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- Computational Investigation of Molecular Optoelectronic and Biological Systems
- The scope of work in this dissertation has comprised several major investigations on applications and theoretical studies of ab initio quantum mechanics and density functional theory where those techniques were applied to the following: (i) investigation of the performance of density functionals for the computations of molecular properties of 3d transition metal containing systems; (ii) guidance for experimental groups for rational design of macrometallocyclic multinuclear complexes with superior π-acidity and π-basicity that are most suitable for p- and n-type semiconductors of metal-organic molecules and nanomaterials; (iii) investigation of the metallo-aromaticity of multi-nuclear metal complexes; (iv) investigation of the kinetics and thermodynamics of copper-mediated nitrene insertion into C-H and H-H bond; and (v) accurate computations of dissociation energies of hydrogen-bonded DNA duplex moieties utilizing the resolution of identity correlation consistent composite approach (RI-ccCA).
- Computational Studies of Inorganic Systems with a Multiscale Modeling Approach: From Atomistic to Continuum Scale
- Multiscale modeling is an effective tool for integrating different computational methods, creating a way of modeling diverse chemical and physical phenomena. Presented are studies on a variety of chemical problems at different computational scales and also the combination of different computational methods to study a single phenomenon. The methods used encompass density functional theory (DFT), molecular dynamics (MD) simulations and finite element analysis (FEA). The DFT studies were conducted both on the molecular level and using plane-wave methods. The particular topics studied using DFT are the rational catalyst design of complexes for C—H bond activation, oxidation of nickel surfaces and the calculation of interaction properties of carbon dioxide containing systems directed towards carbon dioxide sequestration studies. Second and third row (typically precious metals) transition metal complexes are known to possess certain electronic features that define their structure and reactivity, and which are usually not observed in their first-row (base metal) congeners. Can these electronic features be conferred onto first-row transition metals with the aid of non-innocent and/or very high-field ligands? Using DFT, the impact of these electronic features upon methane C—H bond activation was modeled using the dipyridylazaallyl (smif) supporting ligand for late, first-row transition metal (M) imide, oxo and carbene complexes (M = Fe, Co, Ni, Cu; E = O, NMe, CMe2). To promote a greater understanding of the process and nature of metal passivation, first-principles analysis of partially oxidized Ni(111) and Ni(311) surface and ultra-thin film NiO layers on Ni(111) was performed. A bimodal theoretical strategy that considers the oxidation process using either a fixed GGA functional for the description of all atoms in the system, or a perturbation approach, that perturbs the electronic structure of various Ni atoms in contact with oxygen by application of the GGA+U technique was applied. Binding energy of oxygen to the nickel surfaces, charge states of nickel and oxygen, and the preferred binding mode of oxygen to nickel were studied to gain a better understanding of the formation of oxide layers. Using density functional theory, the thermodynamic properties for developing interaction potentials for molecular dynamics simulations of carbon dioxide systems were calculated. The interactions considered are Ni + H2O, Ni + Ni, Ni + CO2, CO2 + CO2, CO2 + H2O and H2O + H2O. These systems were chosen as the possible interactions that can occur when carbon dioxide is stored in the ocean. Molecular dynamics simulations using the results from the DFT studies were also conducted. Finally, thermal conduction analysis was performed on layered functionally graded materials (FGM) subjected to thermal shock by sudden cooling of the material in order to investigate the results obtained from three different mixing laws: linear, quadratic, and half-order. The functionally graded material considered was a composite of nickel and carbon nanotubes at different compositions varying from two to five layers. The middle layers for the three to five layers are composed of graded (i.e., gradually changing) percentages of nickel and carbon nanotube. The thermal conductivity, specific heat and density for the composites were calculated depending on the percentages of materials in each layer, and assuming different rules of mixture.
- Modeling Transition Metal Chemistry for Catalytic Functionalization of Molecules
- The diversity of transition metal complexes allows for a wide range of chemical processes to be mediated by the metal, from catalysis to surface chemistry. Investigations into the structure and electronic configuration of transition metal complexes allow for tuning of desired species by modifications to the ligands and/or metals to achieve more efficient thermodynamics and kinetics for the process of interest. Transition metals, often used in catalysts for a number of important processes, require detailed descriptions of intermediates, transition states and products to fully characterize a reaction mechanism(s) in order to design more active and efficient catalysts. Computational investigations into inorganic catalysts are explored with the aim of understanding the activity of each species and how modifications of supporting ligands, co-ligands and metals vary the interaction along the reaction pathway. Reported results give important insight into the development of the most active complexes in addition to determining the least active complexes to aid experimental development. This report first investigates the mechanisms of two unique transfer reactions: 1) formation of low coordinate nickel-nitrene ((P~P)Ni=NR; P~P = 1,2-bis(dihydrophosphino)-ethane or 1,2-bis(difluoromethylphosphino)-ethane) complexes as catalysts for nitrogen atom transfer and 2) oxidation of a triphosphorus niobium complex, [(η2-P3SnPh3)Nb(OMe)3], for the transfer of the phosphorus synthon, Ph3SnP3. These reactions have utility in the synthesis of nitrogen and phosphorus containing molecules, respectively, and the results presented provide mechanistic insight into the synthesis of the organometallic intermediates. Additionally, a computational approach towards rational catalyst design was performed on the ruthenium based hydroarylation catalyst TpRu(CO)(Ph) [Tp = hydrido-tris(pyrazolyl)borate]. Targeted modifications at the Tp, metal and co-ligand (CO) sites were studied in order to tune the electronics and sterics of the catalyst. Modifications, through computational methods, provided a more cost- and time-efficient way to study the impact of modifications, which provided direct input into attractive synthetic targets. The research described heir in highlights the use of computational chemistry methodologies, specifically DFT, in collaboration with experimental results, for the accurate description of reaction geometries and factors influencing the thermodynamics and kinetics of the systems. Valuable insight is gained by treating inorganic complexes with theoretical methods and additionally provides a fast, cheap way to predict and understand the chemistry of such complex systems.
- Water-soluble Phosphors for Hypoxia Detection in Chemical and Biological Media
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Water-soluble Pt(II) phosphors exist predominantly for photophysical studies. However, fewer are known to be candidates for cisplatin derivatives. If such a molecule could exist, it would be efficient at not only destroying the cancerous cells which harm the body, but the destruction would also be traceable within the human body as it occurred. Herein, research accomplished in chemistry describes the photophysical properties of a water-soluble phosphor. Spectroscopically, this phosphor is unique in that it possesses a strong green emission at room temperature in aqueous media. Its emission is also sensitive to the gaseous environment. These properties have been expanded to both analytical and biological applications. Studies showing the potential use of the phosphor as a heavy metal remover from aqueous solutions have been accomplished. The removal of toxic heavy metals was indicated by the loss of emission as well as the appearance of a precipitate. The gaseous sensitivity was elicited to be used as a potential cancerous cell biomarker. In vivo studies were accomplished in a wide variety of species, including bacteria (E. coli), worms (C. elegans), small crustaceans (Artemia), and fish (D. rerio and S. ocellatus). The phosphor in question is detectable in all of the above. This fundamental research lays the foundation for further expansion into bioinorganic chemistry, and many other possible applications.