Nonalternant aromatic π-electron systems show promises for surface functionalization due to their unusual electronic structure. Based on our previous experiences for metal surfaces, we investigate the adsorption structures, adsorption dynamics and bonding characteristics of azulene and its alternant aromatic isomer naphthalene on the Si(001) surface. Using a combination of density functional theory, ab initio molecular dynamics, reaction path sampling and bonding analysis with the energy decomposition analysis for extended systems, we show that azulene shows direct adsorption paths into several, strongly bonded chemisorbed final structures with up to four covalent carbon–silicon bonds which can be described in a donor–acceptor and a shared-electron bonding picture nearly equivalently. Naphthalene also shows these tetra-σ-type bonding structures in accordance with an earlier study. But the adsorption path is pseudo-direct here with a precursor intermediate bonded via one aromatic ring and strong indications for a narrow adsorption funnel. The four surface-adsorbate bonds formed lead for both adsorbates to a strong corrugation and a loss of aromaticity.

Pulsed laser flash photolysis of M(CO)6 (M = Cr, W) in cyclohexane with a small amount of benzene results in three sequential reactions. The first is the photodissociation of the parent to yield a M(CO)5:C6H12 complex, which takes place faster than the time resolution of our experiments. The second reaction is the replacement of the cyclohexane ligand with benzene to form a M(CO)5:C6H6 complex, in which benzene is coordinated to the metal via one side of the ring. This complex then falls apart in solution as M(CO)5 coordinates with a trace impurity in the solution that is likely water. Kinetic studies over a range of temperatures result in the following activation energies: 39 kJ/mol for the dissociation of W(CO)5:C6H6; 30 kJ/mol for conversion of Cr(CO)5:C6H12 to Cr(CO)5:C6H6; 33 kJ/mol for the dissociation of Cr(CO)5:C6H6. DFT calculations of binding energies for each complex suggest that all reactions proceed through a combination of an associative and dissociative mechanism. Further calculations of carbonyl vibrational frequencies for 13 weak metal–solvent complexes using three different density functionals: B3LYP, M06, and M06-L allowed us to calculate scale factors for predicting experimental vibrational frequencies. The scale factors are: 0.952 for B3LYP, 0.943 for M06, and 0.957 for M06-L. Using these scale factors leads to average errors in predicted experimental vibrational frequencies of less than 1% for each functional.

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We study the structure and energetics of water molecules adsorbed at ceria (111) surfaces below one monolayer coverage using density-functional theory. The results of this study provide a theoretical framework for interpreting recent experimental results on the redox properties of water at ceria (111) surfaces. In particular, we have computed the structure and energetics of various absorption geometries at stoichiometric ceria (111) surface. In contrast to experiment results, we do not find a strong coverage dependence of the adsorption energy. For the case of reduced surface, our results show that it may not be energetically favorable for water to oxidize oxygen vacancy site at the surface. Instead, oxygen vacancies tend to result in water more strongly binding to the surface. The result of this attractive water-vacancy interaction is that the apparent concentration of oxygen vacancies at the surface is enhanced in the presence of water. Finally, we discuss this problem with reference to recent experimental and theoretical studies of vacancy clustering at the (111) ceria surface. We also describe the simulation results for the structure and dynamics of liquid water using the SIESTA electronic structure approach. We find that the structure of water depends strongly on the particular basis set used. Applying a systematic approach to varying the basis set, we find that the basis set which results in good agreement with experimental binding energies for isolated water dimers also provides a reasonable description of the radial distribution functions of liquid water. We show that the structure of liquid water varies in a systematic fashion with the choice of basis set. Comparable to many other first-principle studies of liquid water using gradient-corrected density functionals, the liquid is found to be somewhat overstructured. The possibility of further improvements through a better choice of the basis set is discussed. We find that while improvements are likely to be possible, application to large-scale systems will require use of a computational algorithm whose computational cost scales linearly with system size. Finally, we study the molecular and atomic adsorption of oxygen on the gold nano-clusters. We show multiple stable and metastable structures for atomically and molecularly adsorbed oxygen to the gold cluster. We plan to predict the reaction pathway and calculate activation energy barrier for desorption of molecular oxygen from the atomically adsorbed gold cluster which is very important for any catalytic reaction occurring using gold nanoparticles.

In this thesis, Density Functional Theory (DFT) and Dynamical Mean-Field Theory (DMFT) approaches are applied to study the magnetic properties of transition metal nanosystems of different sizes and compositions. In particular, in order to take into account dynamical electron correlation effects (time-resolved local charge interactions), we have adopted the DFT+DMFT formalism and made it suitable for application to nanostructures. Preliminary application of this DFT+DMFT approach, using available codes, to study the magnetic properties of small (2 to 5-atom) Fe and FePt clusters provide meaningful results: dynamical effects lead to a reduction of the cluster magnetic moment as compared to that obtained from DFT or DFT+U (U being the Coulomb repulsion parameter). We have subsequently developed our own nanoDFT+DMFT code and applied it to examine the magnetization of iron particles containing10-147 atoms. Our results for the cluster magnetic moments are in a good agreement with experimental data. In particular, we are able to reproduce the oscillations in magnetic moment with size as observed in the experiments. Also, DFT+DMFT does not lead to an overestimation of magnetization for the clusters in the size range of 10-27 atoms found with DFT and DFT+U. On application of the nanoDFT+DMFT approach to systems with mixed geometry – Fe2O3 film, which are periodic (infinitely extended), in two directions, and finite in the third. Similar to DFT+U, we find that the surface atom magnetic moments are smaller compared to the bulk. However, the absolute values of the surface atoms magnetic moments are smaller in DFT+DMFT. In parallel, we have carried out a systematic study of magnetic anisotropy in bimetallic L10 FePt nanoparticles (20-484 atoms) by using two DFT-based approaches: direct and the torque method. We find that the magnetocrystalline anisotropy (MCA) of FePt clusters is larger than that of the pure Fe and Pt ones. We explain this effect by a large hybridization of 3d Fe- and 5d Pt-atom orbitals, which lead to enhancement of the magnetic moment of the Pt atom, and hence to a larger magnetic anisotropy because of large spin-orbit coupling of Pt atoms. In addition, we find that particles whose (large) central layer consists of Pt atoms, rather than Fe, have larger MCA due to stronger hybridization effects. Such 'protected' MCA, which does not require protective cladding, can be used in modern magnetic technologies.

This dissertation undertakes theoretical research into the adsorption, pattern formation, and reactions of atoms, molecules, and layered materials on catalyst surfaces. These investigations are carried out from first-principles calculations of electronic and geometric structures using density functional theory (DFT) for predictions and simulations at the atomic scale. The results should be useful for further study of the catalytic activities of materials and for engineering functional nanostructures. The first part of the dissertation focuses on systematic first-principles simulations of the energetic pathways of CO oxidation on the Cu2O(100) surface. These simulations show CO to oxidize spontaneously on the O-terminated Cu2O(100) surface by consuming surface oxygen atoms. The O-vacancy on Cu2O(100) then is subsequently healed by dissociative adsorption of atmospheric O2 molecules. The second part discusses the pattern formation of hydrogen on two and three layers of Co film grown on the Cu(111) surface. It is found that increasing the pressure of H2 changes the hydrogen structure from 2H-(2 × 2) to H-p(1 × 1) through an intermediate structure of 6H-(3 × 3). The third part compares the results of different ways of introducing van der Waals (vdW) interactions into DFT simulations of the adsorption and pattern formation of various molecules on certain substrates. Examinations of the physisorption of five nucleobases on iii graphene and of n-alkane on Pt(111) demonstrate the importance of taking vdW interactions into account, and of doing so in a way that is best suited to the particular system in question. More importantly, as the adsorption of 1,4 diaminebenzene molecules on Au(111) shows inclusion of vdW interactions is crucial for accurate simulation of the pattern formation. The final part carries out first-principles calculations of the geometric and electronic structure of the Moir´e pattern of a single layer of Molybdenum disulfide (MoS2 ) on Cu(111). The results reveal three possible stacking types. They also demonstrate that the MoS2 layer to be chemisorbed, albeit weakly, and that, while Cu surface atoms are vertically disordered, the layer itself is not strongly buckled.

The main focus of the thesis is to have better understanding of the atomic and electronic structures, vibrational dynamics and thermodynamics of metallic surfaces and bi-metallic nanoparticles (NPs) via a multi-scale simulational approach. The research presented here involves the study of the physical and chemical properties of metallic surfaces and NPs that are useful to determine their functionality in building novel materials. The study follows the 'bottom-up' approach for which the knowledge gathered at the scale of atoms and NPs serves as a base to build, at the macroscopic scale, materials with desired physical and chemical properties. We use a variety of theoretical and computational tools with different degrees of accuracy to study problems in different time and length scales. Interactions between the atoms are derived using both Density Functional Theory (DFT) and Embedded Atom Method (EAM), depending on the scale of the problem at hand. For some cases, both methods are used for the purpose of comparison. For revealing the local contributions to the vibrational dynamics and thermodynamics for the systems possessing site-specific environments, a local approach in real-space is used, namely Real Space Green's Function method (RSGF). For simulating diffusion of atoms/clusters and growth on metal surfaces, Molecular Statics (MS) and Molecular Dynamics (MD) methods are employed.

Motivated by our frustration with the lack of quantum chemistry methods for strongly-correlated open-shell systems, we develop quantitative methods for computing the electronic structure of such systems and qualitative tools for analyzing their chemical properties and reactivity. Specifically, we present a modern framework for performing sparse configuration interaction (CI) computations with arbitrary (Slater determinant) N-electron basis sets, using restricted or generalized spin-orbitals, and including computation of spin-polarized 1- and 2- electron reduced density matrices (RDMs). This framework is then used to implement the flexible ansätze for N-electron CI (FanCI) method more efficiently, via increased vectorization in the FanCI equations and use of sparse CI algorithms. We also extended the FanCI approach, including least-squares and stochastic optimization techniques, the computation of spin-polarized 1- and 2- electron RDMs, and transition energies (ionization potentials, electron affinities, and excitation energies). We use these tools to compare various open-shell CI methods and FanCI methods based on various antisymmetrized product of nonorthogonal geminals ansätze. To translate the vast amount of quantitative data present in the energies and (spin-polarized) density matrices of multiple open-shell states, we present a new, internally consistent and unambiguous framework for spin-polarized conceptual density-functional theory (SP-DFT) that reduces to a sensible formulation of spin-free CDFT in an appropriate limit. Using this framework, we were able to generalize the (non-spin-polarized) Parr function. We can also, using this framework, construct promolecules with proatoms having non-integer charges and multiplicities. Finally, we describe an equations-of-motion-based method for computing spin-polarized reactivity descriptors of a chemical system from only the ground state energy and the 1- and 2- electron RDMs from a single-point electronic structure computation, and show some benchmark computations for this method based on various CI and FanCI electronic structure methods. / Thesis / Doctor of Philosophy (PhD)

Due to recent advances in computational hardware and code accessibility, state-of-the-art calculations are currently employed to investigate materials at the nanoscale with varying levels of accuracy. As such, this dissertation highlights a series of materials ranging from one-dimensional wires, to reactive surfaces, to bulk crystals. Initial characterizations for all considered materials are carried out using density functional theory where additional approximations are utilized to obtain more complex quantities. For Millon's salt, first-principles calculations confirm a quasi-one-dimensional description where the metallic backbone influences electronic properties while hydrogen-bonding between ligands results in structural stability. We show that valence band dispersion can be controlled via strain or ligand substitution, pointing to tunable hole-carrier possibilities. Optical properties are also addressed with respect to experimental and theoretical findings. Our focus then shifts to titanium dioxide, a popular and promising photocatalyst. Specific nitrogen doping on the anatase (001) surface introduces intra gap states accessible for photoactivation in the visible. The additional presence of a fluorine dopant or oxygen vacancy enhances the density of these particular states available for transitions. Titanium dioxide also has experimentally displayed involvement in carbon dioxide reduction mechanisms. From first-principles calculations, anatase (001) surfaces containing an oxygen vacancy exhibit an increased potential for carbon dioxide to undergo reduction due to an exposed titanium atom in comparison to the pristine case. Other binding configurations on both types of surfaces suggest the existence of alternative conversion pathways. As a recently realized plasmonic material, titanium nitride proves advantageous in relation to more traditional materials, e.g., gold or silver; one of the main factors stems from its tunable permittivity. We investigate this aspect by theoretically incorporating defects into titanium nitride, which introduces a systematic approach to control plasmonic activity over a broad frequency range. Finally, lifetimes of hot-electrons, originating from plasmonic decay, for instance, possess finite lifetimes in titanium nitride, as well as in other similar materials, that are described by electron-electron interactions through the electron self-energy. Average lifetimes resemble those obtained with a free electron gas model while details of the band structure influence lifetime behavior. Calculations exploring factors affecting these lifetimes are presented.

The results of the application of a density functional theory method incorporating dispersive corrections in the 2010 crystal structure prediction blind test are reported. The method correctly predicted four out of the six experimental structures. Three of the four correct predictions were found to have the lowest lattice energy of any crystal structure for that molecule. The experimental crystal structures for all six compounds were found during the structure generation phase of the simulations, indicating that the tailor-made force fields used for screening structures were valid and that the structure generation engine, which combines a Monte Carlo parallel tempering algorithm with an efficient lattice energy minimiser, was working effectively. For the three compounds for which the experimental crystal structures did not correspond to the lowest energy structures found, the method for calculating the lattice energy needs to be further refined or there may be other polymorphs that have not yet been found experimentally.