2023
OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers
Jorgensen W, Ghahremanpour M, Saar A, Tirado-Rives J. OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers. The Journal Of Physical Chemistry B 2023, 128: 250-262. PMID: 38127719, DOI: 10.1021/acs.jpcb.3c06602.Peer-Reviewed Original ResearchForce fieldStatistical mechanics calculationsUnsaturated hydrocarbonsFree energyPure liquidsFree energy perturbation calculationsStandard force fieldsAtom force fieldAverage unsigned errorOrganic moleculesMechanics calculationsBiomolecular systemsConformational energeticsHeat of vaporizationLarge moleculesKcal/Perturbation calculationsUnsigned errorAverage errorLiquidEtherExperimental dataMoleculesErrorHydration
2007
Why Urea Eliminates Ammonia Rather than Hydrolyzes in Aqueous Solution
Alexandrova AN, Jorgensen WL. Why Urea Eliminates Ammonia Rather than Hydrolyzes in Aqueous Solution. The Journal Of Physical Chemistry B 2007, 111: 720-730. PMID: 17249815, PMCID: PMC2995377, DOI: 10.1021/jp066478s.Peer-Reviewed Original ResearchConceptsAddition/elimination mechanismDecomposition of ureaWater moleculesResonance stabilizationAqueous solutionNH3 eliminationNatural bond order analysisQM/MM Monte Carlo simulationsBond order analysisFree energy perturbation calculationsQM/MMExplicit water modelRate-determining stepElimination mechanismOverall free energyLow activation energySolvent effectsElimination reactionHydrogen bondsPreferred reaction routeReaction routeGas phaseTransition stateZwitterionic intermediateAb initio
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