2017
On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps
Wang J. On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps. Protein Science 2017, 26: 1098-1104. PMID: 28370507, PMCID: PMC5441424, DOI: 10.1002/pro.3169.Peer-Reviewed Original ResearchConceptsAtomic partial chargesPartial chargesQuantum mechanicsForce field parametersAtomic propertiesPartial atomic chargesDensity mapsAtomic chargesField parametersMolecular dynamicsAtomsElectron microscopyProtein backboneNeutral peptide backboneChargeChain atomsComputer simulationsSide-chain atomsDensityPeptide backboneProtein moleculesModel refinementSimulationsPotential densityBackbone
2006
Elucidation of Rate Variations for a Diels−Alder Reaction in Ionic Liquids from QM/MM Simulations
Acevedo O, Jorgensen WL, Evanseck JD. Elucidation of Rate Variations for a Diels−Alder Reaction in Ionic Liquids from QM/MM Simulations. Journal Of Chemical Theory And Computation 2006, 3: 132-138. PMID: 26627159, DOI: 10.1021/ct6002753.Peer-Reviewed Original ResearchQM/MM simulationsIonic liquidsEMI cationTransition stateMM simulationsOPLS-AA force field parametersQM/MM calculationsBasic ionic liquidFree energy perturbation calculationsReaction rateHydrogen bond donorForce field parametersLewis acid effectRelative rate enhancementKey stationary pointsSolute-solvent interactionsEndo/exo ratioAcidic meltsBond donorHydrogen bondingMM calculationsWater moleculesAqueous solutionHydrogen bondsElectrostatic interactions
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