Thesis (M.S.)--University of Hawaii at Manoa, 2006. / Includes bibliographical references. / xi, 133 leaves, bound ill. 29 cm

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 219-226).

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One of the most promising methods for surmounting the high-degree polynomial scaling wall associated with electron correlating wave function methods is the local correlation technique of Pulay and Saebø. They have proposed using a set of localized occupied and virtual orbitals free of the canonical constraint commonly employed in quantum chemistry, resulting in a method that scales linearly (in the asymptotic limit) with molecular size. Pulay and Saeb$oslash; first applied their methods to configuration interaction and later to M$oslash;ller-Plesset perturbation theory. Werner et al. have have extended the local correlation scheme of Pulay and Saeb$oslash; to coupled-cluster theory. One of the pitfalls of the local correlation methods developed by Pulay and Saeb$oslash; is the dependence of domain selection on the molecular geometry. In other words, as the geometry changes the domain structure of the local correlation calculation can change also, leading to discontinuities in the potential energy surface. We have examined the size of these discontinuities for the homolytic bond cleavage of fluoromethane and the heterolytic bond dissociation of singlet ketene and propadienone. Properties such as polarizabilities and optical rotation are realized through linear response theory, where the Hamiltonian is subject to an external perturbation and the wave function is allowed to respond to the applied perturbation. Within the context of local correlation it is necessary to understand how the domain structure alters in response to an applied perturbation. We have proposed using solutions to the CPHF equations (coupled-perturbed Hartree-Fock) in order to predict the correlation response to an applied perturbation. We have applied this technique to the calculation of polarizabilities, with very favorable results, and also to optical rotation, with mixed results. / Ph. D.

Coupled cluster (CC) and density functional theory (DFT) are highly regarded as robust quantum chemical methods for accurately predicting a wide variety of properties, such as molecular structures, thermochemical data, vibrational spectra, etc., but there has been little focus on the theoretical prediction of optical rotation. This property, also referred to as circular birefringence, is inherent to all chiral molecules and occurs because such samples exhibit different refractive indices for left- and right- circularly polarized light. This thesis focuses on the theoretical prediction of this chiroptic property using CC and DFT quantum chemical models. Several small chiral systems have been studied, including (S)-methyloxirane, (R)-epichlorohydrin, (R)-methylthiirane, and the conformationally flexible molecules, (R)-3-chloro-1-butene and (R)-2-chlorobutane. All predicted results have been compared to recently published gas-phase cavity ringdown polarimetry data. When applicable, well-converged Gibbs free energy differences among confomers were determined using complete-basis-set extrapolations of CC energies in order to obtain Boltzmann-averaged specific rotations. The overall results indicate that the theoretical rotation is highly dependent on the choice of optimized geometry and basis set (diffuse functions are shown to be extremely important), and that there is a large difference between the CC and DFT predicted values, with DFT usually predicting magnitudes that are larger than those of coupled cluster theory. / Ph. D.

Accurate theoretical predictions of optical rotation are of substantial utility to the chemical community enabling the determination of absolute configuration without the need for poten- tially lengthy total synthesis. The requirements for robust calculation of gas-phase optical rotation are well understood, but too expensive for routine use. In an effort to reduce this cost we have examined the performance of the LPol and ORP basis sets, created for use in density functional theory calculations of optical rotation, finding that at the coupled cluster level of theory they perform the same or better than comparably sized general basis sets that are often used. We have also examined the performance of a perturbational approach to inclusion of explicit solvent molecules in an effort to extend the calculation of response properties from the gas phase to the condensed phase. This N-body approach performs admirably for interaction energies and even dipole moments but breaks down for optical rotation, exhibiting large basis set superposition errors and requiring higher-order terms in the expansion to provide reasonable accuracy. In addition, we have begun the process of implementing a gauge invariant version of coupled cluster response properties to address the fundamentally unphysical lack of gauge invariance in coupled cluster optical rotations. Correcting this problem, which arises from the non- variational nature of the coupled cluster wavefunction, involves reformulating the response amplitude and function expressions and solving for all necessary amplitudes simultaneously. / Ph. D.

Gyromagnetic Faraday rotation offers a new method to probe limits on properties of simple spin systems such as the possible magnetic moment of asymmetric dark matter or as a polarization monitor for polarized targets. Theoretical calculations predict the expected rotations of linearly polarized light due to the magnetization of spin-1/2 particles are close to or beyond the limit of what can currently be measured experimentally (10−9 rad). So far, this effect has not been verified. Nuclear spin polarized 3He provides an ideal test system due to its simple structure and ability to achieve high nuclear spin polarization via spin-exchange optical pumping (SEOP). To maximize the expected signal from 3He, a SEOP system is built with a modern narrowband pumping laser and a 3He target designed to use with a multipass cavity. Additionally, a sensitive triple modulation apparatus for polarimetry is utilized and further developed to detect Faraday rotations on the order of nanoradians. This works presents the results of the measurement of the magnetic Faraday effect.

The thermal denaturation of proteins has been extensively studied using several methods including differential scanning calorimetry (DSC). A custom-built optical system was used to study thermal effects on protein as an alternative method to DSC measurements. It was used to investigate the thermal stability of bovine serum albumin (BSA) with a focus on comparisons with published DSC data. In the first study, the effect of protein concentration on the thermal denaturation (Td) of BSA was determined and validated using published DSC data for bovine serum albumin (BSA). The optical rotation (OR) and transmitted light (TL) signals indicating protein conformational changes and gel formation, respectively, were collected during the heating of BSA solutions at ~6��C/min from room temperature to ~85��C. The experiments were performed on 1, 2.5 and 5% (w/v) BSA in 0.01 M phosphate buffer at pH 7 and ionic strength (IS) 0.08. BSA���s Td values obtained from this investigation were consistent with published values and had low experimental variability (CV<2.5%). In agreement with some but not all published data, increasing BSA concentration did not affect its thermal stability. Protein gel formation, however, increased with protein concentration. In the second study, changes in the OR and TL signal of BSA in 0.01 M phosphate buffer at pH 6.1, 7 and 7.9 with IS maintained at 0.04, 0.08 and 0.16 were recorded during the heating of BSA solutions at ~6��C/min from room temperature to ~85��C. BSA showed a maximum and minimum thermostability at pH 7 and 7.9, respectively, consistent with published values determined by DSC. BSA formed opaque gel at pH 6.1 approaching the BSA���s pI values. Increasing IS level did not have a significant effect on BSA���s Td value but promoted gel formation. In the third study, the optical method was applied to investigate the heat stability of BSA as affected by low concentrations of sucrose, trehalose or sorbitol. BSA solutions (2.5% w/v) in the presence of 0 5% sucrose, trehalose and sorbitol were heated at ~6��C/min from ambient temperature to ~85��C. In contrast with published work on the thermal stability of BSA in the presence of higher sugar concentrations, this study showed that increasing sugar concentration did not enhance the thermal stability of this protein. Also, the ability to promote protein stability among sucrose, trehalose and sorbitol were not significantly different. The significance of these studies is that they demonstrate that the custom-built optical methods here developed can be used to study heat-induced protein denaturation and the effect of environmental conditions. Future studies will examine other proteins such as ��-lactoglobulin or ��-lacactalbumin. A further advantage of optical systems is their ability to conduct real-time measurements which could be used for food processing control. / Graduation date: 2007

Abstract In this thesis nuclear magnetic resonance (NMR) and magneto-optical rotation (MOR) parameters are investigated for water, paying special attention to the effect of solvation from gaseous to liquid phase. Nuclear magnetic shielding and quadrupole coupling tensors of NMR spectroscopy are studied for gaseous and liquid water. Liquid state is modelled by a 32-molecule Car-Parrinello molecular dynamics simulation, followed by property calculations for the central molecules in clusters cut out from the simulation trajectory. Gaseous state is similarly represented by a one-molecule simulation. Gas-to-liquid shifts for shielding constants obtained this way are in good agreement with experiments. To get insight into the local environment and its effect on the properties the clusters are divided into groups of distinct local features, namely the number of hydrogen bonds. The analysis shows in detail how the NMR tensors evolve as the environment changes gradually from the gas to liquid upon increasing the number of hydrogen bonds to the molecule of interest. The study sheds light on the usefulness of NMR experiments in investigating the local coordination of liquid water. To go a bit further, the above mentioned NMR parameters along with the spin-spin coupling constant are examined for water dimer in various geometries to have insight into solvation and hydrogen bonding phenomena from bottom to top. Characteristic changes in the properties are monitored as the geometry of the dimer is systematically varied from very close encounter of the monomers to distances and orientations where hydrogen bonding between monomers ceases to exist. No rapid changes during the hydrogen bond breaking are observed indicating that the hydrogen bonding is a continuous phenomenon rather than an on-off situation. However, for analysis purposes we provide an NMR-based hydrogen bond definition, expressed geometrically, based on the behaviour of the NMR properties as a function of dimer geometry. Our definition closely resembles widely used definitions and thus reinforces their validity. Magneto-optical rotation parameters, the nuclear spin optical rotation (NSOR) and the Verdet constant, are computed for gaseous and liquid water, in the same manner as the NMR properties above. Recent pioneering experiments including NSOR for hydrogen nuclei in liquid water and liquid xenon have demonstrated that this technique has a potential to be a useful new probe of molecular structure. We reproduce computationally, applying a first-principles theory developed recently in the group, the experimental NSOR for hydrogen nuclei in liquid water, and predict hydrogen NSOR in gaseous water along with the oxygen NSOR in liquid and gaseous water. NSOR is an emerging experimental technique that needs interplay between theory and computation for validation, steering and insight.

In quantum chemistry, scientists aim to solve the time-independent Schrödinger equation by employing a variety of approximation techniques whose accuracy are typically inversely proportional to their computational cost. This problem is amplified when it comes to chiral molecules, whose stereochemical assignments and associated chiroptical properties can be incredibly sensitive to small changes in their three-dimensional structure, requiring highly accurate theoretical methods. On the other hand, due to the polynomial scaling with system size, it is sometimes impractical to apply such methods to chemical compounds of broad scientific interest, especially when a multitude of low-energy conformations have to be accounted for as well. As a result, the assignment of absolute configurations to chiral compounds remains a tedious task. However, the characterization of these compounds is something that many different scientists are significantly invested in. The ultimate goal, then, is twofold: to gain useful insight by utilizing the electronic structure methods at your disposal while simultaneously developing new approximation techniques that can be used to push the boundaries on what is currently capable in computational chemistry. Therefore, we start by applying widely accepted density functional theory methods to predict optical rotations and electronic circular dichroism for naturally occurring antiplasmodial and anticancer drug candidates. We find that by comparing the computational results directly with those obtained through experimental measurement, we can provide reliable absolute config- uraitonal assignments to a variety of chiral compounds with numerous stereogenic centers. We also present the first ever prediction of vibrational circular dichroism with second-order Møller-Plesset perturbation theory. This extension opens the door to systematically improvable correlated wave function methods that can be employed when density functional theory fails or when higher accuracy results are required. / Doctor of Philosophy / Theoretical chemistry aims to draw a line from a molecule's three-dimensional structure to a set of physical observables, allowing for the efficient prediction of such properties. One family of chemical compounds for which this task becomes increasingly difficult is known as chiral molecules. A chiral compound is defined as one that has a non-superimposable mirror image. The concept of chirality is most tangibly seen with a pair of human hands, which demonstrate this same mirror-like behavior. In the same way that a person has left and right hands, a three-dimensonal handedness can be used to characterize many compounds that are essential to life including enzymes, sugars, and proteins. Although procedures have been developed to consistently isolate pure samples of such compounds, the correct identification of each hand poses a much larger task and costs the global pharmaceutical industry tens to hundreds of millions of dollars every year. As such, gaining insight about these incredibly valuable compounds and their associated properties is a never ending goal for many scientists. One such way to gain insight is through the direct comparison of experimental and calculated properties, namely chiroptical properties. These unique properties define how chiral compounds interact with light. While experimental scientists are limited in the degree to which they can probe a molecule's structure, theoretical chemists have the advantage of knowing the exact three-dimensional structure for the compound they are studying. On the other hand, theoretical chemists rely on comparison to experimental results to develop new methods or apply the available techniques to predict molecular properties. This work begins by attempting to match calculated properties to experimentally measured ones in order to confirm the detailed molecular structure of natural product drug candidates. Through multiple such computational studies, it is shown that the current methods are sometimes limited in the knowledge that they can provide. As a result, it is absolutely necessary to continue to improve on the existing methods. We go on to provide a first-of-its-kind implementation that allows for theoretical chemists to compare their results to experiment in a way that was not previously possible.