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Quantum-chemical

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Quantum-chemical

    Quantum-chemical

    258

    20o6.8

    结构化学(JIEGOUHUAXUE)

    Chinese.,.Struct.Chem.

    VOI.25.No.8

    947956

    Quantum?chemicalStudyontheStructuresand

    PropertiesofUracil.BX3(X=F,CI)Complexes?

    ZHANGShiGuo'LIHongYANGPinb?

    (DepartmentofChemist~.andChemicalEngineering,Instituteof MaterialChemistry,BinzhouUniversity,Binzhou256603,China) (KeyLaboratory.ofChemicalBiologyandMolecularEngineeringofMinist~( Education,InstituteofMolecularScience,ShanxiUniversity,Taiyuan030006,China)

    ABSTRACTFortheuracil-BX3(X=F,CI)systems,geometriesandbindingenergieshavebe

    en

    calculatedbyusingtheLeeYoung

    Parrcorrelationfunctionals(B3LYP)methodofdensity functionaltheory(DFT)andthesecondorderMoiler

    Plesset(MP2)methodofabinitioatthe6

    31I+Gor6-311++Gbasisset.Fourisomerswerefoundforeachsystem.andthenthesingle

    point

    energyevaluationswereperformedusingthelargerbasissetsof(6-311+G(2df,p)andaug

    ccpVDZ

    withDFTmethod.InthemoststableisomerofuracilBF3oruracil

    BCI3,theboronatomofBX3(X

    =F,CI)connectstothecarbonyloxygen07ofuracilwithastabilizationenergyof_46.56or-31.

10

    kJ/molattheB3LYP/6

    31l+GlevelfBSSEcorrected).Theanalysesforcombininginteraction

    betweenBX3anduracilwiththeatomin

    moleculetheory(AIM)andnaturalbondorbitalmethod

    (NBO)havebeenperformed.Theresultsindicatethatallisomerswereformedwitha-ptype interactionsbetweenuracilandBX3,inwhichthecarbonyloxygenoffersitslonepairelectronsto

    theemptyPorbitalofboronatomandtheconcomitancesofchargetransferfromuraciltoBX3occur.

    Moreover,thereexistsoneortwohydrogenbondsinmostisomersofuracil-BX3systemandthese

    hydrogenbondscontributetothestabilityofthecomplexsystems.Frequencyanalysissuggeststhat

    thestretchingvibrationofBX3undergoesaredshiftincomplexes.Uracil-BF3complexismore

    stablethanuracil-BCl3althoughthedistanceofB-()isshorterinthelatter.Besides.theconversion

    mechanismsbetweendifferentisomersofuracilBF3havebeenobtained.

    Keywords:B3LYP,Mlr2,intermolecularinteraction,

    uracil-BF3complex,uracil-BCI3complex

    lINTRoDUCTIoN

    TheintermolecularinteractionofbasesinDNAor

    RNAisofimmenseinterestandsignificancetoche

    mistsandbiologists"alike.Theinteractionsofthese

    baseswithmetalcations.solventmoleculesand

    othersmallmoleculesorionswouldaffectthestruc

    tureandbiologicalpropertiesorrecognitionprocess,

    whichhasbeeninvestigatedwidelyt卜剐.

    Boron

containedcompoundsareelectrondeficientcorn

    poundsandhavebeenextensivelyusedascatalysts inchemicalreactions.Therehavebeenmanyexperi? mentalandtheoreticalreports[9''onthedonor-

    acceptercomplexesinvolvingBH3,BF3,BCI3,etc., whicharecalledLewisacidbasecomplexes.Fur-

    thermore.boronisanessentialtraceelementforhu. Receired13December2005;accepted10February2006 ?

    ThisworkwsupportedbytheNationalNaturalScienceFoundationofChina(No.20171031)

    ?Correspondingauthor.Fax:+86351-7011022.E-mail:yaugpin@sxu.edu.cn

    ZHANGS.G.eta1.:Quantum?chemicalStudyontheStructuresand 948PropertiesofUracilBX3(X=F,CI)ComplexesNo.8

    manbeingsorotherbiologyandexcessorscarcity Ofb0ronwillcauseadverseeffecttothem[,?1.

    Recently,ithasbeenfoundthatthecomplexesof nucleotidesorpeptideswithboronhydfidehave antitumoractivitiesandtheinvestigationintoithas beeninprogressi61.SO,weareinterestedin

    studyingwhetherthereisanyinteractionbetween nucleotidesbasesandboroncontainedcompounds andhowtheinteractiontakesplace,whichis meaningfu1.However,tothebestofourknowledge, experimentalandtheoreticalstudiesonthestructure ofcomplexofbasesinDNAorRNAwithboron

    halide,suchasBF3andBCI3,arenotyetreported exceptourpreviousworkonthetheoreticalstudyof adenineorcytosine-boronhalidecomplexes['?l8.In

    thispaper,wechosetheB3LYPmethodofDFFand

    MP2methodofabinitiocalculation,bothincluding thecalculationofelectroncorrectionandthelatter havingbecomeastandardmethodtostudyinter

    molecularinteractionastheelectroncorrectionis evidentinthesesystems,suchastheuracilBX3(X

    =F,C1)system.

    2CALCULATIoNMETHoDS

    AllcalculationswereperformedbyusingCAUS

    SIAN98program'withtheBecke3para-meter

    hybridexchangefunctionalsandLeeYoungParr

    correlationfunctionals(B3LYP)ofDFF.TheMP2 theoryofabinitiocalculationhasbeenusedinpart systemsaswellinordertoconfirmtheconsistency betweentheresultsobtainedfromDFrandMP2.To lookforthestructurewithglobalminimumenergy andallthestructureswithMealminimumenergyfor uracilBX3(X=F,CI)system,allpossibleinitial orientationsofBX3towardsuracilhavebeende

    signed,includingBX3bothoverandbesidethe planeofuracilmolecule.Fulloptimiza-fionsforall theinitialconfigurationswereperformedatthe B3LYP/631I+GandMP2/631I+Glevelsonly

    forpartsystemsasmentionedabove.ForuracilBF3

    oruracilBCI3system,f0isomerscorrespondingto theminimumenergypoints,atwhichtheharmonic frequencyanalysishasbeencarriedoutandthe complexeshavenoimaginaryfrequency,atthemo

    lecularenergyhypersurfacehavebeenobtained, respectively.Singlepointenergycalculationsby

usingmuchlargerbasissetsof(6311+G(2df,p)and

    augccpVDZ)withDPTmethodhavealsobeen carriedoutontheoptimizedconformers.Theana- lysisofintermolecularinteractionsbetweenBX3fX :F.C1)anduracilwithNBOt.,IandAIMhas

    beenperformed231.

    Bindingenergy()isde

    finedasthedifferencebetweentheenergyofthe complexand:hoseofitsfragments.Forthissystem itcanbeexpressedasfollows:

    De=E(C4N2H4Oz--BX3)-E(C4N2H402)E(BX3)

    (X=F,C1)

    TheDecorrectedforthebasissetsuperposition error(BSSE)wasevaluatedbyapplyingthefull Boys-Benrnardicounterpoisecorrectionscheme[.

    Moreover,thecorrectionsofzeropointenergy(ZPE) andvibrationfrequencieswereappliedwitha scalingfactorof0.975referredfromliterature[. Finally,theconversionmechanismbetweendiffe? rentisomersofuracilBF3havebeenobtained,using

    theQST2methodattheB3LYP/6311+Gleve1.

    13RESULTSANDDISCUSSION

    Afteranevaluationofvariouspossibleorienta

    donsofBF3towarduracilfollowedbyfullgeometry optimizationattheB3LYP,63ll+Gleve1.four

    isomers,(a),(a')and(b),(b')wereobtained.Inboth (a)and(a'),BF3connectstoO7,sothetwoisomers aresynantiisomersabouttheC4=O7bond.Based onthesamereason,(b)and(b')aresynantiisomers

    aboutCo=O8.Duringtheprocessofoptimization,

    thoseinitialconfigurations,whichareconstructedby puttingBF3overapyrroletypenitrogenatom(NIor

    Ns),oroveracarbonatomorlayingBF3besidethe uracilfragment,changedtheirconfigurationsinto oneofthefourisomersorseparatedintotwopieces. Thisphenomenonisjustthesameasinadenine-BF3 andcytosineBF3systemsl7?181

    ,

    butitisnotthecase

    inthecomplexesofbenzeneBF3orpyridineBF3as

    20D6VOI.25结构化学(JIEGOUHUAXUE)ChineseStruct.Chem.949 reportedbyP.Tarakeshwart9andChengbuLiu26j.

    Theseresultsshowthat,inuracil-BF3system,there isnominimumenergypointoverpyrroletype

    nitrogenatom,carbonatomorBF3interactedwith thehydrogenatomsofuracil.Consideringthe similarityofthestructuresofBF3andBCI3,we expectthattheinteractionbetweenBCi3anduracil wouldbesimilartothatobservedinuracilBF3

    system.Hencecalculationsatvariousinitialcon

    figurationsforuracilBCI3attheB3LYP/63il+G

    levelwerecarriedout.Asexpected,fourminimum energyisomers(c),(c')and(d),(d')wereobtained. JustasintheuracilBF3system,(c)and(c')aresyn

    antiisomersaboutC(4)=O(7)while(d)and(d')are synantiisomersaboutC(6)=O(8).Forallenergy minimumisomers,theiroptimizedgeometriesand atomiclabelsaleshowninFig.1.Theoptimized geometryparametersoftheeightisomersarelisted

null

(Table2).Inisomer(a),theO(7)B(13)distanceis

    1.628AandthestructureofBchangesfromplane topyramid(ZFBF=Il3.9.).TheC(4)-O(7)distance ofuracillengthensfrom1.215to1.257A.The N(3(4)andC(4)-N(5)distancesareshortenedby 0.023and0.044A,respectively.TheBFbonds

    changefrom1.3l8Ainborontrifluorideto1.355 and1.402A.AfacthasbeennoticedthatNf5)-- H(12)bondformsahydrogenbondwithFi5con? firmedbytheanalysisofAIMmethodwiththe electrondensityof0.0257a.u.(Table5)atthebond criticalpoint(bcp),soBl3-Fl5lengthensto1.402 A.Inisomer(a'),thesynantiisomerof(a),the

    bondlengthsofuracilpartarealmostthesameas thoseinthelatterbuttheB(13).-o(7)distanceisa linleshorter.Besidesthat,thebonddistancesof B(I3F(15)andB(13F(16)arerelativelylonger thantheotherbondresultingfromtheformationof twoweakhydrogenbondsbetweenF(15)andH(11) aswellasF(16)andH(11)confirmedbytheAIM analysisalthoughtheyareweakenough(Table5). F

    ZHANGS.G.eta1.:QuantumchemicalStudyontheStructuresand PropertiesofUracilBX3(X=F,CI)CompleXeS

    (b)

    lI11

    o7

    I10

    1"112J

d)

    BI3

    No.8

    Fig.1.Optimizedstructuresandatomiclabelsofisomersofurcil-BX3complex

    Inisomer(b),theboronatomconnectstocal'- bonyloxygenatom0(8)withtheB(13)-.O(8)dis

    tanceof1.635A.TheB-Fbondsarechangedaccor- dingtothesameruleasthatinisomer(a),thatis,B

    FdistancesarelengthenedandBF3changesits structuretopyramid(ZFBF~I14.0.).Ascarbonyl oxygen0(8)offersitslonepairelectronstoconnect theboronatom,theC(6)__o(8)distancelengthens from1.212to1.256A.Atthesametime,theN(1)

    C(6)andN(5).-C(6)distancesareshortenedby 0.037and0.029A.respectively.Thedistanceof F(16)toH(9)is1.892A.Thusahydrogenbondis formedbetweenFl6andN(1)-H(9)withthe electrondensityof0.0269a.u.atbcp(Table5),. whichisconfirmedbytheanalysisofAIMmethod. SotheB(13)-F(16)bondlengthensgreatlyfrom 1.318to1.405A.Inisomer(b'),theB(13)-.O(8) distancelengthensby0.019Aascomparedtoits isomer(b).ThedistancebetweenF(16)andH(12)is 1.958Aandahydrogenbondisformedinthis isomer.

    Isomers(c)and(c')ofuracilBCI3systemare

    similarto(a)and(a')ofuracil?BF3,inwhichthe boronatomconnectstothecarbonylatom0(7). TheirB(13)_-O(7)distancesare1.554and1.567A,

shorterthanthoseinuracilBF3system.Inisomers(c)

    and(c'),twoweakhydrogenbondsbetweenCl(15), Cl(16)andH(12)orHllareformed.Thedistances 0fClHare2.658and2.843Aandalittleshorter thanthesumofVanderWaalsradiiofhydrogen andchlorine(2.95A).Butinisomer(d),whichis similarto(b)ofuracilBF3,theboronatomconnects

    t00(8)andCI(16)isclosetoH(9),ithadistanceof 2';6A.Asaresult.thehydrogenbondbetween Cl(16)andH(9)isrelativelystrong,whichpossesses electrondensityof0.0l88a.u.atitsbcp.Asto isomer(d'),thesynantiisomeraboutC(6)=0(8)

    bondof(d),atomsCl(14)andCl(16)arenearH(12) andtwoweakhydrogenbondsare~rmedbetween Cl(14(16))andH(12)(Fig.1andTable5,

    ComparedthedataofgeometriesinTablel

    andbindingeaergiesinTable2,wecanseethat(a)

    20o6VoI_25姥构他擘(JIEGOUHUAXUE)Chinesej.Struct.Chem.95l ismorestablethan(b),(c)ismorestablethan(d), andtheBYdistancein(a)and(c)isshorterthan thatin(b)and(d),respectivelythoughtheyareall lessthanthatoftheirisomers(a'),(b'),(c')and(d') respectively,andtheformergroupisomersaremore stablethanthelatterones.

    TableI.PrincipalGeometryParametersforFreeC4N211402andBX3 andforC4N2H402-SX3(X=F,CI)ComplexattheB3LYP/6?311+GLevel DistancesareinAandbondanglesindegree. Yistheclosestatomofuracilfragmenttoboron.A(X-B

    X)istheaverageofthethreeX-B-XanglesinBX3fragment.

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