Using a novel method for determining the coordinate friction for systems that possess bounded diffusion, the rates of kinetic energy partitioning for various elements of solvated carboxy-myoglobin were calculated. Energy redistribution within the heme group and solvent is found to be rapid compared with energy redistribution within the protein. Within the protein, charged residues exhibit much more rapid dispersal than neutral residues. The results suggest that a possible doorway for energy release from the photolyzed heme involves the interaction of its isopropionate groups with the neighboring solvent molecules. The results are analyzed as a function of atom type, protein residue and residue group ͑charged, polar, aliphatic, and aromatic͒ leading to general observations relating to the inherent inhomogeneity in the spatially dependent relaxation rate of the solvated protein. The computational results are used to analyze a variety of estimates of the internal friction, viscosity or damping invoked to interpret experimental measures of protein dynamics. The concluding discussion includes speculations on the origin of internal viscosity in proteins.
The structure of linear water wires with an excess proton was studied at room temperature using ab initio path integral molecular dynamics. The ab initio Car-Parrinello (CP) methodology employed the density functional theory (DFT) description of the electronic structure, and the Feynman path integral approach allowed for quantization of the nuclear degrees of freedom. Thus, the influence of proton tunneling and zero point nuclear vibrations were automatically included. Four or five water molecules were linearly arranged, with an excess proton (H*), to form tetramer and pentamer complexes, respectively. In classical studies of the tetramer complex, the excess proton H*, centered within the wire, formed H 3 O + and H 5 O 2 + ions with the two inner water molecules. In the pentamer complex, the H* was found attached to the inner water molecule, forming a stable H 3 O + ion with two covalent, hyperextended bonds that were hydrogen bonded to neighboring water molecules on both opposite sides. Although the addition of nuclear quantization via path integrals broadened the calculated distribution functions for both complexes, the overall features were unaltered, which suggests that nuclear quantum effects are minimal in these small, linear clusters. However, instantaneous path integral configurations revealed the formation of an extended H 7 O 3 + complex predominantly in the pentamer wire, where the excess proton H* was delocalized over three adjacent water molecules simultaneously. Since the computational demands of CP make long simulations cost-prohibitive, angular distribution functions, requiring much longer simulation times, were obtained using an MP2-based empirical valence bond (EVB) model [
A new empirical valence bond model for proton transfer in bulk water that includes electron correlation effects is presented. The parameters of the model are based on ab initio calculations, in which electron correlation is treated at the MP2 level. Within this model, the properties of the gas-phase H5O2+ complex are in good agreement with recent ab initio path integral studies [M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello, Science. 101, 4878 (1994)] and ab initio molecular dynamics studies [D. Wei and D. R. Salahub, J. Chem. Phys. 106, 6086 (1997)]. Simulations of the solvated H5O2+ complex suggest that at room temperature, the quantum nature of the transferring proton does not affect the essential mechanism of proton transfer and only slightly affects the free energy profile of the asymmetric stretch within the strong hydrogen bond. The predictions of the model are consistent with ab initio molecular dynamics simulations of solvated hydronium using gradient-corrected density functional theory [M. E. Tuckerman, D. Laasonen, M. Sprik, and M. Parrinello, J. Chem. Phys. 103, 150 (1995)].
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