Combined Quantum Mechanical and Molecular Mechanical Methods by Jiali Gao, Mark A. Thompson

By Jiali Gao, Mark A. Thompson

Mixed quantum mechanical and molecular mechanical tools is among the such a lot promising techniques for quantum mechanical calculations of chemical tactics in resolution and in enzymes. This publication offers an in-depth survey of the tools and purposes of those mixed thoughts in chemistry and biochemistry.

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Kollman, P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena, Chem. Rev. 1993, 93, 2395. ; Leong, M.  Comp. Chem. 1997, 63, 1051. ; Garmer, D.  Assignment of the Spectra of Protein Radicals in Cytochrome c Peroxidase, 1993, J. Phys. , 831.  Biol. 1982, 96, 473.  Phys. Chem. 1995, 99, 6273. ; Payling, D. W. A Combined Quantum Mechanical/Molecular Mechanical Model of the Potential Energy Surface of Ester Hydrolysis by the Enzyme Phospholipase A , J. Chem. Soc. Perkin Trans.

ACS Symposium Series; American Chemical Society: Washington, DC, 1998. ch003 41 results fall into these ranges. Figure 1 shows the histogram of the bond angle fluctuations from our HF 6­31G*/TIP3P M C and DFT BP/TIP3P M D simulations.  97° to 113°. It is interesting to note that both the HF and DFT results show similar behaviors in the H O H angle flexibility. In addition to the errors due to statistical fluctuation, another source of error of the present study is due to the use of fixed classical water geometry.

1994.  Hybrid ab initio Quantum Mechanics/Molecular Mechanics (QM(ai)/MM) Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin, J. Phys. Chem. 1997, submitted.  Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches, Chem. Rev. 1993, 93, 2523.  Phys. Chem 1997, 101, 5583.  ChemSol; University of Southern California: Los Angeles, 1997.  Approximate Evaluations of the Electrostatic Free Energy and Internal Energy Changes in Solution Processes, Chem.

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