The vibrational potential energy surfaces in electronic ground and excited states of several ring molecules were investigated using several different spectroscopic methods, including far-infrared (IR), Raman, ultraviolet (UV) absorption, fluorescence excitation (FES), and single vibronic level fluorescence (SVLF) spectroscopies. Based on new information obtained from SVLF and millimeter wave spectra, the far-IR spectra of coumaran were reassigned and the one-dimensional ring-puckering potential energy functions for several vibrational states in the S0 ground state were determined. The barrier was found to be 154 cm-1 and the puckering angles to be ± 25°, in good agreement with the millimeter wave barrier of 152 cm-1 and puckering angles of ± 23°. Moreover, the UV absorption and FES spectra of coumaran allowed the one-dimensional ring-puckering potential energy functions in the S1 excited state to be determined. The puckering barrier is 34 cm-1 for the excited state and the puckering angles are ± 14°. Several calculations with different basis sets have been carried out to better understand the unusual vibrational frequencies of cyclopropenone. It was shown that there is strong interaction between the C=O and symmetric C-C stretching vibrations. These results differ quantitatively from a previous normal coordinate calculation and interpretation. The vapor-phase Raman spectrum of 3,7-dioxabicyclo[3.3.0]oct-1,5-ene was analyzed and compared to the predicted spectrum from DFT calculations. The spectrum further shows it has D2h symmetry, in which the skeletons of both rings are planar. The infrared and Raman spectra of vapor-phase and liquid-phase 1,4-benzodioxan and 1,2,3,4-tetrahydronaphthalene were collected and the complete vibrational assignments for both molecules were made. Theoretical calculations predicted the barriers to planarity to be 4809 cm-1 for 1,2,3,4-tetrahydonaphthalene and 4095 cm-1 for 1,4-benzodioxan. The UV absorption, FES, and SVLF spectra of both molecules were recorded and assigned. Both one and two-dimensional potential energy functions of 1,4-benzodioxan for the ring-twisting and ring-bending vibrations were carried out for the S0 and S1(π,π*) states, and these were consistent with the high barriers calculated for both states. The low-frequency spectra of 1,2,3,4-tetrahydronaphthalene in both S0 and S1(π,π*) states were also analyzed.

Intrinsically conducting polymers (ICPs) with high mechanical strength and electrical conductivity are attractive for several applications spanning the fields of energy, defense, and transportation. Electrochemically processed polythiophene (PTh) films are a class of ICPs that have been demonstrated recently to possess electrical conductivities as high as 1,300 S/cm and be stronger than common types of processed aluminum foils. While these results are promising, the electrical conductivity of PTh is still low compared to metals and the effects of important process conditions such as electrode resistance, distance between working and counter electrodes, and thiophene concentration on the structure and physical properties of electrochemically processed PTh films must be investigated in detail. In this work, electrode resistance and inter-electrode distance were demonstrated to be inversely proportional to the charge efficiency for PTh film growth. A critical concentration of thiophene that produced films with the highest conductivity was also revealed. Anionic surfactants sodium dodecyl sulfate (SDS) and sodium dodeclybenzene sulfonate (SDBS) were used, with and without a proton scavenger, in the Lewis acid boron trifluoride diethyl etherate (BFEE) electrolyte, which allows polymerization of thiophene at low oxidation potentials, to enhance the ordering and conjugation length of PTh through stabilization of the radical cation of thiophene via the dodecyl chain of the anionic surfactants. X-ray diffraction spectra revealed enhanced order and packing when surfactant was used during the processing of PTh films, and measured electrical conductivities were increased by as much as 300% because of the surfactant-mediated structural improvements. Necking behavior observed in tensile test of PTh films with anionic surfactant additives also suggests chain alignment and increased chain length.

This thesis focuses on the construction and role of benchmark quality computations in the area of non-covalent interactions. We have provided a detailed error analysis of focal-point schemes commonly used in benchmark quality computations, as well as provide error and speedup analysis of commonly used approximations to these methods. An analysis of basis set effects on higher-order corrections to MP2/CBS has been carried out, providing the community error bounds on future benchmarks. We demonstrate how these high-level computations can elucidate a better understanding of non-bonded interactions in chemistry as well as provide high-quality reference data to refit existing methods against to increase the overall accuracy of the method.

Animal trypanosomosis is a major constraint in livestock production in Sub-Saharan Africa. With the emergence of resistance against trypanocidal drugs, the cost and environmental concerns raised by vector control, and the challenge of antigenic variation in vaccine development, alternative control measures are being sought. An anti-disease strategy, whereby the immune response or chemotherapy is aimed towards pathogenic factors rather than the parasite itself, constitutes such a novel approach. Congopain is the major cysteine protease in Trypanosoma congolense, and upon release in the bloodstream of infected cattle, acts as a pathogenic factor. It is therefore an attractive candidate for an anti-disease vaccine. It was hence deemed necessary to investigate the variability of congopain-like cysteine proteases before attempting to design drugs and vaccines based on the inhibition of congopain. Most congopain-like cysteine protease genes of T. congolense exist in a single locus of 12-14 copies organised as tandem repeats of 2 kb gene units. A gene unit library of 120 clones was constructed out of several cosmid clones selected in a previous study that contained various lengths of the congopain locus. Some 24 gene unit clones were sequenced, and it was found that congopain genes cluster in three sub-families, named CP1 (8 clones), CP2 (12 clones) and CP3 (4 clones). The latter most characteristically shows a substitution of the active site cysteine by a serine. Isoform specific primers were designed and used to verify the proportions of the three isoforms (one third CP1, half CP2 and a sixth CP3) in the remaining clones of the library. Since this first study was conducted in one isolate, IL 3000, the results were subsequently validated in a large array of isolates, of T. congolense, as well as T. vivax and T. brucei subspecies, by a PCR approach. Finally, to gain access to copies of congopain genes that are not present in the locus, but rather scattered in the genome, an attempt was made to construct a 2 kb size-restricted genomic library. Only 206 clones could be produced, of which a mere 8 coded for congopain-like proteases. The fact that 7 out of 8 of these clones belong to CP3 (thought to be inactive) suggested a cloning artefact, possibly related to the activity of the cloned proteases. Overall, all congopain genes appear very conserved in a given species, with 87-99% identity at protein level. The pre- and pro-region were the most conserved, while the catalytic domain was the most variable, especially around the active site cysteine, with frequent replacement by a serine residue, and in one instance by phenylalanine. The histidine residue of the catalytic triad was also substituted by either a serine or a tyrosine in some instances. The proenzyme cleavage site sequence was also variable, with APEA being the predominant N-terminal sequence. RT-PCR analyses indicated that CP1, CP2 and CP3 mRNA are all present in the bloodstream forms of T. congolense, showing that these variants are likely to be expressed. The conclusion of this study is that, given the high overall conservation of congopain genes in the genome, for the purpose of anti-disease vaccine, it is likely that a single immunogen will suffice to raise antibody able to inhibit all circulating congopain-like cysteine proteases. For chemotherapy however, a more in-depth enzymatic characterisation of the mutants, involving functional recombinant expression, will have to be undertaken. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.

No description available.

Introduction An atom or ion in a solid is associated with a given lattice site. Translational motion can however occur in solids and such diffusion processes can be studied by nuclear magnetic resonance, tracer diffusion and other methods. In ionic compounds the diffusion is also a mechanism for charge transport and hence there is an associated ionic conductivity. [continued in text ...] NOTE: The Abstract contains many indistinct letters in mathematical formulas and it is impracticable to reproduce it here.

A simple theory relating the dynamics of electrons to the long-range properties of the molecular ionic core is developed for asymmetric top molecules in general and water in particular. It is combined with the molecular version of multichannel quantum defect theory developed by Fano and Jungen and applied to the resonance-enhanced multiphoton ionization spectra of Child and Glab (M. S. Child and W. G. Glab, J. Chem. Phys., 2001, 112, 3754-3765), the mass-analysed threshold ionization spectra of Dickinson et al. (H. Dickinson, S. R. Mackenzie and T. P. Softley, Phys. Chem. Chem. Phys., 2000, 2, 4669-4675) and the as-yet unpublished work of Glab on the photoelectron branching ratios of the nd and nf Rydberg lines of the water molecule. The effect of resonances between electronic and rotational motion in Rydberg molecules is investigated using multichannel quantum defect theory with special reference to the time-resolved wave packet experiments of Smith et al. (R. A. L. Smith, J. R. R. Verlet, E. D. Boleat, V. G. Stavros and H. H. Fielding, Faraday Discuss., 2000, 115, 63-70).

The microwave spectrum of the open-shell van der Waals complex NO-HF has been recorded in the region 6-20GHz using a pulsed nozzle Fourier transform microwave spectrometer. This is the first observation of the microwave spectrum of a open-shell van der Waals complex between two molecules. The spectrum exhibits a rich hyperfine structure with the observation of intermolecular hyperfine interactions in an isolated system providing a sensitive probe of electron transfer in the complex. The spectrum consists of four fine structure transitions 5/2(e)-3/2(e), 3/2(e)-1/2(e), 5/2(f)-3/2(f), 3/2(f)-1/2(f) which have been fitted to a semi-rigid Hamiltonian developed to include the effects of the orbital and spin angular momenta of the unpaired electron on NO. A new treatment to account for the intermolecular hyperfine interaction was developed. The structure of the complex has been determined and is significantly bent with an angle of between 37 degrees and 49 degrees between the NO internuclear axis and the a-axis of the complex. The Renner-Teller parameter, epsilon 2, is very large and negative having the value of -10 449.32(4)GHz indicating that configuration with the unpaired electron in the plane of the complex is more stable. The analysis of the hyperfine interactions of the hydrogen and fluorine nuclei uses two constants for each nucleus, one for the spatial relationship between the magnetic moments of the unpaired electron and the nuclear magnetic moment and a Fermi-contact term. The Fermi-contact term for hydrogen is the first strong evidence of intermolecular charge transfer in an isolated van der Waals molecule.

The work presented in this thesis describes an investigation into the properties and behaviour of a new class of nonlinear optical organic chromophores. This study contributes to the optimisation of nonlinear optical molecules through an improved understanding of the relationships between the molecular nonlinear optical properties and the measured macroscopic quantities. A series of highly dipolar non-linear optical chromophores with absorption typically in the range of 350-500 nm have been synthesised by the reactions of amines with tetracyanoquinodimethane (TCNQ). One of the advantages of these materials is the large molecular figure of merit (μβ where μ is the molecular dipole moment and P is the second order polarisability), which theoretically allows large nonlinear optical coefficients to be obtained. The molecular dipole moments of these chromophores were determined both experimentally and theoretically, and were found to agree. The nonlinear optical properties of these compounds in solution were studied using an electric field induced second harmonic generation (EFISH) technique. The measurements of μβ at 1064 nm and 1907 nm in chloroform and acetone are presented. Moderate μβ values were obtained but β is found to be unexpectedly small in chloroform and shows unusual dispersion characteristics in this solvent compared to acetone. Further concentration investigations revealed features that suggest the presence of aggregates within solution. Optical spectroscopy measurements provide evidence of new species whose presence and conformation were found to be solvent-dependent. The results of this work highlight the need for an entire concentration range to be studied if accurate determination of molecular properties of highly dipolar molecules is required. Guest-host polymer films of these materials have been corona poled using a constant current corona triode. Detailed characterisation studies of the second order nonlinearities using second harmonic generation (SHG) were compared to a less dipolar molecule. These investigations showed that the highly dipolar TCNQ derivatives show severe aggregation within the polymer films. The magnitude of the SHG that can be obtained from such systems is therefore limited by this aggregation.

No description available.