Physical Sciences and Mathematics Commons^™

Computationally-Driven Insights Into The Ligand Environments Of Materials For Catalysis And Separations, Stephen Vicchio

All Dissertations

Designing new catalytic and sorption materials is necessary to limit global temperature rise below 1.5 ◦C by 2050, while also meeting global energy demands. Climate change and energy production are not mutually exclusive; global population growth has direct impacts on global energy demands and climate. In both catalysis and adsorption applications, new technologies are needed to address these challenges. Catalysis can provide alternate, low-energy routes for converting low-value gases into higher-value chemical commodities, thus altering our current energy production. Likewise, new sorption materials can capture previously emitted CO₂ from decades of energy production from fossil fuels, thus helping to …

Computational And Experimental Investigation Of Elemental Sulfur And Polysulfide, Jyoti Sharma

Dissertations

Petroleum processing results in the generation of significant quantities of elemental sulfur (S₈), leading to a surplus of sulfur worldwide. Despite its abundance and low cost, the use of sulfur in value-added organic compound synthesis is limited due to its unpredictable and misunderstood reactivity. This dissertation aims to address this issue by tackling it from two angles. Firstly, by utilizing Density Functional Theory (DFT) calculations, the reactivity of sulfur in the presence of nucleophiles is studied. This facilitates the identification of organic polysulfide intermediates that can be generated under different conditions, as well as the corresponding reactivity for …

Advances In One-Electron Self-Interaction-Correction Methods For Accurate And Efficient Self-Interaction-Free Density Functional Calculations, Selim Romero

Open Access Theses & Dissertations

Density functional theory (DFT) is a widely used computational method for studying electronic structures of atoms, molecules, and solids. It provides an exact theory for obtaining ground state energy from the ground state density. However, since the exact exchange-correlation functional remains unknown, approximate exchange-correlation functionals called approximate density approximations (DFAs) are used. The foundation of many DFAs is the local spin density approximation (LSDA). It serves as the starting point for constructing various DFAs. However, DFAs are prone to self-interaction errors (SIE) due to the improper cancellation of the approximate exchange energy and the Coulomb energy. This issue impacts the …

Isolating The Electronic Effects Of Systematic Twist In Highly Substituted Aromatic Hydrocarbons Using Density Functional Theory, Grace Tully, Emily A. Jarvis

Honors Thesis

Density functional theory (DFT) was employed to investigate dodecaphenyltetracene as well as similar molecules containing differing backbone lengths and electron withdrawing groups with interest in manipulating the twist to lower the LUMO level for increased electron mobility. Optimization and frequency time-independent calculations followed by time-dependent (TD-DFT) energy calculations were performed at the B3LYP/G-311G level of theory to analyze electronic trends as a result of increased backbone length and consequently distorted end-to-end molecular twist. These calculations demonstrate a linear relationship with negative slope between the estimated HOMO-LUMO, fundamental, and optical gaps as a function of the number of fused rings along …

Predicting The Reactivities And Reaction Mechanisms Of Photochemically Produced Reactive Intermediates, Benjamin Barrios Cerda

Dissertations, Master's Theses and Master's Reports

Photochemically produced reactive intermediates (PPRIs) such as the hydroxyl radical, carbonate radical (CO₃^•-) singlet oxygen (¹O₂) and triplet state of chromophoric dissolved organic matter (³CDOM^*) are formed in sunlit natural waters upon photoexcitation of chromophoric dissolved organic matter (CDOM). PPRIs react with the organic compounds involved in key environmental processes, resulting in transformation products of smaller molecular weight than their parent compounds. Photochemical transformation of these key water constituents due to their reactions with PPRIs may pose potential effects on human and aquatic ecosystems. Consequently, there is a need …

The Future Of Alternative Energy? Simulating Methyl Stearate Pyrolysis Via Molecular Dynamic Processes, Sarah J. Adeoye

MSU Graduate Theses

The process of extracting and refining crude oil is both expensive and environmentally hazardous. The synthesis of biodiesel sourced from vegetable oils is a renewable process and less hazardous to the environment. Therefore, we seek to understand the pyrolysis procedure at an atomic level in hopes of optimizing future fuel viability. Herein, I analyze methyl stearate (a component of biodiesel) using an in-house database of ab initio trajectories, each simulating 1.0 ps (with 1.0 fs resolution). These jobs were observed for significant bond-breaking/forming events, the type of fragments produced, and the exact position and time for each event. Statistical analysis …

Tethered Axial Coordination As A Control Modality In Rhodium(Ii)-Catalyzed Carbene Transfer Reactions, Anthony Dean Abshire

Doctoral Dissertations

Rhodium(II) paddlewheels are versatile carbene transfer catalyst that are broadly applied in insertion reactions, cycloadditions, and ylide transformations. The effects of axial coordination in rhodium(II)-catalyzed carbene transfer reactions are still little understood due to compounding factors that are difficult to isolate. Traditionally, researchers study axial coordination by addition of Lewis base additives. To ensure interaction between the Lewis base and catalyst, high molar equivalents are used. This can also have the undesired effect of hampering the activity of the catalyst and suppressing the yield of the reaction. We have developed ligands with a tethered Lewis base to overcome these issues. …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

A Study Of Cannabigerolic Acid And Its Derivatives Via Raman Spectroscopy And Density Functional Theory, Trevor Wolfe

Honors Theses

The cannabinoids are a class of molecules endogenous to the cannabis plant. Their scientific relevance has increased in recent years due to the mercurial legal status of marijuana across the United States. Some of the most known are cannabidiol (CBD), δ9-tetrahydrocannabinol (δ9-THC), and δ8-THC due in large part to their widespread use, especially in states where marijuana and related products are legal. However, cannabigerolic acid (CBGA) is arguably the most important cannabinoid; it is enzymatically converted into other acidic cannabinoids, which subsequently undergo non-enzymatic processes (isomerization, thermal decarboxylation, oxidation, etc.) to synthesize further cannabinoids. Although there is a wealth of …

Computational Design Of Two-Dimensional Transition Metal Dichalcogenide Alloys And Their Applications, John Douglas Cavin

Arts & Sciences Electronic Theses and Dissertations

The discovery of bronze as an alloy of copper and tin is arguably the earliest form of material design, dating back thousands of years. In contrast, two-dimensional materials are new to the 21st century. The research presented in this dissertation is at the intersection of alloying and two-dimensional materials. I specifically study a class of two-dimensional materials known as transition metal dichalcogenides (TMDCs). Because of the large number of transition metals, there are many combinations of TMDCs that can be alloyed, making experimental exploration of the phase space of possible alloys unwieldly. Instead, I have applied first-principles methods to study …

Electronic Structure And Dynamics Of Uranyl-Peroxide Species, Ethan T. Hare

Honors Thesis

Uranyl-peroxide nanocapsules are a unique family of self-assembled actinide species. Uranyl ions rapidly self-assemble in basic peroxidic media through a myriad of reactions to coalesce into a single nanocapsule that includes both peroxide and hydroxide bridging groups between the uranyl moieties. A wide variety of capsules can be formed, and it has been proposed that square and pentagonal building blocks assemble prior to nanocapsule formation. We have studied the speciation of the pentagonal 2) uranyl-peroxide nanocapsule building blocks using density functional theory calculations. We predicted the most favorable speciation pathways for the self-assembly of the building blocks prior to cluster …

Molten Alkali Halide Salt-Flux Crystal Growth And Physical Property Determination Of Complex Oxides And Chalcogenides Supported By First Principles Density Functional Theory Calculations, Mohammad Usman

Theses and Dissertations

The primary objective of this dissertation is to inform the reader about more thansixty new materials with potentially attractive physical properties obtained via molten alkali halide flux methods as X-ray diffraction quality crystals. Flux crystal growth carries several advantages over other synthetic methods, including low reaction temperatures and straightforward post-reaction workup. This dissertation consists of 11 chapters, including an introductory chapter, which are organized into two parts, each corresponding to the general structure type of the family of oxides and chalcogenides being investigated. Part 1, which encompasses chapters 2–6, is dedicated to the discussion of crystal growth of complex chalcogenides …

Comparison Of Calculated Normal Mode Molecular Vibrations With Experimental Gas-Phase Infrared Spectroscopy, Anila Renis Sutar

Dissertations and Theses

Computational vibrational spectroscopy serves as an important tool in the interpretation of experimental infrared (IR) spectra. Analysis of computational results provides a perspective over broader wavelength ranges and at higher precision. Although there are issues regarding accuracy, this can be approximated by using a scaling factor. High-resolution gas-phase FTIR spectroscopy at a resolution of 0.125 cm^-1 can partially resolve rovibrational transitions in the P, Q, and R bands and therefore identify fundamental frequencies with approximately 1 cm^-1 precision.

This research has compared high-resolution gas-phase FTIR absorption peaks to calculated vibrational frequencies. In the calculation of normal mode frequencies, …

Determining Material Structures And Surface Chemistry By Genetic Algorithms And Quantum Chemical Simulations, Josiah Jesse Roberts

Theses and Dissertations--Chemistry

With the advent of modern computing, the use of simulation in chemistry has become just as important as experiment. Simulations were originally only applicable to small molecules, but modern techniques, such as density functional theory (DFT) allow extension to materials science. While there are many valuable techniques for synthesis and characterization in chemistry laboratories, there are far more materials possible than can be synthesized, each with an entire host of surfaces. This wealth of chemical space to explore begs the use of computational chemistry to mimic synthesis and experimental characterization. In this work, genetic algorithms (GA), for the former, and …

Developments Of Machine Learning Potentials For Atomistic Simulations, Howard Yanxon

UNLV Theses, Dissertations, Professional Papers, and Capstones

Atomistic modeling methods such as molecular dynamics play important roles in investigating time-dependent physical and chemical processes at the microscopic level. In the simulations, energy and forces, sometimes including stress tensor, need to be recalculated iteratively as the atomic configuration evolves. Consequently, atomistic simulations crucially depend on the accuracy of the underlying potential energy surface. Modern quantum mechanical modeling based on density functional theory can consistently generate an accurate description of the potential energy surface. In most cases, molecular dynamics simulations based on density functional theory suffer from highly demanding computational costs. On the other hand, atomistic simulations based on …

Improving Biodiesel Through Pyrolysis: Direct Dynamics Investigations Into Thermal Decomposition Of Methyl Linoleate, Michael Bakker

MSU Graduate Theses

Dependence on petroleum and petrochemical products is unsustainable as it is both a finite resource and environmentally hazardous. Biodiesel is a proposed alternative, but has complications including possessing poor cold weather operability and lacking the ability to supplement other petrochemical products (e.g., ethylene, hexane, etc.) relied upon in society. Pyrolysis of biodiesel has demonstrated the formation of smaller hydrocarbons comprising many of these petrochemical products. Our aim is to computationally simulate the pyrolysis of methyl linoleate, the most prevalent component in biodiesel formed in the US (from soybean). We make use of unimolecular direct dynamics describing intramolecular processes, introducing Temperature …

Multiscale Modeling Of Structure-Function Relationships Of Organic Semiconductors, Shi Li

Theses and Dissertations--Chemistry

While optoelectronic devices built from organic semiconductors (OSC) continue to find their way into the commercial landscape, there remain numerous challenges to overcome to supplant traditional semiconductors in many technologies. Chief among these are low performance metrics relative to devices with conventional semiconductors and device stability. In order to overcome these challenges, a wide range of new OSC and processing technologies have been developed. However, there remains limited fundamental understanding of the relationship between molecular structure, packing in the solid state, and the resulting materials properties. Here, we make use of multiscale molecular models and utilize classical all-atom molecular dynamic …

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 …

Simulating Hydrogen Bonded Clusters And Zeolite Clusters For Renewable Energy Applications, Qinfang Sun

Doctoral Dissertations

Our research attention is focused on the development of new fuel cell membrane materials and new zeolites which improve biomass conversion rate to meet the increasing demand of renewable and sustainable energy. We have simulated the dynamics of amphiprotic groups (pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, and tetrazole, acetic acid, formic acid, sulfuric acid, and phosphoric acid) as neat liquids and tethered via linkers to aliphatic backbones, to determine how tethering and varying functional groups affect hydrogen bond networks and reorientation dynamics, both factors thought to influence proton conduction. We used the DL_Poly_2 molecular dynamics code with the GAFF force field to …

Nontraditional Hydrogen Bonding In Asymmetric Lewis Acid Catalysis, Brandon Vernier

Electronic Theses and Dissertations

In the field of asymmetric induction, there is a shift from the synthesis of reaction

specific chiral auxiliaries towards a broader mechanistic approach. Our approach is to

develop a theory of asymmetric catalyst design from first principles. The Diels-Alder

reaction of 2-methacrolein and 1,3-cyclopentadiene in the presence of 15 mole % lmenthoxy

aluminum dichloride, reported by Koga, achieved the (S)-exo-Diels-Alder

cycloadduct with 72% ee (0% ee Endo for acrolein). The dramatic change from 72% to 0%

ee is a significant fact that has been overlooked in practical organic synthesis.

In the first phase of this work, the conformational landscape of …

Computational Study Of The Nature Of Tetrel Bond, Yama Aman

Masters Theses

For more than a hundred years, the type of a chemical bond has been distinguished according to the relative electronegativities of chemical units at the ends of a bond. Whereas, the bond of unequally electronegative on both ends is called a polar covalent or even ionic bond or a non-polar covalent bond in case of both equal. Regardless the type of bonded elements, the whole idea for the bond was believed to be electron driven only. In the 20th century the development of the idea, that not just the electronic relation but specific elements are also able to characterize the …

Computational Investigation Of Energetic Materials: Influence Of Intramolecular And Intermolecular Interactions On Sensitivity, Ashley Lauren Shoaf

Chemistry & Biochemistry Theses & Dissertations

The development of novel high energy density materials (HEDMs) with superior energetic properties depends on characterizing how and why detonation occurs. Detonation is highly energetic and a nearly instantaneous process, making experimental studies challenging; thus, computational modeling through density functional theory (DFT) and molecular dynamics (MD) can be used to propose weakened, or activated, bonds that break to initiate explosive decomposition, termed trigger bonds. Bond activation is characterized by the Wiberg bond index (WBI), a measure of interatomic electron density. Trigger bonds in HEDMs are commonly found in explosophores, functional groups that contribute to energetic potential such as X-NO_{2 …}

Determining The Reactivity And Oxidation Intermediates Of An Allylnickel (N-Heterocyclic Carbene) Chloride Complex, Scott W. E. Hendriks

Electronic Thesis and Dissertation Repository

The oxidation of C-H bonds to carbonyl functional groups using molecular oxygen (O₂) is a desirable process as O₂ is environmentally benign and inexpensive. However, oxidations that employ O₂ have lower product selectivity, making it industrially unappealing. The metal complexes NiCl(π-cinnamyl)(NHC) oxidize stoichiometrically with O₂ as the oxidant to selectively form the ketone and aldehyde products.

This thesis details the attempted catalysis with the NiCl(π-allyl)(NHC) complex and the stoichiometric reactivity of NiCl(π-allyl)(NHC) and NiCl(π-cinnamyl)(NHC) complexes upon O₂ exposure. An investigation of the intermediate and decomposition species of the NiCl(π-allyl)(NHC) complex was conducted. The complexes …

Ab Initio Methyl Linoleate Bond Dissociation Energies: First Principles Fishing For Wise Crack Products, Zachary Ryan Wilson

MSU Graduate Theses

With the prices of petroleum reflecting demand for this finite resource, attention has been turned to alternative sources of energy. Biodiesel, defined as fatty acid methyl esters (FAMEs), exhibits many of the same properties as conventional diesel but is derived from biological sources. FAMEs are subsequently thermally cracked to form more light-weight petrochemical products. I aim to further understand the thermal cracking procedure, at an atomic-level, in hopes that this may aid in future engineering of viable fuels. I studied the effective computational modeling of bond disassociations in the FAME methyl linoleate. Bond dissociation in a 44-reaction database with known …

Investigating The Properties Of Superfluid He-4 Through Density Functional Calculations, Matthew Francis Dutra

Doctoral Dissertations

We present a study of isotopically pure He-4 systems evaluated using helium density functional theory (He-DFT) with the intent of better understanding their ground state structural and energetic properties, particularly within the scope of singularly-doped helium droplets. We self-consistently solve for the density profiles and chemical potentials for a wide range of pure helium droplet sizes (up to 9500 atoms) via an imaginary time propagation method, and fit the resultant energetic data to a power law formula to be able to extrapolate values for even larger droplets. Subsequent calculations on singularly-doped droplets within the same size range yield accurate binding …

Rationalizing The Band Gap Tunability Of Semiconductors Via Electronic Structure Calculations, Matthew N. Srnec

Electronic Theses and Dissertations

The polymorphs of titanium dioxide and various diamond-like semiconductor materials are promising candidates in photovoltaic solar cell applications. Several of these polymorphs have been studied with experimental and computational methods, which often aim at tuning the electronic structure, particularly the band gap value of the crystalline solid. Prior studies report that the addition of a substituent into the structure of titanium dioxide decreases its band gap value, but the reasons for this are unknown. Possible explanations for the change in band gap involve the substituent atom's crystal radius, electronegativity, and ionization energy. Understanding the cause of these changes will provide …

A Computational Study Of Silver Doped Cdse Quantum Dots, Heather Gaebler

Theses and Dissertations (Comprehensive)

Due to quantum dot’s ability to emit photons when subjected to light of sufficient energy, they have become optimal candidates for biomedical research and for optoelectronic applications. Fascination towards quantum dots arises from the fact that their properties are easily fine-tuned through a variety of different techniques. Electronic doping is a popular technique used to control the properties of quantum dots through the addition of different elements.

Via density functional theory calculations, this work investigated how the structural energies and HOMO-LUMO gaps were altered by the addition of impurity atoms. First, interstitial and substitutional doping styles were investigated at 0 …

Modeling The 3-Dimensional Structure Of D(Cgcgaattcgcg) And Its 8-Oxo-Da5 Adduct With 1h Nmr Noesy Refinements, Christopher Miles Reynolds

MSU Graduate Theses

Since the characterization of the oligomer d(CGCGAATTCGCG) has been published by Dickerson et al., computational studies have been carried out to produce an accurate 3D model. These models are important for visualizing how certain DNA repair enzymes, such as the glycosylases, recognize sites of damage by signatures of local 3D distortion. Using 1H NOESY-generated internuclear distances to replicate the model of this oligomer and a derivative with an 8-oxo-dA5 lesion, we propose characteristics of helical distortion that DNA glycosylases might use for identifying this form of damage. In addition, this method of comparison can be used to study the repair …

Fractional Charge Methods For Correcting Approximate Kohn-Sham Potentials, Darya N. Komsa

Electronic Thesis and Dissertation Repository

The Kohn-Sham density functional theory relies on approximating the exchange-correlation energy functional or the corresponding potential. The behavior of the exchange-correlation potential as a function of position in a system can be used to detect and correct deficiencies of the parent functional. The too-fast decay of the potentials derived from common density functionals is a major problem, because it causes inaccurate Rydberg excitation energies and erroneous fractional charges in dissociating molecules. An efficient method to correct the shape of the exchange-correlation potential was proposed by Gaiduk et al. [A. P. Gaiduk, D. S. Firaha, and V. N. Staroverov, Phys. Rev. …

Applying Bayesian Machine Learning Methods To Theoretical Surface Science, Shane Carr

McKelvey School of Engineering Theses & Dissertations

Machine learning is a rapidly evolving field in computer science with increasingly many applications to other domains. In this thesis, I present a Bayesian machine learning approach to solving a problem in theoretical surface science: calculating the preferred active site on a catalyst surface for a given adsorbate molecule. I formulate the problem as a low-dimensional objective function. I show how the objective function can be approximated into a certain confidence interval using just one iteration of the self-consistent field (SCF) loop in density functional theory (DFT). I then use Bayesian optimization to perform a global search for the solution. …