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Chemical Nomenclature Lulu Press, Raleigh, N.C. USA

Dr. Pramod Kothari Assistant Professor, Department Of Chemistry Government Post Graduate College, Berinag, District – Pithoragarh Uttarakhand (India)


Copyright Š Creative Commons Attribution-Share Alike 3.0 //creativecommons.org/licenses/by-sa/3.0/ Disclaimer All the material contained in this book is provided for educational and informational purposes only. No responsibility can be taken for any results or outcomes resulting from the use of this material. While every attempt has been made to provide information that is both accurate and effective, the author does not assume any responsibility for the accuracy or use/misuse of this information.

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Preface A chemical nomenclature is a set of rules to generate systematic names for chemical compounds. The nomenclature used most frequently worldwide is the one created and developed by the International Union of Pure and Applied Chemistry (IUPAC). The IUPAC's rules for naming organic and inorganic compounds are contained in two publications, known as the Blue Book and the Red Book, respectively. A third publication, known as the Green Book, describes the recommendations for the use of symbols for physical quantities (in association with the IUPAP), while a fourth, the Gold Book, contains the definitions of a large number of technical terms used in chemistry. Similar compendia exist for biochemistry (the White Book, in association with the IUBMB), analytical chemistry (the Orange Book), macromolecular chemistry (the Purple Book) and clinical chemistry (the Silver Book). These "color books" are supplemented by shorter recommendations for specific circumstances that are published from time to time in the journal Pure and Applied Chemistry. The primary function of chemical nomenclature is to ensure that a spoken or written chemical name leaves no ambiguity concerning which chemical compound the name refers to: each chemical name should refer to a single substance. A less important aim is to ensure that each substance has a single name, although a limited number of alternative names is acceptable in some cases. Preferably, the name also conveys some information about the structure or chemistry of a compound. CAS numbers form an extreme example of names that do not perform this function: each CAS number refers to a single compound but none contain information about the structure. The form of nomenclature used depends on the audience to which it is addressed. As such, no single correct form exists, but rather there are different forms that are more or less appropriate in different circumstances. A common name will often suffice to identify a chemical compound in a particular set of circumstances. To be more generally applicable, the name should indicate at least the chemical formula. To be more specific still, the three-dimensional arrangement of the atoms may need to be specified. In a few specific circumstances (such as the construction of large indices), it becomes necessary to ensure that each compound has a unique name: This requires the addition of extra rules to the standard IUPAC system (the CAS system is the most commonly used in this context), at the expense of having names that are longer and less familiar to most readers. Another system gaining popularity is the International Chemical Identifier (InChI)—

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which reflects a substance's structure and composition, making it more general than a CAS number. The IUPAC system is often criticized for the above failures when they become relevant (for example, in differing reactivity of sulfur allotropes, which IUPAC does not distinguish). While IUPAC has a human-readable advantage over CAS numbering, it would be difficult to claim that the IUPAC names for some larger, relevant molecules (such as rapamycin) are humanreadable, and so most researchers simply use the informal names.

Dr. Pramod Kothari Assistant Professor, Department Of Chemistry Government Post Graduate College, Berinag, District – Pithoragarh Uttarakhand (India)

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Table of Contents Ajmalan ......................................................................................................... 1 Arene substitution pattern ............................................................................. 3 Cahn–Ingold–Prelog priority rules ............................................................... 12 Chirality . ..................................................................................................... 18 Hantzsch–Widman nomenclature ............................................................... 27 Hill system ................................................................................................... 30 International Chemical Identifier .................................................................. 32 InChIKey ..................................................................................................... 35 International Union Of Pue & Applied Chemistry ......................................... 38 Monosaccharide nomenclature ................................................................... 50 Noble metal . ............................................................................................... 58 Oligosaccharide nomenclature .................................................................... 60 Oxidation state . ........................................................................................... 64 Parent hydride ............................................................................................ 73 Phanes (organic chemistry) ......................................................................... 75 Preferred IUPAC name ............................................................................... 76 Primary (chemistry) ..................................................................................... 78 Quaternary (chemistry) . ............................................................................. 79 Secondary (chemistry) ................................................................................. 80 Simplified molecular-input line-entry system . .............................................. 82 Stock nomenclature .................................................................................... 88 Structure Analog………………………………………………………………

89

Subtituent ..................................................................................................... 91

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Systematic element name…………………………………………… ………….94 Tertiary (chemistry) ...................................................................................... 96 Transfermium Wars……………………………………………………………….97 Trivial name .............................................................................................. 101 Ylide…………………………………………………………………………….…108

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Chapter 1: Ajmalan

The conventional representation of the ajmalan skeleton, with numbering

Ajmalan is a parent hydride used in the IUPAC nomenclature of natural products and also in CAS nomenclature. It is a 20-carbon alkaloid with six rings and seven chiral centres. The name is derived from ajmaline, an antiarrhythmic alkaloid isolated from the roots of Rauwolfia serpentina which is formally a dihydroxy-derivative of ajmalan. The –an ending indicates that ajmalan is partially saturated. Ajmaline itself is named after Hakim Ajmal Khan, a distinguished practitioner of the Unani school of traditional medicine in South Asia. The absolute configuration of the seven chiral carbon atoms in ajmalan is defined by convention, as is the numbering system. The stereochemistry is the same as that in naturally-occurring ajmaline, and corresponds to (2R,3S,5S,7S,15S,16R,20S) using conventional numbering. Ajmalan can be systematically named as (1S,4S,5S,7S,8R,16S,17R)-4-ethyl-9-methyl-2,92,7

5,18

diazahexacyclo[14.2.1.0 .0

8,16

.0

10,15

.0

]nonadeca-10,12,14-triene

or as (2S,3S,5S,6aS,11aR,11bS,12R)-4H,11H-3-ethyl-11-methyl-1,2,3,5,6,6a,11a,11boctahydro-2,5,6a-(epiethane[1,1,2]triyl)indolo[2,3-c]quinolizine. Note that the numbering of the atoms in the systematic names is different from the conventional numbering of ajmalan. The ajmalan skeleton is similar to those of certain other alkaloids, and ajmalan could also be given the following semisystematic names: (2β,5β,16R,20β)-1-methyl-1,2,19,20-tetrahydro-5,16-cyclo-16a-homo-17norakuammilan; (2β,5β,7β,16R,20β)-1-methyl-2,7-dihydro-5,16:7,17-dicyclocorynan;

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(2β,7β,16R,20β)-1-methyl-2,7,19,20-tetrahydro-7,17-cyclosarpagan; (2β,3α,7β,20β)-1-methyl-2,7,19,20-tetrahydro-3,4:7,17-dicyclo-22-norvobasan; (2β,5β,7β,16R,20β)-1-methyl-2,7-dihydro-5,16:7,17-dicyclo-17-secoyohimban. However, the relative complexity even of these names justifies the use of ajmalan as a defined parent hydride in alkaloid nomenclature.

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Chapter 2: Arene substitution pattern Arene substitution patterns are part of organic chemistry IUPAC nomenclature and pinpoint the position of substituents other than hydrogen in relation to each other on an aromatic hydrocarbon. Ortho, meta, and para substitution

Main arene substitution patterns. See also: Electrophilic aromatic substitution 

In ortho-substitution, two substituents occupy positions next to each other, which may be numbered 1 and 2. In the diagram, these positions are marked R and ortho.

In meta-substitution the substituents occupy positions 1 and 3 (corresponding to R and meta in the diagram).

In para-substitution, the substituents occupy the opposite ends (positions 1 and 4, corresponding to R and para in the diagram). The toluidines serve as an example for these three types of substitution.

Ipso, meso, and peri substitution 

ipso- substitution.

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meso- substitution. 

peri- substitution. 

Ipso-substitution describes two substituents sharing the same ring position in an intermediate compound in an electrophilic aromatic substitution. Me 3Si, t-Bu, and iPr groups can form stable carbocation, hence are ipso directing groups.

Meso-substitution refers to the substituents occupying a benzylic position. It is observed in compounds such as calixarenes and acridines.

Peri-substitution occurs in naphthalenes for substituents at the 1 and 8 positions.

Cine and tele substitution 

In cine-substitution, the entering group takes up a position adjacent to that occupied by the leaving group. For example, cine-substitution is observed in aryne chemistry.

Tele-substitution occurs when the new position is more than one atom away on the ring.

Origins The prefixes ortho, meta, and para are all derived from Greek, meaning straight or correct, following or after, and akin to or similar, respectively. The relationship to the current meaning is perhaps not obvious. The ortho description was historically used to designate the original compound, and an isomer was often called the meta compound. For instance, the trivial names orthophosphoric acid and trimetaphosphoric acid have nothing to do with aromatics at all. Likewise, the description para was reserved for just closely related compounds. Thus Berzelius originally called the racemic form of aspartic acid paraaspartic acid (another obsolete term: racemic acid) in 1830. The use of the descriptions ortho, meta and para for multiple substituted aromatic rings starts with Wilhelm Körner in the period 1866–1874 although he chose to reserve the ortho prefix for the 1,4 isomer and the meta prefix for the 1,2-isomer. The current nomenclature (different again from that of Körner) was introduced by the Chemical Society in 1879.

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Examples Examples of the use of this nomenclature are given for isomers of cresol: 

o-cresol 

m-cresol 

p-cresol Catechol has two isomers, the meta isomer resorcinol and the para isomer hydroquinone: 

catechol

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resorcinol 

hydroquinone Phthalic acid has two isomers, the meta isomer isophthalic acid and the para isomer terephthalic acid: 

phthalic acid 

isophthalic acid 

terephthalic acid

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Chapter 3: Cahn–Ingold–Prelog priority rules

An example of the prioritisation of structure within the CIP system. Priority is assigned according to the substitution of elements with higher atomic numbers, or other attached groups. In red is the substituent which determines the final priority. The Cahn–Ingold–Prelog priority rules, CIP system or CIP conventions (after Robert Sidney Cahn, Christopher Kelk Ingold and Vladimir Prelog) are a set of rules used in organic chemistry to name the stereoisomers of a molecule. A molecule may contain any number of stereocenters and any number of double bonds, and each gives rise to two possible configurations. The purpose of the CIP system is to assign an R or S descriptor to each stereocenter and an E or Z descriptor to each double bond so that the configuration of the entire molecule can be specified uniquely by including the descriptors in its systematic name. The key article by the three authors setting out the CIP rules was published in 1966. The Cahn–Ingold–Prelog rules are distinctly different from those of other naming conventions, such as general IUPAC nomenclature, since they are designed for the specific task of naming stereoisomers rather than the general classification and description of compounds. Steps for naming The steps for naming molecules using the CIP system are often presented as: 1. Identification of stereocenters and double bonds 2. Assignment of priorities to the groups attached to each stereocenter or doublebonded atom 3. Assignment of R/S and E/Z descriptors Assignment of priorities R/S and E/Z descriptors are assigned by using a system for ranking priority of the groups attached to each stereocenter. This procedure, often known as the sequence rules, is the heart of the CIP system. 1. Compare the atomic number (Z) of the atoms directly attached to the stereocenter; the group having the atom of higher atomic number receives higher priority. 2. If there is a tie, we must consider the atoms at distance 2 from the stereocenter—as a list is made for each group of the atoms bonded to the one directly attached to the stereocenter.

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Each list is arranged in order of decreasing atomic number. Then the lists are compared atom by atom; at the earliest difference, the group containing the atom of higher atomic number receives higher priority. 3. If there is still a tie, each atom in each of the two lists is replaced with a sub-list of the other atoms bonded to it (at distance 3 from the stereocenter), the sub-lists are arranged in decreasing order of atomic number, and the entire structure is again compared atom by atom. This process is repeated, each time with atoms one bond farther from the stereocenter, until the tie is broken. Isotopes If two groups differ only in isotopes, atomic masses are used at each step to break ties in atomic number. Double and triple bonds If an atom A is double-bonded to an atom B, A is treated as being singly bonded to two atoms: B and a ghost atom that has the same atomic number as B but is not attached to anything except A. In turn, when B is replaced with a list of attached atoms, A itself is excluded in accordance with the general principle of not doubling back along a bond that has just been followed, but a ghost atom for A is included so that the double bond is properly represented from both ends. A triple bond is handled the same way except that A and B each carry two ghost atoms instead of one. It needs to be mentioned also that two substituents on an atom may, in rare cases, be geometrical isomers. Consider for example the compound (3Z,6E)-3,5,7-trimethylnona-3,6diene. It soon becomes clear that the 5-carbon is chiral because it has four different substituents. Thus it is necessary to introduce the rule that the Z-isomer has higher priority than the E-isomer. Cycles To handle a molecule containing one or more cycles, one must first expand it into a tree (called a hierarchical digraph by the authors) by traversing bonds in all possible paths starting at the stereocenter. When the traversal encounters an atom through which the current path has already passed, a ghost atom is generated in order to keep the tree finite. A single atom of the original molecule may appear in many places (some as ghosts, some not) in the tree. Assigning descriptors

Stereocenters: R/S

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Two examples of stereocenters. The lowest substituent (number 4) is shown only by a wavy line, and is assumed to be behind the rest of the molecule. Both centers shown are S isomers. After the substituents of a stereocenter have been assigned their priorities, the molecule is oriented in space so that the group with the lowest priority is pointed away from the observer. If the substituents are numbered from 1 (highest priority) to 4 (lowest priority), then the sense of rotation of a curve passing through 1, 2 and 3 distinguishes the stereoisomers. A center with a clockwise sense of rotation is an R or rectus center and a center with a counterclockwise sense of rotation is an S or sinister center. The names are derived from the Latin for right and left, respectively. A practical method of determining whether an enantiomer is R or S is by using the right-hand rule: one wraps the molecule with the fingers in the direction 1→2→3. If the thumb points in the direction of the 4th substitutent, the enantiomer is R. Otherwise, it's S.

(1R,2s,3S)-1,2,3-trichlorocyclopentane It is possible in rare cases that two substituents on an atom differ only in their absolute configuration (R or S). If the relative priorities of these substituents need to be established, R takes priority over S. When this happens, the descriptor of the stereocenter is a lowercase letter (r or s) instead of the uppercase letter normally used. Double bonds: E/Z For alkenes and similar double bonded molecules, the same prioritizing process is followed for the substituents. In this case, it is the placing of the two highest priority substituents with respect to the double bond which matters. If both high priority substituents are on the same side of the double bond, i.e. in the cis configuration, then the stereoisomer is assigned a Z or Zusammen configuration. If, by contrast they are in a trans configuration, then the stereoisomer is assigned an E or Entgegen configuration. In this case the identifying letters are derived from German for 'together' and 'in opposition to', respectively. Examples R/S assignments for several compounds

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The hypothetical molecule bromochlorofluoroiodomethane shown in its R-configuration wou

chiral compound. The priorities are assigned based on atomic number (Z): iodine (Z = 53) >

chlorine (Z = 17) > fluorine (Z = 9). Allowing fluorine (lowest priority) to point away from the v clockwise hence the R-assignment.

In the assignment of L-serine highest priority is given to the nitrogen atom (Z = 7) in the amin the methylalcohol group (CH2OH ) and the carboxylic acid group (COOH) have carbon atoms

given to the latter because the carbon atom in the COOH group is connected to a second ox

in the CH2OH group carbon is connected to a hydrogen atom (Z=1). Lowest priority is given to and as this atom points away from the viewer the counterclockwise decrease in priority over substituents completes the assignment as S. The stereocenter in S-carvone is connected to one hydrogen atom (not shown, priority 4) and

The isopropene group has priority 1 (carbon atoms only) and for the two remaining carb

decided with the carbon atoms two bonds removed from the stereocenter, one part of the priority 2) and one part of an alkene (H,C,C priority 3). The resulting counterclockwise rotation

Multiple descriptors in one molecule If a compound has more than one stereocenter each center is denoted by either R or S. For example, ephedrine exists with both (1R,2S) and (1S,2R) configuration, known as enantiomers. This compound also exists with a (1R,2R) and (1S,2S) configuration. The last two stereoisomers are not ephedrine, but pseudoephedrine. All isomers are 2-methylamino1-phenyl-1-propanol in systematic nomenclature. Pseudoephedrine is chemically distinct from ephedrine with only the three dimensional configuration in space, as notated by the Cahn–Ingold–Prelog rules. Relative configuration The relative configuration of two stereoisomers may be denoted by the descriptors R and S with an asterisk (*). "R*,R*" means two centers having identical configurations (R,R or S,S); "R*,S*" means two centers having opposite configurations (R,S or S,R). To begin, the lowest numbered (according to IUPAC systematic numbering) stereogenic center is given the R* descriptor. To designate two anomers the relative stereodescriptors alpha (α) and beta (β) are used. In the α anomer the anomeric carbon and the reference atom do have opposite configurations (R,S or S,R), whereas in the β anomer they are the same (both R or both S).

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Faces

Acetophenone and Îą-Phenylethanol Stereochemistry also plays a role assigning faces to trigonal molecules such as ketones. A nucleophile in a nucleophilic addition can approach the carbonyl group from two opposite sides or faces. When an achiral nucleophile attacks acetone, both faces are identical and there is only one reaction product. When the nucleophile attacks butanone, the faces are not identical (enantiotopic) and a racemic product results. When the nucleophile is a chiral molecule diastereoisomers are formed. When one face of a molecule is shielded by substituents or geometric constraints compared to the other face the faces are called diastereotopic. The same rules that determine the stereochemistry of a stereocenter (R or S) also apply when assigning the face of a molecular group. The faces are then called the refaces and si-faces. In the example displayed on the right, the compound acetophenone is viewed from the re face. Hydride addition as in a reduction process from this side will form the S-enantiomer and attack from the opposite Si face will give the R-enantiomer. However, one should note that adding a chemical group to the prochiral center from the re-face will not always lead to an S stereocenter, as the priority of the chemical group has to be taken into account. That is, the absolute stereochemistry of the product is determined on its own and not by considering which face it was attacked from. In the above mentioned example, if chloride (Cl-) was added to the prochiral center from the re-face, this would result in an Renantiomer. Text here.

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Chapter 4: Chemical formula Al2(SO4)3

The pictured compound, aluminium sulfate, has a chemical formula Al2(SO4)3

Structural formula for butane. This is not a chemical formula. Examples of chemical formulas for butane are the empirical formula C2H5, the molecular formula C4H10, and the condensed (or semi-structural) formula CH3CH2CH2CH3 A chemical formula is a way of expressing information about the proportions of atoms that constitute a particular chemical compound, using a single line of chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, and plus (+) and minus (−) signs. These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a chemical name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas are more limiting than chemical names and structural formulas. The simplest types of chemical formulas are called empirical formulas, which use only letters and numbers indicating atomic proportional ratios (the numerical proportions of atoms of one type to those of other types). Molecular formulas indicate the simple numbers of each type of atom in a molecule of a molecular substance, and are thus sometimes the same as empirical formulas (for molecules that only have one atom of a particular type), and at other times require larger numbers than do empirical formulas. An example of the difference is the empirical formula for glucose, which is CH2O, while its molecular formula requires all numbers to be increased by a factor of six, giving C6H12O6. Sometimes a chemical formula is complicated by being written as a condensed formula (or condensed molecular formula, occasionally called a "semi-structural formula"), which conveys additional information about the particular ways in which the atoms are chemically bonded together, either in covalent bonds, ionic bonds, or various combinations of these types. This is possible if the relevant bonding is easy to show in one dimension. An example is the condensed molecular/chemical formula for ethanol, which is CH 3-CH2-OH or CH3CH2OH. However, even a condensed chemical formula is necessarily limited in its ability

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to show complex bonding relationships between atoms, especially atoms that have bonds to four or more different substituents. Since a chemical formula must be expressed as a single line of chemical element symbols, it often cannot be as informative as a true structural formula, which is a graphical representation of the spacial relationship between atoms in chemical compounds (see for example the figure for butane structural and chemical formulas, at right). For reasons of structural complexity, there is no condensed chemical formula (or semi-structural formula) that specifies glucose (and there exist many different molecules, for example fructose and mannose, have the same molecular formula C6H12O6 as glucose). Linear equivalent chemical names exist that can and do specify any complex structural formula, but these names must use many terms (words), rather than the simple element symbols, numbers, and simple typographical symbols that define a chemical formula. Chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. While, as noted, chemical formulas do not have the full power of structural formulas to show chemical relationships between atoms, they are sufficient to keep track of numbers of atoms and numbers of electical charges in chemical reactions, thus balancing chemical equations so that these equations can be used in chemical problems involving conservation of atoms, and conservation of electric charge. Overview A chemical formula identifies each constituent element by its chemical symbol and indicates the proportionate number of atoms of each element. In empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these ratio numbers can all be expressed as whole numbers. For example, the empirical formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of ionic compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the formula consists of simple molecules, chemical formulas often employ ways to suggest the structure of the molecule. These types of formulas are variously known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the molecular formula for glucose is C6H12O6 rather than the glucose empirical formula, which is CH2O. However, except for very simple substances, molecular chemical formulas lack needed structural information, and are ambiguous. For simple molecules, a condensed (or semi-structural) formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the condensed chemical formula CH3CH2OH, and dimethyl ether by the condensed formula CH3OCH3. These two molecules have the same empirical and molecular formulas (C 2H6O), but may be differentiated by the condensed formulas shown, which are sufficient to represent the full structure of these simple organic compounds.

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Condensed formulas in organic chemistry implying molecular geometry and structural formulas

Isobutane

structural

formula

Molecular

formula:

C4H10

Condensed or semi-structural chemical formula: (CH3)3CH

Butane Molecular

structural formula:

formula C4H10

Condensed or semi-structural formula: CH3CH2CH2CH3 The connectivity of a molecule often has a strong influence on its physical and chemical properties and behavior. Two molecules composed of the same numbers of the same types of atoms (i.e. a pair of isomers) might have completely different chemical and/or physical properties if the atoms are connected differently or in different positions. In such cases, a structural formula is useful, as it illustrates which atoms are bonded to which other ones. From the connectivity, it is often possible to deduce the approximate shape of the molecule. A condensed chemical formula may represent the types and spatial arrangement of bonds in a simple chemical substance, though it does not necessarily specify isomers or complex structures. For example ethane consists of two carbon atoms single-bonded to each other, with each carbon atom having three hydrogen atoms bonded to it. Its chemical formula can be rendered as CH3CH3. In ethylene there is a double bond between the carbon atoms (and thus each carbon only has two hydrogens), therefore the chemical formula may be written: CH2CH2, and the fact that there is a double bond between the carbons is implicit because carbon has a valence of four. However, a more explicit method is to write H 2C=CH2 or less commonly H2C::CH2. The two lines (or two pairs of dots) indicate that a double bond connects the atoms on either side of them. A triple bond may be expressed with three lines or pairs of dots, and if there may be ambiguity, a single line or pair of dots may be used to indicate a single bond. Molecules with multiple functional groups that are the same may be expressed by enclosing the repeated group in round brackets. For example isobutane may be written (CH3)3CH. This condensed structural formula implies a different connectivity from other molecules that can be formed using the same atoms in the same proportions (isomers). The formula (CH 3)3CH

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implies a central carbon atom attached to one hydrogen atom and three CH3 groups. The same number of atoms of each element (10 hydrogens and 4 carbons, or C 4H10) may be used to make a straight chain molecule, butane: CH3CH2CH2CH3. Chemical names in answer to limitations of chemical formulas The alkene called but-2-ene has two isomers, which the chemical formula CH3CH=CHCH3 does not identify. The relative position of the two methyl groups must be indicated by additional notation denoting whether the methyl groups are on the same side of the double bond (cis or Z) or on the opposite sides from each other (trans or E). Such extra symbols violate the rules for chemical formulas, and begin to enter the territory of more complex naming systems. As noted above, in order to represent the full structural formulas of many complex organic and inorganic compounds, chemical nomenclature may be needed which goes well beyond the available resources used above in simple condensed formulas. See IUPAC nomenclature of organic chemistry and IUPAC nomenclature of inorganic chemistry 2005 for examples. In addition, linear naming systems such as International Chemical Identifier (InChI) allow a computer to construct a structural formula, and simplified molecular-input lineentry system (SMILES) allows a more human-readable ASCII input. However, all these nomenclature systems go beyond the standards of chemical formulas, and technically are chemical naming systems, not formula systems. Polymers in condensed formulas For polymers in condensed chemical formulas, parentheses are placed around the repeating unit. For example, a hydrocarbon molecule that is described as CH 3(CH2)50CH3, is a molecule with fifty repeating units. If the number of repeating units is unknown or variable, the letter n may be used to indicate this formula: CH3(CH2)nCH3. Ions in condensed formulas For ions, the charge on a particular atom may be denoted with a right-hand superscript. For + 2+ example Na , or Cu . The total charge on a charged molecule or a polyatomic ion may also + 2− be shown in this way. For example: H3O or SO4 . For more complex ions, brackets [ ] are often used to enclose the ionic formula, as in 2− [B12H12] , which is found in compounds such as Cs 2[B12H12]. Parentheses ( ) can be nested 3+ inside brackets to indicate a repeating unit, as in [Co(NH 3)6] . Here (NH3)6 indicates that the ion contains six NH3 groups, and [ ] encloses the entire formula of the ion with charge +3. Isotopes Although isotopes are more relevant to nuclear chemistry or stable isotope chemistry than to conventional chemistry, different isotopes may be indicated with a prefixed superscript in a chemical formula. For example, the phosphate ion containing radioactive phosphorus-32 is 32 318 16 PO4 . Also a study involving stable isotope ratios might include the molecule O O. A left-hand subscript is sometimes used redundantly to indicate the atomic number. For 16 example, 8O2 for dioxygen, and 8O2 for the most abundant isotopic species of dioxygen. This is convenient when writing equations for nuclear reactions, in order to show the balance of charge more clearly.

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Trapped atoms

Traditional

formula:

MC60

The "@" notation: M@C60 Main article: Endohedral fullerene The @ symbol (at sign) indicates an atom or molecule trapped inside a cage but not chemically bound to it. For example, a buckminsterfullerene (C60) with an atom (M) would simply be represented as MC60 regardless of whether M was inside the fullerene without chemical bonding or outside, bound to one of the carbon atoms. Using the @ symbol, this would be denoted M@C60 if M was inside the carbon network. A non-fullerene example is 3[As@Ni12As20] , an ion in which one As atom is trapped in a cage formed by the other 32 atoms. This notation was proposed in 1991 with the discovery of fullerene cages (endohedral fullerenes), which can trap atoms such as La to form, for example, La@C 60 or La@C82. The choice of the symbol has been explained by the authors as being concise, readily printed and transmitted electronically (the at sign is included in ASCII, which most modern character encoding schemes are based on), and the visual aspects suggesting the structure of an endohedral fullerene. Non-stoichiometric chemical formulas Main article: Non-stoichiometric compound Chemical formulas most often use integers for each element. However, there is a class of compounds, called non-stoichiometric compounds, that cannot be represented by small integers. Such a formula might be written using decimal fractions, as in Fe0.95O, or it might include a variable part represented by a letter, as in Fe1窶度O, where x is normally much less than 1. General forms for organic compounds A chemical formula used for a series of compounds that differ from each other by a constant unit is called general formula. Such a series is called the homologous series, while its members are called homologs. For example alcohols may be represented by: CnH(2n + 1)OH (n 竕・ 1)

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Hill System The Hill system is a system of writing chemical formulas such that the number of carbon atoms in a molecule is indicated first, the number of hydrogen atoms next, and then the number of all other chemical elements subsequently, in alphabetical order. When the formula contains no carbon, all the elements, including hydrogen, are listed alphabetically. This deterministic system enables straightforward sorting and searching of compounds. See also 

Dictionary of chemical formulas

Element symbol

Nuclear notation

Periodic table

IUPAC nomenclature of inorganic chemistry

Ralph S. Petrucci, William S. Harwood, F. Geoffrey Herring (2002). "3". General Chemistry: Principles and Modern Applications (8th ed.). Prentice-Hall. ISBN 0-13198825-5. OCLC 46872308.

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Chapter 5: Chirality

Two enantiomers of a generic amino acid

(S)-Alanine (left) and (R)-alanine (right) in zwitterionic form at neutral pH A chiral molecule /ˈkaɪərəl/ is a type of molecule that has a non-superposable mirror image. The presence of an asymmetric carbon atom is often the feature that causes chirality in molecules. Achiral (not chiral) objects, such as molecules, are symmetrical, identical to their mirror image. Human hands are perhaps the most universally recognized example of chirality: the left hand is a non-superposable mirror image of the right hand; no matter how the two hands are oriented, it is impossible for all the major features of both hands to coincide. This difference in symmetry becomes obvious if a left-handed glove is placed on a right hand. The term chirality is derived from the Greek word for hand, χειρ (kheir). It is a mathematical approach to the concept of "handedness". In chemistry, chirality usually refers to molecules. Two mirror images of a chiral molecule are called enantiomers or optical isomers. Pairs of enantiomers are often designated as "right-" and "left-handed". Molecular chirality is of interest because of its application to stereochemistry in inorganic chemistry, organic chemistry, physical chemistry, biochemistry, and supramolecular chemistry.

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History The term optical activity is derived from the interaction of chiral materials with polarized light. In solution, the (−)-form, or levorotary form, of an optical isomer rotates the plane of a beam of polarized light counterclockwise. The (+)-form, or dextrorotatory form, does the opposite. The property was first observed by Jean-Baptiste Biot in 1815, and gained considerable importance in the sugar industry, analytical chemistry, and pharmaceuticals. Louis Pasteur deduced in 1848 that this phenomenon has a molecular basis. Artificial composite materials displaying the analog of optical activity but in the microwave region were introduced by J.C. Bose in 1898, and gained considerable attention from the mid-1980s. The term chirality itself was coined by Lord Kelvin in 1894. Different enantiomers or diastereomers of a compound were formerly called optical isomers due to their different optical properties. Symmetry The symmetry of a molecule (or any other object) determines whether it is chiral. A molecule is achiral (not chiral) when an improper rotation, that is a combination of a rotation and a reflection in a plane, perpendicular to the axis of rotation, results in the same molecule - see chirality (mathematics). For tetrahedral molecules, the molecule is chiral if all four substituents are different. A chiral molecule is not necessarily asymmetric (devoid of any symmetry element), as it can have, for example, rotational symmetry. Naming conventions

By configuration: R- and SFor chemists, the R / S system is the most important nomenclature system for denoting enantiomers, which does not involve a reference molecule such as glyceraldehyde. It labels each chiral center R or S according to a system by which its substituents are each assigned a priority, according to the Cahn–Ingold–Prelog priority rules (CIP), based on atomic number. If the center is oriented so that the lowest-priority of the four is pointed away from a viewer, the viewer will then see two possibilities: If the priority of the remaining three substituents decreases in clockwise direction, it is labeled R (for Rectus, Latin for right), if it decreases in counterclockwise direction, it is S (for Sinister, Latin for left). This system labels each chiral center in a molecule (and also has an extension to chiral molecules not involving chiral centers). Thus, it has greater generality than the D/L system, and can label, for example, an (R,R) isomer versus an (R,S) — diastereomers. The R / S system has no fixed relation to the (+)/(−) system. An R isomer can be either dextrorotatory or levorotatory, depending on its exact substituents. The R / S system also has no fixed relation to the D/L system. For example, the side-chain one of serine contains a hydroxyl group, -OH. If a thiol group, -SH, were swapped in for it, the D/L labeling would, by its definition, not be affected by the substitution. But this substitution would invert the molecule's R / S labeling, because the CIP priority of CH2OH is lower than that for CO2H but the CIP priority of CH2SH is higher than that for CO2H. For this reason, the D/L system remains in common use in certain areas of biochemistry, such as amino acid and carbohydrate chemistry, because it is convenient to have the same chiral label for all of the commonly occurring structures of a given type of structure in higher

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organisms. In the D/L system, they are nearly all consistent - naturally occurring amino acids are all L, while naturally occurring carbohydrates are nearly all D. In the R / S system, they are mostly S, but there are some common exceptions. By optical activity: (+)- and (−)- or d- and lAn enantiomer can be named by the direction in which it rotates the plane of polarized light. If it rotates the light clockwise (as seen by a viewer towards whom the light is traveling), that enantiomer is labeled (+). Its mirror-image is labeled (−). The (+) and (−) isomers have also been termed d- and l-, respectively (for dextrorotatory and levorotatory). Naming with d- and l- is easy to confuse with D- and L- labeling and is therefore strongly discouraged by IUPAC. By configuration: D- and LAn optical isomer can be named by the spatial configuration of its atoms. The D/L system, not to be confused with the d- and l-system, see above, does this by relating the molecule to glyceraldehyde. Glyceraldehyde is chiral itself, and its two isomers are labeled D and L (typically typeset in small caps in published work). Certain chemical manipulations can be performed on glyceraldehyde without affecting its configuration, and its historical use for this purpose (possibly combined with its convenience as one of the smallest commonly used chiral molecules) has resulted in its use for nomenclature. In this system, compounds are named by analogy to glyceraldehyde, which, in general, produces unambiguous designations, but is easiest to see in the small biomolecules similar to glyceraldehyde. One example is the amino acid alanine, which has two optical isomers, and they are labeled according to which isomer of glyceraldehyde they come from. On the other hand, glycine, the amino acid derived from glyceraldehyde, has no optical activity, as it is not chiral (achiral). Alanine, however, is chiral. The D/L labeling is unrelated to (+)/(−); it does not indicate which enantiomer is dextrorotatory and which is levorotatory. Rather, it says that the compound's stereochemistry is related to that of the dextrorotatory or levorotatory enantiomer of glyceraldehyde—the dextrorotatory isomer of glyceraldehyde is, in fact, the D- isomer. Nine of the nineteen Lamino acids commonly found in proteins are dextrorotatory (at a wavelength of 589 nm), and D-fructose is also referred to as levulose because it is levorotatory. A rule of thumb for determining the D/L isomeric form of an amino acid is the "CORN" rule. The groups: COOH, R, NH2 and H (where R is the side-chain) are arranged around the chiral center carbon atom. With the hydrogen atom away from the viewer, if the arrangement of the CO→R→N groups around the carbon atom is center is clockwise, then it is the D form. If the arrangement is counter-clockwise, it is the L form. The L form is the usual one found in natural proteins. For most amino acids, the L form corresponds to an S absolute stereochemistry, but is R instead for certain side-chains. Nomenclature 

Any non-racemic chiral substance is called scalemic.

A chiral substance is enantiopure or homochiral when only one of two possible enantiomers is present.

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A chiral substance is enantioenriched or heterochiral when an excess of one enantiomer is present but not to the exclusion of the other.

Enantiomeric excess or ee is a measure for how much of one enantiomer is present compared to the other. For example, in a sample with 40% ee in R, the remaining 60% is racemic with 30% of R and 30% of S, so that the total amount of R is 70%.

Stereogenic centers In general, chiral molecules have point chirality at a single stereogenic atom, which has four different substituents. The two enantiomers of such compounds are said to have different absolute configurations at this center. This center is thus stereogenic (i.e., a grouping within a molecular entity that may be considered a focus of stereoisomerism). Normally when an atom has four different substituents, it is chiral. However in rare cases, two of the ligands differ from each other by being mirror images of each other. When this happens, the mirror image of the molecule is identical to the original, and the molecule is achiral. This is called pseudochirality. A molecule can have multiple stereogenic centers without being chiral overall if there is a symmetry between the two (or more) stereocenters themselves. Such a molecule is called a meso compound. It is also possible for a molecule to be chiral without having actual point chirality. Common examples include 1,1'-bi-2-naphthol (BINOL), 1,3-dichloro-allene, and BINAP, which have axial chirality, (E)-cyclooctene, which has planar chirality, and certain calixarenes and fullerenes, which have inherent chirality. A form of point chirality can also occur if a molecule contains a tetrahedral subunit which cannot easily rearrange, for instance 1-bromo-1-chloro-1-fluoroadamantane and methylethylphenyltetrahedrane. It is important to keep in mind that molecules have considerable flexibility and thus, depending on the medium, may adopt a variety of different conformations. These various conformations are themselves almost always chiral. When assessing chirality, a timeaveraged structure is considered and for routine compounds, one should refer to the most symmetric possible conformation. When the optical rotation for an enantiomer is too low for practical measurement, it is said to exhibit cryptochirality. Even isotopic differences must be considered when examining chirality. Replacing one of the 1 2 two H atoms at the CH2 position of benzyl alcohol with a deuterium ( H) makes that carbon a stereocenter. The resulting benzyl-α-d alcohol exists as two distinct enantiomers, which can be assigned by the usual stereochemical naming conventions. The S enantiomer has [α]D = +0.715°. The identity of the stereogenic atom The stereogenic atom in chiral molecules is usually carbon, as in many biological molecules. However, it may also be a metal atom (as in many chiral coordination compounds), nitrogen, phosphorus, or sulfur. The chiral Carbon

Nitrogen Phosphorus Phosphorus Sulfur

Metal (type of metal)

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atom 1

(phosphates) (phosphines) Serine,

Sarin, VX

Esomeprazole, Tris(bipyridine)ruthenium(II)

stereogenic glyceraldehyde

armodafinil

center

(ruthenium),

cis-

Dichlorobis(ethylenediamine)cobalt(III) (cobalt), hexol (cobalt)

2

Threonine,

stereogenic isoleucine

TrĂśger's Adenosine base

triphosphate

DIPAMP

Dithionous acid

centers 3 or more Met-

DNA

stereogenic enkephalin, centers

leu-enkephalin

Properties of enantiomers Normally, the two enantiomers of a molecule behave identically to each other. For example, they will migrate with identical Rf in thin layer chromatography and have identical retention time in HPLC. Their NMR and IR spectra are identical. However, enantiomers behave differently in the presence of other chiral molecules or objects. For example, enantiomers do not migrate identically on chiral chromatographic media, such as quartz or standard media that have been chirally modified. The NMR spectra of enantiomers are affected differently by single-enantiomer chiral additives such as EuFOD. Chiral compounds rotate plane polarized light. Each enantiomer will rotate the light in a different sense, clockwise or counterclockwise. Molecules that do this are said to be optically active. Characteristically, different enantiomers of chiral compounds often taste and smell differently and have different effects as drugs – see below. These effects reflect the chirality inherent in biological systems. One chiral 'object' that interacts differently with the two enantiomers of a chiral compound is circularly polarised light: An enantiomer will absorb left- and right-circularly polarised light to differing degrees. This is the basis of circular dichroism (CD) spectroscopy. Usually the difference in absorptivity is relatively small (parts per thousand). CD spectroscopy is a powerful analytical technique for investigating the secondary structure of proteins and for determining the absolute configurations of chiral compounds, in particular, transition metal complexes. CD spectroscopy is replacing polarimetry as a method for characterising chiral compounds, although the latter is still popular with sugar chemists. In biology Many biologically active molecules are chiral, including the naturally occurring amino acids (the building blocks of proteins) and sugars. In biological systems, most of these compounds are of the same chirality: most amino acids are L and sugars are D. Typical naturally occurring proteins, made of L amino acids, are known as left-handed proteins, whereas D amino acids produce right-handed proteins. The origin of this homochirality in biology is the subject of much debate. Most scientists believe that Earth life's "choice" of chirality was purely random, and that if carbon-based life

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forms exist elsewhere in the universe, their chemistry could theoretically have opposite chirality. However, there is some suggestion that early amino acids could have formed in comet dust. In this case, circularly polarised radiation (which makes up 17% of stellar radiation) could have caused the selective destruction of one chirality of amino acids, leading to a selection bias which ultimately resulted in all life on Earth being homochiral. Enzymes, which are chiral, often distinguish between the two enantiomers of a chiral substrate. Imagine an enzyme as having a glove-like cavity that binds a substrate. If this glove is right-handed, then one enantiomer will fit inside and be bound, whereas the other enantiomer will have a poor fit and is unlikely to bind. D-form amino acids tend to taste sweet, whereas L-forms are usually tasteless.Spearmint leaves and caraway seeds, respectively, contain R-(–)-carvone and S-(+)-carvone enantiomers of carvone. These smell different to most people because our olfactory receptors also contain chiral molecules that behave differently in the presence of different enantiomers. Chirality is important in context of ordered phases as well, for example the addition of a small amount of an optically active molecule to a nematic phase (a phase that has long range orientational order of molecules) transforms that phase to a chiral nematic phase (or cholesteric phase). Chirality in context of such phases in polymeric fluids has also been studied in this context. D-Amino Acid Natural Abundance The relative abundances of each of the different D-isomers of several amino acids have recently been quantified by collecting experimentally reported data from the proteome across all organisms in the Swiss-Prot database. The D-isomers observed experimentally were found to occur very rarely as shown in the following table in the database of protein sequences containing over 187 million amino acids. D-amino acid

# of Times Experimentally Observed

D-alanine

664

D-serine

114

D-methionine

19

D-phenylalanine 15 D-valine

8

D-tryptophan

7

D-leucine

6

D-asparagine

2

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D-threonine

2

However, the D-isomers are not uncommon as free amino acids. Humans have special enzymes to process then, D-amino acid oxidase and D-aspartate oxidase. D-glutamic acid, D-glutamin, and D-alanine are also extremely common at a part of the peptidoglycan layer in the bacterial cell wall. In addition, D-serine is a neurotransmitter, and produced in humans by serine racemase. Inorganic chemistry

Delta-ruthenium-tris(bipyridine) cation Main article: Complex (chemistry): Isomerism Many coordination compounds are chiral. At one time, chirality was only associated with organic chemistry, but this misconception was overthrown by the resolution of a purely inorganic compound, hexol, by Alfred Werner. A famous example is tris(bipyridine)ruthenium(II) complex in which the three bipyridine ligands adopt a chiral propeller-like arrangement. In this case, the Ru atom is the stereogenic center. The two 2+ enantiomers of complexes such as [Ru(2,2′-bipyridine)3] may be designated as Λ (capital lambda, the Greek version of "L") for a left-handed twist of the propeller described by the ligands, and Δ (capital delta, Greek "D") for a right-handed twist – pictured. Chirality of compounds with a stereogenic "lone pair" When a nonbonding pair of electrons, a lone pair, occupies space, chirality can result. The effect is pervasive in certain amines, phosphines,sulfonium and oxonium ions, sulfoxides, and even carbanions. The main requirement is that aside from the lone pair, the other three substituents differ mutually. Chiral phosphine ligands are useful in asymmetric synthesis.

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Geometric inversion among the lone pair and three bonded groups on a tetrahedral amine Chiral amines are special in the sense that the enantiomers can rarely be separated. The energy barrier for nitrogen inversion of the stereocenter is generally only about 30 kJ/mol, which means that the two stereoisomers rapidly interconvert at room temperature. As a result, such chiral amines cannot be resolved into individual enantiomers unless some of the substituents are constrained in cyclic structures as in Tröger's base.

See also 

Stereochemistry for overview of stereochemistry in general

Supramolecular chirality

Chirality (physics)

Chirality (mathematics)

Pfeiffer Effect

Chemical chirality in popular fiction

External links 

http://www.chirality2009.org/

http://www.chemguide.co.uk/basicorg/isomerism/optical.html#top

http://www.nature.com/horizon/chemicalspace/highlights/s5_nonspec1.html

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IUPAC nomenclature for amino acid configurations.

Michigan State University's explanation of R/S nomenclature

Chirality & Odour Perception at leffingwell.com

Chirality & Bioactivity I.: Pharmacology

Chirality and the Search for Extraterrestrial Life

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Chapter 6: Hantzsch–Widman nomenclature Hantzsch–Widman nomenclature, also called the extended Hantzsch–Widman system, is a type of systematic chemical nomenclature used for naming heterocyclic parent hydrides having no more than ten ring members. Some common heterocyclic compounds have retained names that do not follow the Hantzsch–Widman pattern. Hantzsch–Widman nomenclature is named after the German chemist Arthur Hantzsch and the Swedish chemist Oskar Widman, who independently proposed similar methods for the systematic naming of heterocyclic compounds in 1887 and 1888 respectively. It forms the basis for many common chemical names, such as dioxin and benzodiazepine. A Hantzsch–Widman name will always contain a prefix, which indicates the type of heteroatom present in the ring, and a stem, which indicates both the total number of atoms and the presence or absence of double bonds. The name may include more than one prefix, if more than one type of heteroatom is present; a multiplicative prefix if there are several heteroatoms of the same type; and locants to indicate the relative positions of the different atoms. Hantzsch–Widman names may be combined with other aspects of organic nomenclature, to indicate substitution or fused-ring systems. Prefixes Element

Prefix

Element

Prefix

Fluorine

fluora

Arsenic

arsa

Chlorine

chlora

Antimony

stiba

Bromine

broma

Bismuth

bisma

Iodine

ioda

Silicon

sila

Oxygen

oxa

Germanium germana

Sulfur

thia

Tin

stanna

Selenium

selena

Lead

plumba

Tellurium

tellura

Boron

bora

Nitrogen

aza

Mercury

mercura

Phosphorus phospha The Hantzsch–Widman prefixes indicate the type of heteroatom(s) present in the ring. They form a priority series: If there is more than one type of heteroatom in the ring, the prefix that

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is higher on the list comes before the prefix that is lower on the list. For example, "oxa" (for oxygen) always comes before "aza" (for nitrogen) in a name. The priority order is the same as that used in substitutive nomenclature, but Hantzsch–Widman nomenclature is recommended only for use with a more restricted set of heteroatoms (see also below). All of the prefixes end in "a": In Hantzsch–Widman nomenclature (but not in some other methods of naming heterocycles), the final "a" is elided when the prefix comes before a vowel. The heteroatom is assumed to have its standard bonding number for organic chemistry while the name is being constructed. The halogens have a standard bonding number of one, and so a heterocyclic ring containing a halogen as a heteroatom should have a formal positive charge. In principle, lambda nomenclature could be used to specify a non-standard valence state for a heteroatom but, in practice, this is rare. Stems The choice of stem is quite complicated, and not completely standardised. The main criteria are: 

the total number of atoms in the ring, both carbon atoms and heteroatoms ("ring size")

the presence of any double bonds

the nature of the heteroatoms.

Notes on table: 1. Heteroatom priority is increasing as follows: F, Cl, Br, I, O, S, Se, Te, N, P, As, Sb, Bi, Si, Ge, Sn, Pb, B, Al, Ga, In, Tl, Hg. 2. Names in parenthesis indicate ending when nitrogen is present. Ring size

Saturated Unsaturated

3

-irane

-irene

(-iridine)

(-irine)

-etane

-ete

4

(-etidine) 5

-olane

-ole

(-olidine) 6A O, S, Se, Te; Bi, Hg

-ane

6B N; Si, Ge, Sn, Pb

-inane

-ine

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6C B; F, Cl, Br, I; P, As, Sb

-inine

7

-epane

-epine

8

-ocane

-ocine

9

-onane

-onine

10

-ecane

-ecine

External links 

Hantzsch-Widman nomenclature, IUPAC

Text here.

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Chapter 7: Hill system The Hill system (or Hill notation) is a system of writing chemical formulas such that the number of carbon atoms in a molecule is indicated first, the number of hydrogen atoms next, and then the number of all other chemical elements subsequently, in alphabetical order. When the formula contains no carbon, all the elements, including hydrogen, are listed alphabetically. By sorting formulas according to the number of atoms of each element present in the formula according to these rules, with differences in earlier elements or numbers being treated as more significant than differences in any later element or number — like sorting text strings into lexicographical order — it is possible to collate chemical formulas into what is known as Hill system order. The Hill system was first published by Edwin A. Hill of the United States Patent and Trademark Office in 1900. It is the most commonly used system in chemical databases and printed indexes to sort lists of compounds. Example The following formulas are written using the Hill system, and listed in Hill order: 1. BrI 2. CH3I 3. C2H5Br 4. H2O4S A list of formulas in Hill system order is arranged alphabetically, as above, with single-letter elements coming before two-letter symbols when the symbols begin with the same letter (so B comes before Be, which comes before Br). External links 

Hill notation example, from the University of Massachusetts Lowell libraries, including how to sort into Hill system order

Text here.

Chapter 8: Homology (chemistry) In chemistry, homology refers to the appearance of homologues. A homologue (also spelled as homolog) is a compound belonging to a series of compounds differing from each other by a repeating unit, such as a methylene bridge −CH 2−, a peptide residue, etc.

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serine

homoserine A homolog is a special case of an analog. Examples are alkanes and compounds with alkyl sidechains of different length (the repeating unit being a methylene group -CH2-). Periodic table On the periodic table, homologous elements share many electrochemical properties and appear in the same group (column) of the table. For example, all noble gases are colorless, monatomic gases with very low reactivity. These similarities are due to similar structure in their outer shells of valence electrons. Mendeleev used the prefix eka- for an unknown element below a known one in the same group. See also 

Homologous series

Analog

Congener

Structure-activity relationship

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Chapter 8: International Chemical Identifier

InChI Developer(s)

InChI Trust

Initial release

April 15, 2005

Stable release

1.04 / September 2011

Development status Active Operating system

Microsoft Windows and Unix-like

Platform

IA-32 and x86-64

Size

4.3 MB

Available in

English

License

IUPAC / InChI Trust Licence

Website

http://www.iupac.org/home/publications/e-resources/inchi.html

The IUPAC International Chemical Identifier (InChI /ˈɪntʃiː/ IN-chee or /ˈɪŋkiː/ ING-kee) is a textual identifier for chemical substances, designed to provide a standard and humanreadable way to encode molecular information and to facilitate the search for such information in databases and on the web. Initially developed by IUPAC and NIST during 2000–2005, the format and algorithms are non-proprietary. The continuing development of the standard has been supported since 2010 by the not-for-profit InChI Trust, of which IUPAC is a member. The current version is 1.04 and was released in September 2011. Prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Overview The identifiers describe chemical substances in terms of layers of information — the atoms and their bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information. Not all layers have to be provided; for instance, the tautomer layer can be omitted if that type of information is not relevant to the particular application. InChIs differ from the widely used CAS registry numbers in three respects:

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they are freely usable and non-proprietary;

they can be computed from structural information and do not have to be assigned by some organization;

most of the information in an InChI is human readable (with practice).

InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names. They can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI; for this purpose a format such as PDB can be used. The InChI algorithm converts input structural information into a unique InChI identifier in a three-step process: normalization (to remove redundant information), canonicalization (to generate a unique number label for each atom), and serialization (to give a string of characters). The InChIKey, sometimes referred to as a hashed InChI, is a fixed length (25 character) condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds, since these were problematic with the full-length InChI. It should be noted that, unlike the InChI, the InChIKey is not unique: though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released. This provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string. The standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Format and layers InChI format Internet media type chemical/x-inchi Type of format

chemical file format

Every InChI starts with the string "InChI=" followed by the version number, currently 1. This is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, with each layer providing one specific type of information. The layers and sub-layers are separated by the delimiter "/" and start with a characteristic prefix letter (except for the chemical formula sub-layer of the main layer). The six layers with important sublayers are: 1. Main layer o

Chemical formula (no prefix). This is the only sublayer that must occur in every InChI.

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o

Atom connections (prefix: "c"). The atoms in the chemical formula (except for hydrogens) are numbered in sequence; this sublayer describes which atoms are connected by bonds to which other ones.

o

Hydrogen atoms (prefix: "h"). Describes how many hydrogen atoms are connected to each of the other atoms.

2. Charge layer o

proton sublayer (prefix: "p" for "protons")

o

charge sublayer (prefix: "q")

3. Stereochemical layer o

double bonds and cumulenes (prefix: "b")

o

tetrahedral stereochemistry of atoms and allenes (prefixes: "t", "m")

o

type of stereochemistry information (prefix: "s")

4. Isotopic layer (prefixes: "i", "h", as well as "b", "t", "m", "s" for isotopic stereochemistry) 5. Fixed-H layer (prefix: "f"); contains some or all of the above types of layers except atom connections; may end with "o" sublayer; never included in standard InChI 6. Reconnected layer (prefix: "r"); contains the whole InChI of a structure with reconnected metal atoms; never included in standard InChI The delimiter-prefix format has the advantage that a user can easily use a wildcard search to find identifiers that match only in certain layers. Examples

CH3CH2OH

InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3

ethanol InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 (standard InChI)

InChI=1/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,710H,1H2/t2-,5+/m0/s1 InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,1011H,1H2/t2-,5+/m0/s1 (standard InChI) L-ascorbic acid

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Chapter 9: InChIKey

Morphine structure The condensed, 27 character standard InChIKey is a hashed version of the full standard InChI (using the SHA-256 algorithm), designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, which are not searchable for chemical content. The full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. There is a very small, but finite chance of two different molecules having the same InChIKey, but the probability for duplication of only the first 14 characters has been estimated as only one duplication in 75 databases each containing one billion unique structures. With all databases currently having below 50 million structures, such duplication appears unlikely at present. A recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indicating the version of InChI used, another hyphen, followed by single checksum character. Example: Morphine has the structure shown on right. The standard InChI for morphine is InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4-2-9(14(15)17)811(10)18/h2-5,10-11,13,16,19-20H,6-8H2,1H3/t10-,11+,13-,16-,17-/m0/s1 and the standard InChIKey for morphine is BQJCRHHNABKAKU-KBQPJGBKSA-N. InChI Resolvers As the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure. InChI Resolvers act as a lookup service to make these links, and prototype services are available from NCI, PubChem and ChemSpider Name The format was originally called IChI (IUPAC Chemical Identifier), then renamed in July 2004 to INChI (IUPAC-NIST Chemical Identifier), and renamed again in November 2004 to InChI (IUPAC International Chemical Identifier), a trademark of IUPAC.

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Continuing development Scientific direction of the InChI standard is carried out by the IUPAC Division VIII Subcommittee, and funding of subgroups investigating and defining the expansion of the standard is carried out by both IUPAC and the InChI Trust. The InChI Trust funds the development, testing and documentation of the InChI. Current extensions are being defined to handle polymers and mixtures, Markush structures, reactions and organometallics, and once accepted by the Division VIII Subcommittee will be added to the algorithm. Adoption The InChI has been adopted by many larger and smaller databases, including ChemSpider and PubChem. However, the adoption is not straightforward, and many databases show a discrepancy between the chemical structures and the InChI they contain, which is a problem for linking databases. See also 

Molecular Query Language

Simplified molecular-input line-entry system (SMILES)

Molecule editor

SYBYL Line Notation

External links

Documentation and presentations 

InChI Trust site

IUPAC InChI site

Unofficial InChI FAQ

InChI Technical Manual PDF (335 KB)

[1]

Description of the canonicalization algorithm

Googling for InChIs a presentation to the W3C.

The Semantic Chemical Web: GoogleInChI and other Mashups, Google Tech Talk by Peter Murray-Rust, 13 Sept 2006

IUPAC InChI, Google Tech Talk by Steve Heller and Steve Stein, 2 November 2006

InChI Release 1.02 InChI final version 1.02 and explanation of Standard InChI, January 2009

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Software and services 

NCI/CADD Chemical Identifier Resolver Generates and resolves InChI/InChIKeys and many other chemical identifiers

ChemSpider InChI resolver

Search Google for molecules (generates InChI from interactive chemical and searches Google for any pages with embedded InChIs). Requires Javascript enabled on browser

ChemSketch, free chemical structure drawing package that includes input and output in InCHI format

PubChem online molecule editor that supports SMILES/SMARTS and InChI

ChemSpider Services that allows generation of InChI and conversion of InChI to structure (also SMILES and generation of other properties)

MarvinSketch from ChemAxon, implementation to draw structures (or open other file formats) and output to InChI file format

BKchem implements its own InChI parser and uses the IUPAC implementation to generate InChI strings

CompoundSearch implements an InChI and InChI Key search of spectral libraries

JNI-InChI Java library that wraps the InChI library

the Chemistry Development Kit uses JNI-InChI to generate InChIs, can convert InChIs into structures, and generate tautomers based on the InChI algorithms

Bioclipse generates InChI and InChIKeys for drawn structures or opened files

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Chapter 10: International Union of Pure and Applied Chemistry International Union of Pure and Applied Chemistry

Abbreviation

IUPAC

Motto

Advancing Chemistry Worldwide

Formation

1919

Type

International chemistry standards organization

Location

Zürich, Switzerland

Region served

Worldwide

Official languages English President

Kazuyuki Tatsumi

Website

iupac.org

The International Union of Pure and Applied Chemistry (IUPAC, on lowercase letters: iupac, /ˈaɪjuːpæk/ EYE-ew-pak or /ˈjuːpæk/ EW-pak) is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Council for Science (ICSU). The international headquarters of IUPAC is located in Zürich, Switzerland. The administrative office, known as the "IUPAC Secretariat", is located in Research Triangle Park, North Carolina, United States. This administrative office is headed by the IUPAC executive director. As of 1 August 2012, the Executive Director is Dr. John D. Petersen.

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IUPAC was established in 1919 as the successor of the International Congress of Applied Chemistry for the advancement of chemistry. Its members, the National Adhering Organizations, can be national chemistry societies, national academies of sciences, or other bodies representing chemists. There are fifty-four National Adhering Organizations and three Associate National Adhering Organizations. IUPAC's Inter-divisional Committee on Nomenclature and Symbols (IUPAC nomenclature) is the recognized world authority in developing standards for the naming of the chemical elements and compounds. Since its creation, IUPAC has been run by many different committees with different responsibilities. These committees run different projects which include standardizing nomenclature, finding ways to bring chemistry to the world, and publishing works. IUPAC is best known for its works standardizing nomenclature in chemistry and other fields of science, but IUPAC has publications in many fields including chemistry, biology and physics. Some important work IUPAC has done in these fields includes standardizing nucleotide base sequence code names; publishing books for environmental scientists, chemists, and physicists; and leading the way in improving education in science. IUPAC is also known for standardizing the atomic weights of the elements through one of its oldest standing committees, the Commission on Isotopic Abundances and Atomic Weights. Creation and history

Friedrich August KekulĂŠ von Stradonitz The need for an international standard for chemistry was first addressed in 1860 by a committee headed by German scientist Friedrich August KekulĂŠ von Stradonitz. This committee was the first international conference to create an international naming system for organic compounds. The ideas that were formulated in that conference evolved into the official IUPAC nomenclature of organic chemistry. The IUPAC stands as a legacy of this meeting, making it one of the most important historical international collaborations of chemistry societies. Since this time, IUPAC has been the official organization held with the responsibility of updating and maintaining official organic nomenclature. IUPAC as such was established in 1919. One notable country excluded from this early IUPAC was Germany. Germany's exclusion was a result of prejudice towards Germans by the allied powers after World War I.Germany was finally admitted into IUPAC during 1929. However, Nazi Germany was removed from IUPAC during World War II. During World War II, IUPAC was affiliated with the allied powers, but had little involvement during the war effort itself. After the war, West Germany was allowed back into IUPAC. Since World War II, IUPAC has been focused on standardizing nomenclature and methods in science without interruption.

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Committees and governance IUPAC is governed by several committees that all have different responsibilities. The committees are as follows: Bureau, CHEMRAWN (Chem Research Applied to World Needs) Committee, Committee on Chemistry Education, Committee on Chemistry and Industry, Committee on Printed and Electronic Publications, Evaluation Committee, Executive Committee, Finance Committee, Interdivisional Committee on Terminology, Nomenclature and Symbols, Project Committee, Pure and Applied Chemistry Editorial Advisory Board. Each committee is made from members of different National Adhering Organizations from different countries. The steering committee hierarchy for IUPAC is as follows: 1. All committees have an allotted budget that they must adhere to 2. Any committee may start a project. 3. If a project's spending becomes too much for a committee to continue funding, it must take the issue to the Project Committee. 4. The project committee either increases the budget or decides on an external funding plan. 5. The Bureau and Executive Committee oversee operations of the other committees Committees Table Committee

name Responsibilities

(abbreviation) Bureau

Physical and Biophysical

Discusses and makes changes to which committee has authority over a specific project

Controls finances for all other committees and IUPAC as a whole

Discusses general governance of IUPAC

Organize and promote the international collaboration between scientists in physical and biophysical chemistry and related fields.

Inorganic and inorganic materials chemistry, Isotopes and atomic weights, Periodic Table

Promote the goals of IUPAC in the field of organic and biomolecular chemistry in the broadest sense.

Chemistry Division (Division I) Inorganic

Chemistry

Division (Division II) Organic and Biomolecular Chemistry Division (Division III)

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Polymer Division (Division

Science and technology of macromolecules and polymers.

General aspects of analytical chemistry, separation methods, spectrochemical methods, electrochemical methods, nuclear chemistry methods, applications to human health and the environment.

To provide unbiased and timely authoritative reviews on the behavior of chemical compounds in food and the environment.

Medicinal and clinical chemistry

Chemical Nomenclature and Structure Representation Division (Division VIII)

Maintains and develops standard systems for designating chemical structures, including both conventional nomenclature and computer-based systems.

CHEMRAWN

Discusses different ways chemistry can and should be used to help the world

Coordinates IUPAC chemistry research with the educational systems of the world

Coordinates IUPAC chemistry research with industrial chemistry needs

Designs and implements IUPAC publications

Heads the Subcommittee on Spectroscopic Data Standards

Evaluates every project

Reports back to Executive committee on every project

Plans and discusses IUPAC events

Discusses IUPAC fundraising

Reviews other committees work

IV) Analytical

Chemistry

Division (Division V)

Chemistry

and

Environment

the Division

(Division VI) Chemistry

and

Human

Health Division (Division VII)

Committee

(Chem Research Applied to World Needs) Committee on Chemistry Education (CCE) Committee on Chemistry and Industry (COCI) Committee on Electronic and

Printed

Publications

(CPEP) Evaluation

Committee

(EvC) Executive Committee (EC)

Current Officers of Executive Committee:

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Finance Committee (FC)

Interdivisional

Committee

on Terminology (ICTNS)

Project Committee (PC)

Pure

and

Chemistry

Applied Editorial

President: Moreau, Nicole J.

Vice President: Tatsumi, Kazuyuki

Treasurer: Corish, John

Secretary General: Black, David StC.

Helps other committees properly manage their budget

Advises Union officers on investments

Manages IUPAC Nomenclature

Works through nomenclature

Standardizes measurements

Discusses atomic weight standardization

Manages funds that are under the jurisdiction of multiple projects

Judges if a project is too large for its funding

Recommends sources of external funding for projects

Decides how to fund meetings in developing countries and countries in crisis

Helps to plan, implement, and publish Pure and Applied Chemistry

many

projects

to

standardize

Advisory Board (PAC-EAB)

Nomenclature The IUPAC committee has a long history of officially naming organic and inorganic compounds as mentioned in the Creation and History section. IUPAC nomenclature is developed so that any compound can be named under one set of standard rules to avoid repeat names. The first publication, which is information from the International Congress of Applied Chemistry, is on IUPAC nomenclature of organic compounds can be found from the early 20th century in A Guide to IUPAC Nomenclature of Organic Compounds (1900). Organic nomenclature IUPAC organic nomenclature has three basic parts: the substituents, carbon chain length and chemical ending. The substituents are any functional groups attached to the main carbon chain. The main carbon chain is the longest possible continuous chain. The chemical ending denotes what type of molecule it is. For example, the ending "ane" denotes a single bonded carbon chain, as in "hexane" (C

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6H 14). Another example of IUPAC organic nomenclature is cyclohexanol:

Cyclohexanol 

The substituent name for a ring compound is "cyclo".

The indication (substituent name) for a six carbon chain is "hex".

The chemical ending for a single bonded carbon chain is "ane"

The chemical ending for an alcohol is "ol"

The two chemical endings are combined for an ending of "anol" indicating a single bonded carbon chain with an alcohol attached to it.

Inorganic nomenclature Basic IUPAC inorganic nomenclature has two main parts: the cation and the anion. The cation is the name for the positively charged ion and the anion is the name for the negatively charged ion. An example of IUPAC nomenclature of inorganic chemistry is potassium chlorate (KClO3):

Potassium chlorate 

Potassium is the cation name.

Chlorate is the anion name.

Amino acid and nucleotide base codes IUPAC also has a system for giving codes to identify amino acids and nucleotide bases. IUPAC needed a coding system that represented long sequences of amino acids. This would allow for these sequences to be compared to try to find homologies. These codes can consist of either a one letter code or a three letter code. For example:

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

Alanine: Single letter code: A, Three letter code: Ala

These codes make it easier and shorter to write down the amino acid sequences that make up proteins. The nucleotide bases are made up of purines (adenine and guanine) and pyrimidines (cytosine and thymine or uracil). These nucleotide bases make up DNA and RNA. These nucleotide base codes make the genome of an organism much smaller and easier to read. Publications

Non-series books Book Name

Description

Principles

and Principles and Practices of Method Validation is a book entailing Practices of Method methods on validating and analyzing a many analytes taken from a single aliquot. Also, this book goes over techniques for analyzing Validation many samples at once. Some methods discussed include: chromatographic methods, estimation of effects, matrix induced effects, and the effect of an equipment setup on an experiment. Fundamental

Fundamental Toxicology is a textbook that proposes a curriculum for toxicology courses.Fundamental Toxicology is based on the book Fundamental Toxicology for Chemists.Fundamental Toxicology is enhanced through many revisions and updates. New information added in the revisions includes: risk assessment and management; reproductive toxicology; behavioral toxicology; and ecotoxicology. This book is relatively well received as being useful for reviewing chemical toxicology.

Toxicology

Macromolecular Symposia

Macromolecular Symposia is a journal that publishes fourteen issues a year. This journal includes contributions to the macromolecular chemistry and physics field. The meetings of the IUPAC are included in this journal along with the European Polymer Federation, the American Chemical Society, and the Society of Polymer Science in Japan.

Experimental Thermodynamics book series The Experimental Thermodynamics books series covers many topics in the fields of thermodynamics. Book Measurement

Description of

the Measurement of the Transport Properties of Fluids is a book that is Transport Properties of published by Blackwell Science Inc. The topics that are included in this book are low and high temperature measurements, secondary Fluids coefficients, diffusion coefficients, light scattering, transient methods for thermal conductivity, methods for thermal conductivity, falling-body viscometers, and vibrating viscometers.

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Solution Calorimetry

Solution Calorimetry is a book that gives background information on thermal analysis and calorimetry. Thermoanalytical and calorimetric techniques along with thermodynamic and kinetic properties are discussed in this book. Later volumes of this book discusses the applications and principles of these thermodynamic and kinetic methods.

Equations of State for Equations of State for Fluids and Fluid Mixtures Part I is a book Fluids and Fluid that gives up to date equations of state for fluids and fluid mixtures. This book covers all ways to develop equations of state. It gives Mixtures Part I the strengths and weaknesses of each equation. Some equations discussed include: virial equation of state cubic equations; generalized Van der Waals equations; integral equations; perturbation theory; and stating and mixing rules. Other things that Equations of State for Fluids and Fluid Mixtures Part I goes over are: associating fluids, polymer systems, polydisperse fluids, selfassembled systems, ionic fluids, and fluids near their critical points. Measurement

of

the Measurement of the Thermodynamic Properties of Single Phases is a book that gives an overview of techniques for measuring the Thermodynamic thermodynamic quantities of single phases. It also goes into Properties of Single experimental techniques to test many different thermodynamic states precisely and accurately. Measurement of the Phases Thermodynamic Properties of Single Phases was written for people interested in measuring thermodynamic properties. Measurement

of

the Measurement of the Thermodynamic Properties of Multiple Phases is a book that includes multiple techniques that are used to study Thermodynamic multiple phases of pure component systems. Also included in this Properties of Multiple book are the measurement techniques to obtain activity coefficients, interfacial tension, and critical parameters. This book Phases was written for researchers and graduate students as a reference source. Series of books on analytical and physical chemistry of environmental systems Book Name

Description

Atmospheric Particles

Atmospheric Particles is a book that delves into aerosol science. This book is aimed as a reference for graduate students and atmospheric researchers. Atmospheric Particles goes in depth on the properties of aerosols in the atmosphere and their effect. Topics covered in this book are: acid rain; heavy metal pollution; global warming; and photochemical smog. Atmospheric Particles also covers techniques to analyze the atmosphere and ways to take atmospheric samples.

Environmental Particles: Separation

Colloids

and Environmental Colloids and Particles: Behaviour, Behaviour, Separation and Characterisation is a book that discusses environmental colloids and current information available and on them. This book focuses on environmental colloids and particles in aquatic systems and soils. It also goes over techniques such as: techniques for sampling

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Characterisation

Biophysical

Chemistry

Interactions

Between

environmental colloids, size fractionation, and how to characterize of colloids and particles. Environmental Colloids and Particles: Behaviour, Separation and Characterisation also delves into how these colloids and particles interact.

of Biophysical Chemistry of Fractal Structures and Processes Fractal Structures and in Environmental Systems is meant to give an overview of a technique based on fractal geometry and the processes Processes in Environmental of environmental systems. This book gives ideas on how to use fractal geometry to compare and contrast different Systems ecosystems. It also gives an overview of the knowledge needed to solve environmental problems. Finally, Biophysical Chemistry of Fractal Structures and Processes in Environmental Systems shows how to use the fractal approach to understand the reactivity of flocs, sediments, soils, microorganisms and humic substances. Soil Interactions Between Soil Particles and Microorganisms: Particles and Microorganisms: Impact on the Terrestrial Ecosystem is meant to be read by chemists and biologists that study environmental Impact on the Terrestrial systems. Also, this book should be used as a reference for earth scientists, environmental geologists, environmental Ecosystem engineers, and professionals in microbiology and ecology. Interactions Between Soil Particles and Microorganisms: Impact on the Terrestrial Ecosystem is about how minerals, microorganisms, and organic components work together to affect terrestrial systems. This book identifies that there are many different techniques and theories about minerals, microorganisms, and organic components individually, but they aren't often associated with each other. It further goes on to discuss how these components of soil work together to affect terrestrial life. Interactions Between Soil Particles and Microorganisms: Impact on the Terrestrial Ecosystem gives techniques to analyze minerals, microorganisms, and organic components together. This book also gives a large sections on why environmental scientists working in the specific fields of minerals, microorganisms, and organic components of soil should work together and how they should do so. The Biogeochemistry of Iron in The Biogeochemistry of Iron in Seawater is a book that describes how low concentrations of iron in Antarctica and Seawater the Pacific Oceans are a result of reduced chlorophyll for phytoplankton production. It does this by reviewing information from research in the 1990s. This book goes in depth about: chemical speciation; analytical techniques; transformation of iron; how iron limits the development of High Nutrient Low Chlorophyll areas in the pacific ocean In Situ Monitoring of Aquatic In Situ Monitoring of Aquatic Systems: Chemical Analysis Systems: Chemical Analysis and Speciation is a book that discusses techniques and devices to monitor aquatic systems and how new devices and Speciation and techniques can be developed. This book emphasizes the future us of micro-analytical monitoring techniques and microtechnology. In Situ Monitoring of Aquatic Systems:

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Chemical Analysis and Speciation is aimed at researchers and laboratories that analyze aquatic systems such as rivers, lakes, and oceans. Structure

Surface Structure and Surface Reactions of Soil Particles is a book about soil structures and the molecular processes that Reactions of Soil Particles occur in soil. Structure and Surface Reactions of Soil Particles is aimed at any researcher researching soil or someone in the field of anthropology. It goes in depth on topics such as: fractal analysis of particle dimensions; computer modeling of the structure; reactivity of humics; applications of atomic force microscopy; and advanced instrumentation for analysis of soil particles. Metal

and

Speciation

and Metal Speciation and Bioavailability in Aquatic Systems, Bioavailability in Aquatic Series on Analytical and Physical Chemistry of Environmental Systems Vol. 3 is a book about the effect of Systems, Series on Analytical trace metals on aquatic life. This book is considered a and Physical Chemistry of specialty book for researchers interested in observing the effect of trace metals in the water supply. This book Environmental Systems Vol. 3 includes techniques to assess how bioassays can be used to evaluate how an organism is affected by trace metals. Also, Metal Speciation and Bioavailability in Aquatic Systems, Series on Analytical and Physical Chemistry of Environmental Systems Vol. 3 looks at the limitations of the use of bioassays to observe the effects of trace metals on organisms. Physicochemical Kinetics and Physicochemical Kinetics and Transport at Biointerfaces is a book created to aid environmental scientists in field Transport at Biointerfaces work. The book gives an overview of chemical mechanisms, transport, kinetics, and interactions that occur in environmental systems. Physicochemical Kinetics and Transport at Biointerfaces continues from where Metal Speciation and Bioavailability in Aquatic Systems leaves off. Colored cover book and website series (nomenclature) IUPAC color codes their books in order to make each publication distinguishable. Title

Description

Compendium Analytical Nomenclature

Pure

and

of One extensive book on almost all nomenclature written (IUPAC nomenclature of organic chemistry and IUPAC nomenclature of inorganic chemistry) by the IUPAC committee is Compendium of Analytical Nomenclature – The Orange Book, 1st edition (1978) This book was revised in 1987. The second edition has many revisions that come from reports on nomenclature between 1976 and 1984. In 1992, the second edition went through many different revisions which led to the third edition.

Applied Pure and Applied Chemistry is the official monthly journal of IUPAC. This journal debuted in 1960. The goal statement for Pure and

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Chemistry (journal) Applied Chemistry is to "publish highly topical and credible works at the forefront of all aspects of pure and applied chemistry." The Journal itself is available by subscription, but older issues are available in the archive on the IUPAC website. Pure and Applied Chemistry was created as a central way to publish IUPAC endorsed articles. Before its creation, IUPAC didn't have a quick, official way to distribute new chemistry information. Its creation was first suggested at The Paris IUPAC Meeting of 1957. During this meeting the commercial publisher of the Journal was discussed and decided on. In 1959, the IUPAC Pure and Applied Chemistry Editorial Advisory Board was created put in charge of the journal. The idea of one journal being a definitive place for a vast amount of chemistry was difficult for the committee to grasp at first. However, it was decided that the journal would reprint old journal editions to keep all chemistry knowledge available. Compendium Chemical Terminology

of The Compendium of Chemical Terminology, also known as The Gold Book, was originally worked on by Victor Gold. This book is a collection of names and terms already discussed in Pure and Applied Chemistry.Compendium of Chemical Terminology was first published in 1987. The first edition of this book contains no original material, but is meant to be a compilation of other IUPAC works. The second edition of this book was published in 1997. This book made large changes to the first edition of the Compendium of Chemical Terminology. These changes included updated material and an expansion of the book to include over seven thousand terms. The second edition was the topic of an IUPAC XML project. This project made an XML version of the book that includes over seven thousand terms. The XML version of the book includes an open editing policy, which allows users to add excerpts of the written version. IUPAC Nomenclature of Organic Chemistry, also known as The Blue

IUPAC Nomenclature Organic

of Book, is a website published by Advanced Chemistry Department

Chemistry Incorporated with the permission of IUPAC. This site is a compilation

(online publication) of the books A Guide to IUPAC Nomenclature of Organic Compounds and Nomenclature of Organic Chemistry.

International Year of Chemistry

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International Year of Chemistry Logo IUPAC and UNESCO are the lead organizations coordinating events for the International Year of Chemistry, which took place in 2011. The International Year of Chemistry was originally proposed by IUPAC at the General Assembly in Turin, Italy. This motion was adopted by UNESCO at a meeting in 2008. The main objectives of the International Year of Chemistry is to increase public appreciation of chemistry and gain more interest in the world of chemistry. This event is also being held to encourage young people to get involved and contribute to chemistry. A further reason for this event being held is to honour how chemistry has made improvements to everyone's way of life. Current projects

IUPAC current project list 

Project Number 2009-012-2-200: Coordination polymers and metal organic frameworks: terminology and nomenclature guidelines o

Project Number 2009-032-1-100: Categorizing Halogen Bonding and Other Noncovalent Interactions Involving Halogen Atoms o

The objective of this project is to identify new pollutants and their hazards and to monitor less investigated pollutants. Also, this project will provide strategies for how pollutants should be monitored. The advantages and disadvantages of each monitoring technique will be discussed.

Project Number 2009-034-2-700: Risk Assessment of Effects of Cadmium on Human Health o

The objective of this project is to give a modern definition to the term halogen bonding and to examine and classify halogens as electrophilic species and their intermolecular interactions.

Project Number 2009-048-1-600: Guidance for substance-related environmental monitoring strategies regarding soil and surface water o

The objectives of this project are (1) to produce guidelines for terminology (glossary of terms) and nomenclature (concerning topology, not naming of individual substances) in the area of coordination polymers, (2) to ensure that these guidelines are accepted by a large group of leading researchers in the field, and (3) to have these guidelines implemented or referred to in the instructions to authors of leading general and inorganic chemistry journals.

The objective of this project is to identify the risks and effects of exposure of humans to Cadmium, which is classified as a carcinogenic to humans by the International Agency for Research on Cancer. Also, the objective includes researching how Cadmium enters into the human body.

Project Number 2009-019-2-400: Data Treatment in SEC and Other Techniques of Polymer Characterization. Correction for Band Broadening and Other Sources of Error.

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o

The objective of this project is to provide practical alternatives for improving the accuracy of polymer characterization and measurements. This would allow manufacturers of equipment, such as Size exclusive chromatography (SEC) and other polymer characterization techniques, to sell a product that is more accurate and precise.

See also 

CAS registry number

Chemical nomenclature

Commission on Isotopic Abundances and Atomic Weights

European Association for Chemical and Molecular Sciences

Institute for Reference Materials and Measurements (IRMM)

International Chemical Identifier (InChI)

International Union of Biochemistry and Molecular Biology (IUBMB)

List of chemical elements naming controversies

National Institute of Standards and Technology (NIST)

Simplified molecular-input line-entry system (SMILES)

External links 

Official website

Panel on Biochemical Thermodynamics (1994). "Recommendations for nomenclature and tables in biochemical thermodynamics". G. P. Moss, Queen Mary University of London.

Chapter 11: Monosaccharide nomenclature Monosaccharide nomenclature is a set of conventions used in chemistry to name the compounds known as monosaccharides or "simple sugars" — the basic structural units of carbohydrates, which cannot be hydrolysed into simpler units. Systematic name of molecular graph The elementary formula of a simple monosaccharide is CnH2nOn, where the integer n is at least 3 and rarely greater than 7. Simple monosaccharides may be named generically according on the number of carbon atoms n: trioses, tetroses, pentoses, hexoses, etc.

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Every simple monosaccharide has an acyclic (open chain) form, which can be written as H(CH(OH))x-(C=O)-(CH(OH))y-H; that is, a straight chain of carbon atoms, one of which is a carbonyl group, all the others bearing a hydrogen -H and a hydroxyl -OH each, with one extra hydrogen at either end. The carbons of the chain are conventionally numbered from 1 to n, starting from the end which is closest to the carbonyl. If the carbonyl is at the very beginning of the chain (carbon 1), the monosaccharide is said to be an aldose, otherwise it is a ketose. These names can be combined with the chain length prefix, as in aldohexose or ketopentose. Most ketoses found in nature have the carbonyl in position 2; when that is not the case, one uses a numeric prefix to indicate the carbonyl's position. Thus for example, aldohexose means H(C=O)(CHOH) 5H, ketopentose means H(CHOH)(C=O)(CHOH)3H, and 3-ketopentose means H(CHOH)2(C=O)(CHOH)2H. An alternative nomenclature uses the suffix '-ose' only for aldoses, and '-ulose' for ketoses. The position of the carbonyl (when it is not 1 or 2) is indicated by a numerical infix. For example, hexose in this nomenclature means H(C=O)(CHOH) 5H, pentulose means H(CHOH)(C=O)(CHOH)3H, and hexa-3-ulose means H(CHOH)2(C=O)(CHOH)3H. Naming of acyclic stereoisomers Open-chain monosaccharides with same molecular graph may exist as two or more stereoisomers. The Fischer projection is a systematic way of drawing the skeletal formula of an open-chain monosaccharide so that each stereoisomer is uniquely identified. Two isomers whose molecules are mirror-images of each other are identified by prefixes 'D-' or 'L-', according to the handedness of the chiral carbon atom that is farthest from the carbonyl. In the Fischer projection, that is the second carbon from the bottom; the prefix is 'D-' or 'L-' according to whether the hydroxyl on that carbon lies to the right or left of the backbone, respectively. If the molecular graph is symmetrical (H(CHOH)x(CO)(CHOH)xH) and the two halves are mirror images of each other, then the molecule is identical to its mirror image, and there is no 'L-' form. A distinct common name, such as "glucose" or "ribose", is traditionally assigned to each pair of mirror-image stereoisomers, and to each achiral stereoisomer. These names have standard three-letter abbreviations, such as 'Glc' for glucose and 'Rib' for ribose. Another nomenclature uses the systematic name of the molecular graph, a 'D-' or 'L-' prefix to indicate the position of the last chiral hydroxyl on the Fischer diagram (as above), and another italic prefix to indicate the positions of the remaining hydroxyls relative to the first one, read from bottom to top in the diagram, skipping the keto group if any. These prefixes are attached to the systematic name of the molecular graph. So for example, D-glucose is Dgluco-hexose, D-ribose is D-ribo-pentose, and D-psicose is D-ribo-hexulose. Note that, in this nomenclature, mirror-image isomers differ only in the 'D'/'L' prefix, even though all their hydroxyls are reversed.

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The following tables shows the Fischer projections of selected monosaccharides (in openchain form), with their conventional names. The table shows all aldoses with 3 to 6 carbon atoms, and a few ketoses. For chiral molecules, only the 'D-' form (with the next-to-last hydroxyl on the right side) is shown; the corresponding forms have mirror-image structures. Some of these monosaccharides are only synthetically prepared in the laboratory and not found in nature.

Aldotrioses Trioses D-Glyceraldehyde

Aldotetroses Tetroses D-Erythrose

D-Threose

erythro-

threo-

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Aldopentoses Pentoses D-Ribose

D-Arabinose

D-Xylose

D-Lyxose

ribo-

arabino-

xylo-

lyxo-

Rib

Ara

Xyl

Lyx

Aldohexoses Hexoses D-Allose

D-Altrose

D-Glucose

D-Mannose

D-Gulose

D-Idose

D-Galactose

D-Talose

allo-

altro-

gluco-

manno-

gulo-

ido-

galacto-

talo-

All

Alt

Glc

Man

Gul

Ido

Gal

Tal

Names of aldoses

Names of ketoses Ketotrioses Triuloses

Glycerone

Ketotetrose Tetruloses

D-Erythrulose glycero-

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Ketopentoses Pentuloses

D-Ribulose

D-Xylulose

erythro-

threo-

Rul

Xul

D-Psicose D-Fructose

D-Sorbose

D-Tagatose

ribo-

arabino-

xylo-

lyxo-

Psi

Fru

Sor

Tag

Ketohexoses Hexuloses

Names of 3-ketoses 3Ketopentoses SYM-3-Ketopentose

D-UNS-3-Ketopentose

Penta-3uloses 3Ketohexoses D-RRR-3Hexa-3-

D-RRL-3-

D-RLR-3-

D-RLL-3-

D-LRR-3-

D-LRL-3-

D-LLR-3-

D-LLL-3-

Ketohexose Ketohexose Ketohexose Ketohexose Ketohexose Ketohexose Ketohexose Ketohexose

uloses

Cyclic forms For monosaccharides in their cyclic form, an infix is placed before the '-ose', '-ulose', or 'nulose' suffix to specify the ring size. The infix is "furan" for a 5-atom ring, "pyran" for 6, "septan" for 7, and so on). Ring closure creates another chiral center at the anomeric carbon (the one with the hemiacetal or acetal functionality), and therefore each open-chain stereoisomer gives rise to

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two distinct stereoisomers (anomers). These are identified by the prefixes 'α-' and 'β-', according to the configuration of the anomeric carbon relative to that of furthest stereocenter along the open chain. To determine if the sugar is α or β, the structure is drawn in a Fischer projection; if the endocyclic oxygen (O5) and exocyclic oxygen (O1) are cis, the sugar is α; if they are trans, the sugar is β.

Examples

Glycosides Glycosides are saccharides in which the hydroxyl -OH at the anomeric centre is replaced by an oxygen-bridged group -OR. The carbohydrate part of the molecule is called glycone, the -O- bridge is the glycosisdic oxygen, and the attached group is the aglycone. Glycosides are named by giving the aglyconic alcohol HOR, followed by the saccahride name with the 'e' ending replaced by '-ide'; as in [[phenol D-glucopyrnoside]].

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Modified Sugars

Deoxy sugars Modification of sugar is generally done by replacing one or more –OH group with other functional groups at all position except C-1. Since all these cases involves the removal of an –OH group, they are all deoxy sugars. Rules for Nomenclature of Modified Sugars: 

State the Sugar is deoxy sugar.

Specify the position of deoxygenation.

If there is a substituent other than H in the place of –OH, specify what it is.

Specify the relative configuration of all stereogenic centres (manno, gluco etc.).

Specify the ring size (furanose, pyranose etc.) and anomeric configuration ( a or b).

State the chain length only in situation where –OH is replaced with H.

Alphabetize all the substituent groups (deoxy, -iodo, -amino etc.). Di-, tri- etc. prefixes do not count.

Examples

Protected Sugars Sugars in which –OH is protected by some modification are called protected sugars. Rules for Nomenclature for Protected Sugars: 

Specify the number of particular protecting groups (di, tri, tetra etc.).

List groups alphabetically along with all other substituents ( di, tri prefixes do not count).

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See also 

Carbohydrate conformation

Polysaccharide

Oligosaccharide

Oligosaccharide nomenclature

Chapter 12: Noble metal

A collection of the noble metals, including copper, rhenium and mercury, which are included by some definitions. These are arranged according to their position in the periodic table. The noble metals are metals that are resistant to corrosion and oxidation in moist air, unlike most base metals. They tend to be precious, often due to their rarity in the Earth's crust. The noble metals are most commonly considered to be ruthenium, rhodium, palladium, silver, osmium, iridium, platinum, and gold. Other sources include mercury,rhenium or copper as a noble metal. On the other hand, titanium, niobium, and tantalum are not included as noble metals, although they especially resist corrosion. Noble metals should not be confused with precious metals (although many noble metals have high value).

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Introduction Palladium, platinum, gold and mercury can be dissolved in aqua regia, a highly concentrated mixture of hydrochloric acid and nitric acid, but iridium and silver cannot. (Silver can dissolve in nitric acid, though.) Ruthenium can be dissolved in aqua regia only when in the presence of oxygen, while rhodium must be in a fine pulverized form. Niobium and tantalum are resistant to acids, including aqua regia. This term can also be used in a relative sense, considering "noble" as an adjective for the word "metal". A "galvanic series" is a hierarchy of metals (or other electrically conductive materials, including composites and semimetals) that runs from noble to active, and allows designers to see at a glance how materials will interact in the environment used to generate the series. In this sense of the word, graphite is more noble than silver and the relative nobility of many materials is highly dependent upon context, as for aluminium and stainless steel in conditions of varying pH. In physics, the definition of a noble metal is even more strict. It is required that the d-bands of the electronic structure are filled. Taking this into account, only copper, silver and gold are noble metals, as all d-like bands are filled and do not cross the Fermi level. For platinum two d-bands cross the Fermi level, changing its chemical behaviour; it is used as a catalyst. The different reactivity can easily be seen during the preparation of clean metal surfaces in an ultra-high vacuum; surfaces of "physically defined" noble metals (e.g., gold) are easy to clean and keep clean for a long time, while those of platinum or palladium, for example, are covered by carbon monoxide very quickly. Notes 

R. R. Brooks, "Noble metals and biological systems: their role in Medicine, Mineral Exploration, and the Environment", CRC Press, 1992

External links 

noble metal - chemistry Encyclopædia Britannica, online edition

To see which bands cross the Fermi level, the Fermi surfaces of almost all the metals can be found at the Fermi Surface Database

The following article might also clarify the correlation between band structure and the term noble metal: Hüger, E.; Osuch, K. (2005). "Making a noble metal of Pd". EPL (Europhysics Letters) 71 (2): 276. Bibcode:2005EL.....71..276H. doi:10.1209/epl/i2005-10075-5.

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Chapter 13: Oligosaccharide nomenclature Oligosaccharides and polysaccharides are an important class of polymeric carbohydrates found in virtually all living entities. Their structural features make their nomenclature challenging and their roles in living systems make their nomenclature important. Oligosaccharides Oligosaccharides are carbohydrates that are composed of several monosaccharide residues joined through glycosidic linkage, which can be hydrolyzed by acid to give the constituent monosaccharide units. While a strict definition of an oligosaccharide is not established, it is generally agreed that a carbohydrate consisting of two to ten monosaccharide residues with a defined structure is an oligosaccharide. Some oligosaccharides, for example maltose, sucrose, and lactose, were trivially named before their chemical constitution was determined, and these names are still used today. 

Maltose

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Sucrose 

Lactose Trivial names, however, are not useful for most other oligosaccharides and, as such, systematic rules for the nomenclature of carbohydrates have been developed. To fully understand oligosaccharide and polysaccharide nomenclature, one must understand how monosaccharides are named. An oligosaccharide has both a reducing and a non-reducing end. The reducing end of an oligosaccharide is the monosaccharide residue with hemiacetal functionality, thereby capable of reducing the Tollens’ reagent, while the non-reducing end is the monosaccharide residue in acetal form, thus incapable of reducing the Tollens’ reagent. The reducing and non-reducing ends of an oligosaccharide are conventionally drawn with the reducing-end monosaccharide residue furthest to the right and the non-reducing (or terminal) end furthest to the left. Naming of oligosaccharides proceeds from left to right (from the non-reducing end to the reducing end) as glycosyl [glycosyl] n glycoses or glycosyl [glycosyl]n glycosides, depending on whether or not the reducing end is a free hemiacetal group. In parentheses, between the names of the monosaccharide residues, the number of the anomeric carbon atom, an arrow symbol, and the number of the carbon atom bearing the connecting oxygen of the next monosaccharide unit are listed. Appropriate symbols are used to indicate the stereochemistry of the glycosidic bonds (α or β), the configuration of the monosaccharide residue (D orL), and the substitutions at oxygen atoms (O).Maltose and a derivative of sucrose illustrate these concepts:

Maltose: α-D-Glucopyranosyl-(1→4)-β-D-glucopyranose

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Methyl 2,3,4-tri-O-benzyl-6-deoxy-6-fluoro-α-D-galactopyranosyl-(1→4)-2,3,6-tri-O-acetyl-βD-glucopyranoside In the case of branched oligosaccharides, meaning that the structure contains at least one monosaccharide residue linked to more than two other monosaccharide residues, terms designating the branches should be listed in square brackets, with the longest linear chain (the parent chain) written without square brackets. The following example will help illustrate this concept:

Allyl α-L-fucopyranosyl-(1→3)-[α-D-galactopyranosyl-(1→4)]-α-D-glucopyranosyl-(1→3)-α-Dgalactopyranoside These systematic names are quite useful in that they provide information about the structure of the oligosaccharide. They do require a lot of space, however, so abbreviated forms are used when possible. In these abbreviated forms, the names of the monosaccharide units are shortened to their corresponding three-letter abbreviations, followed by p for pyranose or f for furanose ring structures, with the abbreviated aglyconic alcohol placed at the end of the name. Using this system, the previous example would have the abbreviated name α-L-Fucp(1→3)-[α-D-Galp-(1→4)]-α-D-Glcp-(1→3)-α-D-GalpOAll.

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Polysaccharides Polysaccharides are considered to be polymers of monosaccharides containing ten or more monosaccharide residues. Polysaccharides have been given trivial names that reflect their origin. Two common examples are cellulose, a main component of the cell wall in plants, and starch, a name derived from the Anglo-Saxon stercan, meaning to stiffen. To name a polysaccharide composed of a single type of monosaccharide, that is a homopolysaccharide, the ending ―-ose‖ of the monosaccharide is replaced with ―-an‖. For example, a glucose polymer is named glucan, a mannose polymer is named mannan, and a galactose polymer is named galactan. When the glycosidic linkages and configurations of the monosaccharides are known, they may be included as a prefix to the name, with the notation for glycosidic linkages preceding the symbols designating the configuration. The following example will help illustrate this concept:

(1→4)-β-D-Glucan A heteropolysaccharide is a polymer containing more than one kind of monosaccharide residue. The parent chain contains only one type of monosaccharide and should be listed last with the ending ―-an‖, and the other types of monosaccharides listed in alphabetical order as ―glyco-‖ prefixes. When there is no parent chain, all different monosaccharide residues are to be listed alphabetically as ―glyco-‖ prefixes and the name should end with ―glycan‖. The following example will help illustrate this concept:

((1→2)-α-D-galacto)-(1→4)-β-D-Glucan

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See also 

Oligosaccharide

Carbohydrate Conformation

Monosaccharide

Monosaccharide nomenclature

Chapter 14: Oxidation state The oxidation state, often called the oxidation number, is an indicator of the degree of oxidation of an atom in a chemical compound. The formal oxidation state is the hypothetical charge that an atom would have if all bonds to atoms of different elements were 100% ionic. Oxidation states are typically represented by integers, which can be positive, negative, or zero. In some cases, the average oxidation state of an element is a fraction, such as 8/3 for iron in magnetite (Fe 3O 4). The highest known oxidation state is +8 in the tetroxides (MO 4) of ruthenium, xenon, osmium, iridium, hassium, plutonium, and curium, while the lowest known oxidation state is −4 for some elements in the carbon group. The increase in oxidation state of an atom through a chemical reaction is known as an oxidation; a decrease in oxidation state is known as a reduction. Such reactions involve the formal transfer of electrons, a net gain in electrons being a reduction and a net loss of electrons being an oxidation. For pure elements, the oxidation state is zero. There are various methods for determining oxidation states/numbers. In inorganic nomenclature the oxidation state is determined and expressed as an oxidation number represented by a Roman numeral placed after the element name. In coordination chemistry, oxidation number is defined differently from oxidation state.

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IUPAC definitions of oxidation state and oxidation number

Oxidation state The current definition of the oxidation state listed by IUPAC is as follows: [Oxidation state] is defined as the charge an atom might be imagined to have when electrons are counted according to an agreed-upon set of rules: 1. the oxidation state of a free element (uncombined element) is zero 2. for a simple (monatomic) ion, the oxidation state is equal to the net charge on the ion 3. hydrogen has an oxidation state of 1 and oxygen has an oxidation state of −2 when they are present in most compounds. (Exceptions to this are that hydrogen has an oxidation state of −1 in hydrides of active metals, e.g. LiH, and oxygen has an oxidation state of −1 in peroxides, e.g. H2O2 4. the algebraic sum of oxidation states of all atoms in a neutral molecule must be zero, while in ions the algebraic sum of the oxidation states of the constituent atoms must be equal to the charge on the ion. Oxidation number in naming of inorganic compounds In the nomenclature of inorganic compounds, the oxidation number is represented by a Roman numeral. The oxidation number is equal to the oxidation state using the rules, although they acknowledge other methods can be used. Oxidation numbers must be positive or negative integers, fractional oxidation numbers should not be used and in the event of any uncertainty alternative naming conventions should be used. Oxidation number as used in coordination chemistry The current definition of the oxidation number listed by IUPAC is as follows: Of a central atom in a coordination entity, the charge it would bear if all the ligands were removed along with the electron pairs that were shared with the central atom. It is represented by a Roman numeral. Use in nomenclature In older literature the term is referred to as Stock number, however the use of this term is no longer recommended by IUPAC. The oxidation state in compound naming is placed either as III a right superscript to the element symbol in chemical formula, for example Fe , or in parentheses after the name of the element, iron(III) in chemical names. For example III Fe2(SO4)3 is named iron(III) sulfate and its formula can be shown as Fe 2(SO4)3. This is because a sulfate ion has a charge of -2, so each iron atom takes a charge of +3. Note that fractional oxidation numbers should not be used in naming.

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Determining the oxidation state or number There are two different methodologies for determining the oxidation state of elements in chemical compounds. First, a rule-based approach to determine how the electrons are allocated and this method is based on the rules in the IUPAC definition, and this approach is widely taught. Second, a method-based on the relative electronegativity of the elements in the compound, where in simple terms the more electronegative element is assumed to take the negative charge. Rule based method There are general rules (adopted by IUPAC in 1990) for determining the oxidation states of atoms in simple chemical compounds without the use of structural formulae: [Oxidation state] is defined as the charge an atom might be imagined to have when electrons are counted according to an agreed-upon set of rules: 1. the oxidation state of a free element (uncombined element) is zero 2. for a simple (monatomic) ion, the oxidation state is equal to the net charge on the ion 3. hydrogen has an oxidation state of 1 and oxygen has an oxidation state of −2 when they are present in most compounds. (Exceptions to this are that hydrogen has an oxidation state of −1 in hydrides of active metals, e.g. LiH, and oxygen has an oxidation state of −1 in peroxides, e.g. H2O2 4. the algebraic sum of oxidation states of all atoms in a neutral molecule must be zero, while in ions the algebraic sum of the oxidation states of the constituent atoms must be equal to the charge on the ion. Simple examples 

Any pure element—even if it forms diatomic molecules like chlorine (Cl2)—has an oxidation state of zero. Examples of this are Cu or O 2.

For monatomic ions, the oxidation state is the same as the charge of the ion. For 2− example, the sulfide anion (S ) has an oxidation state of −2, whereas the lithium + cation (Li ) has an oxidation state of +1.

The sum of oxidation states for all atoms in a molecule or polyatomic ion is equal to the charge of the molecule or ion. Thus, the oxidation state of one element can be calculated from the oxidation states of the other elements.

1. An application of this rule is that the sum of the oxidation states of all atoms in a neutral molecule must be zero. Consider a neutral molecule of carbon dioxide, CO 2. Oxygen is assumed to have its usual oxidation state of −2, and so the sum of the oxidation states of all the atoms can be expressed as X + 2(−2) = 0, or X − 4 = 0, where X is the unknown oxidation state of carbon. Thus, it can be seen that the oxidation state of carbon in the molecule is +4. 2. In polyatomic ions, the sum of the oxidation states of the constituent atoms must be equal to the charge on the ion. As an example, consider the sulfate anion, which has 2the formula SO4 . As indicated by the formula, the total charge of this ion is −2. Because all four oxygen atoms are assumed to have their usual oxidation state of

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−2, and the sum of the oxidation states of the all the atoms is equal to the charge of the ion, the sum of the oxidation states can be represented as Y + 4(−2) = −2, or Y − 8 = −2, where Y is the unknown oxidation state of sulfur. Thus, it can be computed that Y = +6. These facts, combined with the fact that some elements almost always have certain oxidation states (due to their very high electropositivity or electronegativity), allows one to compute the oxidation states for the remaining atoms (such as transition metals) in simple compounds. Example for a complex salt: In Cr(OH) 3, oxygen has an oxidation state of −2 (no fluorine or O–O bonds present), and hydrogen has a state of +1 (bonded to oxygen). So, each of the three hydroxide groups has an oxidation state of −2 + 1 = −1. As the compound is neutral, chromium has an oxidation state of +3. Using electronegativity The use of electronegativity in this way was introduced by Pauling in 1947. This method of determining oxidation state is found in some recent text books. This method allows the oxidation state of all atoms in a molecule to be determined whereas the IUPAC 1990/2005 definition does not. In the 1970 rules IUPAC recommended that oxidation state was used in nomenclature and elsewhere in inorganic chemistry as the "charge that would be present on an atom if the electrons were assigned to the more electronegative atom", but with a convention that hydrogen is considered to be positive in combination with non-metals and a bond between like atoms makes no contribution to the oxidation number. In practise the IUPAC 1990/2005 definition is usually extended by adding additional rules based on electronegativity. 

Fluorine has an oxidation state of −1 when bonded to any other element, since it has the highest electronegativity of all reactive elements.

Halogens other than fluorine have an oxidation state of −1 except when they are bonded to oxygen, to nitrogen, or to another halogen that is more electronegative. For example, the oxidation state of chlorine in chlorine monofluoride (ClF) is +1. However, in bromine monochloride (BrCl), the oxidation state of Cl is −1.

Hydrogen has an oxidation state of +1 except when bonded to more electropositive elements such as sodium, aluminium, and boron, as in NaH, NaBH 4, LiAlH 4, where each H has an oxidation state of −1.

In compounds, oxygen typically has an oxidation state of −2, though there are exceptions that are listed below, such as peroxides (e.g. hydrogen peroxide H2O2), where oxygen has an OS of −1.

Alkali metals have an oxidation state of +1 in virtually all of their compounds (exception, see alkalide).

Alkaline earth metals have an oxidation state of +2 in virtually all of their compounds.

Ionic compounds If an ionic compound has two ions with a common element, such as ammonium nitrate, NH 4NO

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3, it is usual to consider the oxidation states for each ion separately. The overall empirical formula of ammonium nitrate is N 2H 4O 3, which leads to an average nitrogen oxidation state of +1, but it is much more useful to consider separately the ions NH+ 4 and NO− 3 with nitrogen oxidation states of -3 and +5 respectively. Calculation of formal oxidation states with a Lewis structure This method can be used for molecules when one has a Lewis structure. It should be remembered that the oxidation state of an atom does not represent the "real" charge on that atom: This is particularly true of high oxidation states, where the ionization energy required to produce a multiply positive ion are far greater than the energies available in chemical reactions. The assignment of electrons between atoms in calculating an oxidation state is purely a formalism, but is a useful one for the understanding of many chemical reactions. For more about issues with calculating atomic charges, see partial charge. The Lewis structure When a Lewis structure of a molecule is available, the oxidation states may be assigned by computing the difference between the number of valence electrons that a neutral atom of that element would have and the number of electrons that "belong" to it in the Lewis structure. For purposes of computing oxidation states, electrons in a bond between atoms of different elements belong to the more electronegative atom; electrons in a bond between atoms of the same element are split equally, and electrons in a lone pair belong only to the atom with the lone pair. For example, consider acetic acid:

The methyl group carbon atom has 6 valence electrons from its bonds to the hydrogen atoms because carbon is more electronegative than hydrogen. Also, 1 electron is gained from its bond with the other carbon atom because the electron pair in the C–C bond is split equally, giving a total of 7 electrons. A neutral carbon atom would have 4 valence electrons, because carbon is in group 14 of the periodic table. The difference, 4 – 7 = –3, is the oxidation state of that carbon atom. That is, if it is assumed that all the bonds were 100% 3ionic (which in fact they are not), the carbon would be described as C . Following the same rules, the carboxylic acid carbon atom has an oxidation state of +3 (it only gets one valence electron from the C–C bond; the oxygen atoms get all the other electrons because oxygen is more electronegative than carbon). The oxygen atoms both have an oxidation state of –2; they get 8 electrons each (4 from the lone pairs and 4 from the

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bonds), while a neutral oxygen atom would have 6. The hydrogen atoms all have oxidation state +1, because they surrender their electron to the more electronegative atoms to which they are bonded. In structural diagrams for organic chemistry, oxidation states are represented by Roman numerals to distinguish them from formal charges (calculated with all bonds covalent). Inequivalent atoms of an element

Structure of the thiosulfate anion An example of a molecule with inequivalent atoms of the same element is the thiosulfate ion 2− (S2O3 ), for which the algebraic sum rule yields the average value +2 for sulfur, where the two ionizing electrons are assigned to the terminal sulfur atom. However, the use of a Lewis structure and electron counting shows that the two sulfur atoms are different. The central sulfur is assigned only one valence electron from the S-S bond and no valence electrons from the S-O bonds, compared to six valence electrons for a free sulfur atom, so the oxidation state of the central sulfur is +5. The terminal sulfur atom is assigned the other electron from the S-S bond plus three lone pairs for a total of seven valence electrons, so its oxidation state is −1. Redox reactions Oxidation states can be useful for balancing chemical equations for oxidation-reduction (or redox) reactions, because the changes in the oxidized atoms have to be balanced by the changes in the reduced atoms. For example, in the reaction of acetaldehyde with the Tollens' reagent to acetic acid (shown below), the carbonyl carbon atom changes its oxidation state from +1 to +3 (oxidation). This oxidation is balanced by reducing two equivalents of silver + 0 from Ag to Ag .

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Elements with multiple oxidation states Main article: List of oxidation states of the elements Most elements have more than one possible oxidation state. For example, carbon has nine integer oxidation states: Integer oxidation states of carbon Oxidation state Example compound –4

CH4

–3

C2H6

–2

CH3Cl

–1

C2H2

0

CH2Cl2

+1

CHCl2—CHCl2

+2

CHCl3

+3

C2Cl6

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+4

CCl4

Oxidation state and formal charge Main article: Formal charge#Formal charge compared to oxidation state The oxidation state of an atom is often different from the formal charge often included in Lewis structures (when it is non-zero). The oxidation state is calculated by assuming that each chemical bond (except between identical atoms) is ionic so that both electrons are assigned to the more electronegative bonded atom. In contrast, the formal charge is calculated by assuming that each bonds is covalent so that one electron is assigned to each + bonded atom. For example, in ammonium ion (NH4 ) the oxidation state of nitrogen is -3, as all eight valence electrons are assigned to the nitrogen atom that is more electronegative than hydrogen. However, the formal charge is +1, calculated by assigning only four valence electrons (one per bond) to nitrogen. For comparison, the nitrogen in ammonia (NH 3) has oxidation state -3 also but a formal charge of zero. On protonation of ammonia the formal charge on nitrogen changes, but its oxidation state does not for molecules that contain nonequivalent atoms of the same element. Oxidation number in coordination compounds Whist oxidation state and oxidation number are often used interchangeably, oxidation number is used in coordination chemistry with a slightly different meaning. In coordination chemistry, the rules used for counting electrons are different. Every electron in a metal-ligand bond belongs to the ligand, regardless of electronegativity, so that the oxidation number is the charge that would remain if all ligands were removed together with the electron pairs shared with the central atom. For most coordination complexes, the metal atom is the less electronegative end of each metal-ligand bond, so that this rule gives the same result as the electronegativity-based rule There are exceptions, however, such as Wilkinson's catalyst RhCl(PPh 3)3 (Ph = phenyl), in which the rhodium atom is more electronegative than phosphorus. Nevertheless the oxidation number of rhodium in this molecule is considered to be +1 and the molecule’s systematic name is chlorotris(triphenylphosphine)rhodium(I), as the Rh-P electrons are assigned to the P atom of the ligand. The electronegativity rule would assign them instead to the Rh with an oxidation state of −5. Spectroscopic oxidation states vs. formal oxidation numbers Although formal oxidation numbers can be helpful for classifying compounds, they are unmeasurable and their physical meaning can be ambiguous. Formal oxidation numbers require particular caution for molecules where the bonding is covalent, since the formal oxidation numbers require the heterolytic removal of ligands, which in essence denies covalency. Spectroscopic oxidation states, as defined by Jorgenson and reiterated by Wieghardt, are measurables that are bench-marked using spectroscopic and crystallographic data. Oxidation state can also have effect on spectroscopic studies of compounds. In infrared spectroscopy of metal carbonyls this effect is illustrated by using spectroscopic studies on metals from oxidation states of –2 to +2.

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Unusual formal oxidation states Main article: High-valent iron Unusual formal oxidation states of metals are important in biochemical processes, the notable ones being Fe(IV) and Fe(V) in Cytochrome P450-containing systems. History of the oxidation number concept Oxidation itself was first studied by Antoine Lavoisier, who believed that oxidation was always the result of reactions with oxygen, thus the name. Although Lavoisier's idea has been shown to be incorrect, the name he proposed is still used, albeit more generally. Oxidation states were one of the intellectual "stepping stones" that Mendeleev used to derive the periodic table. The Stock nomenclature (named for Alfred Stock who suggested it in 1919) was intended to replace the naming that was prevalent at the time. Under the Stock system FeCl 2 was called iron(II) chloride rather than ferrous chloride. The current concept of "oxidation state" was introduced by W. M. Latimer in 1938. In 1940 IUPAC recommended that the term Stock number should be replaced by the term oxidation number. In 1947 Pauling proposed that the oxidation number could be determined using the electronegativity of the atoms to determine the "ions" in the formal determination of oxidation number. In 1970 IUPAC defined oxidation number in terms of electronegativity. In 1990 IUPAC changed course and adopted a rule based determination for the "central atom" rather than using electronegativity. This is the definition in the current gold book for "oxidation state". They also introduced the definition of oxidation number, shown in the current gold book, that appears to make oxidation number specific to coordination chemistry. This may not have been their intention, as in 2005 they issued new recommendations for inorganic nomenclature that define oxidation number in the same terms as the 1990 definition of oxidation state, and that oxidation number is, as in the earlier recommendations, used in the naming of inorganic compounds. Oxidation number versus oxidation state In general, in the wider field of chemistry the IUPAC definitions have not been adhered to and both terms are used interchangeably, as they were when Latimer introduced the concept in 1938. For example, two well-known textbooks use the term oxidation state and represent it in Roman numerals in chemical formulae. The point has been made that, if there is any semantic difference between the terms, then oxidation number refers to the specific numerical value assigned to the entity known as oxidation state, much as IUPAC use the term charge number to refer to the numerical value assigned to the entity know as ionic charge. The IUPAC Gold Book takes the definitions from 1990 IUPAC papers rather than the more recent current IUPAC 2005 recommendations. There is a current IUPAC project, "Towards a comprehensive definition of oxidation state", (project 2008-040-1-200) started in 2009, which has yet to report (March 2013). The project was undertaken because the current definition in the IUPAC Gold Book was seen to be "narrow and circular", and "inapplicable to clusters, Zintl phases and some organometallic complexes". See also 

List of oxidation states of the elements

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

Electrochemistry



Valence (chemistry)

Chapter 15: Parent hydride In IUPAC nomenclature, a parent hydride is an unbranched acyclic or cyclic structure to which only hydrogen atoms are attached. Parent hydrides are parent structures that contain one or more hydrogen atoms. They are the basic structures used in substitutive nomenclature.

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The bonding number of a skeletal atom in a parent hydride is the sum of the total number of valence bonds to adjacent skeletal atoms, if any, and the number of attached hydrogen atoms. In SH2, for example, S has bonding number 2. Parent hydrides in substitutive nomenclature Parent hydrides are compounds with an unsubstituted skeleton, thus with only hydrogens attached to it. They have a defined standard population of hydrogen atoms. Acyclic parent hydrides are always saturated and unbranched. Cyclic parent hydrides are usually either fully saturated or fully unsaturated (containing the maximum number of double bonds). Some combinations of rings or combinations of cyclic and acyclic hydrides may be partially saturated. All elements have 'standard bonding numbers', that is for nitrogen and phosphorus 3, for carbon and silicon 4, etcetera. The names of parent hydrides are ending with 'ane', analogous with the nomenclature for alkanes. Unsaturated hydrides are given the ending 'ene' or 'yne', for example, 'diene' for two double bonds. For non-carbon homocyclic compounds with 3 to 10 membered rings the Hantzsch–Widman nomenclature is preferred. Derivatives of parent hydrides get the name of the parent hydride, along with prefixes or suffixes appropriate to the substituents that replace the hydrogen atoms. Parent hydrides are not only used in organic chemistry nomenclature, but also in inorganic chemistry. Examples Examples of mononuclear parent hydrides (with a single skeletal atom) are: BH3 (borane), CH4 (methane; not carbane!), SiH4 (silane), NH3 (azane), PH3 (phosphane), H2S (sulfane) and H2O (oxidane). Some inorganic parent hydrides

Sulfane

Azane

Cis-diazene

Disilane

See also 

Hydride

Preferred IUPAC name

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Chapter 18: Parent structure

Organic parent structure

Inorganic parent structure In IUPAC nomenclature, a parent structure, parent compound, parent name or simply parent is the denotation for a compound consisting of an unbranched chain of skeletal atoms (not necessarily carbon), or consisting of an unsubstituted monocyclic or polycyclic ring system. Parent structures bearing one or more functional groups that are not specifically denoted by a suffix are called functional parents. Names of parent structures are used in IUPAC nomenclature as basis for systematic names. A parent hydride is a parent structure with one or more hydrogen atoms. Parent hydrides have a defined standard population of hydrogen atoms attached to a skeletal structure. Parent hydrides are used extensively in organic nomenclature, but are also used in inorganic chemistry. To construct a systematic name, affixes are attached to the parent name, which denote substituents that replace hydrogen. See also 

Preferred IUPAC name



Hydride

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Chapter 16: Phanes (organic chemistry)

Phanes are sub-structures of highly complex organic molecules introduced for simplification of the naming of these highly complex molecules. Systematic nomenclature of organic chemistry consists of building a name for the structure of an organic compound by a collection of names of its composite parts but describing also its relative positions within the structure. Naming information is summarised by IUPAC: "Phane nomenclature is a new method for building names for organic structures by assembling names that describe component parts of a complex structure. It is based on the idea that a relatively simple skeleton for a parent hydride can be modified by an operation called 'amplification', a process that replaces one or more special atoms (superatoms) of a simplified skeleton by multiatomic structures". Whilst the cyclophane name describes only a limited number of sub-structures of benzene rings interconnected by individual atoms or chains, 'phane' is a class name which includes others, hence heterocyclic rings as well. Therefore the various cyclophanes are perfectly good for the general class of phanes as well keeping in mind that the cyclic structures in phanes could have much greater diversity.

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Chapter 17: Preferred IUPAC name In chemical nomenclature, a preferred IUPAC name (PIN) is a unique name, assigned to a chemical substance and preferred among the possible names generated by IUPAC nomenclature. The "preferred IUPAC nomenclature" provides a set of rules for choosing between multiple possibilities in situations where it is important to decide on a unique name. It is intended for use in legal and regulatory situations. Currently, preferred IUPAC names are written only for part of the organic compounds (see below). Rules for the remaining organic and inorganic compounds are still under development. The "Preferred names in the nomenclature of organic compounds" (Draft 7 October 2004) replace two former publications: the "Nomenclature of Organic Chemistry", 1979 (the Blue Book) and "A Guide to IUPAC Nomenclature of Organic Compounds, Recommendations 1993". As of May 2010, these draft recommendations have yet to gain formal approval. Definitions A preferred IUPAC name or PIN is a name that is preferred among two or more IUPAC names. An IUPAC name is a systematic name that meets the recommended IUPAC rules. IUPAC names include retained names. A general IUPAC name is any IUPAC name that is not a "preferred IUPAC name". A retained name is a traditional or otherwise often used name, usually a trivial name, that may be used in IUPAC nomenclature. Since systematic names often are not human-readable a PIN may be a retained name. Both "PINs" and "retained names" have to be chosen (and established by IUPAC) explicitly, unlike other IUPAC names, which automatically arise from IUPAC nomenclatural rules. A preselected name is a preferred name chosen among two or more names for parent hydrides or other parent structures that do not contain carbon (inorganic parents). "Preselected names" are used in the nomenclature of organic compounds as the basis for PINs for organic derivatives. They are needed for derivatives of organic compounds that do not contain carbon themselves. A preselected name is not necessarily a PIN in inorganic chemical nomenclature. Basic principles The systems of chemical nomenclature developed by the International Union of Pure and Applied Chemistry (IUPAC) have traditionally concentrated on ensuring that chemical names are unambiguous, that is that a name can only refer to one substance. However, a single substance can have more than one acceptable name, like toluene, which may also be correctly named as "methylbenzene" or "phenylmethane". Some alternative names remain available as "retained names" for more general contexts. For example tetrahydrofuran remains an unambiguous and acceptable name for the common organic solvent, even if the preferred IUPAC name is "oxolane". Substitutive nomenclature (replacement of hydrogen atoms in the parent structure) is used most extensively, for example "ethoxyethane" instead of diethyl ether and "tetrachloromethane" instead of carbon tetrachloride. Functional class nomenclature (also known as radicofunctional nomenclature) is used for acid anhydrides, esters, acyl halides and pseudohalides and salts. Also skeletal replacement operations, additive and subtractive operations and conjunctive operations are applied.

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Retained IUPAC names The number of retained non-systematic, trivial names of simple organic compounds (for example formic acid and acetic acid) has been reduced considerably for preferred IUPAC names, although a larger set of retained names is available for general nomenclature. The traditional names of simple monosaccharides, Îą-amino acids and a large number of natural products have been retained as preferred IUPAC names; in these cases the systematic names are very complicated and virtually never used. Scope of the nomenclature for organic compounds In IUPAC nomenclature all compounds containing carbon are considered as organic compounds. Organic nomenclature only applies to organic compounds containing elements from the Groups 13 through 17. Organometallic compounds of the Groups 1 through 12 are not covered by organic nomenclature.

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Chapter 18: Primary (chemistry) Primary is a term used in organic chemistry to classify various types of compounds (e.g. alcohols, alkyl halides, amines) or reactive intermediates (e.g. alkyl radicals, carbocations). Red highlighted central atoms in various groups of chemical compounds. Primary central atoms compared with secondary, tertiary and quaternary central atoms. primary

secondary

tertiary

quaternary

Carbon atom in an alkane

does not exist

Alcohol

Amine

does not exist

Amide

Phosphine

See also 

Secondary (chemistry)

Tertiary (chemistry)

Quaternary (chemistry)

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Chapter 19: Quaternary (chemistry) Quaternary is a term used in organic chemistry to classify various types of compounds (e. g. amines and ammonium salts). Red highlighted central atoms in various groups of chemical compounds. Quaternary central atoms compared with primary, secondary and tertiary central atoms. primary

secondary

tertiary

quaternary

Carbon atom in an alkane

does not exist

Alcohol

Amine

does not exist

Amide

Phosphine

See also 

Primary (chemistry)

Secondary (chemistry)

Tertiary (chemistry)

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Chapter 20: Secondary (chemistry) Secondary is a term used in organic chemistry to classify various types of compounds (e. g. alcohols, alkyl halides, amines) or reactive intermediates (e. g. alkyl radicals, carbocations). Red highlighted central atoms in various groups of chemical compounds. Secondary central atoms compared with primary, tertiary und quaternary central atoms. primary

secondary

tertiary

quaternary

Carbon atom in an alkane

does not exist

Alcohol

Amine

does not exist

Amide

Phosphine

See also 

Primary (chemistry)

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Tertiary (chemistry)

Quaternary (chemistry)

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Chapter 21: Simplified molecular-input line-entry system SMILES Filename extension .smi Internet media type chemical/x-daylight-smiles Type of format

chemical file format

Generation of SMILES: Break cycles, then write as branches off a main backbone. The Simplified Molecular-Input Line-Entry System or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into twodimensional drawings or three-dimensional models of the molecules. The original SMILES specification was initiated by the author David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo (USEPA) and Albert Leo and Corwin Hansch (Pomona College) for supporting the work, and Arthur Weininger

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(Pomona; Daylight CIS) and Jeremy Scofield (Cedar River Software, Renton, WA) for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc. In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other 'linear' notations include the Wiswesser Line Notation (WLN), ROSDAL and SLN (Tripos Inc). In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more humanreadable than InChI; it also has a wide base of software support with extensive theoretical (e.g., graph theory) backing. Terminology The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings; the exact meaning is usually apparent from the context. The terms Canonical and Isomeric can lead to some confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive. Typically, a number of equally valid SMILES can be written for a molecule. For example, CCO, OCC and C(O)C all specify the structure of ethanol. Algorithms have been developed to ensure the same SMILES is generated for a molecule regardless of the order of atoms in the structure. This SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, and is termed the Canonical SMILES. These algorithms first convert the SMILES to an internal representation of the molecular structure and do not simply manipulate strings as is sometimes thought. Various algorithms for generating Canonical SMILES have been developed, including those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, and the Chemistry Development Kit. A common application of Canonical SMILES is indexing and ensuring uniqueness of molecules in a database. It is important to note that the original paper that described the CANGEN algorithm that claimed to generate unique SMILES strings for graphs representing molecules fails for a number of simple cases (e.g. cuneane, 1,2-dicyclopropylethane) and cannot be considered a correct method for canonizing graphs. There is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and double bond geometry. These are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed Isomeric SMILES. A notable feature of these rules is that they allow rigorous partial specification of chirality. The term Isomeric SMILES is also applied to SMILES in which isotopes are specified. Graph-based definition In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree.

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Examples

Atoms Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as [Au] for gold. Brackets can be omitted for the "organic subset" of B, C, N, O, P, S, F, Cl, Br, and I. All other elements must be enclosed in brackets. If the brackets are omitted, the proper number of implicit hydrogen atoms is assumed; for instance the SMILES for water is simply O. An atom holding one or more electrical charges is enclosed in brackets, followed by the symbol H if it is bonded to one or more atoms of hydrogen, followed by the number of hydrogen atoms (as usual one is omitted example: NH4 for ammonium), then by the sign '+' for a positive charge or by '-' for a negative charge. The number of charges is specified after the sign (except if there is one only); however, it is also possible write the sign as many times 4+ as the ion has charges: instead of "Ti+4", one can also write "Ti++++" (Titanium IV, Ti ). Thus, the hydroxide anion is represented by [OH-], the oxonium cation is [OH3+] and the 3+ cobalt III cation (Co ) is either [Co+3] or [Co+++]. Bonds Bonds between aliphatic atoms are assumed to be single unless specified otherwise and are implied by adjacency in the SMILES string. For example the SMILES for ethanol can be written as CCO. Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES string, which for cyclohexane and dioxane can be written as C1CCCCC1 and O1CCOCC1 respectively. For a second ring, the label will be 2 (naphthalene: c1cccc2c1cccc2 (note the lower case for aromatic compounds)), and so on. After reaching 9, the label must be preceded by a '%', in order to differentiate it from two different labels bonded to the same atom (~C12~ will mean the atom of carbon holds the ring closure labels 1 and 2, whereas ~C%12~ will indicate one label only, 12). Double, triple, and quadruple bonds are represented by the symbols '=', '#', and '$' respectively as illustrated by the SMILES O=C=O (carbon dioxide), C#N (hydrogen cyanide) and [Ga-]$[As+] (gallium arsenide). Aromaticity Aromatic C, O, S and N atoms are shown in their lower case 'c', 'o', 's' and 'n' respectively. Benzene, pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1. Bonds between aromatic atoms are, by default, aromatic although these can be specified explicitly using the ':' symbol. Aromatic atoms can be singly bonded to each other and biphenyl can be represented by c1ccccc1-c2ccccc2. Aromatic nitrogen bonded to hydrogen, as found in pyrrole must be represented as [nH] and imidazole is written in SMILES notation as n1c[nH]cc1. The Daylight and OpenEye algorithms for generating canonical SMILES differ in their treatment of aromaticity.

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Visualization of 3-cyanoanisole as COc(c1)cccc1C#N.

Branching Branches are described with parentheses, as in CCC(=O)O for propionic acid and C(F)(F)F for fluoroform. Substituted rings can be written with the branching point in the ring as illustrated by the SMILES COc(c1)cccc1C#N (see depiction) and COc(cc1)ccc1C#N (see depiction) which encode the 3 and 4-cyanoanisole isomers. Writing SMILES for substituted rings in this way can make them more human-readable. Stereochemistry Configuration around double bonds is specified using the characters "/" and "\". For example, F/C=C/F (see depiction) is one representation of trans-difluoroethene, in which the fluorine atoms are on opposite sides of the double bond, whereas F/C=C\F (see depiction) is one possible representation of cis-difluoroethene, in which the Fs are on the same side of the double bond, as shown in the figure. Configuration at tetrahedral carbon is specified by @ or @@. L-Alanine, the more common enantiomer of the amino acid alanine can be written as N[C@@H](C)C(=O)O (see depiction). The @@ specifier indicates that, when viewed from nitrogen along the bond to the chiral center, the sequence of substituents hydrogen (H), methyl (C) and carboxylate (C(=O)O) appear clockwise. D-Alanine can be written as N[C@H](C)C(=O)O (see depiction). The order of the substituents in the SMILES string is very important and D-alanine can also be encoded as N[C@@H](C(=O)O)C (see depiction). Isotopes Isotopes are specified with a number equal to the integer isotopic mass preceding the atomic symbol. Benzene in which one atom is carbon-14 is written as [14c]1ccccc1 and deuterochloroform is [2H]C(Cl)(Cl)Cl. Illustration with a molecule with more than 9 rings, Cephalostatin-1 (a steroidic trisdecacyclic pyrazine with the empirical formula C54H74N2O10 isolated from the Indian Ocean hemichordate

Cephalodiscus

gilchristi):

Starting with the left-most methyl group in the figure: C[C@@](C)(O1)C[C@@H](O)[C@@]1(O2)[C@@H](C)[C@@H]3CC=C4[C@]3(C2)C(=O)C [C@H]5[C@H]4CC[C@@H](C6)[C@]5(C)Cc(n7)c6nc(C[C@@]89(C))c7C[C@@H]8CC[C@ @H]%10[C@@H]9C[C@@H](O)[C@@]%11(C)C%10=C[C@H](O%12)[C@]%11(O)[C@H]( C)[C@]%12(O%13)[C@H](O)C[C@@]%13(C)CO Note that '%' appears in front of the index of ring closure labels above 9; see section Bonds

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above.

Other examples of SMILES The SMILES notation is described extensively in the SMILES theory manual provided by Daylight Chemical Information Systems and a number of illustrative examples are presented. Daylight's depict utility provides users with the means to check their own examples of SMILES and is a valuable educational tool.

Extensions SMARTS is a line notation for specification of substructural patterns in molecules. While it uses many of the same symbols as SMILES, it also allows specification of wildcard atoms and bonds, which can be used to define substructural queries for chemical database searching. One common misconception is that SMARTS-based substructural searching involves matching of SMILES and SMARTS strings. In fact, both SMILES and SMARTS strings are first converted to internal graph representations which are searched for subgraph isomorphism. SMIRKS is a line notation for specifying reaction transforms.

Conversion SMILES can be converted back to 2-dimensional representations using Structure Diagram Generation algorithms (Helson, 1999). This conversion is not always unambiguous. Conversion to 3-dimensional representation is achieved by energy minimization approaches. There are many downloadable and web-based conversion utilities.

See also SMILES arbitrary target specification SMARTS language for specification of substructural queries. SYBYL Line Notation (another line notation) Molecular Query Language – query language allowing also numerical properties, e.g. physicochemical values or distances Chemistry Development Kit (2D layout and conversion) International Chemical Identifier (InChI), the free and open alternative to SMILES by the IUPAC.

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OpenBabel, JOELib, OELib (conversion)

References 

Anderson, E.; Veith, G. D.; Weininger, D. (1987). SMILES: A line notation and computerized

interpreter

for

chemical

structures.

Duluth,

MN:

U.S.

EPA,

Environmental Research Laboratory-Duluth. Report No. EPA/600/M-87/021.

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Chapter 22: Stock nomenclature Stock nomenclature for inorganic compounds is a widely used system of chemical nomenclature developed by the German chemist Alfred Stock and first published in 1919. In the 'Stock system', the oxidation states of some or all the elements in a compound are indicated in parentheses by Roman numerals. Style Contrary to the usual English style for parentheses, there is no space between the end of the element name and the opening parenthesis: for AgF, the correct style is "silver(I) fluoride" not "silver (I) fluoride". Where there is no ambiguity about the oxidation state of an element in a compound, it is not necessary to indicate it with Roman numerals: hence for NaCl, sodium chloride will suffice; sodium(I) chloride(−I) is unnecessarily long and such usage is very rare. Examples 

FeCl2: iron(II) chloride

FeCl3: iron(III) chloride

K[MnO4]: potassium manganate(VII) (rarely used except in pre-university education, potassium permanganate is ubiquitous)

[Co(NH3)6] : hexaamminecobalt(III)

3+

Mixed-valence compounds 

Co3O4: cobalt(II,III) oxide. Co3O4 is a mixed-valence compound that is more II III 2+ 3+ 2− accurately described as Co Co 2O4, i.e. [Co ][Co ]2[O ]4.

Sb2O4: antimony(III,V) oxide. Sb2O4 is better formulated as Sb Sb O4, i.e. 3+ 5+ 2− [Sb ][Sb ][O ]4.

III

V

See also 

IUPAC nomenclature of inorganic chemistry

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Chapter 23: Structural analog In chemistry, a structural analog (structural analogue), also known as chemical analog or simply analog, is a compound having a structure similar to that of another one, but differing from it in respect of a certain component. It can differ in one or more atoms, functional groups, or substructures, which are replaced with other atoms, groups, or substructures. A structural analog can be imagined to be formed, at least theoretically, from the other compound. Despite a high chemical similarity, structural analogs are not necessarily functional analogs and can have very different physical, chemical, biochemical, or pharmacological properties. In drug development either a large series of structural analogs of an initial lead compound are created and tested as part of a structure-activity relationship study or a database is screened for structural analogs of a lead compound. Examples Carbon-Based Silicon-Based

Methane

Ethane

Silane

Disilane

Acetylene Disilyne

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Propane

Trisilane

Methanol Silanol

See also 

Derivative (chemistry)

Homolog, a compound of a series differing only by repeated units

Functional analog, compounds with similar physical, chemical, biochemical, or pharmacological properties

Transition state analog

External links 

Analoging in ChEMBL — a free web-service for finding structural analogs in ChEMBL.

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Chapter 24: Substituent In organic chemistry and biochemistry, a substituent is an atom or group of atoms substituted in place of a hydrogen atom on the parent chain of a hydrocarbon. The terms substituent, side-chain, group, branch, or pendant group are used almost interchangeably to describe branches from a parent structure, though certain distinctions are made in the context of polymer chemistry. In polymers, side chains extend from a backbone structure. In proteins, side chains are attached to the alpha carbon atoms of the amino acid backbone. The suffix yl is used when naming organic compounds that contain a single bond replacing one hydrogen; -ylidene and -ylidyne are used with double bonds and triple bonds, respectively. In addition, when naming hydrocarbons that contain a substituent, positional numbers are used to indicate which carbon atom the substituent attaches to when such information is needed to distinguish between isomers. The polar effect exerted by a substituent is a combination of the inductive effect and the mesomeric effect. Additional steric effects result from the volume occupied by a substituent. The phrases most-substituted and least-substituted are frequently used to describe molecules and predict their products. In this terminology, methane is used as a reference of comparison. Using methane as a reference, for each hydrogen atom that is replaced or "substituted" by something else, the molecule can be said to be more highly substituted. For example: 

Markovnikov's rule predicts that the hydrogen adds to the carbon of the alkene functional group that has the greater number of hydrogen substituents.

Zaitsev's rule predicts that the major reaction product is the alkene with the more highly substituted (more stable) double bond.

Nomenclature The suffix -yl is used in organic chemistry to form names of radicals, either separate or chemically bonded parts of molecules. It can be traced back to the old name of methanol, "methylene" (coined from Greek words methy = "wine" and hȳlē = "wood"), which became shortened to "methyl" in compound names. Several reforms of chemical chemical nomenclature eventually generalized the use of the suffix to other organic substituents. The use of the suffix is determined by the number of hydrogen atoms that the substituent replaces on a parent compound (and also, usually, on the substituent). According to 1993 IUPAC guidelines: 

-yl means that one hydrogen is replaced.

-ylidene means that two hydrogens are replaced by a double bond between parent and substituent.

-ylidyne means that three hydrogens are replaced by a triple bond between parent and substituent.

The suffix -ylidine (with "ine" instead of "yne" or "ene") is encountered sporadically, and appears to be a variant spelling of "-ylidene". It is not mentioned in IUPAC guidelines.

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For multiple bonds of the same type, which link the substituent to the parent group, the prefixes di, tri, tetra, etc.are used: -diyl (two single bonds), -triyl (three single bonds), tetrayl (four single bonds), -diylidene (two double bonds) For multiple bonds of different bond types, multiple suffixes are added: -ylylidene (one single and one double), -ylylidyne (one single and one triple), -diylylidene (two single and one double) The parent compound name can be altered in two different ways. 

For many common compounds the substituent is linked at one end (the 1 position), which is therefore not explicitly numbered in the formula.The substituent name is modified by stripping ane (see Alkane) and adding the appropriate suffix.This is "recommended only for saturated acyclic and monocyclic hydrocarbon substituent groups and for the mononuclear parent hydrides of silicon, germanium, tin, lead, and boron". Thus, if there is a carboxylic acid called "X-ic acid", an alcohol ending "Xanol" (or "X-yl alcohol"), or an alkane called "X-ane", then "X-yl" typically denotes the same carbon chain lacking these groups but modified by attachment to some other parent molecule.

The more general method omits only the terminal "e" of the substituent name, but requires explicit numbering of each yl prefix, even at position 1 (except for -ylidyne, which as a triple bond must terminate the substituent carbon chain). Pentan-1-yl is an example of a name by this method, and is synonymous with Pentyl from the previous guideline.

Note that some popular terms such as "vinyl" (when used to mean "polyvinyl") represent only a portion of the full chemical name. Methane substituents According to the above rules, a carbon atom in a molecule, considered as a substituent, has the following names depending on the number of hydrogens bound to it, and the type of bonds formed with the remainder of the molecule: CH

methane

no bonds

4 −CH methyl group

one single bound to a non-hydrogen

3

atom

=CH methylene group or methylidene

one double bond

2 −CH methylene bridge or methanediyl

two single bonds

2− ≡CH methylidyne group

one triple bond

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=CH− methine

group,

methanylylidene, one single bond and one double bond

methylylidene >CH− methanetriyl group

three single bonds

≡C− methylylidyne group

one triple bond and one single bond

=C= methanediylidene group

two double bonds

>C= methanediylylidene group

two single bonds and one double bond

>C< methanetetrayl group

four single bonds

Structures In a chemical structural formula, an organic substituent such as methyl, ethyl, or aryl can be 1 2 written as R (or R , R , etc.) This is a generic placeholder, the R derived from radical or rest, which may replace any portion of the formula as the author finds convenient. The first to use this symbol was Charles Frédéric Gerhardt in 1844. The symbol X is often used to denote electronegative substituents such as the halides. Statistical distribution One cheminformatics study identified 849,574 unique substituents up to 12 non-hydrogen atoms large and containing only C,H,N,O,S,P,Se and the halogens in a set of 3,043,941 molecules. Fifty common substituents are found in only 1% of this set, and 438 in 0.1%. 64% of the substituents are unique to just one molecule. The top 5 consists of the phenyl, chlorine, methoxy, hydroxyl, and ethyl substituent. The total number of organic substituents in organic chemistry is estimated at 3.1 million, creating a total of 6.7×10

23

molecules. An

infinite number of substituents can be obtained simply by increasing carbon chain length. For instance, the substituents methyl (-CH3) and pentyl (C5H11).

See also 

Functional groups are a subset of substituents

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Chapter 25: Systematic element name A systematic element name is the temporary name and symbol assigned to newly synthesized and not yet synthesized chemical elements. In chemistry, a transuranic element receives a permanent name and symbol only after its synthesis has been confirmed. In some cases, this has been a protracted and highly political process (see element naming controversy). In order to discuss such elements without ambiguity, the International Union of Pure and Applied Chemistry (IUPAC) uses a set of rules to assign a temporary systematic name and symbol to each such element. This approach to naming originated in the successful development of regular rules for the naming of organic compounds. The IUPAC rules digit

root symbol

0

nil

n

1

un

u

2

b(i)

b

3

tr(i)

t

4

quad

q

5

pent

p

6

hex

h

7

sept

s

8

oct

o

9

en(n) e

The temporary names are derived systematically from the element's atomic number. Each digit is translated to a 'numerical root', according to the table to the right. The roots are concatenated, and the name is completed with the ending -ium. Some of the roots are Latin and others are Greek; the reason is to avoid two digits starting with the same letter (Ex: 0 = nil, 9 = enn, 4 = quad, 5 = pent, 6 = hex, 7 = sept) . There are two elision rules designed to prevent odd-looking names. ď&#x201A;ˇ

If bi or tri is followed by the ending ium (i.e. the last digit is 2 or 3), the result is 'bium' or -'trium', not '-biium' or '-triium'.

ď&#x201A;ˇ

If enn is followed by nil (i.e. the sequence -90- occurs), the result is '-ennil-', not 'ennnil-'.

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The systematic symbol is formed by taking the first letter of each root, converting the first to a capital. The suffix -ium overrides traditional chemical suffix rules, thus 117 and 118 are ununseptium and ununoctium, not ununseptine and ununocton. All elements up to atomic number 112 and elements 114 and 116 have received individual permanent names and symbols. So the systematic names and symbols are only used for unnamed elements 113, 115, 117, 118, and higher. The systematic names are exactly those with 3-letter symbols. Examples Element 122 un + bi + b + ium

= unbibium

(Ubb) (instead of "unbibiium")

Element 167 un + hex + sept + ium = unhexseptium (Uhs) Element 190 un + en + nil + ium Note:

These

= unennilium

examples

show

(Uen) (instead of "unennnilium") conjectured

elements.

As of 2014, ununoctium, element 118, is the highest-numbered element discovered. Examples in Period 8 of the periodic table: External links 

The IUPAC recommendation. Untitled draft, March 2004. (PDF, 143 kB).

http://media.iupac.org/publications/pac/2002/pdf/7405x0787.pdf

American Chemical Society, Committee on Nomenclature, Terminology & Symbols

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Chapter 26: Tertiary (chemistry) Tertiary is a term used in organic chemistry to classify various types of compounds (e. g. alcohols, alkyl halides, amines) or reactive intermediates (e. g. alkyl radicals, carbocations). Red highlighted central atoms in various groups of chemical compounds. Tertiary central atoms compared with primary, secondary and quaternary central atoms.

primary

secondary

tertiary

quaternary

Carbon atom in an alkane

Alcohol

does not exist

Amine

Amide

does not exist

Phosphine

See also 

Primary (chemistry)

Secondary (chemistry)

Quaternary (chemistry)

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Chapter 27: Transfermium Wars The names for the chemical elements 104 to 106 were the subject of a major controversy starting in the 1960s, described by some nuclear chemists as the Transfermium Wars because it concerned the elements following fermium (element 100) on the periodic table. This controversy arose due to disputes between American scientists and Soviet scientists as to which had first isolated these elements. The final resolution of this controversy in 1997 also decided the names of elements 107 to 109. Controversy By convention, naming rights for newly discovered chemical elements go to their discoverers. However, for the elements 104, 105 and 106 there was a controversy between a Soviet laboratory and an American laboratory regarding which one had discovered them. Both parties suggested their own names for elements 104 and 105, not recognizing the other's name. The American name of seaborgium for element 106 was also objectionable to some, because it referred to American chemist Glenn T. Seaborg who was still alive at the time this name was proposed. (Einsteinium and fermium had also been proposed as names of new elements while Einstein and Fermi were still living, but only made public after their deaths, due to Cold War secrecy.) The USSR wanted to name element 104 after Igor Kurchatov, father of the Soviet atomic bomb, which was another reason the name was objectionable to the Americans. Opponents The two principal groups which were involved in the conflict over element naming were: 

An American group at Lawrence Berkeley Laboratory.

A Russian group at Joint Institute for Nuclear Research in Dubna.

and, as a kind of arbiter, 

The IUPAC Commission on Nomenclature of Inorganic Chemistry, which introduced its own proposal to the IUPAC General Assembly.

The German group at the Gesellschaft für Schwerionenforschung (GSI) in Darmstadt, who had (undisputedly) discovered elements 107 to 109, were dragged into the controversy when the Commission suggested that the name "hahnium", proposed for element 105 by the Americans, be used for GSI's element 108 instead. Preferred names Group

Atomic number Name

American 104

Eponym

rutherfordium Ernest Rutherford

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105

hahnium

106

seaborgium Glenn T. Seaborg

Russian 104

Otto Hahn

kurchatovium Igor Kurchatov

105

nielsbohrium Niels Bohr

Proposals

Darmstadt The suggested names for the elements 107 to 109 by the German group were: Atomic number Name

Eponym

107

nielsbohrium Niels Bohr

108

hassium

109

meitnerium Lise Meitner

Hesse, Germany

IUPAC In 1994, the IUPAC Commission on Nomenclature of Inorganic Chemistry proposed the following names Atomic number Name

Eponym

104

dubnium

Dubna, Russia

105

joliotium

FrĂŠdĂŠric Joliot-Curie

106

rutherfordium Ernest Rutherford

107

bohrium

Niels Bohr

108

hahnium

Otto Hahn

109

meitnerium

Lise Meitner

This attempted to resolve the dispute by sharing the namings of the disputed elements between Russians and Americans, replacing the name for 104 with one honoring the Dubna research center, and not naming 106 after Seaborg.

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Objections to the IUPAC 94 proposal This solution drew objections from the American Chemical Society (ACS) on the grounds that the right of the American group to propose the name for element 106 was not in question and that group should have the right to name the element whatever it wanted to. Indeed, IUPAC decided that the credit for the discovery of element 106 should be shared between Berkeley and Dubna but the Dubna group had not come forward with a name. Along the same lines, the German group protested against naming element 108 by the American suggestion "hahnium", mentioning the long-standing convention that an element is named by its discoverers. In addition, given that many American books had already used rutherfordium and hahnium for 104 and 105, the ACS objected to those names being used for other elements. Resolution (IUPAC 97) Finally in 1997, the following names were agreed on the 39th IUPAC General Assembly in Geneva, Switzerland: 104 - rutherfordium 105 - dubnium 106 - seaborgium 107 - bohrium 108 - hassium 109 - meitnerium Thus, the convention of the discoverer's right to name their elements was respected for elements 106 to 109, and the two disputed claims were "shared" between the two opponents. Summary Summary of various proposals and final decision: Atomic Systematic American

Russian

German

IUPAC 94

number

Final

name

(IUPAC 97)

104

unnilquadium rutherfordium kurchatovium —

dubnium

rutherfordium

105

unnilpentium hahnium

nielsbohrium —

joliotium

dubnium

106

unnilhexium seaborgium —

rutherfordium seaborgium

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107

unnilseptium —

nielsbohrium bohrium

bohrium

108

unniloctium

hassium

hassium

109

unnilennium —

meitnerium meitnerium

hahnium

meitnerium

See also 

List of chemical element name etymologies

List of chemical elements naming controversies (Includes Z = 23, 41, 70, 71, 74)

Systematic element name

IUPAC Nomenclature

External links 

Elementymology & Elements Multidict

Picture of a Seaborgium card autographed by Seaborg

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Chapter 28: Trivial name

The element mercury was named after the Greek god (painting by Hendrik Goltzius). In chemistry, a trivial name is a non-systematic name (common name) for a chemical. That is, the name is not recognized according to the rules of any formal system of nomenclature such as IUPAC nomenclature. Generally trivial names are not useful in describing the essential properties of the thing being named. Properties such as the molecular structure of a chemical compound are not indicated. And, in some cases, trivial names can be ambiguous or will carry different meanings in different industries or in different geographic regions. On the other hand, systematic names can be so convoluted and difficult to parse that their trivial names are preferred. As a result, a limited number of trivial chemical names are retained names, an accepted part of the nomenclature. Trivial names often arise in the common language; they may come from historic usages in, for example, alchemy. Many trivial names pre-date the institution of formal naming conventions. Names can be based on a property of the chemical, including appearance (color, taste or smell), consistency, and crystal structure; a place where it was found or where the discoverer comes from; the name of a scientist; a mythological figure; an astronomical body; the shape of the molecule; and even fictional figures. All elements that have been isolated have trivial names. Definitions In scientific documents, international treaties, patents and legal definitions, names for chemicals are needed that identify them unambiguously. This need is satisfied by systematic names. One such system, established by the International Union of Pure and Applied Chemistry (IUPAC), was established in 1950. Other systems have been developed by the American Chemical Society, the International Organization for Standardization, and the

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World Health Organization. However, chemists still use many names that are not systematic because they are traditional or because they are more convenient than the systematic names. These are called trivial names. The word "trivial", often used in a pejorative sense, was intended to mean "commonplace". In addition to trivial names, chemists have constructed semi-trivial names by appending a standard symbol to a trivial stem. Some trivial and semi-trivial names are so widely used that they have been officially adopted by IUPAC; these are known as retained names. Elements Main article: Chemical element#Element names See also: List of chemical element name etymologies and List of chemical elements naming controversies Traditional names of elements are trivial, some originating in alchemy. IUPAC has accepted these names, but has also defined systematic names of elements that have not yet been prepared. It has adopted a procedure by which the scientists who are credited with preparing an element can propose a new name. Once the IUPAC has accepted such a (trivial) name, it replaces the systematic name. Origins

A plaque commemorating a mine in Ytterby where ore was obtained from which four new elements were isolated. Nine elements were known by the Middle Ages – gold, silver, tin, mercury, copper, lead, iron, sulfur, and carbon. Mercury was named after the planet, but its symbol was derived from the Latin hydrargyrum, meaning liquid silver; mercury is also known as quicksilver in English. The symbols for the other eight are also derived from descriptions of their properties in Latin. Systematic nomenclature began after Louis-Bernard Guyton de Morveau stated the need for ―a constant method of denomination, which helps the intelligence and relieves the memory‖. The resulting system was popularized by Antoine Lavoisier's publication of Méthode de nomenclature chimique (Method of Chemical Nomenclature) in 1787. Lavoisier proposed that elements be named after their properties. For the next 125 years, most chemists followed this suggestion, using Greek and Latin roots to compose the names; for example, hydrogen ("water-producing"), oxygen ("acid-producing"), nitrogen ("soda-producing"), bromine ("stink"), and argon ("no reaction") were based on Greek roots, while for naming

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indium, iodine, rubidium, and thallium the Latin root for their color was used. Iridium, which makes compounds of many different colors, takes its name from iris, the Latin for "rainbow". The noble gases have all been named for their origin or properties. Helium comes from the Greek helios, meaning "sun" because it was first detected as a line in the spectrum of the sun (it is not known why the suffix -ium, which is used for metals, was chosen). The other noble gases are neon ("new"), argon ("slow, lazy"), krypton ("hidden"), xenon ("stranger"), and radon ("from radium"). Many more elements have been given names that have little or nothing to do with their properties. Elements have been named for celestial bodies (helium, selenium, tellurium, for the sun, moon, and earth; cerium and palladium for Ceres and Pallas, two asteroids). They have been named for mythological figures, including Titans in general (titanium) and Prometheus in particular (promethium); Greek gods (uranium, neptunium, and plutonium) and their descendents (tantalum for tantalus, a son of Zeus, and niobium for Niobe, a daughter of Tantalus); and Norse deities (vanadium for the goddess Vanadis and thorium for the god Thor). Discoverers of some elements named them after their home country or city. Marie Curie named polonium after Poland; ruthenium, gallium, germanium, and lutetium were based on the Latin names for Russia, France, Germany, and Paris. Other elements are named after the place where they were discovered. Four elements, terbium, erbium, ytterbium, and yttrium were named after a Swedish village Ytterby, where ores containing them were extracted. Other elements named after places are magnesium (after Magnesia), strontium, scandium, europium, thulium (after an old Roman name for the far north of Scandinavia), holmium, copper (derived from Cyprus, where it was mined in the Roman era), hafnium, rhenium, americium, berkelium, californium, and darmstadtium. For the elements up to 92 (uranium), naming elements after people was discouraged. The two exceptions are indirect, the elements being named after minerals that were themselves named after people. These were gadolinium (found in gadolinite, named after the Finnish chemist Johan Gadolin) and samarium (the mineral samarskite was named after a Russian mining engineer, Vasili Samarsky-Bykhovets). Among the transuranium elements, this restriction was relaxed, there followed curium (after the Curies), einsteinium, fermium (Enrico Fermi), mendelevium (Dmitri Mendeleev), nobelium, and lawrencium (after Ernest Lawrence). Relation to IUPAC standards See also: Chemical elements in East Asian languages IUPAC has established international standards for naming elements. The first scientist or laboratory to isolate an element has the right to propose a name; after a review process, a final decision is made by the IUPAC Council. In keeping with tradition, names can be based on a mythological concept or character, astronomical object, mineral, place, property of the element or scientist. For those elements that have not yet been "discovered", IUPAC has established a systematic name system. The names combine syllables that represent the digits of the atomic number, followed by "-ium". For example, "Unnunumium" is element 111 ("un" being the syllable for 1). However, once the element has been found, the systematic name is replaced by a trivial one. The IUPAC names for elements are intended for use in the official languages. At the time of the first edition of the IUPAC Red Book (which contains the rules for inorganic compounds), those languages were English and French; now English is the sole official language. However, other languages still have their own names for elements. The chemical symbol for tungsten, W, is based on the German name wolfram, which is found in wolframite and comes from the German for "wolf's foam", how the mineral was known to Saxon miners. The name

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tungsten means "heavy stone", a description of scheelite, another mineral in which tungsten is found. The German names for hydrogen, oxygen, and nitrogen are Wasserstoff (water substance), Sauerstoff (acid substance), and Stickstoff (smothering substance). The corresponding Chinese names are qingqi (light gas), yangqi (nourishing gas), and danqi (diluting gas). A scheme for translating chemical names into Chinese was developed by John Fryer and Xu Shou in 1871. Where traditional names were well established, they kept them; otherwise, a single character for a name was compounded out of one of the five xing (phases) – metal, wood, water, fire, and earth – and a sound from the English name of the element. Inorganic chemistry Early terminology for compound chemicals followed similar rules to the naming of elements. The names could be based on the appearance of the substance, including all five senses. In addition, chemicals were named after the consistency, crystalline form, a person or place, its putative medical properties or method of preparation. Salt (sodium chloride) is soluble and is used to enhance the taste of food. Substances with similar properties came to be known as salts, in particular Epsom salt (magnesium sulfate, found in a bitter saline spring in the English town of Epsom). Lead acetate was called sugar of lead. However, other names like sugar of lead (lead(II) acetate), butter of antimony (antimony trichloride), oil of vitriol (sulfuric acid), and cream of tartar (potassium bitartrate) borrowed their language from the kitchen. Many more names were based on color; for example, hematite, orpiment, and verdigris come from words meaning "blood-like stone", "gold pigment", and "green of Greece". Some names are based on their use. lime is a general name for materials combining calcium with carbonates, oxides or hydroxides; the name comes from a root "sticking or adhering"; its earliest use was as mortar for construction. Water has several systematic names, including oxidane (the IUPAC name), hydrogen oxide, and dihydrogen monoxide (DHMO). The latter was the basis of the dihydrogen monoxide hoax, a document that was circulated warning readers of the dangers of the chemical (for example, it is fatal if inhaled). Organic chemistry In organic chemistry, some trivial names derive from a notable property of the thing being named. For instance, lecithin, the common name for phosphatidylcholine, was originally isolated from egg yolk. The word is coined from the Greek word for yolk. Many trivial names continue to be used because their sanctioned equivalents are considered too cumbersome for everyday use. For example, "tartaric acid", a compound found in wine, has a systematic name of 2,3-dihydroxybutanedioic acid. The pigment β-Carotene has a IUPAC name of 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-1,3,5,7,9,11,13,15,17nonaenyl]cyclohexene. However, the trivial name can be potentially confusing. Based on their names, one might infer that α-Carotene, β-Carotene, δ-Carotene and ζ-Carotene are closely related in structure, origin or function, but they are not. Shape-based Several organic molecules have semitrivial names where the suffixes -ane (for an alkane) or -ene (for an alkene) are added to a name based on the shape of the molecule. Some are

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pictured below. Other examples include barrelene (shaped like a barrel),fenestrane (having a window-pane motif),ladderane (a ladder shape), olympiadane (having a shape with the same topology as the Olympic rings) and quadratic acid (also known as squaric acid). 

Basketane 

Cubane 

Dodecahedrane 

Housane 

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Olympicene 

Prismane 

Tetrahedrane Based on fiction

The antibiotic Rudolphomycin is named after the character Rodolfo from the opera La Bohème.

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The Bohemic acid complex is a mixture of chemicals obtained through fermentation of a species of actinobacteria. In 1977 the components were isolated and have been found useful as antitumor agents and anthracycline antibiotics. The authors named the complex (and one of its components, bohemamine) after the opera La bohème by Puccini, and the remaining components were named after characters in the opera: alcindoromycin (Alcindoro), collinemycin (Colline), marcellomycin (Marcello), mimimycin (Mimi), musettamycin (Musetta), rudolphomycin (Rodolfo) and schaunardimycin (Schaunard). However, the relationships between the characters do not correctly reflect the chemical relationships. A research lab at Lepetit Pharmaceuticals, led by Piero Sensi, was fond of coining nicknames for chemicals that they discovered, later converting them to a form more acceptable for publication. The antibiotic Rifampicin was named after a French movie, Rififi, about a jewel heist. They nicknamed another antibiotic "Mata Hari" before changing the name to Matamycin. See also ď&#x201A;ˇ

List of chemical compounds with unusual names

Further reading ď&#x201A;ˇ

Andraos, John. "Glossary of Coined Names & Terms Used in Science". careerchem.com. Canaca.com. Retrieved 3 November 2013.

Chapter 7: Vicinal (chemistry)

2,3-dibromobutane (at left) and 1,3-dibromobutane (at right). Carbons containing vicinal functional groups are marked in red. In chemistry vicinal (from Latin vicinus = neighbor) stands for any two functional groups bonded to two adjacent carbon atoms. For example the molecule 2,3-dibromobutane carries two vicinal bromine atoms and 1,3-dibromobutane does not. Likewise in a gem-dibromide the prefix gem, an abbreviation of geminal, signals that both bromine atoms are bonded to the same atom. For example, 1,1-dibromobutane is geminal. Like other such concepts as syn, anti, exo or endo, the description vicinal helps explain how different parts of a molecule are related to each other either structurally or spatially. The vicinal adjective is sometimes restricted to those molecules with two identical functional groups. The term can also be extended to substituents on aromatic rings.

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Chapter 29: Ylide An ylide or ylid (/ˈɪlɪd/ or /ˈɪlaɪd/) is a neutral dipolar molecule containing a formally negatively charged atom (usually a carbanion) directly attached to a heteroatom with a formal positive charge (usually nitrogen, phosphorus or sulfur), and in which both atoms have full octets of electrons. Ylides are thus 1,2-dipolar compounds. They appear in organic chemistry as reagents or reactive intermediates. The class name "ylide" for the compound should not be confused with the suffix "-ylide". Resonance structures Many ylides may be depicted by a multiple bond form in a resonance structure, known as the ylene form:

The actual electron distribution in the molecules and hence the relative importance of the ylide and ylene forms is dependent on the "onium" center and substituent pattern (the identity of the various R groups). Phosphonium ylides

Structure of methylenetriphenylphosphorane. Phosphonium ylides are used in the Wittig reaction, a method used to convert ketones and especially aldehydes to alkenes. The positive charge in these Wittig reagents is carried by a phosphorus atom with three phenyl substituents and a bond to a carbanion. Ylides can be 'stabilised' or 'non-stabilised'. A phosphonium ylide can be prepared rather straightforwardly. Typically, triphenylphosphine is allowed to react with an alkyl halide in a mechanism analogous to that of an SN2 reaction. This quaternization forms an alkyltriphenylphosphonium salt, which can be isolated or treated in situ with a strong base (in this case, butyl lithium) to form the ylide.

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Due to the SN2 mechanism, a less sterically hindered alkyl halide reacts more favorably with triphenylphosphine than an alkyl halide with significant steric hindrance (such as tert-butyl bromide). Because of this, there will typically be one synthetic route in a synthesis involving such compounds that is more favorable than another. Other ylide types

Based on sulfur Other common ylids include sulfonium ylides and sulfoxonium ylides, for instance the Corey-Chaykovsky reagent used in the preparation of epoxides or in the Stevens rearrangement. Based on oxygen +

-

Carbonyl ylides (RR'C=O C RR') can form by ring-opening of epoxides. Oxonium ylides + (RR'-O -C R'R) are prepared by reaction of ethers with diazo compounds. Based on nitrogen Certain nitrogen-based ylides also exist such as azomethine ylides with the general structure:

These compounds can be envisioned as iminium cations placed next to a carbanion. The substituents R1, R2 are electron withdrawing groups. These ylides can be generated by condensation of an Îą-amino acid and an aldehyde or by thermal ring opening reaction of certain N-substituted aziridines. Stable carbenes also have a ylidic resonance contributor e.g.:

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Other Halonium ylides can be prepared from allyl halides and metal carbenoids. After a [2,3]rearrangement a homoallylhalide is obtained. The active form of Tebbe's reagent is often considered a titanium ylide. Like the Wittig reagent, it is able to replace the oxygen atom on carbonyl groups with a methylene group. Compared with the Wittig reagent, it has more functional group tolerance. Ylide reactions An important ylide reaction is of course the Wittig reaction (for phosphorus) but there are more. Dipolar cycloadditions Some ylids are 1,3-dipoles and interact in 1,3-dipolar cycloadditions. For instance an azomethine ylide is a dipole in the Prato reaction with fullerenes. Dehydrocoupling with silanes In the presence of the group 3 homoleptic catalyst Y[N{SiMe3)2}3], triphenylphosphonium methylide can be coupled with phenylsilane. This reaction produces H 2 gas a by product, and forms a silyl-stabilised ylide.

Sigmatropic rearrangements Many ylids react in sigmatropic reactions. The Sommelet-Hauser rearrangement is an example of a [2,3]-sigmatropic reaction. The Stevens rearrangement is a [1,2]rearrangement. A [3,3]-sigmatropic reaction has been observed in certain phosphonium ylids

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Allylic rearrangements Wittig reagents are found to react as nucleophiles in SN2' substitution:

The initial addition reaction is followed by an elimination reaction. See also 

1,3-dipole

Zwitterion: a neutral molecule with one or more pairs of positive and negative charges

Betaine: a neutral molecule with an onium cation and a negative charge

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Line notation Source: https://en.wikipedia.org/w/index.php?oldid=553809309 Contributors: Billy Rushton, Clicketyclack, Dthomsen8, Itub, Jeodesic, Joerg Kurt Wegner, John Vandenberg, Oleg Alexandrov, Rich Farmbrough, 2 anonymous edits

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Monosaccharide nomenclature Source: https://en.wikipedia.org/w/index.php?oldid=589502409 Contributors: AdventurousSquirrel, D6, Dineshts, Glycoform, Hystrix, Jkwchui, Jorge Stolfi, LilHelpa, M-le-mot-dit, Marek69, Matt18224, Mdewman6, Odysseus1479, Omegakent, Selkie upsilon, Tabletop, Δ, 9 anonymous edits

Noble metal Source: https://en.wikipedia.org/w/index.php?oldid=577233342 Contributors: Abdull, Achim1999, Amberroom, Art LaPella, Asfarer, Bcharles, Benbest, Bgpaulus, Bluemoose, Borgx, Chem-awb, Chemicalinterest, Christophenstein, Cmjayakumar, Common Man, Cybercobra, Donfbreed, DopefishJustin, Double sharp, Edgar181, EgraS, Enochlau, Enz, Everyking, Fangjian, Furrykef, Gioto, Hari Eswar SM, Hede2000, Heeero60, Icairns, Ike9898, Itub, Jimp, Knuckles, KoshVorlon, Kpjas, Magog the Ogre 2, Mandarax, Materialscientist, McDoobAU93, Mccready, Metre01, Michał Sobkowski, Mtz1010, N2e, PhilKnight, Physchim62, Piledhigheranddeeper, Pinethicket, Polyparadigm, Rami radwan, RandomP, Rayc, Rich Farmbrough, Rifleman 82, Rune.welsh, Rursus, Sanya3, Sasakubo1717, Satori Son, Scientific29, Scyldscefing, Seth Nimbosa, Shad0, Skittle, Sligocki, Smackeldorf, Softballbaby984, T.J.S.1,

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Nomenclature of monoclonal antibodies Source: https://en.wikipedia.org/w/index.php?oldid=583808107 Contributors: Anypodetos, Arcadian, Aztec Master, Blake3522, BlakeCS, Circeus, ClickRick, DO11.10, Danierrr, Flacruzb, Jfdwolff, Knowledge Seeker, Knowledgejwl, Kwamikagami, MarcoTolo, NCurse, Nephron, Night Gyr, Renji143, Rjwilmsi, Swpb, Tyranitar Man, 12 anonymous edits

Nomenclature of Organic Chemistry Source: https://en.wikipedia.org/w/index.php?oldid=564588948 Contributors: Alansohn, Fadesga, Physchim62, Rhadamante, Thorwald, Wickey-nl, 6 anonymous edits

Oligosaccharide nomenclature Source: https://en.wikipedia.org/w/index.php?oldid=483313691 Contributors: Alice.haugen, Ccostell, Giraffedata, Glycoform, Harbinary, Headbomb, IceCreamAntisocial, JHunterJ, Odysseus1479, Omegakent, Prishly, Rifleman 82, Sadads, ‫ال بط ع لي ح سن‬

Organic nomenclature in Chinese Source: https://en.wikipedia.org/w/index.php?oldid=570612491 Contributors: Anthony Appleyard, ArnoldReinhold, Benlisquare, Bumm13, Colonies Chris, PamD, SchreiberBike, Visik, Wavelength, Wyang, Ymwang42, 24 anonymous edits

Ortho acid Source: https://en.wikipedia.org/w/index.php?oldid=545352121 Contributors: Christian75, Itub, Kupirijo, Sadads, TimVickers

Oxidation state Source: https://en.wikipedia.org/w/index.php?oldid=593785441 Contributors: 28bytes, AThing, Addihockey10, Ahoerstemeier, Aisteco, Aitias, Akiioni, AlanPalgut, Alchemy Heels I, Alsandro, Am088, Amcg0722, Andre Engels, Angorohovski, Anoop.m, AxelBoldt, Axiosaurus, Benbest, Bgwhite, Bigbuck, Biopresto, Bmdavll, Bomac, Brane.Blokar, Bsadowski1, Bsimmons666, Bucketsofg, Charles Gaudette, Chem-helsinki, Christian75, Cornellrockey, Cyanos, Daniel Bonniot de Ruisselet, Delirium, DemonThing, Difluoroethene, Dirac66, DoSiDo, Double sharp, DragonflySixtyseven, Drphilharmonic, Dwmyers, Eivindgh, EtymAesthete, Exercisephys, Extasic Wale, Eyreland, Felix Wan, Femto, Foodeatingperson, GB fan, Gentgeen, Gscshoyru, Gunderberg, HMSSolent, Hang Li Po, Hellbus, Hood0023, Hqb, Hvn0413, IW.HG, InverseHypercube, Itub, JSquish, James Crippen, Jaxl, Jj137, John Cumbers, Julesd, Kingpin13, Kjkolb, Klilidiplomus, Knotgoblin, LedgendGamer, Lee1026, Lifeformnoho, Looxix, Marqueed, Mat-C, Materialscientist, Maxxicum, Mirwin, Mister Macbeth, Mário, NBeddoe, Narayansg, Nczempin, Nergaal, Niceguyedc, Nneonneo, Octahedron80, Olly150, PEarley (WMF), Palica, Peter Karlsen, Physchim62, Pinethicket, Pranav1195, Puppy8800, Radon210, Ramendoctor, Riana, Richard001, RolfSander, Rpm2004, S Schaffter, Sbharris, ScAvenger lv, Scarian, Sewebster, Siim, Smallman12q, Smokefoot, Snowolf, Sodium, Spinning quirK, Stifynsemons, Sulfurio, TYelliot, Ta bu shi da yu, TheEditrix2, Thechamelon, This, that and the other, Tlroche, Tsemii, Urocyon, V8rik, Vader Terence, Vanished user vjhsduheuiui4t5hjri, Vsmith, Walkerma, WaysToEscape, Wickey-nl, Wtmitchell, Yuetyanli, Zeimusu, Јованвб, 236 anonymous edits

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Parent hydride Source: https://en.wikipedia.org/w/index.php?oldid=405875633 Contributors: Wickey-nl

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Parts-per notation Source: https://en.wikipedia.org/w/index.php?oldid=587256411 Contributors: A. di M., Aeropedia, Andre Engels, AndrewHowse, Andros 1337, Angr, Bernoullies, Bgwhite, Bkell, Blair P. Houghton, Bobblewik, Bobrayner, Bookandcoffee, CALR, Candymishal, Carbuncle, Ceyockey, Chtfn, Classicalecon, ClickRick, Closedmouth, Cool3, Crd721, Crissov, Davidomackay, DeadEyeArrow, Den fjättrade ankan, DmitTrix, Ehrenkater, El Irlandés, Electron9, Epbr123, Erasmus, Eric-Wester, Espoo, Firien, Frosted14, Gaius Cornelius, Gene Nygaard, Gerrit, Gh5046, Greg L, Ground Zero, Hadlock, Heron, Hooperbloob, Hydrargyrum, Icairns, Ignoramibus, InverseHypercube, Itub, J. W. Love, Jclerman, Jeepo, Jeronimo, Jianhui67, Jimp, Keenan Pepper, KnowledgeOfSelf, KudzuVine, Lodgerease, Magioladitis, Marshlight, Maxim Razin, Mbeychok, Mike Dillon, Mnmngb, Mokhtari, Muad, Mwtoews, NCDane, NHSavage, Nonagonal Spider, Not-just-yeti, Oleg Alexandrov, Orzetto, OutPhase, OwenX, Oxymoron83, PabloStraub, Pakaraki, Patrick, Physchim62, Pm, Pzavon, Q Science, R8R Gtrs, Radius, RedKnight7, RolfSander, SEWilco, Saippuakauppias, Sarregouset, Savantas83, Savonnn, SebastianHelm, Shadowjams, Shell Kinney, Shellreef, Sligocki, Smsarmad, Spiffy sperry, Spinningspark, Srleffler, The Ultimate Koopa, Thecurran, Thorwald, Thumperward, Tomchiukc, Tommy2010, TransUtopian, Trevor Andersen, Violetriga, Vsmith, Vuo, Yamlikha, Zosma, Zyxwv99, ‫زادگ ان ق لی‬, 146 anonymous edits

Phanes (organic chemistry) Source: https://en.wikipedia.org/w/index.php?oldid=544477214 Contributors: Khatru2, LouisBB, Nagelfar, V8rik

Preferred IUPAC name Source: https://en.wikipedia.org/w/index.php?oldid=562797565 Contributors: Cantukarol, Chris the speller, Dcirovic, Lamro, NuclearWarfare, O.Koslowski, Physchim62, Wickey-nl, 4 anonymous edits

Primary (chemistry) Source: https://en.wikipedia.org/w/index.php?oldid=551848536 Contributors: DMacks, Jü, Odysseus1479, 1 anonymous edits

Quantities, Units and Symbols in Physical Chemistry Source: https://en.wikipedia.org/w/index.php?oldid=586328070 Contributors: BD2412, Bookinvestor, ChrisGualtieri, DeMk9D76, Derek farn, Drechem, Fadesga, FizykLJF, Kehrli, Pegship, Physchim62, PlasmaDragon, Rhinde, Rifleman 82, Trunks ishida, 3 anonymous edits

Quaternary (chemistry) Source: https://en.wikipedia.org/w/index.php?oldid=551868567 Contributors: DMacks, Fvasconcellos, Jü, Odysseus1479, 2 anonymous edits

Redox gradient Source: https://en.wikipedia.org/w/index.php?oldid=538352214 Contributors: Oliverjknevitt, Pdcook, Santryl, Senator2029, 1 anonymous edits

Retained name Source: https://en.wikipedia.org/w/index.php?oldid=580103186 Contributors: Physchim62, RockMagnetist, Wickey-nl

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Secondary (chemistry) Source: https://en.wikipedia.org/w/index.php?oldid=551953763 Contributors: DMacks, Fvasconcellos, Jü, Odysseus1479, 2 anonymous edits

Simplified molecular-input line-entry system Source: https://en.wikipedia.org/w/index.php?oldid=593918429 Contributors: 129.186.19.xxx, AManWithNoPlan, Adrian J. Hunter, Albmont, Alex17nico, Altenmann, Andersneld, Andreww, AxelBoldt, Bigeard2007, Bryan Derksen, CALR, Cacycle, Cantukarol, CapitalR, ChemConnector, Chester Markel, Chinasaur, Chris Dybala, Christian75, Conversion script, DMacks, David Eppstein, Decastries2007, Dirac1933, Dugwiki, Edgar181, EgonWillighagen, Egonw, Eoseth, Extremo88, FghIJklm, Firien, Gaius Cornelius, Geracudd, Glrx, Gmutizabal, GregorB, Gringer, Hvn0413, JaGa, JesseAlanGordon, Jesshhiieee, Joerg Kurt Wegner, JonHarder, Katnap01, Keenan Pepper, Kevinmon, Kku, KnightRider, Lahiru k, M1ss1ontomars2k4, Malatinszky, Maneesh, Marj Tiefert, MaxSem, McGeddon, Meco, Michael Hardy, Mikeblas, Mikespedia, Millsey, Mlessard, Mykhal, Nneonneo, Nono64, Nowyouseeme, Oiseau Furtif, Paul Drye, Peak, Philip Trueman, Physchim62, Pit, Planetneutral, Plasmic Physics, Quasar Jarosz, R'n'B, Ringill, Rjwilmsi, RyanJones, Sarvagna, Saucepan, ShelfSkewed, Shyamal, Sidhu 2201, Silverhill, Slashme, Sleigh, SpK, Spiff, Stewartadcock, Tony1, Virtualx, Wayne Slam, X14n, Yikrazuul, Yohananw, Ysangkok, Yworo, Zephalis, Zurrr, ~K, 125 anonymous edits

Stock nomenclature Source: https://en.wikipedia.org/w/index.php?oldid=545895366 Contributors: Benjah-bmm27, Christian75, Rjwilmsi, Wavelength

Structural analog Source: https://en.wikipedia.org/w/index.php?oldid=591092540 Contributors: Anrnusna, Apayne, Arch dude, Cacycle, Can't sleep, clown will eat me, ChemGardener, Ctdunstan, Dcirovic, Dreg743, Elvim, Eric Martz, ForestAngel, Freestyle-69, Gklambauer, Guanxi, Jamesters, Jmjanzen, Kku, Mets501, NeutralLang, Rjwilmsi, SimonP, Telewatho, Vsmith, Westfall, Wickey-nl, 17 anonymous edits

Substituent Source: https://en.wikipedia.org/w/index.php?oldid=590837844 Contributors: Alan Liefting, Anthony Appleyard, Arcadian, Bluemoose, Bobo192, Borgx, Chessphoon, Christian75, Cwkmail, Darkwind, Dcirovic, Drphilharmonic, Edgar181, Epbr123, Hoschimobi, Jorge Stolfi, Kupirijo, Lazypenguin13, Lfstevens, LilHelpa, Loutre en goguette, Melamed katz, Mike Serfas, Mrloloo, Paddles, Patrick, Patrickg, Pucesurvitaminee, Puppy8800, SchreiberBike, Smappy, Thumperward, Tonyrex, Tungstic, V8rik, Wickey-nl, Widr, 26 anonymous edits

Substrate analog Source: https://en.wikipedia.org/w/index.php?oldid=545605753 Contributors: Cacycle, Jesse V., Rawkergirl, Vector209

SYBYL line notation Source: https://en.wikipedia.org/w/index.php?oldid=563041630 Contributors: Cantukarol, Decastries2007, Endorf, Gigacephalus, Glrx, Joerg Kurt Wegner, Tony1, WebsterHomer, 1 anonymous edits

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