Molecular mechanics dynamics

Virshup AM, Punwong C, Pogorelov TV, Lindquist BA, Ko C, Martinez TJ (2009) Photodynamics in complex environments ab initio multiple spawning quantum mechanical/molecular mechanical dynamics. J Phys Chem B 113 3280-3291... 

We have recently started to explore a type of calculations in which DFT treatment of the quantum mechanical (QM) site is combined with either continuum electrostatics treatment of the protein, or with microscopic molecular mechanics/dynamics treatment of the protein, or with a combined molecular mechanics and continuum electrostatics treatment of the protein in a truly multiscale type of calculations. All these calculations have a spirit of QM/MM (quantum mechanics combined with molecular mechanics) method, which is currently in wide use in protein calculations. The DFT and the solvation energy calculations are performed in a self-consistent way. The work aims at both improving the QM part of p/ calculations and the MM or electrostatic part, in which of the protein dielectric properties are involved. In these studies, an efficient procedure has been developed for incorporating inhomogeneous dielectric models of the proteins into self-consistent DFT calculations, in which the polarization field of the protein is efficiently represented in the region of the QM system by using spherical harmonics and singular value decomposition techniques [41,42]. 

Tailoring Adhesion of Adhesive Formulations by Molecular Mechanics/Dynamics... 

Erom QM to Molecular Mechanics/Dynamics Eorce Eields. 11... 

Virshup, A. M., Punwong, C., Pogorelov, T. V., Lindquist, B. A., Ko, C., 8c Martinez, T. J. (2009). Photodynamics in complex environments Ab initio multiple spawning quantum mechani-cal/molecular mechanical dynamics. The Journal of Physical Chemistry B, 113(11), 3280-3291. doi 10.1021/Jp8073464... 

The conversion of DHF to THE catalysed by DHFR has been used in this chapter as a reaction model to present the evolution and difficulties on computational methods to describe chemical reactions in enzymes, since the early calculations based at semiempirical level carried out in gas phase to the recent sophisticated simulations based on hybrid Quantum Mechanical/Molecular Mechanics Dynamics schemes. 

Calculations of the above type have not yet been applied to reactive systems" and there is clearly a perceived need for both quantitative kinetic measurements and complementary molecular mechanics/dynamics simulations for model intrazeolite reactions. In what follows, we describe the first experiments designed to fill this void. 

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