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In this thesis, a combination of density functional theory (DFT) based calculations and nonequilibrium Green’s functions are employed to investigate electron transport in molecular switches, molecular cords and nanoscale devices.   Molecular electronic devices have been proposed as an approach to complement today’s silicon based electronic devices. However, engineering of such miniature devices and design of functional molecular components still present significant challenges.   First, the way to connect a molecule to conductive electrodes has to be controlled. We study, in a nanoelectrode-nanoparticle platform, how structural changes affect the measured conductance and how current fluctuations due to these structural changes can be decreased. We find that, for reproducible measurements, it is important to have the molecules chemically bonded to the surfaces of adjacent nanoparticles. Furthermore, we show by a combination of DFT and theoretical modeling that we can identify signals from single-molecules in inelastic electron spectroscopy measurements on these devices.   Second, active elements based on molecules, some examples being switches, rectifiers or memory devices, have to be designed. We study molecular conductance switches that can be operated by light and/or temperature. By tuning the substituents on the molecules, we can optimize the shift of the most conducting molecular orbital and increase the effective coupling between the molecule and the electrodes when going from the OFF to the ON-state of the switches, giving high switching ratio (up to three orders of magnitude). We also study so called mechanoswitches that are activated by a mechanical force elongating the molecules, which means that these switches could operate as sensors.   Furthermore, we have studied two different classes of compounds that may function either as rigid molecular spacers with a well-defined conductance or as molecular cords. In both cases, we find that it is of great importance to match the conjugation of the anchoring groups with the molecular backbone for high conductance.   The last part of the thesis is devoted to another interesting semiconductor material, diamond. We have accurately calculated the band structure and effective masses for this material. Furthermore, these results have been used to calculate the Hall coefficient, the resistivity and the Seebeck coefficient.

The maximum theoretical energy efficiency of fuel cells is much larger than those of the steam-power-turbine cycles that are currently used for generating electrical power. Similarly, direct hydrocarbon fuel cells, DHFCs, can theoretically be much more efficient than hydrogen fuel cells. Unfortunately the current densities (overall reaction rates) of DHFCs are substantially smaller than those of hydrogen fuel cells. The problem is that the exchange current density (catalytic reaction rate) is orders of magnitude smaller for DHFCs. Other work at the University of Ottawa has been directed toward the development of polymer electrolytes for DHFCs that operate above the boiling point of water, making corrosion rates much slower so that precious metal catalysts are not required. Propane (liquefied petroleum gas, LPG) was the hydrocarbon chosen for this research partly because infrastructure for its transportation and storage in rural areas already exists. In this work nickel based catalysts, an inexpensive replacement for the platinum based catalysts used in conventional fuel cells, were examined using density functional theory, DFT. The heats of propane adsorption for 3d metals, when plotted as a function of the number of 3d electrons in the metal atom, had the shape of a volcano plot, with the value for nickel being the peak value of the volcano plot. Also the C-H bond of the central carbon atom was longer for propane adsorbed on nickel than when adsorbed on any of the other metals, suggesting that the species adsorbed on nickel was less likely to desorb than those on other metals. The selectivity of the propyl radical reaction was examined. It was found that propyl radicals

Hydrogen bonds are of great interest in the solid state due to their importance in structural, functional and dynamical properties of chemical systems. Moderate hydrogen bonds have been linked with proton transfer, whereas the short, strong hydrogen bonds enable proton migration. Previous work in our group on relatively simple hydrogen bonded adducts relied on the combination of ab initio computational modelling (molecular dynamics) with variable temperature diffraction results (X-ray and neutron). These demonstrated that the interplay of these techniques was successful in studying the phenomena of proton transfer and migration. The present work follows on from that, and focuses on the effects of temperature and pressure on proton transfer and migration using both experimental and computational methods. The systems studied continue to encapsulate adducts with N…O and O…O hydrogen bonds. The study of the adduct formed between squaric acid and 4,4’-bipyridine was found to exhibit proton transfer associated with a single-crystal to single-crystal phase transition at 450 K that is coupled to a colour change (yellow to red). X-ray and neutron diffraction initially revealed the heavy atom structure and secondly the location of the hydrogen atoms along the moderate N…O hydrogen bond (ca. 2.6 Å). Computational modelling supported this and deduced the reason for the striking colour change. Pressure studies also determined that the adduct underwent two phase-transitions with a similar colour change, indicating that proton transfer is also a factor here, but with powder patterns different from the high temperature form, indicating that further polymorphs for this interesting system must exist. In an attempt to lower the temperature at which proton transfer would occur the base was changed to one of a more basic nature, i.e. co-crystallisation of squaric acid and 2,2’-dimethyl–4,4’-bipyridine was pursued. This lead to the formation of two red crystals that were found to posses the base doubly protonated at all temperatures studied (from 300 K to 100 K). The adduct of N,N-dimethylurea with phosphoric acid was obtained from a systematic study designed to follow the success of a previously reported system that showed proton migration (the adduct of urea and phosphoric acid). The new material was found to crystallise as the 2:1 adduct and maintained the short, strong hydrogen bonds characteristic of the parent structure. As part of the systematic approach undertaken throughout the research presented here, co-crystallisation of a combination of acids and bases were attempted in order to synthesise new materials containing short, strong hydrogen bonds. These yielded the adducts between oxalic acid and 2,2’-dimethyl-4,4’-bipyridine, and oxamic acid and 4,4’-bipyridine. In addition to these adducts some compounds ended up reacting to create new ones, e.g. the fusing of dimethyl urea and squaric acid to give N-(2-hydroxycyclobutene-3,4-dione)-N’,N’-dimethylurea and N-(2- hydroxycyclobutene-3,4-dione)-N,N'-dimethylurea, while a new polymorphs of one of the precursors on its own was also obtained (N,N’-dimethylurea). The resulting co-crystallisations did not all follow the design quite as intended. They did, however, yield interesting new structures, some of which have the potential to be proton migration and transfer systems.

Chapter one is an introduction to the less common coordination and oxidation chemistry of palladium; complexes containing Pd-OR, Pd-NR2 and those in the oxidation states of +IV. An outline of PdII/IV catalysed ligand-directed oxidative functionalisation is also included. Chapter two covers the design and synthesis of a range of tethered N-heterocyclic carbene (NHC) complexes of Pd. In addition, the syntheses of a number of new tethered NHC ligands are described. The use of Density Functional Theory (DFT) to model the complexes in this thesis was explored. Chapter three describes the synthesis and characterisation of PdIV halide complexes. The relevance of these compounds to PdII/IV catalysed ligand-directed oxidative functionalisation is explored. DFT was used to probe the reaction pathway for N-bromosuccinimide and iodobenzene dichloride. Chapter four examines reactions with oxidants used to form C-O and C-C bonds. The reaction pathway for iodobenzene diacetate was investigated using DFT. Chapter five contains experimental details and characterising data for the compounds reported.

Negative Poisson’s ratio, or auxetic, materials present the possibility of designing structures and components with tailored or enhanced mechanical properties. This thesis explores the phenomenon of auxetic behaviour in cubic crystals using classical and quantum modelling techniques and assesses the validity of these techniques when predicting auxetic behaviour in cubic elemental metals. These techniques are then used to explore the mechanism of this behaviour. The findings of the atomistic modelling are then used as a template to create networks of bending beams with tailored Poisson’s ratio behaviour.

The structural and electronic properties of covalently and non-covalently functionalized graphene are investigated by means of first-principles density-functional-theory. The electronic characteristics of non-covalently functionalized graphene by a planar covalent organic framework (COF) are investigated. The aromatic central molecule of the COF acts as an electron donor while the linker of the COF acts as an electron acceptor. The concerted interaction of donor acceptor promotes the formation of planar COF networks on graphene. The distinctive electronic properties of covalently functionalized fluorinated epitaxial graphene are attributed to the polar covalent C–F bond. The partial ionic character of the C–F bond results in the hyperconjugation of C–F σ-bonds with an sp2 network of graphene. The implications of resonant-orbital-induced doping for the electronic and magnetic properties of fluorinated epitaxial graphene are discussed. Isolation of single-walled carbon nanotubes (SWNTs) with specific chirality and diameters is critical. Water-soluble poly [(m- phenyleneethynylene)- alt- (p- phenyleneethynylene)], 3, is found to exhibit high selectivity in dispersing SWNT (6,5). The polymer’s ability to sort out SWNT (6,5) appears to be related to the carbon–carbon triple bond, whose free rotation allows a unique assembly. We have also demonstrated the important role of dispersion forces on the structural and electronic stability of parallel displaced and Y-shaped benzene dimer conformations. Long-range dispersive forces play a significant role in determining the relative stability of benzene dimer. The effective dispersion of SWNT depends on the helical pitch length associated with the conformations of linkages as well as π-π stacking configurations. We have revisited the constructing schemes for a large family of stable hollow boron fullerenes with 80 + 8n (n = 0,2,3,...) atoms. In contrast to the hollow pentagon boron fullerenes the stable structures constitute 12 filled pentagons and 12 additional hollow hexagons. Based on results from density-functional calculations, an empirical rule for filled pentagons is proposed along with a revised electron counting scheme. We have also studied the relative stability of various boron fullerene structures and structural and electronic properties of B80 bucky ball and boron nanotubes. Our results reveal that the energy order of fullerenes strongly depends on the exchange-correlation functional employed in the calculation. A systematic study elucidates the importance of incorporating dispersion forces to account for the intricate interplay of two and three centered bonding in boron nanostructures.

The work in this thesis mainly focuses on the assessment of density functional methods for computing structures and energies of organic and bioorganic molecules. Previous studies found dramatic conformational and stability changes from B3LYP to MP2 geometry optimization for some Tyr-Gly conformers. Possible reasons could be large intramolecular basis set superposition errors (BSSEs) in the MP2 calculations and the lack of dispersion in the B3LYP calculations. The fragmentation method and three kinds of rotation methods were used to investigate intramolecular BSSE. It is concluded that the rotation method cannot be used to correct intramolecular BSSE along a rotation profile. Another methodology is to employ modern density functionals. We focused on M06-L with the Tyr-Gly conformer ‘book6’. Potential energy profiles were determined by computing the energy for geometries optimized at various fixed values of a distance that controls the degree of foldedness of the structure. M06-L manifested itself as a very promising method to investigate the potential energy surface of small peptides containing aromatic residues. To predict Tyr-Gly structures, 108 potential conformers were created with a Fortran program. The geometry optimizations were done using M06-L/6-31G(d) and M05-2X/6-31+G(d). Two schemes were employed and the most stable conformers were compared to the 20 stable conformers found by B3LYP. Both schemes found 10 conformers similar to one of the B3LYP stable conformers, as well as several newly found conformers. The study of a missing B3LYP stable conformer showed that the possible reason of missing conformers may be the lack in dispersion in B3LYP theory. To study the hydration effect, we studied the conformations of neutral and zwitterionic 3-fluoro-γ-aminobutyric acid (3F-GABA) in solution using different solvation models, mainly the explicit water molecule models. Zwitterionic forms of 3F-GABA are preferred in solution. M06-2X performs better in calculating transition energy profiles than MP2.

First-principles calculations have been carried out to investigate structural and electronic properties of graphene on SiC and diamond substrates and for a study of doping of fluorographene with various surface adsorbates. New insight is given into the problem of the decoupling of the graphene layers from SiC substrates after epitaxial growth. Mechanisms of hydrogen penetration between graphene and SiC(0001) surface, and properties of hydrogen and fluorine intercalated structures have been studied. Energy barriers for diffusion of atomic and molecular hydrogen through the interface graphene layer with no defects and graphene layers containing Stone-Wales defect or two- and four-vacancy clusters have been calculated. It is argued that diffusion of hydrogen towards the SiC surface occurs through the hollow defects in the interface graphene layer. It is further shown that hydrogen easily migrates between the graphene layer and the SiC substrate and passivates the surface Si bonds, thus causing the graphene layer decoupling. According to the band structure calculations the graphene layer decoupled from the SiC(0001) surface by hydrogen intercalation is undoped, while that obtained by the fluorine intercalation is p-type doped. Further, structure and the electronic properties of single and double layer graphene on H-, OH-, and F- passivated (111) diamond surface have been studied. It is shown that graphene only weakly interacts with the underlying substrates and the linear dispersion of graphene pi-bands is preserved. For graphene on the hydrogenated diamond surfaces the charge transfer results in n-type doping of graphene layers and the splitting of conduction and valence bands in bilayer graphene. For the F- and OH-terminated surfaces, charge transfer and doping of graphene do not occur. Finally, the possibility of doping fluorographene by surface adsorbates have been investigated. The structure and electronic properties of fluorographene with adsorbed K, Li, Au atoms, and F4-TCNQ molecule are described. It is shown that adsorption of K or Li atoms results in electron doping of fluorographene, while Au atoms and F4-TCNQ introduce deep levels inside the band gap. The calculated value of the fluorographene work function is extremely high, 7.3 eV, suggesting that p-type doping is difficult to achieve.