High resolution nuclear magnetic resonance studies of biologically significant molecules

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Nightmare from which you will never awake: Electronic to vibrational spectra

This dissertation is comprised of seven chapters: Chapter 1 provides the theoretical background of ab initio methods and density functional theory, which are relevant to the computational methodologies presented in the following chapters. Chapter 2 examines the anharmonicity associated with weakly bound metal cation dihydrogen complexes using the vibrational self-consistent field (VSCF) method and characterizes the interaction between a hydrogen molecule and a metal cation. Chapter 3 illustrates a study of molecular hydrogen clustering around the lithium cation and their accompanied vibrational anharmonicity employing VSCF. Chapter 4 provides a qualitative interpretation of solvent-induced shifts of amides and simulated electronic absorption spectra using the combined time-dependent density functional theory/effective fragment potential method (TDDFT/EFP). Chapter 5 elucidates an excited-state solvent assisted quadruple hydrogen atom transfer reaction of a coumarin derivative using micro solvated quantum mechanical (QM) water and macro solvated EFP water. Chapter 6 presents a dispersion correction to the QM-EFP1 interaction energy. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 7

Ambident properties of phosphoramidates and sulphonamides

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POLYCYCLIC POLYAMINES: SYNTHESIS AND CONFORMATIONAL ANALYSIS

The synthesis, conformational analysis, and reactivity of a homologous series of tricyclic orthoamides is discussed. The tricyclic orthoformamides, orthoacetamides, orthopropionamides, and orthobenzamides were synthesized by the uncatalyzed condensation of macrocyclic triamines with amide acetals. The conformations were studied spectrally (IR, (\u271)H NMR, (\u2713)C NMR, DNMR) and by the application of empirical force field calculations (MM2). In most (but not all) cases the minimized conformations as generated by MM2 were found to be in agreement with the experimentally determined conformations. The alkylation, acylation, and hydrolysis of these compounds is also discussed. Efforts towards the synthesis of the spherically shaped host molecule 1,5,9,13,-tetraazatricyclo{7.7.3.3(\u275,13)}-docosane are described. A classical acylation-reduction sequence was employed in this synthesis. Cyclizations were carried out under high dilution conditions. The design and construction of a new high dilution apparatus is described. High yields of monomeric cyclic intermediates were obtained. Monomeric cyclic intermediates were purified by preparative gel permeation chromatography (GPC). The modification of a Waters 200 analytical GPC unit are described as are the column packing procedures for preparative GPC columns

Extension of the B3LYP - Dispersion-Correcting Potential Approach to the Accurate Treatment of both Inter- and Intramolecular Interactions

We recently showed that dispersion-correcting potentials (DCPs), atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys. Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the application of B3LYP-DCP for the {\beta}-scission of the cumyloxyl radical led a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We show in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C-C covalent-bonding region. In this work, we present a new C-DCP with a form that was expected to influence the electron density farther from the nucleus. Tests of the new C-DCP, with previously published H-, N- and O-DCPs, with B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular interactions, giving mean absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively. Additional testing on the S12L database of complexation systems gave an MAE of 2.6 kcal/mol, showing that the B3LYP-DCP/6-31+G(2d,2p) approach is one of the best-performing and feasible methods for treating large systems dominated by non-covalent interactions. Finally, we showed that C-C making/breaking chemistry is well-predicted using the newly developed DCPs. In addition to predicting a barrier height for the {\beta}-scission of the cumyloxyl radical that is within 1.7 kcal/mol of the high-level value, application of B3LYP-DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights and energies, isomerization energies and relative conformation energies gives performance that is amongst the best of all available dispersion-corrected density-functional theory approaches

Distributed Multipoles from a Robust Basis-Space Implementation of the Iterated Stockholder Atoms Procedure

The recently developed iterated stockholder atoms (ISA) approach of Lillestolen and Wheatley (<i>Chem. Commun.</i> <b>2008</b>, 5909) offers a powerful method for defining atoms in a molecule. However, the real-space algorithm is known to converge very slowly, if at all. Here, we present a robust, basis-space algorithm of the ISA method and demonstrate its applicability on a variety of systems. We show that this algorithm exhibits rapid convergence (taking around 10–80 iterations) with the number of iterations needed being unrelated to the system size or basis set used. Further, we show that the multipole moments calculated using this basis-space ISA method are as good as, or better than, those obtained from Stone’s distributed multipole analysis (<i>J. Chem. Theory Comput.</i> <b>2005</b>, <i>1</i>, 1128), exhibiting better convergence properties and resulting in better behaved penetration energies. This can have significant consequences in the development of intermolecular interaction models

The Electron Density of the Hydrogen Bond

The general features of the electron density in hydrogen bonds, as derived from recent diffraction investigations and quantum mechanical calculations, are summarized. In hydrogen bonds of weak and intermediate strengths, the electron distribution can be considered simply as a superposition of the densities of the undisturbed, constituent monomers. The· modification actually taking place as the molecules interact with each other in the crystal, constitutes only a second-order effect, hardly detectable in the experimental maps. In very strong hydrogen bonds, however, a modification of the original monomer densities is quite noticeable. Special interest is concentrated on the electron distribution in the lone-pair region