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Browsing by Author "Dixon, David A."

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Accelerating the insertion reactions of (NHC)Cu-H via remote ligand functionalization
(Royal Society of Chemistry, 2021) Speelman, Amy L.; Tran, Ba L.; Erickson, Jeremy D.; Vasiliu, Monica; Dixon, David A.; Bullock, R. Morris; United States Department of Energy (DOE); Pacific Northwest National Laboratory; University of Alabama Tuscaloosa
Most ligand designs for reactions catalyzed by (NHC)Cu-H (NHC = N-heterocyclic carbene ligand) have focused on introducing steric bulk near the Cu center. Here, we evaluate the effect of remote ligand modification in a series of [(NHC)CuH](2) in which the para substituent (R) on the N-aryl groups of the NHC is Me, Et, Bu-t, OMe or Cl. Although the R group is distant (6 bonds away) from the reactive Cu center, the complexes have different spectroscopic signatures. Kinetics studies of the insertion of ketone, aldimine, alkyne, and unactivated alpha-olefin substrates reveal that Cu-H complexes with bulky or electron-rich R groups undergo faster substrate insertion. The predominant cause of this phenomenon is destabilization of the [(NHC)CuH](2) dimer relative to the (NHC)Cu-H monomer, resulting in faster formation of Cu-H monomer. These findings indicate that remote functionalization of NHCs is a compelling strategy for accelerating the rate of substrate insertion with Cu-H species.
Boron-Substituted 1,3-Dihydro-1,3-azaborines: Synthesis, Structure, and Evaluation of Aromaticity
(Wiley-VCH, 2013) Xu, Senmiao; Mikulas, Tanya C.; Zakharov, Lev N.; Dixon, David A.; Liu, Shih-Yuan; University of Oregon; University of Alabama Tuscaloosa
A comparison of hydrogen release kinetics from 5-and 6-membered 1,2-BN-cycloalkanes
(Royal Society of Chemistry, 2021) Giustra, Zachary X.; Chen, Gang; Vasiliu, Monica; Karkamkar, Abhijeet; Autrey, Tom; Dixon, David A.; Liu, Shih-Yuan; Boston College; University of Alabama Tuscaloosa; United States Department of Energy (DOE); Pacific Northwest National Laboratory
The reaction order and Arrhenius activation parameters for spontaneous hydrogen release from cyclic amine boranes, i.e., BN-cycloalkanes, were determined for 1,2-BN-cyclohexane (1) and 3-methyl-1,2-BN-cyclopentane (2) in tetraglyme. Computational analysis identified a mechanism involving catalytic substrate activation by a ring-opened form of 1 or 2 as being consistent with experimental observations.
Computational Predictions for the Interactions of Lewis Acid Gases with Each Other and with Materials of Interest
(University of Alabama Libraries, 2021) Lee, Zachary Ryan; Dixon, David A.; University of Alabama Tuscaloosa
This dissertation focuses on the computational chemistry predictions of the mechanisms and products of Lewis acid gases with materials of interest to understand the chemistry of these systems and to aid in the design of practical sorbents for acid gas separations and conversions. A detailed computational investigation of the species present prior to the introduction of a sorbent was performed. The barriers and overall thermodynamics of H2SO4, H2SO3, H2S2O3, and H2S2O2 formation from the reactions of SOx (x = 2 or 3) with H2O and H2S in both gas phase and in aqueous solution as well as the resulting acidities of these BrÃ¸nsted acids were predicted. These calculations were performed using the Feller-Peterson-Dixon (FPD) methodology with implicit MP2/aug-cc-pVTZ/COSMO corrections included for predicting energies in aqueous solution and predict favorable formation of strongly acidic H2SO4 and the experimentally elusive H2S2O3. The thermodynamics of a novel type of NO2 adsorption to Groups IV and VI transition metal oxide clusters, calculated at the CCSD(T)//B3LYP level, are compared directly to the previously predicted binding energies of CO2, SO2, and H2O to these oxides and correlated with the M-O bond dissociation enthalpy, vertical excitation energy, electron affinity, and ionization potential trends of the bare metal oxides themselves. The results provide key insight into the importance of band gaps and M-O bond strengths for the selection of metal oxides for NOx separations. The role of 4f electrons and the surrounding ligand environment on the acid gas interactions of H2O, NO2, and SO2 with a promising class of metal-organic frameworks (MOFs), the rare-earth 2,5-dihydroxyterephthalic acid frameworks, was studied using DFT for both a cluster model which explicitly treats the lanthanide 4f electrons and a periodic model to predict bulk interactions without the inclusion of active 4f electrons. Insight into the reaction mechanisms of the promising post-combustion capture of CO2 by aqueous and solid-state amines was studied primarily using the composite G3(MP2) methodology. As a whole, these studies provide a detailed understanding of the chemical thermodynamics and kinetics relevant to acid gas capture by promising materials of interest.
Computational Predictions of the Thermochemical Properties of Metal Oxides and Hydrolysis of Actinide Oxides
(University of Alabama Libraries, 2024) Lontchi, Eddy Mfopah; Dixon, David A.; Street, Shane C.
Actinide oxides play an important role in the energy sector in terms of fuels for nuclear power generation to reduce our carbon footprint and for fuel reprocessing and management of spent fuel. Pa and Group V transition metals share a similar pentavalent oxidation state, but Pa oxides with 5f valence orbitals are less explored than the transition metal oxides. The structures and thermochemical properties of various M2O5 (M = V, Nb, Ta, Pa) isomers were predicted together with single metal oxides, hydroxides, and fluorides using the Feller-Peterson-Dixon (FPD) approach at the coupled cluster CCSD(T)/CBS (complete basis set) level of calculation. The structure of Pa2O5 exhibits actinyl character dominated by the interaction of PaO2+ groups with a bridging O2-. The results provide insights into Pa being a transitional element between actinide character as found for U and transition metal character as found for Ac and Th. Hydrolysis reactions play an important role in processes across the nuclear enterprise and are important in the transformation of metal oxides to hydroxides. A detailed computational investigation was made to predict the hydrolysis of various high oxidation state actinide oxides (An = Th - Pu). Reaction coordinates were calculated based on geometries at the DFT/B3LYP level with additional energetics at the higher MP2, and/or CCSD(T) levels. Hydrolysis is initiated by the formation of a Lewis acid/base adduct with H2O adding to the actinide followed by proton transfer to an adjacent oxygen. The initial physisorption (physical adsorption) energy of H2O on the An was predicted to fall between −20 to −30 kcal/mol. The stability of the chemisorption (chemical adsorption) product varied across the actinide series and the structural conformation of the products. Thorium oxides (ThnO2n) (n = 1 - 6) were predicted to have a high propensity for hydrolysis, readily forming hydroxide products over hydrated complexes. The hydrolysis reactions of Pa monomer and dimers were also predicted to be exothermic. Hydrolysis reactions of U, Np, and Pu were predicted to be the least capable of achieving full hydrolysis.In addition, this dissertation covers studies of a fuel based on a blend of ammonia borane, methylamine borane, and methanol as an alternative to carbon-based fuel for use in high velocity combustion systems. The work describes experiments performed to test the spray characteristics, ignition delay, and ignition methods. Ignition and combustion of the fuel was performed using a combustion apparatus and the burns were characterized using high framerate imaging.
Computational studies of atmospheric chemical processes, flexible catalysts, and of new materials for chemical hydrogen storage
(University of Alabama Libraries, 2014) Garner, Edward B.; Dixon, David A.; University of Alabama Tuscaloosa
Advanced electronic structure methods on high performance computers have been used to study new materials for technology applications and for atmospheric chemical processes of the halogens. Chapter 2 is focused on the thermodynamics of halogen oxides relevant to stratospheric ozone depletion chemistry. We calculated the thermodynamic properties of various key species to better understand what is happening in the atmosphere to help minimize our impact on the environment. This research is particularly important because of the lack of experimental data on these species. Chapter 3 is focused on the design of flexible catalysts for single electron transfer reactions using neutral Group 6B (Cr, Mo, W) pentacarbonyl complexes M(CO)5-L. It was found that various P-ligands such as phosphines, phosphalkenes, and phospha-quinomethanes can form radical cations and anions under redox conditions and that the radical site can be localized either on the metal or on the "non-innocent" ligand. More polar solutions will drive single electron transfer reactions to form the cationic and anionic metal based complexes with the appropriate oxidizing and reducing agents. Chapter 4 is the study of chemical hydrogen storage systems with a focus on borane amines. The goal was to develop economically viable and energy efficient processes to regenerate spent fuel formed by the release of hydrogen from ammonia borane. The thermodynamics for fuel regeneration processes of spent ammonia borane fuel, modeled as polyborazylene, were accurately predicted. A method using a modified Pictet-Trouton rule and calculated boiling points was used to estimate heats of formation of liquids for the prediction of the thermodynamics of reactions in the liquid phase. An effective tin catalyst with the potential to lower the cost for ammonia borane regeneration at an industrial scale was designed in collaboration with Los Alamos National Laboratory. However, it was found that at an industrial scale the process was limited due to the cost of transporting the tin catalyst around the spent fuel regeneration plant. Therefore, it was necessary to find a new method for regenerating spent ammonia borane fuel, and hydrazine was found to work very effectively in a one pot approach.
Computational Studies of Interactions Between Transition Metals and Main Group Elements
(University of Alabama Libraries, 2022) Mason, Marcos Mcallister; Dixon, David A.; University of Alabama Tuscaloosa
The interactions between main group elements and d- and f-block metals are important in many chemical applications. Calculated bond dissociation energies (BDE) and heats of formation of the Group 3 metal halide dimers (MX, where M = Sc, Y, La and X = F, Cl, Br, I) for the X1Σ+ and a3δ state were used to explain the chemiluminescent reactions of the Group 3 metals Sc and Y with F2, Cl2, Br2, ClF, ICl (Sc), IBr (Y) and SF6 and La with F2, SF6, Cl2, and ClF and show that the observed spectra are due to metal monohalide emission. The BDE calculations were performed using the Feller-Peterson-Dixon (FPD) approach including molecular spin-orbit (SO) corrections. The initial steps in the selective catalytic reduction (SCR) of NO by TiO2 supported vanadium oxides and surface adsorbed NH3 were predicted at the density functional theory (DFT) level with the B3LYP functional benchmarked at the coupled cluster CCSD(T) level. Different proton transfer pathways which depend on the initial neutral or protonated sites coupled with addition of NO lead to formation of a NH2NO surface species and reduction of a vanadium and spin transfer to the metal oxide surface. NH2NO subsequently desorbs and decomposes in the gas phase following a series of intramolecular rearrangements with barriers comparable to its generation on the surface. Spectroscopic observation of surface adsorbed NH3 and NH4+ in the SCR reaction is supported by vibrational frequency calculations. However vanadium bound NH2 is not predicted to be present in significant amounts, consistent with experiment. NO2 may also be present in combustion gas streams with the NO so the interactions of NO2 with cluster models of vanadium oxides and supported vanadium oxides were studied at the CCSD(T)//B3LYP level. A qualitative covalent vs, ionic bonding model is further developed, and the key factors in the favorability of nitrate formation on vanandium oxides are proposed. Calculations predict that saturating the vanadia with V-O bonds strengthens the V=O bond, raises the excitation energy, and precludes NO2 chemisorption so that only weak physisorption will occur. A series of organic ligands is investigated for metal selectivity in the separation of actinides (An) from lanthanides (Ln) at the DFT level couples with self-consistent reaction field calculations using the COSMO parameters to predict free energies in aqueous and organic solvents. A novel ligand to metal charge transfer in Eu complexes is predicted.
Computational studies of Lewis acidic gas adsorption to transition metal oxide nanoclusters and metal organic frameworks
(University of Alabama Libraries, 2017) Flores, Luis Antonio; Dixon, David A.; University of Alabama Tuscaloosa
Computational studies of the interaction of Lewis acid gases with metal oxide clusters and metal organic frameworks show how these gases interact with and degrade these materials at the molecular level. The calculations were done at the levels of density functional theory and correlated molecular orbital theory ((CCSD(T))). Group VI metal oxides clusters physisorb CO_2 near or below to 298K, and chemisorption of CO_2 by carbonate formation is an endothermic process. SO_2 physisorbs to Group VI clusters near or below 298K. Group VI metal oxides chemisorb SO_2 by forming sulfites with positive free energies of binding at 298K. The formation of sulfates is thermodynamically allowed for Cr clusters because Cr clusters have a higher reducibility than do Mo or W clusters. Group IV metal oxide clusters prefer chemisorption of both gases by carbonate and sulfite formation. Mo and W oxides may function as long lived sorbents for these gases, whereas Cr and Group IV metal oxides would degrade upon exposure to these gases as sulfites, sulfates, or carbonates form on their surfaces. Uranium trioxide clusters are predicted to chemisorb CO_2 by uranyl carbonate formation. The exposure of nuclear waste to CO_2 could cause uranium oxides to degrade leading to ground water contamination. The physisorption of the Lewis acid gases (CO_2, SO_2, H_2O, H_2S, CO, and NO_2) to M-MOF-2 systems (M = Zn, Cu, Co), was investigated. The MOFs are predicted to bind H_2O, H_2S, and SO_2 more strongly than the other gases. The binding energies are larger for Zn and Co than for Cu. Zn-MOF-2 clusters will degrade faster than Cu.
Computational studies of solid state materials for practical applications
(University of Alabama Libraries, 2012) Stott, Amanda C.; Dixon, David A.; University of Alabama Tuscaloosa
The Ni-rich Ni55Ti45 composition of the NiTi alloy is a promising material for aerospace bearing materials. Spiral orbit tribometry friction tests performed on Ni-rich Ni55Ti45 titanium ball bearings indicate that this alloy is a promising candidate for future aerospace bearing applications. Microstructural characterization of the bearing specimens was performed using transmission electron microscopy and energy dispersive spectroscopy, with NiTi, Ni4Ti3, Ni3Ti, and Ni2Ti4Ox phases identified within the microstructure of the alloy. Density functional theory (DFT) was applied to predict the electronic structure of the NixTiy phases, including the band structure and site projected density of states. Ultraviolet photoemission spectroscopy was used to verify the density of states results from the density functional theory calculations, with good agreement observed between experiment and theory. Plane wave ab initio DFT calculations of the B2 NiTi (100), (110), and (111) surfaces, the B2 and B19´ phases of NiTi, and the supercell structures of NiTi, Ni4Ti3 and Ni3Ti are also reported. Electronic energies from the electronic structure calculations are used to assess relative stability of the different surface and supercell geometries. DFT was applied using a plane wave approach for solids to determine the band gap energies in a series of Pb3C6X6 semiconducting extended-network organic structures, to determine the phase stability in the NiTi alloy system, and to study the surface of the (bcc) B2 phase of NiTi. To reveal the molecular structure and optoelectronic properties of these materials, a detailed ab-initio theoretical investigation of the solid-state properties was performed. Density functional theory was applied to predict the electronic structure of the NixTiy phases, including the band structure and site projected density of states. Organo-metallic compounds are also an important class of materials for organic electronic devices due to their semiconducting properties. Ground state geometries, band structure, density of states, and charge density were calculated using density functional theory using the PBE exchange-correlation functional as well as the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional. The results show that the optical properties and band gap energies can be easily tuned by chemical modifications of the substituent X atom in Pb3(C6X6). Calculations of substituent atoms S, O, Se, and Te are presented. TiV-based alloys are promising candidates for NiMH batteries, as it is well established that the V-based (bcc) solid solution phase acts as the major hydrogen absorbing phase wguke the (hcp) Ti phase acts mainly as a catalyst for electrochemical hydrogenation and dehydrogenation. To achieve improved electrochemical performance a precise knowledge of the microstructure is required. Therefore, the influence of the interfacial energy on the material phase stability was investigated for a series of TiV multi-laminate thin films. Experiments revealed that at a higher layer thickness, the α (hcp) phase is the most stable. As the layer thickness is reduced, a transformation from the α (hcp) phase to the ß (bcc) phase occurs. Atomic-scale characterization of the transformed specimen by atom probe tomography reveals V interfacial diffusion between the layers. Equivalent crystal theory based calculations confirm the V interfacial diffusion mechanism. The predicted segregation profiles match those obtained experimentally.
Computational studies of the catalytic reactions of group ivb and vib transition metal oxide clusters
(University of Alabama Libraries, 2014) Fang, Zongtang; Dixon, David A.; University of Alabama Tuscaloosa
Computational chemistry approaches have been used to study the reactivity of Group IVB and VIB transition metal oxide clusters. The hydrolysis of MCl₄ (M = Zr, Hf) as the initial steps on the way to form zirconia and hafnia nanoparticles has been studied with density functional theory (DFT) and coupled cluster [CCSD(T)]theory. Instead of the direct production of MOCl₂ and HCl or MO₂ and HCl, the hydrolysis reaction starts with the formation of oxychlorohydroxides followed by the release of HCl due to the large endothermicities associated with the direct path to form gas phase MO₂. The formation of MO₂ nanoparticles by the high temperature oxidation method is complicated and is associated with the potential production of a wide range of intermediates. The interaction between H₂O and small (MO₂)n (M = Ti, Zr, Hf, n = 1−4) nanoclusters has been studied for the first step to understand the reaction mechanism of photocatalytic water splitting with the presence of (MO₂)n as catalysts. Both the singlet and the first excited potential energy surfaces (PESs) are studied. The hydrolysis reactions begin with the formation Lewis acid-base adducts followed by proton transfer from H₂O to the nanclusters. The reactions are highly exothermic with very small activation energies. Thus, H₂O should readily decompose to generate two OH groups on (MO2)n nanoclusters. The generation of H₂ and O₂ starting from the hydroxides formed in the hydrolysis step has been studied with the same computational methods as used for the hydrolysis study. The water splitting reactions prefer to take place on the first excited triplet potential energy surface (PES) due to its requirement of less energy than that on the singlet PES. A low excess potential energy is needed to generate 2H₂ and O₂ from 2H₂O if the endothermicity of the reaction is overcome on the first excited triplet PES using two visible photons. Hydrogen generation occurs via the formation of an M−H containing intermediate and this step can be considered to be a proton coupled, electron transfer (PCET) reactions with one or two electrons being transferred. Oxygen is produced by breaking two weak M−O bonds on the triplet PES. Ethanol (CH3CH2OD) conversions on cyclic (MO3)3 (M = Mo, W) clusters have been studied experimentally with temperature programmed desorption and computationally with both DFT and CCSD(T) methods. The addition of two alcohol molecules is required to match experiment. The reaction begins with the elimination of water with the formation of an intermediate of dialkoxy species for further reaction. The dehydration reaction proceeds through a β hydrogen transfer to a terminal MVI = O atom without the involvement of a redox process. The dehydrogenation reaction is through an α hydrogen transfer to an MoVI = O with redox involved or a WVI avoiding redox. The same computational methods have been used to study the other alcohol species such as methanol, n-propanol and isopropanol. The reactions with single, double and triple alcohols per M3O9 cluster have been studied. The dehydrogenation and dehydration for single alcohol reactions is via a common intermediate of metal hydroalkoxide formed by the dissociation of alcohol. The dehydration is through a β hydrogen transfer to OH group. The lowest energy pathway for dehydrogenation is the same for different alcohols in both single and double alcohol reactions. Three alcohols involved condensation reaction may lower the reaction barrier tremendously by the sacrifice of an alcohol to form a metal hydroalkoxide, a strong gas phase Brønsted acid. This is a Brønsted acid driven reaction different from dehydrogenation and dehydration reactions governed by the Lewis acidity of the metal center and its reducibility.
Computational studies of the fundamental thermodynamic properties of amino acids and small peptides
(University of Alabama Libraries, 2015) Stover, Michele Leigh; Dixon, David A.; University of Alabama Tuscaloosa
In 2011, the Human Proteome Project (HPP) was launched with the main goal of experimentally mapping the entire human proteome. Determining a protein’s sequence is a first step to understanding its structure and function, which are of great importance in biological, biochemical, and medical studies. The sequencing of peptides and proteins by mass spectrometry (MS) has become a major tool in proteomics research because it is a cost effective and highly reproducible analytical technique. The analysis of biomolecules by mass spectrometry requires an understanding of proton transfer reactions because the two most commonly used ionization techniques, electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI), involve the addition and removal of protons. The sites of proton transfer reactions can affect the fragmentation patterns of peptide ions, which consequently impacts the sequence information that can be obtained from mass spectrometry experiments. Thermodynamic values, such as the gas-phase acidity (GA or ∆Gacid), the ΔG for the deprotonation reaction AH → A- + H+, provide valuable information to help in understanding the less studied negative ion peptide fragmentation mode by mass spectrometry. The study of gas-phase proton transfer reactions provides unique insights into the structures and energetics of the peptides. Changing the protonation state can impact the hydrogen bonding in the molecule and result in decreased or increased properties such as solubility, hydrophobicity, and electrostatic interactions. By combining these experimentally obtained results with the results from high level electronic structure theory calculations, an improved understanding of the structures and energetics of polypeptides can be obtained. Herein we describe computational studies using reliable, correlated molecular orbital methods of the gas-phase properties, including acidities and heats of formation, and solution-phase acidities of amino acids (AAs) and small peptides including substituted molecules such as AA amides and phosphorylated AAs. This dissertation will focus on the prediction of fundamental thermodynamic properties of AAs and small peptides that are of interest in the area of biochemistry, proteomics, and the Human Proteome Project.
Computational studies of transition metal catalysts
(University of Alabama Libraries, 2010) Craciun, Raluca; Dixon, David A.; University of Alabama Tuscaloosa
High level electronic structure calculations were used to evaluate reliable, self-consistent thermochemical data sets for the second and third row transition metal hexafluorides, as well as for metal phosphines (M=Ni, Pd, Pt). For the transition metal hexafluorides, the electron affinities, heats of formation, first (MF₆ → MF₅ + F) and average M-F bond dissociation energies, and fluoride affinities of MF₆ (MF₆ + F⁻ → MF₇⁻) and MF₅ (MF₅ + F⁻ → MF₆⁻) were calculated. For the transition metal phosphines, the first metal-phosphine binding energy in MPH₃, M(PH₃)₂, MPH₃Cl₂ and M(PH₃)₂Cl₂ was calculated. The electron affinities, which are a direct measure for the oxidizer strength, increase monotonically in the second and third row series, from WF₆ to AuF₆, and from MoF₆ to AgF₆. The hexafluorides of the last two elements of each series, Pt, Au in the third row and Pd and Ag in the second, form extremely powerful oxidizers. The inclusion of spin orbit corrections is necessary to obtain the correct qualitative order for the electron affinities. The calculated electron affinities increase with increasing atomic number, are in good agreement with the available experimental values and, for the third row are: WF₆ (3.15 eV), ReF₆ (4.58 eV), OsF₆ (5.92 eV), IrF₆ (5.99 eV), PtF₆ (7.09 eV), and AuF₆ (8.20 eV). The electron affinities of the second row hexafluorides are even larger than for the second row: MoF₆ (4.23 eV), TcF₆ (5.89 eV), RuF₆ (7.01 eV), RhF₆ (6.80 eV), PdF₆ (7.95 eV), AgF₆ (8.89 eV). A wide range of density functional theory exchange-correlation functionals were also evaluated and only three gave satisfactory results as compared to the higher level electronic structure calculations. The corresponding pentafluorides are extremely strong Lewis acids. The optimized geometries of the corresponding MF₇⁻ anions show classical structures with M-F bonds for W through Ir and for Mo, Tc and Rh; however, for PtF₇⁻, AuF₇⁻, RuF₇⁻, PdF₇⁻, and AgF₇⁻ nonclassical anions were found with a very weak external F-F bond between an MF₆⁻ fragment and a fluorine atom. These anions are text book examples for "superhalogens" and can serve as F atom sources under very mild conditions.
Computational Studies of Transition Metals and Small Molecules
(University of Alabama Libraries, 2021) Persaud, Rudradatt Randy; Dixon, David A.; University of Alabama Tuscaloosa
The chemistry that transition metals can access due to their d orbitals has expanded the horizons of many fields in chemistry. The work covered in this dissertation focuses on designing a computer system for performing computational studies, and a wide range of computational chemical studies of transition metals in various applications including predictions of bulk properties, homogenous/heterogenous catalysis, and the acidity of solvated transition metals for use in proteomics. Utilizing high-performance computers allows chemists to explore the d-block elements to aid in the analysis of experimental results or to explore new chemistry cheaply, safely, and ‘greenly’. Although a handful of high-performance computer cluster building recipes are available for general use, a free-open source recipe geared towards computational chemistry with compatibility for a broad range of computer hardware is provided. High level MO theory studies of coinage-metal trimers were done to study their potential energy surfaces. While exploring these potential energy surfaces, a novel, vibrationally bound, local minimum for the gold trimer was discovered, one of the first examples of bond angle isomerism. The normalized clustering energies of small metal clusters (n = 2-20) of the coinage metals were extrapolated to predict the cohesive energy of the bulk metal. The importance of spin orbit coupling for the binding energies of gold clusters was found. Density functional theory was used to calculate the binding energies of organic molecules including cyclohexane and benzene on a model of the rutile TiO2(110) surface, an important first step in heterogeneous catalysis of these species on a transition metal oxide. The calculated vibrational frequencies were used to predict reliable prefactors for analysis of temperature programmed desorption experiments. Mechanisms for the homogenous catalysis of the reduction of CO2 to formate using a triphosphine-ligated Cu(I) catalyst were developed. A mechanism of enhanced protonation involving transition metals in an electrospray ionization source in mass spectrometry for proteomic applications was developed.
The computational studies on the chemistry of titanium dioxide nanoparticles
(University of Alabama Libraries, 2010) Wang, Tsang-Hsiu; Dixon, David A.; University of Alabama Tuscaloosa
The chemistry of TiO_2 and SiO_2 nanoclusters is studied using computational methods. The potential energy surfaces (PESs), thermochemistry of the intermediates, and the reaction paths for the initial steps of the hydrolysis of TiCl_4 were calculated. Transition state theory and RRKM unimolecular rate theory are used to predict the rate constants. Clustering energies and heats of formation are calculated for neutral clusters, and the calculated heats of formation were used to study condensation reactions. The reaction energy is substantially endothermic if more than 2 HCl are eliminated. The calculations show that the reported values for ΔH_f^0(TiOCl_2) should be remeasured. Transition metal oxides such as TiO_2 can be used as photocatalysts to control chemical transformations for energy production. An important applications for TiO_2 is its use to photochemically split water to produce H_2 and O_2. The PES for splitting water on the ground and first excited state surfaces of (TiO_2)_n (n=1-4) nanoparticles have been studied up through the coupled cluster CCSD(T)/complete basis set level. Water is readily split to form hydroxyl groups without the need for a photon. Experimental measurements of the photoconversion of ketones (C(O)RR') on the rutile TiO_2 (110) surface show that one can eliminate R or R'. The bond dissociation energies of R=CH_3 and a wide range of R' for the gem-diols CRR'(OH)_2 were calculated at the density functional theory (DFT) and G3(MP2) levels. The calculated bond dissociation energies are in excellent agreement with the experimental values. The calculations show that most of the photodissociation processes are under thermodynamic control except for R'=CF_3. X-ray photoelectron spectroscopy (XPS) and DFT electronic structure calculations were used to study the average formal oxidation state of silicon in fumed silica (CAB-O-SIL®). The results show that the average surface oxidation state of the silicon in fumed silica is predominantly +1 and suggest a notably less hydrophilic character for CAB-O-SIL® than the oxides of silicon with Si in the formal +3 and +4 oxidation states. Once the +3 oxidation state is formed, water on the silica surface facilitates the conversion of the Si^+3 to the Si^+4 oxidation state.
Computational study of the fundamental thermodynamic properties of iridium and osmium clusters
(University of Alabama Libraries, 2017) Zhang, Shengjie; Dixon, David A.; University of Alabama Tuscaloosa
Computational studies of a model of a recently synthesized Ir_4 cluster with phosphine-calixarene ligands have been made to better understand how the catalytic properties can be controlled by creating a selective nanoscale environment. The calculations show that the binding energy of C_2H_4 on the apical site is lower than on the basal-plane site by 4 – 9 kcal/mol, and does not depend on the size of the phosphine. Electronic effects dominate in controlling the selective binding. The energetic low-lying structures of Irx(PH3)y(CO)z were optimized using density functional theory (DFT). The energies of small clusters were calculated using DFT and coupled cluster theory (CCSD(T)) was used to benchmark the DFT calculations. The best exchange-correlation functional, ωB97X-D, was used to predict the energies of the Ir_4 clusters. The calculations predict as carbonyls are replaced by PH_3 that the ligands dissociation energies (LDEs) of CO increase due to stronger π-back-bonding. The LDEs of PH3 decrease for the smaller clusters, and exhibit no discernable trend for the Ir4 clusters. The structures and LDEs of Irx(CO)y(NHC)z have been calculated using the same approach as for the Irx(PH_3)y(CO)z clusters, except that the CAM-B3LYP functional was found to be better and it was used to predict the energies of the Ir_4 clusters. The results were compared to experiment and the Irx(PH_3)y(CO)z results. The NHC ligands act as stronger σ-donors and have larger LDEs than CO’s. The trend for how the LDEs change is consistent with the trend for Irx(PH3)y(CO)z results. The Ir4 cluster with phosphine-calixarene ligands was treated oxidatively, leading to an increase in the rate of hydrogenation of C_2H_4. The Ir_4L_3 clusters (L = PMe_3 and PMePh_2) before and after oxidative treatment and the transition states for the hydrogen atom transfer to form C_2H_6 have been studied. The DFT calculation predicted that the reductive elimination reaction is more exothermic after oxidation, and that the oxidation decreases the barrier of the reactions. New site-isolated Os complexes in various oxidation states have been studied for different models ofh Os on an MgO lattice. The calculated bond lengths and C-O frequencies were compared with experiments to determine the possible structures.
Computational Study of Thermodynamics of Metal Carbonates and Catalytic Properties of Group IV Transition Metal Oxides
(University of Alabama Libraries, 2023) Hu, Yiqin; Dixon, David A.
This dissertation describes computational studies of the thermodynamics of metal carbonates, the sequestration of CO2 by group IV transition metal oxides, the reactivity of ethanol on group IV transition metal oxides as a model for biofuel conversion, and halogen atom oxidation of magnesium clusters. Gas phase heats of formation using the Feller-Peterson-Dixon (FPD) approach were predicted for carbonates, bicarbonates and hydroxides for Mg, Ca, and various first-row transition metals. These reliable FPD values were used to benchmark a range of density functional theory exchange-correlation functionals that are used in modeling larger systems and solids. None of the functionals show good chemical accuracy of ±1 kcal/mol, most likely due to issues with properly treating oxygen. The FPD results can be used to predict cohesive energies and metal atom exchange reactions. The addition of CO2 to M3O6 and M3O6- was studied at the CCSD(T) using weighted core correlation consistent basis sets. The calculations showed that prior predictions on the Ti structures were not correct as the results require the use of weighted core functions. The calculations enabled comparisons of CO2 binding energies to the neutral and anionic clusters as well the role that CO2 binding has on the electron affinity of the cluster. Ethanol dehydration and dehydrogenation on (TiO2)n nanoclusters, n = 2 to 4, which serve as models for the bulk TiO2 surface were studied at the CCSD(T)/aD//B3LYP/DZVP2 level to provide insights into how metal oxides can be used to convert biofuel into fuels or feedstocks for the chemical industry. The Lewis/Brønsted acidity and basicity on the Ti and O sites were correlated with various energetics. The oxidation of small Mg clusters by F and Cl was studied to interpret the observed chemiluminescence. The computational results provide the best available energetics for these species and are critical to interpreting the experiments which date back more than 40 years.
Computational thermodynamic studies of alkali and alkaline earth compounds, olefin metathesis catalysts, and borane -- azoles for chemical hydrogen storage
(University of Alabama Libraries, 2010) Vasiliu, Monica; Dixon, David A.; University of Alabama Tuscaloosa
Geometry parameters, frequencies, heats of formation and bond dissociation energies are predicted for the alkali (Li, Na and K) hydrides, chlorides, fluorides, hydroxides, and oxides and alkaline earth (Be, Mg and Ca) fluorides, chlorides, oxides and hydroxides at the coupled cluster theory [CCSD(T)] level extrapolated to the complete basis set (CBS) limit. The calculations including core-valence correlation corrections with the aug-cc-pwCVnZ basis sets (n = D, T, Q and 5) are mostly in excellent agreement with the available experimental measurements. Additional corrections (scalar relativistic effects, vibrational zero-point energies, and atomic spin-orbit effects) were necessary to accurately calculate the total atomization energies and heats of formation. The results resolve a number of issues in the literature. CCSD(T)/CBS level calculations with additional corrections are used to predict the heats of formation, adiabatic and diabatic bond dissociation energies (BDEs) and Bronsted acidities and fluoride affinities for the model Schrock-type metal complexes M(NH)(CRR')(OH)_2 (M = Cr, Mo, W; CRR' = CH_2, CHF, CF_2) and MO_2(OH)_2 transition metal complexes. The metallacyclobutane intermediates formed by addition of C_2H_4 to M(NH)(CH_2)(OH)_2 and MO_2(OH)_2 are investigated at the same level of calculation. The electronegative groups bonded to the carbene carbon lead to less stable Schrock-type complexes as compared to the complexes with a CH_2 substituent. The Schrock compounds with M = Cr are less stable than with M = W or Mo. The heats of formation and bond dissociation energies (BDEs) for the pyrrole, pyrazole, imidazole, triazole and tetrazole borane adducts were predicted using an isodesmic approach based on G3MP2 calculations. As potential hydrogen storage substrates, dehydrogenation energies for the elimination of one H_2 molecule were predicted as well as thermodynamic properties relative to their acid-base behavior. The H_3B-N bonds to an sp^2 nitrogen are much stronger than those to an sp^3 nitrogen for the 5-membered rings. The B-N BDEs for the azolylborate adducts are much larger than for the neutral azole borane adducts. The azole adducts with more number of nitrogens in the ring and with more BH_3 molecules to the azole nitrogens are more acidic.
Computational Thermodynamics of Gas and Solution Phase Anions
(University of Alabama Libraries, 2020) McNeill, Ashley Shari; Dixon, David A.; University of Alabama Tuscaloosa
The work in this dissertation focuses on the computational analysis of the thermodynamics of anions in the gas phase and in aqueous solution to provide unique insights into the chemistry of a range of biologically and geochemically relevant chemical species. This often involves calculating properties for these species such as electron affinities and hydration free energies of the anions, which can be difficult or impossible to obtain experimentally. Systems of interest in this work include small peptides, enzyme-catalyzed biological reactions, and the gas phase and solvation energetics of a variety of anionic species including CO2-, H-, X- (halides), OX- (hypohalites), and YH- (chalcogen hydrides). The peptide work, performed largely with the composite correlated molecular orbital theory G3(MP2) method, is compared directly to experiments conducted with low-energy collision-induced dissociation negative ion mode mass spectrometry. Isotope fractionation studies, of significant use in many geochemical applications, are conducted on the overall reaction by the alanine transaminase enzyme (+H3NCH(CH3)COO? + ?OOCCH2CH2C(O)COO? ? CH3C(O)COO? + +H3NCH(CH2CH2COO?)COO?) in order to predict that 13C preferentially collects in the C2 site of pyruvate over alanine by 9‰ at equilibrium. This prediction, calculated from gas phase- and aqueous-optimized clusters with explicit H2O molecules at the MP2/aug-cc-pVDZ with and without the COSMO self-consistent reaction field for implicit solvation, is reflected in simpler models: without explicit solvation, with simpler analogues formaldehyde and methylamine, and from canonical functional group frequencies and reduced masses for R2C=O and R2CH-NH2. Solvation studies of the CO2-, H-, X-, OX-, and YH- anions and corresponding neutrals gave adiabatic electron affinities, reduction potentials, and gas phase and aqueous acidities that are generally in excellent agreement with experiment. These studies used a variety of computational methods, including heavy application of coupled cluster calculations with the Feller-Peterson-Dixon method to obtain high accuracy thermodynamic values. Absolute hydration free energies are determined for neutral and anionic species clustered with 4 to 8 explicit H2O molecules using a supermolecule-continuum approach.
Crystallographic evidence of Watson-Crick connectivity in the base pair of anionic adenine with thymine
(National Academy of the Sciences, 2020) Mishra, Manish Kumar; Kelley, Steven P.; Smetana, Volodymyr; Dixon, David A.; McNeill, Ashley S.; Mudring, Anja-Verena; Rogers, Robin D.; University of Alabama Tuscaloosa; Stockholm University; University of Minnesota Twin Cities; University of Missouri Columbia
Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N-4444](+)) or tetrabutylphosphonium ([P-4444](+)) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N-4444][Ad]center dot 2H(2)O, and thymine, [P4444][Thy]center dot 2H(2)O, as well as the double salt cocrystal, [P-4444](2)[Ad][Thy]center dot 3H(2)O center dot 2HThy. The cocrystal includes the anionic [Ad-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson-Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.
Development and applications in computational chemistry for inorganic catalysis
(University of Alabama Libraries, 2013) Chen, Mingyang; Dixon, David A.; University of Alabama Tuscaloosa
A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the meta data. The indexed meta data can be used for data analysis and data mining. A novel tree growth - hybrid genetic algorithm (TG-HGA) was developed to search the global minimum of small clusters. In the TG algorithm, the clusters grow from a small seed to the size of interest stepwise. New atoms are added to the smaller cluster from the previous step, by analogy to new leaves grown by a tree. The initial structures for the search for the global minimum of TiO_2 nanoclusters were generated by TG-HGA, and new low energy structures that have not been previously reported were found. Low energy isomers of Agn, n = 2 - 99, were studied at different computational level depending on the size of Agn. The geometries of Agn, n = 2 - 8, were optimized using density functional theory (DFT), and the energies were calculated at the CCSD(T)/CBS level. The Agn, n = 9 - 20, were initially generated by the TG-HGA builder with an EAM potential, and optimized using the DFT method. The relative energies and normalized atomization energies for the optimized structures were calculated at the CCSD(T) level with a small basis set. For larger Agn, 20 < n < 100, the low energy structures were generated using TG-HGA with an EAM potential, and the energies were calculated at the DFT level with a small basis set. A range of DFT functionals were benchmarked with the normalized atomization energies at the CCSD(T) level for the small Agn clusters. PW91 and ω-B97XD provided best results for predicting the normalized atomization energies. The normalized atomization energies for Agn start to converge slowly to the bulk at n = 55. At n = 99, the normalized atomization energy is predicted to be ~50 kcal/mol. The low energy isomers of the Irn(CO)m complexes (n=1, 2, 3, 4, and 6) were investigated using electronic structure methods at the density functional theory and coupled cluster (CCSD(T) theory levels. Ir4(CO)12 is predicted to be the most favored complex for reactions of Irn(CO)m with CO at low temperature, and Ir6(CO)16 is predicted to be formed above room temperature. Smaller Irn(CO)m clusters will nucleate to form Ir4(CO)12 spontaneously. Low-lying structures of the small iridum clusters Irn (n = 2 - 8) were optimized using DFT methods. Ir2 and Ir3 were also optimized using the CASSCF method. MRCI-SD (for Ir2) energies and CCSD(T) (for Ir2 and Ir3) energies of the leading configurations from the CASSCF calculations were done to predict the low-lying states. The normalized atomization energies for Irn (n = 2 - 8) were calculated at the CCSD(T) level up to the complete basis set (CBS) limit in some cases using the B3LYP optimized geometries. Inclusion of the spin orbit corrections in the normalized atomization energies for Irn is critical and will decrease the normalized atomization energies by ~ 15 kcal/mol for n ≥ 4. Several molecular models were used to characterize various binding sites of the metal complexes in the zeolites. The calculated structures and energies indicate a metal-oxygen (M(I)-O) coordination number of two for most of the supported complexes but a value of three when the ligands include C2H5 or H. The results characterizing various isomers of supported metal complexes incorporating hydrocarbon ligands indicate that some carbene and carbyne ligands could form. A set of ligand bond dissociation energies is reported to explain reactivity trends. The Pd-L ligand bond dissociation energies (BDEs) of cis- and trans-[L-Pd(PH3)2Cl]+ were predicted using coupled cluster CCSD(T) theory and a variety of density functional theory (DFT) functionals at the B3LYP optimized geometries. For cis-[L-Pd (PH3)2Cl]+ complexes, the Pd-L bond energies are 28 kcal/mol for CO; ~40 kcal/mol for AH3 (A = N, P, As, and Sb), norbornene, and CH3CN; and ~53 kcal/mol for CH3NC, pyrazole, pyridine, and tetrahydrothiophene at the CCSD(T) level. The benchmarks show that the dispersion-corrected hybrid, generalized gradient approximation, DFT functional ω-B97X-D is the best functional to use for this system. Use of the ω-B97X-D/aD functional gives predicted BDEs within 1 kcal/mol of the CCSD(T)/aug-cc-pVTZ BDEs for cis-[L-Pd(PH3)2Cl]+ and 1.5 kcal/mol for trans-[L-Pd(PH3)2Cl]+ . Lanthanide metal atoms, produced by laser ablation, were condensed with CH3F in excess Ar at 8 K. New infrared absorption bands are assigned to the first insertion CH3LnF and oxidative addition methylene lanthanide hydride fluoride CH2LnHF products on the basis of 13C and deuterium substitution and density functional theory calculations of the vibrational frequencies. For Ln = Eu and Yb only CH3LnF is observed. CH3LnF in the Ln formal +2 state is predicted to be more stable than CH2LnHF with the Ln in the formal +3 oxidation state. CH3-LnF forms a single bond between Ln and C and is a substituted methane. The calculated potential energy surface for the CH3F + La → CH3-LaF/CH2-LaHF shows a number of intermediates and transition states on multiple paths. The reaction mechanism involves the potential formation of LaF and LaHF intermediates.