Physical Sciences and Mathematics Commons^™

Computational Quantum Chemistry Studies Of The Stabilities Of Radical Adducts Formed During The Oxidation Of Melatonin Derivatives, James Horne

Electronic Theses and Dissertations

Melatonin is a natural antioxidant that has been investigated for properties as a potential spin trap to identify short-lived free radicals. Computational quantum chemistry studies have been performed for the oxidation of melatonin to N¹-acetyl-N²-formyl-5-methoxykynuramine. This research focused on modification of melatonin into derivatives and analyzing the change in total molecular energy from melatonin to its oxidation product, as well as the corresponding derivatives. Each of the molecular geometries were optimized at the DFT/B3LYP/6-31G(d), DFT/B3LYP/cc-pVXZ (X = D, T), HF/6-31G(d), HF/cc-PVXZ (X = D, T), MP2/6-31G(d), and MP2/cc-PVXZ (X = D, T) levels of theory. …

Role Of Defect Type In Optimizing Photoelectrochemical Hydrogen Production Catalysts, Mohamed Mahrous

Theses and Dissertations

The search for new energy sources has become a global challenge due to the increasing demand for energy and the negative impact of traditional energy sources on the environment. The photoelectrochemical water splitting has emerged as a promising alternative source for producing hydrogen, which can be used as a clean fuel. However, it is necessary to tailor the properties of the light-active material that will be used to absorb sunlight and split water. This research project aimed at providing detailed insights into the effect of varying the type and concentration of defects on the optical and electronic properties of diamond …

Advances In Structure Elucidation Of Small Molecules And Peptides By Nuclear Magnetic Resonance Spectroscopy And Mass Spectrometry, Ryan D. Cohen

Seton Hall University Dissertations and Theses (ETDs)

This dissertation reports on improvements in nuclear magnetic resonance (NMR) and mass spectrometry (MS) structure determination methods of organic compounds, with particular focus on challenging cyclic peptides. A recent and important innovation in NMR spectroscopy is the combination of theoretical property predictions, such as chemical shifts, using density functional theory (DFT) to aid in challenging NMR structure assignments, such as determination of regio- and stereo-configurations. In the first part of this thesis, a comprehensive benchmark study of DFT chemical shift prediction methods was performed using experimental NMR data collected from 50 well curated compounds, which was referred to as the …

Quantum Mechanical Studies Of Water Splitting Reaction With (Zno)3 Nanoclusters As Catalysts, Duwage C. Perera

Electronic Theses and Dissertations

With the current energy crisis, H₂ production through the water-splitting reaction has drawn attention recently. In this thesis, I studied the structural (geometry) and electronic properties (vertical detachment energy and electron affinity) of ZnO monomers and dimers using density functional theory. ZnO is a metal oxide with a 3.37 eV band gap and can be a commercially cheaper photocatalyst in hydrogen (H₂) production. The B3LYP/DGDZVP2 pair was selected after investigating different pairs of exchange functionals and basis sets to study the hydration, hydrolysis, and water-splitting reaction. The singlet-triplet energy gaps of small (ZnO)_n clusters (n=1-6) of …

Theory Of Aqueous Solvation: Uninterrupted, Cyclic Hydrogen-Bonding Essential For Accurate Keto-Enol Energies And Grotthuss Tautomerism Of Acetone, Mark Recznik

Electronic Theses and Dissertations

Keto-enol tautomerization (KET) is a fundamental process impacting a range of molecular phenomena in organic and biochemistry. However, the accurate computation of solution-phase KET energies remains a challenge, even for prototypical acetone.

In Part I, keto-enol tautomers of acetone were incorporated into solvent clusters that interact via uninterrupted, cyclic hydrogen-bonding (UCHB) networks. An empirical model was created to predict accurate KET energies, E_taut, of simple carbonyl compounds. Based on the availability of experimental data and structural simplicity, acetone was selected as a prototype. A discrete-continuum strategy was employed – accounting simultaneously for local noncovalent interactions and bulk-phase effects …

Low-Lying Spin-Flip Excitonic States Of ����12��12 (��������)16 [��2��]4 Molecule (Mn12 − ����), Karma Dema

Open Access Theses & Dissertations

Molecules and materials constructed from Mn atoms offer diverse assortments of geomet- rical and spin structures. The diversity of structures, in comparison with other transition metals, along with nature’s decision to use a Mn-based molecule to catalyze solar-driven water splitting and oxygen evolution, suggests that there is indeed something special about the location of Mn valence electrons, both energetically and geometrically, that endows Mn with its multifaceted behaviors that, in turn, provide such chemical, physical and mag- netic diversity. Based upon recent work on the Mn3 monomer and the Mn(taa) there is an expectation that Mn�� �� �� centers can …

Structural Analysis Of [Ni(Dippe)] Fragment Using Computational Methods, Jennifer L. Sanchez

Theses and Dissertations

The structural analysis of the Nickel (Bisdiisopropylphospino)ethane, also known as [Ni(dippe)H]2, has been heavily studied in our group in collaboration with William D. Jones's group. A computational analysis of the [Ni(dippe)] fragment was performed to determine the structural relationship between the nickel center and its phosphine ligand, due to phosphines having both electronic and steric properties. The reactivity of the Nickel will be most dependent on the dippe ligand. A conformational search generated 244 conformers after a thorough minimization using Molecular Mechanic (MM) calculations where a thorough minimization was performed and then re-minimized using a SEED command until unique conformers …

Computationally Assisted Nmr Crystallography: A Path To Unusually High-Resolution Crystal Structures, Luther Wang

Theses and Dissertations

Crystallography has traditionally been studied by diffraction methods involving X ray or neutron radiation. These methods have some limitations, from requiring the substance under study to form single crystals to the limited ability of X rays to locate hydrogen atoms. While neutron radiation can characterize hydrogens, it is expensive, not readily available and has its own particular limits on resolution. It this dissertation, it is demonstrated that NMR is extraordinarily sensitive to atomic positions, with variations of mere tens of femtometers creating statistically distinguishable chemical shift changes. To date, no other means of measurement can detect structural changes at this …

Computational Study Of The Reactions Of Heteroatomic Compounds On Ceo2, Suman Bhasker Ranganath

LSU Doctoral Dissertations

The mechanisms of ambient-temperature reactions of heteroatomic compounds catalyzed by ceria (CeO₂), an archetypical reducible oxide, for enzyme mimetics, environmental protection, and chemical synthesis are investigated in this dissertation using theoretical methods. CeO₂ is modeled with thermodynamically stable low-index surfaces exposed by commonly studied ceria thin films and nano particles. To understand phosphatase-like dephosphorylation activity, stable adsorption states and surface reactions of model phosphates are examined. Binding of the central P-atom to surface lattice oxygen (O_latt) supplemented by phosphoryl O-Ce interaction is the only stable adsorption state for the un-dissociated molecule. Deprotonation of phosphate monoesters, …

Quantum Capacitance Investigation Of Different Tas2 Polymorphs For Energy Storage Applications – First Principles Study, Mahmoud Elattar

Theses and Dissertations

Energy is an essential requirement, which has a growing demand due to the growth of population and the world transformation into electronic. More than 70% of energy resources are fossil-fuel based which has an environmental impact due to the CO₂ emissions. Energy hubs for Fossil-fuel to electric energy conversion, controlled CO₂ emissions processing units, and energy storage system are key factors for a smooth transition to green energy without lack of energy supplies, where electrical energy storage systems (ESS) are key enablers to achieve that. One of the effective components which determines the ESS efficiency is the electrode …

Effects Of Vacancies And Electron Temperature On The Electron Phonon Coupling In Cubic Silicon Carbide And Their Connection To The Inelastic Thermal Spike, Salah Al-Smairat

Doctoral Dissertations

“The electron-phonon interaction is an important interaction in many solids as it influences transport phenomena and related quantities such as the electrical and thermal conductivities, especially in nuclear and space applications. The importance of the electron-phonon interaction in primary damage production in 3C-SiC is the subject of this research.

The electron-phonon coupling factor was calculated using a hybrid Density Functional Perturbation Theory - Classical Electron Gas model. The coupling factor was calculated as a function of electron temperature in pristine and defective 3C-SiC, and relaxed defective cells. The electron-phonon coupling is found to depend strongly on the electronic temperature and …

Theoretical Investigation Of The Co-C Bond Activation In Methylcobalamin And Adenosylcobalamin-Dependent Systems: Mechanistic Insights., Arghya Pratim Ghosh

Electronic Theses and Dissertations

The vitamin B₁₂ derivates, otherwise known as cobalamin (Cbl), are ubiquitous organometallic cofactors. The biologically active forms of Cbl, such as methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), act as cofactors in different physiological reactions for both prokaryotes and eukaryotes. A crucial aspect of the Cbl-mediated systems is the activation of the organometallic Co-C bond that plays a critical role in its catalytic activity. One of the most remarkable features of this Co-C bond is its unusual activation in AdoCbl-dependent enzymatic reactions, where a trillion-fold rate acceleration of the Co-C bond cleavage is observed inside the enzyme compared to the isolated …

First Principle Studies Of The Effects Of Alkali-Metal Intercalation On Structural Transition From Black To Blue Phosphorene And The Adsorption Of N2h4 On Ws2 Layers., Md Rajib Khan Musa

Electronic Theses and Dissertations

A comprehensive density functional theory calculation has been conducted to seek a potential structural transition from black to blue phosphorene layers, with a focus on the roles played by alkali-metal intercalation in black phosphorene/phosphorus. This study reveals that at sufficiently high Li concentration and specific, well-defined configurations, a phase transition from black to blue phosphorene can take place. The Li atoms intercalated in black phosphorene could act as a “catalyst” in the“reactive region” of the lone pair of P atoms, leading to a P-P bond breaking and, subsequently, a local structural transformation from an orthorhombic lattice to an assembly of …

Transport Properties Of Binary And Doped Diborides, Alin Babu Niraula

MSU Graduate Theses

A systematic computational study to evaluate the electronic structures and transport properties including resistivity, thermal conductivity of several binary diborides (ZrB2 , TiB2 , TaB2 , CrB2 , and AlB2 ) and the ZrB2 alloyed with Cr, Al, Ti and Ta has been performed. Due to the p-d hybridization, the characteristic pseudo gap at the Fermi energy level (Ef) from the density of states (DOS) is presence in the DOS of both ZrB2 and TiB2 in contrast to those of TaB2 and CrB2 with only a partial occupation on the anti-bonding states. AlB2 is also similarly shown the presence of …

Investigations Into Effects Of Modified Prolines On Cis-Trans Isomers And Polypeptide Secondary Structure & Prediction Of Spectroscopic Properties Of Phthalonitriles For Characterization, Jeffrey Raab

Seton Hall University Dissertations and Theses (ETDs)

Proline is a unique amino acid because it is the only amino acid whose side chain wraps around and bonds back to the peptide backbone. This ring shape helps proteins form conformations which would otherwise not be possible such as hairpin turns. The cis/trans isomerization of the peptide bond between the preceding amino acid (X_aa) and Proline is important in determining how the secondary structure folds. Thus, being able to control the cis/trans isomerization is important when a specific conformation is desired; Proline can be modified to get make the equilibrium shift whichever way is needed. The modifications …

Investigation Of The C—Cn Bond Activation Of Fluorinated Benzonitriles With [Ni(Dmpe)] And Dft Benchmarking Study With [Ni(Dippe)], Dominique C. Gallegos

Theses and Dissertations

Carbon-carbon bond activation has become a rapidly growing area of research due to its extensive range of applications. Despite the significant progress that has been made in this field, the cleavage of kinetically inert and thermodynamically stable C—C σ-bonds under mild homogeneous conditions remains a challenge. The activation is primarily limited to systems in which either relief of strain or aromatization serves as a driving force. A notable exception to this is the oxidative addition of unstrained C—CN bonds of nitriles. In this study, we are looking at the effect of fluoro substituents. We hypothesized …

Extension Of Restricted Open-Shell Kohn-Sham Methodology To A Density-Functional Tight-Binding Framework, Reuben Szabo

WWU Graduate School Collection

The restricted open-shell Kohn-Sham (ROKS) approach for singlet excited states provides some advantages over the ∆-self-consistent-field (∆SCF) method, requiring only a single SCF procedure and avoiding the problem of variational collapse. While ROKS is a powerful tool for DFT, its application to density functional tight-binding (DFTB) could offer significant improvements in time complexity when compared to DFT, enabling excited-state simulations of extended molecular systems on longer timescales than ROKS. In this work we discuss the implementation of an RO-DFTB approach in the DFTB+ package, as well as its suitability for the study of organic dyes and photoactive compounds. For benchmarking, …

Recovery Of Phosphorus From Florida Phosphatic Waste Clay, Amir Eskanlou

Graduate Theses, Dissertations, and Problem Reports

This MS thesis examines the recovery of phosphorus (P) from Florida waste clay (WC). A comprehensive literature review revealed that: (i)-The most important values being lost to WC are P and rare earth elements (REEs). For the recovery of these values from WC, two crucial attempts are the removal of extremely fine-sized clays, followed by the recovery of phosphate content, which can pave the path for the recovery of REEs; (ii)-Any scientific/ technological solution should, at the same time, be economically and environmentally attractive to the industry. As such, moving from mostly chemical separation processes to the primarily physical/ physicochemical …

Computational Study Of Radical Cation Rearrangements, Mi'kayla D. Word

Theses and Dissertations

A radical cation is a molecule that has one unpaired electron that holds a positive charge. The unpaired electron within a radical cation causes the molecule to be reactive. The high reactivity of these species allows for radical cations to be commonly studied experimentally using mass spectrometry and other multi-mass imaging techniques. However, these methods often cannot resolve the reaction mechanisms for these fast reactions. Specifically, radical cation rearrangement mechanisms are particularly unresolved within experiments. For this reason, radical cation rearrangements are computationally investigated to explain complex reaction pathways for processes to understand reactions leading to the initiation of detonation …

A Generic Implementation Of Fast Fourier Transforms For The Bpas Library, Colin S. Costello

Electronic Thesis and Dissertation Repository

In this thesis we seek to realize an efficient implementation of a generic parallel fast Fourier transform (FFT). The FFT will be used in support of fast multiplication of polynomials with coefficients in a finite field. Our goal is to obtain a relatively high performing parallel implementation that will run over a variety of finite fields with different sized characteristic primes. To this end, we implement and compare two Cooley-Tukey Six-Step fast Fourier transforms and a Cooley-Tukey Four-Step variant against a high performing specialized FFT already implemented in the Basic Polynomial Algebra Subprograms (BPAS) library. We use optimization techniques found …

In Silico Investigation For The Conversion Of Methyl Oleate To Gasoline, Arkanil Roy

MSU Graduate Theses

Petroleum products are found in all walks of life. From the plastic casing on a cell phone to the gasoline that runs most vehicles, a lot is derived from petroleum. Ubiquitous use of petroleum has adversely affected the environment. Toxic substances such as SOx and NOx are released into the atmosphere during the processing and usage of petroleum products, which contributes to global warming. Inevitable oil spills cause devastating effects to marine ecosystems. The rate of regeneration of petroleum is much slower than the rate of usage that would lead to it being exhausted in the recent future. Hence, a …

First-Principles Studies Of Anion Engineering In Functional Ceramics, Steven Timothy Hartman

McKelvey School of Engineering Theses & Dissertations

Ceramic materials display a wide variety of valuable properties, such as ferroelectricity, superconductivity, and magnetic ordering, due to the partially covalent bonds which connect the cations and anions. While many breakthroughs have been made by mixing multiple cations on a sublattice, the equivalent mixed-anion ceramics have not received nearly as much attention, despite the key role the anion plays in the materials’ properties. There is great potential for functional ceramics design using anion engineering, which aims to tune the materials properties by adding and removing different types of anions in existing classes of ceramic materials. In this dissertation, I present …

Computational Quantum Study Of Intermediates Formed During The Partial Oxidation Of Melatonin, Oladun Oladiran

Electronic Theses and Dissertations

Melatonin is a neurohormone produced by the pineal gland in the brain. It functions as an antioxidant to scavenge free radicals. Free radicals are reactive species; they often oxidize the cells leading to oxidative stress which may lead to severe health complications. Reaction of melatonin with free radicals is known to be stepwise, as such the stability of the intermediates can be examined. Thus, the possibility of using melatonin as an in vivo spin trap can be determined. Spin traps allow characterization of unstable radical species using electron spin resonance spectroscopy. In this research, ab initio quantum chemistry techniques were …

Hydroponic And Soilless Culture Systems And Transplant Practices Influence Production Of Basil (Omicum Basilicum L.), Samuel Warren Edward Doty

Graduate Theses and Dissertations

Two controlled-environment greenhouse experiments evaluated (1) plant growth and morphology of basil (Omicum basilicum L.) grown in three different hydroponic and soilless substrate systems and (2) seedling tray cell-count and transplant date into hydroponic culture effects on basil growth and yield at harvest. For the first experiment, four basil cultivars (‘Genovese’, ‘Mrs. Burns Lemon’, ‘Sweet Thai’, and ‘Cinnamon’) were grown in deep flow technique (DFT) hydroponics, nutrient film technique (NFT) hydroponics, and a novel shallow aggregate ebb-and-flood (SAEF) soilless substrate system and were harvested after 21 d. Plant yield and morphological characteristics measured at harvest included shoot fresh mass, shoot …

Computational Modeling Of Photolysis And Catalysis Reactions In Vitamin B12-Dependent Enzymes., Abdullah Al Mamun

Electronic Theses and Dissertations

Vitamin B₁₂ is a complex organometallic molecule, the derivatives of which such as adenosylcobalamin (AdoCbl) and methylcobalamin (CH₃Cbl) act as a cofactor in numerous enzymatic reactions. These two biologically active cofactors contain a unique organometallic Co-C σ bond. Important feature of this Co-C bond is that it can be activated by both thermally and photolytically inside the enzymatic environment as well as in the solution. In the case of enzymatic reactions where AdoCbl molecule act as a cofactor, the cleavage of the Co-C bond constitutes the key catalytic step. The most intriguing features of this cleavage is …

An Atomistic Study Of The Effects On Mechanical Properties And Bonding Interactions Of Carbon Nanofillers In Nylon 6 Nanocomposites, Michael Roth

Dissertations

Polymers have potential for a wide range of applications. The effectiveness of polymers can be further enhanced through the addition of nanofillers that improve thermal, mechanical, and electrical properties of the polymer. Carbon based nanofillers such as carbon nanotube (CNT), graphene, and carbon nanofibre (CNF) are of particular interest due to their high properties and high aspect ratios. However, limited understanding of the governing interactions of these nanofillers with polymers limits the effectiveness of the final nanocomposite.

The first facet of this dissertation focuses on determining the dominating interactions between pristine CNT and graphene with nylon 6 monomer and the …

Magnetism In Γ-Fesi2 Nanostructures: A First Principles Study, Sahil Dhoka

Dissertations, Master's Theses and Master's Reports

First-principles calculations are performed on γ-FeSi₂ nanostructures grown on Si (111) and (001) substrate. An attempt to explain the origin of emergent magnetic properties of the metastable gamma phase of iron di-silicide (γ-FeSi₂) is made, which show ferromagnetic behavior on nanoscale, unlike its possible bulk form. Many papers try to explain this magnetism from factors like bulk, epitaxial strain, interface, surface, edges, and corners but doesn’t provide an analytical study for these explanations. Density functional theory is used to analyze the magnetic effects of these factors. The results for the epitaxial structures show no magnetic behavior for …

Quantum Chemical Pka Estimation Of Carbon Acids, Saturated Alcohols, And Ketones Via Quantitative Structure-Activity Relationships, Corey Adam Baldasare

Browse all Theses and Dissertations

Acid dissociation constants, often expressed as pKa values, afford vital information with regards to molecular behavior in various environments and are of significance in fields of organic, inorganic, and medicinal chemistry. Several quantitative structure-activity relationships (QSARs) were developed that correlate experimental pKas for a given class of compounds with a descriptor(s) calculated using density functional theory at the B3LYP/6-31+G** level utilizing the CPCM solvent model. A set of carbon acids provided a good final QSAR model of experimental aqueous pKas versus ΔEH2O (R2 = 0.9647) upon removal of three aldehydes as outliers. A study of saturated alcohols offered a final …

A Density Functional Theory Study Of Palladium Nanoparticles And Their Redox Properties On Graphene, Billie A. Radcliffe

Theses and Dissertations

Nanoparticles exhibit characteristics that are different from bulk materials as well as from atoms resulting in their application in numerous fields of applied material science. In particular, small palladium nanoparticles supported on graphene have been found to be outstanding catalysts for the Suzuki cross-coupling reaction. One explanation as to why these supported nanoparticles are such outstanding catalysts is because they may act as both electron donors and acceptors. Charge donating ligands are known to lower the ionization energy of clusters, making the clusters better donors. In this project, it is hypothesized that graphene supports may also act like charge donating …

Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur

Biological Sciences

Many recent theoretical and experimental techniques have been developed to probe the structurefunction relationships of complex biomolecules. The roles of RNAs are dependent upon various intricate structural motifs and interactions, including hairpins, pseudoknots, long range territory contacts, bulges and internal loops, that are not easily captured by these methods. We had previously developed an enhanced replica exchange molecular dynamics method that incorporated secondary structure information in the form of distance restraints in order to effectively overcome kinetic barriers and sample conformational space. In several structures, restrained RNA base pairs near large bulges displayed a preference for stacking over hydrogen bonding …