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<p>The X-ray absorption spectrum of silicon in of SiCl4 has been calculated for the LIII and LII edges. The resulting spectrum has been vibrationally resolved by considering the symmetric stretch vibrational mode and the results has been compared to experiment [4]. One peak from the experiment was found to be missing in the calculated vibrationally resolved spectrum. The other calculated peaks could be matched to the corresponding experimental peaks although significant basis set effects are present. An investigation of one peak beyond the Franck–Condon principle shows it to be a good approximation in the case of the studied system.</p>

Thesis (Ph. D.)--Institute of Paper Chemistry, 1976. / Includes bibliographical references (p. 138-139).

The electrostatic field created by the inward pointing dipole moments of an oriented membrane leaflet has never been measured directly, but is thought to have an important influence on membrane function. Here we present the first direct measurement of the membrane dipole field in lipid bicelles using vibrational Stark effect spectroscopy which is based on the sensitivity of a nitrile oscillator’s vibrational frequency to its local electrostatic environment. The nitrile probe was introduced as the artificial amino acid p-cyanophenylalanine (CN-Phe) in four different locations of a α-helical peptide composed of alternating alanine and leucine residues. This peptide was intercalated into bicelles composed of mixtures of the long chain lipids 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and the short chain lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) formed in two different sizes, 5 nm and 15 nm in radius. Formation of the bicelle above the phase transition temperature of the lipid mixture was confirmed by ³¹P NMR, and the structure of the [alpha]-helix within the bicelle was confirmed by circular dichroic spectroscopy. The absorption energy of the nitrile probe at 4 positions along the helical axis was measured by Fourier transform infrared spectroscopy, from which we estimate the magnitude of the membrane dipole electrostatic field to be -6 MV/cm. Then we successfully manipulated the dipole field in q = 0.5 DMPC/DHPC bicelles by incorporating the small molecule phloretin into the membrane and measured the corresponding ratiometric fluorescence signal of the co-intercalated voltage gated dye di-8-ANEPPS. We measured 0.7 ± 0.2 cm⁻¹ blue shift in absorption energy of the nitrile probe due to the decrease in dipole field caused by phloretin, corresponding to a dipole field of -4.2 MV/cm. This change was essentially identical to what has been estimated through ratiometric fluorescence methods, indicating that VSE spectroscopy will be useful tool for measurement of the biological effects of electrostatic fields in lipid membranes. / text

Noncovalent factors, such as shape complementarity and electrostatic driving forces, almost exclusively cause the affinity and specificity for which two or more biological macromolecules organize into a functioning complex. The human oncoprotein p21Ras (Ras) and a structurally identical but functionally distant analog, Rap1A (Rap), exhibit high selectivity and specificity when binding to downstream effector proteins that cannot be explained through structural analysis alone. Both Ras and Rap bind to Ral guanine nucleotide dissociation stimulator (RalGDS) with affinities that differ tenfold instigating diverse cellular functions; it is hypothesized that this specificity of RalGDS to discriminate between GTPases is largely electrostatic in nature. To investigate this hypothesis, electrostatic fields at the binding interface between mutants of RalGDS bound to Rap or Ras are measured using vibrational Stark effect (VSE) spectroscopy, in which spectral shifts of a probe oscillator’s energy is related directly to that probe’s local electrostatic environment and measured by Fourier transform infrared spectroscopy (FTIR). After calibration, the probe is inserted into a known position in RalGDS where it becomes a highly local, sensitive, and directional reporter of fluctuations of the protein’s electrostatic field caused by structural or chemical perturbations of the protein. The thiocyanate (SCN) vibrational spectroscopic probe was systematically incorporated throughout the binding interface of RalGDS. Changes in the absorption energy of the thiocyanate probe upon binding were directly related to the change of the strength of the local electrostatic field in the immediate vicinity of the probe, thereby creating a comprehensive library of the binding interactions between Ras-RalGDS and Rap-RalGDS. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations with the results highlighting the complex structural and electrostatic nature of protein-water interface. Additional SASA studies of the nine RalGDS mutants that bind to Ras or Rap verified that experimentally measured thiocyanate absorption energies are negatively correlated with exposure to water at the protein-water interface. By changing the solvent composition, we confirmed that the cyanocysteine residues that are more exposed to solvent experienced a large difference in absorption energy. These studies reinforce the hypothesis that differences in the electrostatic environment at the binding interfaces of Ras and Rap are responsible for discriminating binding partners. / text

The functional aspects of proteins are largely dictated by highly selective protein- protein and protein-ligand interactions, even in situations of high structural homology, where electrostatic factors are the major contributors to selectivity. The vibrational Stark effect (VSE) allows us to measure electrostatic fields in complex environments, such as proteins, by the introduction of a vibrational chromophore whose vibrational absorption energy is linearly sensitive to changes in the local electrostatic field. The works presented here seek to computationally quantify electrostatic fields measured via VSE, with the eventual goal of being able to quantitatively predict electrostatic fields, and therefore Stark shifts, for any given protein-interaction. This is done using extensive molecular dynamics in the Amber03 and AMOEBA force fields to generate large ensembles the GTPase Rap1a docked to RalGDS and [superscript p]²¹Ras docked to RalGDS. We discuss how side chain orientations contribute to the differential binding of different mutations of Rap1a binding to RalGDS, where it was found that a hydrogen-bonding pocket is disrupted by the mutation of position 31 from lysine to glutamic acid. We then show that multi-dimensional umbrella sampling of the probe orientations yields a wider range of accessible structures, increasing the quality of the ensembles generated. A large variety of methods for calculating electrostatic fields are presented, with Poisson- Boltzmann electrostatics yielding the most consistent, reliable results. Finally, we explore using AMOEBA for both ensemble-generation as well as the electrostatic description of atoms for field calculations, where early results suggest that the electrostatic field due to the induce dipole moment of the probe is responsible for predicting qualitatively correct Stark shifts.

The weakly bound association products of atmospherically relevant radical species (O₂, OH, NO₂, HO₂ and NO) have been studied theoretically using quantum-chemical methods. The thermodynamic stabilities, which are crucial to determining the probability of formation in Earth's atmosphere, were calculated for the hydrotrioxy radical (HOOO) and peroxynitrous acid (HOONO, an isomer of nitric acid) relative to the radical dissociation products. In the case of HOONO, the experimentally determined values were confirmed. For HOOO, the predicted stability was significantly lower than the experimentally determined value; a conclusion that was supported by later experimental work and indicates that HOOO will not form in significant quantities in Earth's atmosphere. The fundamental and multi-quantum vibrational transitions were also predicted for both the HOONO and HOOO systems. The theoretical work on the HOONO system aided the assignment of experimental spectra and was used to correct equilibrium rotational constants. The HOOO system presented a challenge for the methods used here and work to apply other approaches in describing the vibrational modes is ongoing. Second-order vibrational perturbation theory, combined with a correlated quantum-chemical method and a moderately sized basis set, provides a method for accurately predicting fundamental and low-order multi-quantum transition energies and intensities for many systems (HOOO being an exception). Here coupled cluster theory, at a level which treats one- and two-electron correlation with a correction for three-electron correlation, and atomic natural orbitals basis sets were used in the vibrational calculations. To predict the dissociation energies of weakly bound species with the precision required (due to the small energy differences involved), high-order correlation contributions (a full treatment of three-electron correlation and a correction for four-electron correlation) are included, as is extrapolation to the basis set limit. Other contributions, such as that for the zero-point energy, were also considered. For the HOOO system, one-dimensional potential curves along the dissociation and torsional coordinates were constructed with standard single-reference and equation-of-motion coupled-cluster methods. The latter is better able to describe the nature of a system in the bond-breaking region and the complex electronic structure of a species formed from two radical fragments, one doubly degenerate in the ground state: X²[Pi] OH and X³[Sigma] O₂. A possible barrier to dissociation and the torsional potential for HOOO were investigated. / text

The thermo-chemical relaxation of nitrogen hypersonic flows behind strong shocks and in nozzle expansions is investigated with 1D flow simulations and detailed vibrational kinetics. This work aims at deriving from detailed vibrational models accurate reduced models easy to implement in multidimensional reentry flow codes. First, nonequilibrium couplings between vibrational excitation, dissociation and recombination reactions are considered. Vibrational kinetics is described using accurate vibrational state-to-state rate constant databases of the literature completed with the forced harmonic oscillator model. The key role of multiquanta vibration-translation processes on the relaxation of the vibrational distribution function and the dissociation/recombination processes is put forward behind shocks and in nozzles. The vibrational distributions, which deviate strongly from equilibrium for nozzle expansions, are driven by vibration-translation processes and dissociation/recombination processes. A macroscopic model using groups of vibrational levels is developed to derive consistently the chemical and vibrational energy source terms from the vibrational state-to-state database.This model successfully reproduces the thermal, chemical and vibrational distribution function dynamics predicted by the state-to-state model with one group of levels behind a shock wave, and with three groups of levels in nozzle expansions. In a second step, the detailed vibrational model is extended to ionized nitrogen flows, including in particular a detailed modeling of the resonant electronvibration processes. Behind shocks, these processes control the rate of ionization by feeding energy to the electrons, up until the time when the elastic electron-ion exchanges takes over. It is shown that the widely used assumption of equilibrium between the electron and vibration temperatures predicts a too fast relaxation behind shock waves. In nozzle expansions, it is shown that for low electron concentration, the electron temperature is driven by electronvibration processes. Moreover, it is found that electrons are strongly coupled to low vibrational levels, and that more levels are coupled when the electron temperature increases. Coupling of the flow field with radiation is performed using the tangent slab approximation, and it is shown that the population of a metastable and two higher electronic levels are strongly impacted. Finally, the macroscopic model is extended to ionized nitrogen flows and is successfully applied on shock waves with one group of levels and with three groups of levels in nozzle expansions. In particular, the proposed macroscopic model represents more accurately the electron-vibration coupling than the widely used Landau-Teller model.

A new intermolecular potential energy surface, rovibrational transition frequencies, and line strengths are computed for OCS-OCS and CO2-CS2. The potentials were made by fitting energies obtained from explicitly correlated coupled-cluster calculations and fit using an interpolating moving least squares method. Rovibrational transition frequencies are also calculated for four isotopologues of the N2O dimer using a previously presented potential energy surface. The rovibrational Schroedinger equation for all three dimers is solved with a symmetry-adapted Lanczos algorithm and an uncoupled product basis set. All four intermolecular coordinates are included in the calculation. On the OCS-OCS potential energy surface, a previously unknown, cross-shaped isomer is found along with polar and non-polar isomers. For CO2-CS2, the previously found cross-shaped minima is found along with a slipped-parallel configuration. The associated wavefunctions and energy levels for each of these isomers is presented. To identify states that have a permanent dipole, both calculations of line strengths and vibrational parent analysis is used. For non polar states of, OCS-OCS, and N2O-N2O isotopologues, and all CO2-CO2 states, only vibrational parent analysis was used. Calculated rotational constants differ from their experimental counterparts by less than 0.001 wavenumbers for OCS-OCS and CO2-CS2, and less than 0.002 wavenumbers for any N2O-N2O isotopologue. / Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2012-08-23 13:19:45.294

The potential of filling carbon nanotubes in polymers has been widely acknowledged for composites with exceptional new properties owing to the high strength of carbon nanotubes. In the thesis, by employing Materials Studio 4.0 software, the buckling behaviour and vibration of polyethylene and carbon nanotube matrix composites are first discussed using molecular mechanics simulations. The research is aimed to acquire a high strength design of PE-CNT matrix with proper PE/CNT ratio as well as discovering the dynamic characteristics of the PE-CNT composites. Investigation results show that as the number of PE chains increases, the buckling strain and the resonance frequency will decrease. Van der Waals forces are collected to explain the relation of the PE chains to the buckling strain and the resonance frequency of the composites.