or Ior

THE DEAMINATION OF CYTOSINE, AN ADINITIOSCF MOSTUDY

by

JieXu

A ThesisSubmittedinPartial Fulfillment ofthe RequirementIortheDegree of

MASTER OF SCIENCE

Graduate ProgrammeinCh,ttlistry Memorial University

o r

Newfoundland

St.John's,Newfoundlaod June 1990

11 +0

^{of Canada}

"""""'"

Theauthorhas granted an jrrevoce b le non- exciuslve licen c eallow ingtheNationalUbrary ofCanadatorep roduce ,loan,distl~~uleorsen copiesofhisfher thesi sbyany meansand In any fonnor format.makingthisthesis available to interes ted pe rsons.

Theauthorretains ownership ofthe copynght in hiS/herthesis.Neither the thesis IlQ(

subStantial extractsfromit maybeprintedOf otherwisereprod ucedwithouthislher per- mission .

L'auteur a accords unelicenceirre vocabl eet nonexc lusive permetl ant

a

taBibliolhequ e nationaledu Canadadereproduire.preter. dislrib uer ou vendredescopie sdesathese dequelqu e manlereatsous quelqueform e que cesotpourmettredes exemplairesde cettetheseitIadisposition despersoroe s intere sse es.

L'auteurconservela propfiltedodroit d'auteu- quiprotegecathese.NiIat:U:;ienidesextraits substantielsde ceae-crne doivent etre lmpnrnes ou autremenlrep(odui ts sansson autolisat ioo.

ISSN 1J- 3 15-6185 0-7

Canada

ABSTRACT

In1014,Lindah landNybergstud iedthe rate ofduminationofl'ytO!lin~

residues insingleanddoublestranded DNA.After~lu dy in gthe rall"",lH''l'ral temperaturesthe activationenergyrortheconversionofcyl()llinttouracilwa."

estimatedto be121kJ{moJ.

Possiblemechanismslordeamination

o r

cytosinearestudiedusing Dbinitio SCF molecularorbitalealeulations. Ab initioca lculat ions with81'O.3G,3-210 and 6-310-basisset!bevebeenperform edtoinvestigat ethe optimizedst ruc- turesandener gies.

riDtthe,I ,JUinlltioDoramidineis st udiedu amodelcompound andthe calculatioDl!arethen extendedto cylosine.Theres ultsJorbothtalculatioosindio eetetbatther.t~det.erminiD &step [seece dstep) withOU·ba.~a barrier

or

200 kJ/molandwitb "20 hasa barrieror174kJ/mol.Theresults showtha~the reactionillthermodyu micallyfavourable butkinetk allynotveryfavourabl e.

ACKNOWLEDGEMENTS

Iamdeeply andgreatly indebt ed tomysupervisorDr.RaymondA. Poirier fot all his patie nceand a lotofhelpduringmystudies. I wouldliketothank the NewfoundlandandLaboradorCompute rServices (NLCS) and MemorialUniver- sityofNewfoundla ndComputi ngServices fo rtheirgenerousallocation of com- puter time.

iii

Tomy IoveJYlob

TABLE OFCO NTENT S

ABST RA CT 11

ACKNOWLEDGEMENTS Itt

DEDiCAT IO N Iv

TABLE OF CON'l E NTS .,.

LIST OF TABLES ~111

LIST OF FIGURES x1

CHAPTER I INTRODUCTION I

1.1GeneralIntrod uction.... . 1

1.2Experimental Results 10

CHAPTER

n

MO THEORY AND COMPUTATIONDETAILS .

2.1MO Theory .

2.2 BasisSetExpaaslona ..

. 24

. 26

2.3Hartree-Foek Theory andSCF Theory 28

2.4Comp ut at ional Meth od! 30

CHAP TE Rill RES ULTSANDDISCUSSIO N .

•a.I Method

3.2 TheReaction orAmidine withOU-,

.»••• • • • • • • • •••••32 ....33

..•....78 3.3TheReactionof Amidincwith 1120 5·1 3.4Effect ofBasi~Sets ontheDeamin ation

of Amidincwith011-and H₂₀ 74

3.5Comparison of the Deamin atioDof Arnidine with OH-and1120 .

3.6OptimizedStructure ofCytosine ,_ 79

3.7The Reaction01Cytosinewith011- .

3.8 TheReaction 01Cytosinewith H20. 3.9Effect01 Basi! Sets onCyto! ine with

3.10Comparison of theDeaminat ion ofCytos ine

. 79

. 107

...139

withOH~and H₂₀ 143

3.11Comparison or the Deaminationor

Cytosine and AmidinewitbOH- 1..6

3.12ComparisonIo tbe Deemlaeuce or

Cytosineand Amidlne with. H20 147

vi

3.13Comparisonof the Experiment al and

Calculated Results . . 148

CONCLUSION 161

APPENDIX 163

REF ER EN CE S 167

vii

LISTOF TABLES

TBoie

1.ST O-3G, 3-210 and 6-310*opt imized geometries (underC.symmetry)

fortheamidine-hydroxidecomplex (I.I·

2. STO-3G,3-21G and 6-3lG*optimized geometries (under C.symmetry) forthe amidine-hydroxidecomplex(I,)

3. STO.3G,3-21G and6-3IG. optimizedgeometries forthe amidine-hydroxide intermediate(It

1

of,STO-3G,3-21Gand 6-31G*optimized geometries lor the amidine-hydroxide transit ion state(I~) 5.STO-3G,3-21G and6-31G.optimizedgeometries lor thelormamide ion-ammoniacomplex(r,) 6.Total energies lor the amidine-hydroxidestruct ures·f. -It 7.Relative energieslortheamidine-hydroxidestructures· I. _.It 8.STO-aG,3-21Gand 6-31G. optimized geomet ries

lor the amidine-water complexID. ) O.STD-3G, 3-21G and6-3!G* optim.zedgeomet ries

lorthe emidine-water complex (0,)

viii

forthe amidine-wa ter interm ediat e(DeI 0.STO· ,10,3-210and6-31G*optimizedgeomet ries

fortheamidine-wat erinterm ediate(D" ) 12. STO· 3G,3-2:nend6·310*opt imizedgeomet ries

fortheemidlne-wete rtra nsitio nsta le(II.J 13. ST().3 G. 3-21G and 6-3I G* opti mizedgeometries

fortheform amid e-ammoniacomplex (II, ) 14.Totalenergieslorth eemidine-wuterstruct ures" II••• lI, 15.Relati veenergieslorthe amid ine-waterslrudures·Ii.-0, 16.STO- 3Gand 3-210 op timized geometries(under C.symmetry )

for cytosine

17. ST Q.a G and 3-21G op timized geometries(under C.symmetry ) for the cytosine-hydroxide complex (ill.)

18.ST0-3Gand 3-21Gopt imizedgeometries (underC, symmetry ) lorthe eytosine-hydroxidecomplex (ill. )

10.STo-an Al1d 3-21G optimizedgeometri esfor thecytosine-hyd roxide interm ediate(D1.J 20.ST Q-aG and 3-21Gopti mized geometri esfor

ix

thecytosine-hydroxide transitionstate(ill.) 21. STO·3Gand 3-21G opt imized geometriesfor

the uracilion-ammoniacomplex (W. J

22.Totalenergies forthecytosine-hydroxide structures"111•••Ill, 23.Relative energiesfor thecytosine-hyd roxidestr uctures"III.--Ill, 24. ST O-.3G and 3-21GoptimizedgeometrleeCor

thecytosine-watercomplex(IV. ) 25.8To-3Gand 3-210 optimizedgeometrleaCor

the cytosine-watercomplex(IV.I 26.STO-3G and 3-210 optimizedgeometr ies Cor

the cytosine-water int ermediat e ( IVe ) 27.81'O-3Gand3-21Goptimizedgeometries Cor

thecytosine-waterintermediate (IV~) 28. STO-3G and J.21Goptimizedgeomet riesCor

the cytosine-watertransitionst at e (IVe ) 29.STo-3G and 3-21G optimized geometries for

the uracil-a mmoniacomplex( IVI )

30. Totalenergies for the cytosine-waterstruct urcs'.IV.--rvl 31.Relativeenergies Cor the cytosine-watt'rstruc tu res'IV.-IVI

LISTOF FIGURES

Figure

I.l Thestruct e reof DNA.The pairof"ribbons"represen tsthe

!ugar· pbC''lphate backbonechains.

1.2 Thetwo-dim ensio nal struct ureof DNA.

1.3 Mecbenlsm for the deamina tion

or

cy tosine {IOI. B· = bufl'eranion.

1.4 Mechanismtorthedeeminer lcu ofcyt osine(101, B·=b ufl'eranion.

1.5 Methanis.'Ilfat the deamin atio nofcytosine

1 1 41,

HB-=H50 £ ;H_2PO..-.

•.6The tautomerism

o r

cytosine.

3.1The du rnin atioD ofCl 108iOe witbOH·, 3.2Thednminatiooorcytosin e with H20. 3.3Thedeaminatiooofemidinewitb OH-•

•1.-4Thedeamin alion ofamidinewith H20.

3.5Theetruet u eeeforthe durninatioD ofamidi newith hydroxid e.

I,andI, are amidine-hydr oxide com plex (react ant), Ieis an iutermediete,I,.isthetrans itionst a l e Ior the bydrogenrearr angemen tand I.istheformamid eion- ammo niacomplex (p roduct) .

3.6Schematicenergy profile for thede&.minationofamidinewit h011-. 3.7The struct ures for the deaminat ionofamidi newith water.

II. and Il&are emidine-watercomplex [react ant], Il, andnilareint er mediat es,II,isthe tra Qsition stateforthehydrogen rea rrangementand UI is the formamide-ammonill.complex(product).

3.8Sch ematic energy profile(orthedeamination01amidine with H₂₀. 3.0Numberinglor thecytosinestructure.

:J.lO The structu res lor the cytosine-hydroxidecomplex (reactant).

3.11 The str uctu re forthe cytos ine-hydroxide intermediat e.

3.12 Thestruct ureof thetransition sta tefor the hydrogen r@arr angement(cytosine-hydroxide).

J.l3 The struc t ure fortheuracilion-a mmoniacomplex (product) . 3.1"Schemati c energy profilerorthe deamination ofcytosine with

on-.

3.15 The struc t ures forthecytosine-wate rcomp lex (react ant).

3.16Thestr uct uresfor the cytosine-wat erintermediate.

3.17The str uct ure01the transit ion sta te forthehydrogen rearr angement(cytosine-water).

3.18Thestruct ure lortheurac il-ammon ia complex (product).

xii

3.10Sehemetle energy profile(01'tbe deemlnetloa o( cytosine with 1120 . 3.20 Reaction ecbernes lor the formation of the cytosine-water and

cytosine-hydroxide intermediates.

xiii

CHAPTER I

Introduction

1.1 Generallntroductlon

The fundament al unit of anyhigher organismisthe cell.Eacbdaughtercell prod ucedatcell divisioncont ains an identical copy of the genetic material.The inst ructions whichenable these many intr a-cellular reactions to takeplace, the geneticinfor mation,areencoded in the chromosomes.

The geneticinformation liesin the chemica:substance knownasdeoxyr i- bon ucleicacid,orDNA, for this is the geneti c materieland themostimportant const ituentofthechromosomes,DNAilla very long polymerknownasapolynu- eleotide, mad eup of fourtypes ofbuilding blockunits ornucleotides; adenin e (A),thymine [T],guanine(G) andcytosine(C) .

The6rstimporta nt featur e of theWat son andCrick modelfor the str uct u re of DNAisthat (usu ally) the moleculeisnotjust one polynucleotide chainhut two suchchainstwistedaround each otherin theform ofadoublehelix-rat her liketwopiecestitstringthat have beentwisted toget her (Fig.l.l).

The st ruct ure or DNA.Thepa.irof"ribbons" represent sthe sugar-phosphate backbonech ains.The points representbases(i.e.,adenine,thymine,guanineand cytosine).

Theseco n d important fea t ureis thAt the pairing ofthe basesisnotrandom. Ie^{themoleculeis}to be regulr.randundistorted then itsdimensionsare such that thereisnoroomtoaccomodatea pairofthe largepurinebasesIAandGlwhilea pairofpyrimidines[CandT)is too small.Asa consequ enceone cha in isalways comp lementarytotheother chain. Thetwo-dimensionalstructure ofDNAis showninFig.I.2.

Inawide varietyoforga nisms, hotb procaryotesand euca ryotes ,chemicals whichalterthe struct ureof the geneticmaterialDNA(or sometimesRNA)can causeheritable changesormutations.So impo rtantisthe exactsequenceofthe strueturn lunitsinagene,which may be up to1500 structuralunitslong,that thereplacementoronestruct ural un itby a differentstructura lunit(mutation) maycomplet elydestro),the norma lactivityof the gene.Itseemsclear thatgene mutationoccursbyal~i"";ngthe sequence of nu cl eotides alongtheDNAmolecu le so that thefun cti oningofthegene and, ultima tely, the phenotypeoCtheorga n- ism is affected. We now recog n ise tha tgene mutation can changethe informa- tionalcontentofa gene inatle ast two ways,first,by a base substitutionchan g- ingonebasepa ir to adifferent basepair (or inasingle-strand edaacleieacid by cbangin g one baseroeanother )and,second,by adu Ofdeleti ngoneormore base pairs.

Figure1.2

The two-dlmeaeioualstr ucture of DNA, wher e A=Adenine, T=Th~·mine, G-=Guanine, C= C ylosine and P=Phospbal e.

1

Agentswhichchemicallyalterthebases, whichare adenine(Al,thymine(T ), guanine (Glandcytosine (C) inDNA,havebeen importanttools ror research in mutagenesis and carcinogenesis.Recentlyehemieally modified DNA has beenused to study the~ffectoralteredbase pairson DNA duplextbcrmostability(l-21.or the manypossiblechemicalalterationsorDNA, includingdepurtneuo n,dcpyrimi- dinntion,alkylationanddeaminat ion,onlydeaminationCll.IIS('Snltl'r:l.lion~which resemble themismatchedbase pairs whichmight arisehom a transition mula- tion.

Nucleotidesconsistorthreecomponents,i.e.,ribose,base (purineand pyrimidine)and phosphate.Theprincipalpyrimidines roundinRNA are uracil and cytosine;inDNAthey arethymineandcytosine.Cytcslne and methylcyto- sineeau undergo deaminationto yielduraciland thymin e.respectively.Itbas been confirmed by UV spectrophotomet rythatcytosi neandcyt idine deaminate touracil andundine,respectively,atallpHvalues. These productsslowly degraderurtherinstronglyalkalinesolut ions.

Spontaneousmutagenesismayinvolve a varietyoCdistinctmechanisms(3-51.

One exampleoCa sponta neouschemicalchsnge that has muta tiona lconsequences isthe deaminat ionoCcyt osinetouracil (see Scheme I).

Scheme l The deamination01cytosine touracil.

H L H HH~H

o A)lH'

^{H,O -}

_o~JlH+

^HH.

I I

H H

1.2Experimental Re8ults

Therol e whichchemica! mutagens playin thedeamin ation of cytosine to uracil derivat ives hasbeenthe subjectofseveral iovllStigatioo sdirect ed toward eluc idatio nofin vivomechanismsof mutagenic activity [6-IOJ.

InIg66, R.Shapi roan dR.S.Klein

ItoJ

report ed that cytidine andcytosine are deaminat edat 05' Cbya varietyofaqueous buffers ofpH

<

6.0 .Based on the experime ntal data,they proposedtwokinetically equiva le nt mechanismsfor the deamioation orcytosine which areoutl ined in Fig.L3 and Fig.1.4.Both mech anisms combinespecific hydrogen-ioncatalysiswith general basecatalysis bybuffer anion, B-.The sim plemechanismdescribedin Fig.l.aisanalogous to thehydrolysisofen amide. However ,little direct evidencebas beenreportedto suppo rtitsoccurrencein knownreactionsinvolvingnucleophilicdisplacementof the aminegroupor cytosine . Th e eeeccd rne -hani smisdescribed inFig.1. 4 where followingprot oDation, thebufferanion B-addsto the5,6 doublebond with the resu lt ing dihyd rccytoeieeintermedia t e,undergoingdeaminationtogive a uracil derivative.This route is sim ilar tothatesta blishedIll)forthe reaction of thepotentmutagen,hydroxylamine ,withcytosinederiva tives.Isolation or the componentsin reactionmixtures reve aledonlycyto sine and uracil. No inte r- media.t es corr e ponding to bufferanio nadditio nwere detected,therefore, making it impossibletodistinguish bet ween thesetwomeehanisms .

11

Figure 1.3

Mechanismforthedeamina tionof cytosine (10),B-= bufJer anion.

:): ^N~'

^H

N

I

O~N

^"H

HI

: ] :

0 H

HN

I

OJ-- N H HI

NJCOH

HN H

O~N ^I

^H+BH

I H

13

Figure 1.4

Mechanism(orthedeamination01cytosine(101,B-=bulJer anion.

O.t.NJlH NJ:H

~

..

o,,~:

NH,_{I B} H

1&

SchusterandSchramm (121 foundthatdeaminetic nof the aminogroups

o r

thecytosine,adenine,andguanilleresid uesorthenueleieacids could be effeded bynit rousacid.Jordan1131sbowedthatc)'to"Iiot' andguanine couldbedu m- inlltedunderst rong acidic conditions. Quantitative dataonthebujler-alleeted deamin utiouofc)'IMine arabinoside wasgiven by Nata li(14)andNatali etal, (15-161. whoreportedtbatcytosinenuelecsidesunderwent deaminationinvllri~lIs bullet sbetweenpH3.4 and 7.7.Thework focusedonthedeamiaat ionofcyto- sinederivat ive!to the corresponding uracil derivativC'laftertheformat ion ofa reversibl yhydr olyzingsaturated5,~doublebondadductwith bisulfiteion ,(the bisulfite ion acting as a catalyst ). Suchareactionmnybe responsiblefor muta genicactionbytransrormingthe cytosicemoietiesin RNA andDNA(17.

211 ·

Nof.a.ri(1-4)proposed amechanismforthe hydrol,tiedeam inat ioooreytceie e iraaqueous buBer,whichisdescribed in Fig.1.5.Thekinetics of hydrolyt icdeaml- nationorcytosinehavebeenstudied as aIuneticnorpH,temperature,and buBer eomposlu on.Thereactioncomponentswereisolated,ident ified,andquantitie-d. Theprimecrite ri aroreatalysisby aeuelecphtlesucb...HB-,areShOWDtobe (a)sufficientnucJeopbilicity to attackthe 6-positi oD following theinitial pec te ns- tion at the 3-posit ion and (b) theabilityto subsequentlydonate0.prot onreeuu- ing in the compl et esaturationof the5,6-doublebond.

Mterst udyingthemechanism[or the hydrolyt icdeo.mination orcytosine in

'6

Figure1.5

Mechanismforthedeaminationofcytosine 1141.00-=HSOi;H₂P0₄-.

HNU ;"~JzH

o ~ Be

\-NH,

<H,o ..

17

aqueous buffer,Nataliet all161 invr:sLigatedtheintermolecularand intramolecu -

lar nta lysis in dfllminali oD 01cyto:!lne nucleoside'S. fberalnofdeam ina lionor eytostne ara bi noside,cytidine and cytosin e areeomp eredintbepresenceaDdin

theabsence ofcatal),tic buffers.Thepseudo-first orde rrateeonstents fordeami- nationof1.8X10.3 McytOllineat1fte,pll3.75.re2A8-3..~OX10·^trorsen·ral huITereompon enta116J anelat700C,pH7.P:Iare0.723-0.815X10.4,Theresults lndleatethat pseudo-firstorderdeaminal toDrate consta nts,kitfot cytidineand cytosineshowed alineardependencyonouO'erconcentration.Bot h cytidineaod cytceine were suscep t ibleto gene ral-ad dandgene ra l-basecnla lysi!lbythebuffer

components.Itishypot hesizedthatcytosine arabinosideissubjecttogenerel- base typeofintramolecularcatalysis by the2'.bydroxyl groupandthusonly intermoleculargeneral-acidcat alysis is observed.

Thesolvolyticdeaminal iono( cytosineand cytidine are reportedbyGarrett aad Tsau122)in1072. Therconfirmed usingUVspect rophotomet ryand TLC that cytosine and cytidi neduminateto eraeiland uridine,respectively,atallpll nlneJ 122).Theresulb show thattheuse ofuidi6edlIOIutions(ortheestimation or rate consta nbwere preferred since thedifference in>...values betweeneyto- sine and its product,uracil.was the greatest inthis solution. The spectral changesoftheacidi6ed solutionsor react ingcytosine followedthe same pattern for allsolutions more acidic than 0.1N NaOH: ahypsocbromic shiftin>'mufrom

"

cytosine(274nm)touradt(2S9nmI 122).Thecalculatedlil'!lt-orderrateroostaab from the linearplo~re-the3OIvolyticdeamioatio nofcytosineandcytidineAlt givco

1221.

The firat-order ratec:onslanllforthe dumioaliODofcytm ineand cytidinebecome pHindependent between pH5 aDd 0and indicateeitherWlll "'f attack on theneutral speciesoritskineticequivalent,hydroxyl-ion aHar k onthe protonatedspecies.Thedeaminationratescbaradefizedbythe -Ietermmedrale ecnstantk_lforbotheytcs ineand cytidineabovepHg ate catalyzedbyhydroxyl ions.Alinea rincreaseoflog k,wit hincreasingpHataslopecloseto unityindi- eet edaspecifichydr oxyl-ioncata lyzed reaction. Forcytosine,the energiesof activatio nattheseveral pHvalues were(kJ/mal,pll):53,1.0;51,1.0; and 97, D.8.Forcyti dine, theywere:49,2.0;54,7.0;aDd74,11.0.

In 1974,Lindahland Nyberg(23)9tud ied therat eofdeaminat ioD ofcytosine residuesinsingle-and double-str andedDNA. Theacti. .ticnenergy (or the conversionofcytosinetouracil wasestimatedtobe121 U/mol,based ontbe deaminationof cytosineindiffer ent forms(poly(dGI'pol, (dC),pol,( dC) and -ic.JMPldCMP=deoxycltidine5'-monopbospba~)),mll!uuredatleveraltemper.- turee.Tbeybavealsoreported124]aD activationenergyof131±8 U/mol(or thedepurins fionof DNAinneut ral solution.

The heat-in duceddeam inati onconversionof5-met hylcytosine residues to thymin eresidu esandorcytO!linli!to uracil resid ues insingle-st ra ndedDNAwas

'0

stud iedbyEhrlichand Nor ris[251.Theyinvestigatedtherates of deaminati on of S-mcthylcytosinc and cytosine residuesinsingle-st ra nded DNA at pbyeiclcgieel pI!and for temp eratur es of 70°,80°,P!)oand110°0 to allow prediction ofthe ratesat 31°0.The results indicatethatthe calculated ratesfor the deamination of5-met hylcytosi neandcytosineat 37°0and pH7.4 were 9.5 X10-¹⁰and 2.1X 10.105·' , respecti vely and that the Arrhen iusplots ofthe temp era tur e dependent!'of the deaminationrates gave approximateactivationenergiesof 100 and 113 kJ/m olfordeamination of s-metbyleytcs tne and cytosine residues, respectively125).

Anoth erODCstep mechanismtormutati on isthe1,3-bydrogcn shift reaction.

Tauto me ricstruct uresca n bewrittenfora variety of molecul arformulae, such as amidine,form amid e and acet aldehydefor example. Thetheoret icalst udies for amldlne,Icrmamideand othersystemsestimate thBtthebarrierIor 1,3-hydrog en shirt rang efrom166kJjmol to 450kJjmolfortheform ic acid-formic acidand propen e-propenereactions,respectively 1261.Ineproticsolution, however,1,3- hydrogen shirts arefacilitatedby directinvolvement ofone watermolecule.The mechanism for the C-hy droxy;min e-forma midetau tomerism has beenstudied 127).Whilein a gasphase the barrier (orthe hydrog en atomtra nsfer is251 kl/mol (271,when reactantand product aresolvat ed byone or twowater moleculest.bis barrier goes down to46kJ/moland 8 kJ/mol,respet',heJy(27).

Thehydrogenatomtransfertakesplacethrougha cha inof watermolecules.A1J shown in Fig.1.6,1,3-hydr ogen shift,themigrat ion ofproto n fromI-nitrogen,

21

leadsto theformation ofthe enoltautomerofcytosine.

figure1.6 The tautomerism

or

cytosine.

23

CHAPTERU

MOTheoryendCo m p u b. t1on a lDe t ai ls

2.1MOTheory

Thekey to theoreticalchemistryismolecular quant um mechanics.Thisis the science rela tingmolecular properties(.0the motion and interact ions ofelec- trons end nuclei.

Ahinitiocalculations have long promisedto becomeamajor tool tor the studyof molecular problems01structure,stability,andreactionmechanism.The fund ament al techniques,suchasmolecular orbita ltheory,datebacktotheearii- est days of quantu mmechanicsmore than hall a centu ryago. However, widespreadquant itativeapplications have only becomepracticallypceslblein recent times,primarilybecauseDCexplosive development s incompute r hardwar e andassociatedachievements in the designof efficient math emat ical algorithms.

At the presenttime,the subject has become sufficiently matur e andthe technol- ogysulli~ientlystable for practici ngexperimenta lchemiststo use quantum mechanicalmethods directlyfor theirownpart icular applicat ions,ratherthan to relyoncollabora tion with atheoretician.

Accordingto quantumrneehaaics {281,the~n~rcandman,.properties of the statioo:uy state ofamolecule canbeobtainedby solut ionof thetime- independent S('brodingerpartia.ldifferentialequation,

li~=E~ III

HereilistheHamiltonian,adifferentialoperato rt('present ini!: thetotalenergy, F.isthenumericalvalue ofthe energyofthest..-',tbatis,the energyrelativeto astate in whieh the constituentpart icles(nucleiandel~etrons)areinfinitely separat ed and atred and~isthewevelueence.Theweveruu cuondependson theposit ioncoordinates ofall particles(whi{'hmaytakeany valuefrom-00to +00)andalso on thespincoordinates(alpha orbeta spin).

Molecularorbitaltheoryisanapproachto molecular quantummechanics whichuses one-electronfunction!! ororbitalsto approximate tbefull wu e(unc·

tion.AmolecularorbitalJo(x,,.,%),illafund ionoftheposition coordinatesx,r.% ofasingle elect ron.

The completewavdunetion forasingleelectronistheproductofamolecu- tar or bital andaspin (unction, J(x,r, l )o{Oor'1x,y,z)~e).Itilltermed..spin orbital,X(x,y,l,eJ.To ensureantisymmetry, the spinorbitalsmar bearranged in a det erminant al wavefunction.

Withtheseleatures, wecauwritedownDfull mauy-electt onmolecularorbi- tal wavefunctioDforclosed-shellground stateofa moleculewith nteven} elec- trons,doubly occupying n/2orbitals:

~,(')o(l) ",(1111( 1) ~21 1 Io (l ) ~

,.

" (I)P(II

~,(2)o( 2) ".I2IPl2) ~2(2)o( 2 1 ~"1 2 IPl21

r

~=~

⁽²¹

~,( n)oln)~,( nIptn) \112(n )cr(n ) '

,.

. I n )Pln }

2.2Bss isSet ExpanslDDs

Above,we describedhow8many-electr onweverueetl oais eons trueted from molecular orbitals in theform ofa single determina nt.In practicalapplicati ons of thetheor y,theindividua l molecular orb ita lsareexpressedas alineareombiue- tion ofa finitesetofNprescribed one-elect ron Iueetioesknownas basisrune- tions.Uthebasisfunctionsare4>1,92I•••'~N,t benan individualmolecular orbital

'Pi

canbewritten

131

where

a

pi are themolecularorbitalexpa nsion coefficjenu.Thesecoefficients providethe orbitalsdescriptionwithsome8exibility.but clearly doDotallowfor complete freedom unlessthe~pdefine acompleteset.However,the problem of finding the orbitalsillreducedlrcm findingcomple t e descri ptlcusoftheth ree- dimensional function¢Ii to finding only^&finite setoflinear coefficientsroreacb

27

orbital.

In simplegeneralversionsof molecularorbita ltheory,atomic orbitalsofcon- st ituent atom !areusedasbreisfunctions. Such treatmentsareonendescrib ed asLCAO (linear combination ofatomicorb ital ) theoeles.

Gauss ian-type functions (GTF) were introducedintomolecularorbita lcom- putationsbyBoys[201.Theyare lesssat isfactorythan 81'0',(SlaterType Orbi- tals) asre present a ti onsofatomic orbitals,particula rlybecausethey do nothave a cuspat the origin.Nevertheless,they havethe importantadvantagethat all in tegrals in thecomputations ca n be evaluated explicity withoutrecourse to numerical integration.The basic advantageof GTF'sisdue to the fact thatthe productof any two Gaussian,isalso a Gaussian. Consequently,allintegrals have explicit analytica lexpressionsand maybe evaluatedrapidly. A similar theoremdoes not existforSTD's.

VeryoftenSTO'sareexpanded interms ofGTF's[l.e.alinear combination orGTF'sistailoredto fit tbeebepeofSTO's(STO-NGbasisset)). Tbismet hod of usicgfixedlinear combinationsof GTF'sandstoringonlyAO integrals(to reduce the storagespace needed)iscalledcontract ion. Witbout contract ion many calculationson tbeelectronicstruct ureoflar gemolecules wouldbe quite impossible.In ourcalculationstandardsetsof GTF'sare used.

2.3 Uartree-Fock Theol7 and SOF Theol'7

Uptothillpoint,webavedescribedbowdeterm iu ntalwan(unction"may be constructed from molecularorbit ab ,and howtheorbita lsmay, inturn, be expanded in termsof• set01basisIuncticns.Themethodrordeter mining the expa nsionc:oefficienbisintherealm01Hert ree-Fcek(HF) theory.

HFtheory isbased on thevariational method in quantummeeheuica1301. We dealwiththese equations(orclosed-shellsystems. The Ha rtree-Fc ek equa tions are

E(F,."N -f,S,...IC,,,=0 _I

wit h theDormalb at ioD rooditioos N N

E E

0;;5,.0,,;- I.

,.- 1 - 1

p=1.2•...•N (4)

(5)

Here,i;istheceeelectroneneru01molecularorbital

" i.

^{S "..are the elements}

ofanNXNmatrixtermedthe overlap matr ix.

endF,,,,are theelements

o r

anotherNXNmatrix,theFoekmetrlx, (6)

10 thisexpression,H~~"is.matrix rE'presentingthe energy

o r

asingleelectron

in Afieldwhichisfixed.Its elements Are

HereZAis theAtomic Dumber ofatomA,and the sum mationis carriedoutover allatoms. The quan t ities(pill>'0')ap pearing in (7) aretwo-electronrepulsion integrals:

Here(I'll

I

>'0')aregivenin chemist 's notation.They are multiplied by the element! of the one-electron densitymatrix,P)....,

P)....=2Ec ~i C.,,·

i -I

(10)

The summat ionisover occupiedmolecularorbitals on ly. Thefactorof two iudi- cates that twoelectronsoccupyeach molecularorhital,and theasteriskdenotes comp lexconj ugat ion (requiredif the molecularor bitals arenot real functions).

The electronic ene r gy.E",isgiven by (11),

E^U =

t ,._1_1 f EPjl"lF,." +H~-:')

which, when addedto(12). accounting forthein t ernuclear repulsion, (11)

(12)

(whereZ,4.andZ8aretheatomicnumbersofatomsA and B,and_{R AB}is their sepatat lon ] yieldsanexpression fatthetotalenergy.

TheHaetree-Fock equations(4)areDo tlinear sincetbe FockmatrixFp ..

itselr depends onthemolecularorbitalcoefficients,Cpi ,throughthe density matrix expression(10).Solutionnecessarilyinvolves an iterativeprocess. Since theresultingmolecula rorbita ls are detlvedfrom theirowneffectivepote ntial,the techniqueisfrequentlycalledselj-eonsistent-fleld(SCF) theory.

2." Com p u t a t loDalMethods

During the past decade,theanalyt icalcalculat ionofthe firstderivatives of the energyhasbecom e practica landefficient forab initiomolecularorbit al methods (31J.ForSCFcalculations,analyticalgradientscanprovidean orderof magnitu demore informationabouta moleculetha ntheenergy compu tati on alone.Analyticalderivative calculations recentl yhavebeenext ended tomethods thatincludecorrelatio nenergy[32-35).Energy gradients werefirstused tocalcu- late vibrationa lforceconstants [36,37).However,geomet ry optimizationhas now become the most widesprea dapplication.

Optimizationof moleculargeometryis oneofthemost impor ta nt procedures incontemporary theoretical chemistry. The traditiona lapplicationof geometry optimizatio n has beenthedete rminationofequilibrium geometr iesfromab initio

31

calculatio ns,andextensive literat ure[38)hlL'l demonstrated that ebinitiostrut- tureaare generall yingood agreementwithexper imenta l data.Thisractrecorn- mendsab initio geometry optimizat ionasapowe rfultool forinf e.gligatingmolec- ular stru ctu reswhichare notexperimentallyknow n.

Molecularorbitalcalculat ionsgenerallyinvolv e threebasicsteps:(a)calcula- tion ofintegrals , (b)solut ionof theself-consistent equations and (e) evalua t ionof theenergy gradient.

CHAP TE R lU

ResultsandDteeueejo n

3.1Method

ClosedshellSCFabinitiocalculat ions wereperformed using the MUN- GAUSS program 1391.Aminim al STO-3G[40,411and split-valence3-21G basis set(42-45) wasusedthroughout.In addition,calculat ionswere performed with the 6-31G*basisset(461forthedeamination

o r

emidine .Thegeometrieswere optimized usinggradient optimizationtechniques(41,48J.Except ror transition statest r uctures, all the geometryoptimizations were performedusing the optimallyconditionedmethodofDavidon andNazareth 14Q,50).Thecriterionlor convergencewasthenorm ofthegradien tlength being less than 5.0X10.⁴rndyu, a condit ionwhich normally givesbond lengths towithin0.0001

A

andanglesto within 0.01⁰or th eirtrue optimumvalues 1511 .Transit ion state structu reswere det erminedusing the VAOS sum

o r

squaresoptimizationtechnique152J. The for ce cons tantma t rixwas calcula te dusingVA05 to determine theorder

o r

acme or the sta tionarypoint!.

33

Wehave stud iedthe deamination ofcytosine using ab init ioSCF MO calcu- latlc ne.Thetwo mechanisms invest igated inthis workfotthe deamination

o r

cy tosine areoutlinedin Fig.3.1and Fig.3.2. Fjg. 3.1showsthatthe nucleophilic att ac k by thehydroxide at position4,followedby1,3-byd rogenrearra ngement and elimina tionof NH₃togivethe uracilanion.Asim ilarmechanism with1120 isshownin Fig.3.2where the 6rs1 step involvesprotoualionof thenitrogen at position3and nucleoph ilicattack byhyd roxideat position4.The secondstep is followed by a 1,3-hyd rogen rearrangement andsubsequent eliminationof Nils,to give uracil.

Because01the sizeof moleculesinvolved,as afirs t step,weinvestig atedone (withoutintermediate inFig.3.3)andtwo step mechanis ms for the deamination ofamidineasAmode lforcytosine (F ig.3.3 and 3.4).

Unlessotherwisespecified,allcalculate dvalues rep o rtedinthis chapte r refer to the resul tsfrom calculatio ns using the3-21Gbaais set.

3.2The Reaction or Amldlnewith OH-

A one step mech anismforthedeamiaatiou ofami dine withhydr oxidehas beenstudied. The structu resinvolved inthe emidiee-h ydrcxide comp lex (rea c- tant) and Corm ami te ion-ammoniacomplex (pro duct)will bedis cussedin thetwo stepmechani sms.Tbetransit ion state st ructu re(d.Table I inappendix) forthe

Thedeaminat iou01cytosinewit hOH-.

0

~ %-~ffi

% %

o ~ . , +

p>

0

^';

!;l

x- z ,,'

- Z

~

%

x.

%

X

o}- "

,0

l;l

~

~

~l;l

x-z _

~

~

% X

~ %_~\ _~

% ~

~ O~ :t ^z

~ %-~ - :

^~

O }.~

% %

%-~O

% X

+

Z

:

Figure3.2

Tbe deaminatio n orcytosine with H20.

o ~'"

^{z 0}

%-

_

"

,'"

z'

%

r.:

+

J

"'-~~ o

'" :x:

+

if

o

Figure J.3

The deami oa tioDoramidiDewith OH-.

3'

+

.t

z

Figure 3.4 Thedeamina ti on ofamidine with H20.

+

.. z

ODe stepmechanismshowsthattheOs-Ctbondistorming andC-N2 bondis breakingtorming Nit"a.9a leaving group.This st ructure is afirst ordersaddle pointonthe pote ntialenergysurfaee, thatis,thetort e consta ntmatrixhas only onenegativeeigenvalue. The resultsofthesecalculationsindicate thattheeon- certedreact ionhas abarrierof424kJ/m a!.Theonestepmechanismwasnot consideredanyfurtherbecause ofthe bighbarr ier.Thetrans itionstal estr uct ure and relatedinlormatioc are givenintheappendix.

The structures (two step mechanisms)involved inthereactionofamidi ne with hydroxide areshown inFig.3.5.Thecorresponding geom etriestorallstruc- tures,amidine-hydrox ide complex(J. andIb),intermediat e(

r, ),

transition sta te(J"JandIormamide ion-ammoniacomplex(I. ) are givenin Tables1-5 andthe corresponding energies are giveninTable6.Thetwo conformationsot the amidine-hydroxidc'complex(I.andI, ) wereconstrained tohaveC.sym- metr y.These two structu resdifferonlyinthe orien tati onoftheon·.The cal- eulat ed OV-CI bondlengts in I. i, foundto be3.54

A.

Thecalculated Oo-Cl bondlengt hinI.isfoundtobe:'>.64

A.

StructureI.iss;,ghtlymorestll.bletha n I~by2 kJ{m ol(c.r.Table7).

Thei.nterm ediat e( Ie)resulti ngfromadditionof OH-to amidine,has cal- culated OV-Cl andCl·N2 bondlength s or 1.52

A .

Compa rison ofthe09-Cl andCI-N2bondlengt hsinI. and I. showthattheOa-OtbondlengthinI. is getti ngshorte r than thatin I.by2.03

A

^andCI-N2bondlengt h in I.isgetti ng longer thanthat in I. by0.12

A.

43

Figure3.5

The st ruct uresfor thedeamiaation

o r

amidinewit b bydroxide.I. andI. are amidine-bydroxidecomplex(reactant),Ifisan intermediate,I~isthetransition ate te forthe hydrogen rearr angement andIfi!theform amide ion-ammoniacorn- plex(product ).

N4

H5

10 H'

• •

09<~

^,NO

" ~.' ^NO

"

_'..CI

N4

H'

H5 I>

£

^Hi

^{N' e,}

^H6

09\~ •.•.••H4

.•\ N3

..

Ie

~ H8 '''''''''H1

71..•·N2

"f

_He ⁰

_....

_H4

N3 td H1

• He

~ ^{O' :/} H9~6

-N4 H3

H'

1.

"

Table1STQ.3G,3-210 and6-310' optimized geometries(under 0,symmetry) Icrtile amidine-hydroxl decomplex ( I,I'

Bond lengths STO·3G 3-2lG 6-310*

N2Cl 1.4360 1.4043 1.4')10

H3Cl 1.1052 1.0S98 1.0916

N'GI ^{1.2015 1.2658} L2S01

H5N4 1.0487 1.0170 1.0070

H1N2 L09S1 1.0366 10157

09Cl 3.20BS 3.5401 3.70:;0

H600 1.0173 D.gOn 0,0563

Bondangles

I13CIN2 113.50 113.01 113.15

N4CIN2 127.58 127.10 126.03

HsN4Cl 101.25 112.50 l00A1

HIN2el }09.22 115.37 112.16

QUGIN, 88. 10 92.60 02.32

H609Cl 85.80 80.51 81.66

Torsionan gles

1I1N2CIH3 +140.58 +131.36 +129.88 H2N2CIH3 -140.58 -131.36 -129.88 a.Bond lengthsare given in angstroms and bond angles in degreesrotall tables.

Table 2 STO.3G,3-2lG and6-31G*opti misedgeomet ries(underC.symmet ry) for the amid ine-byd roxidecom plex (I.I

Bondlengths STO·aG 3-2lG 6-310_

N2CI 1.4377 1.4034 1.4011

H3Cl L10S0 l.OOO4 (,0918

N4Cl 1.2908 1.2652 1.2585

HSN4 1.0489 1.011 1 1.0070

HIN' 1.0957 1.0335 1.0145

osci

3.2055 3.6367 3.1949

H60 9 1.02 17 a,gg 07 0,9569

Bon dangles

HaCIN' 113.51 112,91 113.05

N4C I N2 127.60 127.34 127.07

H5N4Ct 107.26 112.42 100.40

HIN2Cl lORIS lIB.55 112.96

agCI N4 87.8 1 97.06 91 .14

!I00g CI 127.46 111.08 110.64

Tcraion angle!

HIN, C1H3 -+:140.21 +129,91 +128.94 112N2CIH 3 -140.21 -129,9} -128.94

41

Table3ST0-aG,3-21G and6-alC.optimised geometriesforemidine-byd roxlde intermediate (

r, )

Bond lengths STO·3G 3-21G 6-3IG·

N2Cl 1.5440 1.5211 1.4027

NaCt 1.1344 1.3869 1.3796

H4N3 1.0646 1.0379 1.0213

H6N2 1.0389 1.0102 1.0045

H7N2 1.0392 1.0100 1.006 2

H8C1 1.1009 1.0854 1.0928

OgCI 1.4697 1.6165 1.4631

HI09 O,9913 0.9684 0,9411

Bondangles

N2CIN3 118. 78 118 .70 118.80

H4NaG! 00.82 106.04 105.401

H6Nzei 103.43 106.60 104.31

H7N2C l 104.30 107.31 105.72

H8CIN2 103 .23 106.92 105.63

OgCIN2 101.94 100.04 10 1.S9

H10 gCl 100.91 100.81 99.81

Table 3 continued

Torsion angles

I14N3CI N2 57.26 50.17 52.58

116N2CIN3 48.63 23.04 34.43

H7N2CIN3 303.oI 265.90 283.61 HBCIN2Na 237.95 234.78 236.88 09CIN2N3 127.65 12·U 5 126.3 2 H10 9CI N3 ·9,49 ·17.63 -18.39

,.

Table 4 ST0-3G,~2lGand 6-31G_optimizedgoometries lor the amidine- hydroxide transitionstate {I..I

Bondlengths STO-aG 3-21G 6-31C.

N2Cl 2.og9Z 2.0440 2.0362

NaCl l.30QS UIHO 1.2897

H4N3 1.0482 1.0109 1.0096

H6N2 1.0451 1.0270 1.0120

H7N' 1.0 438 1.0248 1.0123

HSC1 1.1038 1.0756 1.0708

0001 1.4053 1.4193 1.3849

HI N2 1.5040 1.7675 1.0477 Bond angles

N2CINa 118.78 118.47 IHI.20 H4N3C1 10 4.53 100.78 107.3 5 H6N,Ct 118.80 110.02 105.73 H7N2Cl 118.74 IM.70 10 1.60

HaCI N, IH.IO 90.79 89.62

Q9CIN2 80.29 86.04 so,17

HtN2CI 55.80 56.90 5..t50

Table4 continued

Torsionangles

lIotNaCIN2 81.12 81.68 84.0 2 H6N2CI N3 112.23 90,S9 81.0 0 H7N2CI N3 348.71 348.01 334.17 HSCIN2N3 240.28 238.58 230.28

09CIN2Na 124.51 124.84 125.97

HIN2CIN3 232.90 231,88 225.04

51

Table5 STO-3G,3-21G and~3lG.optimized geometries forthetcrmemtde ion-ammonia complex ( If)

Bond leugt be STO·3G 3-210 6-310*

agel

1.2828 1.2700 I.Hto

H3Ct 1.1HI7 1.1118 1.1163

N4CI 1.32Da 1.291& 1.2971

H5N' 1.0 483 1.0188 1.0082

HD09 1.4333 1.8285 2.0087

N6H' 1.0950 1.0210 1.0153

H7N6 1.0366 1.0101 10054

HaN6 1.0367 1.0 10 2 1.00&4 Bondangles

H3C10 9 116.23 115.17 U5.03

N'CIO' ^125.96 127.75 128.29

H5N,CI 104.80 110.40 101.54

HgQgCt 113 .30 125.25 126.63 N6H90 9 176.01 169,64 164.49 H7N6H' 103.70 100.12 104.69 R8NaRD 103.84 109.13 104.66

Table5 continued

Tor sion angles

N4C109H3 180.03 180.05 lSO.03

115N4CllU 0.10 0.12 0.10

li9Q9CIH3 0.85 3.43 4.51

NaHgOgCI 150,93 155.23 156,95

H1N611g0 Q 52.69 59,14 5517

HSN6H9QQ -52.69 -59,14 -55.17

53

Table 6 Tota lenergies fot the amidine-bydroxide struct ures·I. -I.

Energies(bartrees) Compound ( OH-)

STO-3G 3-21G 6-31Ct

I, -22 1.2550 13 A223.135347 -224.418&09 I, ·221.254l:l0 4 -223.1~4560 ·224.417703 I, -221.385775 -223. 17646g -224.443556 I, -221.329240 -223.1 53612 -224.41732tJ

I, -221.40168 1 -223.236483 -224.511773

a.See Fig.3.5tor thest ruct ures.

Thetransitionstat e(I~) tor thel,a.-hydrogenrearrangement(d.Fig.3.5) indicatesthat the Og·Clbondis shortening and CI -N2bond is breakingformi ng NII3^:ISa.leaving group. Theorderofthestat io n al}' point ,whichwasdeter- minedusi ng VA05, indicatedthat this struct ure isa6r~tordersa d dlepoin t on thepotentialenergysurface, that is,the forc econstantmatrixhasODenegative eigenvalue . The ca lculated 00-01bondlength in the transitionsta tetl<i ) is foundtobe1.42

A

,whichis betweenthe single00·01bond(1.52

A)

inIeand tbe 01J-Cldoublebond (1.27

A)

^inI•.

Inthe final product(I. ),theIormamideion-ammoniacomplex,theNHa is hydrogenbonded totheoxygen witb atypicallylinearhydrogenbond .

Therelativeenergiesof the emidlee-hyd roxtdecomplex,intermed iate, tra os i- tioostateaod productaresummarized in Tat'':!7.Aschematic energy profileCor th edceminarionor amidinewithoH-isshow n ill Fig.3.6.Thcresults showthat the second stepbasacarrierof 60kJ/molL...dthat theproductismore st a ble than theI.by258kJ/mol.Therefore,these results indicatetbat thisreactionis both thermodynamicallyand kineticallyfavou ra ble.

3.3TheReeeelcaorAml d lDe withH20

Thestru ctures involvedin thereaction of amidinewithwaterareshownio Fig.3.7.The correspon dinggeometriesforall etrueturee,amidine-water com:>lex

55

Table 7Rela t iveener gies for tbl!amidine-bydro xidest r uctures' 1. -If

Relati v e energies(kJjmol) Compou nd(OW)

STQ.3G 3-210 6-3 lG_

I, 400.83 265.53 244.86

I, 40Ll2 267.60 246.98

r,

57.51 157.57 17Q.l0

I, 206.95 217.58 247.97

I, 0.00 0.00 0.00

a.SeeFig.3.6

figure3.6

Sche,,!:lt ieenergy profile(orthedeemineuceof amidinewith OH-.Am+OH4

IDd FM-+NH, ener gies jus t tbe or tbe energies

E(Am+OR-)=E(Am)+E(OW) aDd E(Fo,-+N H,) =E(Fo '-)+E(NII,)_ Wh", R..w...OH-corresponds toI.,I"'....OH- to1"TA ......OH""to14 endPf.,;:.N~toIf'

57

o

g ...

_o

o

..

Ii

.. ..

"

Ir ⁶

.0

l"i

!

^t

h-ir !

⁰

¹

0

1 1

-J :: iJi

;

.;;0

~

, 2

~~ ...

^;Z:z:

Figure 3.7

The struct uresfor the deamioation

o r

amidinewith water.U. sod 0, are amidine-watercomp lex(reactant), Dc andIII areintermediates,0,isthetransi- tionstate for the hydrogenrearra ngementand II, isthe rcrm ermde-emmcn le complex (product ).

~~f? _i",,~

N~ ~

~

n.

K~~~

^{H2 " ' 0}

" ~

~ Ub

0

^~

^"

^~

^{~--~ a ~}

I11. &lidU. I,intermediate{ U,.and 01 I.transitionstate ( U. ) and form 3.mid~ammoDiacomplexIOJ )are given in TabletS.13.Thetotal eom- puted f'oergiesarereported inTable14.Two st ructuresIorthe amidiee-water com p lexeor reapcadin glotwodiffeccnlorienta tionsoflit O (II.and II, )are obta ined.Theoe.crbond lengthinU.iscalculated tobe 3.15

A.

The calcu- lated OO-Cl bondlength in01 is obtain ed tobe 3.48

A.

Str udure U. is predieted to bemorestablethan theII.by03 kJjmol{d.Table15).

In thetwo confo rmersof theintermediate (U. and U₁)resu ltingfrom addit ionor hydroxide atCl andproto nationatN3,the 09-C land Qo-HIbond lcngth,are calculatedtobe1.4~and 0.07

A

respectively.TheHoeNtors ion eugles inD,. andU~ are_30⁰end160°,respectively.Str uct ure04isslightly more stabletbaDtheU, byUkJ/mol .

The calc uleted Oo-CIADdN2-CIbondlen~bsrorthe.,3-byd rogenrear·

rlngcmenttran~itionsta le( II. Jareroundtobe1.37aDd 1.68

A

^Ire3peclively.

AKaintbe transitionstatestr ucture(::I,) indicatesthattheQ9.CIbondisebor- teningeed theN2·CILundillbreAking rormingNH"&Saleaving group. The joree constan t matri x indi<:ate'ltbat thisisI.61St ordersaddle point.FromTable 11·12 itiscleartbat theOg...CI bondlengthdecreeaeain goin g homint ermediate to tr e nelucn stateby 0.06

A.

and the N2·Ctbondlengthincr easein going(rom interme diatetotransition sta te by0.22

A.

61

Table8STO-aG,3-21Gand6-310*optimizedgeometriesIor the amidine-water complex (U. )

Bondlengths STO·3G 3-21G 6-31(;·

N2Cl 1..1198 1.3491 1.3560

11301 1.0956 1.0798 1.0833

N4C. 1.2823 1.27 19 1.2627

115N< 1.0413 1.0070 1.0010

H6N2 1.0 385 1.0 086 1.0008

H7N2 1.0261 0.9934 0.9938

osci

3.1355 3.1509 3.37&8 H109 O.{l864 0.9665 OJ l474

"209 0.9884 0.g863 0.9578 Bond angles

1130 l N2 114.28 114.23 113.50 N4Cllla 124.92 123.&1 123.33

HsN4Cl 108.99 115 .3 1 111.49

H6N2Cl 109.61 117.02 116.68

117N20 1 111.82 12 1.71 118.25

OOCl N4 63.43 60.40 58.93

1110'01 113.13 1B.70 115.50

820 9H l l00 ,99 108.10 105.24

Ta.ble8 continued

Torsion angles

N1C!H 3N2 176.66 179,81 178.21

H5N4C1ll3 -1.00 0.20 -0,07

116N2CI N4 18.0 2 2.00 12.32

U7N2CIN4 142.52 177.77 159.31

O{lCIN4 N2 13 .68 0.50 0.00

1I10 9CIN2 85.\16 96.24 94.17 H209HIO I -5 4.23 -45 .47 -42.56

63

Ta.ble 9 STQ.3G,3-21G end 6-31G*opti mised geometriestor tbe amidine-water eomplex( 0_{6 )}

Bondlengths STO-3G 3-21G 6-31C·

N2Cl 1.4672 1.4304- 1.4225

H3Ct 1.0976 1.0825 1.0866

N4CI 1.2723 1.2508 1.2464

USN4 1.0466 1.0126 1.0048

H6N2 1.0340 UlO40 1.0037

H7N2 1.0340 1.0048 1.0037

0001 3.5562 3.479} 3.6300

"109 0.0873 0.0660 0.9482

H2O' ^{0,9876 a.g70T 0.9510}

Bond angles

H3CIN2 116.81 116.26 116.85

N4C 1H3 124.23 122.80 122.69

HSN4Ct 108.98 UU4 110.9S H6N2Ct 107.71 114.80 110.40

H7N2C1 107.7 4 114.83 110.42

O'CIN4 63.48 60.44 61.47

1120901 65.31 64.111 64.88

H200m gO.a9 103.84 102.39

".

Table 9 cont inued

Tcrelonangles

N4ClH 3N2 180.0 7 180 .07 180.03

I15N4ClH3 -0.04 ·0.07 -0.0 2

HaN2CJII3 S8.2 4 66.30 58.gS

H7N2CUl3 -56 .24 -66. 30 -S8.98

09CIN4N2 -1.81 -1.29 -1.21

HIOgC1N2 181.86 181.54 181.28 11209HI01 ·1.90 -1.39 -1.25

65

Table10ST O·3G, 3-21Gand 6-31Ge, --timizoo geometriesrOttheemidi ne-water intermediate(DeI

Bondlengths STO-3G 3--210 6-3IG...

N2Cl 1.4845 1.14 48 1.4376

N ac.

1.4865 1.4575 1.4491 II.N3 1.0314 1.0019 1.0018 HSN3 1.0328 1.0 0 43 1.0036

H6N2 1.0328 1.0002 1.0010

H7N2 1.0336 1.0014 1.0024

HBC! 1.1020 1.0 812 1.0850

0901 1.4381 1.4255 1.3868

HlO' 0.gg02 0,9656 0,0419

Bondangles

N2CINa 111.47 117.15 118,08 H. N3CI 108.S9 115 .86 111.64 H5N3C1 108.89 114.42 110.53 lIoN2CI 106,58 116.04 1l1.33 117N2Cl 107.49 113.53 110.31 118CIN2 107.a9 100.33 107.54 OgCIN2 107.78 104.33 105.45 HlOgCI I04.1J6 lOS.15 107.61

Ta bleJOeoutieued

Torsionangles

114NaCI N2 ·173.84 -87.3 0 -60,27 HsNaCIH4 244.84 (34.25 120.48

H6N2CI Na 52.08 40,14 53.12

H7N2C1N3 2110.78 272.35 202.H H8CIN' N3 243041 230.11 230.77 OllCIN2N3 128.13 110.71 120.71

HIOgCIN a 1.23 -38.5' -43.12

67

Table 11 ST0-3G, 3-21Gand6-310_optimized geometries fertheamidine-wa ter intermediate(

n, )

Bondlengths STO·3G 3-21G f)...31G·

N2C l 1.4852 1.4494 1.4380

NaC} 1.4848 1.4429 1.4342

II'N3 1.0326 1.0051 1.0000

"5Na 1.0338 1.0061 1.00 42

HGN2 1.0321 1.0036 1.0019

117N2 1.0334 U")62 1.0038

H8Cl 1.1029 1.0798 1.0849

0.01 1.4302 1.4341 l.agS2

1110' ^0.9891 a,9aog 0.9490 Bond angles

N2CtNa 112.40 113.52 113 .65

II'N301 107.11 113.04 100.81

HSNaG. 106.14 112.23 109.38

H6N2C l 107.02 113.11 110.12

H7N2Ct 10 7.25 112.72 100.9]

IIsC1N2 107.31 107.87 107.67

QgCIN2 100.23 107.85 lOS.3 0

"t09Ol 103.64 109.06 108.21

Table 11conti nued

Torsionangles

1J4N3CI N2 -173.2 5 -t71.07 0176. 19 HSNaOIH", 2-18.55 23 4.23 2,13.33

H6N2CINa 61.51 86.02 5Q.4 4

H1N2 CI Na aOD,50 208.20 301.00 H8CIN2 Na 24Ul5 240.73 241.28 OQCIN2Na 120,08 121.00 122.06

HI09CINa 160,55 168.50 171.71

09

Table 12STO-3G,3-210and &-310.optimized geometrieslor tbeamidine-wate r transition stat e (D,)

Bondlengths STO·3G 3-210 6-3IC'

N2Cl 1.8 121 1.6569 1.6253

NaG! 1.4075 1.4062 1.390 4

H4N3 1.0135 0.g077 0.0920

H5N3 1.0139 O.gggg o,goao

lioN, 1.0328 1.0000 1.0046

117N2 1.0325 1.0081 1.0038

11801 1.1112 1.0817 1.088 3

09CI 1.3236 1.3691 1.3253

IIIN' 1.1425 1.2124 1.2085

Bondeugles

NZCIN3 111.11) 109.S9 H2.53

H..NaG! 122.24 119.62 122.73

H5N3Cl n9.55 113.13 117.67

HaN2el 121.80 117.66 117.03

H7N2C I 121.25 112.67 115.8 1

118N' C l 08.88 10 4.34 104.35

OOCIN2 87.52 92.15 93.48

IIIN' CI 67.76 71.77 70.35

Table12cont inued

Torsionangles

114N3CIN2 ·{lS.57 -113.25 -S5.45 IISNaCIN2 88.20 102.40 80.01 H6N2CINa 126.8 7 130.41 13lo71 H1N2CiII3 345.68 351.60 358.35 H8C1N2N3 24 4.04 :l3g.42 293.68 OgCIN2 N3 121.88 llV.02 119.45

H1N2CINa 23 6.58 242,07 24UO

71

Table13 STQ.3G ,3-21G andlJ.31G.optimized geometriesfor the formamide- ammo nia complex(II ,I

Bond lengt h! ST().3 G 3-2lG 6-31( ;-

oo ct

1.218·' 1.2207 1.1983

H3C1 i.ion 1.0784 1.0871

N4Cl 1.42911 1.3493 1.3·mO

HSN4 1.0255 0,0053 O,9930

H6N4 1.0263 0.9981 0.09 55

HlOO 1.0371 2.1100 2.2973

N711l 1.0336 1.0061 1.0043

H8N7 1.0310 1.0030 1.0030

HON7 1.0320 1.0039 1.0029

Bond angles

H3ClOO 123.87 121.18 121,08 N4C100 123.76 124.52 124.32

HSN4Cl 112.75 121.74 121.66

H6N4CI 112.44 119.61 119.44

H10.Cl 113.17 94.70 96.11

N7H109 174.65 H4.15 146.40 H8N7Hl 104.40 112.53 101.32 HON7H1 104.30 112.34 101.31

Table13 continued

Torsion angles

N.f,CI09H3 176.09 179.95 180.06

HsN4C!Ha -36.24 0.02 0.23 JI6NotCll13 107.94 170,79 179.8&

IU09 C1H3 3.68 0.27 0.77

N7HIOgCI 4.08 -3.33 -1.20

H8N7Hl":"Q 133.45 121.03 122.53 HON7HIH8 108.64 126.74 114.62

73

Table14 Total energies for the emidlne-weteestr uctures" U. -U f

Energies[hartr eee]

Compound(112 0I

STO·3G 3-21G 6-3IC·

u, -222.133981 ·223.863695 -225.102779

u,

-222.115357 -223.818 174 -225.078.'; 2·1

u ,

-222.183429 ·223.8 49440 -225.009238

n,

·222,103799 -223.854666 -225.105232

n, -222.057560 -223.785 155 -225.0 15579

n_l -222.152181 -223.870066 -225.122167

a.SeeFig.3.7forthestructures

Inthe finalprodu ct(°1),theformamide-ammonia complex,theNH3is hydrogenbondedtotheoxygenwith8typically linear hydrogenbond.Cern- perieon(J(thestr uctures ofUJ,lit and II,show the Og·CIbond gettingshorter in goingfrom thesingleOG-CI bondinUJ(1.43

A

J.to theOc-Ctdouble bond 11.22 A) i nU /·

Therelati ve energiesofamidine-hydroxidecomplex,int ermediates,transition st ate and Iormemide-emm oniecomplexareeummensc din Table15. The results indicat etbat thesecond stephasabarrier of182 kJ/m ol and thattbeproductis moresta ble than thecomplex (II. )by42 kJ/m ol.Fig.3.8illustr ates tbatthe reactionofemidlnewit h wat eristhermodynamically favourable but kinetically notfavour able.

8.4Effectof Baele Sct8 on the Deamlnallon or Amldlne with08-

Comparingsomeor theimportantgeometrical parametersof theST0-3G, :J.21Gand 6-31G. opti mized geometries a.number or trendsappear.The3-21G and &-31G. basis setconsistentlygiveshorterN·C, H-C,H-Nand H-Obond lengths tban thosefromST0-3 G basissetand longer0-Cbond lengths of the order of0.015-0.430

A.

The:J.21Gand6-3!G. H3CIN2 . N4CI N2, H5N4Cl.

HIN2Cl , 02C1N4 andH602 01bondangiesdiffer by lessthan3⁰,except in the transitionstate st ructures, wheretheanglesvary byas muchas 4°,Inaddit ion,

75

Table15 Relativeenergies fortbeamidine-waterstructures-II. - U,

Relativeeuergiee(k J/m al) Compound ( Hz 0 )

STO·3G 3-210 ~3lG*

II, 47.48 42.08 50.00

II, 06.68 138.2·1 1H.58

II, -82.04 54.14 60.20

II, -100.27 40.43 44.46

II, 248.43 222.03 270.85

0,

^{0.00 0.00 0.00}

a.See Fig.3.8

7'

Figure3.8

Sebemetleenergy profiletor the deamlnati on of emdlne with 11₂0 . Am+ H20and For+N H₃energies arejustthe sumoftheenergiesE(Am+~O)=E(Am)+ E( H20) and E(For+N H₃J=E(For)+ E(NH3). Where RA,"...~O corresponds to D., J~II\...

¥

tolIe.l~m...Hp to Dol.TAm.•.Hp tolieandPF..~...NH3toU, .

11

0

..

0

..

0 ^;;;0 ^Oi0

8 '" t

M: ^{~ "'}

: ;t

12

~~

⁰

,

.. ^~

I N :

i !{

:

~H

! _{.=~ -}

! ! ~

i

^:

ⁱ "M ~

^{3 i}

!

!

⁰

^{I .}

, ^{' ,} . "f

, ,

iii

i :

^N

I

I·~ ^{::l ~~}

! ^{f '"}

^I

I'~ 'I ~

I I I

'"

themostnoticeable chuge in thegf'Ometry01thetransition,tate involvesacoo- siderable narrowing01 theOe Ntbond angle which iaereeses in goingIrom STO·

aG,3-21G to_{~3IG' 1}wheretheOeNtbond angleincreasesby4-10°.

3.&Co m parlso n

or

theDea mlnaUoD

or

Amld iDe"11th08-an d RIO

Table7 and Table15summarizedtherelati ve energiesteethe deaminatioD ofemidine with OWandH20 , respectively.The schematicenergy profileIcrthe deamin ati onotamidincwithOH-and H₂0 ore shownin Fig.3.6andFig.J.8, respectively.Ccmpereon01theresulls01thereactionlorthedeaminet lou01 arnldiee wit hhydroxideand waterindicatethat emldine-bydroxideintermediate( I~)ismor establethlDamidine-bydroxide complex by110 kJ/molandtbatthe amidine-waterintermediate(0.)isonly sightly morestable thaDtbe amidine- water complex by 3kJ/mol.The secondstep withhydroxidebasabarrierof60 kJlmol and wit h water bas a barrier01182kJ/mol. Thebarrierlor thedeami- nation or amidinewitb hydro xideillsignifiuotlylowertbantbe deamination01 amid ine wit hwa;";:-.Bot h relat in energiesshow thattbe reeence01amidine with OH-isboththermodynamica lly andkinetically ravourable and the reaction or amidine with H20^isthermodyn amicallybu~kineticallyDotveryCavourabl e.

70

3.8Optimised Str ud ure

or

Cytoa1De

Theoptimizedstruc t ure(d.Fig.3.GlorQumberinr;)01eytosinelJ~inr;ST O- 3Gand 3-21GbasissetarereportedinTable16andeoruparedwiththeesperl- mentalelyslaleteueture

1531 .

Thecomputed bonddist a nt"inthering are longerthanthe~xperimeDtaldist ances.exceptlor N.jCI,caC2,N3CJ andOIG·1 whicbareshorte rby0.04 ,0.01,0.003 andJ.02

A

,respectivel y.Thecompute d boodangleswithin thering are inleirlygood agreement withthe experiment ai values, the largestdiscrepan cybeinga diITerence015.4° intheIll N2C l angle.

3.7The Rer.etlonorC7toalnewithOU-

The au logou5 struct ureslor thedeamination01amidine with hydroxidr wereinvestigatedlorthe deaminatio nofcytosinewith hydrox ide.Thesh udure involved in thereactionorcytosine with hyd roxideare sho wn in Fip.3.1D-3.13.

Therorralponding geometri esIoraUstr u ctures,cytOlline-brd roxidecomplexI W.

and01.).interm ediate(OI, ), transit ion stat e(OI~)and uracilion-ammon ia ecmptexIIll, ) aregivenin T ..:)Ie9 11-21and tbetolal compu ted enerciesare repor tedinTable 22.

The structu restorthe crtoslne-bydrcx ldecomplex(10.and

m. )

wereeon- strainedtobaveC.symmetry.These two eteuet ureedifferonly intheorient...

tionotthe OH-.Str ucture 10.lsslightlymorestable tban

m.

by 5.1kJ/mol.

Figure 3.9 Numbering for thecytosinestructure.

81

01

82

Table 16STo-aG and 3-210optimizedgeometries (under0, symmetry) Ior cytosine

Bond lengths Experimental STO-3G 3-21G

N2CI 1.330 1.3018 ^1.3439

0201 1.424 1.4715 1.4431

N4.Cl 1.337 1.3095 1.2iI73

HIN2 0.87 1.0141 O,g074

H2N2 0.86 1.0132 0,(10013

H3C2 0.87 1.0764 1,0661

0302 1.342 1.3298 1.3378

H4Ca 1.01 1.0876 1.0701

N3C3 1.357 1.3876 1.3044

H5N3 0.88 1.0198 0.0084

C4N4 1.384 1.44.04 1.3686

orca 1.234 1.2209 1.2113

N3C. 1.374 1.4.. 53 1.4147

83

Table16 eontlaued

Bond englee

C2CIN2 11~.98 119.15

NotCIN2 118.2 116.tlO 118.0 8

HIN2et 123.0 1111.16 117.64

H2N2Cl 124.0 121.60 122.16 H302C1 123.0 120.37 121.78

030201 117.3

m.oo

116.08

H4CJC2 122.0 123.76 122.43

N3C3C2 120.1 llg,99 120.80

H5NaC3 117.0 119.88 121,33 C4N4Cl 119,9 117.24 122.23 OlC4Na 110,8 n9.51 118.90

Figure 3.10

The structureslortheeytcelne-hydrcxldecomplex (reactant).

m.

m.

.6

Figure3.11

Thestructure torthe cytosine-hydroxideintermed iate.

87

ille

H2

Figure3.12

Thestructure01the transitionstate forthe hydrogen resnengemeut(cytosine- hydroxide).

8.

H4

00

Figure 3.13

The structure lor the uracil ion-ammonia complex (product).

Q1

H80 " ' "f

:::

__ _ ___ He N3

HI

HZ

m.

Table 17 ST().3G and 3-21G optimized geometries (underC.symmetry) for the cytosine-hydroxidecomplex( UI. )

Bondlen~thll STQ-3G J.21G

N2Cl 1.4151 1.3848

0201 1.4045 1.4554

N'C' ^{1.3270 1.3012}

HIN2 1.1266 1.0515

H302 1.0782 1.0849

C3C. 1.3224 1.3311

U,C3 1.0860 1,0712

N3C3 1.3085 l.3668

USN3 1.0184 0,9068

C4N4 1...310 1.3733

01C4 1.2288 1.2194

0201 3.1378 3.5375

H602 1.0 124 0,9943

03

Table 17continued

Bondangles

C2CIN2 114.44 114.89

N.C1N2 123.88 124.86

HIN2e. 100.33 111.16

HaC2Cl 118.06 118.34

C3c.CI 120.11 118.22

H..C3e 2 124.91 123.75

N3C3C2 119,18 110.81

HSN3C3 120.18 121.53

C.N.CI 110,10 122.90

OlC4N3 117.07 118.32

02CIN' 83.00 04.81

H602CI 127.26 115.38

Torsion angles

HIN2CI C2 +143.06 +133.00 H2N2CIC2 -143.06 -133.06

Table 18STQ-aGand 3-21Goptimized geometries (underC. symmetry)lorthe cytosine-hydroxidecomplex(01.)

Bond lengths STO-3G 3-21G

N2Cl 1.4067 1.3828

C2Cl 1.4953 1.4543

N4Cl 1.3322 1.3030

H1N2 1.1404 1.0606

H3C2 1.0783 1.0640

0302 1.3223 1.3312

H4C3 1.0860 1.0713

NaC3 1.39S5 1.3669

H5N3 1.0183 0.9067

Cm4 1,4267 1.3710

OlC4 1.2298 1.2201

0201

aosso

^3.4078

H602 1.11047 0.9S90

85 Tab le 18continued

Bondangles

C2CIN , 114.80 115.27

N4CIN 2 123.72 124.20

HIN2Cl 108.74 114.02

H3G201 118.08 US.37

(J3C2Cl 120.16 118.17

~i4C3C2 124.86 123.60

N3CaC2 110.21 nO.81

HsNaC3 120.16 121.53

C4N4Cl IHJ.26 122.94

OlC4Na 117.78 118.21

O~CIN4 8U lO 88.32

8602C1 85.15 8306

Torsionangles

HIN2CIC2 +144.28 +135.81 H2N2CIC2 -144.28 -135.81

..

Table10STO-3Gand3-21GoptimizedKeomet, jjorC1~iDe-b1droddeinter- mediate(W, )

Bced lengths ST0-3G 3-21G

N2CI l.S100 1.4805

0201 1.S330 1.5010

N4CI 1.4722 1.4296

HIN2 1.0388 .1.0to5

H2N2 1.0388 1.0100

11302 1.0702 1.06ll8

C3C2 1.3130 1.3198

H4C3 1.0881 1.0745

N3C3 1,4268 1.3782

HSN3 1.0205 0.9931

C4N4 1.3502 1.3182

010 4 1.24SS 1.2451

0201 1.4537 1.4600

H602 0._ 0.9680

07 Table10eoatinued

Bend anlles

C'CIN' ^{107.84 10 7.0 4} N4CIN2 108.42 112.15 IIIN2C1 10 3.03 107.16 H2N2Cl 104.08 107.50 HaCt O] lUU 7 117.05 CJC2CI 117.sg 1111.31 H.CJC2 123.&1 122.43 N3C3C, 120.02 12 1.30 H5N3CJ 111.54 122.12 C4iN4.Cl 115.81 123.85 OIC.N 3 113.74 114.91 02CIN' 105 .48 103.77 H60'CI 101.30 102 .407

os

Table 19continued

Torsion angles

N.CI N2C2 233.36 231.42

IIIN2CIN. 50.00 61.61

H2N2C1N. 304.24 31l.21

H3C2CIN2 27.67 55.21

C3C2C1H3 -179.19 -179.48

H.C3C2H3 0.75 -0.10

N3C3C2H. 177.50 170,90

HSN3C3H4 -25.51 0.66

C4N4CIC2 30,80 -1.53

QIC'N3H5 23.82 0.08

02CIN2N4 -117.86 -115.53

H602CIN. -11.69 2,22