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A solute molecules is exposed to an external electrostatic field generated by the surrounding solvent molecules. The contributions to the field originating from rapid electron density fluctuations in the solvent molecules cause the attractive dispersion interaction. They are approximately homogeneous, isotropic, and are identical in polar and nonpolar solvents. Therefore, they do not specifically change the electron density and the associated force field within the solute. As a consequence, its vibrational modes are hardly affected by solvation in nonpolar solvents. In polar solvents, however, the additional contributions originating from the permanent dipoles in the structured and slowly fluctuating solvent shells add up to the field generated by the nuclei, to which, according to Born-Oppenheimer approximation, the electrons of the solute instantaneously adjust. These added fields generate the electronic polarization, and correspondingly, change the effective electronic potential of nuclear motion.
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These parameters were taken from the file parmallh3x.pro contained in the distribution of the MD program XPLOR 3.1 by A. Brünger, The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 1992. We do not consider the choice of the Lennard-Jones parameters to be critical for our purposes.
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To exclude other algorithmic causes, we have carefully checked by visual inspection that the MD trajectory of the dipole moment M(t) is everywhere smooth and bears no signatures of algorithmic noise, which might arise from the multiple time-step procedures applied for the integration of the Newtonian equations or from the multiple scale approach used for the computation of the electrostatics (see Eichinger for a discussion of accuracy issues in DFT/MM-MD simulations).
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