Thesis (Ph. D.)--Michigan State University. Chemistry, Biochemistry and Molecular Biology, 2008. / Title from PDF t.p. (viewed on July 2, 2009) Includes bibliographical references. Also issued in print.

Thesis (M.S. in environmental engineering)--Washington State University, August 2009. / Title from PDF title page (viewed on Aug. 7, 2009). "Department of Civil and Environmental Engineering." Includes bibliographical references (p. 73-76).

Thesis (Ph. D.)--University of Virginia, 1999. / Includes bibliographical references (p. 136-159). Also available online through Digital Dissertations.

No description available.

The problem with which this investigation is concerned is that of measuring the rate coefficients for termolecular charge transfer reactions of He2+ in atmospheric pressure afterglows with the minority reacting species. Of particular interest was the discovery that the presence of a third body can change an improbable charge transfer reaction involving He+2 into a very probable one, as in the case of the reaction with argon. For example, in Tables II and II it was shown that less than a 300 torr pressure of helium was required to double the effective rate of reaction of argon with He2+ while over 3000 torr was required for CH4. The sensitivity of the method has been sufficient to detect termolecular components as small as 2 x 10-30 cm /sec and values were found to range widely from 2 x 10 for Ne to 67 x 10-30 cm6/sec for CO2. The size of these termolecular rates not only served to explain specific anomalous efficiencies of the charge transfer process observed in atmospheric pressure lasers but also suggested the general importance of three-body ion-molecule reactions in higher pressure plasmas.

Philosophiae Doctor - PhD / This thesis describes research work undertaken to study neutron pairing correlations in 136Ba via the 138Ba(p, t) pair transfer reaction and to perform high-precision spectroscopy of low-lying states in 136Cs using the 138Ba(d, ) reaction. The aim of this project was to provide useful spectroscopic information relevant for matrix element calculations of 136Xe neutrinoless double beta decay. This work is relevant because neutrinoless double beta decays are standard-model-forbidden lepton number violating processes, which if observed, would establish the Majorana nature of the neutrinos and also determine the absolute mass scale of the light Majorana neutrinos. Our experiments show a signi cant fragmentation of the two-neutron transfer (p, t) strength to excited 0+ states in 136Ba, which could signi cantly affect future matrix element calculations. Additionally we obtain information on 65 new states in 136Cs observed in this work. It is anticipated that these new information will play a vital role in improving the precision of calculated matrix elements for 136Xe double beta decays.

The axilla is a major source of human body odour from which the characteristic musky, urinous or acidic odours emanate, and are predominantly due to bacterial metabolism of the protein-rich fluid secreted by the apocrine and sebaceous glands located in this area (Senol and Fireman, 1999). Clothing has been implicated in contributing to body odour intensity, possibly even increasing the intensity (Dravnieks, et al., 1968; Shelley, et al., 1953) by the transfer of secretions, skin debris and bacteria from the body to the fabric substrate. Despite much anecdotal evidence indicating that some fibres and fabrics are better at limiting odour intensity than others, there appears to be no published research confirming this. The purpose of this study therefore, was to determine whether fabrics varying in fibre content (cotton, wool, polyester) and fabric knit structure (interlock, single jersey, 1x1 rib) differed in the extent to which they retained and emanated axillary odour following wear, and whether the intensity of odour was linked to the number of bacteria transferred to the fabrics. A procedure for collecting odour on fabrics was developed as was a method for evaluating odour through use of a sensory panel. Total aerobic bacteria and aerobic coryneform bacteria extracted from the fabrics were counted to determine if an association between bacterial counts and fabrics existed. Sensory analysis recognises the unique capability of humans as odour-detecting instruments whereas, instrumental analysis has the potential to offer information on the concentration and identification of axillary compounds, which a human assessor cannot. To investigate a new method for detecting axillary odour on apparel fabrics, proton transfer reaction mass spectrometry (PTR-MS) was used to analyse volatiles emitted from fabrics differing in fibre type. After removal of garments from the human body, axillary odour can be detected on fabrics, with the intensity of odour being strongly influenced by the fibre type from which the fabrics had been made. Polyester fabrics emanated odour of high intensity, cotton that of mid-low odour intensity, and wool fabrics were low odour. Fabric structural properties such as thickness, mass per unit area and openness of knit structure also had an effect on odour intensity. However, as the principal factor influencing odour intensity was fibre, only fabrics characterised by a high intensity (i.e. polyester) were influenced by structural properties. Differences in odour intensity among fabrics were not necessarily related to bacterial numbers, and no �inherent antimicrobial� properties were evident for any of the fabrics. Bacterial populations persisted in all fabrics up to 28 days. A decline in numbers was apparent for high-odour polyester fabrics, while numbers in low-odour wool fabrics remained relatively stable. PTR-MS detected compounds likely to be short-chain carboxylic acids which increased in the headspace above the polyester fabrics after 7 days. However, this increase was not evident for either the wool or cotton fabrics. Therefore, bacterial numbers per se cannot be a predictor of the odour intensity emanating from fabrics at least on the basis of these fabrics and fibres. The intensity of axillary odour emanating from fabrics was found inversely related to fibre hygroscopicity. Keywords:fibre content, fabric structure, axillary odour, sensory analysis, bacteria, corynebacteria, instrumental analysis, PTR-MS

Free energy simulations have been widely employed to compute the thermodynamic properties of many important biochemical processes. In the first part of this dissertation, two important biochemical processes, protonation/deprotonation of acid in solution and solvation of small organic molecules, are investigated using free energy simulations. Accurate computation of the pKa value of a compound in solution is important and challenging. To efficiently simulate the free energy change associated with the protonation/deprotonation processes in solution, a new method of mixing Hamiltonian, implemented as an approach using a fractional protonin the hybrid quantum mechanics/molecular mechanics (QM/MM) scheme, is developed. This method is a combination of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theoretical and technical details of this method, along with the calculation results of the pKa value of methanol and methanethiol molecules in aqueous solution, are discussed. The simulation results show satisfactory agreement with experimental data. Though the QM/MM method is one of the most useful methods in the modeling of biochemical processes, little attention has been paid to the accuracy of QM/MM methods as an integrated unit. Therefore, the solvation free energies of a set of small organic molecules are simulated as an assessment of ab initio QM/MM methods. It shows that the solvation free energy from QM/MM simulations can vary over a broad range depending on the level of QM theory / basis sets employed. Diffuse functions tend to over-stabilize the solute molecules in aqueous solution. The deviations pose a pressing challenge to the future development of new generation of MM force fields and QM/MM methods if consistency with QM methods becomes a natural requirement. In the second part of the dissertation, the dynamic and energetic properties of two molten globule (MG) protein molecules, α-lactalbumin(α-LA) and monomeric chorismate mutase (mCM) are investigated using molecular dynamics simulations. The exploring of the molecular mechanism of protein folding is a never-settled battle while the properties of MG states and their roles in protein folding become an important question. The MGs show increased side chain flexibility while maintain comparable side-chain coupling compared to the native state, which partially explains the preserving of native-like overall conformation. The enhanced sampling method, temperature-accelerated molecular dynamics (TAMD), is used for the study of the hydrophobic interactions inside both biomolecules. The results suggest that these hydrophobic cores could overcome energy barriers and repack into new conformation states with even lower energies. The repacking of the hydrophobic cores in MGs might be served as a criterion for recognizing the MGs in large class of biomolecules. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

This thesis is concerned with the use of Lewis base organocatalysts for carboxyl and acyl transfer reactions. Chapter 1 introduces the ability of organic Lewis bases other than DMAP-type to promote a range of asymmetric O-, N- and C-acyl transfer processes. This chapter summarizes the developments in catalyst architectures and approaches to these processes that have been disclosed to date in this dynamic area of asymmetric organocatalysis. Chapter 2 introduces studies into the synthesis of pyrrolyl carbonates via cyclization of gamma-amino esters and ring closing metathesis (RCM) of N-allylamides. The ability of a range of Lewis bases to promote the regioselective O- to C-carboxyl transfer of pyrrolyl carbonates is also presented. Chapter 3 introduces isothiourea DHPB as an efficient Lewis base catalyst for the diastereoselective C-acylation of silyl ketene acetals with anhydrides or benzoyl fluoride, giving 3-acyl-3-aryl or 3-acyl-3-alkylfuranones in excellent yields and stereoselectivities (up to 99:1 dr). Chapter 4 introduces C(2)-aryl substituted DHPB derived-isothioureas as efficient Lewis base catalysts for the enantioselective C-acylation of silyl ketene acetals with propionic anhydride, giving 3-acyl-3-aryl or 3-acyl-3-alkylfuranones in good isolated yields and enantioselectivities (up to 98% ee). This chapter also demonstrates that these chiral isothioureas are required for high reactivity and asymmetry in related acylation manifolds. Chapter 5 presents and overall conclusion for chapters 2,3 and 4. Chapter 6 contains full experimental procedures and characterization data for all compounds synthesized in Chapters 2, 3 and 4.

The axilla is a major source of human body odour from which the characteristic musky, urinous or acidic odours emanate, and are predominantly due to bacterial metabolism of the protein-rich fluid secreted by the apocrine and sebaceous glands located in this area (Senol and Fireman, 1999). Clothing has been implicated in contributing to body odour intensity, possibly even increasing the intensity (Dravnieks, et al., 1968; Shelley, et al., 1953) by the transfer of secretions, skin debris and bacteria from the body to the fabric substrate. Despite much anecdotal evidence indicating that some fibres and fabrics are better at limiting odour intensity than others, there appears to be no published research confirming this. The purpose of this study therefore, was to determine whether fabrics varying in fibre content (cotton, wool, polyester) and fabric knit structure (interlock, single jersey, 1x1 rib) differed in the extent to which they retained and emanated axillary odour following wear, and whether the intensity of odour was linked to the number of bacteria transferred to the fabrics. A procedure for collecting odour on fabrics was developed as was a method for evaluating odour through use of a sensory panel. Total aerobic bacteria and aerobic coryneform bacteria extracted from the fabrics were counted to determine if an association between bacterial counts and fabrics existed. Sensory analysis recognises the unique capability of humans as odour-detecting instruments whereas, instrumental analysis has the potential to offer information on the concentration and identification of axillary compounds, which a human assessor cannot. To investigate a new method for detecting axillary odour on apparel fabrics, proton transfer reaction mass spectrometry (PTR-MS) was used to analyse volatiles emitted from fabrics differing in fibre type. After removal of garments from the human body, axillary odour can be detected on fabrics, with the intensity of odour being strongly influenced by the fibre type from which the fabrics had been made. Polyester fabrics emanated odour of high intensity, cotton that of mid-low odour intensity, and wool fabrics were low odour. Fabric structural properties such as thickness, mass per unit area and openness of knit structure also had an effect on odour intensity. However, as the principal factor influencing odour intensity was fibre, only fabrics characterised by a high intensity (i.e. polyester) were influenced by structural properties. Differences in odour intensity among fabrics were not necessarily related to bacterial numbers, and no �inherent antimicrobial� properties were evident for any of the fabrics. Bacterial populations persisted in all fabrics up to 28 days. A decline in numbers was apparent for high-odour polyester fabrics, while numbers in low-odour wool fabrics remained relatively stable. PTR-MS detected compounds likely to be short-chain carboxylic acids which increased in the headspace above the polyester fabrics after 7 days. However, this increase was not evident for either the wool or cotton fabrics. Therefore, bacterial numbers per se cannot be a predictor of the odour intensity emanating from fabrics at least on the basis of these fabrics and fibres. The intensity of axillary odour emanating from fabrics was found inversely related to fibre hygroscopicity. Keywords:fibre content, fabric structure, axillary odour, sensory analysis, bacteria, corynebacteria, instrumental analysis, PTR-MS