Computational Chemistry Commons^™

Exploration And Synthesis Of Half-Heusler And Disordered Ternary Intermetallic Single Crystals, Md Fahel Bin Noor

Graduate Theses/Dissertations

Due to their distinct physical and chemical characteristics, half-Heusler compounds are intermetallic materials that have undergone substantial research. The general formula for these compounds is XYZ, where X and Y are transition metals and Z is a p-block element. Thermoelectricity is among the half-Heusler compounds' most exciting potential uses, but additional possible applications include spintronics, magnetic refrigeration, and superconductivity, among others. Recently, half-Heuslers (and Heuslers) have emerged as candidates for catalysts for hydrogenation. The CoNbSn half-Heusler compound, as well as another unique intermetallic ternary compound, the disordered Mn_4-xCr_xAl₁₁, were successfully grown as single crystals …

Molecular Dynamics Modeling Of Polymers For Aerospace Composites, Swapnil Sambhaji Bamane

Dissertations, Master's Theses and Master's Reports

Polymer matrix composite materials are widely used as structural materials in aerospace and aeronautical vehicles. Resin/reinforcement wetting and the effect of polymerization on the thermo-mechanical properties of the resin are key parameters in the manufacturing of aerospace composite materials. Determining the contact angle between combinations of liquid resin and reinforcement surfaces is a common method for quantifying wettability. It is challenging to determine contact angle values experimentally of high-performance resins on CNT materials such as CNT, graphene, bundles or yarns, and BNNT surfaces. It is also experimentally difficult to determine the effect of polymerization reaction on material properties of a …

Multilevel Computational Investigation Into The Catalytic Mechanisms Of Matrix Metalloproteinase-1 And Fat Mass And Obesity-Associated Enzyme, Ann Varghese

Dissertations, Master's Theses and Master's Reports

Enzymes are biological macromolecules, typically proteins, that efficiently accelerate the rate of chemical reactions. Their remarkable catalytic power plays a vital role in essential processes across all kingdoms of life. Nowadays, computational chemistry methods provide valuable insights into enzymatic functions aiding our understanding of biological processes and providing advancements in fields such as biomedical sciences, biomimetic catalysis, drug design and biotechnology. This dissertation employs multilevel computational chemistry methods to investigate the structure-function relationships and the catalytic mechanisms of two metalloenzymes -Zn(II)-dependent matrix metalloproteinase-1 (MMP-1) and non-heme Fe(II)/2-oxoglutarate (2OG) dependent fat-mass and obesity-associated (FTO) enzyme. Chapter 2 explores the role of …

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 …

Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed

Dissertations, Master's Theses and Master's Reports

Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps …

Computational Comparison Of Platinum, Base Metals, And Binary Intermetallic Compounds’ Efficiency In Hydrogenation Catalysis, Lauren M. Sayler

Graduate Theses/Dissertations

In the petroleum industry, platinum is used as a catalyst in hydrogenation reactions during petroleum refining. Although platinum is extremely effective as a catalyst, it is expensive. This is an investigation into platinum and what characteristics make it so efficient, with the end goal of finding intermetallic compounds composed of base metals that are as effective in hydrogenation catalysis. The metals used in this investigation are Fe, Co, Ni, Mo, and W. The research performed here is computational and used to support and direct decisions made in the laboratory. The computation is first-principle, which is accomplished using Vienna Ab initio …

Computational Investigation Of The Ionization Potential Of Lead Sulfide Quantum Dots, Jessica Beyer

Scripps Senior Theses

The purpose of this work was to determine the impact of quantum dot size on ionization potential and to determine how the presence of carbonyl-based ligands affect the ionization potential of lead sulfide quantum dot systems. Ionization potential (IP) is defined as the energy required to remove an electron from an atom, molecule, or material. IP helps scientists determine how reactive the material of interest is, which is crucial information when manufacturing nanomaterials. Accurate quantum chemical calculations of ionization potential are challenging due to the computational cost associated with the numerical solution of the Dyson equation. In this work, the …

Global Minimum Search For The Largest Ge Cage Stabilized By A Single Interstitial Metal Atom, Alexis Kiefer

Williams Honors College, Honors Research Projects

Recent joint experimental and theoretical studies showed that the largest Ge cage-like cluster features 14 Ge atoms that encapsulate a single transition metal atom in the [Nb@Ge₁₄]^3- cluster. The next larger experimentally confirmed Ge cluster exhibiting a cage-like geometry was found to be viable only when stabilized by two transition metal atoms in the [Co₂@Ge₁₆]^4- cluster. So, as of now, it is not clear whether a cage-like cluster made out of 15 Ge atom stabilized by a single transition metal is viable. Hence, the aim of this project is to find the …

Developing Novel Femtosecond Time-Resolved Mass Spectrometry Techniques For Analysis Of Energetic Materials, Shane L. Mcpherson

Theses and Dissertations

Energetic materials and the unimolecular dissociation dynamics attributed to their initiation and subsequent bimolecular detonation have been a subject of interest for defense agencies such as the Department of Defense (DoD) for decades. The timescale in which these initial dynamics exist ranges from several picoseconds to dozens of femtoseconds, necessitating equally fast time-resolved experiments to capture and characterize these events. Our lab specializes in one such laser-based technique: femtosecond time-resolved mass spectrometry (FTRMS). FTRMS is an essentially nondiscriminatory pump-probe laser technique with nearly infinite modifications via pulse shaping, intensity, and wavelength modulation that can readily examine previously undefined dissociation pathways …

The Design And Characterization Of Gold Nanoclusters As Elementary Building Blocks, Heather Gaebler

Theses and Dissertations (Comprehensive)

Gold nanoclusters with diameters in the quantum size regime (< ~2 nm) are promising building blocks for the design of novel nanomaterials as they exhibit unique size-dependent properties that can be altered and fine-tuned. The research outlined in this PhD thesis employs density functional theory to construct and analyze small ligand-protected cage and rod-shaped nanoclusters. Chapter 2 reports stable halide-protected gold nanocages that were engineered to have a closed-shell valence electron count of 18. This study finds that nanocages comprised of 19 and 20 gold atoms can be converted into stable magic number species containing 18 valence electrons by modifying their charged states via adsorption of halide ligands to the cage’s surface. Chapter 3 reports stable ligand-protected gold nanoclusters with a tetrahedral Au₄ core that were engineered to have a closed-shell valence electron count of 2. This study investigates the structural and electronic effects of halide and alkoxy ligands on the tetrahedral nanocluster and concludes that the results support the broader conclusion that it’s possible to fine-tune the stability and electronic properties of small gold nanoclusters using appropriate ligands. Chapter 4 reports stable gold nanorods that have diameters in the quantum regime that were constructed from elementary building blocks that contain “halide-staples”. This study presents different orientations of the “halide-staple” motifs on …

Computational Studies Of The Effects Of Substitutions On Silatranes And Ring Strain Energies, As Well As Determination Of Aromaticity And Complexation In Polypnictogen Analogues Of The Cyclooctatetraenyl Dianion, Alexander Stuart Pixler

Graduate Research Theses & Dissertations

The work in this dissertation computationally examines four areas involving variations on archetype molecules and how they affect reactivity and physical properties. Studies in Chapters 2 and 3 assess substituent effects on cyclic systems, while those in Chapters 4 and 5 explore both partial and complete substitution of ring component atoms as well as the chemical implications of the substitution.The effect of substituents on molecular reactivity is a critical concept that affects every branch of chemistry. Previous work within our group showed that 1-hydridosilatrane was an effective and selective reducing agent for a variety of compounds. Fully 3,3,7,7,10,10-substituted silatranes have …

Molecular Understanding Of Zwitterions And Quantum Computing For Sustainability, Manh Tien Nguyen

Theses and Dissertations--Chemical and Materials Engineering

The sustainable development of society needs sustainable energy solutions and the mitigation of greenhouse gas emissions. One key subject in this area is the development of safe and efficient ion-based batteries. Moreover, CO₂ capture is a crucial pathway in mitigating emissions from the combustion of fossil fuels. Ongoing efforts are to improve both technologies' safety and efficiency. This thesis presents our efforts to conduct computational research on understanding advanced zwitterionic electrolytes and CO₂ capture. Chapters 2-4 illustrate the computational research to understand ionic solvation in zwitterionic electrolytes. Solid-state electrolytes are essential for safer batteries. While solid polymer electrolytes …

Translating Chemistry, Structure, And Processing To The Solid-State Morphology And Function Of Organic Semiconductors Through Computational Modeling And Simulations, Chamikara D. Karunasena

Theses and Dissertations--Chemistry

The immense synthetic design space and material versatility have driven the exploration and development of organic semiconductors (OSC) over several decades. While many OSC designs focus on the chemistries of the molecular or polymer building blocks, a priori, multiscale control over the solid-state morphology is required for effective application of the active layer in a given technology. However, molecular assembly during solid-state formation is a complex function interconnecting the building block chemistry and the processing environment. Insufficient knowledge as to how these aspects engage, especially at the atomistic and molecular scales, has so far limited the ability to predict …

Developing And Deploying Data-Driven Tools For Accelerated Design Of Organic Semiconductors, Vinayak Bhat

Theses and Dissertations--Chemistry

Organic semiconductors have gained widespread attention due to their potential applications in flexible, low-cost, lightweight electronics, energy storage and generation technologies, and sensing applications. However, developing new organic semiconductors with improved performance remains a significant challenge due to the vast chemical space of possible molecular and materials structures. Furthermore, the high cost and time-consuming nature of experimental synthesis and characterization hinder the rapid discovery of new materials. To overcome these challenges, this dissertation presents a data-driven approach to organic semiconductor discovery. The primary focus of this work is the development of data-driven tools, namely machine learning models, to predict critical …

Water-Soluble Palladium, Copper, And Nickel Catalysts And Their Formation In Ligand-Free Suzuki-Miyaura Cross-Coupling Reactions, Priya Karna

Theses and Dissertations--Chemistry

Transition-metal catalyzed Suzuki-Miyaura (SM) cross coupling is a powerful synthetic method for constructing carbon-carbon and carbon-heteroatom bonds in designing organic compounds, agrochemicals, pharmaceuticals, and precursors for materials. However, the nature of catalysis and identity of the transition metal catalysts used in these reactions remain under debate or unknown. This dissertation reports the studies of three metals: Pd, Cu, and Ni. Pd-nanocluster catalysts and their formation in ligand-free SM reactions with Pd(II) nitrate as a precatalyst was investigated. The catalysts are water-soluble neutral Pd tetramer and trimer in their singlet electronic states as identified by UV-Vis absorption spectroscopy and are formed …

First Principles Calculations To Investigate Surface And Catalytic Properties Of Materials For Green Energy Generation, Keerthan Raghavendra Rao

Theses and Dissertations--Chemistry

Climate change due to greenhouse gas build up in the earth’s atmosphere is an existential threat to humanity. To mitigate climate change, a significant shift from fossil fuels is necessary. Over the years, several renewable energy sources like solar, wind, geothermal etc. have been explored with the aim providing carbon-free energy. In this work, we focus on using density functional theory (DFT) methods to investigate key functional properties of materials of interest for applications in solar cells and catalytic conversion for energy generation. We show geometric effects of carboxylic acid binding on a transition metal surface to impact the deoxygenation …

Computational Studies On Molecular Mechanisms For Dysregulation Of Monoamine Transporters By Hiv-1 Tat And Drug Discovery Of Novel Phosphodiesterase-2 Inhibitors, Charles A. Adeniran

Theses and Dissertations--Chemistry

Computational chemistry methods have been greatly used and has great potential in drug discovery and understanding the detailed molecular mechanism of biological processes. Scientific questions can initially be addressed using computational modeling and simulation studies. The common feature in this work is to understand intermolecular interactions related to protein targets in the brain, as it relates to HIV infection and Alzheimer’s Disease. HIV is among the world’s most deadly infectious diseases. Recent therapeutic advancements have begun to increase the life expectancy of people living with this virus. The mechanisms that lead to neurobiological complications known as HIV- associated neurocognitive disorders …

Structural Analysis Of Polar Aggregates And Inter-Ionic Distances In Room Temperature Ionic Liquids, Emily Elizabeth Dalbey

Graduate Research Theses & Dissertations

Ionic liquids have a wide variety of applications in chemistry due to their unique properties such as low flammability, low volatility, and high thermal and chemical stability. These properties make them great solvents, electrolytes for lithium-ion batteries, and more. Ionic liquids are salts whose components are mis-matched in size and shape leading to low melting points. To design an ionic liquid with a desired property it is key to first understand their structure. Lineshape analysis of the charge alternation peak from the experimentally measured or computationally calculated X-ray scattering data can give information about the size of the polar aggregates …

Machine Learning For Electronic And Atomistic Simulations, Jun Yang

Dartmouth College Ph.D Dissertations

The demand for accurate and efficient atomistic simulations and electronic structure calculations in materials science and quantum chemistry has motivated the development of novel computational methodologies. The rapid evolution of machine learning has brought new techniques for advancing the accuracy, efficiency, and predictive power of atomistic simulations and electronic structure calculations.

In this thesis, we explore the symmetry requirements and physics intuitions needed for developing machine-learning interatomic potentials, which are the most critical component in atomistic simulations. Specifically, we introduce a novel physics-inspired graph neural network interatomic potential that enables accurate and efficient atomistic simulations of complex materials. The machine …

Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …