Biomedical subjects

Christian J Burnham

Publications and source records attributed to Christian J Burnham.

4 recordsLinked to original sources

PubMed2006

The properties of ion-water clusters. II. Solvation structures of Na+, Cl-, and H+ clusters as a function of temperature.

Ion-water-cluster properties are investigated both through the multistate empirical valence bond potential and a polarizable model. Equilibrium properties of the ion-water clusters H+(H2O)100, Na+(H2O)100, Na+(H2O)20, and Cl-(H2O)17 in the temperature region 100-450 K are explored using a hybrid parallel basin-hopping and tempering algorithm. The effect of the solid-liquid phase transition in both caloric curves and structural distribution functions is investigated. It is found that sodium and chloride ions largely reside on the surface of water clusters below the cluster melting temperature but are solvated into the interior of the cluster above the melting temperature, while the solvated proton was found to have significant propensity to reside on or near the surface in both the liquid- and solid-state clusters.

Algorithms↗

PubMed2005

The properties of ion-water clusters. I. The protonated 21-water cluster.

The ab initio atom-centered density-matrix propagation approach and the multistate empirical valence bond method have been employed to study the structure, dynamics, and rovibrational spectrum of a hydrated proton in the "magic" 21 water cluster. In addition to the conclusion that the hydrated proton tends to reside on the surface of the cluster, with the lone pair on the protonated oxygen pointing "outwards," it is also found that dynamical effects play an important role in determining the vibrational properties of such clusters. This result is used to analyze and complement recent experimental and theoretical studies.

Adsorption↗

PubMed2004

Anomalously soft dynamics of water in a nanotube: a revelation of nanoscale confinement.

Quasi-one-dimensional water encapsulated inside single-walled carbon nanotubes, here referred to as nanotube water, was studied by neutron scattering. The results reveal an anomalously soft dynamics characterized by pliable hydrogen bonds, anharmonic intermolecular potentials, and large-amplitude motions in nanotube water. Molecular dynamics simulations consistently describe the observed phenomena and propose the structure of nanotube water, which comprises a square-ice sheet wrapped into a cylinder inside the carbon nanotube and interior molecules in a chainlike configuration.

Computer Simulation↗

PubMed2004

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.

A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H(2)O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials.

Journal Article↗