3d removal

function of the photon energy. In particular,

states presented a very interesting trend as a

the non-bonding O 2p part decreases strongly

function of bandwidth and band-filling control:

and the weak V 3d band diminishes at higher

(i) The bandwidth control from SrVO3 to CaVO3

photon energies. In fact, the high energy

transferred spectral weight from the coherent

photoemission spectrum is dominated by

to incoherent feature. (ii) The band-filling from

the bonding O 2p – V 3d band, whereas the

CaVO3 to LaVO3 inhibited the coherent charge

non-bonding O 2p part is strongly suppressed,

fluctuations, opening the band gap. (iii) Finally,

and the V 3d region appears diminished. In a

the bandwidth control from LaVO3 to YVO3

first approximation, the changes observed in the

reduced the width of the remaining incoherent

spectra are related to the photoemission cross

structure. There was also a considerable

section. The calculated spectra resemble the

contribution from V 3d removal states mixed

Science Highlights

in the O 2p band region. These results suggest that O 2p states play an important role in the Mott-Hubbard transition. Some of these changes

Acknowledgments This work was partially supported by the

are unexpected and cannot be explained by the

Brazilian research funding agencies CNPq

current Mott-Hubbard theories.

and CAPES.

References 1. Imada, M.; Fujimori, A.; Tokura, Y. Metalinsulator transitions. Reviews of Modern Physics, v. 70, n. 4, p. 1039-1263, 1998.

2. Fujimori, A. et al. Evolution of the spectral function in Mott-Hubbard systems with d1 configuration. Physical Review Letters, v. 69, n. 12, p. 1796-1799, 1992.

3. Morikawa, K. et al. Spectral weight transfer and mass renormalization in Mott-Hubbard systems SrVO3 and CaVO3: influence of long-range Coulomb interaction. Physical Review B, v. 52, n. 19, p. 13711-13714, 1995.

4. Liebsch, A. Surface versus bulk Coulomb correlations in photoemission spectra of SrVO3 and CaVO3. Physical Review Letters, v. 90, p. 096401, 2003.

5. Nekrasov, I. A. Comparative study of correlation effects in CaVO3 and SrVO3.

Physical Review B, v. 72, p. 155106, 2005.

6. Abbate, M. et al. The soft X-ray spectroscopy beamline at the LNLS: technical description and commissioning results. Journal of Synchrotron Radiation, v. 6, n. 5, p. 964-972, 1999.

7. Mossanek, R. J. O. et al. Minimal model needed for the Mott-Hubbard SrVO3 compound. Physical Review B, v. 79, p. 033104, 2009.

8. Pen, H. F. et al. Electronic structure of Y1-xCaxVO3 studied by high-energy spectroscopies. Physical Review B, v. 59, n. 11, p. 7422-7432, 1999.

Activity ActivityReport Report 2009 2008 |

61

10

First crystal structure and catalytic mechanism of a bacterial glucuronosyltransferase

Máximo Barreras, Silvina R. Salinas, Matías A. Kampel and Luis Ielpi Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad de Buenos Aires C1405BWE, Argentina

Xanthomonas campestris GumK (β-1,2-glucuronosyltransferase) is a membraneassociated protein involved in the biosynthesis of xanthan, an exopolysaccharide crucial for this bacterium’s phytopathogenicity. Xanthan is also used in many important industrial applications. The x-ray crystal structure of apo-GumK was solved at 1.9 Å resolution. The enzyme has two well defined Rossmann domains with a catalytic cleft between them. Recently, the crystal structure of GumK complexed with the donor substrate was also solved. We identified a number of catalytically important residues, including Asp157, which serves as the general base in the transfer reaction. The biological and structural data reported here shed light on the molecular basis for donor and acceptor selectivity in glucuronosyltransferases.

Facility: MX1 Publication: J. Biol. Chem. (2008) Sep 5;283(36):25027-35.

Funding: ANPCyT and UBACyT

Science Highlights

Introduction

In particular, many details of UDP-

Glycosylation events are among the most common and important enzymatic reactions in nature. Glycosyltransferases are enzymes that catalyze the transfer of a sugar moiety from a donor to an acceptor molecule, and are involved in the biosynthesis of glycolipids,

glucuronosyl transferase (UGT) structures and mechanisms remain elusive, and only a segment of the carboxy-terminal domain of human UGT2B7 has been crystallized5.

Nor much is known about bacterial UGTs. These enzymes play an important role in

polysaccharides, glycoproteins, and a vast range

the synthesis of oligo- and polysaccharides.

of metabolites. Accordingly, glycosyltransferases

Some extracellular polysaccharides display

display a wide array of acceptor molecules,

rheological and physical properties that are

including oligosaccharides, lipids, proteins, and

useful for industrial applications. Such is

glycolipids1, 2. In contrast, donor substrates are

the case of xanthan, an exopolysaccharide

mostly activated glyconucleotides. The numerous

produced by the phytopathogen Xanthomonas

compounds synthesized by glycosyltransferases

campestris. X. campestris UGT GumK is a

have central roles in cellular biochemistry (e.g.,

membrane-associated protein responsible

in cell signaling, immune response, and bacterial

for the addition of a GlcA residue during the

virulence, among other processes)3, 4.

formation of xanthan 6, 7. The crystal structure

Nα6

Nα6

a

Nα5

4

Nα

4

Nα

Nα8

B1

N

UDP

Cα 1

Cα3 CB5

CB6

Cβ4

CB1 CB2 CB3

Cα6

Figure 1

Cα2

Nα3

7

Cα4

Cα5

Nα2

Cα

Nα8

Cα4

Nβ4 Nα1

NB7

NB8

Nα3

7

NB3

NB2

1

Nα2

Cα

Nα7

Nβ4 Nα1

Cα

N

NB2

NB7

NB8

6 NB NB5

NB3

B1

6 NB NB5

Nα7

b

Nα5

Cα5

Cα3 CB5

CB6

Cβ4

CB1 CB2 CB3

Cα6

Cα2

Overall structure of GumK and the GumK-UDP complex. a, the apoprotein is shown as a ribbon diagram with β-strands in magenta and α-helices in cyan. b, GumK-UDP complex.UDP is drawn as a stick model Activity ActivityReport Report 2009 2008 |

63

Catalytic mechanism of a bacterial glucuronosyltransferase

of GumK with its donor substrate, together

homology (r.m.s. deviation = 2.02 over 88 C-α),

with site-directed mutagenesis, provided the

which confirms that despite the low sequence

first insights into the active site of this enzyme

homology between these domains, the same

and also its transfer mode of action.

fold is adopted. The N- and C-domains are

Figure 1 shows that GumK is a two-

joined by a linker between the eighth β-strand

domain molecule with an overall size of

and the first α-helix of the C-domain. This

50 × 50 × 65 Å. The N-domain is composed

interdomain linker, together with the loop

of 10 α-helices surrounding a core of eight

connecting Cα6 and Cα7, defines the floor of

mostly parallel β-sheets. The C-domain

the cleft between the two domains. The cleft

consists of a core of six β-sheets shielded by

is ~20 Å deep and 15 Å across at its widest

six α-helices. The β-strands and α-helices

point.

of both domains are ordered as in a typical

Figure 2 shows the position of UDP in its

Rossmann fold8 and exhibit high structural

binding pocket. This pocket is located on the

a

b

c

d Cα3

Y292 M231

K307

UDP C4

E272

M306 M273

C4

Q310

Figure 2

64

Substrate binding in GumK. a, ribbon representation of GumK, showing UDP bound on the C-terminal face of the catalytic cleft. b, surface representation of the UDP-binding pocket. c, final (2Fo-Fc) electron density map for UDP (contoured at 1σ). Residues contacting UDP are shown as stick representations. Hydrogen bonds are depicted as dashed lines. d, GumK C-terminal α/β/α motif involved in donor substrate binding

| Activity Report 2008

Science Highlights

C-terminal face of the cleft, in a positively charged

(Figure 3b). The degree of this interaction and

surface. The UDP-binding pocket is an α/β/α

the relative importance of individual residues

motif defined by Cα3, Cβ4, and Cα4 and the linkers between them (Figures 1b and 2d). This structural motif is highly conserved throughout glycosyltransferases9,10 as an alternative way

of the basic cluster, together with surrounding hydrophobic residues, are currently being investigated in our laboratory.

to coordinate the negative charge of the phosphates in the nucleotide-sugar.

N-terminal

Discussion

Nα4

a

Nα2

Subcellular localization experiments showed that GumK associates with the cell membrane in X. campestris . The calculated electrostatic 6

Basic (arginine) cluster

D157

surface potential for GumK structure reveals a polar protein with a positively charged

Catalytic cleft

C-terminal

N-domain (theoretical pI 9.97) and a negatively charged C-domain (theoretical pI 6.20). A cluster of basic and hydrophobic residues

Periplasm

(in helices Nα2 and Nα4 and in the linker

b

region between Nα4 and Nβ4) lies at the tip of the N-terminal domain (Figure 3a). This

Membrane

arrangement suggests possible involvement of the region in membrane interactions. A model for other glycosyltransferases proposes a mixed hydrophobic-electrostatic interaction between an equivalent basic region in the

Man-Cel-P-P-lipid

N-terminal

N-terminal domain and the membrane 11. In

D157

this model, there is a first contact between UDP-GlcA

the negatively charged membrane and the C-terminal

positive charges of a cluster of basic residues.

Subsequently, the contact is strengthened by the interaction of the membrane lipids with the hydrophobic residues. Furthermore, the location of the basic patch is consistent with the proposed acceptor binding site.

Membrane association in this region would bring the middle cleft closer to the membrane surface, where the soluble UDP-GlcA donor is coupled to the membrane anchored acceptor glycolipid, mannose-cellobiose-P-P-polyprenyl

Figure 3

Proposed membrane binding by GumK. a, the proposed binding surface between GumK and the X. campestris membrane.

Helices Nα2 and Nα4 and loop 8, which contain residues Arg58, Lys60, Arg86, Arg95, Arg96, Arg100, and Arg108, are shown in blue. b, model for the proposed interaction between the inner membrane and GumK N-terminal basic patch (arginine cluster). The soluble donor substrate (UDP-GlcA) and the acceptor mannose-cellobiose-P-P-polyprenyl protruding from the membrane are depicted as stick models. The surface representation of GumK is colored by electrostatic potential (red, -2kT; blue, +2kT; white, neutral, where k represents the Boltzmann constant and T is temperature), calculated using the APBS program and visualized with Pymol. Membrane, GumK, and substrates are depicted in scale Activity ActivityReport Report 2009 2008 |

65

Catalytic mechanism of a bacterial glucuronosyltransferase

Summary and Conclusion

the catalytic base and the donor substrate, as

To identify the catalytic residue, all acidic residues lying in the catalytic cleft that could act as the general base were mutated. Mutations E192A, D207A or D234A showed no effect on GumK activity either in vitro or in vivo. On the contrary, we observed a lack of activity in GumK mutants D157A/Q/N. The lack of activity in Asp157 mutants, after replacement of the charge (Asp to Asn mutation) or the

CH2 OH O

HO

HO

structure of mutant D157A as apoprotein using

Asp-157, the acceptor nucleophile can attack

the D03B-MX1 beamline at LNLS (Protein Data

the anomeric position of UDP-GlcA to form

Bank code 3CUY). The r.m.s. deviation for all

a new glycosidic bond with an inverted

residues between native GumK and mutant

configuration (Figure 4). The side product

D157A is 0.28 Å, showing that the mutant

UDP dissociates at the same time. According

structure has not undergone any structural

to this hypothesis, the anomeric carbon is

changes. A model of the binding of the

located between the acceptor nucleophile, the

mannose-cellobiose-P-P-polyprenyl acceptor

C2-OH of mannose, and the leaving group

can be constructed based on the location of

UDP, the geometry that is consistent with an

CH2OH O

HOOC

D157 O

OH O

P

P

NH3+

O

Man-Cel-P-P-lipid

O CH2OH O

O OH

O

– O

UDP

HO COOH O HO

O

OH

Transition state

O

O

OH

OH P-P-lipid OH

OH O + UDP–

OH OH

Uridine

NH2

COOH O

HO

OH

O

OH

+

OH

CH2 OH O

O

residue. The side chain of Asp157 is also

Upon deprotonation of the C2-OH group by

O

O

could deprotonate the 2-OH of the mannose

folding errors, we crystallized and solved the

O

O

accommodated. The carboxylate of Asp157

glucuronic acid in the GumK-UDP complex.

HO –

where the glycolipid acceptor could be

as the catalytic residue. To check for potential

OH O H

below this N-terminal hydrophobic pocket,

putative location of the anomeric carbon of

OH

OH

(Figure 3b). Asp157 is located immediately

in vivo and in vitro assays, implicates Asp157

P-P-lipid

O

is complementary to the shape of the cleft

positioned immediately adjacent to the

HO CH2OH O

site cleft. The shape of the acceptor substrate

length of the side chain (Asp to Glu) in both

CH2 OH O O

well as the shape and orientation of the active

Reaction products

OH

S K307

M306

Y292

Enzyme-substrate complex Figure 4

66

Proposed catalytic mechanism of GumK. Asp157 serves as the general base. Residues Lys307, Met306, and Tyr292, which interact with UDP phosphates, are depicted in blue

| Activity Report 2008

Science Highlights

in-line displacement mechanism (45 JBC).

of the UDP ligand was exactly the same as

Indirect evidence supporting this hypothesis

in wild type GumK (Protein Data Bank code

is that GumK showed hydrolytic activity

3CV3). Unfortunately, the position of the GlcA

toward UDP-GlcA after a 1-h incubation

moiety was not observed, suggesting that

in the absence of the acceptor. Under the

the molecular motion of this portion of the

same conditions, mutant D157A was unable

molecule in the “open” conformation of GumK

to hydrolyze UDP-GlcA, even after a 24-h

does not allow seeing it by crystallographic

incubation. In an attempt to find the GlcA

methods.

portion of bound UDP-GlcA, we performed soaking experiments with crystals of the

Acknowledgments

D157A mutant in the presence of UDP-GlcA

The authors are grateful for being given

and the structure was solved using the

access to the facilities of the D03B-MX1

D03B-MX1 beamline at LNLS. The position

beamline at the LNLS.

RefeRences 1. Breton, C. et al. Structures and mechanisms of glycosyltransferases. Glycobiology, v.

16, n. 2, p. 29R-37R, 2006.

2. Bowles, D. et al. Glycosyltransferases: managers of small molecules. Current Opinion Plant Biology, v. 8, n. 3, p. 254-263, 2005.

3. Doores, K. J. et al. Exploring and exploiting the therapeutic potential of glycoconjugates.

Chemistry-A European Journal, v. 12, n.

22, p. 656-665, 2006.

4. Feizi, T.; Mulloy, B. Carbohydrates and glycoconjugates: Glycomics: the new era of carbohydrate biology. Current Opinion in Structural Biology, v. 13, n. 5, p. 602-604, 2003.

polysaccharide synthesis. Glycobiology, v. 14, n. 3, p. 233-241, 2004.

7. Katzen, F. et al. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence.

Journal of Bacteriology, v. 180, n. 7, p.

1607-1617, 1998.

8. Baker, P. J. et al. Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold: implications for nucleotide specificity.

Journal of Molecular Biology, v. 228, n.

2, p. 662-671, 1992.

9. Hu, Y.; Walker, S. Remarkable structural similarities between diverse glycosyltransferases. Chemistry & Biology, v. 9, n. 12, p. 1287-1296, 2002.

5. Miley, M. J. et al. Crystal structure of the cofactor-binding domain of the human phase II drug-metabolism enzyme UDPglucuronosyltransferase 2B7. Journal of Molecular Biology, v. 369, n. 2, p. 498-511, 2007.

10. Davies, G. J.; Gloster, T. M.; Henrissat, B. Recent structural insights into the expanding world of carbohydrate-active enzymes.

Current Opinion in Structural Biology, v.15, n. 6, p. 637-645, 2005.

6. Barreras, M; Abdian, P. L.; Ielpi, L. Functional characterization of GumK, a membraneassociated ß-glucuronosyltransferase from Xanthomonas campestris required for xanthan

11. Lind, J. et al. High cationic charge and bilayer interface-binding helices in a regulatory lipid glycosyltransferase. Biochemistry, v. 46, n. 19, p. 5664-5677, 2007.

Activity ActivityReport Report 2009 2008 |

67

11

Coherent X-ray beam with a compact X-ray pathway

Marcelo Goncalves Hönnicke,1 Edson Massayuki Kakuno,2 Guinther Kellermann,3 Irineu Mazzaro,4 Daniel Abler4 and Cesar Cusatis4 1

NSLS II, Brookhaven National Laboratory, Upton, NY, USA 2 Universidade Federal do Pampa, Bage, RS, BRAZIL 3 Laboratório Nacional de Luz Síncrotron – LNLS, Campinas, SP, BRAZIL 4 Departamento de Fisica, UFPR, Curitiba, PR, BRAZIL

Coherent X-ray beams are achieved by setting the experimental hutch as far as possible from the source. A long X-ray pathway is presented, based on an X-ray back-diffraction cavity for experiments requiring high coherent X-ray beams. The setup was tested and used for propagation-based X-ray phase contrast imaging (PBI).

This setup proved useful for PBI purposes, with the advantage of being more compact (3 m long) than long X-ray synchrotron beamlines.

Facilily: XRD2 Publication: Applied Physics Letters, 92: 264103-1-3 (2008).

Funding: FUNPAR/UFPR and CNPq

Science Highlights

Introduction

incident o-beam. In this geometry, the widths

High coherent X-ray beams are provided by long X-ray pathways.1,2 This can be checked by a simple mathematical relation for the lateral coherence(lt), which is given by: lt =

λ.d 2σ x

of single crystal rocking curves are much larger (∼10–3 rad) than those of conventional X-ray diffraction angles (∼10–6 rad). The experimental difficulty of this type of measurement lies in the detection of the diffracted h-beam, which

(1)

where λ is the wavelength of the incoming X-ray beam, d is the source to sample distance, and σx is the source size.

Coherent X-ray beams can be used for phase contrast X-ray imaging. This imaging technique has been used for several applications in many fields of knowledge3,4 to reveal structures that are invisible by attenuation contrast X-ray imaging (conventional radiography).

Propagation-based X-ray phase contrast imaging (PBI)5,6 is the most simple phase contrast

involves the need for semi-transparent detectors or very long distances between the crystal and the detector.

A synchrotron setup based on a “virtual” long X-ray pathway is presented here. The idea is to have a far distance source using an X-ray back-diffraction cavity in which two Si crystals are used in multi-bounce diffraction. Such a setup is compact when compared with long X-ray beam pathways presented elsewhere.1,2

Experiment

X-ray imaging technique since it requires no

The experiment was carried out at the XRD2

sophisticated optics. The only requirement

beamline of the LNLS (Brazilian Synchrotron

is a small source size with high brilliance,

Light Laboratory) (Figure 1). The energy of the

provided by conventional microfocus X-ray

incoming white beam X-ray was selected by

sources or by high brilliance and low emittance

the beamline monochromator (Si 111, placed at

third generation synchrotron sources.

8.7 m from the source) at 9.684 keV. The X-ray

X-ray back-diffraction7,8 is characterized by

back-diffraction cavity was mounted downstream

the overlapping of a diffracted h-beam and an

FROM the monochromator: a non-dispersive

Vaccum path

First crystal: Si 660

LNLS ring

Second crystal: Si 660

CCD detector

XRD2 beamline monochromator Si 111 Figure 1

3.3 m

D

Sample

PBI setup based on a multi-bounce X-ray back-diffraction cavity Activity ActivityReport Report 2009 2008 |

69

Coherent X-ray beam with a compact X-ray pathway

double crystal Si 660 setup in back-diffraction

was used with only 4 bounces (2 in each crystal)

geometry. The first Si 660 crystal was set at

with a diffraction angle of 89.56º. The sample

19 m from the source. The second Si 660 was

was placed behind the cavity, thus increasing

placed 3.3 m further downstream. A vacuum

the beam pathway by 13.2 m, i.e., the source

path was set up between them to reduce the

to sample distance was increased to 32.2 m.

attenuation/scattering of the beam in the air.

The vertical source size (σx) at LNLS’s XRD2

The crystals were 130 mm long and 40 mm

beamline is about 170 µm. Equation (1) gives

wide. These crystals, which were oriented, cut

the transverse coherence length of 12 µm. With

and chemically polished (etching) to a precision

such lateral coherence, the XRD2 beamline

greater than 0.1º, were designed to work with

becomes competitive, for example, with the

a 2 mm high × 40 mm wide beam and a total

SYRMEP beamline at ELETTRA9 (lt ∼ 15 µm

of 10 bounces in the cavity (5 in each crystal).

at 9.7 keV) for PBI purposes (radiography and

However, in the present work, the X-ray cavity

tomography) in edge detection geometry.

a

b

5 mm

5 mm

1.2

1.2

1.0

1.0

0.8 0.6 0.4 0.2 –2

–1

0

1

2

Position on the CCD (mm)

| Activity Report 2008

0.8 0.6 0.4 0.0

–3

70

d

0.2

0.0

Figure 2

1.4

c Intensity (a.u)

Intensity (a.u)

1.4

3

–3

–2

–1

0

1

2

3

Position on the CCD (mm)

Images of the polypropylene tube: (a) Conventional synchrotron radiography at D = 0 mm; (b) PBI at D = 700 mm. Exposure time: 10 min; (c) image cross-section profile of (a); (d) image cross-section profile of (b). The phase effects (dashed circles) are more pronounced at larger sample-to-detector distances (D)

Science Highlights

a

5 mm Figure 3

b

5 mm

Propagation-based X-ray phase contrast images (PBIs) of a tree leaf at two different sample-todetector distances: (a) 160 mm; (b) 700mm. The vessels and cork warts (indicated by dashed circles) are more well-defined in the image recorded at a longer distance (b). Phase effects at the sample border are also more strongly emphasized in the image (b): see, for instance, an edge enhancement effect at the top of the figure. Exposure time: 10 min

In the present setup, the sample-to-detector

An image of a tree leaf was also recorded

distance (D, Figure 1) can vary from 0 mm

(Figure 3). Details of the leaf, such as the vessels

(sample in contact with the CCD detector) to

and cork warts, are much more well-defined

1 m. This means that conventional synchrotron

at longer sample-to-detector distances. As

radiography (CSR) and PBI can be performed

mentioned previously, this is because phase

in the same setup. The images were recorded

effects are more strongly emphasized at longer

with a direct conversion CCD detector, which

sample-to-detector distances, as can also be

has 1242 × 1152 pixels of 22.5 × 22.5 µm2 each.

confirmed by the edge enhancement at the top

Coupled translators for sample and detector, each

border of the leaf (Figure 3b).

with a range of 100 mm, were also employed.

The results indicate that the idea of creating a compact long X-ray pathway based on an

Results Figure 2 shows images and cross sections of a polypropylene tube at two different sample-to-detector distances. It is easy to see that phase effects at the tube edges are much

X-ray back-diffraction cavity works, i.e., phase effects were detected as a result of the improved lateral coherence.

Conclusions

more visible when the detector is placed at

An effective long X-ray path was demonstrated

longer distances from to the sample. This can

for phase contrast X-ray imaging purposes over

be quantified by examining the cross sections

a short distance, using X-ray back-scattering

of the images. The contrast at the edges (phase

diffraction geometry (Bragg angles of about π/2)

effects) increases with the sample-to-detector

to fold the beam multiple times. Such a setup

distance due to the strong phase jumps at the

is shown to be useful for propagation-based

external and internal borders of the tube.

X-ray phase contrast imaging (PBI).

Activity ActivityReport Report 2009 2008 |

71

Coherent X-ray beam with a compact X-ray pathway

It is worth noting that, with a good vacuum

the cavity, since the bandwidth of the upstream

path, one could achieve 10 bounces in the

Si 111 is about 10–4. However, despite this loss

back-diffraction cavity, enabling improvement

of intensity, this setup seems reasonable since

of the lateral coherence so that in-line beam

exposure times of 10 minutes were employed.

holography could be performed. However,

Short exposure times can be achieved working

it should also be noted that the crystals must

with third generation synchrotron sources.

operate at specific energies on the distinct

With regard to the use of this setup at

allowed diffraction planes. At the X-ray

LNLS, we point out that it can be used as an

energy employed here, about 2% is lost in

alternative to the standard analyzer-based

each diffraction (photoelectric absorption),

X-ray phase contrast imaging setup10, with the

indicating that 20% of intensity can be lost

advantage of being an easier phase contrast

after 10 bounces. Also, the bandwidth (∆λ/λ)

imaging technique, particularly for purposes of

of the back-diffraction cavity is about 10–6,

tomography (post-image processing). Moreover,

which means that the intensity loss (photon

other experiments requiring coherent X-ray

flux) is about two orders of magnitude after

beams can be developed with this setup.

References 1. Espeso, J. I. et al. Conserving the coherence and uniformity of third-generation synchrotron radiation beams: the case of ID19, a `long’ beamline at the ESRF. Journal of Synchrotron Radiation, v.

5, n. 5, p. 1243-1249, 1998.

2. Hönnicke, M. G. et al. Propagationbased x-ray phase-contrast imaging with broad focus conventional x-ray sources. Disponível em <http://arXiv. org > cond-mat > arXiv:0710.1286> (2009).

3. Westneat, M. W. et al. Tracheal respiration in insects visualized with synchrotron x-ray imaging. Science, v. 299, n. 5606, p. 558-560, 2003.

4. Hönnicke, M.G. et al. Preliminary studies of enhanced contrast radiography in anatomy and embryology of insects with Elettra synchrotron light. Nuclear Instruments and Methods in Physics Research A, v. 548, n. 1-2, p. 207-212, 2005.

5. Antunes, A. et al. X-ray imaging in advanced studies of ophthalmic diseases.

Medical Physics, v. 33, n. 7, p. 2338-2343, 2006.

72

| Activity Report 2008

6. Wilkins, S. W. et al. Phase-contrast imaging using polychromatic hard x-rays. Nature, v. 384, n. 6607, p.335-338, 1996.

7. Snigirev, A. et al. On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation. Review of Scientific Instruments, v. 66, n. 12, p.

5486-5492, 1995.

8. Caticha, A.; Caticha-Ellis, S. Dynamical theory of x-ray-diffraction at Bragg angles near PI/2. Physical Review B, v. 25, n.

2, p. 971-982, 1982.

9. Cusatis, C. et al. X-ray back-diffraction profiles with an Si(111) plate. Acta Crystallographyca A, v. 52, n. 4, p. 614620, 1996.

10. Arfelli, F. et al. Digital mammography with synchrotron radiation. Review of Scientific Instruments, v. 66, n.2, p.13251328, 1995.

11. Hönnicke, M. G. et al. Enhanced contrast radiography with channel-cut crystals at the LNLS. Review of Scientific Instruments, v. 76, n.9, p. 093703, 2005.

Science Highlights

Activity ActivityReport Report 2009 2008 |

73

12

Calculation of the mixed iron valence (Fe+3/Fe+2) ratio in hexacyanoferrates (Prussian Blue materials) using synchrotron X-ray powder diffraction Fabio Furlan Ferreira1, Paulo Roberto Bueno2 and Grazielle de Oliveira Setti2

2

1 Laboratório Nacional de Luz Síncrotron, Campinas, SP, Brazil Universidade Estadual Paulista, Instituto de Química, Araraquara, SP, Brazil

Resonant X-ray diffraction analysis can be used as a tool to calculate the Fe+3/ Fe+2 ratio in hexacyanoferrate materials, thanks to the ability of resonant X-ray diffraction to enhance the sensitivity of one of the iron ions by tuning the wavelength above the Fe +2 absorption edge and below the Fe+3 one.

Experiments performed on the D10B-XPD beamline revealed that this information is crucial for a thorough understanding of such compounds.

The proposed approach is applicable to other hexacyanometallates and to various other molecular compounds of mixed valences.

Facility: XPD Publication: Applied Physics Letters, 92: 264103-1-3 (2008) Funding: FAPESP

Science Highlights

There is great interest in the study of molecular-

of ~1.0 mm (vertical) × ~2 mm (horizontal) to

based compounds, e.g., hexacyanometallate

the sample’s position in order to increase the

materials, alternatively referred to as mixed

energy resolution of the beamline, which was

transition metal valence compounds. A typical

~1.5 eV at wavelengths near the Fe absorption

example is Prussian blue (PB) material,

edge (λ1 = 1.76140 Å and λ2 = 1.74156 Å). The

which is a subclass of hexacyanometallates, a

diffracted beam was analyzed with a pyrolytic

hexacyanoferrate which is known to exhibit

graphite HOPG(002) and detected with a

identical metal atoms existing in different spin

Na(Tl)I scintillation counter with a pulse-

and/or oxidation states.1 This kind of compound is

height discriminator in the counting chain.

of particular interest for applications in magnetic,2

The incoming beam was also monitored by

electrochromic and optical fields. Within this

a scintillation counter to normalize the decay

class of materials, a particular type is based on

of the primary beam. The powder sample

molecular entities with unpaired electron spins

(herein referred to as KhFek[Fe(CN)6]l·mH2O)

residing in d- or f-orbitals. Ensembles of these

was loaded into a 0.5 mm-diameter borosilicate

molecules form a solid structured 3D network

glass capillary, after being scratched off from

3

4

in which spins reside in orbitals (d or f) of the individual metallic entities.

Consequently, the electronic or magnetic state of the metal atoms at particular sites can be tailored by external conditions, such as magnetic field,2 light, and/or by changes in a specific local crystal environment (due to electrochemical compositional in situ variation, for example).1 In other words, the hexacyanometallate crystal structure tolerates different electronic spins, limiting the super-exchange interactions across CN-bridges, thus allowing tunneling of magnetism and coloration properties. Specifically, tunneling on the properties depends on the metal-ligand bond length between high-spin and low-spin states.

High-intensity synchrotron X-ray powder diffraction data were collected at the X-ray Powder Diffraction (D10B – XPD) beamline5 of the Brazilian Synchrotron Light Laboratory (LNLS, Campinas, Brazil), placed after a dipolar source. X-rays of λ1 = 1.76140(8) Å, λ2 = 1.74156(2) Å and λ3 = 1.37862(2) Å wavelengths were selected by a double-bounce Si(111) monochromator. A vertically collimated beam was used in the experiments on a spot

Figure 1

Schematic planar representation of a Fe+2(CN)6 vacancy environment in the whole framework of the FeHCF compound.

The arrows indicate the Fe+3 (Fe+3(NC)5OH- clusters or entities) where electronic charge is located preferentially before the changeover and the electrochromic processes take place Activity ActivityReport Report 2009 2008 |

75

Calculation of the mixed iron valence (Fe +3/Fe +2) ratio in hexacyanoferrates (Prussian blue materials)...

sixty 90-nm thin films, in order to obtain

It is well known that the choice of an

enough material for the structural analyses,

incident wavelength far removed from the

and data were recorded at room temperature

absorption edge of the constituent elements

for 10 s at each 2θ in steps of 0.06° from 10° to

makes the atomic scattering factor independent

90°. Details of the electrochemical preparation

of the energy.9 Now, if one chooses an incident

methodologies6,7.

wavelength near the absorption edge of the constituent elements, the real and imaginary

refined by the Rietveld method using the

components of the anomalous dispersion term,

General Structure Analysis System (GSAS)

f’ and f”, respectively, become significant.9 Due

program and its graphical user interface,

to this characteristic of the scattering theory,

EXPGUI. The space group was Fm3m and

data collected at ~73 eV below the Fe K-edge

the lattice parameter was a = 10.175(2) Å. The

(7.112 keV = 1.7433 Å) were used to minimize

model proposed by us,8 obtained from an X-ray

the imaginary anomalous scattering term (f”) of

diffraction profile analysis, was considered

iron. In order to differentiate the ratio between

as the initial structural model and was able

Fe+2 and Fe+3 ions, thus taking into account the

to provide a precise analysis of the PB-type

fact that the Fe+2 would undergo absorption,

compound’s main structure.

a resonant X-ray diffraction experiment was

(200)

The PB powder diffraction patterns were

a

c

(400)

b

(222)

2000

(111)

Counts (arb. units)

(220)

4000

0 20

30

40

20

30

40

20

30

2 (degrees) Figure 2

76

| Activity Report 2008

Rietveld refinements (selected regions) of the KhFek[Fe(CN)6]l·mH2O structure measured at three distinct wavelengths: (a) λ1 = 1.74156(2) Å, (b) λ2 = 1.76140(8) Å, and (c) λ3 = 1.37862(2) Å. (+) observed, (red line) calculated, (blue line) difference, and (magenta symbol) Bragg reflections. Various selected indexed reflections are indicated and the (222) one is indicated by a dashed green ellipse to emphasize the differences in integrated intensities

Science Highlights

performed between the absorption edges of

on the occupancy of crystallographic sites as

the two Fe ions (above the Fe+2 edge and below

determined by Rietveld analysis and depicted

the Fe one), which are separated by ~5 eV. In

in Figure 1 as a planar representation.

+3

this condition, the dependence of the atomic

Figure 2 shows the Rietveld plots of selected

scattering factor of the Fe+3 was enhanced in

2胃 ranges of the X-ray diffractograms measured

contrast to the Fe+2, thus indicating certain

with (a) 位1, (b) 位2 and (c) 位3 where the most

vacancies in some crystallographic sites, based

intense reflections of PB are located. The fact

Figure 3

Linear schematic representation of Fe+2(CN)6 vacancy environment, and changeover and electrochromic mechanisms during electronic charging of FeHCF compound. (a) Illustrates penta-coordinated Fe+3 in 4a crystallographic sites (octahedral coordinated

by N atoms), i.e., Fe+3(NC)5OH- clusters before electronic charging starts. The arrows in (a) indicate the OH- entities where ionic compensating charges (H+, H3O+ or K+) must be located. (1) Indicates the Fe+3 that does not have a water substructure adjacent to it. On the other hand, (2) illustrates the Fe+3 in 4a crystallographic sites adjacent to the water substructure. b) and c) represent the stage of the mechanism in which the changeover and bleaching process described in the text occur. (d) Represents the final stage in which the FeHCF compound is fully charged, when all the Fe+3 has been converted into Fe+2 Activity ActivityReport Report 2009 2008 |

77

Calculation of the mixed iron valence (Fe +3/Fe +2) ratio in hexacyanoferrates (Prussian blue materials)...

that the (111) reflection is not totally absent may

vacant Fe[(CN)6] group is occupied by water

be attributed to a face-centered cubic lattice

molecules coordinated to the structure and

with Fe ions located at the corners and at the

K+ ions to counterbalance the charge. What

center of the faces of the cubes and a partial

is more, this is a key point in the changeover

occupation of the octahedral sites by Fe+2 ions.

in the properties during in situ compositional

This is evidenced experimentally even in the

variation.10 It is important to clarify that the

cases where the wavelengths did not differentiate

OH- entity is a consequence of the presence

the two iron ions, i.e., for λ1 and λ3. Although

of the first water shell coordinated with the

the differences take place along the various

main structure framework (coordinated

reflections, the most prominent effect occurs at

water).8 It is a very important and particular

the (222) reflection, indicating that the vacant

environment of this structure because it is

[Fe(CN)6] group can be evaluated in spite of a

the bridge between the water substructure

full-pattern Rietveld refinement. Knowing what

and the main framework represented by

the integrated intensity of a given reflection

the Fe+2-CN-Fe Fe+3 chains. This bridge or

is and measuring the same sample at no less

connection is made mainly by means of the Fe+3

than two selected wavelengths allows one to

atoms at 4a crystallographic sites chemically

quantify the vacant sites in the sample.

bound to OH- entities (first coordinated water

+3

Initially, we considered the f’ value for each

substructure), as displayed schematically in

iron ion as being equal to the scattering factor

Figure 3. The water crystalline substructure

of the neutral atom for each wavelength. The

is a non-stoichiometric environment, and this

scattering factors of the C, N, O, and K atoms

characteristic is very important to control the

are much smaller than the Fe and were not

occupancy of ionic sites by K+, H+, and/or

considered to vary. Refinements of the f’ terms

H3O+ entities.8

for the Fe+2 and Fe+3 ions yielded the values of

In summary, synchrotron X-ray powder

−3.4(2) and −4.1(2) for λ1 and −8.0(3) and −9.7(3)

diffraction experiments were conducted to

for λ2, respectively. This is an interesting result

determine the Fe+3/Fe+2 ratio in Prussian blue

because, if one considers the fact that the number

compounds, which were elected as an example of

of electrons decreases, the same effect should

the use of this approach. As a result, a resonant

occur with the intensity of the peaks. That is

X-ray diffraction measurement provided direct

true for most of them, but in the specific case

evidence that the vacant [Fe(CN)6] group was

of the (222) reflection, its integrated intensity

randomly absent from ~31% of the structure,

is increased. Considering that the absorption

which was indicated by structural differences

effects are the same for all the reflections, this

caused by variations in the anomalous dispersion

higher integrated intensity is explained by the

term. These findings are very important for a

differences in the occupation of the jth site. It is

deeper understanding of the changes occurring

known from the structural model considered

in properties during in situ compositional

here that the PB structure has ~25% missing

variations.

Fe+2 ions (in fact, it is the Fe[(CN)6] group that

This work was supported by the São Paulo

is vacant). It should be noted that, according

state research funding agency (FAPESP), project

to the structural model, Fe and Fe ions do

No. 02/06693-3. We thank LNLS for the use of

not occupy the same crystallographic site. The

its beamline.

+2

78

| Activity Report 2008

+3

Science Highlights

RefeRences 1. Sato, O.et al. Photoinduced magnetization of a cobalt iron cyanide. Science, v. 272, n. 5262, p. 704-705, 1996.

electrodes: an electrochemical preparation method. Journal of the Electrochemical Society, v. 129, n. 7, p. 1498-1500, 1982.

2. Hayami, S. et al. First observation of light-induced excited spin state trapping for an iron(III) complex. Journal of the American Chemical Society, v. 122, n.

29, p. 7126-7127, 2000.

7. Agrisuelas, J. et al. Usefulness of F (dm/ dQ) function for elucidating the ions role in PB films. Journal of the Electrochemical Society, v. 154, n.6, p. F134-F140, 2007.

3. Mortimer, R. J.; Reynolds, J. R. In situ colorimetric and composite coloration efficiency measurements for electrochromic Prussian blue. Journal of Materials Chemistry, v. 15, n. 22, p. 2226-2233, 2005.

4. Sato, O. et al. Photoinduced long-range magnetic ordering of a cobalt竏段ron cyanide.

Inorganic Chemistry, v. 38, v. 20, p. 44054412, 1999.

5. Ferreira, F. F. et al. X-ray powder diffraction beamline at D10B of LNLS: application to the Ba2 Fe ReO6 double perovskite.

Journal of Synchrotron Radiation, v. 13, n. 1, p. 46-53, 2006.

6. Itaya, K.; Akahoshi, H.; Toshima, S. Electrochemistry of Prussian blue modified

8. Bueno, P. R. et al. Synchrotron structural characterization of electrochemically synthesized hexacyanoferrates containing K+: a revisited analysis of electrochemical redox. The Journal of Physical Chemistry C, v. 112, n. 34, p. 13264-13271, 2008.

9. Waseda, Y. Nature of anomalous x-ray scattering and its application to the structural analysis of crystalline and non-crystalline systems. In: ________.

Anomalous x-ray scatterings for materials characterization. Berlin: Springer, 2002. p. 21-38.

10. Bueno, P. R. et al. Changeover during in situ compositional modulation of hexacyanoferrate (Prussian blue) material.

Journal of the American Chemical Society, v. 128, n. 51, p. 17146-17152, 2006.

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13

Structural properties of novel Ce-Zr mixed oxide nanotubes

Leandro M. Acuña1, Diego G. Lamas1, A. Gabriela. Leyva2, Richard T. Baker3 and Rodolfo O. Fuentes1, 1

Centro de Investigaciones en Sólidos (CINSO, CITEDEF-CONICET), Villa Martelli, Buenos Aires, Argentina 2 Departamento de Física, Centro Atómico Constituyentes (CNEA), San Martín, Buenos Aires, Argentina 3 School of Chemistry, University of St. Andrews, St. Andrews, Fife, United Kingdom

Since CeO2-ZrO2 solid solutions have been demonstrated to have better catalytic properties than pure CeO2, they may also have properties that make them attractive for application as hydrocarbon reforming or hydrocarbon activation catalysts in Solid Oxide Fuel Cells (SOFCs). Moreover, the redox behavior, thermal stability and catalytic performance of zirconia-ceria mixed oxides are strongly related to their crystal structure. In the present work, novel ZrO2-CeO2 mixed oxide nanotubes with 50, 70 and 90 mol% CeO2 were synthesized following a very simple, high yield procedure and their structural properties were characterized mainly by synchrotron radiation X-ray diffraction (SR-XRD) and by high resolution transmission electron microscopy (HRTEM).

Facility: XPD, XAFS1

Publication: Chemistry of Materials, 20: 7356-7363 (2008) Funding:

CONICET and ANPCyT

Science Highlights

ZrO2-CeO2 substitutional solid solutions

forms, all belonging to the P42/nmc space group.

have attracted much interest in recent years

The stable tetragonal form is called the t-form.

due to their extensive use in different fields,

There is also a t’-form with a wider solubility,

for example, as active supports or “oxygen

but unstable in comparison with the mixture of

buffers” in three-way catalysts (which are

the t-form and cubic phase. Finally, the t’’-form

applied for controlling the emissions of NOx,

has an axial ratio, c/a, of unity, but with the

CO and hydrocarbons from automotive exhausts). In particular, the metastable forms of the tetragonal phase have been widely investigated since they are the most suitable for technological applications.1,2 The wide use of these systems as catalyst components has prompted a renewed interest in the preparation of these materials in the form of nanosized, high surface area powders. In this context, the

oxygen atoms displaced along the c axis from the ideal sites of the cubic phase, Fm3m space group (Figure 1).3-5 Recently, Gonzalez-Rovira et al. reported the synthesis of CeO2 nanotubes. The catalytic activity of these novel materials for the CO oxidation reaction is compared to that of a polycrystalline powder CeO2 sample prepared

present contribution describes the synthesis

by a conventional route. The activity of the CeO2

of Ce-Zr mixed oxide nanotubes, by a novel,

nanotubes is shown to be in the order of 400

simple and high-yielding method, and the

times higher per gram of oxide at 200°C.6

structural and chemical characterization of Zirconia-ceria solid solutions have better catalytic properties than pure ceria, which makes these compositions of potential interest for application in catalysts for solid oxide fuel cell (SOFC) systems. Since the range of desirable operating temperatures of such systems extends from around 600 to 1000°C, an

Crystal structure (400)

Cubic Fm3m space group O2–  1/4 1/4 1/4 c/a = 1

Intensity (a.u.)

these materials.

Tetragonal P42 /nmc space group O2–  1/4 1/4 z(O) c/a > 1 (t’-form) c/a = 1 (t’’-form)

important additional advantage in this respect

Cation: Ce4+; Zr4+

stability of the solid solutions over pure ceria. materials is provided by the particular case of their application in automotive catalytic converters, in which CeO2 is present as a solid

Intensity (a.u.)

Evidence for the improved stability of these

(200)

ZrO2, CeO2 deactivates rapidly. In contrast, CeO2-ZrO2 mixtures maintain their activity for

20

solutions is the existence of three tetragonal

(331) (420)

(333) (422)

(400) (004)

(112) 30

40

50

60

70

80

90

100

2 (°)

many years under very harsh environments. compositionally homogeneous CeO2-ZrO2 solid

(400)

(400)

solution with ZrO2. Without the addition of

One of the most notable characteristics of

(311)

ZC70 ZC50

(400)

66 67 68 69 70 71 72 73 74 75 2 (°)

(222)

ZC90

ZC70

ZC50

(111) (220)

(400)

(004)

Anion: O2–

is the much improved thermal and chemical

ZC90

Figure 1

Crystal structure of Ce-Zr mixed oxide. Synchrotron XRD pattern recorded at room temperature for the three nanotube compositions with inset showing the region of the 400 and 004 peaks Activity ActivityReport Report 2009 2008 |

81

Structural properties of novel Ce-Zr mixed oxide nanotubes

However, so far, the literature is lacking reports

In the present work, we report for the first

on ZrO2-CeO2 nanotubes. The preparation of

time on the preparation of CeO2-ZrO2 mixed

nanotubes of Zr-Ce mixed oxides is attractive

oxide nanotubes using a template synthesis

for several reasons, particularly in the case of

method (Figure 2) and employing polymeric

nanotubes with sufficiently small dimensions,

filtration membranes.7,8 Three compositions were

which would have high specific surface areas

prepared using a commercial polycarbonate

(SSAs) that would lead to high activity, good atomic efficiency and rapid response to changing conditions in catalyst systems.

membrane (with pore size of 800 nm) as a template, with CeO2 contents of 50, 70 and 90 mol%, which are hereinafter referred to as ZC50, ZC70 and ZC90, respectively.

Synchrotron XRD patterns recorded at room temperature for the ZC50, ZC70 and ZC90

1) Template: porous polycarbonate films

nanotube samples (Figure 1) exhibited resolvable peaks but with relatively severe line broadening.

This broadening was ascribed to the presence of 3) Denitrification of the confined precursor in a microwave oven

small crystallites. The 2θ region in the vicinity of the 400 and 004 reflections is inset in Figure 1. A splitting of these peaks is expected for the tetragonal phase, indicating c/a > 1. However, although this splitting is not evident in the ZC50

2) Pores was filled with the nitrate precursor solution

sample, its peak shows a strong asymmetry.

In addition, by assuming the existence of two peaks here, a better fit of this profile is obtained.

In contrast, the ZC70 and ZC90 samples show

4) Template was burnt off in a standard furnace

only one peak, indicating that the cations are in the ideal fluorite sites (c/a = 1).

SR-XRD was carried out on the ZC50 nanotube material to detect the very weak 112 reflection. However, because the small 5 m

crystallites (4.8 nm) gave rise to very broad Bragg reflections, the 112 peak was not observed, although long step-counting times (20 s step–1) were used to improve the signal to noise ratio.

For the ZC90 composition, which has a cubic structure, the 112 reflection is forbidden, while in compositions close to the tetragonal-cubic

1 m Figure 2

82

Schematic representation of the template method used to obtain the nanonotubes. SEM images of ZC90 nanotubes at different magnifications showing the high yield of nanotubes and the structure of individual nanotubes

| Activity Report 2008

phase boundary, i.e., 70 mol% CeO2, this peak is extremely difficult to detect because it is rather weak and, in this particular case, it undergoes significant line broadening because of the small crystallite size (~6 nm).

Science Highlights

The ZC50 nanotube sample exhibited a

sample. Although the presence of Ce3+ ions in

tetragonal structure (P42/nmc space group),

the nanotube samples cannot be completely

specifically the t’-form, whereas the ZC90

excluded, based on the comparison with the

sample exhibited a cubic structure (Fm3m

reference compound, the Ce atoms appear to

space group). However, in the case of the ZC70

be mainly in the tetravalent state.

sample, both P42/nmc and Fm3m structural

HRTEM results are presented in Figure 4 for

models yielded similar agreement factors, so

the ZC90 sample. Firstly, in the SAED patterns

it was not possible to determine if this material

obtained from the ends of the nanotubes of

underwent an oxygen displacement.

the three different compositions, the fact that

The pseudo-cubic lattice parameter values,

the concentric diffraction rings are essentially

a* = (2a + c)/3, of the nanotube materials of the

continuous implies that the samples consisted

present study, ZC50, ZC70 and ZC90, were

of many very small crystallites. Interplanar

found to be consistently larger than those of

spacings were calculated from the three patterns

the nanopowders of the same composition

and can be indexed to the cubic fluorite or the

reported in a previous work.5 The authors

tetragonal t’ phase of CexZe1-xO2–δ in all three

reported that their nanopowders had average

cases. No rings that could be assigned solely

crystallite sizes of about 18-20 nm. In CeO2ZrO2

to the t’ phase were visible. These would be

solid solutions, a unit cell contraction is

expected to be much fainter than the rings

expected to occur because of the replacement of

that were observed here. This is corroborated

Ce4+(1.01Å) by Zr4+(0.89Å). Nevertheless, a cell

by the SR-XRD pattern (Figure 1) in which the

expansion may also occur by reduction of Ce4+

(112) reflection, for example, is very weak, even

to Ce3+(formation of O2- defects), because the

for the ZC50 composition, where it would be

ionic radius of Ce3+(1.14Å) is larger than that of Ce4+. For nanocrystallites, an O2- defect structure 3.0

can be stabilized through surface phenomena,

Ce3+

whose importance decreases as the crystallite larger a* values in the nanotube materials can be explained by a partial reduction of the Ce4+ to Ce3+, accompanied by stabilization of the defect structure, which would be favored by the small primary particles present in the nanotube samples.

In Figure 3, the Ce LIII XANES spectra of the ZC90 nanotube sample is compared with that of the CeO2 reference powder (Ce4+) and cerium nitrate (Ce3+). Two main peaks (labeled 1 and 2) separated by approximately 7 eV are observed in the CeO2 spectrum. These two components were also detected in the ZC90 sample, with an intensity ratio close to that found in the CeO2

2.5 Normalized absorbance (a.u.)

size increases. It appears, therefore, that the

1

2

2.0 Ce4+

1.5 1.0 0.5 0.0 5.71

5.72

5.73

5.74

5.75

Photon energy (KeV) Figure 3

Ce LIII-edge XANES normalized absorption spectra for bulk ceria (Ce4+), cerium nitrate (Ce3+) and ZC90 nanotube sample (circles) Activity ActivityReport Report 2009 2008 |

83

Structural properties of novel Ce-Zr mixed oxide nanotubes

expected to be the strongest. Secondly, a series

zone axis. Thirdly, the width of a number of

of HRTEM images of increasing magnitude

these nanoparticles was measured from each

are presented for each nanotube composition.

set of TEM images. The size distribution for

These show the shape of a single nanotube in

these nanoparticles is presented in the form of

the low magnification images and, at higher

a histogram. Volume-corrected particle sizes

magnifications, one of the ends of these

were calculated from the TEM data (4.7-7.6 nm,

nanotubes, whose walls are composed of a

with increasing%Ce). These can be compared

thin, curved sheet of nanoparticles. The highest

directly with the values obtained from the

magnification images clearly show several

SR-XRD data using the Scherrer equation

individual nanoparticles making up the edge of

(5.6-6.9 nm, with increasing%Ce), and they

these sheets. Digital Diffraction Patterns (DDP)

show very good agreement.

for selected individual crystallites are inset in

In summary, novel ZrO2-CeO2 mixed oxide

these images. The DDPs can all be indexed

nanotubes of 50, 70 and 90 mol% CeO2 were

to the fluorite phase viewed along the [011]

successfully synthesized at high yield by the pore

a 1.53 2.95

(111)

c

b

1.77

2.52

(200)

(311)

(220) 0.5 m 

d



0.2 m 

e

f

 Frequency





20 nm Figure 4

84

  5 nm

   





      Crystallite size (nm)

(a) SAED of part of a ZC90 nanotube. Interplanar spacings (in Å) and the corresponding Miller indices are given. TEM images of a typical nanotube are given in (b) at low magnification; (c, d) intermediate magnification images of the end of a nanotube showing the curved sheet of nanoparticles and (e) high resolution image of individual nanocrystals showing their internal crystal planes. DDPs from two of the nanocrystals are inset.

These can be indexed to the fluorite or t’ structure viewed along the [011] zone axis. Miller indices are given. (f) Particle size distribution for the primary nanoparticles which make up the Ce0.9Zr0.1O2 nanotubes

| Activity Report 2008

Science Highlights

Gas

ZC90NT

Pd Pd

Pd

Pd Figure 5

Pd

5 nm

Schematic representation of metal supported nanotubes for catalytic applications and TEM image of ZCE nanotubes impregnated with Pd

wetting method. Nanotubes of 90 mol% CeO2

on nanopowders of the same compositions.

exhibited the highest surface area, indicating

Finally, it is important to emphasize that there

that this composition is a good candidate for

is also interest in using ceria-based nanotube

application in catalyst systems. The formation

structures9 as catalyst supports for metal

of O2– defects (by reduction of Ce4+ to Ce3+)

nanoparticles, and that their catalytic activity

seems to be responsible for the larger unit cell

will be the subject of investigation in future

dimensions than were found in previous work

work (Figure 5).

RefeRences 1. Di Monte, R.; Kaspar, J. Nanostructured CeO2– ZrO2 mixed oxides, Journal of Matererials Chemistry, v. 15, n.6, p.

633-648, 2005.

2. Kaspar, J.; Fornasiero, P. Structural properties and thermal stability of ceria-zirconia and related materials. In: Trovarelli, A. (Ed.) Catalysis by ceria and related materials. London: Imperial College Press, 2002. p. 217-241.

3. Yashima, M. et al. Raman-scattering study of cubic-tetragonal phase-transition in Zr1-X CeX O2 solid-solution. Journal of the American Ceramic Society, v. 77, n. 4, p. 1067-1071, 1994.

4. Lamas, D. G. et al. Synchrotron x-ray diffraction study of the tetragonal-cubic phase boundary of nanocrystalline ZrO2- CeO2 synthesized by a gelcombustion process. Journal of Applied Crystallography, v. 38, p. 867-873, 2005.

5. Fuentes, R. O.; Baker, R. T. Synthesis of nanocrystalline CeO2− ZrO2 solid solutions by a citrate complexation route: a thermochemical and structural study.

Journal of Physical Chemistry C, v. 113, n. 3, p. 914-924, 2009.

6. González-Rovira, L. Single-step process to prepare CeO2 nanotubes with improved catalytic activity. Nano Letters, v. 9, n.

4, p. 1395-1400, 2009.

7. Martin, C. R. Nanomaterials: a membranebased synthetic approach. Science, v.

266, n. 5193, p.1961-1966, 1994.

8. Leyva, A. G. et al. Microwave assisted synthesis of manganese mixed oxide nanostructures using plastic templates.

Journal of Solid State Chemistry, v. 177, n. 11, p. 3949-3953, 2004.

9. Fuentes, R. O. et al Preparation and characterisation of nanostructured gadolinia-doped ceria tubes. Journal of Materials Chemistry, v.18, n. 46, p.

5689-5695, 2008.

Activity ActivityReport Report 2009 2008 |

85

88 Accelerator development and operation 102 Beamlines 108 Center for Structural Molecular Biology (CeBiME) 112 Nanoscience and nanotechnology 118 Cesar Lattes Nanoscience and Nanotechnology Center (C2Nano) 120 Industrial research activities 124 Main Events 128 Facts and figures

1

Accelerator development and operation CrĂŠdito: Gustavo Tilio

In 2008, the LNLS UVX light source achieved its best performance since it started operating as an open facility for users of synchrotron light.

The year was marked by excellent overall reliability of the light source, with a significant reduction in injection time and in the number of machine failures.

This achievement was the result of a series of improvements and upgrades of the light source over recent years, an effort that involved the entire Accelerator Division. Together with reliability, beam stability is another fundamental and permanent issue on the accelerator teamâ&#x20AC;&#x2122;s agenda. The enhancement in the machineâ&#x20AC;&#x2122;s performance achieved through improvements and upgrades began with a careful analysis of the critical subsystems by dedicated task forces whose main purpose was to improve beam stability. In particular, the new high-brilliance beamlines now under construction, the PGM, and the materials science wiggler beamline, are known to demand very high performance from the light source, thus creating the requirement for improved stability and reliability.

Facility Report

Introduction The central mission of LNLS is to provide a propitious environment and maintain its open facilities in excellent operational conditions, thus enabling its users to carry out outstanding science. As the cornerstone of these facilities, the UVX synchrotron light source has been operating for external users since 1997, assuming a fundamental role in the success of LNLS

the ring – allowing for direct monitoring of the position of the photon beam.

Concurrently, a second task force was established to identify means of reducing the time spent on the injection process. Because injection takes place at low energy, the time spent on injection has a considerable impact on beam motion caused by transient thermal drifts in the vacuum chamber. Moreover, synchrotron light to the beamlines is switched off during

as a National Laboratory. The delivery of a

injection, which can result in thermal drifts in

high-quality beam operating according to the

the optical components. The need for faster

published schedule is particularly important,

injection led to upgrades in the injector system

and is therefore one of the main operational

and to several modifications in injection and

goals for the light source. This allows LNLS

ramping procedures. The crowning moment

users to optimize their use of the limited beam

of all the improvements implemented over the

time available. Allied to the effort to expand

past years came when the operator took less

the spectrum of light available to its users,

than 6 minutes to deliver the beam back to the

beam stability and reliability have been a core

users, the fastest injection ever achieved. This

aspect of the improvements implemented in

feat, which was achieved in September 2008,

the machine in recent years.

represented a huge advance from the typical

The Beam Stability Task Force was set up in 2004 to coordinate the continuing efforts

injection time of 40 minutes at the time the task force was established.

toward more stable electron and photon beams.

Accelerator Operations

identification of the causes of beam motion

operated routinely 24 hours a day, providing 4500

and minimize the causes of beam motion.

4000

These actions include the development of a

3500

and construction of X-ray beam position monitors – installed in some beamlines around

Figure 1

2008

0 2007

the storage ring tunnel; and the development

500 2006

to achieve better temperature control within

1000

2005

thus heating, the chamber’s walls; the effort

1500

2004

to prevent synchrotron light from reaching, and

2000

2003

introduction of masks in the vacuum chamber

2500

2002

sensitive to vacuum chamber thermal drifts; the

3000

1997

new model of beam position monitor – less

User beam time (hours)

been taken to improve the monitoring system

2001

system. Based on these efforts, actions have

through Saturday mornings, the light source

2000

of the electron beam position monitoring

From January to October 2008, Monday

1999

and on the source of instrumental problems

1998

The Task Force concentrated its efforts on the

Total beam time delivered to users since 1997 Activity Report 2008 |

89

year due to the continuous improvements in

300

beam lifetime and in average beam current in

200

usersâ&#x20AC;&#x2122; shifts (Figures 3 and 4). During most of

100

the operational time, the machine was run in

0

multi-bunch mode. Single bunch mode was

Figure 2

2008

400

2007

charge (Figure 2) was the same as in the previous

2006

500

2005

year ever (Figure 1). The total delivered beam

2004

600

2003

time delivered in 2007, which was the best

2002

700

2001

users. This was very close to the total beam

2000

800

1999

4,128 hours of beam time to synchrotron light

1998

900

1997

Beam charge (A.h)

Accelerator development and operation

delivered for two weeks to meet demands for UV and soft X-ray beamlines in time-resolved

Total beam charge delivered to users since 1997

experiments.

The overall reliability of the source (defined as the ratio of delivered to scheduled beam time)

Average beam lifetime (hours)

25

reached 98%, which, along with 2003, is the best performance since user operations began in

20

1997 (Figure 5). The continuous improvements in reliability, injection efficiency, and beam

15

orbit stability over the last years are the result 10

of a systematic approach to fault logging and analysis, and corresponding investments in

5

critical subsystems to overcome bottlenecks and weaknesses. The mean time between

Figure 3

2008

2007

2006

2005

2004

2003

2002

2001

2000

1999

1998

1997

0

failures was 72 hours, a 15% improvement over 2007 and the best result since this parameter started to be measured in 2006. The mean time

Average beam lifetime in usersâ&#x20AC;&#x2122; shifts since 1997

to recovery was slightly over 1 hour, basically the same as in the previous year.

A great deal of effort was dedicated to

250 Average beam current (mA)

automating operational procedures to reduce 200

susceptibility to human errors and standardize the procedures. This contributed to the

150

achievement of a marked reduction in injection time during 2008.

100 50

Insertion Devices Elliptically Polarizing Undulator

Figure 4

90

Average beam current in usersâ&#x20AC;&#x2122; shifts since 1997

| Activity Report 2008

2008

2007

2006

2005

2004

2003

2002

2001

2000

1999

1998

1997

0

The first LNLS Elliptically Polarizing Undulator (EPU) was installed in the storage

Facility Report

ring and successfully commissioned in 2007.

to master the cryogenics handling techniques

Designed and produced in the LNLS workshops,

and procedures.

the undulator is a 2.87 m long device that uses

All necessary changes to the storage ring to

pure permanent magnets with 50 mm periods

allow for the installation of the wiggler were

and 22 mm gaps, and is optimized to cover the

designed and implemented in 2008, including

100 eV to 1 keV photon energy range, providing

new vacuum chambers and photon shutters

linearly, elliptically, and circularly polarized

with cooling systems ready to withstand the

light. In October 2008, a preliminary setup of

large heat load from the wiggler radiation. With

the PGM beamline was used to perform the

the gradual installation of insertion devices

first quantitative measurements of the radiation

over the years, the need arose to operate with

produced by the undulator. Photoemission spectroscopy studies of gold plates confirmed the undulatorâ&#x20AC;&#x2122;s expected yield and also provided

100 98

the first opportunity for the accelerator team to

96

routine user runs, thus putting the undulator active orbit compensation system to work under real conditions, with no observable detrimental effects on other beamlines.

Reliability (%)

act on the undulatorâ&#x20AC;&#x2122;s gap and phase during

94 92 90 88 86

the LNLS storage ring will be a superconducting

2008

2007

2006

2005

2004

2003

2002

The third insertion device to be installed in

2001

80 2000

Materials Sciences

1999

82 1997

Superconducting Wiggler for

1998

84

Figure 5

Machine reliability in usersâ&#x20AC;&#x2122; shifts since 1997

Figure 6

General view of the LNLS 4.0 T superconducting wiggler in the workshop at Budker Institute in Novosibirsk

wiggler optimized to enhance the photon flux in the 10 to 20 keV photon energy range (Figures 6 and 7). The device is in its final stages of construction at the Budker Institute in Novosibirsk and is scheduled for installation in the LNLS storage ring in November 2009.

It consists of a 31 pole, 60 mm period, 4.0 T peak field device with 14 mm beam stay clear gap, and will allow the photon flux at 20 keV to be increased by more than three orders of magnitude over the corresponding photon flux from the storage ring dipoles. Plans for the beamline aim at reaching energies of 30keV, which are currently unavailable at the other beamlines. This will be the first superconducting device in the LNLS machine and considerable effort is being devoted by the machine team

Activity Report 2008 |

91

Accelerator development and operation

reduced vertical aperture, which is particularly

sections, was implemented and commissioned

important when operating with a 14 mm vertical

by the end of 2008.

aperture superconducting wiggler. To cope with this restricted aperture, a new operation mode for the storage ring, with low (~0.8 m) vertical betatron functions in all six long straight

Orbit Stability From the very outset, the efforts of the LNLS Beam Stability Task Force concentrated

Photon flux (photons/sec/mrad hor/0.1% bw)

on understanding the source of long-term orbit drifts, produced mainly by a variety of thermal

1015

drifts. Throughout 2007, data were collected

1014

and analyzed from the prototype button type

1013

electron beam position monitors (BPMs) installed

12

10

in the straight section which houses the EPU,

1011

as well as from the BPMs in section 12 (where

1010

new water-cooled absorbers were added to the vacuum chamber in 2006). These analyses led to

109

the conclusion that a variety of short and long

E = 1.37 GeV I = 250 mA

108 107 0.1

2

3

4 5 6 78

timescale instrumental problems in the current 1

2

3

4 5 6 78

10

2

3

4 5 6 78

100

Photon energy (keV) Superconducting Wiggler (4.0 T, 31 poles) Figure 7

Dipole

Calculated flux from the 4.0 T superconducting wiggler compared to photon flux from the existing dipole magnets

BPM system could be solved by implementing a large scale replacement program of the old stripline BPMs and by upgrading the vacuum chamber cooling system. Even though the short-term difficulties could essentially be solved by improvements in BPM electronics (and by custom-made solutions for a few specific mechanical problems), the encouraging results obtained from the prototypes indicated that the replacement of all electron BPMs in the storage ring was indeed the next step to overcome orbit stability limitations. A final design for the new button type BPM was developed in 2008 and a set of monitors were built and characterized (Figure 8)1. A bulky and sturdy support for these BPMs was also developed and built out of manganese brass alloy for its suitable thermal properties. One third of the storage ring BPMs and vacuum chambers were replaced in a large scale operation during the 2008 machine shutdown. The new BPMs feature much better cooling and mechanical stability than

Figure 8

92

New button-type BPM being prepared for RF characterization

| Activity Report 2008

the previous models (Figure 9). In addition to

Facility Report

replacing BPMs, a series of cooling masks were

a

incorporated to the storage ring vacuum system to prevent chamber heating from synchrotron radiation and the resulting unwanted chamber motion. Beam measurements (using position gauges and beam-based alignment) confirmed that thermally induced BPM deformation and motion have been reduced significantly and are now acceptable (Figure 10). Substitution of the remaining stripline BPMs is planned for the next two years.

Orbit stability was constantly monitored by means of X-ray BPMs at a diagnostic beamline and stability figures of merit were recorded for various time scales. The measurements confirmed previous observations that short-term stability was adequate, but avoiding longer-term drifts was much more challenging. Typical curves for changes in photon beam position, observed with a blade BPM at a diagnostic beamline,

b

show +/â&#x20AC;&#x201C;10 Âľm drifts over a few user shifts (Figure 42). These drifts are expected to be reduced when the RF BPM replacement program is completed.

Other diagnostics systems that have been added to the accelerators in recent years include an automated transverse electron beam size measurement device based on an X-ray pinhole camera; a system embedded in the control software to automate tune measurements in the storage ring; and commercial (LIBERA) digital BPM electronics with single turn capability.

Tests were initiated to use these modules for mapping transverse (betatron) phase space, which should lead to important insights into non-linear dynamics in the storage ring. More importantly, this is the first step toward the complete specification of an active feedback system to overcome collective instabilities in the LNLS storage ring.

Figure 9

a) The old stripline BPM; and b) new button BPM installed in the storage ring. Note the cooling mask, decoupling bellows, and robust support in the new modelv Activity Report 2008 |

93

Accelerator development and operation

storage ring quadrupole power supplies was

15 200

10 5

150

0 100

–5 –10

Beam current (mA)

BPM mechanical centre shift (m)

In 2007, a new set of active shunts for the

250 a

20

50

–15 –20 5:00 PM

6:00 PM

7:00 PM

8:00 PM

were built and installed in all storage ring quadrupoles during the 2008 machine shutdown.

These shunts allowed for the beam-based alignment of the BPM electrical centers and the redefinition of a reference orbit that goes through the magnetic center of the quadrupoles. So far,

0 9:00 PM

the main benefits that have been observed as a result of the improved offset determination

11/28/2008 BPM 04A

built and successfully tested. Thirty-six units

BPM 08A

are a reduced sensitivity of the orbit to tune

Current

changes (due to better centering of the beam in 250 b

40

200

30 150 20 100

10

reduces betatron coupling effects.2

Injector Improvements

6: 00 PM

7: 00 PM

8: 00 PM

The injector upgrade program, started in 2006 with the aim of reducing the total refill

0 9: 00 PM

time of the storage ring, brought its first results

11/28/2008 BPM 04A

in 2007 and was completed in 2008. In fact, the

BPM 08A

typical injection time, i.e. the time between

Current

Figure 10 a) Thermally induced motion; and b) deformation of the BPM body of an old (BPM 04A) and a new (BPM 08A) BPM, as observed with position gauges 30

10

150

0 100

–10 –20

50

–30

0 00: 00

12: 00

26/09/2008

magnitude. A record 5 min 28 second injection

00: 00

injection method implemented in 2006 (which became the routine procedure in 2007) and also of various improvements to the injector hardware, such as the upgrade of the booster synchrotron RF system, commissioned in 2007, which – with a new power plant based on solid state amplifiers – increased the total available

27/09/2008 Current

Blade monitor

Figure 11 Photon beam stability measured with a blade monitor in a diagnostic beamline along three user shifts. The X-BPM is located 8.5 m away from the photon source | Activity Report 2008

next shift, was reduced by nearly one order of

This is a result of the new low energy top-up Beam current (mA)

200

the end of a user shift and the start of the

time was achieved in October 2008 (Figure 12).

250

20 Beam position (m)

the beam along the machine sextupoles, which

50

0 –10 5: 00 PM

94

quadrupoles), and a 10% reduction in vertical beam size, possibly due to better centering of

Beam current (mA)

BPM body deformation (m)

50

2.

Liu L. et al. Beam-Based Alignment of the LNLS UVX Storage Ring BPMs. In: Proceedings of the Particle Accelerator Conference; 2009; Vancouver.

Facility Report

1.0

Normalized frequency

0.8

0.6

0.4

0.2

0.0 0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

Injection time (minute) 2006

2007

2008

Figure 12 Normalized frequency histogram of injection times from 2006 to 2008

RF power by a factor of more than 2, to a total

RF power source for the booster synchrotron in

of 2 kW at 476 MHz.

2001 (using 250 W amplifier modules, which

Our efforts to reduce injection time included

at that time was a world record in power

improving the automation of the injection

per single module at this frequency), the

process, such as the use of orbit feedback

accelerator team continued its involvement

during energy ramps, closing and opening of

in the development of RF power sources.

insertion devices, and other previously manual

These sources can provide an alternative to

procedures. These improvements provided not

commercial UHF klystron or tetrode tubes,

only faster but also more repeatable injections. A

which are becoming increasingly expensive to

short injection time is very beneficial in reducing

purchase and operate. Solid state systems offer

thermal transients of the orbit associated with

the advantage of much higher efficiency and

the injection process.

modularity, leading to significant reduction in electricity costs. In fact, klystron tubes are

Development of Solid State RF Power Sources

typically not only much less efficient, but they also present essentially fixed power consumption, regardless of the instantaneous

Following the successful design, construction,

power needs of the accelerator. Solid state

and commissioning of a 1 kW, 476 MHZ solid state

devices, on the other hand, will consume only Activity Report 2008 |

95

Accelerator development and operation

whatever electric power is needed for a given

two towers. Also, power combiners, dividers,

RF power demand. Moreover, the intrinsic

and directional couplers have been designed,

modularity is also expected to bring enhanced

prototypes have been built successfully, and

reliability, since the amplifier is capable of

some of the newly developed components

continuing operation even in the event of

were used for the booster RF system upgrade

failure of one or several modules.

in 2007. A schematic drawing of the amplifier

In 2007, a project was approved by the federal funding agency FINEP to design and

and photos of its main components are shown in Figure 13.

build two solid state amplifier towers capable

The two amplifier towers are scheduled

of providing a total of 100 kW of power at

for assembly and testing in the RF lab

476 MHz. Detailed design of the system

by the end of 2009 and installation in the

began in 2008, in close collaboration with

storage ring is expected to take place in

the SOLEIL RF group. These amplifiers are

2010. The difference in efficiency between

slated to replace the two commercial klystron

the two systems is so remarkable that we

tubes currently in operation in the storage

estimate the investment in this project will

ring RF system. By the end of 2008, the power

be fully recovered in approximately three

transistors, which are the heart of the system,

years of operation through the reduction in

had been specified, the 300 W amplifier

electricity costs. We also expect this to be

modules had been successfully tested, and

the technology of choice for the LNLS-2 RF

orders had been placed for the construction

power sources.

of the several hundred units needed for the

Beam Dynamics and Modeling The Accelerator Physics group has worked on a variety of new operation modes for the storage ring in recent years. In early 2008, a low-emittance mode was implemented in test trials, demonstrating the possibility of reducing the storage ring emittance by a factor of about two if the dispersion matching constraint of the Double Bend Achromat (DBA) lattice is removed.

Moreover, various optical configurations with low vertical betatron function at the center of the insertion straight sections were designed and implemented and have been routinely 300 W Amplif ier module

10-way divider

8-way divider

Two-way 50 kW combiner

2.5 kW combiner & 40 dB dir coupler

10-way 25 kW combiner

Figure 13 The proposed 476 MHz, 50 kW solid state RF power amplifier with its main components

96

| Activity Report 2008

employed as nominal operation modes for users operation. These are very useful because they allow for the installation of narrow gap insertion devices. In fact, special modes with low vertical betatron function were implemented in specific

Facility Report

straight sections, along with the installation

the orbit response matrix measurements and

of the 2.0 T hybrid multipolar wiggler and

streamlining the modeling analysis. The linear

the elliptically polarizing undulator. In 2008,

modeling analysis, coupled with the recent

as part of the preparation for the upcoming

availability of shunts for all quadrupoles in

installation of a superconducting wiggler, a new

the storage ring, opens the possibility for

mode (BBY6) was commissioned, in which the vertical betatron function is reduced to about 0.8 m at the center of all six long straight sections.

LNLS UVX BBY6T Mode

This was considerably more challenging than

30

the previous low beta modes, which could be

25

via a smooth migration from the standard mode,

20

because now a new injection configuration at 500 MeV also had to be determined to avoid crossing integer resonances. By the end of

x, y (m)

reached at high energy, without any beam loss,

15 10

2008, successful injection and ramping in the

5

new mode was demonstrated and, starting

0

in early 2009, this became the routine user operation mode.3

0

20

x

the transverse beam size. The effect of insertion and BBY6 modes is shown in Figure 15. A larger dynamic aperture leads to longer beam lifetime

80

s (m)

new BBY6 mode, which are closely related to devices on the dynamic aperture of standard

60

40

Figure 14 shows the betatron functions of the

y

Figure 14 Measured (dotted) and calculated (solid curves) betatron functions in the BBY6T mode with the wiggler closed. Red (blue) curves are related to the horizontal (vertical) plane. The betatron functions were measured by changing quadrupole strengths

and greater injection efficiency, allowing for easier implementation of the mode.

Throughout 2008, work on linear modeling

Standard without IDs

+ Wig

+ Wig + compensation

BBY6T without IDs

+ Wig

+ Wig + compensation

of the storage ring lattice by analysis of orbit response matrix measurements was intensified, making use of the much improved quality of the available BPM data. In fact, previous attempts at this type of modeling were hampered over recent years by limitations of the beam position measurement system. Most of the efforts in 2008 were devoted to automating

3.

Liu L. et al. A New Mode for Operation with Insertion Devices at UVX. In: Proceedings of the Particle Accelerator Conference; 2009; Vancouver.

Figure 15 Dynamic aperture for the Standard (top row) and BBY6T (bottom row) modes. From left to right: the lattice without IDs, with the 2.0 T wiggler without compensation, and with compensation.

Horizontal and vertical axes show the normalized coordinate u/√βu and span from –0.01 to +0.01 m1/2 in both axes Activity Report 2008 |

97

Accelerator development and operation

the implementation of storage ring optical

Minister of Science and Technology during

symmetrization procedures, with beneficial

the inauguration of the new Center for Nano-

effects on beam lifetime and stability .

Science and Nano-Technology in early March.

4

Beam-based alignment procedures are

In November 2008, the Ministry of Science and

now fully automated as well, allowing for

Technology allocated initial funding for the

the definition of a new reference orbit with

preparation of a Conceptual Design Report for

improved characteristics.

a new synchrotron light source to be built at LNLS. A Preliminary Conceptual Design Report

Conceptual Design for a New Light Source

is being prepared, describing a state-of-the-art light source based on a 2.5 GeV electron storage ring with about 300 m circumference and an

Internal discussions about a future light

emittance below 1 nm.rad. The Preliminary

source for LNLS gained momentum in 2008.

Design Report will be the basis of the discussions

A preliminary scientific case was prepared by

during the First LNLS-2 Workshop, to be held

the in-house scientific staff and delivered to

immediately after the 2009 edition of the LNLS

President Luiz InĂĄcio Lula da Silva and to the

Usersâ&#x20AC;&#x2122; meeting.5

4.

5.

98

| Activity Report 2008

Resende XR. et al. Analysis of the LNLS Storage Ring Optics Using LOCO. In: Proceedings of the Particle Accelerator Conference; 2009; Vancouver.

Tavares, P. et al. LNLS-2: A New High Performance Synchrotron Radiation Source for Brazil. In: Proceedings of the Particle Accelerator Conference; 2009; Vancouver.

Facility Report

Activity Report 2008 |

99

A New Light for LNLS Initial Design Efforts on the Next Light Source: LNLS-2 Scientific research and technological development with synchrotron radiation have experienced enormous growth all around the world over the past 20 years. In fact, today there are more than 70 synchrotron light sources operating around the globe. Some of them have come into operation quite recently, such as the Swiss (Swiss Light Source – SLS), British (Diamond), French (SOLEIL), Canadian (Canadian Light Source – CLS) and Australian (Boomerang) facilities. All these projects represent responses by various countries to the explosive growth of the demand for synchrotron radiation. This growth is due to the wide range of scientific and technological

period of 10 years and started user operations in July 1997.

In addition to the numerous scientific results obtained using the source – which in 2007 reached more than 200 papers published in refereed journals, the equivalent of about 1.5% of Brazil’s total scientific output in all fields of research – in its 10+ years of operation, LNLS installations have undergone continuous improvements and upgrades, reaching significantly higher performance levels than originally foreseen in its design.

However, in recent years, the capabilities of the LNLS-1 light source, in terms of new beamlines and of upgrades to its accelerators (comprising the injector chain and the UVX storage ring) have approached their physical limits and can no longer withstand further

applications made possible by the availability of storage

expansions. At the same time, technological innovations

ring-based ultraviolet and X-ray sources with several

are continually introduced all over the world, and new

orders of magnitude stronger brightness than that

synchrotron light sources are currently being designed or

obtainable from conventional, laboratory-scale sources.

built in other countries, such as NSLS-II in Brookhaven

Those applications involve the determination of the

(USA) and MAXIV in Lund (Sweden), with much higher

structural and chemical properties of a wide range of

performance levels than can be obtained today at the

materials at the molecular and atomic level. Knowledge

existing Brazilian source.

of the detailed inner workings of these materials is key

In order to keep Brazil’s scientific and technological

for the development of new technologies and compounds

community competitive over the next decades, it is

for everyday use as well as for the application of known

essential to provide it with the tools required to perform

materials in new environments. In this context, synchrotron

materials analyses at the molecular and atomic scales

light emerges as an essential tool which allows scientists

under increasingly demanding experimental conditions.

and technologists to actually see matter at the nanoscopic

In the field of synchrotron radiation, this means

level, unraveling its most intimate nature.

providing light beams that are much more intense and

Brazil has kept up with this tendency and, beginning

brighter than those that can be obtained at LNLS today,

in the late 80s and throughout the 90s, developed its

which can be focused down to sub-micrometric spots

own technology for the production of synchrotron light,

and reach the more penetrating, hard X-ray region of

designing and building LNLS-1, the first synchrotron light

the electromagnetic spectrum, with controllable time

source in the Southern Hemisphere, and still the only one

structure and polarization properties. All of this is only

in Latin America. Brazil’s source was built at LNLS over a

possible through the construction of a new synchrotron

100 | Activity Report 2008

Preliminar study on the design of the new source building

light source based on a storage ring with higher energy

Inácio Lula da Silva and to the Minister of Science

and a larger circumference.

and Technology, Sergio Machado Resende, during the

The year 2008 marked the beginning of the efforts

opening ceremony for the Cesar Lattes Building on the

toward the design and construction of this new light source

LNLS campus in early March 2008. A few months later,

at LNLS, called LNLS-2. Following a recommendation

in late November 2008, R$ 2 million was added to the

by the LNLS Scientific Advisory Committee in 2007,

ABTLuS budget for 2008, earmarked specifically to

discussions on possible parameters for a new light source

initiate the LNLS-2 design efforts. In the first few months

were initiated in early 2008, involving the in-house

of 2009, a task force will be set up at LNLS to prepare

scientific staff and the accelerator and instrumentation

a Preliminary Conceptual Design Report, which will

development groups. These discussions led to the

be presented to the LNLS user community at the First

preparation of a report entitled “LNLS-2: A New High

LNLS-2 Workshop to be held immediately following

Performance Synchrotron Light Source for Brazil – Proposal

the 19th LNLS Users´ meeting. This workshop will bring

for the Preparation of a Conceptual Design Report”. This

together the scientific community interested in LNLS-2

document described a preliminary scientific case for the

and representatives of funding agencies, to discuss the

new facility, listed a series of phases for the development

economic viability of LNLS-2.

of the project, and established a R$15 million budget

All this makes 2008 a remarkable year in the history

request for the preparation of a Conceptual Design

of LNLS pointing to an exciting and bright future for

Report. The document was delivered to President Luiz

the entire lab.

Activity Report 2008 | 101

2

Beamlines

CrĂŠdito: Gustavo Tilio

As part of its mission as a national laboratory, LNLS has a continuous effort on building and upgrading its beamlines. These improvements are essential to attend the demands of the user community for new methods and techniques. The evolution of the beamlines is, therefore, driven towards the implementation of new setups, which inherently bring additional flexibility to the research performed in each installation. Such evolution is followed by a constant development of user friendly systems that allow researchers to better control these facilities and to extract the best scientific results from their experiments.

Facility Report

Presently, there are thirteen beamlines at LNLS in full-time operation for users, one

of ice on the crystal during data collection at cryogenic temperatures.

beamline in construction (PGM), one ready to be commissioned (SAXS-1) and one already commissioned but still not open to users (VUVF).

Other two beamlines are dedicated to beam diagnostics and are for internal use. The beamlines are organized in five groups, Macromolecular Crystallography and Spectroscopy, X-ray Absorption and Fluorescence, X-ray Diffraction, X-ray Scattering and Ultraviolet and Soft-X-ray Spectroscopies. Most scientific instrumentation developed at the beamlines during this year, had special emphasis on automation of alignment procedures and in situ experiments.

These improvements followed guidelines designed to meet the demands from the users, both academic and industry related. Several other minor improvements on computational capabilities and usability of the beamlines were performed which are sensed by the users during their shifts. In the following we list the major improvements that have been implemented in the beamlines during 2008.

X-ray Absorption and Fluorescence Currently, three absorption spectroscopy beamlines are operational at LNLS. Two of them are conventional energy scanning and allow for the performance of most standard transmission and fluorescence experiments.

The third one, an energy dispersive beamline, is dedicated to time resolved and extreme condition experiments. As a major improvement to the absorption beamlines, the mechanisms of alignment and optimization of the monochromator and optics of the D04B:XAFS1 beamline were automated. Several improvements were made in the D08B:XAF2 beamline data acquisition and detection system in fluorescence and transmission modes. One of the main projects under development at the D06A:DXAS beamline is the installation of a 6.5 T superconducting coil. This system is flexible, compatible with UHV experiments and can also be used at SXS, SGM, and the upcoming PGM beamlines, as well as for stand-alone experiments. A new layout

Macromolecular crystallography and spectroscopy

for the beamline was designed to allow for the installation of the superconducting coil.

This group has two protein crystallography

A major effort for implementation of combined

beamlines, one with tunable energy (W01B:MX2)

techniques has also been undertaken at LNLS

using a wiggler source and capable of doing MAD experiments, and one with fixed energy (D03B:MX1). The wiggler-based beamline (W01B â&#x20AC;&#x201C; MX2) received an upgrade in the thermal control of its optical components, which, with the additional improvements in progress, will enhance its energy resolution and stability. The other beamline (D03B â&#x20AC;&#x201C; MX1) gained a much awaited improvement in sample conditioning, namely, a hutch at the sample position to prevent the formation and deposition

Figure 1

Mass spectrometer installed at the DXAS beamline Activity Report 2008 | 103

Beamlines

to add new capabilities to the absorption and

spectrometry with XAFS for the in situ study

other beamlines. One of the highlights of

of chemical reactions (Figure 1).

these experiments is the association of mass

A new laboratory, with all the necessary tools for mounting and preparation of high pressure

a

cells, is now available for users conducting in situ experiments under extreme conditions.

The X-ray fluorescence beamline serves a broad, multi-disciplinary community of users involved mainly in environmental sciences, chemistry, and biophysics applications. This beamline received several improvements during 2008. In collaboration with the University of Córdoba – Argentina, polycapillary focusing optics were designed to allow for micro-XRF using the confocal geometry technique in studies

c

b

of locally three-dimensional distribution of the samples’ elemental composition. A grazing incidence XRF set-up for chemical compositions, which is sensitive to trace levels and combines TXRF and XANES spectroscopy in fluorescence mode, was also installed for studies of toxic elements at trace levels in environmental and

Figure 2

biological samples. An energy dispersive X-ray

Setup for in situ measurements: (a) furnace with imaging plate system; (b) furnace mounted at the Huber diffractometer; (c) gas supply system

reflectivity set-up was also developed for the study of self-assembled multilayer structures of organic materials as a function of temperature (40 to 200º C).

X-ray Diffraction 0.5 mm capillar

Zoom lenses

This group has three X-ray diffraction beamlines: D10A:XRD2, D10B:XPD and D12A:XRD1 working in collaborative mode, with the users’ requests distributed among them according to the best possible use of the beamlines’ characteristics, their scientific instrumentation, and time allocation. The major

Goniometric head

improvements in the X-ray diffraction beamlines aimed to increase their ability to perform in

Device for the rotation of the sample

situ measurements, including furnaces, gas supply, and gas analyzer integrated with data

Figure 3

Capillary system for powder diffraction measurements

104 | Activity Report 2008

collection (Figure 2). A capillary system for

Facility Report

diffraction measurements was also developed,

MX2

tested and installed (Figure 3).

On the D10B:XPD beamline, several incremental improvements were implemented to render it more robust and user-friendly, e.g., a sample environment furnace (1000 ยบC), cryostats (12-475

SAXS1

K, 1.7-300 K) and a B4C pressure cell (0-1 GPa).

Finally, a multi-analyzer detector stage was designed and its first tests conducted.

SAXS2

X-ray Scattering LNLS has two X-ray scattering beamlines

Figure 4

New position of the D11A:SAXS1 beamline

Figure 5

Sample holder for SAXS experiments, allowing for the automatic change of up to 12 samples

to meet the research requirements of several soft-matter and inorganic nanostructured systems. To make room for the undulator UV beamline, SAXS1, one of the first beamlines at LNLS, was dismantled in October 2006 and its reassembly in the new position (Figure 4) began in July 2007. Several improvements were made during its reassembly: the shielding was improved, the slit system was upgraded, a new hutch was built following the design Foto:

of the other beamlines, and a new viewport and cooled Be window were installed. This beamline will now receive a Pilatus 300k area detector (from Dectris) and will be available to users in the second semester of 2009.

A new sample holder based on a capillary

range (D04A:SXS), and for the construction of

or mica window was adapted to the beamline

the first undulator beamline at LNLS, named

setup and a sample holder for in-vacuum solid samples was developed for the SAXS2, to be used also on the SAXS1, when it becomes operational.

U11A:PGM, which will provide a highly brilliant photon flux in the 100 to 1000 energy range.

The sample holder allows up to 12 samples to

The UV and soft-X-ray beamlines were among

be changed automatically (Figure 5).

the first ones installed at LNLS and a program has been initiated to upgrade them. D08A:SGM

Ultraviolet and Soft-X-ray Spectroscopies The group is responsible for three existing

has already undergone part of its refurbishment and is showing promising results. This beamline has also received a new higher harmonic filter,

beamlines, two in the UV range (D05A:TGM

which improved beam quality considerably in

and D08A:SGM) and one in the soft-X-ray

the energy interval of 240 to 370 eV. Activity Activity Report Report2008 2009| 105 |

Beamlines

The D04A:SXS beamline is undergoing

Nickel and rhodium mirror reflectivity

1.0

complete refurbishment. A new mirror was installed with nickel and rhodium layer

0.8

depositions and much better reflectivity that

Reflectivity

will provide a higher flux in the 3 to 5 keV energy range (Figure 6). A new monochromator

0.6

purchased from ACCEL was installed. It is equipped with a high vacuum (10-9 mbar),

0.4

double-crystal Huber goniometer and has two operation modes: constant offset and

0.2

channel-cut. The first crystals will be maintained below 300 ºC by a water cooling system. This

0.0 1000

2000

3000

4000

5000

6000

Photon energy (eV) Rhodium – old  = 12.4 g/cm3  = 1.00  = 3.3 Å

beamline is slated to become available for users in the first half of 2010.

Two new circular dichroism chambers that

Nickel – new  = 8.9 g/cm3  = 0.60  = 1.4 Å

can be shared by the 3 operational beamlines have also been made available to users. One of the chambers has a fixed magnetic field of 1 Telsa,

Figure 6

Comparison of X-ray reflectivity spectra of the old and new mirrors of the SXS beamline

and the other has coils that allow for control of the magnetic field applied to the sample.

The major step forward on the UV / soft X-ray beamlines, however, will be reached with the completion of the U11A:PGM, a high-brilliance

Au 4f excited with the 3rd harmonic at U11

and high-resolution UV-soft X-ray beamline

EK = Hv ~ 30 eV

whose construction is underway. During the single-bunch mode of operation, experiments with the white beam were conducted in November 2008, allowing some components of the beamline to be tested and the light emitted by the undulator to be characterized. Briefly, the experiments consisted of placing the undulator gap where the first harmonic was at 100 and 110 eV, respectively. Using a very small aperture (300 µ) the light from the undulator illuminated a gold sample. The photoelectrons ejected from the

190

200

210

220

230

240

250

Photoelectron kinetic energy (eV) 1st harmonic at ~100 eV Figure 7

1st harmonic at ~110 eV

Characterization experiments on the U11A:PGM beamline

106 | Activity Report 2008

gold sample by the third undulator harmonic were collected by an electron energy analyzer (EA). Figure 7 shows the spectrum of the 4f gold photoelectrons, demonstrating that the undulator is operating as expected.

Facility Report

Activity Activity Report Report2008 2009| 107 |

3

Center for Structural Molecular Biology (CeBiME) Crédito: Gustavo Tilio

The Center for Structural Molecular Biology – CeBiME houses unique instrumentation used for the determination of macromolecular three-dimensional structures. The energy-tunable MX2 is one of the most sophisticated beamlines at LNLS and is dedicated to protein crystallography. Facilities for macromolecular crystallography also include the MX1 beamline and a rotating anode X-ray generator. This instrumentation, together with the NMR 500 MHz and 600 MHz spectrometers – the latter equipped with a cryogenic probe –, comprise an open facility available to the structural biology community.

Facility Report

Macromolecular crystallography at LNLS To optimize the use of the MX1 and MX2 beamlines, a rotating anode X-ray generator (Figure 1) is available for external users with the main purpose of performing preliminary crystal diffraction screens. This X-ray generator also serves as a back-up source for the macromolecular crystallography community during maintenance shutdowns and upgrades of the synchrotron machine. It is equipped with a VariMax optical system to optimize flux and focus at the sample position; a 345 mm image plate detector (Mar345, Rayonix); and a cryogenic system (Oxford Cryosystem series 700). Requests for the use of the X-ray generator may be submitted at any time. To expedite the process of time assignments for external users, a fast track mode of proposal evaluation was implemented.

The MX1 and MX2 beamlines operated for external users throughout the year, using different phasing methods to solve new structures. Nonetheless, the beamlines require continual maintenance and improvements.

At the MX1 beamline, one of the first operational beamlines of the Brazilian Synchrotron Light Laboratory, a new cabin was installed to cover the goniometer and prevent ice from building up over the sample. The energy-tunable MX2 beamline (Figure 2) has been under rigorous scrutiny for the causes of energy oscillations. Careful measurements of beam instability are currently being performed at this beamline and should provide the basis for a solution of the energy oscillation problems. The computers available for users of both beamlines have also been upgraded.

Figure 1

View of the rotating anode X-ray generator available at LNLS for the macromolecular crystallography community

Figure 2

View of the MX2 beamline (upper panel) and its experimental hutch (lower panel) Activity Report 2008 | 109

Center for Structural Molecular Biology (CeBiME)

Dynamic light scattering for protein stability and aggregation studies Determination of three-dimensional protein structure by crystallography or nuclear magnetic resonance (NMR) requires the reconstitution of in vitro conditions that keep a protein purified to near homogeneity, i.e., as close as possible to its natural folding state. During the protein purification process, great care must be taken to handle samples under conditions that ensure the prevention of denaturation and aggregation. Many factors contribute toward the stability of a purified protein, especially the physicochemical properties of its surface, the buffer components, and the temperature. Dynamic light scattering (DLS) is well known as an efficient method to provide information on size distributions and polydispersity of macromolecules such as proteins. Polydispersity is related to the

state of aggregation while monodispersity is associated with higher crystallization success. Protein stability studies will be greatly facilitated by the use of a DLS plate reader, purchased from Wyatt Technology Co. (Figure 3), which allows DLS experiments to be carried out in a high-throughput mode with automated temperature control. Among the applications of the DLS plate reader for protein studies are characterization of homogeneity, determination of size and thermal stability, association kinetics experiments of macromolecular assemblies, and screening of compounds that may lead to protein aggregation. For purposes of protein crystallization and NMR analyses, the information obtained from DLS will be used to determine the best buffer conditions to stabilize the proteins in solution, thus preventing aggregation and sample loss during the extraction and purification processes. This is expected to increase the success of protein crystallization and to provide stable samples for NMR analyses.

Light and temperature-controlled rooms for regeneration of citrus plants

Figure 3

Light and temperature-controlled rooms for regeneration of citrus plants. Top: tissue culture and regenerative growth room. Bottom: transgenic plants in the acclimatization room

110 | Activity Report 2008

During the past four years we have studied the interaction between Xanthomonas citri and orange plants, aiming to understand the molecular mechanisms governing citrus canker development. Based on global gene expression analysis and protein-protein interaction studies, we have been able to identify a number of citrus proteins implicated in disease development, as well as in citrus defense against the pathogen. Therefore, we are now envisaging new ways of obtaining

Facility Report

citrus plants resistant to Xanthomonas citri. To accomplish this, a series of modifications of the genetic background of citrus plants are being performed and knowledge of how to transform and regenerate citrus plants has become a major goal to be achieved by CeBiME researchers. To support research in this area, two growth rooms equipped with temperature and light control systems were

Figure 4

built at CeBiME for seedling development and plant tissue culture (Figure 4). One of the rooms is dedicated to sweet orange transformation and tissue culture. After a period of regenerative growth and rooting, the plantlets are moved to the second growth room for acclimatization, shoot development, and experiments involving challenges by pathogens.

Light and temperature-controlled rooms for regeneration of citrus plants. Top view: tissue culture and regenerative growth room. Bottom view: transgenic plants in the acclimatization room Activity Activity Report Report2008 2009| 111 |

4

Nanoscience and nanotechnology CrĂŠdito: Nelson Chinalia

The nanoscience and nanotechnology activity at the Brazilian Synchrotron Light Laboratory started more than a decade ago, involving efforts in synchrotron radiation-based experiments, physical and chemical syntheses of 2D and 3D nanostructures, theoretical modeling, manipulation, microfabrication, scaling from the nano-scale to the micro-scale, and advanced use of microscopies based on electrons (SEM, TEM, and STEM) and scanning probes (AFM and STM). These combined efforts seeks the understanding of the materials unique behavior and properties and at the nano-scale, the development of new materials, the precise control over these materials production, and most important, the search for useful applications for this new generation of materials and devices.

Facility Report

In order to achieve its goals as a national laboratory and in agreement with the effort of the Brazilian community in the field of nanoscience and nanotechnology LNLS installations operate as open and multiuser facilities with strong activity on the training of specialized human

Electron microscopy The electron microscopy facility was transferred to the new C2Nano center and began welcoming users at this new location in July 2008. Details of the new building’s advanced design, its construction, and commissioning

resources. The internal research and technical

are presented elsewhere in this report. Part of

team works on the development of new

the new developments at the center included

methodologies and dedicated instrumentation,

the installation and commissioning of two new

which are linked to both, the in-house and

transmission electron microscopes, funded

users word-class research.

mainly by FAPESP (State of São Paulo Research

Among the open facilities related to the nanoscience and nanotechnology program are the x-ray diffraction beam-lines, the electron microscopy laboratory, the scanning probe microscopy laboratory, and the thin-films and

Support Foundation).

The new microscopes installed at the C2Nano building are: A 200 keV TEM-STEM-FEG (1.9 Å point resolution) coupled to STEM BF-DF, and HAADF detectors, a TV-rate CCD camera, a

microfabrication laboratory. In addition, a set

4-megapixel CCD camera, a large collection

of installations dedicated to in-house research

angle energy dispersive X-ray spectrometer

for chemical synthesis of nanostructures and

(XEDS), and an electron energy loss spectrometer

molecules manipulation are part of this great

(EELS) capable of energy filtered imaging. This

effort of a small group of technicians, engineers, physicists, and researchers in nanoscience and nanotechnology at LNLS. As a result of this long-term effort with count-less outstanding results and important

instrument will be used mainly in studies of the crystallographic, chemical, and electronic properties of functional nanostructured materials.

The system’s installation has been completed and its commissioning and debugging are under way.

impact on the Cesar Lattes Nanoscience and Nanotechnology Center (C2Nano) was open for users in 2008 with the presence of the Brazilian President, Luis Ignacio Lula da Silva and the Minister of Science and Technology, Sérgio Machado Rezende, among other ministers of state and personalities. This new center will host an important part of the actual and future LNLS efforts in this field.

The overview of the main activities and new developments in this area during 2008 is presented below.

Figure 1

Disposable salicylicate sensors obtained by deposition of Ti/Au on acetate Activity Report 2008 | 113

Nanoscience and nanotechnology

A 200 keV TEM-STEM-MSC (2.5 Å point

It has been nearly 10 years since the electron

resolution) coupled to a TV-rate CCD camera,

microscopy laboratory opened its doors to users

a 1-megapixel CCD camera, and an XEDS

from all over Brazil and South-America. Since

spectrometer. This instrument will be used mainly

then, it has delivered more than 48,300 hours

for the study of crystallographic and chemical

of electron microscopy to 1,140 external users,

properties of nanostructured functional and

resulting in 332 indexed journal publications.

structural materials, and for the development

In 2008 alone, approximately 5,440 hours of

of in situ experiments. Commissioning and

TEM and SEM were delivered to external

LNLS personnel training were completed and

users involved in 129 research projects, which

the system opened for users in July 2008. In

resulted in 49 indexed journal articles. As a

addition to user training, 14 research projects

central part of the nanoscience program at

were initiated in 2008.

LNLS, the electron microscopy laboratory

The previously existing microscopes are:

continues to train electron microscopists.

A 300 keV TEM-HR (1.7 Å point resolution,

Several programs are in place for theoretical

1.2 Å information limit) coupled to a TV-rate

and practical training.

CCD camera, a 1-megapixel CCD camera, and

Six specialized graduate level courses are

an XEDS spectrometer, which is used for the

offered at nearby universities (UNICAMP and

study of crystallographic and chemical aspects

USP), some of which are available via the LNLS

of nanostructured materials.

website at no charge. A 3-week summer course

A 30 keV SEM-FEG (1.5 nm resolution)

also gives users located far from LNLS the

coupled to an XEDS spectrometer and plasma

opportunity to receive a comprehensive theoretical

based anti-contaminator, employed in studies

education and practical training on HRTEM,

of the morphological, crystallographic and

sample preparation, and data analysis.

chemical aspects of micro- and nanostructured materials.

Figures: images of the installed TEMs and sample Preparation room are suggested.

A 30 keV SEM-LV (3.0 nm resolution) coupled to an XEDS spectrometer, EBSD, and stages for in situ experimentation, dedicated mainly to the

114 | Activity Report 2008

Scanning probe microscopy

study of the morphological, crystallographic

After a commissioning step following some

and chemical properties of microstructured

technical difficulties, the UHV-STM is now

materials and advanced in situ experiments

open for users. Currently, the base pressure

involving heating and deformation.

is pressure is in its mid 5E-12 Torr, thanks

The SEMs listed above and the sample

to several additions: a 400l/s ion pump and

preparation facilities have already been

a non-evaporable getter pump in the main

transferred to the C2Nano Building. The

chamber; and for the load-lock (LL) chamber,

300 keV TEM-HR and some sample preparation

Ar plasma treatment is applied to all samples

equipment will be moved to this new building in

and tips brought into the main chamber.

2009. The new sample preparation laboratories

With a base pressure of 5E-8 Torr or better,

provide users with more adequate and complete

the LL chamber also has an Ar bombardment

installations for the preparation of SEM and

system, a gas manifold allowing for O2 and

TEM samples from a wide variety of hard and

N2 plasmas, and a lamp heating system. The

soft materials.

main chamber currently has Ge, Hf and Ag

Facility Report

e-beam evaporation sources, all of which were

to name just two examples, the development of

developed at LNLS. Current experiments

disposable amperometric biosensors (Figure 1) for

involve the reactive deposition of Hf on Si,

salicylicate-based on screen-printed electrodes; and

and metal surface science.

the development of micro-meshes for the study

The scanning probe facility also offers two

of DNA irradiation damage by soft X-ray.

AFM systems (Veeco DI Ns3a, and a NTMDT Solver Pro) for a variety of experiments, including MFM, EFM, etc.

Molecular manipulation Ensemble biochemical analyses provide excellent quantitative and qualitative descriptions,

Microfabrication and thin films

but fail to describe details of phenomena at

While resident scientists use this facility

the molecular level. The micromanipulation of

extensively, it is also frequently utilized by

individual cells (Figure 2) and molecules opens

visiting users and for industrial projects such as,

the possibility of performing single molecule

a

Figure 2

b

 2.2 m

 3.5 m

10 m

10 m

Scanning electron microscope images of metal mesh filters with different geometrical parameters to control exposed areas on the samples (upper panels). Cells were irradiated for 6 min using filters with openings of 2.2 µm (left) or 3.5 µm in diameter (right), fixed 5 min later and stained for DNA (blue) and γH2AX (red). The scale bar has 10 µm size Activity Report 2008 | 115

Nanoscience and nanotechnology

force spectroscopy. The kinetics, mechanics,

elasticity as a function of the enzyme activity or

and variations in structure, function, and

the environmentâ&#x20AC;&#x2122;s conditions. Single molecule

interactions can thus be explored, leading to a

techniques such as Atomic Force Microscopy,

more complete understanding of physiological

and Optical and Magnetic tweezers are used to

processes.

characterize molecules on the nanometric scale,

Due to Brownian motion, a molecule experiences many fluctuations in the environment in which it performs its functions. An enzyme bound to a polymer, such as DNA, RNA or a carbohydrate, is subject to collisions with water and other molecules that make the entire system move rather rapidly. For a thorough characterization of the interactions between these molecules, it is desirable to restrict these

range. Applications of these techniques shed light into important biological mechanisms such as transcription and translation, and also into studies of the elasticity of cellulose derivatives.

The implementation of magnetic tweezers set-ups (Figure 3) is an ongoing effort that integrates biology and physics expertise and opens new research opportunities at the

movements. One way of accomplishing this

Nanoscience and Nanotechnology laboratory.

is through the application of a unidirectional

This effort is cosupported by CNPq through

force that stretches the polymer, and subsequent

the Scanning Probe Microscopy Network and

monitoring of the changes in the polymerâ&#x20AC;&#x2122;s

by ABTLuS.

Figure 3

116 | Activity Report 2008

with force measurements in the piconewton

Magnetic tweezer setup for manipulation of biological samples

Facility Report

Activity Report 2008 | 117

Cesar Lattes Nanoscience and Nanotechnology Center – C2Nano A state-of-the-art Building for a unique Facility The Cesar Lattes Nanoscience and Nanotechnology center building was funded by FINEP (Brazilian Research and Projects Financing). The center was finished in October 2007, comissioned and occupied by

nanoscience and nanotechnology efforts at LNLS will be concentrated at this new center, which already houses the electron microscopy laboratory and whose office space is occupied by researchers, engineers, and technical staff. Future nanoscience laboratories will also be established at this center in future. The area reserved for electron microscopy comprises six rooms containing

the electron microscopy laboratory and other groups

scanning and transmission electron microscopes (SEMs

during 2008. This new center, named after Brazilian

and TEMs). This building has special characteristics: it

physicist Cesar Lattes, was officially inaugurated in

was designed to reduce external sources of interference

March 2008 by President Luiz Inácio Lula da Silva,

such as wind, temperature variations, and ground-

with the attendance of the Minister of Science and

transmitted vibration, etc., and to minimize the use of

Technology, Sergio Machado Rezende, along with

steel reinforcements and conductor loops within the

other ministers of state and distinguished guests. The

concrete structure, thus requiring special electrical wiring encased in shielding to reduce electromagnetic field interference. Computer-designed concrete inertia

Crédito: Gustavo Tilio

blocks (35 to 70 tons) and mechanically insulated air-conditioning ducts were designed to minimize noise and mechanical vibration. The building also has an acoustic damping system to minimize noise, and a high performance air conditioning system with injection diffusers, controlled air speed, natural convention air flow, and radiation cooling panels to provide high temperature stability (± 0.5 °C/h and 2 °C per day) and very low noise.

This major undertaking resulted in high quality rooms for the SEMs and TEMs. Ongoing fine tuning of the AC system and the electromagnetic shielding will

C2Nano building

118 | Activity Report 2008

provide the necessary levels of mechanical and thermal

stability and electromagnetic noise reduction to ensure that the current and future sophisticated instrumentation installed in this building will be used to the best possible advantage. The next step in the expansion of the LME is the completion of another sample preparation room in the C2Nano building to house the instrumentation development group, the electrochemical polishing system, cryo-ultramicrotome, and thermal and electron beam evaporators.

The electron microscopy area at the C2Nano center, comprising six rooms reserved for scanning and transmission electron microscopes

Transmission Electron Microscopes (TEM) configured for materials science and in situ experiments Activity Report 2008 | 119

5

Industrial research activities

Crédito: William Brabosa

The industrial program at LNLS is designed to offer Brazil’s industrial sector access to the laboratory’s unique infrastructure and to the specialized know-how of its scientific and technical staff. The resounding success of the LNLS industrial program led to a revision of its guidelines in 2008 to enable it to respond rapidly to the increasing demand for new projects.

Long-term partnerships and joint-projects are becoming the preferred mechanisms to contribute to the advancement of the industrial sector’s R&D efforts in new technological developments, in challenging problem-solving situations, and in exploratory projects.

Facility Report

The success of the LNLS industrial program

technology to join materials through friction

continued to grow in 2008, as reflected by the

stir welding (FSW) and hydro pillar welding.

significant increase in investments in facilities,

Such technologies are seen as strategic for

infrastructure, and human resources, all funded

exploration and production in new Brazilian

by industrial contracts. Through their special

oil and gas fields. The outstanding results

programs, funding agencies such as FINEP

in mechanical performance obtained so far

and FAPESP have also supported joint projects.

suggest that this new technology (FSW) should

Several groups representing different areas

be considered viable for the construction,

within LNLS are involved in this expansion

implementation, and repair of current and

effort, and these long-term partnerships have

future infrastructures.

brought numerous technological advances

Due to the results in this very competitive

and additional know-how on both sides. The

area, LNLS and Petrobras are already planning

most relevant projects undertaken in 2008 are

a much larger follow-up project to bring the

described below.

technology closer to the implementation stage. In addition to these focused projects,

Structural characterization of advanced materials – Petrobras Petrobras has become the major industrial partner of LNLS, with projects in different areas: Materials characterization: Since 2006, a major effort has been made to improve the beamlines’ capabilities to perform in situ

LNLS and Petrobras are developing advanced infrastructure to meet current and future needs in the area of structural materials characterization. As part of this effort, in order to achieve unique thermomechanical physical simulation capabilities, construction is under way that includes a high-performance physical simulation unit and a dedicated

materials characterizations using synchrotron

1.6

techniques such as X-ray Diffraction and X-ray Absorption. The work has been coordinated

1.4

by LSQ and funded by the Petrobras Network

1.2

Refining Industry”. It has been possible already, for example, to monitor catalytic reactions and to probe simultaneously the morphological, structural, and electronic modifications of the catalyst (in situ measurements). The

Norm. Intensity

through the “Materials Center for Petroleum

1.0 0.8

instrumentation that has been developed is

0.4

available for all LNLS users.

0.2

Advanced Structural Materials Simulation, Joining, and Characterization: Several projects were developed in this strategic area. One of the highlights is an ongoing project whose objective is to acquire the fundamental knowledge and develop the

Activation

0.6

0.0 8960

8980

9000

9020

9040

9060

Energy (ev) Figure 1

Modification of the CuO phase of an industrial catalyst during activation, followed by in situ measurements at the XAFS2 beamline Activity Report 2008 | 121

Industrial research activities

synchrotron installation, to be used for in situ thermomechanical experiments. This has been led by LME and involves several other groups at LNLS. The Synchrotron

Joining and bonding in steel meshes – DFB Técnicas para Soldagem de Metais Ltda

simulator will be installed on a dedicated

The purpose of this joint project is to develop

hutch at the XRD1 beamline to allow for

the capability to manufacture in-country the

in situ materials characterization by X-ray

Premium screens that are used for sand control

Diffraction, the world’s sole installation of

during petroleum extraction. The sand control

its kind. An effort to develop residual stress

process is widely used by Petrobras, but its

mapping through X-ray Diffraction is also

filtering element still has to be imported due

ongoing (Figures 1 to 3).

to the lack of a Brazilian technology to weld by diffusion bonding.

In 2008, successful diffusion bonding of several 316L stain-steel meshes was achieved and the filtering elements were mechanically tested. The next step is to determine the process parameters for other pairs of materials, such as Inconel 600. This project is co-funded by FINEP and conducted by the LNLS Materials group and DFB.

Search for new catalysts – Oxiteno This partnership, which began in 2005 to hasten the development and scale-up of new catalysts, continued in 2008. Several catalyst families were characterized by the LSQ team, Figure 2

FSW machine. Right upper detail shows the friction stir welding process

using synchrotron and electron microscopy techniques. The team then compared the resulting morphological, structural and electronic data against the catalyst performance and the production process employed by the OXITENO research group.

The next step in this successful partnership began in late 2008 as a new project funded

by FAPESP-OXITENO. The purpose of this project is to explore new routes to produce catalysts for the fabrication of polyols from glycerol, an important step to produce

Figure 3

Gleeble 3800® and Synchrotron Gleeble®, thermomechanical physical simulators, expected to be commissioned in 2010

122 | Activity Report 2008

chemicals with greater added value from renewable sources.

Facility Report

Cleaning of optical fibers – Padtec Cleaning procedures for the removal of acrylate in optical fibers is of great importance to

Semiconductor-based devices for quantum computation – Hewlett-Packard (HP)

the industry, because the quality of metallization

The partnership between LNLS and HP has

on the fiber is strongly related to this step. In this

completed its 6th year in 2007 and was concluded

project, the microfabrication laboratory (LMF)

in 2008. Advances in high-level basic research

at LNLS developed a simple, cost-effective

with emphasis on quantum computation,

cleaning process that can be adapted easily to

epitaxial growth of semiconductors, deposition

operating conditions in manufacturing. The

of nanostructured dielectric materials and

next step was the development of a double ring

development of scanning probe microscopy

metallization process (Ti/Au/Ni/Au) around the

based lithography techniques were achieved

fiber core for welding in special applications. An

during the partnership period. Finally, the direct

experimental setup has already been installed at

improvements in scientific instrumentation

the Padtec plant for the production of 80 fibers

were crucial to the formation of qualified

per run (Figure 4).

human resources.

Microfabrication for catalysis – Novocell

b

a

NOVOCELL is looking for improvements in the microfabrication process of high-conductivity bipolar plates for fuel cells. The goal is to achieve a large-scale plate, thereby adding functionalities to the plate, e.g., i) to exponentially increase the surface area and reduce contact resistance; ii) improve the catalytic function by speeding the removal of electrons from the

Figure 4

catalyst site; iii) improve the gas distribution

Optical fiber showing residual acrylate (left) and after cleaning process (right)

properties and the removal of humidity from the components; and iv) allow for better liquid water management to and from the vicinity of catalytic sites (Figure 5).

New methods on bio-industry – Natura A partnership between CeBiME-LNLS and the company NATURA Inovação Tecnológica LTDA was established in July 2008. The main purpose of this partnership is to develop novel methods to assay for toxic molecules with potential action against skin aging, using DNA micro-array based 25 kV

global gene expression analysis. The research activities are expected to start in 2009.

Figure 5

× 80

200 m

Ni mold for production of texturized graphite plates Activity Activity Report Report2008 2009| 123 |

6

Main Events

CrĂŠdito: Arquivo LNLS/MCT

The events organized by the LNLS aim to inform and discuss new techniques, research results and advances in instrumentation.

Along the whole year seminars, workshops and meeting are realized with the participation of the academic and non-academic community.

In this report we discuss the main events that took place in 2008.

Facility Report

One of the workshops, in its 2nd edition,

Users’ Meeting The 18th LNLS Annual Users’ Meeting (RAU, in Portuguese) was held at the LNLS Campus in Campinas on February 18 and 19, 2008,

was attended by about 60 participants and focused on in-situ experiments performed under extreme conditions using synchrotron

with the participation of about 330 researchers

radiation. The workshop’s main objective was

and students. The Annual Users’ meeting

to bring together LNLS users with potential

is an important forum where users have an

interest in in situ studies of materials subjected

opportunity to publicize their scientific results

to extreme conditions of pressure, magnetic field,

and meet with LNLS scientists to discuss the

and temperature. Main goals were established

status of the infrastructure currently available

for four central topics:

and to communicate the user community’s needs and wishes, thus contributing toward better

i. Demonstrate opportunities and applications

planning for the construction and installation

of in situ experiments under extreme

of new facilities.

conditions using synchrotron radiation. To

To complement the meeting’s program,

this end, we plan to invite two international

two satellite workshops were conducted on

experts: François Baudelet (SOLEIL) and

February 19 and 20, 2008.

Daniel Haskel (APS).

Poster session at 18th LNLS Annual Users’Meeting Activity Activity Report Report2009 2008 | | 125

Main Events

ii. Present the current status and prospects for

chemistry, physics, biology, and materials

the infrastructure for experiments under

science; as well as to several areas of industry,

extreme conditions;

particularly those acting in the polymers, food

iii. Discuss new scientific cases for the implementation of new instrumentation;

and cosmetics sectors. The main objective of this workshop was to bring together the community

iv. Debate users’ needs and where to direct

of interest and to gather information on the

efforts to develop experiments under extreme

potential demand for the use of the above

conditions at LNLS.

described facilities.

The two aforementioned international experts, Dr. François Baudelet (SOLEIL – France) and Dr. Daniel Haskel (APS – USA), participated in this workshop.

The second workshop, which was attended by about 40 participants, focused on applications of synchrotron radiation on soft matter. Polymers, emulsions, colloids and liquid crystals are among the main examples of these materials. The challenge of soft matter physics is to understand the macroscopic behavior of these materials based on their basic microscopic properties, independently of chemical details. In this context, synchrotron-related techniques are essential for the study of the fundamental properties of soft materials, and for understanding their multiple scales of spatial organization.

LNLS has invested in this area and intends

126 | Activity Report 2008

SRMS-6 The 6th International Conference on Synchrotron Radiation in Materials Science brought together leading researchers from around the world and was a celebration of the increasingly important relationship between materials science and synchrotron radiation research. The conference, which was held at the Campinas Business Institute Convention Center from July 20 to 23, 2008, brought together 120 scientists – 65 from the Brazilian community and 55 from abroad. The Brazilian Synchrotron Laboratory (LNLS) was the principal organizer of the SRMS-6, with support from several Brazilian and Latin-American Agencies and Universities.

to expand its capabilities through collaborations

Special attention was given to the contribution

with industry and with government agencies.

of Synchrotron Radiation techniques to the solution

Several of the laboratory’s beamlines, such as

of key unsolved problems in Materials Science.

the small angle scattering (SAXS1 and SAXS2),

Among the topics covered in the conference were

crystallography of macromolecules (MX1), and

selected studies on: Archaeological Materials,

high resolution x-ray diffraction (XRD2), are

Catalysts and Clusters, Complex Oxides,

used in the study of soft materials. In addition,

Data-storage and Materials Engineering, Thin

the instrumentation at LNLS offers advanced

Films, Surfaces and Interfaces, Geophysics,

features – such as electron microscopy and

Molecular Electronic Materials, Glasses and

atomic force microscopy, mass spectroscopy,

Ceramics, Liquids, Nano-magnetism, Studies

and nuclear magnetic resonance – that allow for

of Materials under Extreme Conditions (high

the execution of experiments complementary

pressure, etc.), Metals and Alloys, Metamaterials,

to those that use using synchrotron light. The

Multiferroics, Nano-structured Materials, Self-

possibility of performing these experiments in

assembly Processes, Polymers and Biomaterials,

soft-matter systems at LNLS is of interest to

Micro- and Nano-focusing X-ray Techniques,

the Brazilian academic community, including

Strongly Correlated Materials, Superconductivity,

Facility Report

Industrial Use of Synchrotron Radiation, and recent instrumentation developments.

– Beamline features and available instrumentation – Sample preparation and the choice of

Practical Training In 2008, several courses, workshops, and an international conference were held to promote the experimental capabilities available at LNLS. These courses included: a) 2nd Theoretical-Practical Course on

suitable standards – The choice of a detection mode 6) Examples of applications and data analysis of a variety of systems, including liquids, amorphous and glassy systems, nanostructures, and crystals.

Transmission Electron Microscopy: The main goal of this course was to popularize Transmission Electron Microscopy (TEM) techniques, with emphasis on training the participants to use the new microscopes that are installed in the Cesar Lattes building. b) VUVF Beamline Workshop: This workshop covered basic and practical aspects involved in the use of the Visible Ultraviolet Fluorescence (VUVF) Beamline. The topics included presentations on the fundamental and experimental details of the beamline, descriptions of what types of experiments are possible, and analysis of results.

Plenary talk at SRMS-6

c) Introduction to EXAFS Data Analysis: The main objective of this short course was to present the basic techniques and methodologies of EXAFS data analysis, with emphasis on the use of FEFF and IFEFFIT packages. The audience was composed mainly of graduate students and young researchers.

The following topics were covered: 1) Review of the basic radiation-matter interaction processes; 2) Principles of EXAFS data analysis; 3) ATHENA, ARTEMIS and FEFF programs; 4) Some traps in EXAFS data analysis (and how to avoid them); 5) Planning of a XAFS experiment – Preparing and submitting a proposal

Poster session at SRMS-6 Activity Activity Report Report2008 2009| 127 |

7

Facts and figures

CrĂŠdito: MĂĄrio Belloni

The mission of the Brazilian Synchrotron Light Laboratory (LNLS) is to operate as a national facility available to the community as a multi-user and interdisciplinary installation. The mission of the laboratory is to provide integrated solutions to complex scientific and technological challenges in several fields of research such as nanotechnology, biotechnology, materials science, particle accelerators and scientific instrumentation.

Facility Report

The Brazilian Association for Synchrotron

the new PGM beamline was successfully

Light Technology (ABTLuS) is a non-profit

executed. The results attest to the quality of

organization that operates the LNLS through a

the undulator, which was designed and built

management contract signed with the Ministry

by the LNLS team.

of Science and Technology (MCT) and the

The creation of the Center of Nanoscience

National Council for Scientific and Technological

and Nanotechnology (C2Nano) and the official

Development (CNPq), in line with Executive

opening of the Cesar Lattes building on March 4

Order 2405 of November 26, 1997.

was another achievement in 2008. President Luiz

ABTLuS comprises the Synchrotron facility

Inácio Lula da Silva and the Minister of Science

(LNLS), the Center of Structural Molecular

and Technology, Sergio Machado Rezende, were

Biology (CeBiME) and the recently incorporated

present at the opening ceremony. This center

Bioethanol Science and Technology Center

includes a building designed specifically to

(CTBE). These three associated centers work

house high-resolution electron microscopes.

in synergy with the other laboratories operated

The building required special engineering to

by ABTLuS to advance areas of knowledge that

reduce vibration effects and is currently one

are strategic to the country. Future plans for the

of the most sophisticated structures in the

establishment of the Center of Nanoscience and

country in this field. Two new microscopes have

Nanotechnology (C2Nano) as an independent

already been installed, one of them operating

associated center are under consideration.

for external users.

The year 2008 was remarkable in that, for the

Interactions with industrial partners in 2008

first time, the Ministry of Science and Technology

showed considerable improvements in terms of

allocated a specific budget for preparation of

hours allocated for specific work and volume

the project of the second Brazilian Synchrotron

of monetary resources applied to proprietary

Light Source (provisionally called LNLS-2).

research. New contracts involving soft matter

Building this new machine represents a crucial

and biological sciences were established,

step for the existing community as well as an

expanding the scope of industrial research at

expansion of Brazil’s scientific aspirations and

LNLS. The partnership with PETROBRAS and

horizons.

its research center CENPES was expanded to

The LNLS synchrotron source operated with

include contracts involving several thematic

remarkable efficiency in 2008, repeating its

research networks and allow for remodeling

historical record of 98% reliability achieved in

and continuity of the partnership program.

2003. This achievement is the result of planned

The whole ensemble of LNLS’s open

efforts dedicated to the improvement of injection

facilities was used in 2008 to execute a total of

and operation procedures on the source.

660 proposals, which resulted in 241 scientific

In October 2008, a preliminary experiment for the characterization of components of

publications – 14 with an impact factor higher than 5.

Activity Report 2008 |

129

Facts and figures

600

2500

500

2000

400 1500

300

1000

200

500

100

0

0

Shifts Requested

Proposals

Accepted Shifts in 2008

500

Shifts

400 300 200

Beamlines Requested Proposals in 2008

120

Proposals

100 80 60 40 20

Beamlines Submitted

130

| Activity Report 2008

Accepted

XRD1

SAXS2

XPD

XRD2

XRF

SGM

DXAS

TGM

XAFS1/XAFS2

SXS

MX1/MX2

0

Accepted

XRD1

SAXS2

XPD

XRD2

XRF

SGM

DXAS

TGM

XAFS1/XAFS2

MX1/MX2

0

SXS

100

Facility Report

Proposals executed from 1998 to 2008

150

143

161

138

129

96 112 86

358

74 226

169

181

142

1998

2000

466

434

423

379

438

231

2002

2004

2006

2008

Year Electronic microscopy

Synchrotron

Geographical distribution of proposals at the beamlines 15%

15%

15%

15%

15%

20%

23%

25%

23%

28%

65%

2000

62%

2001

60%

2002

62%

57%

2003

2004

17%

16%

32%

33%

51%

51%

2005

2006

17%

18%

39%

36%

44%

46%

2007

2008

Year S達o Paulo state

Other states

Other countries

Staff chart employees 2008 Engineers & technicians 61%

Administrative & support 28%

Staff chart employees 2007 Engineers & technicians 60%

Administrative & support 32%

Researchers 11% Researchers 8%

Activity Activity Report Report2008 2009| 131 |

Facts and figures

Publications from 1998 to 2008 258

254

246

2005

2006

241

199 172

159 141

83 55 30

1998

1999

2000

2001

2002

2003

2004

2007

2008

Year

Evolution of publications with impact factor higher than 5 18 15

13

16 13

11

14

8 5

1999

5

2000

2001

2002

2003

2004

2005

2006

Year

Increase of beamline time 60000 50000 40000 30000 20000 10000 0

1998

1999

2000

2001

2002

2003 Year

132

| Activity Report 2008

2004

2005

2006

2007

2008

2007

2008

Facility Report

Activity Activity Report Report2008 2009| 133 |

134

| Activity Report 2008

Small-Angle X-ray Scattering

Small-Angle X-ray Scattering

Macromolecular Crystallography

Soft X-ray Spectroscopy

X-ray Absorption Fine Structure

Toroidal Grating Monochromator

Visible and Ultraviolet Fluorescence Dispersive X-ray Absorption Spectroscopy

W01B

D01B

D02A

D03B

D04A

D04B

D05A

D05B

A

Detectors

Hemispherical Electron Analyzer

XRD1

Applications

Power Diffraction Studies in Materials Science

Magnetic Scattering, Grazing Incidence, Nanostructures

Environment and Geochemistry, Biophysics and Agriculture

Materials Science

Materials Science, thin films and diluted systems

â&#x20AC;&#x153;Testing new applications in Protein Radiolysis. Desorption measurementsâ&#x20AC;?

Surface and Interfaces. Atomic and Molecular Physics

Materials Science, In-situ Studies, Magnetic Dichroism

Chemistry and Biology

Surface, Atomic and Molecular Physics; Time-of-Flight

Materials Science, thin films and diluted systems

Photoabsorption and photoemission spectroscopy

Structural Molecular Biology

Glasses and Nanocrystals, Polymers and Molecular Biology

Glasses and Nanocrystals, Polymers and Molecular Biology

Structural Molecular Biology using MAD technique

Differential Scanning Calorimeter (DSC)

Low Temperature Furnance (up to 300K)

High Temperature Furnance (up to 1000K)

Sample Environment

Reference

A

A

A

A

A

N 2 Cryojet

Cryostat

Thermal Bath

Surface and Interfaces. Atomic and Molecular Physics, X-ray Magnetic Dichroism Focusing Double crystal 5-15 keV Single crystal diffraction, Multiple Beam Diffraction

Planar Grating 100-1200 eV

Solid State Detector (with energy resolution)

X-ray Diffraction

D12A

PGM

Focusing Double crystal 5-15 keV

Photodiode

High Resolution VUV Spectroscopy

U11A

XPD

Focusing Double crystal 5-15 keV

Total Electron Yield

X-ray Powder Diffraction

D10B

XRD2

White beam or double crystal 5-25 keV

CCD (2D detector)

X-ray Diffraction

D10A

XRF

SCW

Focusing Double crystal 5-15 keV

Spherical Grating 240-1000 eV

Filtered white beam 5-20 keV

One single-bent crystal 5-12 keV

Gratings 2-6 eV

Toroidal Grating 12-300 eV

Channel cut 3-25 keV

Double crystal 1800-3000 eV

One single-bent crystal 6-12 keV

One single-bent crystal 6-12 keV

One single-bent crystal 6-12 keV

Image Plate (2D)

Superconducting Wiggler BeamLine X-ray Fluorescence

W09B

XAFS2

Monochromator Focusing Double crystal 5-15 keV

Cintilator

X-ray Absorption Fine Structure

D08B

SGM

DXAS

VUVF

TGM

XAFS1

SXS

MX1

SAXS2

SAXS1

MX2

Acronym

Position Sensitive Detector (1D)

Spherical Grating Monochromator

D08A

D09B

White beam (previously X-ray Lithography)

D06B

D06A

Name

Macromolecular Crystallography

Dipole

Low Pressure Cell (up to 1.2Gpa)

High Pressure Cell (up to 10Gpa)

Status

Operational

Construction

Operational

Operational

Operational

Design

Operational

Operational

Under test

Operational

Comissioning

Operational

Operational

Operational

Operational

Operational

Commissioning

Operational

Eletrochemichal Cell

Microfocus (Capillary)

Sample Enviroment

Magnetic field (up to 1T)

Detectors

Facts and figures

Scientific Reports in the CD-Rom Biology

Chemistry

Role of the SR-mXRF methodology in the assessment of protective capacity of antioxidant therapy during as exposure

Carbon Nanotubes Decorated with both Gold Nanoparticles and Polythiophene

G. A. Bongiovanni; C. A. Pérez; R. D. Pérez; P. N. Rubatto Birri; M. Rubio

Thermal and Chemical Stability of Ovorubin, a Protease Inhibitor from the eggs of Pomacea Canaliculata.

Functional Implications M. Ceolin; H. Heras; S. Ituarte; M. S. Dreon

Hyperthyroidism Bone Analysis L4 Vertebrae Site I. Lima; R. T. Lopes; M. L. F. Farias; D. Rosenthal; E. Sales; V. M. Costa

Hyperthyroidism Bone Analysis L4 Vertebrae Site I. Lima; R. T. Lopes; M. L. F. Farias; D. Rosenthal; E. Sales; V. M. Costa

Hyperthyroidism Bone Analysis L4 Vertebrae Site I. Lima; R. T. Lopes; M. L. F. Farias; D. Rosenthal; E. Sales; V. M. Costa

Internal Structure of Monoolein:Oleic acid Nanoparticles containing Phthalocyanines and Protoporphyrin IX M. V. L. B. Bentley; L. V. Depieri; M. C. A. Fantini; F. C. Rossetti

M. M. Oliveira; A. J. G. Zarbin

Valence and inner shell dissociation dynamics of sulfur-containing amino acids photo-excited by synchrotron radiation R. L. Cavasso Filho; A. F. Lago; A. Naves de Brito

Structural study of modified layered materials C. Airoldi; C. T. G. V. M. T. Pires

Synchrotron Radiation X-Ray Fluorescence (SR-XRF) and Principal Component Analysis (PCA) to study cryogenic soils from Maritime Antarctica M. B. B. Guerra; E. R. Pereira Filho

SR-XRD in Archaeology: compositional study of prehistoric pigments (Carriqueo rock shelter, Argentina ) S. Boeykens; A. M. Maury; O. M. Palacios; C. Vázquez

An exafs study of the binding of copper on raw and calcined clays A. F. de Almeida Neto; M. G. C. da Silva

Activity Report 2008 | 135

Electronic effects on Pt-Ru/C catalysts for methanol oxidation D. R. M. Godoi; J. Perez; H. M. Villullas

XPS Analyses of La2-x MxCuO4, where M is Ce, Ca and Sr. E. M. Assaf; S. S. Maluf

Ceramic and metal tube atomizers in atomic absorption spectrometry: characterization using scanning electron microscopy and chemometrics tools E. R. Pereira Filho

Composition and morphology studies of a magnetically recoverable gold nanoparticle-catalyst L. M. Rossi; R. L. Oliveira

Study of the Physical and Electrochemical Properties of Pt/RhO2/C and Pt/RuO2/C Electrocatalysts K. S. Freitas; P. P. Lopes; E. A. Ticianelli

Pt3Sn Electrocatalyst in the Anode of a Direct Ethanol Fuel Cell: analysis of the Pt LIII XANES region.

F. Colmati; E. R. Gonzalez; R. Sousa

Micellar Solutions and Microemulsions formed with Ionic Surfactants applied as Corrosion Inhibitors: Characterization by Small-Angle X-Ray Scattering A. A. Dantas Neto; T. N. C. Dantas; A. Gurgel; E. F. Moura; A. O. Wanderley Neto

Evaluation of selenium in protein spots in plasma and muscle and liver tissue of Nile tilapia (Oreochromis niloticus) using SR-XRF after 2DPAGE separation M. A. Z. Arruda; M. A. O. da Silva; P. M. Lima; R. C. F. Neves; P. M. Padilha; C. A. PĂŠrez; F. A. Santos; F. A. Silva

Stability of PtNi/C and Pt/C electrocatalysts as cathode materials for polymer electrolyte fuel cells E. Antolini; F. Colmati; E. R. Gonzalez; C. S. Zignani

Synthesis, characterization and stability studies of carbon supported Pt-Sn-Pd nanoparticles for the oxidation of ethanol.

E. Antolini; F. Colmati; E. R. Gonzalez

Synthesis, characterization and stability studies of carbon supported Pt-Sn-Pd nanoparticles for the oxidation of ethanol.

E. Antolini; F. Colmati; E. R. Gonzalez

Synthesis, characterization and stability studies of carbon supported Pt-Sn-Pd nanoparticles for the oxidation of ethanol.

E. Antolini; F. Colmati; E. R. Gonzalez

Effect of the Structure of The Grafted Metallocene Species on Microporous and Mesoporous Supports on the Molecular Weight of the Produced Polymer M. C. M. Alves; J. H. Z. dos Santos; F. Silveira

Cu catalysts analyzed by XANES E. M. Assaf; S. S. Maluf

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The influence of ethanol and temperature on the binary system Renex-100/water

Worm-like micelles of CTAB and sodium salicylate: effect of temperature and flow

C. A. Bertran; D. D. P. Campos; R. B. R. Garcia; E. Y. Kawachi; A. S. Pascoli

M. A. da Silva; R. K. Rodrigues; E. Sabadini

The effect of addition of the Ru and Pt on the reduction behavior of Co/ MgAl2O4 catalyst: In situ XANES study E. M. Assaf; L. P. R. Profeti; E. A. Ticianelli

Ni catalysts studied by XAFS E. M. Assaf; O. L. S. Ferreira; L. P. R. Profeti

XANES and EXAFS study of dodecanethiol-stabilized platinum nanoparticles prepared by twophase route E. G. Castro; M. M. Oliveira; R. V. Salvatierra; A. J. G. Zarbin

Structural study related to the proton exchanged K4Nb6O17 layered phase M. A. Bizeto; V. R. L. Constantino; F. Leroux; A. L. Shiguihara; M. L. A. Temperini

XANES studies of Ni catalysts prepared from precursors MgAl hydrotalcite-type.

E. M. Assaf; J. D. A. Bellido; A. F. Lucrédio

On the temperature stability of extracellular hemoglobin of Glossoscolex paulistus in met form: SAXS studies P. J. W. Carvalho; P. S. Santiago; M. Tabak

Hematites of Fazendão Deposit, quadrilátero ferrífero, Minas Gerais J. D. Fabris; F. F. Ferreira; A. R. P. Pereira; F. J. Rios; C. A. Rosière

Dissociative Photoionization of ClC(O)SCH2CH3 following sulfur 2p and chlorine 2p excitations R. L. Cavasso Filho; Carlos O. Della Védova; Mauricio F. Erben; Mariana Geronés; Lucas Rodriguez Pirani; Rosana M. Romano

Co content (employed as marker) in ruminal fluid by EDXRF and SRTXRF techniques A. A. Menegário; E. Almeida; D. P. D. Lanna; L. C. Leite; P. R. Massoni; V. F. Nascimento Filho

XANES experiments on the thermally induced charge transfer in Co3(Mn(CN)5NO)2.xH2O M. Ceolin; B. Soria; M. A. Taylor

Systems formed by anionic polymers and cationic surfactants: Phase equilibrium and structural characterization D. R. Catini; W. Loh; A. M. Percebom

Surface functionalization of Polystyrene by monochromatic synchrotron radiation and oxygen exposure F. Kessler; G. V. S. Mota; D. E. Weibel

Condensed methanol bombarded by cosmic rays: Relevance to solid state astrochemistry D. P. P. Andrade; H. M. Boechat-Roberty ; E. F. da Silveira; M. G. P. Homem; R. Martinez Rodriguez; M. L. M. Rocco

Planar waveguides based on Er3+ doped SiO2-Ta2O5 J. L. Ferrari; R. R. Gonçalves Activity Report 2008 | 137

Structural characterization of cellulose acetate nanocomposites by 2D-SAXS/WAXS. Part II

Colloidal Systems containing Silicone Compounds: structure and phase equilibria

R. Bonzanini; M. C. Gonçalves

M. S. Ferreira; W. Loh; H. Westfahl Jr.

Identification of substances isolated from plant extracts active against the coffee leaf miner

Colloidal Systems containing Silicone Compounds: structure and phase equilibria

R. C. R. Chagas; D. F. Oliveira; P. Paula; H. M. dos Santos Júnior; M. A. I. Santos

M. S. Ferreira; W. Loh; H. Westfahl Jr.

Ni- ZSM-5 catalysts: detailed characterization of metal sites for proper catalyst design A. J. Maia; M. M. Pereira

Application of NMR to Study the Mechanisms of Action of antitumor Compounds J. E. Carvalho; A. de Fatima; F. C. Macedo Jr.; M. S. Mantovani; A. Ruiz; I. S. Scarminio

Colloidal Systems containing Silicone Compounds: structure and phase equilibria M. S. Ferreira; W. Loh; H. Westfahl Jr.

Colloidal Systems containing Silicone Compounds: structure and phase equilibria M. S. Ferreira; W. Loh; H. Westfahl Jr.

Colloidal Systems containing Silicone Compounds: structure and phase equilibria M. S. Ferreira; W. Loh; H. Westfahl Jr.

Colloidal Systems containing Silicone Compounds: structure and phase equilibria M. S. Ferreira; W. Loh; H. Westfahl Jr.

138

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Niobian Iron Oxides As Heterogeneous Fenton Catalysts for Environmental Remediation J. D. Fabris; L. M. Menezes; E. Murad; D. Q. L. Oliveira; L. C. A. Oliveira; A. C. Silva

Metallocene Supported on Silica - Characterization of Metalocene Structure by Exafs and Particles Size and Shape By SAXS and AFM M. C. M. Alves; J. H. Z. dos Santos; F. Silveira

Structural Studies of Lignin in Different Oxidation Conditions T. Batista; A. F. Craievich; A. R. Gonçalves; D. S. Machado; P. Maziero; M. Oliveira Neto; I. Polikarpov

Preparation of containing silver nanoparticles phylosilicates and morphology-structure relationship C. Airoldi; J. C. P. Melo; C. T. G. V. M. T. Pires

Environment Geosciences

and

Evaluation of heavy metals in atmospheric emissions of automotive industry by SR-TXRF S. Moreira; J. Weber Neto

Monitoring and Evaluation of Metals in Ducts and Stationary Sources of Ceramic Industries from Santa Gertrudes, Limeira and Cordeirópolis region.

Roney J. Fonseca; S. Moreira

Assessment of the applicability of tree bark to heavy metal air pollution monitoring employing the total reflection X-ray fluorescence with synchrotron radiation technique H. Carreras; C. A. Pérez; E. D. Wannaz

Elemental analysis of lead and calcium content of primary teeth by m-SRXRF A. P. Almeida; R. C. Barroso; D. Braz; S. C. Cardoso; C. de Souza Guerra; R. F. Gerlach; S. Moreira; L. F. Oliveira; N. G. V. Pinto; C. L. Silva

Manganese removal from synthetic wastewaters by limestone - XANES investigation G. Duarte; V. A. Leão; A. M. Silva; M. C. Teixeira

Morphological aspects of UreaIntercalated and Delaminated Kaolinites used for Adsorption Kinetics Involving Copper and Lead

Instrumentation Current Status of the Wavelength Dispersive System of the XRF Beamline H. J. Sánchez; C. A. Pérez

Current Status of the Wavelength Dispersive System of the XRF Beamline H. J. Sánchez; C. A. Pérez

Current Status of the Wavelength Dispersive System of the XRF Beamline H. J. Sánchez; C. A. Pérez

Current Status of the Wavelength Dispersive System of the XRF Beamline H. J. Sánchez; C. A. Pérez

Current Status of the Wavelength Dispersive System of the XRF Beamline H. J. Sánchez; C. A. Pérez

Current Status of the Wavelength Dispersive System of the XRF Beamline

C. Airoldi; D. J. L. Guerra; C. T. G. V. M. T. Pires

H. J. Sánchez; C. A. Pérez

Chromium levels in muscle, liver and gonad of fish species from São Francisco River of the Paraná Brazilian State by using SR-TXRF technique

Current Status of the Wavelength Dispersive System of the XRF Beamline

F. R. Espinoza Quiñones; M. A. Rizzutto; A. N. Módenes; S. M. Palacio; N. Szymanski; R. A. Welter

H. J. Sánchez; C. A. Pérez

XRFCT under various excitation conditions M. J. Anjos; C. Calza; R. T. Lopes; G. R. Pereira; C. A. Pérez; H. S. Rocha

Activity Report 2008 | 139

Characterization of polycapillary lenses to depth profiling analysis by confocal XRF H. J. Sánchez; C. A. Pérez; R. D. Pérez; M. Rubio; V. Sbarato

Materials Science Grazing-incidence X-ray fluorescence analysis of Sn0.9Cu0.1O films 2 A. M. Mudarra Navarro; F. Golmar; C. A. Pérez; C. E. Rodríguez Torres

Analyses of intrinsic heterogeneities and metal segregation in samples of GeSe2-Se system with Ag and Fe solutes.

B. Arcondo; M. Erazú; M. Fontana; J. A. Rocca; M. A. Ureña

Microstructural characterization of rapidly solidified Ti-Si-B alloys by HRTEM K. C. G. Candioto; G. C. Coelho; C. A. Nunes; P. A. Suzuki

Synthesis and characterization of Gd3+ ions doped in NaYF4 nanocrystals L. M. Holanda; P. G. Pagliuso; C. Rettori; J. M. Vargas; W. Iwamoto

Prussian Blue Analogues: Prototype of Porous Solids for H2 Storage and of Tunable Molecular Magnets R. Martínez-García; E. Reguera; J. RodriguezHernandez

Materials for Hydrogen Storage: Low temperature Structural Transformation in Pillared 2D Solids, T[Ni(CN)4].2pyz, T =Mn, Zn, Cd A. A. Lemus-Santana; M. Avila; E. Reguera; J. Rodriguez-Hernandez

Materials for Hydrogen Storage: Use of the Pattern Background to Obtain Structural Information in Porous Solids A. Gómez; E. Reguera; J. Rodriguez-Hernandez

Molecular orientation of injection molded polypropylene by X-ray pole figures M. C. Branciforti; Bretas; M. M. Favaro

Preparation and Characterization of Ti-Zr-V Non-Evaporable Getter Films to Be Used in Ultra-High Vacuum M. J. Ferreira; P. A. P. Nascente; D. A. Tallarico

Ordered mesoporous structure of zirconia-based oxide hybrids R. Bacani; M. C. A. Fantini; R. O. Fuentes; D. G. Lamas; T. S. Martins; J. R. Matos

SAXS study of organic-inorganic hybrid matrixes for drug delivery devices L. A. Chiavacci; L. Lopes; S. H. Pulcinelli; C. V. Santilli; V. H. V Sarmento

Post-Silicidation Annealing Effects on Electrical and Structural Properties of NiPt Germanosilicide I. Doi; M. Eleotério

140

| Activity Report 2008

SAXS evaluation of Renex-based self-assembly for nanostructured mullite preparation

Characterization of polyurethane nanocomposites containing ocular drugs using SAXS

C. A. Bertran; D. D. P. Campos; R. B. R. Garcia; E. Y. Kawachi; A. S. Pascoli

E. Ayres; A. S. Cunha Jr. ; R. L. Orefice; G. R. Silva

Microstructure of polyurethane films

nanoteflon/

J. I. Amalvy; P. S. Anbinder; O. R. Pardini; P. J. Peruzzo

Nanocrystalline diamond films grown on porous silicon substrate from a solid carbon source of reticulated vitreous carbon M. R. Baldan; A. F. Beloto; N. G. Ferreira; C. R. B. Miranda

Structural properties of nanostructured Ce-Zr mixed oxides synthesized by different routes: nanopowders and nanotubes L. M. AcuĂąa; R. O. Fuentes; D. G. Lamas

Blends of Polyaniline and Cardanol/ Furfural Bioresin - A X-ray diffraction study under pressure R. C. Michel; M. T. D. Orlando; F. G. Souza Jr.

Optimization of parameters for the synthesis of TiO2-CeO2 core-shell nanoparticle via layer-by-layer in mesoporous silica D. B. Almeida; D. N. Correa; I. O. Mazali; E. B. Santos

Evaluation of the amorphous to crystalline phase transition in TiSi-B alloys by High Temperature Synchrotron Radiation XRD. K. C. G. Candioto; G. C. Coelho; C. A. Nunes; P. A. Suzuki

Electrical characterization of a polythiophene derivative: application in sensors for volatile organic compounds D. T. Balogh; B. M. Nunes; C. A. Olivati; V. C. Gonçalves

Local structure of ZrO2 spherical nanoparticles studied by XANES. L. Andrini; P. M. Arnal; F. G. Requejo

Lamellae orientation and structural periodicity of blown films C. A. G. Beatrice; M. C. Branciforti; R. E. S. Bretas; J. Marini

Study of the supramolecular structure of PSSNa T. Batista; A. F. Craievich; D. S. Machado; M. G. Neumann; M. Oliveira Neto; I. Polikarpov; C. C. Schmitt

Vanadium Pentoxide Nanostructures: An Effective Control of Morphology and Crystal Structure in Hydrothermal Conditions W. Avansi; E. R. Leite; V. R. Mastelaro; C. Ribeiro

Cellulosic paper sheets modified with polyaniline nanoparticles - A morphological study by SAXS G. E. Oliveira; J. C. Pinto; F. G. Souza Jr

Orientational Study in Liquid Crystals Drops by Small - Angle X-Ray Scattering (SAXS) N. R. Demarquette; L. S. Gomes; I. L. Torriani

Activity Report 2008 | 141

Determination of monosodic alendronate presence in osteoporosis affected human bones.

I. O. Fábregas; M. E. Fernández de Rapp; D. G. Lamas

XAS studies of Pb1-xRxZr0.40Ti0.60O3 (R=La,Ba) ferroeletric ceramics V. R. Mastelaro; A. Mesquita; A. Michalowicz

Study of nanostructured ZnO thin films prepared by sol-gel spincoating technique A. F. Craievich; C. D. Bojorge; H. R. Cánepa; J. R. Casanova; E. Heredia; G. Kellermann

Local structure of the tetragonal phase in nanocrystalline ZrO2 -Sc</ sub>2</sub>O3 powders P. M. Abdala; A. F. Craievich; M. C. A. Fantini; D. G. Lamas

Nitrogen adsorption and small angle X ray diffraction studies of pore size in ordered SBA-15 A. Sousa; E. M. B. Sousa; R. G. Sousa; K. C. Souza

Mesoporous silica/magnetite nanocomposite synthesized by using a neutral surfactant A. Sousa; J. D. Ardisson; E. M. B. Sousa; K. C. Souza; W. A. A. Macedo

Nanostructured Synthetic Hydroxyapatite and Dental Enamel Heated e Irradiated By ER,CR:YSGG: characterized by FTIR AND XRD. P. A. Ana; S. L. Baldochi; V. L. Mazzocchi; J. S. Rabelo; M. E. G. Valerio; D. M. Zezell

Structural changes in Polymer/Clay melted Nanocomposites induced by Electric Fields G. J. Silva; E. N. Azevedo; J. O. Fossum; T. S. Plivelic;

142

| Activity Report 2008

S. M. L. Silva; M. H. Sousa; Z. Rozynek

Characterization of human fluorotic enamel by X-ray diffraction A. P. G. Almeida; R. C. Barroso; D. Braz; R. Droppa Jr.; R. F. Gerlach; M. V. C. Gonçalves; L. F. Oliveira; I. M. Porto

Real time x-ray diffraction on in situ hydration of cement based materials D. C. C. Dal Molin; A. P. Kirchheim; P. J. M. Monteiro; D. T. Pagnussat; A. A. Silveira

Lattice distortions in oxygen deficient SrMnOy 2.8<y<3 compounds with disordered vacancies.

B. Dabrowski; R. Faccio; A. W. Mombrú; L. Suescun

Atypical Coordination in Transition Metal Hexacyanometallates M. Avila; E. Reguera; J. Rodriguez-Hernandez

Mixed Valence State Systems in Cobalt Iron Hexacyanides M. Knobel; R. Martínez-García; E. Reguera

Electron withdrawing groups effect on self-assembling of nanofibers derived from glucose solutions.

M. F. Abreu; D. R. dos Santos; C. Gatts; R. A. Giacomini; P. C. M. L. Miranda; L. Vitorazi

For Copper: A Unique Behaviour within Prussian Blue Analogues E. Reguera; J. Rodriguez-Hernandez

Microstructural characterization of rapidly solidified Ti-Si-B alloys by HRTEM. K. C. G. Candioto; G. C. Coelho; C. A. Nunes; P. A. Suzuki

Er probing and influence of pH of starting suspension, investigated

by XPS and photoluminescence, in sol-gel SnO2

Degradation of the N,N’-bis-(1n a p h t h y l ) - N , N’ - d i p h e ny l - 1 , 1 ’ biphenyl-4,4’-diamine by photon irradiation

A. Tabata; L. P. Ravaro; L. V. A. Scalvi

M. R. M. Chagas; M. Cremona; G. V. S. Mota; A. M. J. C. Neto; W. G. Quirino; M. L. M. Rocco; E. A. Sousa

The structural dynamics of FDU-1 ordered mesoporous silica calcination process

Characterization of welding regions at Friction taper plug welded joints

M. C. A. Fantini; F. Mariano-Neto; T. S. Martins; J. R. Matos; L. C. C. Silva

C. R. M. Afonso; T. F. Hermenegildo; M. T. Piza; A. J. Ramirez; J. Unfried

Evaluation of the orientation and lamellae periodicity in injection molded polypropylene/talc composites by SAXS

XAFS study of Zn0.7Co0.3O powders prepared by ball milling

M. C. Branciforti; C. A. Oliveira; J. A. Sousa

Location site of lanthanides in ZnO

Electrochemical behavior centrifuged cast Ti-Cu alloys

of

R. Caram; A. Cremasco

SAXS study of radial homogeneity of silica glass boule synthesized by VAD method E. Ono; J. S. Santos; C. K. Suzuki

Carbon nanotubes growth directly over TEM grids to evaluate the nucleation and growth processes S. A. Moshkalev; C. Verissimo

Porous Transition Metal Hexacyanoferrates (II) with High Available Free Volume: Framework Stability M. Avila; E. Reguera; J. Rodriguez-Hernandez

A. M. Mudarra Navarro; C. E. Rodríguez Torres; L. C. Damonte

H. R. Cánepa; E. Otal; N. E. Walsoe de Reca

SAXS spectra of composite electrolytes Nafion-Silica and Nafion-Titania: a morphological study.

M. A. Dresch; F. C. Fonseca; R. A. Isidoro; M. Linardi; B. R. Matos; J. F. Q. Rey; E. I. Santiago

Negative thermal expansion Y2Mo3O12 at low temperatures

of

M. Ari; P. M. Jardim; B. A. Marinkovic; F. Rizzo

Study of valence state of europium in low silica calcium aluminosilicate glasses M. L. Baesso; M. C. Filadelpho; A. N. Medina; J. H. Rohling; J. A. Sampaio

Photoelectrocatalysts for Methanol Oxidation W. A. Alves; M. C. Santos; A. S. Polo; P. M. Takahashi

Activity Report 2008 | 143

Structural characterization in injection molded PTT, PBT and their nanocomposites with MMT M. C. Branciforti; R. E. S. Bretas; M. M. Favaro

XANES and XMCD investigation on the thermal evolution of FePt nanoparticles P. de La Presa; S. J. A. Figueroa; S. J. Stewart

Retention of metastable phases in nanocrystalline ZrO2-Sc2O3 solid solutions P. M. Abdala; A. F. Craievich; M. C. A. Fantini; D. G. Lamas

Effect of curing in blastfurnace slag cement concrete: ettringite formation G. Camarini; E. L. Ferreira Jr

Thermal expansion of In2Mo3O12 in monoclinic and orthorhombic structure M. Ari; R. R. de Avillez; P. M. Jardim; B. A. Marinkovic; F. Rizzo

KDP:Mn piezoelectric coefficients obtained by X-ray diffraction C. M. R. Remedios; L. P. Cardoso; A. S. de Menezes; A. O. dos Santos; E. J. L. Gomes

KDP:Mn piezoelectric coefficients obtained by X-ray diffraction C. M. R. Remedios; L. P. Cardoso; A. S. de Menezes; A. O. dos Santos; E. J. L. Gomes

KDP:Mn piezoelectric coefficients obtained by X-ray diffraction

E. N. S. Muccillo; J. F. Q. Rey; E. C. C. Souza

Strong CTR-cap-layer coupling for X-ray scattering in InAs/GaAs (001) quantum dots systems

P. R. C. Couceiro; A. C. Doriguetto; J. D. Fabris; A. T. Goulart; J. M. Delgado; F. D. da Silva

Synchrotron Radiation Multiple Diffraction as high resolution probe to analyze Mn impurity in KDP C. M. R. Remedios; L. P. Cardoso; A. S. de Menezes; A. O. dos Santos

AFM/EFM Study of SiO2/SnO2/Cgraphite composites electrodes J. Arguello; Y. Gushikem | Activity Report 2008

E. N. S. Muccillo; J. F. Q. Rey; E. C. C. Souza

Small angle X-ray study of nanostructured samaria-doped ceria: effect of different alcoholic media on scattering characteristics Crystallographic Changes Accompanying the Verwey Transition in a Magnetite from Steatite

144

Small angle X-ray study of nanostructured samaria-doped ceria: effect of thermal treatment on scattering characteristics

C. M. R. Remedios; L. P. Cardoso; A. S. de Menezes; A. O. dos Santos; E. J. L. Gomes

R. O. Freitas; S. L. Morelh達o; A. A. Quivy

Development of Conducting Polyaniline/Poly(lactic acid) Nanofibers by Electrospinning P. H. S. Picciani; B. G. Soares

Development of Conducting Polyaniline/Poly(lactic acid) Nanofibers by Electrospinning P. H. S. Picciani; B. G. Soares

Development of Conducting Polyaniline/Poly(lactic acid) Nanofibers by Electrospinning P. H. S. Picciani; B. G. Soares

Development of Conducting Polyaniline/Poly(lactic acid) Nanofibers by Electrospinning P. H. S. Picciani; B. G. Soares

Development of Conducting Polyaniline/Poly(lactic acid) Nanofibers by Electrospinning P. H. S. Picciani; B. G. Soares

Development of Conducting Polyaniline/Poly(lactic acid) Nanofibers by Electrospinning P. H. S. Picciani; B. G. Soares

Microscopy Microfabrication

and

M. C. A. Fantini; S. M. Gheno; A. L. Gobbi; A. C. Machado; P. A. P. Nascente; P. I. Paulin Filho; P. J. M. Silva

Development of a Silicon Carbide Piezoresistive Pressure Sensor M. A. Fraga; H. S. Maciel; M. Massi; I. C. Oliveira

Behavior

in

S. M. Gheno; P. I. Paulin Filho; V. L. Pimentel

Effect of Heat Treatments on Fatigue Resistance of Ti-35Nb Applied as Biomaterial R. Caram; A. Cremasco

F. Veiga; C. B. Woitiski

Integration of electrodes conductometric detection the fabrication process glass microfluidic devices electrophoresis

for to of for

E. Carrilho; W. K. T. Coltro; L. H. Mazo; T. P. Segato

Projeto de Chaves e Indutores Tridimensionais para Aplicaçþes em RF A. S. A. Tavora; P. F. B. Atanazio; C. E. Capovilla; L. C. Kretly; M. W. B. Silva

Fabrication of nanochannels in SU-8 using AFM tip E. Carrilho; G. R. M. Duarte; Marcelo A Pereira-daSilva

Au-Pd Bilayered Films Deposited on Si(100) By DC Magnetron Sputtering

Potential Barrier Bicuvox Materials

Nanoscale analysis of biopolymeric nanoparticles for orally dosed insulin using atomic force microscopy

Fabrication of nanochannels in SU-8 using AFM tip E. Carrilho; G. R. M. Duarte; Marcelo A Pereira-daSilva

Physics Magnetoelastic Effects in DyNiBC and TbNiBC Studied by High Resolution Synchrotron X-ray Scattering M. Alzamora; E. Baggio-Saitovitch; D. Berthebaud; M. B. Fontes; M. Kumaresavanji; D. R. Sanchez

Synthesis and characterization of Gd3+ ions doped in NaYF4 nanocrystals L. M. Holanda; P. G. Pagliuso; C. Rettori; J. M. Vargas; W. Iwamoto

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Characterization of Self-Assembled Monolayers of Aliphatic and Aromatic Thiols and Selenols on Au(111) H. Ascolani; F. P. Cometto; G. Zampieri

Synthesis and characterization of Gd3+ ions doped in NaYF4 nanocrystals L. M. Holanda; P. G. Pagliuso; C. Rettori; J. M. Vargas; W. Iwamoto

Surface structural characterization of a 3 ML Pd film deposited on Au(111) by angle-scanned X-ray photoelectron diffraction M. F. Carazzolle; A. de Siervo; G. G. Kleiman; R. Landers; P. A. P. Nascente; A. Pancotti; D. A. Tallarico

Carbamazepine from raw materials to tablets analyzed through Rietveld Method S. G. Antonio; F. F. Ferreira; M. A. S. Guerreiro; C. O. Paiva-Santos; P. C. P. Rosa

Quantitative phase analysis of carbamazepine forms I and III using synchrotron X-ray powder diffraction data and the Rietveld method.

S. G. Antonio; F. R. Benini; F. F. Ferreira; C. O. PaivaSantos; P. C. P. Rosa

Quantitative Phase Analysis of Tibolone Polymorphs Using Highthroughput Synchrotron X-Ray Diffraction S. G. Antonio; G. L. B. Araujo; F. M. S. Carvalho; F. F. Ferreira; M. A. S. Guerreiro; J. R. Matos; C. O. PaivaSantos

Grazing incidence investigation of structural evolution of CdTe/Si(111) quantum dots S. O. Ferreira; A. Malachias; J. Oliveira; I. R. B. Ribeiro; J. Suela

Study of (1s,3p) resonant inelastic x-ray scattering processes in Cr, Mn and Cu G. Stutz; G. Tirao

A multi-coincidence study of the multiple photoionization of CH4 and NH3 molecules A. C. F. Santos; R. L. Cavasso Filho; E. C. Montenegro; S. Pilling; L. Sigaud; W. Wolff

Multielemental Analysis of Prostate Tissues by SR-TXRF M. J. Anjos; C. G. L. Canellas; R. C. Correia; L. C. Ferreira; R. G. Leit茫o; R. T. Lopes; L. E. Nasciutti; A. J. Palumbo

Determination of Low-z Elements In Human Serum of Patients with Idiopathic Thrombocytopenic Purpura by Txrf Spectrometry M. J. Anjos; C. G. L. Canellas; S. M. F. Carvalho; E. F. O. de Jesus; R. T. Lopes

Shape changes in Pt nanoparticles induced by support effect.

L. J. Giovanetti; J. M. Ramallo-L贸pez; F. G. Requejo

Structural Modeling of PtxPd1-x (x = 1, 0.7 or 0.5) Bimetallic Nanoparticles by in-situ XAS A. Traverse; M. C. M. Alves; F. Bernardi; C. W. Scheeren; J. Dupont; J. Morais; D. O. Silva

Electronic and Structural Properties of PtxPd1-x (x = 0.7 or 0.5) Bimetallic Nanoparticles M. C. M. Alves; F. Bernardi; J. Morais

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Analysis of trace elements in normal, benign and malignant breast tissues measured by total reflection x-ray fluorescence

Study of Co/Ru and NiFe/Ru multilayers by X-ray diffraction

J. J. G. Costa; M. E. Poletti; M. P. Silva; O. L. A. D Zucchi

Study of Co/Ru and NiFe/Ru multilayers by X-ray diffraction

Study of biological structures of some tissues between 0.15 and 8.50nm-1 using Small Angle X-ray Scattering

W. Alayo; E. Baggio-Saitovitch; Miguel Tafur; V. P. Nascimento

A. L. C. Conceição; M. E. Poletti; I. Torriani

Compositional modulation and surface stability in InGaP films J. Bettini; J. R. R. Bortoleto; M. A. Cotta; H. R. Gutiérrez

Thermal stability of CaC2O4.H2O

W. Alayo; E. Baggio-Saitovitch; Miguel Tafur; V. P. Nascimento

XRD investigation of thermally induced structural and chemical changes in iron oxide nanoparticles embedded in porous carbons A. G. Cunha; E. Nunes; Francisco G. Emmerich; J. C. C. Freitas; Miguel A. Schettino Jr.; M. K. Morigaki; E. C. Passamani

Structural Biology

Molecular

H. P. S. Corrêa; L. G. Martinez; M. T. D. Orlando

Designing spatial correlation of quantum dots J. Bettini; J. R. R. Bortoleto; M. A. Cotta; H. R. Gutiérrez; J. G. Zelcovit

Oxidation state quantification for Mn oxide mix samples by high resolution Kb spectra C. Quintana; S. Ceppi; G. Stutz; G. Tirao

Oxidation state quantification for Mn oxide mix samples by high resolution Kb spectra C. Quintana; S. Ceppi; G. Stutz; G. Tirao

Study of b-FeSi2 synthesized during Fe+ ion implantation process in Si(001) by means of Synchrotron Radiation X-ray Multiple Diffraction L. Amaral; L. P. Cardoso; A. S. de Menezes; A. O. dos Santos; R. Lang; E. A. Meneses

Preparation and Crystallization of Schizolobium parahyba Chymotrypsin Inhibitor in Complex with Chymotrypsin J. A. R. G. Barbosa; G. F. Esteves; S. M. Freitas; C. R. Santos; A. J. Silva; R. C. L. Teles

Frequency-domain Fluorescence lifetime of the Schizolobium parahyba Chymotrypsin Inhibitor A. C. M. Álvares; J. A. R. G. Barbosa; S. M. Freitas; F. A. Schaberle; A. J. Silva; R. C. L. Teles

Crystallization and X-ray analyses of peroxiredoxins interacting with vitamin C. L. S. Cavalcante; K. F. Discola; G. Monteiro; L. E. S. Netto

Low resolution structural studies of human Stanniocalcin-1 J. Kobarg; M. S. Navarro; J. C. Silva; I. Torriani; D. M. Trindade

Activity Report 2008 | 147

Expression, purification and molecular modelling of the phosphate-binding protein from Xanthomonas axonopodis pv. citri A. Balan; J. A. R. G. Barbosa; L. N. Güttlein

Thermolability of major Royal Jelly Protein 1 (MRJP1) Caused by Calcium J. A. R. G. Barbosa; G. C. N. Cruz; S. M. Freitas; L. Garcia; M. V. Sousa

SAXS analysis of the human kinase Nek6 J. Kobarg; D. C. F. Lanza; G. V. Meirelles; J. C. Silva; I. Torriani

Hydrodynamic Features of the Leucyl Aminopeptidase from Leptospira interrogans A. C. M. Álvares; J. A. R. G. Barbosa; S. M. Freitas; J. M. Santana; A. J. Silva

Structural Studies of Trypanosoma brucei Prolyl Oligopeptidase J. A. R. G. Barbosa; I. M. D. Bastos; S. M. Freitas; M. M. Lima; F. J. Medrano; D. Neves; J. M. Santana

The FEZ1 protein dimerizes via its N-terminus by a disulfide bond M. R. Alborghetti; A. S. Furlan; J. Kobarg; J. C. Silva; I. Torriani

Structural Determination of a new cyclic peptide from Jatropha curcas L. W. F. Altei; E. M. Cilli; V. B. da Silva; G. Giesel; H. Verli

Crystallization and preliminary X-ray diffraction analysis of the lectin from Canavalia boliviana Piper seeds K. L. L. Alencar; R. G. Benevides; E. H. S. Bezerra; G. A. Bezerra; M. J. B. Bezerra; B. S. Cavada; P. Delatorre; T. R. Moura; C. S. Nagano; B. A. M. Rocha; A. H. Sampaio

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Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides W. F. Azevedo Jr.; R. G. Benevides; G. A. Bezerra; B. S. Cavada; P. Delatorre; F. B. M. B. Moreno; T. R. Moura; C. B. Nobre; T. M. Oliveira; B. A. M. Rocha

Crystallization and preliminary X-ray diffraction analysis of the leptospiral protein LIC12922 M. V. Atzingen; P. O. Giuseppe; B. G. Guimarães; A. L. T. O. Nascimento; N. I. T Zanchin

The leptospiral antigen Lp49 is a two-domain protein with putative protein binding function P. O. Giuseppe; B. G. Guimarães; A. L. T. O. Nascimento; F. O. Neves

Effect of temperature and Additives on the Structure of Trypanosoma brucei Prolyl Oligopeptidase J. A. R. G. Barbosa; I. M. D. Bastos; S. M. Freitas; M. M. Lima; F. J. Medrano; D. Neves; J. M. Santana

Low Resolution Structure of DNA and Ligand Binding Domains of Peroxisome Proliferator-activated Receptors g F. A. H. Batista; A. Bernardes; A. F. Craievich; A. C. M. Figueira; M. Oliveira Neto; I. Polikarpov

Interaction of Cytochrome-c with Biomimetic systems L. R. S. Barbosa; R. Itri; P. Mariani; S. Mazzoni

Low Resolution Structure of the hTRa1 DBD-LBD Dimer A. Bernardes; A. F. Craievich; A. C. M. Figueira; M. Oliveira Neto; I. Polikarpov

Data collection and processing of the crystal from alkanesulfonatebinding protein from Xanthomonas axonopodis pv. Citri

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions

J. A. R. G. Barbosa; F. Tofoli

M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Low Resolution Structures of monomer hPPARgLBD and heterodimer hPPARgLBDhRXRaLBD F. A. H. Batista; A. Bernardes; A. F. Craievich; A. C. M. Figueira; M. Oliveira Neto; I. Polikarpov

Thermodynamic Characterization of the Interaction Between H-NS protein from Xylella fastidiosa and DNA: pH dependence of Higher Order Structure Formation A. P. de Souza; M. G. de Oliveira; L. K. Rosselli; R. C. Sassonia; M. L. Sforรงa; A. C. Zeri; A. Zeri; A. C. M. Zeri

Thermodynamic Characterization of the Interaction Between H-NS protein from Xylella fastidiosa and DNA: pH dependence of Higher Order Structure Formation A. P. de Souza; M. G. de Oliveira; L. K. Rosselli; R. C. Sassonia; M. L. Sforรงa; A. C. Zeri; A. Zeri; A. C. M. Zeri

Thermodynamic Characterization of the Interaction Between H-NS protein from Xylella fastidiosa and DNA: pH dependence of Higher Order Structure Formation A. P. de Souza; M. G. de Oliveira; L. K. Rosselli; R. C. Sassonia; M. L. Sforรงa; A. C. Zeri; A. Zeri; A. C. M. Zeri

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Activity Report 2008 | 149

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Characterization of the interaction between C-terminal half of human juvenile myoclonic epilepsy protein EFHC1 and Ca2+ and Mg2+ ions M. G. Oliveira; I. Lopes-Cendes; M. J. Murai; R. C. Sassonia

Thermodynamic Characterization of the Interaction Between H-NS protein from Xylella fastidiosa and DNA: pH dependence of Higher Order Structure Formation A. P. de Souza; M. G. de Oliveira; L. K. Rosselli; R. C. Sassonia; M. L. Sforรงa; A. C. Zeri; A. Zeri; A. C. M. Zeri

Structural stability of Oligopeptidase B from Trypanosoma cruzi Under Different pHs J. A. R. G. Barbosa; I. M. D. Bastos; S. M. Freitas; F. S. N. Motta; J. M. Santana

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