Molecular mechanical energy model

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

As the SIBFA approach relies on the use of distributed multipoles and on approximation derived form localized MOs, it is possible to generalize the philosophy to a direct use of electron density. That way, the Gaussian electrostatic model (GEM) [2, 14-16] relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. It offers the possibility of a continuous electrostatic model going from distributed multipoles to densities and allows a direct inclusion of short-range quantum effects such as overlap and penetration effects in the molecular mechanics energies. 

Shirts, M. R. Pande, V. S., Solvation free energies of amino acid side chain analogs for common molecular mechanics water models, J. Chem. Phys. 2005,122, 134508. 

The following definition of computational chemistry was published in 1985 (6) quantitative modeling of chemical behavior on a computer by the formalisms of theoretical chemistry. Some quantum theoreticians naturally would like to see computational chemistry as a subset of their field (7). However, today the number of scientists employed as computational chemists well exceeds the number employed as theoreticians (8). A recent textbook author (9) views computational chemistry as encompassing not only quantum mechanics, but also molecular mechanics, [energy] minimization, simulations, conformational analysis, and other computer-based methods for understanding and predicting the behavior of molecular systems. ... 

Molecular modeling using either Monte-Carlo simulations or molecular dynamics is used to apply molecular mechanics energy minimizations to very complex systems [348]. In complex flexible molecules such as proteins or nucleic adds, the number of variable parameters, i.e., bond torsion angles, is such that the global search for energy minima becomes impossible The same problem occurs with theoretical calculations of water structure in aqueous solutions or in heavily hydrated crystals. 

The quantum mechanical/molecular mechanical aerosol model was developed to describe the interaction between gas phase molecules and atmospheric particles. This method has been utilized for the calculation of interaction energies and... 

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