水分子三聚體的ab initio和ABEEM-MM方法研究及配體和受體間的結(jié)合自由能計(jì)算方法的評(píng)述.pdf

1、遼寧師范大學(xué)碩士學(xué)位論文水分子三聚體的abinitio和ABEEMMM方法研究及配體和受體間的結(jié)合自由能計(jì)算方法的評(píng)述姓名：劉慧波申請(qǐng)學(xué)位級(jí)別：碩士專業(yè)：原子與分子物理指導(dǎo)教師：楊忠志20090401水分子三聚體的abinitio和ABEEM／MM方法的研究及配體和受體間的結(jié)合自由能計(jì)算方法的評(píng)述AbstractContent：Therearetwocentralpartsofworkinpropertiesofthewatertrim

2、ershavebeenstudied，thispaperFirstlytheconfigurationsandusingabinitiomethodsandABEEM／MMfluctuatingchargeforcefieldSecondly，variousmethodsofcalculatingbindingfreeenergiesarereviewed，thenthelongstandingproblemsandchallenges

3、intheprocessofcalculatingbindingfreeenergiesarealsodiscussedNowadays，thestudiesofwaterclustershavebeenoneofthepopscientificresearches，especiallythesmallwaterclustersItisofgreatimportancetounderstandthepropertiesofwaterso

4、lventThewatertrimerisoneoftheprototypesystemstoinvestigatetheaccuratethreebodycontributionstotheintermolecularpotentialenergysurfaces(PESs)，andisalsothefirststepfromthewell—characterizeddimertowardsthebulkTheinvestigatio

5、nsofwatertrimerhavefocusedontheglobalminimum，andtherearefewresearchestostudytheotherstationarypointsHighlevelabinitiomethods，ABEEM／MMmodelwereusedtostudythepropertiesoftheeightstationarypointsonthewatertrimerPESsFullgeom

6、etryoptimizationoftheeightwatertrimers’structuresareperformedwiththemethodsmentionedaboveVariouspropertiesoftheeightstationarypointsonthewatertrimerPESs，suchasgeometries，bindingenergies，harmonicvibaritionfrequencies，ABEE

7、Mchargedistributions，havebeencomputedbytheabovemethodsAsforcomparisonandanalysis，someotherforcefieldmethodsareusedtocalculatethebindingenergiesComparingwiththehighlevelabinitiomethods，theresultsofABEEM／MMmodelisconsonant

8、withtheresultsofhighlevelabinitiomethodsConsequently，theaboveresultsofferreliableargumentstovalidatereasonableness，validityandtransferabilityoftheparametersofABEEM／MMmodelMeanwhile，well—knitfoundationisalsoestablishedtoc

9、ognizethemiddlingandthebiggerwaterclustersAccuratepredictionofbindingfreeenergiesforligandsandreceptorsisoneofthemostimportantgoalsincomputationalchemistryFirstofall，vadousmethodsofcalculatingbindingfreeenergiesarereview

10、edfromtwopointsofview(ieapproacheswithoutknowledgeofthereceptorstructureandapproachesbasedonknowledgeofthereceptorstructure)，whiletheadvantagesanddisadvantagesofthesemethodsarecommentedThenwealsotalkaboutthelong—standing

11、problemsandchallengesintheprocessofcalculatingbindingfreeenergies，includingmodelsofpotentialenergyfunctionandofsolvation，thelossoftranslational，rotationalandconfigurationalentropiesintheprocessofassociationFinallysomeele

12、mentarytentativesofcalculatingbindingaffinitiswithABEEM／MMcombiningwithGBSAandLIECEareintroducedinbriefKeywords：Abinitiomethod；AtomBondElectronegaliVityEqualizationMethod／MolecularMechanics(ABEEM／MM)；Watertrimer；Bindingf