Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations.
A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.
Woodcock
H Lee
HL
National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892.
Hodošček
Milan
M
Center for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
Gilbert
Andrew T B
ATB
Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia.
Gill
Peter M W
PMW
Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia.
Schaefer
Henry F
HF
Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2556.
Brooks
Bernard R
BR
National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892.
D000838:Anions / Q000737:chemistry; D002384:Catalysis; D002826:Chorismate Mutase / Q000378:metabolism; D003198:Computer Simulation; D019281:Dimerization; D008956:Models, Chemical; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D012964:Sodium / Q000737:chemistry; D012984:Software; D014867:Water / Q000737:chemistry
D000838:Anions; D014867:Water; D012964:Sodium; D002826:Chorismate Mutase