Molecular dynamics systems, chemical reaction efficiency

Chemical studies usually deal with a solute which can be a single molecule or a molecular complex or transition state in a chemical reaction. In such systems, the role of the solvent is mainly a physical perturbation which can be simulated at a lower theoretical level than that required for the study of the subsystem of chemical interest. The success of continuum models confirms this statement. In order to describe the solution at the molecular level and to perform full statistical mechanics computations on a model of macroscopic sample, one may set up some computationally efficient approaches by limiting the quantum chemical study to the solute and using one of the usual classical force-fields to represent the solvent molecules. The computation of the statistical averages can be done by means of either Monte Carlo or molecular dynamics algorithms. The so-called QM/MM models are now widely used in such chemical studies. 

The most recent method considered is DFT-D3 [35]. Previous DFT-D methods did not distinguish between different valence states of an atom in a molecule, that is the dispersion coefficients in Eq. (11.1) for sp and sp carbon atoms should differ, as dispersion coefficients decrease upon oxidation of an atom and increase upon reduction. To obtain accurate dispersion coefficients, the concept of atomic fractional coordination number was introduced in DFT-D3. The dispersion coefficients in Eq. (11.1) depend on the atomic fractional coordination number and the latter depends on an atom s geometrically closest neighbors. The D3-correction has continuous dispersion coefficients C even if chemical reaction occurs in a model system (i.e., dispersion coefficients change smoothly when an atom s valence or oxidation state changes), which is very efficient. Indeed, this allows smooth forces and therefore may be used in quantum molecular dynamics. For example, in the simple transition state of the Sj.j2 reaction [F CHj F ], the fractional coordination number of the carbon atom is 4.1 and that of fluorine atom is 0.57. DFT-D3 contains eighth-order terms with w = 8 and the eighth-order dispersion coefficients Cg in Eq. (11.1) are computed from for the same atom pairs. 

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