Biomedical subjects

R T Downs

Publications and source records attributed to R T Downs.

5 recordsLinked to original sources

PubMed2006

Classification of metal-oxide bonded interactions based on local potential- and kinetic-energy densities.

A classification of the hydrogen fluoride H-F-bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio /Vr(c)/ / Gr(c) where /Vr(c)/ is the magnitude of the local potential-energy density and Gr(c) is the local kinetic-energy density, each evaluated at a bond critical point r(c). A calculation of the ratio for the M-O bonded interactions comprising a relatively large number of oxide molecules and earth materials, together with the constraints imposed by the values of inverted Delta2rho r(c) and the local electronic energy density, Hr(c) = Gr(c) + Vr(c), in the H-F study, yielded practically the same classification for the oxides. This is true despite the different trends that hold between the bond critical point and local energy density properties with the bond lengths displayed by the H-F and M-O bonded interactions. On the basis of the ratio, Li-O, Na-O, and Mg-O bonded interactions classify as closed-shell ionic bonds, Be-O, Al-O, Si-O, B-O, and P-O interactions classify as bonds of intermediate character with the covalent character increasing from Be-O to P-O. N-O interactions classify as shared covalent bonds. C-O and S-O bonded interactions classify as both intermediate and covalent bonded interactions. The C-O double- and triple-bonded interactions classify as intermediate-bonded interactions, each with a substantial component of covalent character and the C-O single-bonded interaction classifies as a covalent bond whereas their local electronic energy density values indicate that they are each covalent bonded interactions. The ratios for the Be-O, Al-O, and Si-O bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between the ratio and the character of the bonded interactions is consistent with trends expected from electronegativity considerations. The ratio increases as the net charges and the coordination numbers for the atoms for several Ni-sulfides decrease. On the contrary, the ratio for the Si-O bonded interactions for the orthosilicate, forsterite, Mg2SiO4, and the high-pressure silica polymorph, stishovite, decreases as the observed net atomic charges and the coordination numbers of Si and O increase in value. The ratio for the Ni-Ni bonded interactions for the Ni-sulfides and bulk Ni metal indicate that the interactions are intermediate in character with a substantial component of ionic character.

Journal Article↗

PubMed2005

Electron density distributions calculated for the nickel sulfides millerite, vaesite, and heazlewoodite and nickel metal: a case for the importance of ni-ni bond paths for electron transport.

Bond paths and the bond critical point properties (the electron density (rho) and the Hessian of rho at the bond critical points (bcp's)) have been calculated for the bonded interactions comprising the nickel sulfide minerals millerite, NiS, vaesite, NiS(2), and heazlewoodite, Ni(3)S(2), and Ni metal. The experimental Ni-S bond lengths decrease linearly as the magnitudes of the properties each increases in value. Bond paths exist between the Ni atoms in heazlewoodite and millerite for the Ni-Ni separations that match the shortest separation in Ni metal, an indicator that the Ni atoms are bonded. The bcp properties of the bonded interactions in Ni metal are virtually the same as those in heazlewoodite and millerite. Ni-Ni bond paths are absent in vaesite where the Ni-Ni separations are 60% greater than those in Ni metal. The bcp properties for the Ni-Ni bonded interactions scatter along protractions of the Ni-S bond length-bcp property trends, suggesting that the two bonded interactions have similar characteristics. Ni-Ni bond paths radiate throughout Ni metal and the metallic heazlewoodite structures as continuous networks whereas the Ni-Ni paths in millerite, a p,d-metal displaying ionic and covalent features, are restricted to isolated Ni(3) rings. Electron transport in Ni metal and heazlewoodite is pictured as occurring along the bond paths, which behave as networks of atomic size wires that radiate in a contiguous circuit throughout the two structures. Unlike heazlewoodite, the electron transport in millerite is pictured as involving a cooperative hopping of the d-orbital electrons from the Ni(3) rings comprising Ni(3)S(9) clusters to Ni(3) rings in adjacent clusters via the p-orbitals on the interconnecting S atoms. Vaesite, an insulator at low temperatures and a doped semiconductor at higher temperatures, lacks Ni-Ni bond paths. The net charges conferred on the Ni and S atoms are about a quarter of their nominal charges for the atoms in millerite and vaesite with the net charge on Ni increasing with increasing Ni-S bond length. Reduced net charges are observed on the Ni atoms in heazlewoodite and are related to its Ni-Ni metal bonded interactions and to the greater covalent character of its bonds. Local energy density and bond critical point properties of the electron density distributions indicate that the Ni-S and Ni-Ni bonded interactions are intermediate in character between ionic and covalent.

Journal Article↗

PubMed2005

Comparison of the electron localization function and deformation electron density maps for selected earth materials.

The electron localization function (ELF) and experimental and theoretical deformation electron density maps are compared for several earth materials and one representative molecule. The number and arrangement of the localized one-electron probability density domains generated in a mapping of the ELF correspond to the number and arrangement of the localized electron density domains generated in a mapping of the deformation electron density distribution, a correspondence that suggests that the two fields are homeomorphically related. As a homeomorphic relationship has been established previously between the Laplacian of the electron density distribution and the ELF, the relationship suggests that the deformation electron density distribution is also homeomorphically related to the Laplacian of the distribution.

Journal Article↗

PubMed2001

Systematic generation of all nonequivalent closest-packed stacking sequences of length N using group theory.

An algorithm has been developed that generates all of the nonequivalent closest-packed stacking sequences of length N. There are 2(N) + 2(-1)(N) different labels for closest-packed stacking sequences of length N using the standard A, B, C notation. These labels are generated using an ordered binary tree. As different labels can describe identical structures, we have derived a generalized symmetry group, Q approximately equal to D(N) x S(3), to sort these into crystallographic equivalence classes. This problem is shown to be a constrained version of the classic three-colored necklace problem.

Journal Article↗

PubMed2001

Quantifying distortion from ideal closest-packing in a crystal structure with analysis and application.

A parameter, U(cp), that quantifies the distortion of the anion skeleton in a crystal from ideal closest-packing has been developed. It is a measure of the average isotropic displacement of the observed anions from their ideal equivalents. An ideal closest-packed structure can be fit to an observed structure by varying the radius of the ideal spheres, orientation and translation, such that U(cp) is minimized. Ideal structures were fit to the M1M2TO(4) polymorphs, pyroxenes and kyanite. The distortions of these crystals were analyzed in terms of the two parameters, U(cp) and the ideal radius. Changes in structures due to temperature, pressure and compositional effects were characterized in terms of these parameters.

Journal Article↗