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ChemistryattheFrontierwithPhysics andComputerScience

TheoryandComputation

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Chemistryatthe FrontierwithPhysics andComputerScience

TheoryandComputation

SergioRampino

FacultyofScience

Pisa,Italy

Elsevier

Radarweg29,POBox211,1000AEAmsterdam,Netherlands

TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates

Copyright©2022ElsevierInc.Allrightsreserved.

Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans, electronicormechanical,includingphotocopying,recording,oranyinformationstorageand retrievalsystem,withoutpermissioninwritingfromthepublisher.Detailsonhowtoseek permission,furtherinformationaboutthePublisher’spermissionspoliciesandourarrangements withorganizationssuchastheCopyrightClearanceCenterandtheCopyrightLicensingAgency, canbefoundatourwebsite: www.elsevier.com/permissions.

Thisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythe Publisher(otherthanasmaybenotedherein).

Notices

Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchand experiencebroadenourunderstanding,changesinresearchmethods,professionalpractices,or medicaltreatmentmaybecomenecessary.

Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgein evaluatingandusinganyinformation,methods,compounds,orexperimentsdescribedherein.In usingsuchinformationormethodstheyshouldbemindfuloftheirownsafetyandthesafetyof others,includingpartiesforwhomtheyhaveaprofessionalresponsibility.

Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors, assumeanyliabilityforanyinjuryand/ordamagetopersonsorpropertyasamatterofproducts liability,negligenceorotherwise,orfromanyuseoroperationofanymethods,products, instructions,orideascontainedinthematerialherein.

ISBN:978-0-323-90865-8

ForinformationonallElsevierpublications visitourwebsiteat https://www.elsevier.com/books-and-journals

Publisher: SusanDennis

AcquisitionsEditor: CharlesBath

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ProductionProjectManager: SruthiSatheesh

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ToCécile,JulieandLilas

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6.Thepotential-energysurface

7.Theoreticaltreatments

8. Fromtheorytocomputing :collinearreactivescattering withrealwavepackets

9.Fromreactiondynamicstochemicalkinetics

11.Towardscomplexity

13. Fromtheorytocomputing :theHartree–Fockmodel

13.1TheRoothaan–Hallequations

13.3Basisfunctionsandone-andtwo-electronintegrals

14.Theatomandthebond

14.1Partitioningschemes

15. Fromtheorytocomputing :analyzingthe electron-chargeredistribution

15.1Object-basedprogramming

16. Application:donationandbackdonationin coordinationchemistry

16.1Themetal–carbonylcoordinationbond

17.Relativityandchemistry 17.1Relativisticquantumchemistry

PartIV

Chemistryandcomputerscience

19.Virtualreality

19.1Scientificvisualizationandvirtualreality

20.Data-drivenchemistry

Biography

SergioRampino

SergioRampinowasborninMesagne(Apulia,Italy)in1984.Hegraduated withhonorsinChemistry(2007)andItalianLanguageandLiterature(2012)at theUniversityofPerugia,wherehealsoobtainedhisPhDinChemistry(2011). In2017hewasappointedlecturerinTheoreticalandComputationalChemistry attheScuolaNormaleSuperioreinPisa,wherehepresentlyteachesbothundergraduateandPhDstudents.Hisresearch,partlycarriedoutatseveralEuropean researchandcomputingcenters,hasfocusedonseveraltopicsofgeneral,physicalandinorganicchemistryrangingfromthequantumdynamicsofelementary reactionstorelativisticdensity-functionaltheory,theanalysisofchemicalbonding,andtheuseofvirtual-realitytechnologyforchemistry.In2016hewas awardedthe‘EoloScrocco’prizebytheDivisionofTheoreticalandComputationalChemistryoftheItalianChemicalSociety.

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Preface

Ognipetraàzaparete. (‘everystonemakesthewallalittlehigher’,oldapuliansaying)

WhenIenteredtheclassroomtoattendmyfirstuniversitylesson,thiswasageneralchemistryoneandIwasaneighteen-year-oldstudentwithabackgroundin artsandhumanitiesandwithnoideaofwhattoexpectforthenextfiveyears.It tookmeseveralmonthstobecomeacquaintedwithanewparadigmofconceivingandrelatingtoreality,andacoupleofyearsofclassesandlaboratoriesof organic,physical,inorganicandbiologicalchemistrybeforemycompasscould findtheNorthinahighlyfascinating,albeitlesspopular,facetofchemistryat thecrossroadswithphysicsandcomputerscience.

Itisinthissubdisciplineofchemistry,labeledbytheadjectives‘theoretical andcomputational’,thatIhavepursuedtheacademicpathsincethestartofmy PhDprojectin2007.InaboutfifteenyearsofresearchIhavebeenluckyenough toworkonsuchdiverseandfascinatingsubjectsasthedynamicsofchemical reactions,theanalysisofchemicalbonding,theeffectsofrelativityonchemistry,andtheintegrationofimmersivevirtualrealityinchemicalapplications.I metextraordinarypeopleandhadthechanceofvisitingresearchandcomputing centersinwonderfulplacessuchasEdinburgh,Bristol,Toulouse,Paris,Zurich, BarcelonaandCracow,thefondmemoriesofwhichshallforeverbeinextricably linkedwiththetopicsofmyresearch.

InJuly2020,IreceivedaninvitationbythePublishertoauthoranewbook inthefieldoftheoreticalandphysicalchemistry,andIhadnohesitationinacceptingasIregardeditasanopportunitytosumuptheworkofalltheseyears andofferapersonalperspective,withconcreteexamplesfrommyownresearch activity,onthedisciplineonwhichIhad,overtime,specialized.Iamextremely gratefultotheacquisitionseditorAnnekaHessforthatcontact.Duringthefollowingmonths,IreceivedprecioushelpfromprojectmanagersDevlinPerson andVeronicaIIISantos,andfromthepermissionscoordinatorNarmathaMohan.Iamgratefultothemfortheirsupportduringthevariousstagesofthebook production.IwouldalsoliketothankVickyPearsonEsserforherexcellent

jobindesigningthebookcover,andtheproductionmanagerSruthiSatheesh, togetherwithanyotherpersonwhowasinvolvedintheproductionofthebook.

Theorganizationofthisbookpartlyreflectsthestructureandcontentofthe coursesthatIheldattheScuolaNormaleSuperioreinPisa,Italy,from2017to 2022,andofaseriesofoutreachlecturesthatIdeliveredforayoungeraudience withintheinitiative‘LaNormaleaScuola’organizedbytheScuolaNormale Superioreasasupporttohigh-schoolstudentsduringtheCovid-19globalhealth emergency.Iamgratefultoallthestudentswhoattendedmycoursesoverthese yearsfortheirpreciousfeedback.Inturn,thepresentationofthetheoretical aspectsofthebook,especiallythoserelatedtothefundamentalsofquantum mechanics(Chapter 2)andelectronic-structuretheory(Chapter 12 andpartof Chapter 13),drawsontheintroductorycoursesintheoreticalchemistryheldby Prof.FrancescoTarantelliattheUniversityofPerugiain2005–2007,whilethe descriptionoftheVerletalgorithminSection 7.1 drawsonusefullecturenotes byProf.HannesJónsson.

IamverygratefultomyacademicmentorsProf.AntonioLaganàand Prof.VincenzoBarone,fortheopportunityofworkingwiththemandforthe many,manystimulatingdiscussions,andtoallthepeoplewhohavecollaboratedwithmeovertheyears,manyofwhomfigureascoauthorsofthearticles citedinthisbook.Inparticular,IamgratefultoStefanoCrocchianti,Dimitrios Skouteris,andLorianoStorchiforinitialguidancein,respectively,scientific programming,quantumreactivescattering,andparallelcomputing,andtoProf. AntoninoPolimenoandProf.MircoZerbettofortheopportunityofworking oninterestingnewtopicsopeningnewperspectivesinmyresearch.Iamalso gratefultoDr.KennethLawley,Prof.KimBaldridge,Prof.StefanoEvangelisti, Prof.GabrielBalint-Kurti,Prof.ErnestoGarcía,Prof.IreneBurghardt,Dr.MariuszSterzel,andProf.CaroleMorrisonforhostingshort-termscientificvisitsto theirgroupsfinancedbytheEuropeanCOSTandHPC-Europaprogrammes. SpecialthanksarefinallyduetomyyoungercollaboratorswhoseworkIhad thechanceofsupervisingandtowhomIwishthebestfortheirfuture:Matteo DeSantis,LorenzoPaoloni,SimonePotenti,SurajitNandi,BernardoBallotta, LucaSagresti,SilviaAlessandrini,andGiovanniNottoli.

ThewritingofthisbookhasoccurredtomeatatimewhentheIrishflute enteredwildlyintomylife.IamgratefultofellowmusiciansStefanoBattaglia, YuriBernardini,DiegoCeccarelli,LorenzoDelGrande,AntonioMalacarne, NicoMarraccini,CarloRogo,andGiovanniSteaforthehundredsofjigsand reelsandforthememorable craic,andtomaestroCarloIpataforseveralfruitfulandlivelyflutelessons.Ithasalsooccurredinnotsoeasytimesofprecarity, sometimesparadoxicallymadeharderbythesametransdisciplinaryvocation thatanimatesthisbook,andthathardlyreconcileswiththehighdegreeofspecializationthatcharacterizesthecurrentacademicworld.Fortheirsupportand theirpresence,Iamgratefultomyfamily,CécilePirat,JulieandLilasRampino, tomyfamilyoforigin,GabrieleRampino,IreneandLuciaAmmaturo,Ade-

Preface xv

laide,Guido,GiulianaandDanieleRampino,toDrs.PaoloCatanzaroandAriannaLuperini,andtoAriannaFederici. TothelovingmemoryofJonMikelAzpiroz.

SergioRampino ScuolaNormaleSuperiore March2022

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Chapter1

Introductionandscope

1.1Introductionandscope

Thisbookisanintroductiontotheoreticalandcomputationalchemistrythat aimsatframingchemistrybetweenitsneighboringdisciplinesphysicsandcomputerscience.Modernchemistrymaybedefinedasthebranchofsciencethat aimsatmodelingandunderstandingthepropertiesandbehaviorofmatteratthe atomicandmolecularlevel.Theoreticalandcomputationalchemistry,asopposedtoexperimentalchemistry,isasubdisciplineofchemistrypursuingthe sameobjective‘comfortably’frombehindadesk,withtheaidofpenandpaper aswellasofmoderninformationandcommunicationtechnology,ratherthanin alaboratory.Inotherwords,itusesthelawsofphysicstopredictthebehavior ofmolecularsystemsintermsoftheirconstitutingparticles,thenucleiandthe electrons.

Thiswellexplainsthefirstadjective(‘theoretical’)1 ofthedyadthatcharacterizesthisdisciplineandthatappearsasasubtitletothisbook.Thesecond adjective(‘computational’)2 owesitsraisond’êtretothefactthatthemathematicalapparatusinvolvedbythetheoryissocomplexthattheuseofacomputer ismandatoryinordertoefficientlyperformtherequirednumberofoperations andtohandletheinvolved(oftenhuge)amountofdata.

Theoryandcomputationarealsothetwoextremesofajourneywithintermediatestagesthatleadsfromphysicstochemistrythroughmathematicsand computerscience,andthatfitswellintothefollowinghierarchicalscheme:

• Theory

• Model

• Method

• Implementation

• Computation

Thesefivestages,whichreflectthedailyactivityofatheoreticalandcomputationalchemist,maybedescribedasfollows.Thephysicaltheoryrequiredfor anaccuratemodelingofatomsandmoleculesturnsouttobetoocomplexand oneroustobeusedasis,sothatapproximationsareoftenintroducedthrough

1 Theword‘theory’curiouslyderivesfromaGreekrootmeaning observation,whichisthemain activityofthe‘experiment’.Theoryisindeedconstructedbyrationalizingtheoutcomeofobservation,andthenusedtomakepredictionsonnewobservations:onemaysuccinctlysaythatitfollows observationinordertoprecedeit.

2 Theword‘computation’hasaLatinrootmeaningtocount,tocalculate.

modelsthatsimplifythephysicalandmathematicaltreatment.Modelsareput intoactionthroughmethods,whichinturnrequireaneffectiveimplementation onacomputer.Thisleadstothelaststage,computation,wherecalculationsare performedandtheiroutcomeiselaboratedandtransformedintochemicalinsight.

Thepurposeofthisbookistoillustrate–andaccompanythereader through–thisjourneybyconjugatingthebigpicturetothemostpracticalimplicationsor,inotherwords,byframingchemistryintheoverallcontextwhereit relatestophysicsandcomputersciencewhileatthesametimeofferingpractical examplesofhowtosolveachemicalproblemfromatheoreticalandcomputationalperspective,goingfromtheorytomodels,methods,implementation,and computation.Forthatpurpose,thetwocentralconceptsinchemistryofchemicalreactionandchemicalbondingwillbetakenasleadingthemestoillustrate thetreatmentofthetwobasicparticlesthatconstitutematterattheatomic andmolecularlevel:thenucleiandtheelectrons,respectively.Accordingly, afterreviewingthephysicsofmolecularsystemsandintroducingtheBorn–Oppenheimerapproximation,whichallowsfortheseparationofthenuclearand electronicmotions,theconceptsofchemicalreactionandchemicalbonding areexploredwithreferencetotheunderlyingnucleardynamicsandelectronic structure.

Constantattentionisgiventhroughoutthebooktopracticalaspectsconnectedtothenumericalresolutionoftherelevantequationsandtherelated implementationincomputerprograms,whichhaveplayedakeyroleinthe developmentofthedisciplineitself.Forachoiceofthreephysicalproblems (wavepacketdynamics,Hartree–Fockequations,electron-cloudredistribution) adetailedaccountfromtheorytoimplementationisgiventhroughtheseries ofchapters Fromtheorytocomputing,whiletheapplicationofthediscussed methodologiestorelevantchemicalproblemsfromtheauthor’sresearchareillustratedthroughthechapterseries Applications.Computer-codeexampleswill begivenintheFortran95programminglanguage,andshouldbefullyaccessible toreaderswithintermediate-levelexperienceincomputerprogramming.Onthe otherhand,therelationbetweenchemistryandcomputerscienceisnowadays rapidlyevolvingduetotheconstantprogressininformationandcommunicationtechnology,sothattheroleofcomputerscienceinchemistrygoeswell beyondthetraditionalaspectofscientificcomputing.Thefinalpartofthebook dealswiththemostrecentperspectivesduetotheconnectionofchemistrywith computerscience.

Inmoredetail,thebookisstructuredasfollows:

InPart I, Physicsandchemistry,thephysicsofmolecularsystemsisreviewedwithemphasisontheparadigmchangefromclassicaltoquantummechanics(Chapter 2).Chapter 3 explorestherelationbetweenphysicsandchemistryandprovidesanintroductiontotheconceptsofchemicalreactionsand chemicalbondingthatwillbedevelopedinParts II and III,respectively,witha focusontheperspectiveofachemistasopposedtothatofaphysicist.Chapter 4

providesabriefhistoricalaccountonthebirthandevolutionoftheoreticaland computationalchemistrywithreferencetothetopicstreatedinthisbook.

Part II, Nucleardynamicsandchemicalreactions,isdevotedtothetreatment ofthenuclearmotionandtheillustrationofthemodelingofchemical-reaction dynamics.Inparticular,Chapter 5 revisitschemicalreactionsfromthephysical perspectiveofcollisiontheory.Chapter 6 isdevotedtoacornerstoneconcept inchemistry,thatofthepotential-energysurface.Chapter 7 reviewsthemain theoreticalapproachesforthetreatmentofthenuclearmotion.Chapter 8,the firstoftheseries Fromtheorytocomputing,focusesontheimplementationof aquantummethodformodelingtheevolutionofasimplereaction.InChapter 9,therelationbetweenthemicroscopicviewofsinglecollisionalprocesses andthemacroscopiconeofchemicalkineticsisaddressed.Chapter 10 illustratesthestudyofanastrochemicalreactionthroughthepreviouslydiscussed methodologies.Finally,Chapter 11 providesanoverviewofthemainmethods tacklingnucleardynamicsinmorecomplexcontexts.

InPart III, Electronicstructureandchemicalbonding,wemoveontothe othersideoftheBorn–Oppenheimerapproximationanddealwiththetreatment oftheelectronsandtheirroleinchemicalbonding.Afterillustratingthefundamentalelectronic-structuretheory(Chapter 12),theimplementationofabasic electronic-structureprogramisdiscussedinChapter 13 (secondoftheseries Fromtheorytocomputing).Thenthechemicalconceptsofatomsandbonds arerevisitedintermsofthepreviouslyintroducedmathematicalandphysicalformalism(Chapter 14),andtheimplementationofacomputerprogram foranalyzingtheelectron-chargeredistributionoccurringuponchemicalbondingisdiscussed(Chapter 15,thirdoftheseries Fromtheorytocomputing). Chapter 16,throughastudyofchemicalbondinginadiverseclassofmetal–carbonylcomplexes,illustrateshowthechemicalconceptsof σ -donationand π -backdonationcanbemodeledthroughthepreviouslydiscussedmethodologiesrootedinthequantummechanicsoftheelectrons.Chapter 17,thelast chapterofPart III,dealswiththefrontiertopicoftheeffectsofrelativityin chemistry,withafocusonthechemistryoftheso-calledsuperheavyelements.

Part IV, Chemistryandcomputerscience,thefinalpartofthebook,explores theconnectionsbetweenchemistryandcomputerscience.Inparticular,Chapter 18 focusesonthetraditionalaspectofscientificcomputing.Afterreviewing thebasicsofcomputerprogramming,thetopicofparallelcomputing(inits high-performanceandhigh-throughputflavors)isdiscussed,andaconcreteexampleofparallelizationofarelativisticelectronic-structureprogramisgiven. Chapter 19 showshowstate-of-the-artvirtual-realitytechnologycanenhance scientificresearchandeducationinchemistrythroughthedescriptionoftwo applicationsdirectlyrelatedtothemodelingofchemicalreactionsandtheanalysisofchemicalbondingdiscussedinParts II and III ofthebook,respectively.

InChapter 20,emergingparadigmsbasedonartificialintelligenceandmachine learningforadata-drivenapproachtochemistryarediscussed.Theconcluding

chapter,Chapter 21,dealswithchallengesandimplicationsofthemostrecent perspectiveofchemistryasanopenscience.

1.2Notationandconventions

Forthereader’sconvenienceasummaryofthenotationandconventionsadopted inthebookisgiveninthefollowing.Aselectionofthemostrelevantsymbols usedinthebookisgivenbelow.Symbolsaregroupedtogetheronthebasisofthe domaintowhichtheyarerelevant,andlistedinanorderthatlargelyreflectstheir appearanceinthebook.Afewsymbolsareusedwithdifferentmeaningindifferentpartsofthebooksoastoadheretoconventionalnotationsspecifictosome topics(e.g.,thescatteringmatrixinnucleardynamicsandtheoverlapmatrixin electronicstructurearebothoftennotatedwith S ).However,thisshouldhave noeffectontheoverallreadabilityasitshouldalwaysbeclearfromthecontext whattherepeatedsymbolsreferto.Insomepartsofthebook,wheredeclared, useismadeofatomicunits,wherebythemassoftheelectron me ,thecharge oftheelectron |e |,Planck’sconstant = h 2π ,andtheBohrradius a

areallsettounity(fromtheexpressionof a0 ,itfollowsthatalsotheCoulomb constant kc isequalto1inatomicunits).Lowercaseanduppercaseboldcharactersaregenerallyadoptedforvectorsandmatrices,respectively.Curlybrackets areusedtoindicatesetsofvariables.The i subscriptdenotesvariablesrelated tothe i thelectron,the a subscriptdenotesvariablesrelatedtothe a thnucleus. Whenmorethanonesubscriptisnecessary, i , j , k , l areusedforelectronsor molecularorbitals, a and b areusedfornuclei,and p , q , r , s areusedforatomic orbitals(basisfunctions).Thesymbol δij indicatestheKroneckerdelta(δij = 0 if i = j , δij = 1if i = j ).SomeintegralsareexpressedinDirac(orbra-ket) notation,whereby

Generaltheory

P(x) probabilitydistribution

p(x) probabilitydensity

ξ collectivecoordinate

p momentumvector

ˆ p momentumoperator

r positionvector

ˆ r positionoperator

Molecularquantummechanics

{r i } setofelectroniccoordinates

{r a } setofnuclearcoordinates

Ψ molecularwavefunction nuclearwavefunction

ψ electronicwavefunction

Za atomicnumberofnucleus a

ma massofnucleus a

me massofelectron

e chargeofelectron Planck’sconstant

kc Coulomb’sconstant

E totalenergy

ˆ U time-evolutionoperator

ˆ H Hamiltonianoperator

ˆ T kinetic-energyoperator

ˆ V potential-energyoperator

ˆ TN nuclear–kineticenergyoperator

ˆ He electronicHamiltonian

εn energyofelectronicstate n

Nucleardynamics

b impactparameter

σ crosssection

re diatomicequilibriumdistance

ke diatomicforceconstantatequilibriumdistance

De diatomicdissociationenergy

n bond-ordercoordinate

β bondorder–exponentialmappingparameter

rBC , rAB interatomicdistances ABCangle

R , r , θ reactantJacobicoordinates

R , r , θ productJacobicoordinates

γv vibrationalwavefunction

εv energyofvibrationalstate v

χ wavepacket

S scatteringmatrix

k(T) thermalrateconstant(functionoftemperature T )

k(E) microcanonicalrateconstant(functionofenergy E )

ρ(E) densityofstates

vR reactionrate

Electronicstructure

ϕ molecularorbital

χ atomicorbital(basisfunction)

εi energyoforbital i

ChemistryattheFrontierwithPhysicsandComputerScience

μ labelfor N -tupleofmolecularorbitals

μ Hartreeproductassociatedwith N -tuple μ

μ Slaterdeterminantassociatedwith N -tuple μ

ˆ h one-electronpartoftheelectronicHamiltonian

ˆ j (j) Coulomboperatorfororbital j

ˆ J totalCoulomboperator

ˆ k (j) exchangeoperatorfororbital j

ˆ K totalexchangeoperator

ρ electrondensity

S overlapmatrix

C molecular-orbitalcoefficientmatrix

D densitymatrix

F Fockmatrix

h one-electronpartoftheFockmatrix

J Coulombmatrix

K exchangematrix

Theoriginalfiguresofthisbookwereproducedusingthefollowingsoftware:Gnuplot,Pymol,andthePSTricksLATEXpackage.

PartI

Physicsandchemistry

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Chapter2

Thephysicsofmolecular systems

2.1Classicalandquantummechanics

AsalreadymentionedinChapter 1,weshallbeconcernedwiththemodelingof thestructureandbehaviorofmatterattheatomicandmolecularlevel.Atthis levelofdetail,weshallconsiderthenucleiandtheelectronsasthe‘elementary’ particlesofmatter,andweshallthereforefocusonthelawsofphysicsthat governtheirbehavior.

Now,howdoweimaginenucleiandelectrons?Mostlikely,inthefirstinstance,asparticles–moreorlesspoint-like–possessingamassandacharge, andlocalizedinagivenpointofthethree-dimensionalphysicalspace.Thisis certainlyhownucleiandelectronsappearinpopulartextbookrepresentations, suchastheatommodelofRutherfordorBohr,withtheorbitingelectronsarrangedaroundanucleusandcaughtasinaphotograph,ortheLewisdiagramsof electron-pairsharinginchemicalbonding,withnonbondedelectronsdepicted asdotsneartherespectivenuclei.Boththeserepresentationsarerootedina classicalviewofphysics:withinsuchaframework,modelingandpredicting thebehaviorofamolecularsystemultimatelymeansbeingabletosimulatethe evolutionintimeofthepositionofitsconstitutingparticles.Inclassicalmechanics,thiscanbeeasilyachievedthroughNewton’slawsofmotion,which areiconicallyrepresentedbythemathematicalexpressionforNewton’ssecond law1

AccordingtoNewton’slaws,givenaparticleofmass m inagivenpointof space,theevolutionofitspositionintimecanbeeasilydeterminedoncethe forcesactingontheparticleareknown.Thinkingofnucleiandelectronsas chargedpointparticlesinteractingthroughaCoulombelectrostaticpotential andgeneralizingEq.(2.1)tothemultiparticlecase,onewouldreadilyobtainthe toolsforsimulatingtheevolutionoftheresultingmolecularsystem.However, whileclassicalmechanicsfindswidespreadusageintheoreticalandcomputationalchemistryfordealingwith‘higher-level’,coarse-grainedaspectsofchemistry(see,forinstance,Chapters 7 and 11 ofthisbook),itunfortunatelyfailsin

1 AsmentionedinChapter 1,Section 1.2,vectorswillgenerallybeindicatedwithlowercasebold charactersthroughoutthebook.Uppercaseboldcharacterswillbeusedformatrices.

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