Quantum chemistry is plagued by the presence of high-rank quantities, stemming from the N-body nature of the electronic Schrödinger equation. These high-rank quantities present a significant mathematical and computational barrier to the computation of chemical observables, and also drastically complicate the pedagogical understanding of important interactions between particles in a molecular system. The application of physically-motivated rank reduction approaches can help address these to problems. This thesis details recent efforts to apply rank reduction techniques in both of these arenas. With regards to computational tractability, the representation of the 1/r Coulomb repulsion between electrons is a critical stage in the solution of the electronic Schrödinger equation. Typically, this interaction is encapsulated via the order-4 electron repulsion integral (ERI) tensor, which is a major bottleneck in terms of generation, manipulation, and storage. Many rank reduction techniques for the ERI tensor have been proposed to ameliorate this bottleneck, most notably including the order-3 density fitting (DF) and pseudospectral (PS) representations. Here we detail a new and uniquely powerful factorization - tensor hypercontraction (THC). THC decomposes the ERI tensor as a product of five order-2 matrices (the first wholly order-2 compression proposed for the ERI) and offers great flexibility for low-scaling algorithms for the manipulations of the ERI tensor underlying electronic structure theory. THC is shown to be physically-motivated, markedly accurate, and uniquely efficient for some of the most difficult operations encountered in modern quantum chemistry. On the front of chemical understanding of electronic structure theory, we present our recent work in developing robust two-body partitions for ab initio computations of intermolecular interactions. Noncovalent interactions are the critical and delicate forces which govern such important processes as drug-protein docking, enzyme function, crystal packing, and zeolite adsorption. These forces arise as weak residual interactions leftover after the binding of electrons and nuclei into molecule, and, as such, are extremely difficult to accurately quantify or systematically understand. Symmetry-adapted perturbation theory (SAPT) provides an excellent approach to rigorously compute the interaction energy in terms of the physically-motivated components of electrostatics, exchange, induction, and dispersion. For small intermolecular dimers, this breakdown provides great insight into the nature of noncovalent interactions. However, SAPT abstracts away considerable details about the N-body interactions between particles on the two monomers which give rise to the interaction energy components. In the work presented herein, we step back slightly and extract an effective 2-body interaction for each of the N-body SAPT terms, rather than immediately tracing all the way down to the order-0 interaction energy. This effective order-2 representation of the order-N SAPT interaction allows for the robust assignment of interaction energy contributions to pairs of atoms or functional groups (the A-SAPT or F-SAPT partitions), allowing one to discuss the interaction in terms of atom- or functional-group-pairwise interactions. These A-SAPT and F-SAPT partitions can provide deep insight into the origins of complicated noncovalent interactions, e.g., by clearly shedding light on the long-contested question of the nature of the substituent effect in substituted sandwich benzene dimers.

The molecular theory of the second light-scattering virial coefficient Bp describing the effects of interacting pairs of molecules on the depolarization ratio p of Rayleigh-scattered light is reviewed, both for interacting linear and nonlinear molecules. The molecular tensor theory of Bp for nonlinear molecules is extended for the first time to include in the scattered intensity p those contributions arising from field gradient effects and induced quadrupole moments in the molecular interactions. The expressions for contributions to Bp are evaluated numerically for the nonlinear polar molecule dimethyl ether. We have used an existing light-scattering apparatus to investigate the pressure-dependence of the depolarization ratio p for dimethyl ether, allowing Bp to be extracted. The measured value is compared with the calculated value, theory and experiment being found to agree to within 9%. This success in modelling Bp for dimethyl ether spurred us on to extend our investigation to the second Kerr-effect virial coefficient BK • The molecular-tensor theory of BK for nonlinear molecules is reviewed, and is applied in this work to dimethyl ether. The calculated BK values generally lie within the uncertainty limits of the available measured data over their full range of temperatures. We have used a recently-commissioned Kerr cell to undertake our own measurement of BK for dimethyl ether at room temperature. This value is in good agreement with the findings of our molecular model, and is in reasonable agreement with the other measured data. This thesis serves to reaffirm recent claims that comprehensive dipole-induced-dipole theories of molecular interaction effects explain the observed phenomena adequately provided one works to higher orders in the molecular tensors so that the series of contributing terms has converged to a meaningful numerical result, and provided the full symmetry of the molecules is allowed for. / Thesis (M.Sc.) - University of Natal, Pietermaritzburg, 2000.

Van der Waals molecules are complexes of two or more atoms or molecules bound by weak intermolecular forces rather than a conventional chemical bond. This thesis contains a high resolution molecular beam study of the rotational spectra of two such species, ArNO and NeNO. A new hamiltonian is presented to account for the spectra of these open-shell complexes. The theory is similar to that already known for the uncomplexed diatom, nitric oxide, but is modified to an asymmetric top form appropriate for these non-linear species. Two novel interactions require inclusion. The first models a slight quenching of the NO orbital angular momentum by the rare gas atoms. The second is a large centrifugal distortion associated with the effects of the bending motion on the projection of the electronic angular momentum on the complex's a-inertial axis. A comparatively rich, though incomplete, spectrum is obtained for ArNO. Most of the transitions that originate from the lower rotational states are assigned and fitted to within a few MHz using the modified open-shell hamiltonian. Possible sources are suggested for the origins of the small residual errors between the observed and calculated transition frequencies. A vibrationally-averaged structure is derived from the fitted molecular parameters indicating an equilibrium geometry which is quite close to a T-shape. The hyperfine structure in the spectrum which is associated with the ¹⁴ N nucleus is well fitted by the hamiltonian; however, the magnetic hyperfine parameters are significantly perturbed from the values that best fit the lambda-doubling spectrum of the uncomplexed diatom. The implications of this with respect to the nature of the rare gas-nitric oxide intermolecular interaction are discussed. Greater experimental difficulties are encountered in trying to record the radiofrequency and microwave spectrum of NeNO and so fewer transitions have been measured than for ArNO. A partial analysis yields approximate values for the structural parameters. The complex exhibits a larger deviation from the T-shaped geometry than is observed for ArNO. The spectrum also provides an estimate of the magnitude of the quenching of the orbital angular momentum. The quenching interaction is somewhat larger in the neon complex.

Thesis (Ph. D.)--University of Washington, 1997. / Vita. Includes bibliographical references (leaves [193]-203).

Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2008. / Committee Chair: Gallivan, Martha A.; Committee Member: Hess, Dennis; Committee Member: Lee, Jay H.; Committee Member: Li, Mo; Committee Member: Ludovice, Pete.

The research conducted for this thesis has led to the development of an intramolecular gold-catalysed direct arylation protocol whereby tethered arenes and aryltrimethylsilanes are coupled (Scheme 1). In Chapter 1, the key synthetic and mechanistic studies that have ultimately led to the conception of this project are introduced. In Chapter 2, the substrate scope of intramolecular direct arylation is assessed. The reaction tolerates a wide range of substrates with tether lengths between one and five units (containing C, N and O) generating 5- to 9- membered rings. Substrates that lead to 5-membered rings (1 → 2) can tolerate a broad electronic range of substituents and proceed under the mildest reaction conditions (≤ 1 mol% catalyst, room temperature) and with excellent yields. A smaller collection of examples is demonstrated for the cyclisation to 6- and 7- membered rings (3 → 4, 5 → 6), but no heating is required and good yields are maintained throughout the series. The synthetically challenging synthesis of 8- and 9- membered rings (7 → 8, 9 → 10) is successful, albeit with slightly more forcing conditions (4 mol%, up to 50 °C). The methodology was subsequently applied in the successful 10-step synthesis of natural product allocolchicine 11. In Chapter 3, the operative reaction mechanism is elucidated. Reaction monitoring techniques allowed for the detailed study of linear free energy relationships (LFERs) and kinetic isotope effects (KIEs), which in turn allowed for deduction of the reaction turnover-limiting step (TLS) and thus the first quantitative experimental data on the effects of aryl electron demand and conformational freedom on the rate of reductive elimination from diarylgold(III) species. The mechanistic investigation led to the observation of complex kinetic profiles for specific substrates. The origin of these unusual effects is the focus of Chapter 4. By combining experiment with kinetic simulation, an off-cycle catalyst inhibition pathway was identified and the understanding of this process allowed for a re-optimisation of reaction conditions. In Chapter 5, the general kinetic parameters that could govern any domino reaction combining inter- and intramolecular direct arylation are deduced through kinetic analysis and simulation of hypothetical systems. The results of the kinetic analysis were proved experimentally through the successful combination of intra- and intermolecular gold-catalysed direct arylation. The products of intramolecular cyclisation 2, generated in-situ, are demonstrated to couple with intermolecular aryltrimethylsilanes 12, resulting in a rapid increase in molecular complexity from simple substrates in one pot.

Nonheme iron(II) oxygenases within a common 2-His-1-carboxylate binding motif catalyze a wide range of oxidation reactions involved in biological functions like DNA repair and secondary metabolic processes. The mechanism of O2 activation catalyzed by this enzyme family has been examined by spectroscopic, crystallographic, and computational studies, where it is clear the iron(II) center works with substrate, and cosubstrate to activate O2 by forming a highly oxidizing iron species (iron(IV)-oxo). From a thermodynamic perspective, substrate and/or co-substrate binding organizes the active site for O2 activation, and understanding the interactions among metal, substrate, cosubstrate, and enzyme provides insight into the intramolecular contacts that guide the reaction catalyzed by the enzymes. This dissertation is focused on elucidating the interactions between metal, substrate, and co-substrate in a representative enzyme subfamily of nonheme iron(II) oxygenases, namely the 2-oxoglutarate dependent dioxygenases. Specifically, we investigated the thermodynamic properties of divalent metal ions binding to taurine-dependent dioxygenase (TauD), using Mn2+, Fe2+, and Co2+ ions. Additionally, the thermodynamics associated with substrate and co-substrate binding to Fe·TauD and iron(II)-ethylene forming enzyme (Fe·EFE) were explored using calorimetry and other biophysical techniques.

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Submitted by Edileide Reis (leyde-landy@hotmail.com) on 2013-04-23T14:35:12Z No. of bitstreams: 1 Yuji Watanabe.pdf: 3696013 bytes, checksum: 64d732d452c08c675e78db3f991bf851 (MD5) / Made available in DSpace on 2013-04-23T14:35:12Z (GMT). No. of bitstreams: 1 Yuji Watanabe.pdf: 3696013 bytes, checksum: 64d732d452c08c675e78db3f991bf851 (MD5) Previous issue date: 2002 / Este trabalho é constituído de três etapas, a saber: · planejamento e construção de um aparato experimental para medidas de fluorescência total (LIF) e depolarização fluorescente (PLF) em sistema de injeção em fluxo (FI); testes operacionais visando otimizar parâmetros experimentais; avaliação fotoquímica/fotofísica da cinética e dinâmica molecular duma reação química em FI. O aparato experimental automatizado é constituído de um sistema de detecção de fluorescência, um sistema FI e um sistema ótico. Permite a aquisição com alta resolução espacial (20mm) de perfis de distribuição de concentração (LIF) e de orientação molecular vertical e horizontal (PLF) em função do tempo de transporte do fluxo. Os perfis interpolados em mapas bidimensionais fornecem informações sobre a cinética e a dinâmica molecular dos processos de dispersão axial e radial de amostras em fluxo carregador. Foram medidas tensões interfaciais estáticas, pelo método do ângulo de contato, para escolher a constituição química do percurso analítico e minimizar a sua influência na cinética e na dinâmica molecular de dispersão. Foi determinada a influência da aceleração gravitacional e do número de injeções por período de amostragem, dentre outros parâmetros usuais, no processo de dispersão.Observou-se a existência de padrões de dispersão diferenciados para a Rodamina B (RB) a depender da sua orientação espacial. Isto foi atribuído ao grupo benzóico perpendicular ao grupo xantênico e comprovado pela utilização da Rodamina 6G (R6G) sob as mesmas condições. A contribuição da cinética e da dinâmica moleculares de dispersão no rendimento de uma reaçãoquímica em fluxo foi avaliado com adição de Ca(II), um agente supressor da fluorescência da RB. / Salvador

The thesis entitled “Exploring Intermolecular Space by Charge Density Analysis in Molecular Crystals” consists of five chapters. A short introductory note highlights the importance of intermolecular interactions and presents the current status of charge density analysis to obtain insights into such interactions. Charge density analysis of crystalline materials by using high resolution X-ray diffraction data has become routine and enables derivation of reliable one electron properties associated with the electron density. The results obtained from single crystal X-ray diffraction data at low temperature have been compared with periodic theoretical calculations using B3LYP/6-31G** methods to unequivocally establish the nature of weak interactions. Chapter 1 describes the quantitative analysis of Cl∙∙∙Cl intermolecular interactions in compounds 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine and 2-chloro-3-chloromethyl-8-methylquinoline, which are corresponding to type I (trans and cis) and type II (L) geometries of Cl∙∙∙Cl interactions respectively. The 3D static deformation density plots from charge density analysis unequivocally suggest that both ‘cis’ and ‘trans’ type I geometries show decreased repulsion whereas type II geometry is attractive based on the nature of “polar flattening” of the electron density around the Cl atom. The topological features derived at bond critical point (BCP) of Cl∙∙∙Cl interactions also support the observed results. Chapter 2 discusses hetero-halogen (Cl∙∙∙F) and homo-halogen (F∙∙∙F) intermolecular interactions involving “organic fluorine” in compounds 2-chloro-4-fluorobenzoic acid and 4-flurobenzamide respectively. Charge density distributions show polar flattening effects at both atoms Cl and F, however the extent of polarization is small on F in comparison with that of the Cl atom. 3D static deformation density plots depict δ+ ∙∙∙δ− interactions for Cl∙∙∙F intermolecular interactions while F∙∙∙F interactions show small decreased repulsion features. The topological properties of F∙∙∙F interactions bring out the similarity between F∙∙∙F and Cl∙∙∙Cl interactions. Chapter 3 describes the nature of C−Cl∙∙∙O=C halogen bond in 2, 5-dichloro-1, 4-benzoquinone, a molecule specifically chosen to depict this interaction dominantly. The topological values at bond critical point, three dimensional static deformation density features and electrostatic potential isosurfaces unequivocally establish the attractive nature of C−Cl∙∙∙O=C halogen bond in the crystalline lattice. Chapter 4 discusses the generation of multi-component systems (for example cocrystals and salts) of active pharmaceutical ingredients (API). Two systems associated with nicotinamide, one with salicylic acid and the other with oxalic acid as coformers resulting in 1:1 molecular complexes have been analyzed. The charge density analysis, particularly at the proton transfer region clearly bring out the differences between cocrystal and salt thus providing insights into the continuum in the proton transfer pathways in molecular crystals. Chapter 5 describes a new methodology [supramolecular synthon based fragment approach (SBFA)] concerning transferability of experimental charge density multipole parameters and building a database using well defined supramolecular synthons. The modularity and robustness of supramolecular synthons are used to transfer experimental charge density multipole parameters of synthons derived from a high resolution X-ray diffraction study to target molecules possessing these synthons as fragments in the crystalline lattice. The synthesized charge density and derived topological properties on target molecules using routine single crystal diffraction data are comparable with both experimental and theoretical charge density results. SBFA thus is expected to provide an additional database which can be applied to include intermolecular interactions space in the modeling directly unlike the available ones such as ELMAM, INVARIOM and UBDB. Further, SBFA approach can be extended to the determination and synthesis of charge density properties in macromolecules such as polypeptides, nucleic acids and proteins. APPENDIX contains reprints of the articles published which comprises of the work carried out in addition to the above five chapters.