Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 10, Issue 5, Pages 2185-2193Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct500033w
Keywords
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Funding
- Spanish MIC INN [IPT2011-0964-900000, SAF2011-13156-E, FIS2010-16046]
- European Commission [DIVINOCELL FP7 HEALTH-F3-2009-223431, COST-CMTS Action CM1002]
- Comunidad de Madrid [S2009/MAT-1467]
- European Social Fund
- National Science Foundation (NSF), through the Scientific Software Innovations Institutes [NSF S12-SSE (NSF114876)]
- NVIDIA, Inc.
- Department of Energy [DE-FG02-10ER16164]
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [1148276] Funding Source: National Science Foundation
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In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (FIREBALL) with the AMBER force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.
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