Born dynamical charge

X. Gonze and C. Lee. Dynamical matrices, born eflFective charges, dielectric permittivity tensors, and interatomic force constants from density-functional perturbation theory. Phys. Rev. B, 55(16) 10355-10368, 1997. 

We wanted to extend this approach to include dynamical effects on line shapes. As discussed earlier, for this approach one needs a trajectory co t) for the transition frequency for a single chromophore. One could extract a water cluster around the HOD molecule at every time step in an MD simulation and then perform an ab initio calculation, but this would entail millions of such calculations, which is not feasible. Within the Born Oppenheimer approximation the OH stretch potential is a functional of the nuclear coordinates of all the bath atoms, as is the OH transition frequency. Of course we do not know the functional. Suppose that the transition frequency is (approximately) a function of a one or more collective coordinates of these nuclear positions. A priori we do not know which collective coordinates to choose, or what the function is. We explored several such possibilities, and one collective coordinate that worked reasonably well was simply the electric field from all the bath atoms (assuming the point charges as assigned in the simulation potential) on the H atom of the HOD molecule, in the direction of the OH bond. 

Since many of these developments reach into the molecular domain, the understanding of nano-structured functional materials equally necessitates fundamental aspects of molecular physics, chemistry, and biology. The elementary energy and charge transfer processes bear much similarity to the molecular phenomena that have been revealed in unprecedented detail by ultrafast optical spectroscopies. Indeed, these spectroscopies, which were initially developed and applied for the study of small molecular species, have already evolved into an invaluable tool to monitor ultrafast dynamics in complex biological and materials systems. The molecular-level phenomena in question are often of intrinsically quantum mechanical character, and involve tunneling, non-Born-Oppenheimer effects, and quantum-mechanical phase coherence. Many of the advances that were made over recent years in the understanding of complex molecular systems can therefore be transposed and extended to the study of... 

In contrast to the above situation, based on an average charge density (pa), one may identify another dynamical regime where the solvent electronic timescale is fast [50-52] relative to that of the solute electrons (especially, those participating in the ET process). In this case, H F remains as in Equation (3.106), treated at the Born-Oppenheimer (BO) level (i.e., separation of electronic and nuclear timescales), but HFF is replaced by an optical RF operator involving instantaneous electron coordinates [52] ... 

The perplexing difficulties that arise in the crystallization of macromolecules, in comparison with conventional small molecules, stem from the greater complexity, lability, and dynamic properties of proteins and nucleic acids. The description offered above of labile and metastable regions of supersaturation are still applicable to macromolecules, but it must now be borne in mind that as conditions are adjusted to transport the solution away from equilibrium by alteration of its physical and chemical properties, the very nature of the solute molecules is changing as well. As temperature, pH, pressure, or solvation are changed, so may be the conformation, charge state, or size of the solute macromolecules. 

M. V. Basilevsky and G. E. Chudinov, Dynamics of charge transfer chemical reactions in a polar medium within the scope of the Born-Kirkwood-Onsager model, Chem. Phys. 157, 327-344 (1991). 

A computationally efficient analytical method has been developed for the crucial calculation of Born radii, which is required for each atom of the solute that carries a (partial) charge, and the Gpoi term has been parameterized to fit atomic polarization energies obtained by Poisson-Boltzmann equation [57]. The GB/SA model is thus fully analytical and affords first and second derivatives allowing for solvation effects to be included in energy minimizations, molecular dynamics, etc. The Gpoi term is most important for polar molecules and describes the polarization of the solvent by the solute. As force fields in general are not polarizable, it does not account for the polarization of the solute by the solvent. This is clearly an important limitation of this type of calculations. 

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