The main body of this thesis describes how to calculate scanning tunneling microscopy (STM) images from first-principles methods. The theory is based on localized orbital density functional theory (DFT), whose limitations for large-vacuum STM models are resolved by propagating localized-basis wave functions close to the surface into the vacuum region in real space. A finite difference approximation is used to define the vacuum Hamiltonian, from which accurate vacuum wave functions are calculated using equations based on standard single-particle Green’s function techniques, and ultimately used to compute the conductance. By averaging over the lateral reciprocal space, the theory is compared to a series of high-quality experiments in the low- bias limit, concerning copper surfaces with adsorbed carbon monoxide (CO) species and adsorbate atoms, scanned by pure and CO-functionalized copper tips. The theory compares well to the experiments, and allows for further insights into the elastic tunneling regime. A second significant project in this thesis concerns first-principles calculations of a simple chemical reaction of a hydroxyl (oxygen-deuterium) monomer adsorbed on a copper surface. The reaction mechanism is provided by tunneling electrons that, via a finite electron-vibration coupling, trigger the deuterium atom to flip between two nearly identical configurational states along a frustrated rotational motion. The theory suggests that the reaction primarily occurs via nuclear tunneling for the deuterium atom through the estimated reaction barrier, and that over-barrier ladder climbing processes are unlikely.

In this thesis, density functional theory is employed in the study of two kinds of systems that can be considered to be biomimetic in their own ways. First, three binuclear metal complexes, synthesized by the group of Prof. Ebbe Nordlander, have been investigated. The complexes are designed to resemble the active sites of phosphatase enzymes and have been examined in complexes where either two Zn(II) ions or one Fe(III) and one Mn(II) ion are bound. These dinuclear compounds were studied as catalysts for the hydrolysis of bis(2,4-dinitrophenyl) phosphate and the transesterification of 2-hydroxypropyl p-nitrophenyl phosphate, which are model systems for the same reactions occurring in DNA or RNA. It was found that the two reactions take place in similar ways: a hydroxide ion that is terminally bound to one of the metal centers acts either as a nucleophile in the hydrolysis reaction or as a base in the transesterification. The leaving groups depart in an effectively concerted manner, and the formed catalyst-product complexes are predicted to be the resting states of the catalytic cycles. The rate-determining free energy barriers are identified from the catalyst-product complex in one catalytic cycle to the transition state of nucleophilic attack in the next. Another type of biomimetic modeling is made with an aim of imitating the conceptual features of selective binding of guests and screening them from solute-solvent interactions. Such features are found in so-called nanocontainers, and this thesis is concerned with studies of two capsules synthesized by the group of Prof. Julius Rebek, Jr. First, the cycloaddition of phenyl acetylene and phenyl azide has experimentally been observed to be accelerated in the presence of a capsule. Computational studies were herein performed on this system, and a previously unrecognized structure of the capsule is discovered. Two main factors are then identified as sources of the rate acceleration compared to the uncatalyzed reaction, namely the reduction of the entropic component and the selective destabilization of the reactant supercomplex over the transition state. In the second capsule study, the alkane binding trends of a water-soluble cavitand was studied. It is found that implicit solvation models fail severely in reproducing the experimental equilibrium observed between binding of n-decane by the cavitand monomer and encapsulation in the capsule dimer. A mixed explicit/implicit solvation protocol is developed to better quantify the effect of hydrating the cavitand, and a simple correction to the hydration free energy of a single water molecule is proposed to remedy this. The resulting scheme is used to predict new hydration free energies of the cavitand complexes, resulting in significant improvement vis-à-vis experiments. The computational results presented in this thesis show the usefulness of the quantum chemical calculations to develop understanding of experimental trends observed for substrate binding and catalysis. In particular, the methodology is shown to be versatile enough such that experimental observations can be reproduced for such diverse systems as studied herein. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

As the demand for clean and renewable energy sources continues to grow, much attention has been given to solid oxide fuel cells (SOFCs) due to their efficiency and low operating temperature. However, the components of SOFCs must still be improved before commercialization can be reached. Of particular interest is the solid electrolyte, which conducts oxygen ions from the cathode to the anode. Samarium-doped ceria (SDC) is the electrolyte of choice in most SOFCs today, due mostly to its high ionic conductivity at low temperatures. However, the underlying principles that contribute to high ionic conductivity in doped ceria remain unknown, and so it is difficult to improve upon the design of SOFCs. This thesis focuses on identifying the atomistic interactions in SDC which contribute to its favourable performance in the fuel cell. Unfortunately, information as basic as the structure of SDC has not yet been found due to the difficulty in experimentally characterizing and computationally modelling the system. For instance, to evaluate 10.3% SDC, which is close to the 11.1% concentration used in fuel cells, one must investigate 194 trillion configurations, due to the numerous ways of arranging the Sm ions and oxygen vacancies in the simulation cell. As an exhaustive search method is clearly unfeasible, we develop a genetic algorithm (GA) to search the vast potential energy surface for the low-energy configurations, which will be most prevalent in the real material. With the GA, we investigate the structure of SDC for the first time at the DFT+U level of theory. Importantly, we find key differences in our results from prior calculations of this system which used less accurate methods, which demonstrate the importance of accurately modelling the system. Overall, our simulation results of the structure of SDCagree with experimental measurements. We identify the structural significance of defects in the doped ceria lattice which contribute to oxygen ion conductivity. Thus, the structure of SDC found in this work provides a basis for developing better solid electrolytes, which is of significant scientific and technological interest. Following the structure search, we perform an investigation of the electronic properties of SDC, to understand more about the material. Notably, we compare our calculated density of states plot to XPS measurements of pure and reduced SDC. This allows us to parameterize the Hubbard (U) term for Sm, which had not yet been done. Importantly, the DFT+U treatment of the Sm ions also allowed us to observe in our simulations the magnetization of SDC, which was found by experiment. Finally, we also study the SDC surface, with an emphasis on its structural similarities to the bulk. Knowledge of the surface structure is important to be able to understand how fuel oxidation occurs in the fuel cell, as many reaction mechanisms occur on the surface of this porous material. The groundwork for such mechanistic studies is provided in this thesis.

Solid-state nuclear magnetic resonance (SSNMR) has proven to be a useful tool in the characterization of non-covalent interactions such as hydrogen bonding and cation-π interactions. In recent years, the scientific community has manifested a renewed interest towards an important class of non-covalent interaction, halogen bonding (XB), as it has applications in various fields such as crystal engineering and biological processes. This dissertation demonstrates that NMR parameters measured in the solid state are sensitive to changes in electronic structure, which are caused by halogen bonds. A series of halogen bonded compounds exhibiting interactions between different diiodoperfluorobenzenes (p- C6F4I2, o- C6F4I2, sym- C6F3I3, p- C6H4I2) and various halogen bond acceptors have been synthesized as part of this work. These new halogen bonded compounds were characterized with a combined theoretical and experimental SSNMR, X-ray diffraction (XRD) methods. The complete multinuclear magnetic resonance spectroscopy of the nuclei involved directly in the halogen bond (13C, 14/15N, 31P, 77Se, 35/37Cl and 79/81Br) were recorded at multiple magnetic fields (4.7, 9.4, 11.75 and 21.1 T). The specialized SSNMR experiments provided high-resolution spectra of quadrupolar nuclei, which were WURST-QCPMG or solid-echo type experiments combined with the variable offset cumulative spectral (VOCS) method, as for spin 1/2 nuclei cross polarization magic angle spinning (CPMAS) experiments were usually appropriate. This dissertation will discuss successful applications of SSNMR spectroscopy to characterize halogen bonds, it will demonstrate the significant changes in NMR observables in the presence of XB interaction and thus establish that NMR parameters are very sensitive to halogen bonding interaction. Furthermore, this work explains why the NMR parameters are correlated with the halogen bonding interaction. The different trends observed between the NMR observables and the halogen bonding were further understood with a ZORA-DFT natural localized molecular orbital (NLMO) study.

Ce travail consiste en l'étude théorique DFT des mécanismes de couplage. Le couplage déshydrogénant de stannanes implique la formation in situ d'un stannylène, formation possible grâce à l'inertie de la paire libre et au caractère acide de Lewis des stannylènes. Le couplage entre un carboxylate aromatique et un arène Ar-H commence par la décarboxylation en 2 étapes (isomérisation et désinsertion de CO2) sur un complexe de Pd(II) et se poursuit par une étape de CMD. Celle-ci est facilitée par la présence de fluors en ortho sur Ar-H essentiellement en raison du renforcement de la liaison M-C qu'ils induisent. Le couplage entre un arène et un alcyne catalysé par Ni(0)L présente une étape originale de transfert d'hydrogène de l'arène sur l'alcyne concerté avec la création de deux liaisons M-C (M-aryl et M-vinyl). Cette étape est à nouveau associée à une barrière d'activation plus basse en présence de fluors sur l'arène. L'hydroboration avec ouverture de cycle d'alkylidenecyclopropane en présence de Rh(I) nécessite la création de deux sites vacants pour que l'étape souhaitée d'ouverture de cycle soit favorisée par rapport à une étape d'élimination réductrice C-B. / This work is a theoretical study with DFT method of coupling reactions. The dehydrogenating coupling of stannanes proceeds via the formation of stannylene. This is made possible because of the chemical inertness of the lone pair and the Lewis acid character of stannylene. Coupling an aromatic carboxylate and an arene Ar-H on a Pd(II) complex is initiated by a 2-step reaction (isomerization and decarboxylation). The CMD reaction that follows is facilitated by ortho fluorine subtituents on the arene ArH because of the strengthening of the resulting Pd-C bond. The coupling between an arene and an alkyne by a Ni(0)L catalyst starts by an unusual hydrogen transfer from the arene to the alkyne, concerted with the formation of two NiC (aryl and vinyl) bonds. The energy barrier of this elementary step is lowered by fluorine subtituents on the arene. The hydroboration with ring opening of alkylidenecyclopropane in presence of Rh(I) complex is feasible only with two empty coordination sites during the key ring-opening step. Under these conditions, the ring opening is favored over the reductive elimination C-B.

Lithium Ion Batteries (LIBs) are important in today's society, powering cars and mobile devices. LIBs consist of a negative anode commonly made of graphite, and a positive cathode commonly made from transition metal oxides. Between these electrodes are separators and organic solvent based electrolyte. Due to the high potential of LIBs the electrolyte is reduced at the anode. The electrolyte reduction results in the formation of a layer called the Solid Electrolyte Interphase (SEI), which prohibits the further breakdown of the electrolyte. Despite being researched for over50 years, the composition formation of the SEI is still poorly understood. The aim of this project is to develop strategies for efficient identification and classification of various active and intermediate components in the SEI, to, in turn, gain an understanding of the reactions taking place, which will help find routes to stabilize and tailor the composition of the SEI layer for long-term stability and optimal battery performance. For a model gold/li-ion battery electrolyte system, Raman spectra will be obtained using Surface Enhanced Raman Spectroscopy (SERS) in a spectroelectrochemical application where the voltage of the working gold electrode is swept from high to low potentials. Spectra of common components of the SEI as well as similar compounds will be simulated using Density Functional Theory (DFT). The DFT data is also used to calculate the spontaneity of reactions speculated to form the SEI. The simulated data will be validated by comparing it to experimental spectra from pure substances. The spectroelectrochemical SERS results show a clear formation of Li-carbonate at the SERS substrate, as well as the decomposition of the electrolyte into other species, according to the simulated data. It is however shown that there are several issues when modelling spectra, that makes it harder to correlate the simulated spectra with the spectroelectrochemical spectra. These issues include limited knowledge of the structure of the compounds thought to form on the anode surface, and incorrect choices in simulational parameters. To solve these issues, more work is needed in these areas, and the spectroelectrochemical methods used in this thesis needs to be combined with other experimental methods to narrow down the amount of compounds to be modelled. More work is also needed to avoid impurities in the electrolyte. Impurities leads to a thick inorganic layer which prohibits the observation of species in the organic layer.

abstract: Single-layer pentagonal materials have received limited attention compared with their counterparts with hexagonal structures. They are two-dimensional (2D) materials with pentagonal structures, that exhibit novel electronic, optical, or magnetic properties. There are 15 types of pentagonal tessellations which allow plenty of options for constructing 2D pentagonal lattices. Few of them have been explored theoretically or experimentally. Studying this new type of 2D materials with density functional theory (DFT) will inspire the discovery of new 2D materials and open up applications of these materials in electronic and magnetic devices.In this dissertation, DFT is applied to discover novel 2D materials with pentagonal structures. Firstly, I examine the possibility of forming a 2D nanosheet with the vertices of type 15 pentagons occupied by boron, silicon, phosphorous, sulfur, gallium, germanium or tin atoms. I obtain different rearranged structures such as a single-layer gallium sheet with triangular patterns. Then the exploration expands to other 14 types of pentagons, leading to the discoveries of carbon nanosheets with Cairo tessellation (type 2/4 pentagons) and other patterns. The resulting 2D structures exhibit diverse electrical properties. Then I reveal the hidden Cairo tessellations in the pyrite structures and discover a family of planar 2D materials (such as PtP2), with a chemical formula of AB2 and space group pa ̄3. The combination of DFT and geometries opens up a novel route for the discovery of new 2D materials. Following this path, a series of 2D pentagonal materials such as 2D CoS2 are revealed with promising electronic and magnetic applications. Specifically, the DFT calculations show that CoS2 is an antiferromagnetic semiconductor with a band gap of 2.24 eV, and a N ́eel temperature of about 20 K. In order to enhance the superexchange interactions between the ions in this binary compound, I explore the ternary 2D pentagonal material CoAsS, that lacks the inversion symmetry. I find out CoAsS exhibits a higher Curie temperature of 95 K and a sizable piezoelectricity (d11=-3.52 pm/V). In addition to CoAsS, 34 ternary 2D pentagonal materials are discovered, among which I focus on FeAsS, that is a semiconductor showing strong magnetocrystalline anisotropy and sizable Berry curvature. Its magnetocrystalline anisotropy energy is 440 μeV/Fe ion, higher than many other 2D magnets that have been found. Overall, this work not only provides insights into the structure-property relationship of 2D pentagonal materials and opens up a new route of studying 2D materials by combining geometry and computational materials science, but also shows the potential applications of 2D pentagonal materials in electronic and magnetic devices. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2020

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Although band theory is about a century old, it remains relevant today as a tool for the treatment of electrons in solids. The confluence of mathematical ideas like geometry and topology with band theory has proven to be a ripe avenue for research in the past few decades. The importance of Fermi surface geometry, especially in conjunction with electronic correlation, has been well recognized. One particular thread in this direction is probing the occurrence of non-trivial Fermi surface geometry, and its influence on macroscopic properties of materials. A notable example of exotic Fermi surface geometry arises from singular points of the dispersion, and these have been known since 1953. The investigation into these was reignited recently, culminating in the work presented in this thesis. In this dissertation, I investigate two broad categories of singular points in bands. At a singular point, either the dispersion or the Fermi surface fail to be smooth. This may cause distinct signatures in transport and spectroscopic properties when the singular point occurs close to the Fermi level. In the two dimensional setting, I classify using catastrophe theory, the point singularities arising from higher order saddles of the dispersion. These are the more exclusive cousins of the regular van Hove saddle that cause, among other things, a power law divergence in the density of states. The role of lattice symmetries in aiding or preventing the occurrence of these singularities is also carefully explored. In the case of three dimensional bands, I investigate the spectroscopic properties of the nodal point singularity, arising from a linear band crossing. In particular, I determine the distinct signature of nodal points in the analytic, momentum resolved, joint density of states (JDOS) and the numerically calculated resonant inelastic x-ray scattering (RIXS) spectrum, within the fast collision approximation that ignores core hole effects. The results presented here will be the stepping stone towards a careful future calculation, incorporating the potential edge singularity effects through core hole potential. Such a calculation may be directly comparable with ongoing experiments.