A molecule can crystallise in more than one crystal structure, a common phenomenon in organic compounds known as polymorphism. Different polymorphic forms may have significantly different physical properties, and a reliable prediction would be beneficial to the pharmaceutical industry. However, crystal structure prediction (CSP) based on the knowledge of the chemical structure had long been considered impossible. Previous failures of some CSP attempts led to speculation that the thermodynamic calculations in CSP methodologies failed to predict the kinetically favoured structures. Similarly, regarding the stabilities of co-crystals relative to their pure components, the results from lattice energy calculations and full CSP studies were inconclusive. In this thesis, these problems are addressed using the state-of-the-art CSP methodology implemented in the GRACE software. Firstly, it is shown that the low-energy predicted structures of four organic molecules, which have previously been considered difficult for CSP, correspond to their experimental structures. The possible outcomes of crystallisation can be reliably predicted by sufficiently accurate thermodynamic calculations. Then, the polymorphism of 5- chloroaspirin is investigated theoretically. The order of polymorph stability is predicted correctly and the isostructural relationships between a number of predicted structures and the experimental structures of other aspirin derivatives are established. Regarding the stabilities of co-crystals, 99 out of 102 co-crystals and salts of nicotinamide, isonicotinamide and picolinamide reported in the Cambridge Structural Database (CSD) are found to be more stable than their corresponding co-formers. Finally, full CSP studies of two co-crystal systems are conducted to explain why the co-crystals are not easily obtained experimentally.

The interfacial electronic structure of the organic material- tris(8-hydroxyquinolinato)aluminum (Alq3) forming an interface with cobalt metal has been investigated in this research. The primary characterization method used in this research was near-edge X-ray absorption fine structure (NEXAFS) spectroscopy which probes the unoccupied molecular orbitals of a material. Density functional theory (DFT) calculations have also been employed to calculate the partial density of states (PDOS) of all constituent elements present in Alq3 molecule. The DFT calculations helped to determine the molecular orbital structure of Alq3 and to understand how the orbital structure is influenced by forming an interface with ferromagnetic Co layer. The experimental NEXAFS spectra measured in total fluorescence yield (TFY) showed that the lowest unoccupied molecular orbital (LUMO) and LUMO+1 states of Alq3 were not affected by the presence of Co when Co is deposited onto Alq3. On the other hand, a charge transfer between Co and Alq3 led the loss or reduction of LUMO+2 state for a Co(top)/Alq3 bilayer sample when compared to pristine Alq3 reference sample (without Co deposition). This selective effect of Co on the orbital configuration of Alq3 suggests that Co atoms diffuse into Alq3 and interact with preferred sites in Alq3. By comparing the spectral change in the experimental NEXAFS spectra to the calculated PDOS of Alq3, the preferred interaction sites between Co and Alq3 could be successfully determined. This work suggests that the spectroscopic approach using synchrotron-radiation X-ray spectroscopy can serve as a powerful means for studying the interfacial electronic structure between magnetic metals and organic semiconductors and can contribute to the research and development of high performance organic spintronics.

The chemistry of actinides in aqueous solution is important, and it is essential to build adequate conceptual models and develop methods applicable for actinide systems. The complex electronic structure makes benchmarking necessary. In the thesis a prototype reaction of the water exchange reaction for uranyl(VI), for both ground and luminescent states, described with a six-water model, was used to study the applicability of density functional methods on actinides and different solvation models. An excellent agreement between the wave function methods CCSD(T) and MP2 was obtained in the ground state, implying that near-minimal CASPT2 can be used with confidence for the reaction in the luminescent state of uranyl(VI), while density functionals are not suited to describe energetics for this type of reaction. There was an ambiguity concerning the position of the waters in the second hydration sphere. This issue was resolved by investigating a larger model, and prop- erly used the six-water model was found to adequately describe the water exchange reaction. The effect of solvation was investigated by comparing the results from conductor-like polarizable continuum models using two cavity models. Scattered numbers made it difficult to determine which solvation model to use. The final conclusion was that the water exchange reaction in the luminescent state of uranyl(VI) should be addressed with near-minimal CASPT2 and a solvation model without explicit cavities for hydrogens. Finally it was shown that no new chemistry appears in the luminescent state for this reaction. The thesis includes a methodological investigation of a multi-reference density functional method based on a range separation of the two-electron interaction. The method depends on a universal parameter, which has been determined for lighter elements. It is shown here that the same parameter could be used for actinides, a prerequisite for further development of the method. The results are in that sense promising.

London or dispersion interactions are weak van der Waals (vdW) interactions. They are important in determining the structure and properties of many chemical and biochemical systems. In this thesis, an optimizer using the nonempirical generalized gradient approximation (GGA) functional PW86+PBE+XDM, to capture van der Waals interactions, is presented. The work in this thesis covers the assessment of a variety of basis sets for their ability to reproduce accurate GGA repulsive and binding energies. Selected basis sets were then used to compute binding energies of 65 vdW complexes at equilibrium. This functional was also tested for binding energies of two sets of vdW complexes at distorted geometries. The last part deals with forces to investigate their accuracy using PW86+PBE+XDM in order to build an optimizer for vdW complexes using a nonempirical DFT method. Eventually, after confirming a high reproducibility of the optimizer on the geometries and binding energies, it was used in two biologically relevant applications. This optimizer is a unique tool to compute deformation energies with a nonempirical DFT method. The second part of this thesis covers a biologically relevant application where a conventional DFT is used. This application is related to the carrier of the genetic codes in living cells, DNA. DNA undergoes harmful mutations under external perturbations such as applied external electric fields. In this study, DNA base pairs were first mimicked by a simpler model, namely, the formic acid dimer. The effect of applied external electric fields on the geometries of the formic acid dimer is studied. The effect of these applied fields on the potential energy surface, the barrier height and the frequency of the double proton transfer in the formic acid dimer are also investigated. The study was then repeated on DNA base pairs to study the effect of an external applied electric field on the tunneling corrected rate constants of the double proton transfer reactions in AT and GC.

This work presents a study of the electronic structure of four transition metal oxides (TMOs) using spectroscopic data and a variety of theoretical models. TMOs are a class of materials made from d-block metals in the periodic table, and one or more oxygen atoms. The nature of d-electrons is examined and theoretical models used to treat d-electron systems are tested against experimental data. Background theory of condensed matter physics is outlined. An overview of density functional theory (DFT) as a theoretical model for calculating the electronic structure of materials is presented. A variety of exchange-correlation (XC) functionals used within the DFT framework are outlined and tested for their applicability to the TMO systems in question. X-ray spectroscopy is briefly outlined and used to test the validity of the different XC functionals. All four compounds, AgO, Ag2O, CuO, and Cu2O require a Hubbard U term in the XC functional to most accurately reproduce experimental results. The effects of varying the value of U is examined in depth. The oxygen K-edge X-ray emission spectra (XES) exhibits a“two peak” structure for all compounds; the effect of varying the U value is to change the intensity ratio of the two peaks. The ratio of the two peaks as a function of U shows a linear trend in all compounds. A simple line is fit to the peak ratio vs. U curve. A common line between all compounds would provide an important metric with which to predict the appropriate U value needed in similar materials based on simple experimental data. However, the parameters of the fitted line were not common between the four compounds and any metric derived from this method would be system-dependent and not widely applicable to other systems. There are, however, interesting trends in the data when the U value is varied that provide subjects for future research. A number of fundamental quantities are determined both from experiment and theoretical calculations. Calculated bandgap values are shown to be lower than the experimental values for most functionals tested. This is not unexpected as DFT methods are known to predict much smaller bandgaps than expected. The Heyd-Scuseria-Ernzerhof (HSE) functional used for Ag2O and Cu2O does predict the bandgaps very accurately. The core-hole effect is estimated and proven to be negligible in these systems. Charge transfer and on-site Coulomb repulsion energies, important quantities in the electronic behaviour of TMOs, are determined and compared to previously reported values.

A summary of research conducted since September 2007 at the University of Toronto in the laboratory of Professor Robert A. Batey is presented in this thesis, which is divided into four chapters. The first chapter contains a two-part introduction, where aryl- and aliphatic-Claisen rearrangements are discussed in part 1, and the nucleophilic addition of organoboron reagents to unsaturated C–N functionalities is described in part 2. Chapter 2 contains research involving synthetic and theoretical studies of aryl-Claisen rearrangements and other sigmatropic reactions. The work towards developing the lanthanide-catalyzed domino aryl-Claisen rearrangement for the synthesis of contiguous aryl–C(sp³) moieties is presented first. This is followed by computational studies involving E/Z-selectivity differences for the aryl-Claisen rearrangement, which was an issue noted for the domino aryl-Claisen reaction of a linear substrate. The mechanistic origins of E/Z-selectivity differences for the mono aryl-Claisen rearrangement, which was experimentally ambiguous for over 40 years, is resolved through computational methods. A theoretical analysis of selectivity differences for the allylic azide rearrangement is also described. The third section contains a discussion of Eu(fod)3-catalyzed aryl-Claisen rearrangements on vinyl bromide systems and preliminary studies involving application of the substrates in cross-coupling reactions, and other attempted mono- and domino sigmatropic rearrangements are presented in the fourth section. In chapter 3, the search for computational methods that can accurately predict experimental free energy of activation barriers for the aliphatic-Claisen rearrangement through benchmarking studies with a priori kinetic barrier and kinetic isotope effect data is described. Methods were found to predict new valid transition states and predict ΔG‡ values with a mean unsigned error of 0.3 kcal/mol relative to experimental values. In chapter 4, the development of new allylboration reaction is outlined, involving the double allylboration of nitriles and anhydrides, and initial studies towards the first aminoallylboration reactions of N-aluminoaldimines to form 1,2-diamines.

Metal-cyclic hydrocarbon complexes were prepared in a laser-vaporization molecular beam source and studied by single-photon zero electron kinetic energy (ZEKE) and IR-UV resonant two-photon ionization (R2PI) spectroscopy. The ionization energies and vibrational frequencies of the metal complexes were measured from the ZEKE spectra. Metal-ligand bonding and low-lying electronic states of the neutral and ionized complexes were analyzed by combining the ZEKE measurements with density functional theory (DFT) calculations. In addition, C-H stretching frequencies were measured from the R2PI spectra. In this dissertation, metal complexes of 1, 3, 5, 7-cyclo-octatetraene (COT), toluene, p-xylene, mesitylene, hexamethylbenzene, biphenyl, naphthalene, pyrene, perylene, and coronene were studied. For each metal-ligand complex, different effects from the metal coordination have been identified. Although free COT is a nonaromatic molecule with a tub-shaped structure, the group III transition metal atoms (Sc, Y, and La) donate two electrons to a partially filled π orbital of COT, making the ligand a dianion. As a result, metal coordination converts COT into a planar, aromatic structure and the resulting complex exhibits a half-sandwich structure. For the Sc(methylbenzene) complexes, the benzene rings of the ligands are bent and the π electrons are localized in a 1, 4-diene fashion due to differential Sc binding with the carbon atoms of the rings. Due to differential metal binding, the degenerate d orbitals split and the Sc-methylbenzene complexes prefer the low-spin ground electronic states. In addition, as the number of methyl group substituents in the ligand increases, the ionization energies (IEs) of the Sc-methylbenzene complexes decrease. However, Ti, V, or Co coordination does not disrupt the delocalized π electron network within the carbon skeleton in the high-spin ground states of the metal complexes. For group VI metal (Cr, Mo, and W)-bis(toluene) complexes, methyl substitution on the benzene ring yields complexes with four rotational conformers of 0°, 60°, 120°, and 180° conformation angles between two methyl groups. In addition, variable-temperature ZEKE spectroscopy using He, Ar, or their mixtures has determined the totally eclipsed 0° rotamer to be the most stable. When there are two equivalent benzene rings, the metal (Ti, Zr or Hf) binds to both the benzene rings of biphenyl, or the metal (Li) binds to one of the benzene rings of naphthalene. On the other hand, the metal (Li) favors the ring-over binding site of the benzene ring with a higher π electron content and aromaticity in pyrene, perylene, and coronene.

Solid oxide fuel cells are considered as one of the main alternatives for future sources of clean energy. To further improve their performance, theoretical methods able to describe the diffusion process in candidate electrolyte materials at finite temperatures are needed. The method of choice for simulating systems at finite temperature is molecular dynamics. However, if the forces are calculated directly from the Schrödinger equation (first-principles molecular dynamics) the computational expense is too high to allow long enough simulations to properly capture the diffusion process in most materials. This thesis introduces a method to deal with this problem using an external force field to speed up the diffusion process in the simulation. The method is applied to study the diffusion of oxygen ions in Sm-doped ceria, which has showed promise in its use as an electrolyte. Good agreement with experimental data is demonstrated, indicating high potential for future applications of the method.

This thesis deals with inelastic effects in electronic currents. We developed a time-dependent technique and show that this approach gives rich insight into electron-phonon coupling during transport. We compare our results with a time-independent technique and analyse the validity of our model. Finally, the results of a quantum chemistry calculation are presented in the framework of scanning tunneling miscroscopy (STM). We study the chemisorption of a tetrathiafulvalene molecule on a gold surface by performing the calculation of the charge transfer, the induced dipole, and the STM images using the density functional theory.

This dissertation research is focused on first principles studies of graphene and single organic molecules for nanoelectronics applications. These nanosized objects attracted considerable interest from the scientific community due to their promise to serve as building blocks of nanoelectronic devices with low power consumption, high stability, rich functionality, scalability, and unique potentials for device integration. Both graphene electronics and molecular electronics pursue the same goal by using two different approaches: top-down approach for graphene devices scaling to smaller and smaller dimensions, and bottom-up approach for single molecule devices. One of the goals of this PhD research is to apply first-principles density functional theory (DFT) to study graphene/metal and molecule/metal contacts at atomic level. In addition, the DFT-based approach allowed us to predict the electronic characteristics of single molecular devices. The ideal and defective graphene/metal interfaces in weak and strong coupling regimes were systematically studied to aid experimentalists in understanding graphene growth. In addition, a theory of resonant charge transport in molecular tunnel junctions has been developed. The first part of this dissertation is devoted to the study of atomic, electronic, electric, and thermal properties of molecular tunnel junctions. After describing the model and justifying the approximations that have been made, the theory of resonant charge transport is introduced to explain the nature of current rectification within a chemically asymmetric molecule. The interaction of the tunneling charges (electrons and holes) with the electron density of the metal electrodes, which in classical physics is described using the notion of an image potential, are taken into account at the quantum-mechanical level within the tight binding formalism. The amount of energy released onto a molecule by tunneling electrons and holes in the form of thermal vibration excitations is related to the reorganization energy of the molecule, which is also responsible for an effective broadening of molecular levels. It was also predicted that due to the asymmetry of electron and hole resonant energy levels with respect to the Fermi energy of the electrodes, the Joule heating released from the metallic electrodes is also non-symmetric and can be used for the experimental determination of the type of charge carriers contributing to the molecular conductance. In the second part of the dissertation research ideal and defective graphene/metal interfaces are studied in weak and strong interface coupling regimes. The theoretical predictions suggest that the interface coupling may be controlled by depositing an extra metallic layer on top of the graphene. DFT calculations were performed to evaluate the stability of a surface nickel carbide, and to study graphene/carbide phase coexistence at initial stages of graphene growth on Ni(111) substrate at low growth temperatures. Point defects in graphene were also investigated by DFT, which showed that the defect formation energy is reduced due to interfacial interactions with the substrate, the effect being more pronounced in chemisorbed graphene on Ni(111) substrate than in physisorbed graphene on Cu(111) substrate. Our findings are correlated with recent experiments that demonstrated the local etching of transfered graphene by metal substrate imperfections. Both graphene and molecular electronics components of the PhD dissertation research were conducted in close collaboration with several experimental groups at the University of South Florida, Brookhaven National Laboratory, University of Chicago, and Arizona State University.