86.Dang,L.X.,IntermolecularInteractionsofLiquidDichloromethaneandEquilibriumPropertiesofLiquid-VaporandLiquid-LiquidInterfaces:aMolecularDynamicsStudy,J.Chem.Phys.1999,110:
10113-10122.
87.Chang,T.M.;Dang,L.X.,MolecularDynamicsSimulationsofCCl4-H2OLiquid-liquidInterfaceWithPolarizablePotentialModels,J.Chem.Phys.1996,104:6772-6783.
88.Dang,L.X.,CharacterizationofWaterOctamer,Decamer,andIodine-WaterInteractionsUsingMolecularDynamicsTechniques,J.Chem.Phys.1999,110:1526-1532.
89.Dang,L.X.,ComputerSimulationStudiesofIonTransportacrossaLiquid/LiquidInterface,J.Phys.
Chem.B1999,103:8195-8200.
90.Dang,L.X.;Feller,D.,MolecularDynamicsStudyofWater-BenzeneInteractionsattheLiquid/VaporInterfaceofWater,J.Phys.Chem.B.2000,104:4403-4407.
91.Hermida-Ramon,J.M.;Rios,M.A.,ANewIntermolecularPolarizablePotentialforaFormaldehydeDimer.ApplicationtoLiquidSimulations,J.Phys.Chem.A1998,102:10818-10827.
92.Mannfors,B.;Palmo,K.;Krimm,S.,ANewElectrostaticModelforMolecularMechanicsForceFields.J.Mol.Struct.2000,556:1-22.
93.Ding,Y.;Bernardo,D.N.;Krogh-Jespersen,K.;Levy,R.M.,SolvationFreeEnergiesofSmallAmidesandAminesfromMolecularDynamics/FreeEnergyPerturbationSimulationsUsingPairwiseAdditiveandMany-bodyPolarizablePotentials.J.Phys.Chem.1995,99,11575-11583.
94.Gresh,N.;EnergeticsofZn2+BindingtoaSeriesofBiologicallyRelevantLigants:aMolecularMechanicsInvestigationGroundedonAbInitioSelf-ConsistentFieldSupermoleculeComputations,J.Comput.Chem.1995,16:856-882.
95.Gresh,N.;Garmer,D.R.,ComparativeBindingEnergeticsofMg2+,Ca2+,Zn2+andCd2+toBiologicallyRelevantLigants:CombinedAbInitioSCFSupermoleculeandMolecularMechanicsInvestigation,J.Comput.Chem.1996,17:1481-1495.
96.Garmer,D.R.;Gresh,N.;Roques,B.P.,ModelingofInhibitor-metalloenzymeInteractionsandSelectivelyUsingMolecularMechanicsGroundedinQuantumChemistry,Proteins1998,31:42-60.
97.Tiraboschi,G.;Roques,B.-P.;Gresh,N.,JointQuantumChemicalandPolarizableMolecularMechanicsInvestigationofFormateComplexeswithPenta-andhexahydratedZn2+.ComparisonbetweenEnergeticsofModelBidentates,Monodentate,andThrough-WaterZn2+BindingModesandEvaluationofNonadditivityEffects,J.Comput.Chem.1999,20:1379-1390.
98.Gresh,N.;Sponer,J.,ComplexesofPentahydratedZn2+withGuanine,Adenine,andtheGuanine-CytosineandAdenine-ThymineBasePairs.StructuresandEnergiesCharaterizedbyPolarizableMolecularMechanicsandAbInitioCalculations,J.Phys.Chem.B1999,103:
11415-11427.
99.Tiraboschi,G.;Gresh,N.;Giessner-Prettre,C.;Pedersen,L.G.;Deerfield,D.W.,ParallelAbInitioandMolecularMechanicsInvestigationofpolycoordinatedZn(II)ComplexeswithModelHardandSoftLigands:VariationsofBindingEnergyandofItsComponentswithNumberandChargesofLigands,J.Comput.Chem.2000,21:1011-1039.
100.Rogalewicz,F.;Ohanessian,G.;Gresh,N.,InteractionofNeutralandZwitterionicGlycinewithZn2+inGasPhase:AbInitioandSIBFAMolecularMechanicsCalculations,J.Comput.Chem.2000,21:963-973.
101.Wang,J.;Cieplak,P.;Kollman,P.A.HowWellDoesaRestrainedElectrostaticPotential(RESP)ModelPerforminConformationalEnergiesofOrganicandBiologicalMolecules,J.Comput.Chem.
2000,21:1049-1074.
102.Meng,E.C.;Caldwell,J.W.;Kollman,P.A.,InvestigatingtheAnomalousSolvationFreeEnergiesofAmineswithaPolarizablePotential,J.Phys.Chem.1996,100:2367-2371.
103.Stern,H.A.;Kaminski,G.A.;Banks,J.L.;Zhou,R.;Berne,B.J.;Friesner,R.A.,FluctuatingCharge,PolarizableDipole,andCombinedModel:ParameterizationfromAbInitioQuantumChemistry,J.Phys.Chem.B1999,103:4730-4737.
104.Banks,J.L.;Kaminski,G.A.;Ruhong,Z.;Mainz,D.T.;Berne,B.J.;Friesner,R.A.ParamitrizingaPolarizableForceFieldfromAbInitioData.I.TheFluctuatingPointChargeModel,J.Chem.
Phys.1999,110:741-754.
105.Kaminski,G.A.;Stern,H,A.;Berne,B.J.;Friesner,R.A.;Yixiang,X.C.;Murphy,R.B.;Ruhong,Z.;Halgren,T.A.,DevelopmentofaPolarizableForceFieldforProteinsviaAbInitioQuantumChemistry:FirstGenerationModelandGasPhaseTests,J.Comput.Chem.2002,23:1515-1531.
106.Gresh,N.;Guo,H.;Salahub,D.R.;Roques,B.P.;Kafafi,S.A.,CriticalRoleofAnisotropyfortheDimerizationenergiesofTwoProtein-proteinRecognitionMotifs:Cis-N-methylacetamideversusaBeta-sheetConformerofAlanineDipeptide.AJointAbInitio,DensityFunctionalTheory,andMolecularMechanicsInvestigation,J.Am.Chem.Soc.1999,121:7885-7894.
107.Dixon,R.W.;Kollman,P.A.,AdvancingbeyondtheAtom-centeredModelinAdditiveandNonadditiveMolecularMechanics,J.Comput.Chem.1997,18:1632-1646.
108.Patel,S.,Brooks,C.L.,III.CHARMMFluctuatingChargeForceFieldforProteins:I.
ParameterizationandApplicationtoBulkOrganicLiquidSimulations,J.Comput.Chem.2004,25:1-15.
109.Patel.S.,Mackerell,A.D.,Jr.,Brooks,C.L.,III.,CHARMMFluctuatingChargeForceFieldforProteins:II.Protein/SolventPropertiesfromMolecularDynamicsSimulationsUsingaNonadditiveElectrostaticModel,J.Comput.Chem.2004,25:1504-1514.
110.Ogawa,T.;Kitao,O.;Kuiita,N.;Sekino,H.;Tanaka,S.,ConsistentChargeEquilibrationMethodCombinedwithUniversalForceField:ApplicationtoAminoAcidMolecules,Chem-Bio.InformaticsJ.2003,3:78-85.
111.Ren,P.;Ponder,J.W.,PolarizableAtomicMultipoleWaterModelforMolecularMechanicsSimulation,J.Phys.Chem.B2003,107:5933.
112.Grossfield,A.;Ren,P.;Ponder,J.W.,IonSolvationThermodynamicsfromSimulationwithaPolarizableForceField,J.Am.Chem.Soc.2003,125:15671.
113.Ren,P.;Ponder,J.W.,ConsistentTreatmentofInter-andIntramolecularPolarizationinMolecularMechanicsCalculations,J.Comput.Chem.2002,23:1497-1505.
114.Thole,B.T.,MolecularPolarizabilitiesCalculatedwithaModifiedDipoleInteraction,Chem.Phys.
1981,59:341.
115.Mulder,F.;vanHemert,M.C.;Wormer,P.E.S.;vanderAvoird,A.,Theor.Chim.Acta.1977,46:
39.
116.vanHemert,M.C.;Blom,C.E.,Mol.Phys.1981,43:229.
117.Btcher,C.F.;Bordewijk,P.,TheoryofElectricPolarization,Elsevier:Amsterdam,1978.