Density functional theory (DFT) is a popular approach to solving the many-electron Schrödinger equation, in order to investigate the properties of matter from first principles. While DFT can give the exact ground state electronic density of a system, in practice, an approximation is required for the many-body effects contained in the exchange-correlation functional. The accuracy of calculations performed using DFT is strongly related to the choice of approximation. In this thesis we will investigate and build upon a fully non-local approach to modeling exchange-correlation in the form of the weighted density approximation (WDA). Central to the WDA is the model function chosen for the coupling-constant averaged pair-correlation function (PCF). We show that a model PCF can be selected from a set to give excellent bulk properties for a particular system. However, this model is not necessarily transferable to other systems and there is no method of selecting an appropriate model from this set a priori. We suggest that the model PCF can be improved systematically by satisfying known physical constraints. One such constraint is the Kimball cusp condition, which we include in our model and implement. We demonstrate that surfaces are systems that require a non-local treatment of exchange-correlation by applying the WDA to metal surfaces and investigate the dissociative adsorption of H2 on the Cu(100) surface. A new framework for a model PCF with spin resolution is developed, providing a route for more physical constraints to be satisfied within a weighted spin density approximation (WSDA). A simple model is suggested and implemented and comparisons are made to the coupling-constant averaged PCF in the homogeneous electron gas. We then apply a selection of our new models to a number of materials and show that our model for the WSDA gives improved band gaps over the local density approximation. Application of the WSDA to spin polarised materials reveals shortcomings in our simple model. We then suggest further refinements to our implementation of the WSDA. It is expected that the inclusion of additional physical constraints will systematically improve results given in a weighted-density based approximation to exchange-correlation.

The objective of this study was to elucidate the nature and extent of drift by the aquatic insect populations of the Brazos River, Texas.

PhD, Faculty of Health Sciences, University of the Witwatersrand / Many studies have shown a negative effect of depot-medroxyprogesterone acetate (DMPA) hormonal contraception on bone mineral density (BMD) in women. There is limited information on the effect of norethisterone enanthate (NET-EN) on BMD and the effect of combined oral contraceptives (COCs) on BMD is inconclusive, however emerging evidence is showing that low-dose COCs maybe detrimental to BMD in young women. The aim of this research was to evaluate, in a 5-year follow-up study, the possible effect of DMPA, NET-EN and COCs on BMD among young (15-19 years) and older (40-49 years) South African women. Method: This prospective study was conducted at the Commercial City Family Planning clinic in Durban, South Africa between 2000 and 2007. In the adolescent group women with no history of hormonal contraception who were initiating use of DMPA (n=115), NET-EN (n=115) or COCs (n=116) and 144 nonuser controls were recruited. In the older group, one hundred and twenty seven users of DMPA, 102 NET-EN users and 106 COC users of at least one year were compared to 161 nonuser controls. BMD was measured at the distal radius and midshaft of the ulna using dual x-ray absorptiometry. In the crosssectional component of the study conducted at the end of the longitudinal phase, BMD was measured at the hip, spine and femoral neck in a sub-group of 96 of the younger women. Results: In the longitudinal study of adolescents, BMD increased in all four groups during follow-up (p<.001). There was evidence for lower BMD increases per annum in NET-EN (p=.050) and COC (p=.010) users compared to nonusers but no difference between DMPA and nonusers (p=.76). In 14 NET-EN discontinuers, an overall reduction of 0.61% per year BMD was followed, upon cessation, by an increase of 0.69% per year (p=.066). The cross-sectional sub-study found that young women in the injectables-only user group had lower BMDs compared to the non-user group after adjusting for BMI at the spine (p=0.042), hip (p=0.025), and femoral neck (p=0.023). The mixed COC/injectable user group BMD values were lower than controls; however, they were not significant at any of the three sites. In the older women, there was no significant difference in radius BMD between the contraceptive user groups and the non-user controls (p=.26) with and without adjustment for age at baseline, or after two and a half years of follow-up (p=0.52). Conclusion: This study suggests that BMD increases in adolescents may be less in NETEN and COC users; however, recovery of BMD in NET-EN users was found in the small sample of adolescents followed post-discontinuation. The cross-sectional sub-study showed similar findings in long-term injectable users, but not when women had mixed injectable and COC use. There was no evidence that long-term use of DMPA, NET-EN and COCs affected BMD in the older women.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, in fulfillment of the requirements for the degree of Doctor of Philosophy, April 2013. / Density functional theory (DFT) and time dependent-DFT (TD-DFT) was applied to investigate the geometric and electronic properties of cobalamin (Cbl) models. Model compounds of the type, [B–(Co(III)(L)4–X)–Y]n+ were used, where B and Y were comprised of the alpha (α) and β axial ligands, (L)4 represented the equatorial ligand(s) and X was either hydrogen or a substituent of electron donating or withdrawing character, quantified by the Hammett constant (σp), at C10 of the corrin. All calculations were conducted in the gas phase or implicit solvent medium at the BP86/6-31+G(d,p) level of theory. High-resolution crystal structures of B12, extracted from the Cambridge Crystal Structural Database (CCSD), were used as the source of initial coordinates. DFT was used to explore the trans influence of the lower (α) axial ligand, the cis influence of various equatorial ligands and the cis influence of a substituted corrin ring at the C10 position on the Gibbs free energy (ΔG) and bond dissociation energies (BDEs) of the Co(III)–Cβ bond. Other geometric parameters such as ring distortion, axial bond lengths, equatorial bond lengths and partial charges on the Co metal centre, donor atom of the upper and lower axial ligands as well as the N-donor atoms of the macrocyclic ring are documented and discussed. The use of a broad range of alpha (α) ligands in the cobalamin models from charged and neutral N-donor ligands (NH3, NH2–, NH2–, NH2F, NHF–, NF2–, NH2CH3, NHCH3, NH(CH3)2, N(CH3)3), to naturally occurring amino acids or realistic models of their metal-coordinating side chains (methanethiol, dimethylsulfide, cysteine, methanethiolate, glycine, p-aminopyridine, imidazole, histidine, acetate, 2-propanol, serine and tyrosine), provided significant information on the trans influence of these ligands on the BDE of the Co(III)–C bond (upper axial ligand). The ligands NH3, NH2–, NH2–, NH2F, NHF–, NF2–, NH2CH3, NHCH3, were used to explore electronic effects while NH3, NH2CH3, NH(CH3)2, and N(CH3)3 were used to investigate steric effects. The naturally occurring amino acids or their models focused primarily on exploring why nature chooses an N-donor ligand such as histidine or imidazole instead of an S-donor or O-donor ligand that is also readily available from protein side chains. As the basicity of the α ligand increased in the series NH2F < NH3 < CH3NH2 < (CH3)2NH < (CH3)3N < NHF– < NHCH3– < NH2– < NF2– < NH2–(as assessed by the proton affinities) a normal trans influence was observed between the axial ligands. While the Co(III)–C bond was observed to increase in length, the Co(III)–Nα bond length decreased. The weakening of the Co(III)–C bond was paralleled by the decrease in the Co(III)–C BDE. On the other hand, as the steric bulk of the α ligand (NH3, NH2CH3, NH(CH3)2, and N(CH3)3) increased (assessed by the molar volume and Tolman cone angle), an inverse trans influence (in other words, simultaneous lengthening or shortening) between the upper and lower axial bonds was observed. The Co(III)–C bond showed a marginal increase in length while the Co(III)–Nα bond length steadily increased as the molar volume of the α ligand increased. Interestingly, the large difference in the Co–Nα bond length from the 5-coordinate to the 6-coordinate complex (later referred to as ΔCo–Nα(5c-6c)), paralleled the decrease of the Co(III)–C BDEs. It also became evident from calculations with the amino acids posing as α ligands that the nature of the α ligand (assessed by the absolute chemical hardness (η) of the ligand, with the greater the η value the harder the ligand) plays a major role in the labilisation of the organometallic bond. As the η of the α ligand increased, the Co(III)–C BDE increased. The trans influence of the α ligands resulted in the strengthening (hard ligand) and weakening (soft ligand) of the Co(III)–C bond, as was affirmed by the electron density at the bond critical point (bcp) of the Co(III)–C bond. The N-donor ligands (described as having an intermediate character as the η- values were between the hard and soft ligands) were found to be catalytically suitable (31.89 – 32.45 kcal mol -1), rather than the soft and hard donor ligands. The trans influence of the latter two ligands on the upper axial bond revealed a weakly and strongly bound alkyl group to the Co metal centre, giving Co(III)–C BDEs values of 29.39–32.27 kcal mol-1and 32.54–34.96 kcal mol-1, respectively. In addition to the corrin macrocycle, other equatorial ligands like cobaloxime, corrole, porphyrin, methylcobalt(III) pentaamine, [14-ane]N4, [15-ane]N4 and [16-ane]N4 were used in calculations to explore the cis influence on the labilisation of the Co(III)–C bond. These ligands included saturated and unsaturated cyclic rings. The results showed that the flexibility of the ring increased as the size of the equatorial ligand increased and thus affected the displacement of the Co(III) metal centre from the defined mean plane. This subsequently affected the strength of the organometallic bond, which paralleled the BDEs. The hydrogen atom at C10 of the corrin ring was substituted by electron donating (CH3, OH and NH2) or –withdrawing groups (NO, NO2, CN, COOH and Br) and the cis influence of these groups on the organometallic bond was investigated. A normal trans influence between the axial ligands was observed. As the electron density from the substitutents increased towards the ring, the Co(III)–C bond strengthened and the Co(III)–Nα bond weakened. The increased electron density from the C10 substituents influenced the contraction of the Co–Nα bond length. The greater difference in contraction of the Co–Nα bond length from the 5-coordinate to the 6-coordinate complex (ΔCo–Nα(5c-6c)) resulted in lower Co(III)–C BDEs. The TD-DFT method was used to generate both the absorption and circular dichroism (CD) spectra where the vertical electronic excited states of Co(III) cobalamin species that differ with respect to their upper axial ligand, including FCbl, ClCbl, BrCbl,SeCNCbl and CH3Cbl were calculated. The cis influence for each of the species was analysed within the framework of TD-DFT to assign the major spectral features, in other words, the α/β, D/E and γ bands in the predicted UV-visible spectra. These studies reveal that the “typical” and “atypical” absorption exhibit a high degree of σ-donation from the β-ligand to the Co(III) metal centre and the subsequent destabilisation of the corresponding d-orbitals of Co. Furthermore, as the donor ability of the β ligand increased, the contributions from the antibonding d z2 orbital to the HOMO increased, leading to a strong Co(III)–Nα σ-antibonding interaction, which is consistent with the observed lengthening of the same bond from FCbl, ClCbl, BrCbl, SeCNCbl to CH3Cbl.

No description available.

Chiu Lai Fan. / Thesis submitted in: December 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves [74-77]). / Abstracts in English and Chinese. / ABSTRACT (ENGLISH) --- p.iii / ABSTRACT (CHINESE) --- p.v / ACKNOWLEDGMENTS --- p.vi / TABLE OF CONTENTS --- p.vii / LIST OF FIGURES --- p.ix / LIST OF TABLES --- p.xi / LIST OF SYMBOLS --- p.xiii / Chapter CHAPTER ONE --- INTRODUCTION AND BACKGROUND --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- The nature of hydrogen bonding interactions --- p.2 / Chapter 1.3 --- Evidences of hydrogen bonding interactions --- p.4 / Chapter 1.4 --- Three-centered hydrogen bond --- p.4 / Chapter 1.4.1 --- Literature review of three-centered H-bonds --- p.6 / Chapter 1.4.2 --- Review of three-centered H-bonds characterization --- p.8 / Chapter 1.5 --- Cooperative effect --- p.12 / Chapter 1.6 --- Scope of thesis --- p.13 / Chapter CHAPTER TWO --- THEORY AND METHODOLOGY --- p.15 / Chapter 2.1 --- Introduction --- p.15 / Chapter 2.2 --- Theory --- p.16 / Chapter 2.2.1 --- Density Functional Theory (DFT) --- p.16 / Chapter 2.2.2 --- Natural Bonding Orbital Theory (NBO) --- p.19 / Chapter 2.2.3 --- Spin-Spin coupling constants --- p.22 / Chapter 2.2.4 --- Wiberg Bond Index --- p.24 / Chapter 2.3 --- Methodology --- p.25 / Chapter CHAPTER THREE --- RESULTS AND DISCUSSION --- p.32 / Chapter 3.1 --- The nature of three-centered hydrogen bond interaction --- p.32 / Chapter 3.1.1 --- Geometries --- p.32 / Chapter 3.1.2 --- Natural bond orbital analysis - Donor-acceptor interactions --- p.41 / Chapter 3.1.3 --- Spin-Spin coupling across the hydrogen bonds --- p.46 / Chapter 3.1.4 --- Wiberg bond index --- p.51 / Chapter 3.1.5 --- Proton transfer -Hydrogen bond strengths on the effect of remote proton transfer --- p.53 / Chapter 3.1.6 --- Cooperactive character in hydrogen bonding clusters --- p.65 / Chapter CHAPTER FOUR --- CONCLUSING REMARKS --- p.71 / REFERENCES / APPENDIX

Lee, Shun Hang = 密度泛函理論計算的壓力修正 / 李信恆. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (p. 67-69). / Abstracts in English and Chinese. / Lee, Shun Hang = Mi du fan han li lun ji suan de ya li xiu zheng / Li Xinheng. / Chapter 1 --- Introduction --- p.1 / Chapter 2 --- Theoretical backgrounds --- p.4 / Chapter 2.1 --- Density Functional Theory --- p.4 / Chapter 2.2 --- Pseudopotential approximation --- p.6 / Chapter 2.3 --- Car-Parrinello Molecular Dynamics --- p.8 / Chapter 3 --- Simulation details --- p.10 / Chapter 3.1 --- Simulation overview --- p.10 / Chapter 3.2 --- Electronic minimization --- p.11 / Chapter 3.2.1 --- The need and setting of electronic minimization --- p.11 / Chapter 3.2.2 --- Results and convergence of electronic minimization --- p.13 / Chapter 3.3 --- Atomic minimization --- p.13 / Chapter 3.4 --- CPMD runs and parameter settings --- p.14 / Chapter 3.4.1 --- The NVE ensemble --- p.14 / Chapter 3.4.2 --- The NVT ensemble --- p.14 / Chapter 3.5 --- Taking the average --- p.20 / Chapter 3.6 --- Check for valid stress tensors and pressure --- p.22 / Chapter 3.7 --- Check for the structure --- p.24 / Chapter 3.7.1 --- The need for structure checks --- p.24 / Chapter 3.7.2 --- Methods to check the structures --- p.24 / Chapter 4 --- Pressure Correction --- p.30 / Chapter 4.1 --- Theoretical Basis for the Correction --- p.30 / Chapter 4.2 --- CPMD Calculation Results --- p.32 / Chapter 4.2.1 --- E(V) at different T --- p.34 / Chapter 4.2.2 --- Results of stress tensor checks --- p.35 / Chapter 4.2.3 --- The EOS's found in this study --- p.38 / Chapter 4.2.4 --- Comparisons with others´ة work --- p.39 / Chapter 4.2.5 --- Difference between LDA and GGA results --- p.42 / Chapter 5 --- Magnesium Silicate (MgSiO3) --- p.45 / Chapter 5.1 --- Simulations for MgSiO3 perovskite --- p.47 / Chapter 5.1.1 --- Simulation parameters and various check --- p.47 / Chapter 5.1.2 --- Results for MgSiO3 perovskite --- p.50 / Chapter 5.2 --- Simulations for MgSiO3 post-perovskite --- p.53 / Chapter 5.2.1 --- Simulation parameters and various check --- p.53 / Chapter 5.2.2 --- Results of MgSiO3 post-perovskite --- p.55 / Chapter 6 --- Discussions --- p.58 / Chapter 6.1 --- Other thermodynamic quantities --- p.58 / Chapter 6.2 --- Asymptotic behaviour of ΔP(V) --- p.59 / Chapter 6.3 --- Applications to the exact XC functional --- p.60 / Chapter 7 --- Conclusion --- p.61 / Chapter 8 --- Appendix --- p.62 / Chapter 8.1 --- Efficient method to perform electronic minimization --- p.62 / Chapter 8.2 --- Efficient method to perform atomic minimization --- p.63 / Chapter 8.3 --- Other related settings --- p.64 / Chapter 8.4 --- Typical input files for CPMD calculations using Quantum-Espresso --- p.65 / Bibliography --- p.67

"March 2003" / Corrections inside front cover. / Includes bibliographical references (leaves 111-167) / x, 167 leaves : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Medicine, 2003

"February 2004" / Bibliography: leaves 150-168. / 168 leaves : ill., plates ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Medicine, 2004

Immersion energies for an impurity in a homogeneous electron gas with a uniform positive background charge density have been calculated numerically using density functional theory. The numerical aspects of this problem are very demanding and have not been properly discussed in previous work. The numerical problems are related to approximations of infinity and continuity, and they have been corrected using physics based on the Friedel sum rule and Friedel oscillations. The numerical precision is tested extensively. Immersion energies are obtained for non-spin-polarized systems, and are compared with published data. Numerical results, such as phase shifts, density of states, dielectric constants, and compressibilities, are obtained and compared with analytical theories. Immersion energies for excited systems are obtained by varying the number of electrons in the bound states of an impurity. The model is extended to spin-polarized systems and is tested in detail for a carbon impurity. The spin-coupling with an external magnetic field is considered mainly for a hydrogen impurity. These new results show very interesting behavior at low densities. / Graduation date: 2005