By Jiali Gao, Mark A. Thompson
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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Additional info for Combined Quantum Mechanical and Molecular Mechanical Methods
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.
Combined Quantum Mechanical and Molecular Mechanical Methods by Jiali Gao, Mark A. Thompson