Quantum and molecular mechanical Monte Carlo techniques for modeling condensed-phase reactions

摘要: A recent review (Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic enzymatic reactions. Acc Chem Res 2010, 43:142–151) examined our use development of a combined technique modeling included the pairwise-distance-directed Gaussian (PDDG)/PM3 semiempirical QM (SQM) method, computation multidimensional potentials mean force (PMF), incorporation on-the-fly Monte Carlo simulations, polynomial quadrature method rapidly treating proton-transfer This article serves as follow-up on progress. Highlights include new reactions, alternative SQM methods, polarizable OPLS field, novel solvent environments, e.g., ‘on water’ room temperature ionic liquids. The methodology is strikingly accurate across wide range condensed-phase antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, pericyclic classes. Comparisons are made to systems treated with continuum-based solvents ab initio or density functional theory (DFT) methods. Overall, QM/MM provides detailed characterization reaction paths, proper configurational sampling, several advantages over implicit models, reasonable computational cost. WIREs Comput Mol Sci 2014, 4:422–435. Conflict interest: authors have declared no conflicts interest this article. For further resources related article, please visit website.