Biomedical subjects

D Jayatilaka

Publications and source records attributed to D Jayatilaka.

4 recordsLinked to original sources

PubMed2006

Si-O bonded interactions in silicate crystals and molecules: a comparison.

Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, rho(r), calculated for silicates such as quartz and gas-phase molecules such as disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in silica are short-ranged and molecular-like. Using the G(rc)/rho(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc)= G(rc) + V(rc), and the coordination number of the Si atom decrease and as the accumulation of the electron density at the bond critical point, rho(rc), and the Laplacian, inverted Delta2 rho(rc), increase. The G(rc)/rho(rc) and H(rc)/rho(rc) ratios categorize the bonded interaction as observed for other second row atom M-O bonds into discrete categories with the covalent character of each of the M-O bonds increasing with the H(rc)/rho(rc) ratio. The character of the bond is examined in terms of the large net atomic charges conferred on the Si atoms comprising disiloxane, stishovite, quartz, and forsterite and the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is an intermediate interaction between Al-O and P-O bonded interactions rather than being a closed-shell or a shared interaction.

Journal Article↗

PubMed2006

Bond length and local energy density property connections for non-transition-metal oxide-bonded interactions.

For a variety of molecules and earth materials, the theoretical local kinetic energy density, G(r(c)), increases and the local potential energy density, V(r(c)), decreases as the M-O bond lengths (M = first- and second-row metal atoms bonded to O) decrease and the electron density, rho(r(c)), accumulates at the bond critical points, r(c). Despite the claim that the local kinetic energy density per electronic charge, G(r(c))/rho(r(c)), classifies bonded interactions as shared interactions when less than unity and closed-shell when greater, the ratio was found to increase from 0.5 to 2.5 au as the local electronic energy density, H(r(c)) = G(r(c)) + V(r(c)), decreases and becomes progressively more negative. The ratio appears to be a measure of the character of a given M-O bonded interaction, the greater the ratio, the larger the value of rho(r(c)), the smaller the coordination number of the M atom and the more shared the bonded interaction. H(r(c))/rho(r(c)) versus G(r(c))/rho(r(c)) scatter diagrams categorize the M-O bonded interactions into domains with the local electronic energy density per electron charge, H(r(c))/rho(r(c)), tending to decrease as the electronegativity differences for the bonded pairs of atoms decrease. The values of G(r(c)) and V(r(c)), estimated with a gradient-corrected electron gas theory expression and the local virial theorem, are in good agreement with theoretical values, particularly for the bonded interactions involving second-row M atoms. The agreement is poorer for shared C-O and N-O bonded interactions.

Kinetics↗

PubMed2001

Wavefunctions derived from experiment. I. Motivation and theory.

An experimental wavefunction is one that has an assumed form and that is also fitted to experimental measurements according to some well defined procedure. In this paper, the concept of extracting wavefunctions from experimental data is critically examined and past efforts are reviewed. In particular, the importance of scattering experiments for wavefunction fitting schemes is highlighted in relation to the more familiar model, the Hamiltonian paradigm. A general and systematically improvable method for fitting a wavefunction to experimental data is proposed. In this method, the parameters in a model wavefunction are determined according to the variational theorem but subject to an imposed constraint that an agreement statistic between the calculated and observed experimental data has a certain acceptable value. Advantages of the method include the fact that any amount of experimental data can be used in the fitting procedure irrespective of the number of parameters in the model wavefunction, the fact that a unique answer is obtained for a given choice of the model wavefunction, and the fact that the method can be used to model different experiments simultaneously. The wavefunction fitting method is illustrated by developing the theory for extracting a single-determinant wavefunction for a fragment of a molecular crystal, using data obtained from elastic X-ray scattering data. Effects due to thermal motion of the nuclei, secondary extinction of the X-ray scattering and different choices for the crystal fragment are treated.

Journal Article↗

PubMed2001

Wavefunctions derived from experiment. II. A wavefunction for oxalic acid dihydrate.

A wavefunction has been derived for the oxalic acid dihydrate molecule using accurate low-temperature X-ray electron-density structure-factor data. The electron density from this constrained theoretical wavefunction is compared to those of unconstrained theoretical wavefunctions. Fitted electron densities around hydrogen atoms show significant deviation compared to Hartree-Fock calculations. In particular, hydrogen bonding appears enhanced in the crystal over theoretical predictions, while the density usually attributed to lone-pair electrons of the oxalic acid oxygen atoms is decreased. The constrained fitting procedure improves the overall agreement of the calculated structure factors even for structure factors that were not used as input to the fitting procedure. The pictures obtained from the constrained fitting procedure are insensitive to random errors introduced into the data. Similarly, the fitting procedure is able to reproduce features that arise from more accurate theoretical calculations. However, we are unable to fit our wavefunction to within the experimentally quoted error bounds without allowing an unreasonably large change in the energy of the constrained wavefunction. Large Hartree-Fock and density functional theory (DFT) cluster calculations involving up to 86 atoms in size also do not show significantly improved agreement with the experimentally observed structure factors. Derived properties from the constrained wavefunction fragments, such as the kinetic energy, electrostatic potential and the electron localization function, are also presented. In general, there are no difficulties in extracting experimental wavefunctions and the associated derived properties from elastic X-ray scattering data for crystal fragments of the order of 20 atoms.

Journal Article↗