Biomedical subjects

Steven W Rick

Publications and source records attributed to Steven W Rick.

5 recordsLinked to original sources

PubMed2006

Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water.

A vast array of experimental data on water provides a global view of the liquid that implicates its tetrahedral hydrogen-bonding network as the unifying molecular connection to its observed structural, thermodynamic, and dielectric property trends with temperature. Recently the classification of water as a tetrahedral liquid has been challenged based on X-ray absorption (XAS) experiments on liquid water (Ph. Wernet et al., Science, 2004, 304, 995), which have been interpreted to show a hydrogen-bonding network that replaces tetrahedral structure with chains or large rings of water molecules. We examine the consequences of tetrahedral vs. chain networks using three different modified water models that exhibit a local hydrogen bonding environment of two hydrogen bonds (2HB) and therefore networks of chains. Using these very differently parameterized models we evaluate their bulk densities, enthalpies of vaporization, heat capacities, isothermal compressibilities, thermal expansion coefficients, and dielectric constants, over the temperature range of 235-323 K. We also evaluate the entropy of the 2HB models at room temperature and whether such models support an ice I(h) structure. All show poor agreement with experimentally measured thermodynamic and dielectric properties over the same temperature range, and behave similarly in most respects to normal liquids.

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PubMed2005

Simulations of proton order and disorder in ice Ih.

Computer simulations of ice Ih with different proton orientations are presented. Simulations of proton disordered ice are carried out using a Monte Carlo method which samples over proton degree of freedom, allowing for the calculation of the dielectric constant and for the examination of the degree of proton disorder. Simulations are also presented for two proton ordered structures of ice Ih, the ferroelectric Cmc2(1) structure or ice XI and the antiferroelectric Pna2(1) structure. These simulations indicate that a transition to a proton ordered phase occurs at low temperatures (below 80 K). The symmetry of the ordered phase is found to be dependent on the water potential. The stability of the two proton ordered structures is due to a balance of short-ranged interactions which tend to stabilize the Pna2(1) structure and longer-range interactions which stabilize the Cmc2(1) structure.

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PubMed2005

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials.

A new method for performing molecular dynamics simulations with fluctuating charge polarizable potentials is introduced. In fluctuating charge models, polarizability is treated by allowing the partial charges to be variables, with values that are coupled to charges on the same molecule as well as those on other molecules. The charges can be efficiently propagated in a molecular dynamics simulation using extended Lagrangian dynamics. By making a coordinate change from the charge variables to a set of normal mode charge coordinates for each molecule, a new method is constructed in which the normal mode charge variables uncouple from those on the same molecule. The method is applied to the TIP4P-FQ model of water and compared to other methods for implementing the dynamics. The methods are compared using different molecular dynamics time steps.

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PubMed2004

Hydration free energies and entropies for water in protein interiors.

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein hydrogen bonds, and one which is more hydrophobic, forming only one water-protein hydrogen bond. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the nonpolar cavity is entropically favorable. For both proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increased length and weakened strength of protein-protein hydrogen bonds near the cavity.

Animals↗

PubMed2004

A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums.

The five-site transferable interaction potential (TIP5P) for water is most accurate at reproducing experimental data when used with a simple spherical cutoff for the long-ranged electrostatic interactions. When used with other methods for treating long-ranged interactions, the model is considerably less accurate. With small modifications, a new TIP5P-like potential can be made which is very accurate for liquid water when used with Ewald sums, a more physical and increasingly more commonly used method for treating long-ranged electrostatic interactions. The new model demonstrates a density maximum near 4 degrees C, like the TIP5P model, and otherwise is similar to the TIP5P model for thermodynamic, dielectric, and dynamical properties of liquid water over a range of temperatures and densities. An analysis of this and other commonly used water models reveals how the quadrupole moment of a model can influence the dielectric response of liquid water.

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