By Jiali Gao, Mark A. Thompson
ISBN-10: 0841235902
ISBN-13: 9780841235908
Mixed quantum mechanical and molecular mechanical equipment is likely one of the such a lot promising techniques for quantum mechanical calculations of chemical techniques in resolution and in enzymes. This booklet offers an in-depth survey of the tools and purposes of those mixed strategies in chemistry and biochemistry.
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Extra info for Combined Quantum Mechanical and Molecular Mechanical Methods
Sample text
The new development can potentially further extend the applicability of molecular dynamics and Monte Carlo simulations to phenomena that involve large environmental changes, such as water near interfaces, supercritical fluids, and salt solutions. A n important property charactering a flexible water model is the average geometry of water in the liquid state. However, there is a tremendous ambiguity from various flexible water models (Table I). Table I. 6° (49). On the experimental side, neutron diffraction experiments indicate that there is an increase in the OH bond length, and only small geometrical variations in the bond angle, although the prediction of the water geometry is complicated by inelastic scattering and data analyses (12,13).
Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis, Science 1989, 244, 1069. On the Nature of Phosphate Ester Hydrolysis in Aqueous Solution: Associative Versus Dissociative Mechanisms, J. Phys. Chem. 1997, submitted. Frisch, M . M . ; Johnson, B. ; Robb, . ; Cheeseman, J. ; Petersson, G. ; Montgomery, J. ; AlLaham, . ; Andres, J. ; Martin, R. ; Pople, J. : Pittsburgh PA, 1995. ; Kluwer Academic Publishers: Dordrecht, Boston, London, 1997. Kollman, P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena, Chem.
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. Essentially the same structural changes are obtained, suggesting the effect from the flexible model is minimal. 0° from DFTBP/TZVP M D simulations. 7° (12), in accord with the present simulation results. 8° (13). 6° greater than the gas phase value.
Combined Quantum Mechanical and Molecular Mechanical Methods by Jiali Gao, Mark A. Thompson
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