Thesis (Ph. D.)--West Virginia University, 2001. / Title from document title page. Document formatted into pages; contains viii, 113 p. : ill. (some col.). Includes abstract. Includes bibliographical references.

Thesis (Ph.D.)--Drexel University, 2007. / Includes abstract and vita. Includes bibliographical references (leaves 148-150).

Graduation date: 1987

The primary focus of this dissertation is the advancement of the correlation consistent composite approach (ccCA) methodology from its original formulation to the current implementation. Although for large main group test sets which contained both first- (Li-Ne) and second-row (Na-Ar) species ccCA produced chemical accuracy (generally estimated as a deviation of ~1 kcal mol-1 from reliable experiment), the second-row species were smaller in molecular size in comparison to their corresponding first-row species. Previous theoretical work has shown that the accuracy for theoretical calculations involving second-row species (specifically sulfur-containing species) are more basis set dependent than first-row species. Therefore, an analysis of the accuracy of ccCA for sulfur-containing species is warranted. The ccCA methodology is used to evaluate both enthalpies of formation and bond dissociation energies of sulfur-containing species as well as examine isomerization energies for three sets of sulfur-containing isomers. During the testing of ccCA for sulfur-containing species two observations were made which led to further investigations. First, there is no agreement between different theoretical methodologies on the lowest energetic isomer between SNO and NSO. In fact, G3 and G3B3 which differ only by the geometry of the single-point calculations do not agree on the lowest isomer. For this reason, larger, more complete theoretical treatments of SNO and NSO are investigated. Second, for open-shell sulfur-containing systems the accuracy of the ccCA methodology begins to degrade when spin-contamination becomes non-negligible. Therefore, we investigate the accuracy of the ccCA methodology when spin-contamination is removed from the wavefunction. Finally, the ccCA methodology is utilized in a multilayer ONIOM approach as the high level of theory in conjunction with density functional theory as the low level for the C-H bond dissociation energies of anthracene and fluorene analogues.

Phosphoryl transfers are essential chemical reactions in key life processes, including energy production, signal transduction and protein synthesis. They are known for having extremely low reaction rates in aqueous solution, reaching the scale of millions of years. In order to make life possible, enzymes that catalyse phosphoryl transfer, phosphoryl transferases, have evolved to be tremendously proficient catalysts, increasing reaction rates to the millisecond timescale. Due to the nature of the electronic structure of phosphorus atoms, understanding how hydrolysis of phosphate esters occurs is a complex task. Experimental studies on the hydrolysis of phosphate monoesters with acidic leaving groups suggest a concerted mechanism with a loose, metaphosphate-like transition state. Theoretical studies have suggested two possible concerted pathways, either with loose or tight transition state geometries, plus the possibility of a stepwise mechanism with the formation of a phosphorane intermediate. Different pathways were shown to be energetically preferable depending on the acidity of the leaving group. Here we performed computational studies to revisit how this mechanistic shift occurs along a series of aryl phosphate monoesters, suggesting possible factors leading to such change. The fact that distinct pathways can occur in solution could mean that the same is possible for an enzyme active site. We performed simulations on the catalytic activity of β-phosphoglucomutase, suggesting that it is possible for two mechanisms to occur at the same time for the phosphoryl transfer. Curiously, several phosphoryl transferases were shown to be able to catalyse not only phosphate ester hydrolysis, but also the cleavage of other compounds. We modeled the catalytic mechanism of two highly promiscuous members of the alkaline phosphatase superfamily. Our model reproduces key experimental observables and shows that these enzymes are electrostatically flexible, employing the same set of residues to enhance the rates of different reactions, with different electrostatic contributions per residue.

The solubility of cellobiose in 18 organic liquids and water was measured at 20°C. Hydrogen bond acceptors were the most effective solvents. Three models were analyzed to evaluate their accuracy and to understand factors that affect cellobiose solubility: Hansen solubility parameters (HSP), linear free energy relationship (LFER), and UNIQUAC functional-group activity coefficients (UNIFAC). The HSP of cellobiose were determined and the model was able to distinguish between most good and poor solvents, however, proved to be occasionally unreliable due to a false negative. The LFER model produced an empirical equation involving contributions from solvent molar refraction, polarizability, acidity, basicity, and molar volume, which predicted cellobiose solubilities to within ±2 log units. LFER indicated that good solvents were highly polarizable and had low molar volume, which was consistent with the good solvents found for cellobiose. A modified version of UNIFAC that includes an association term (A-UNIFAC) predicted the solubility of cellobiose in water and alcohols to within ±0.6 log units, indicating that A-UNIFAC can be used to predict the solubility of cellobiose and other carbohydrates provided additional data to extend the model to solvents other than water and alcohols.

Yes / Many in-vitro methods for prediction of skin permeability have been reported in literature. Cerasome electrokinetic chromatography is one of the most sophisticated approaches representing a maximum level of similarity to the lipid phase of the stratum corneum. One goal of this study was to investigate the affinity pattern of Cerasome and to compare it with the permeability profile of human skin. Another purpose was to study the applicability of Hansen solubility parameters for modelling skin permeation and to investigate the predictive and explanatory potential of this method. Visualisation in Hansen diagrams revealed very similar profiles of Cerasome electrokinetic chromatography retention factors and skin permeability coefficients. In both cases, the characteristic pattern with two clusters of highly retained or highly permeable substances could be shown to be mainly caused by two groups of compounds, one of them with high affinity to ceramides, fatty acids and lecithin and the other being more affine to cholesterol. If based on a sufficiently comprehensive experimental dataset, model-independent predictions of skin permeability data using three-component Hansen solubility parameters are able to achieve similar accuracy as calculations made with an Abraham linear free energy relationship model in which the compounds are characterized by seven physicochemical descriptors.

yes / Experimental values of permeability coefficients, as log Kp, of chemical compounds across human skin were collected by carefully screening the literature, and adjusted to 37 °C for the effect of temperature. The values of log Kp for partially ionized acids and bases were separated into those for their neutral and ionic species, forming a total data set of 247 compounds and species (including 35 ionic species). The obtained log Kp values have been regressed against Abraham solute descriptors to yield a correlation equation with R2 = 0.866 and SD = 0.432 log units. The equation can provide valid predictions for log Kp of neutral molecules, ions and ionic species, with predictive R2 = 0.858 and predictive SD = 0.445 log units calculated by the leave-one-out statistics. The predicted log Kp values for Na+ and Et4N+ are in good agreement with the observed values. We calculated the values of log Kp of ketoprofen as a function of the pH of the donor solution, and found that log Kp markedly varies only when ketoprofen is largely ionized. This explains why models that neglect ionization of permeants still yield reasonable statistical results. The effect of skin thickness on log Kp was investigated by inclusion of two indicator variables, one for intermediate thickness skin and one for full thickness skin, into the above equation. The newly obtained equations were found to be statistically very close to the above equation. Therefore, the thickness of human skin used makes little difference to the experimental values of log Kp.

Yes / The high-performance liquid chromatography (HPLC) method employing stationary phases immobilized with plasma proteins was used for this study to investigate the structural properties governing drug-plasma protein binding. A set of 65 compounds with a broad range of structural diversity (in terms of volume, hydrogen-bonding, polarity and electrostatic force) were selected for this purpose. The Abraham linear free energy relationship (LFER) analyses of the retention factors on the immobilized HSA (human serum albumin) and AGP (α1-acid glycoprotein) stationary phases showed that McGowan’s characteristic molecular volume (V), dipolarity/polarizability (S) and hydrogen bond basicity (B) are the three significant molecular descriptors of solutes determining the interaction with immobilized plasma proteins, whereas excess molar refraction (E) is less important and hydrogen bond acidity (A) is not of statistical significance in both systems, for electrically neutral compounds. It was shown that ionised acids, as carboxylate anions, bind very strongly to the immobilized HSA stationary phase and that ionised bases, as cations bind strongly to the AGP stationary phase. This is the first time that the effect of ionised species on plasma protein binding has been determined quantitatively; the increased binding of acids to HSA is due almost entirely to acids in their ionised form.

Yes / We have set out an equation for partition of 87 neutral molecules from water to o-nitrophenyl octyl ether, NPOE, an equation for partition of the 87 neutral molecules and 21 ionic species from water to NPOE, and an equation for partition of 87 neutral molecules from the gas phase to NPOE. Comparison with equations for partition into other solvents shows that, as regards partition of neutral (nonelectrolyte) compounds, NPOE would be a good model for 1,2-dichloroethane and for nitrobenzene. In terms of partition of ions and ionic species, NPOE is quite similar to 1,2-dichloroethane and not far away from other aprotic solvents such as nitrobenzene.