Combined Quantum Mechanical and Molecular Mechanical Methods - download pdf or read online

By Jiali Gao, Mark A. Thompson

ISBN-10: 0841235902

ISBN-13: 9780841235908

Mixed quantum mechanical and molecular mechanical tools is without doubt one of the such a lot promising techniques for quantum mechanical calculations of chemical procedures in resolution and in enzymes. This publication offers an in-depth survey of the equipment and functions of those mixed ideas in chemistry and biochemistry.

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2 fs. The system is first equilibrated using the potential for a sphere of water for 100 ps. The coordinate for a water molecule near the center of the sphere is chosen for the Q M molecule. ; ACS Symposium Series; American Chemical Society: Washington, DC, 1998. 5 ps for data collection. Coordinates for the Q M atoms are saved on each dynamics integration step, from which normal coordinate autocorrelation functions are determined to yield the vibrational frequencies. The Lennard­Jones parameters needed for the Q M atoms (last terms in equations 2 and 3) have been developed for the combined AI/TIP3P potential at the HF/3­21G level, and have been shown to yield excellent results for the water dimer both when the Q M molecule is treated as a hydrogen bond donor and an acceptor (23).

Alternatively, molecular dynamics simulations can be carried out using the forces derived from the hybrid Q M / M M Bom­Oppenheimer potential energy surface. The related Newton's equations of motion are x c where j specifies either a solute or a solvent atom, and m: are the atomic masses. The DFT program developed by St­Amant (31) nas been used for the Kohn­ Sham DFT calculations. The implementation features expansion of the wave functions and charge density in terms of a linear combination of Gaussian type orbitals (LCGTO) (32).

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. 2 1991, 225.  Am. Chem. Soc. 1995, 117, 11345. Alden, R. ; Chu, .  Am. Chem. Soc. 1995, 117, 12284.  Rational modification of enzyme catalysis by engineering surface charge, Nature 1987, 328, 496.  Biol. Chem. 1996, 271, 10010. Fothergill, M . ; Warshel, A.  Chem. Soc. 1995, 117, 11619.  Biol.

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

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