Melatonin (N-acetyl-5-methoxytryptamin, MLT) is a naturally occurring antioxidant which has shown some potential for use as a spin trap. Spin traps react with short lived hydroxyl radicals (HO·) to produce more stable products called spin adducts which may be characterized by electron paramagnetic resonance spectroscopy. However, the relative stability of hydroxyl spin adducts of melatonin derivatives (MLTD) compared to 2-hydroxymelatonin (HO-MLT) has not been examined computationally. Computational studies have been done on four selected MLTD; methylmelatonin (Me-MLT), chloromelatonin (Cl-MLT), cyanomelatonin (CN-MLT), and nitromelatonin (NO2-MLT). Geometry of the structures were optimized at the HF/6-31G(d), cc-pVXZ, (X=D and T) and DFT/B3LYP/6-31G(d), cc-pVDZ and cc-pVTZ levels of theory and extrapolated to the complete basis set limit using cc-pVXZ (X=D, T) basis sets. The lowest relative energy was found to be a mix of results for 2-OH-MLT-Me at HF and 2-OH-MLT-NO2 at DFT.

Topological materials have discovered ultrahigh magnetoresistance, chiral anomalies, the inherent anomalous Hall effect, and unique Fermi arc surface states. Topological materials now include insulators, metals, and semimetals. Weyl semimetals (WSM) are topological materials that show linear dispersion with crossings in their band structure which creates the pair of Weyl nodes of opposite chirality. WSMs have topological Fermi arc surface states connecting opposing chirality Weyl nodes. Spin-orbit coupling can result in the band opening in Dirac nodal rings, and creating the pair of Weyl nodes either by breaking the time-reversal or spatial inversion symmetry (but not both) 1-3. The chirality of a Weyl node is set by the Berry flux through a closed surface in reciprocal space around it. The purpose of this thesis was to characterize and investigate the thermodynamic stability of WSM. To accomplish these goals, quantum mechanical modeling at the level of density functional theory (DFT) was used. WloopPHI, a Python module, integrates the characterization of WSMs into WIEN2k, a full-potential all-electron density functional theory package. It calculates the chirality of the Weyl node (monopole charge) with an enhanced Wilson loop method and Berry phase approach. First, TaAs, a well-characterized Weyl semimetal, validates the code theoretically. We then used the approach to characterize the newly discovered WSM YRh6Ge4, and we found a set of Weyl points into it. Further, we study the stability of the kagome-based materials A3Sn2S2, where A is Co, Rh, or Ru, in the context of the ternary phase diagrams and competing binary compounds using DFT. We demonstrated that Co3Sn2S2 and Rh3Sn2S2 are stable compounds by examining the convex hull and ternary phase diagrams. It is feasible to synthesize Co3Sn2S2 by a chemical reaction between SnS, CoSn and Co9S8. Moreover, Rh3Sn2S2 can be produced by SnS, RhSn and Rh3S4. On the other hand, we found that Ru3Sn2S2 is a thermodynamically unstable material with respect to RuS2, Ru3S7 and Ru. Our work provides some insights for confirming materials using the DFT approach. 1. S. M. Young et al. Dirac Semimetal in Three Dimensions. Physical Review Letters108(14) (2012), 140405. 2. J. Liu and D. Vanderbilt. Weyl semimetals from noncentrosymmetric topological insulators. Physical Review B 90(15) (2014), 155316. 3. H. Weng et al. Weyl Semimetal Phase in Noncentrosymmetric Transition-Metal Monophosphides. Physical Review X 5(1) (2015), 011029. / Thesis / Master of Applied Science (MASc)

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)