We report a study on different ionization states and conformations of the bimolecular (Gly)(2) system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug-cc-pVTZ and B3LYP/6-311+G(2df,2p) methods on B3LYP/6-31+G(d,p) optimized structures (some single-point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion-zwitterion or neutral-zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (-4 kcal mol(-1)). Thus, according to our results, zwitterion-zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α-glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion-zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.
Translational and rotational diffusion coefficients of
liquid water
have been computed from molecular dynamics simulation with a recent
polarizable potential at 298, 400, and 550 K at very high pressure.
At 298 K, the model reproduces the initial increase and the occurrence
of a maximum for the translational and rotational diffusion coefficients
when the pressure increases. At 400 and 550 K, translational and rotational
diffusion coefficients are found to monotonically decrease when pressure
increases in the gigapascal range, with the translational coefficient
decreasing faster than the rotational one. At 400 K, such an evolution
of the rotational diffusion coefficient contrasts with quasielastic
neutron scattering results predicting a near independence of the rotational
diffusion with a pressure increase above ≃0.5 GPa. An interpretation
is proposed to explain this discrepancy. The pressure dependence of
the translation–rotation coupling is analyzed. The anisotropy
of rotational diffusion is investigated by computing the rotational
diffusion tensor in a molecular system of axes and the reorientational
correlation times of rank 1 and rank 2 of the inertia axes and of
the OH bond vector. Deviation of the simulation data with respect
to the predictions of the isotropic Debye model of rotational diffusion
are quantified and can be used to estimate experimental rotational
diffusion coefficients from experimental reorientational correlation
times.
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