Prediction and Calculation of Crystal Structures: Methods and Applications PDF
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Topics in Current Chemistry 345 Şule Atahan-Evrenk Alán Aspuru-Guzik Editors Prediction and Calculation of Crystal Structures Methods and Applications 345 Topics in Current Chemistry EditorialBoard: K.N.Houk,LosAngeles,CA,USA C.A.Hunter,Sheffield,UK M.J.Krische,Austin,TX,USA J.-M.Lehn,Strasbourg,France S.V.Ley,Cambridge,UK M.Olivucci,Siena,Italy J.Thiem,Hamburg,Germany M.Venturi,Bologna,Italy C.-H.Wong,Taipei,Taiwan H.N.C.Wong,Shatin,HongKong Forfurthervolumes: http://www.springer.com/series/128 Aims and Scope TheseriesTopicsinCurrentChemistry presentscriticalreviews ofthepresent and futuretrendsinmodernchemicalresearch.Thescopeofcoverageincludesallareasof chemical science including the interfaces with related disciplines such as biology, medicineandmaterialsscience. Thegoalofeachthematicvolumeistogivethenon-specialistreader,whetherat theuniversityorinindustry,acomprehensiveoverviewofanareawherenewinsights areemergingthatareofinteresttolargerscientificaudience. Thuseachreviewwithinthevolumecriticallysurveysoneaspectofthattopicand placesitwithinthecontextofthevolumeasawhole.Themostsignificantdevelop- mentsofthelast5to10yearsshouldbepresented.Adescriptionofthelaboratory procedures involved is often useful to the reader. The coverage should not be exhaustiveindata,butshouldratherbeconceptual,concentratingonthemethodolog- icalthinkingthatwill allowthenon-specialistreaderto understandtheinformation presented. Discussionofpossiblefutureresearchdirectionsintheareaiswelcome. Reviewarticlesfortheindividualvolumesareinvitedbythevolumeeditors. Readership:researchchemistsatuniversitiesorinindustry,graduatestudents. Şule Atahan-Evrenk Alán Aspuru-Guzik l Editors Prediction and Calculation of Crystal Structures Methods and Applications With contributions by (cid:1) (cid:1) (cid:1) C.S. Adjiman A. Aspuru-Guzik S. Atahan-Evrenk (cid:1) (cid:1) (cid:1) (cid:1) G.J.O. Beran J.G. Brandenburg S. Grimme G. Hautier (cid:1) (cid:1) (cid:1) (cid:1) Y. Heit R.G. Hennig Y. Huang A.V. Kazantsev (cid:1) (cid:1) (cid:1) (cid:1) K. Nanda A.R. Oganov C.C. Pantelides B.C. Revard (cid:1) (cid:1) (cid:1) (cid:1) R.Q. Snurr W.W. Tipton S. Wen C.E. Wilmer (cid:1) X.-F. Zhou Q. Zhu Editors S¸uleAtahan-Evrenk Ala´nAspuru-Guzik Dept.ofChemistryandChemicalBiology HarvardUniversity Cambridge Massachusetts USA ISSN0340-1022 ISSN1436-5049(electronic) ISBN978-3-319-05773-6 ISBN978-3-319-05774-3(eBook) DOI10.1007/978-3-319-05774-3 SpringerChamHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2014938743 #SpringerInternationalPublishingSwitzerland2014 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerpts inconnectionwithreviewsorscholarlyanalysisormaterialsuppliedspecificallyforthepurposeofbeing enteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework.Duplication ofthispublicationorpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthe Publisher’s location, in its current version, and permission for use must always be obtained from Springer.PermissionsforusemaybeobtainedthroughRightsLinkattheCopyrightClearanceCenter. ViolationsareliabletoprosecutionundertherespectiveCopyrightLaw. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. While the advice and information in this book are believed to be true and accurate at the date of publication,neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityfor anyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,with respecttothematerialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Thepredictionofcrystalstructureforachemicalcompoundisstillachallenge.It requiresadvancedalgorithmsforexhaustivesearchesofthepossiblepackingforms and highly accurate computational methodologies to rank the possible crystal structures. This book presents some of the important developments in crystal structurepredictioninrecentyears.Thechaptersdonotcovereveryareabutrather presentawiderangeofmethodologieswithapplicationsinorganic,inorganic,and hybridcompounds. The blind tests organized by the Cambridge Crystallographic Data Center (CCDC) showed a notable improvement for the crystal structure prediction of organic compounds over recent years. The first two chapters of this book present two of the methodologies contributed to the success in recent blind tests. The chapter “Dispersion Corrected Hartree–Fock and Density Functional Theory for OrganicCrystalStructurePrediction”byBrandenburgandGrimmeisdedicatedto recent advances in the dispersion-corrected Hartree–Fock and density functional theory. Another important areashowingremarkableprogressistheefficienttreat- mentoftheinternalflexibilityofmoleculeswithmanyrotatablebonds.Thechapter “GeneralComputational Algorithms forAbInitioCrystalStructure Prediction for Organic Molecules” by Pantelides et al. summarizes some of the algorithms that have contributed to this success. In addition, the chapter “Accurate and Robust Molecular Crystal Predictions Using Fragment-Based Electronic Structure Meth- ods” by Beran et al. illustrates how fragment-based electronic structure methods canprovideaccuratepredictionofthelatticeenergydifferencesofpolymorphsof organiccompounds. One research area that would benefit tremendously from the crystal structure prediction of organic compounds is the design of organic semiconductors. In the chapter “Prediction and Theoretical Characterization of Organic Semiconductor Crystals for Field-Effect Transistor Applications” by S¸ule Atahan-Evrenk and Ala´n Aspuru-Guzik, discuss some aspects of theoretical characterization and pre- dictionofcrystalstructuresofp-typeorganicsemiconductorsfororganictransistor applications. The chapter also provides information about the structure–property relationshipsinorganicsemiconductors. v vi Preface In organic systems, thanks to the internal constraints of molecular structures, randomsamplingmethodscanbeusedsuccessfully.Ininorganiccrystals,however, there are no constraints other than the chemical compositions. Therefore, the challenge in the crystal structure prediction of inorganic compounds is the search problem,andthemethodologiesthatspanthesearchspaceeffectivelyarecrucial. ThechaptersbyHautier,byRevardetal.,andbyZhuetal.arededicatedtocover recentadvancestowardsachievinginorganiccrystalprediction.Thechapter“Data MiningApproachestoHigh-ThroughputCrystalStructureandCompoundPredic- tion”byHautierdiscussesdataminingapproachesandthechaptersbyRevardetal. and by Zhu et al. cover evolutionary algorithms for compound prediction. In particular, the chapter “Structure and Stability Prediction of Compounds with Evolutionary Algorithms” by Revard et al. presents different methodologies adaptedfortheevolutionaryalgorithmsapproachesandthechapter“CrystalStruc- turePredictionandItsApplicationinEarthandMaterialsSciences”byZhuaetal. focusesonthestateoftheartoftheUSPEXmethodology. The prediction of hybrid materials such as metal-organic frameworks posits a specificsetofchallengesforstructureprediction.Thechapter“Large-ScaleGener- ation and Screening of Hypothetical Metal-Organic Frameworks for Applications in Gas Storage and Separation” by Wilmer and Snurr discusses the large-scale generationandscreeningofmetal-organicframeworks.Withpossibleapplications in storage, catalysis, pharmaceuticals, and electrochemistry, these methodologies showgreatpotentialfordevelopmentofhybridsystems. Webelievecrystalstructurepredictionwillbeoneofthemostimportanttoolsin solid-statechemistryinthenearfuture.Applicationsrangingfrompharmaceuticals toenergytechnologieswouldbenefittremendouslyfromcomputationalprediction ofthesolidformsofmaterials.Webelievethisbookprovidesup-to-date,concise, andaccessiblecoverageofthesubjectforawideaudienceinacademiaandindustry andwehopethatitwillbeusefulforchemistsandmaterialsscientistswhowantto learn more about the state-of-the-art in crystal structure prediction methods and applications. WewouldliketothankSpringereditorsBirkeDaliaandElizabethHawkinsfor invitingustoeditthisvolumeandalltheauthorsfortheircontributions.Lastly,we would like to thank all the members of the Aspuru-Guzik Group for their support andcamaraderie. Cambridge,MA,USA S¸uleAtahan-EvrenkandAla´nAspuru-Guzik December2013 Contents DispersionCorrectedHartree–FockandDensityFunctionalTheory forOrganicCrystalStructurePrediction .................................... 1 JanGeritBrandenburgandStefanGrimme GeneralComputationalAlgorithmsforAbInitioCrystalStructure PredictionforOrganicMolecules ............................................ 25 ConstantinosC.Pantelides,ClaireS.Adjiman,andAndreiV.Kazantsev AccurateandRobustMolecularCrystalModelingUsingFragment-Based ElectronicStructureMethods ................................................ 59 GregoryJ.O.Beran,ShuhaoWen,KaushikNanda,YuanhangHuang, andYonatonHeit PredictionandTheoreticalCharacterizationofp-TypeOrganic SemiconductorCrystalsforField-EffectTransistorApplications ........ 95 S¸uleAtahan-EvrenkandAla´nAspuru-Guzik DataMiningApproachestoHigh-ThroughputCrystalStructure andCompoundPrediction ................................................... 139 GeoffroyHautier StructureandStabilityPredictionofCompoundswithEvolutionary Algorithms .................................................................... 181 BenjaminC.Revard,WilliamW.Tipton,andRichardG.Hennig CrystalStructurePredictionandItsApplicationinEarthandMaterials Sciences ....................................................................... 223 QiangZhu,ArtemR.Oganov,andXiang-FengZhou vii viii Contents Large-ScaleGenerationandScreeningofHypotheticalMetal-Organic FrameworksforApplicationsinGasStorageandSeparations .......... 257 ChristopherE.WilmerandRandallQ.Snurr Index .......................................................................... 291 TopCurrChem(2014)345:1–24 DOI:10.1007/128_2013_488 #Springer-VerlagBerlinHeidelberg2013 Publishedonline:13November2013 Dispersion Corrected Hartree–Fock and Density Functional Theory for Organic Crystal Structure Prediction JanGeritBrandenburgandStefanGrimme Abstract We present and evaluate dispersion corrected Hartree–Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electroncorrelation,alsoknownasvanderWaals(vdW)interaction,ispointedout andsomemethodologicalissuessuchasinclusionofthree-bodydispersiontermsare discussed. One of the most efficient and widely used methods is the semi-classical dispersioncorrectionD3.Itsapplicabilityforthecalculationofsublimationenergies isinvestigatedforthebenchmarksetX23consistingof23smallorganiccrystals.For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometryisinvestigatedandverygoodagreementwithexperimentaldataisfound. Since these calculations are carried out with huge plane-wave basis sets they are rathertimeconsumingandroutinelyapplicableonlytosystemswithlessthanabout 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screeningofmanystructures,apre-sortingwithfastermethodsismandatory.Small, atom-centered basis setscan speed upthe computation significantlybut theysuffer greatlyfrombasisseterrors.Wepresenttherecentlydevelopedgeometricalcounter- poisecorrectiongCP.Itisafastsemi-empiricalmethodwhichcorrectsformostof theinter-andintramolecularbasissetsuperpositionerror.ForHFcalculationswith nearlyminimalbasissets,weadditionallycorrectforshort-rangebasisincomplete- ness.WecombineallthreetermsintheHF-3cdenotedschemewhichperformsvery wellfortheX23sublimationenergieswithanMADofonly1.5kcal/mol,whichis closetothehugebasissetDFT-D3result. Keywords Counterpoise correction (cid:1) Crystal structure prediction (cid:1) Density FunctionalTheory(cid:1)Dispersioncorrection(cid:1)Hartree–Fock J.G.BrandenburgandS.Grimme(*) MullikenCenterforTheoreticalChemistry,Institutfu¨rPhysikalischeundTheoretische ChemiederUniversita¨tBonn,Beringstraße4,53115Bonn,Germany e-mail:[email protected];[email protected]
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