Modeling systems in liquid is imperative to chemistry, as many reactions take place in liquid, and nearly all of biochemistry is in the liquid state. Solvation Model 12 (SM12) is the newest Generalized Born Approximation iteration of a series of solvation models from Minnesota, it shows great promise for accurate, description of solutions. Shown is the full implementation of SM12 in to the pure Slater Type Orbital code, the Amsterdam Density Functional (ADF) package in particular. The model performs as well as its Gaussian Type Orbital counterpart. The model has been extended to account for periodic boundary conditions, as presented by the ADF-BAND code. The extension to infinite boundaries creates interesting edge effects that need to be taken into consideration, and are accounted for through cut off approximations and a screening function to ensure the potential is well-behaved. / October 2016

The physical and chemical properties of materials are intimately related to their underlying crystal structure: the detailed arrangement of atoms and chemical bonds within. This thesis uses computational methods to predict crystal structure, with a particular focus on structures and stable phases that emerge at high pressure. We explore three distinct systems. We first apply the ab initio random structure searching (AIRSS) technique and density functional theory (DFT) calculations to investigate the high-pressure behaviour of beryllium, magnesium and calcium difluorides. We find that beryllium fluoride is extensively polymorphic at low pressures, and predict two new phases for this compound - the silica moganite and CaCl$_2$ structures - to be stable over the wide pressure range 12-57 GPa. For magnesium fluoride, our results show that the orthorhombic `O-I' TiO$_2$ structure ($Pbca$, $Z=8$) is stable for this compound between 40 and 44 GPa. Our searches find no new phases at the static-lattice level for calcium difluoride between 0 and 70 GPa; however, a phase with $P\overline{6}2m$ symmetry is energetically close to stability over this pressure range, and our calculations predict that this phase is stabilised at high temperature. The $P\overline{6}2m$ structure exhibits an unstable phonon mode at large volumes which may signal a transition to a superionic state at high temperatures. The Group-II difluorides are isoelectronic to a number of other AB$_2$-type compounds such as SiO$_2$ and TiO$_2$, and we discuss our results in light of these similarities. Compressed hydrogen sulfide (H$_2$S) has recently attracted experimental and theoretical interest due to the observation of high-temperature superconductivity in this compound ($T_c$ = 203 K) at high pressure (155 GPa). We use the AIRSS technique and DFT calculations to determine the stable phases and chemical stoichiometries formed in the hydrogen-sulfur system as a function of pressure. We find that this system supports numerous stable compounds: H$_3$S, H$_7$S$_3$, H$_2$S, H$_3$S$_2$, H$_4$S$_3$, H$_2$S$_3$ and HS$_2$, at various pressures. Working as part of a collaboration, our predicted H$_3$S and H$_4$S$_3$ structures are shown to be consistent with XRD data for this system, with H$_4$S$_3$ identified as a major decomposition product of H$_2$S in the lead-up to the superconducting state. Calcium and oxygen are two elements of generally high terrestrial and cosmic abundance, and we explore structures of calcium peroxide (CaO$_2$) in the pressure range 0-200 GPa. Stable structures for CaO$_2$ with $C2/c$, $I4/mcm$ and $P2_1/c$ symmetries emerge at pressures below 40 GPa, which we find are thermodynamically stable against decomposition into CaO and O$_2$. The stability of CaO$_2$ with respect to decomposition increases with pressure, with peak stability occurring at the CaO B1-B2 phase transition at 65 GPa. Phonon calculations using the quasiharmonic approximation show that CaO$_2$ is a stable oxide of calcium at mantle temperatures and pressures, highlighting a possible role for CaO$_2$ in planetary geochemistry, as a mineral redox buffer. We sketch the phase diagram for CaO$_2$, and find at least five new stable phases in the pressure/temperature ranges 0 $\leq P\leq$ 60 GPa, 0 $\leq T\leq$ 600 K, including two new candidates for the zero-pressure ground state structure.

<div>Partition Density Functional Theory (P-DFT) is a formally exact method to find the ground-state energy and density of molecules via self-consistent calculations on isolated fragments. It is being used to improve the accuracy of Kohn-Sham DFT (KS-DFT) calculations and to lower their computational cost. Here, the method has been extended to be applicable to semi-infinite and periodic systems. This extension involves the development of new algorithms to calculate the exact partition potential, a central quantity of P-DFT. A novel feature of these algorithms is that they are applicable to systems of constant chemical potential, and not only to systems of constant electron number. We illustrate our method on one-dimensional model systems designed to mimic metal-atom interfaces and atomic chains. From extensive numerical tests on these model systems, we infer that: 1.) The usual derivative discontinuities of open-system KS-DFT are reduced (but do not disappear completely) when an atom is at a nite distance from a metallic reservoir; 2.) In situations where we do not have chemical potential equalization between fragments of a system, a new constraint for P-DFT emerges which relates the fragment chemical potentials and the combined system chemical potential; 3.) P-DFT is an ideal method for studying charge transfer and fragment interactions due to the correct ensemble treatment of fractional electron charges; 4.) Key features of the partition potential at the metalatom interface are correlated to well-known features of the underlying KS potential; and 5.) When there is chemical potential equalization between an atom and a metal surface it is interacting with, there is strong charge transfer between the metal and atom. In these cases of charge transfer the density response to an innitesimal change in the chemical potential is located almost exclusively around the atom. On the other hand, when the fragment chemical potentials do not equalize, the density response only aects the surface Friedel oscillations in the metal.</div>

Doctor of Philosophy / Department of Chemical Engineering / Bin Liu / In the course of mitigating our dependence on fossil energy, it has become an urgent issue to develop unconventional and innovative technologies based on renewable energy utilization for fuels and chemicals production. Due to the lack of fundamental understanding of catalytic behaviors of the novel chemical compounds involved, the task to design and engineer effective catalytic systems is extremely challenging and time-consuming. One central challenge is that an intricate balance among catalytic reactivity, selectivity, durability, and affordability must be achieved pertinent to any successful design. In this dissertation, density functional theory (DFT), coupled with modeling techniques derived from DFT, is employed to gain insights into molecular interactions between elusive intermediates and targeted functional catalytic materials for novel electrochemical and heterogeneous catalytic processes. Two case studies, i.e., electroreduction of furfural and step-catalysis for cyclic ammonia production, will be discussed to demonstrate the capability and utility of DFT-based theoretical modeling toolkits and strategies. Transition metal cathodes such as silver, lead, and nickel were evaluated for furfuryl alcohol and 2-methylfuran production through detailed DFT modeling. Investigation of the molecular mechanisms revealed that two intermediates, mh6 and mh7 from mono-hydrogenation of furfural, are the key intermediates that will determine the product formation activities and selectivities. Nickel breaks the trends from other metals as DFT calculations suggested the 2-methylfuran formation pathway is most likely different from other cathodes. In this work, the Brønsted–Evans–Polanyi relationship, derived from DFT energy barrier calculations, has been found to be particularly reliable and computationally efficient for C-O bond activation trend predictions. To obtain the solvation effect on the adsorptions of biomass-derived compounds (e.g., furfural and glycerol), influence of explicit solvent was probed using periodic DFT calculations. The adsorptions of glycerol and its dehydrogenation intermediates at the water-platinum surface were understood via various water–adsorbate, water–water, and water–metal interactions. Interestingly, the bond-order-based scaling relationship established in solvent-free environment is found to remain valid based on our explicit solvent models. In the second case study, step-catalysis that relies on manganese’s ability to dissociate molecular nitrogen and as a nitrogen carrier emerges as an alternative route for ammonia production to the conventional Haber-Bosch process. In this collaborative project, DFT was used as the primary tool to produce the mechanistic understanding of NH3 formation via hydrogen reduction on various manganese nitride systems (e.g., Mn4N and Mn2N). Both nickel and iron dopants have the potential to facilitate NH3 formation. A broader consideration of a wide range of nitride configurations revealed a rather complex pattern. Materials screening strategies, supported by linear scaling relationships, suggested the linear correlations between NHx (x=0, 1, 2) species must be broken in the development of optimal step catalysis materials. These fundamental findings are expected to significantly guide and accelerate the experimental material design. Overall, molecular modeling based on DFT has clearly demonstrated its remarkable value beyond just a validation tool. More importantly, its unique predictive power should be prized as an avenue for scientific advance through the fundamental knowledge in novel catalysts design.

We present a theoretical framework based on an extension of Dynamical Density Functional Theory (DDFT) to describe the structure and dynamics of cells in living tissues and tumours. DDFT is a microscopic statistical mechanical theory for the time evolution of the density distribution of interacting many-particle systems. The theory accounts for cell pair-interactions, different cell types, phenotypes and cell birth and death processes (including cell division), in order to provide a biophysically consistent description of processes bridging across the scales, including the description of the tissue structure down to the level of the individual cells. Analysis of the model is presented for a single species and a two-species cases, the latter describing competition between a cancerous and healthy cells. In suitable parameter regimes, model results are consistent with biological observations. Of particular note, divergent tumour growth behaviour, mirroring metastatic and benign growth characteristics, are shown to be dependent on the cell pair-interaction parameters.

Keggin-based aluminum nanoclusters have been noted to be efficient sorbents for the adsorption of arsenic, copper, lead, and zinc from water. Obtaining a molecular-level understanding of the adsorption processes associated with these molecules is of fundamental importance and could pave the way for rational design strategies for water treatment. Furthermore, due to their size and the availability of experimental crystal structures, Al nanoclusters are computationally tractable at the atomistic modeling level. The adsorption of contaminants onto metal-oxide surfaces with nanoscale Keggin-type structural topologies has been established, but identification of the reactive sites and the exact binding mechanism are lacking. In more common surface studies the two main factors that affect reactivity have been found to be charge and functional group identity. Since Al nanoclusters each have a distinct shape we introduce the effects of shape as a third factor. In all the work presented in this dissertation, it is extremely apparent that the shape of the aluminum particle plays the most important role in nanoparticle reactivity studies. We first focus on the reactivity of three aluminum polycations: [Al13O4(OH)24(H2O)12]7+ (Al13), [Al30O8(OH)56(H2O)26]18+ (Al30), and [Al32O8(OH)60(H2O)30]20+ (Al32). Using outer-sphere adsorption of sulfate and chloride as probe adsorbents, density functional theory (DFT) calculations determined that the reactivity can be represented as a function of particle topology, and not functional group identity or charge. Further exploring the shape-reactivity relationship of Al30 we reveal that cations and anions have opposing trends and ion reactivity can be generalized. It is determined that all cations favor the adsorption sites on the caps of Al30 and all anions favor adsorption in the beltway (middle) region. This result is supported by the visualization of the electrostatic potential of Al30 and three-dimensional induced charge density maps. The middle of the cluster is more positive than the caps, and this promotes anion adsorption in the beltway and cation adsorption on the caps. Next we explore the reactivity of co-adsorption (outer-sphere anions and inner-sphere cations) onto Al30 through a collaborative approach. Al30 with two surface-bound Cu2+ cations (Cu2Al30-S) was experimentally crystallized in the presence of disulfonate anions; however, in the Cu2Al30-S structure the cations bind to the beltway region of the cluster. Using DFT we determined that the counter anions play a key (and governing) role in the crystallization of Cu2Al30-S. This result that outer-sphere adsorption dictates inner-sphere adsorption does not appear in surface calculations, it is unique to Keggin studies. Seeing that all anions favor adsorption to the beltway region and all cations favor adsorption to the cap region we set out to determine if any reactivity patterns can be reversed. In order to do this inner-sphere As(V) and P(V) adsorption is modeled onto Al30 through another collaborative approach. The experimental crystal structure of (TBP)2[Al2(μ4-O8)(Al28(μ2-OH)56(H2O)26)]14+ (where TBP = t-butylphosphonate (CH3)3CPO3) has been synthesized, and using DFT calculations we can alter the R-group of P(V) or the DFT As(V) analogue to see if the inner-sphere anion ever prefers to bind to the cap region instead of the beltway. We observe that no matter the intrinsic properties of the R-group the anion always prefers to bind to the beltway region, which once again shows that the shape-reactivity relationship plays a major role in Keggin based structure reactivity. Since As(V) is such a harmful ion we extend our As(V) adsorption studies to aluminum surfaces. As(V) has been experimentally shown to bind to aluminum surfaces in a bidentate binuclear configuration. By modeling a variety of configurations we can confirm and explain that the bidentate binuclear configuration is most stable due to the least amount of strain on the As(V) atom. Aluminum surfaces are common DFT models to study but are computationally expensive, due to this fact some people choose to model small Al octahedral cluster models instead. Comparing the reactivity of both systems we see a significant difference in energy magnitudes and ranges and can conclude that small Al octahedral cluster models cannot take place of aluminum surfaces. All in all, the work presented in this dissertation provides an important contribution in our understanding of Keggin based Al compounds. Keggin based compounds are very sparsely studied computationally and this work helps to fill a knowledge gap. Hopefully the insights obtained from this work can help guide future Keggin based studies.

Abstract Detailed in this manuscript is a methodology to model ground state properties of 4He droplets at zero pressure and zero Kelvin using a density functional theory of liquid helium. The density functional approach examined here consists of two noted functionals from the literature and corresponding mean field definitions. A mean field and trial density are defined for each system and optimized to self-consistency using a matrix diagonalization technique. Initial calculations of planar slabs are performed and demonstrate reasonable agreement with experiment and with prior studies using density functional theory. Quantum properties of droplets and droplets containing atomic dopants are calculated. Three different He-dopant potentials are examined to test the limits of the functional methods. For each impurity interaction, an average of 12 atoms were found to reside in the first solvation shell with an atomic dopant placed at the droplet center. Maximum densities in the first solvation shell reached those of solid helium as predicted by DF methods.

Cerium(IV) oxide (CeO2), ceria, is an active metal oxide used in solid oxide fuel cells and for the purification of exhaust gases in vehicle emissions control. Behind these technically important applications of ceria lies one overriding feature, namely ceria's exceptional reduction-oxidation properties. These are enabled by the duality of the cerium ion which easily toggles between Ce4+ and Ce3+. Here the cerium 4f electrons and oxygen vacancies (missing oxygen ions in the structure) are key players. In this thesis, the nature of ceria's f electrons and oxygen vacancies are in focus, and examined with theoretical calculations. It is shown that for single oxygen vacancies at ceria surfaces, the intimate coupling between geometrical structure and electron localisation gives a multitude of almost degenerate local energy mimima. With many vacancies, the situation becomes even more complex, and not even state-of-the-art quantum-mechanical calculations manage to predict the experimentally observed phenomenon of vacancy clustering. Instead, an alternative set of computer experiments managed to produce stable vacancy chains and trimers consistent with experimental findings from the literature and revealed a new general principle for surface vacancy clustering. The rich surface chemistry of ceria involves not only oxygen vacancies but also other active oxygen species such as superoxide ions (O2−). Experiments have shown that nanocrystalline ceria demonstrates an unusually large oxygen storage capacity (OSC) and an appreciable low-temperature redox activity, which have been ascribed to superoxide species. A mechanism explaining these phenomena is presented. The ceria surface is also known to interact with SOx molecules, which is relevant both in the context of sulfur poisoning of ceria-based catalysts and sulfur recovery from them. In this thesis, the sulfur species and key mechanisms involved are identified.

The phase behaviors and microstructures of various realistic and model mixtures of macro and micro molecules, such as polyolefin solutions and nanoparticle block copolymer composites, have been accurately predicted by the application of Statistical Associating Fluid Theory (SAFT) based approaches through various extensions that improve both the physical description of molecular interactions and efficiency of computations. The extensions are presented in a generic sense that is applicable to other studies. These rigorously derived theories have been demonstrated to capture material structure-property relationships and can be applied broadly to other fields including biology, medicine and energy industry. On the phenomenogical scale, the novel SAFT-Dimer equation of state has been extended to study the liquid-liquid phase boundary (cloud point) in polyolefin solutions. A simplified model of the polyolefin molecules has been followed and the effect of various parameters, such as temperature, molecular weight, solvent quality and comonomer content, on the phase behavior has been successfully captured by the theoretical model through comparison with experimental measurements. The presented approach requires less parameters than previous methods and is of critical value to the industrial productions of polymers, especially polyolefins with long branches. On the molecular scale, the interfacial SAFT (iSAFT) Density Functional Theory (DFT) has been extended to include a dispersion free energy functional that explicitly accounts for molecular correlations. The Order-Disorder Transition (ODT) between lamellar and disordered phase has then been investigated for pure block copolymer and copolymer nanocomposite systems. The extension has been shown to dramatically improve the ODT predictions of iSAFT as well as the self assembled microstructures in nanocomposites over previous DFT calculations, in comparison to coarse grained molecular simulations. The behavior of the equilibrium spacing of ordered structures is also examined against the variation of copolymer size and interactions. An efficient numerical scheme, Fast Fourier Transform (FFT), has been implemented and shown to drastically increase the computation efficiency. The theory has then been extended to study block copolymer morphologies with density variations in multiple dimensions. Comprehensive phase diagrams including lamellar, cylindrical and disordered phases have been obtained for copolymer nanocomposites for the first time using a single framework molecular theory. In addition, the nanoparticle induced morphological transition between cylindrical and lamellar phase has been studied using a pseudo arc-length continuation method. Transition evolution is tracked and metastable morphologies are examined and compared with existing experimental reports and theoretical calculations. With these extensions, iSAFT offers a powerful prediction tool that closely relates molecular structure to thermophysical properties and provides an efficient alternative to screen parameter space for specified material properties.

The chloro and pyridinate derivatives of rhenium(I) tricarbonyl complexes containing the diimine ligands 2,2’-bipyrazine (bpz) and 5,5’-dimethyl-2,2’-bipyrazine (Me2bpz) are discussed. When compared to similar rhenium(I) tricarbonyl complexes of 2,2’-bipyridine (bpy) and 2,2’-bipyrimidine (bpm), the Me2bpz complexes are comparable to bpm derivatives and their properties are intermediate between those of bpy and bpz complexes. Also discussed is the synthesis and properties of two new analogues of ruthenium(II) tris-bipyridine, a monomer and dimer. The complexes contain the ligand 6,6’-(1,2-ethanediyl)bis-2,2’-bipyridine (O-bpy) which contains two bipyridine units bridged in the 6,6’ positions by an ethylene group. Crystal structures of the two complexes formulated as [Ru(bpy)(O-bpy)](PF6)2 and [(Ru(bpy)2)2(O-bpy)](PF6)4 reveal structures of lower symmetry than D3 which affects the electronic properties of the complexes as revealed by Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TDDFT) calculations. Iron(II) tris-bipyrazine undergoes dissociation in solution with loss of the three bipyrazine ligands. The rate of the reaction in acetonitrile depends on the concentration of anions present in the solution. The rate is fastest in the presence of Cl- and slowest in the presence of Br-. In a second discussion DFT calculations are used to explore four iron(II) diimine complexes. DFT calculations show the higher energy HOMO (highest occupied molecular orbital) orbitals of the four complexes are metal centered and the lower energy LUMO (lowest unoccupied molecular orbitals) are ligand centered. / Dissertation(Ph.D.)--Wichita State University, College of Liberal Arts and Sciences, Dept. of Chemistry