Journal
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
Volume 4, Issue 5, Pages 422-435Publisher
WILEY
DOI: 10.1002/wcms.1180
Keywords
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Funding
- National Science Foundation [CHE-1149604, CHE-0446920]
- National Institutes of Health [GM32136]
- DARPA
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [1149604] Funding Source: National Science Foundation
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A recent review (Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 2010, 43: 142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modeling organic and enzymatic reactions. Advances included the pairwise-distance-directed Gaussian (PDDG)/PM3 semiempiricalQM(SQM) method, computation of multidimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. This article serves as a follow-up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e. g., `on water' and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost. (C) 2014 John Wiley & Sons, Ltd.
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