Computational Chemistry Commons^™

Unraveling The Reactivity Of Nitrate Ester Explosives: Insights From Femtosecond Time-Resolved Mass Spectrometry And Computational Chemistry, Erica Britt

Theses and Dissertations

This dissertation uncovers the ultrafast molecular mechanisms underlying the decomposition of nitrate ester explosives—nitroglycerin (NG), ethylene glycol dinitrate (EGDN), and amyl nitrate—through the integration of femtosecond time-resolved mass spectrometry and advanced computational chemistry. Although these compounds play fundamental roles in both military and civilian contexts, the precise molecular dynamics governing their pronounced reactivity and impact sensitivity have remained inadequately characterized. Our research establishes that low O–NO2 bond dissociation energies are the primary driver of ultrafast fragmentation and high reactivity in all three esters. The distinctive molecular architectures of these esters dictate their explosive properties: NG’s tri-nitrate configuration leads to exceptional …

Theoretical Investigation Of Hydrogen Abstraction From Fluorinated Propanones And Fluorinated Propanals, Laurel Washburn

Honors Theses

Per- and polyfluoroalkyl substances (PFAS) are a class of thousands of industrially used compounds often called “forever” chemicals because of their slow degradation process that leads to accumulation in soil, dust, drinking water, and the body. PFAS are used for their grease and water resistance properties but some of these compounds are toxic at extremely low levels. To better understand the effects of these types of compounds, the main pathways of their degradation need to be further investigated. This study analyzes computationally the hydrogen abstraction reactions by both hydroxyl radical and triplet oxygen atom for all possible fluorinated propanones and …

Methods For Computing Rovibrational Spectral Data With Applications To Inorganic Oxides And Hydrocarbons, Alexandria Watrous

Honors Theses

Computational chemistry focuses on finding solutions to the time-independent Schrödinger equation for systems of interest to study their molecular properties such as rovibrational spectral data. Any molecule containing more than one electron cannot be solved explicitly but coupled cluster theory offers one of the best approximations. One such application of this method is to molecules of astrochemical interest to support observation and experimental data. Chapters 2, 3, and 4 look at the performance of new couple cluster theory methods including composite and hybrid methods for ground and excited state rovibrational data. Chapters 5 - 9 use the previously mentioned methods …

Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust

Graduate Theses/Dissertations

The world today relies on hydrocarbon combustion for many reasons, including its high energy density that provides ease of transportation. However, hydrocarbons sourced from fossil fuels are not expected to last forever. Biodiesel, a renewable alternative, has many attractive benefits but comes with other downsides. Biodiesel can gel in cold environments and may leave residue in an engine. Pyrolysis of biodiesel has shown promise in addressing these common detriments. Inducing pyrolysis on biodiesel feedstock (commonly soybean oil in the USA) would be an attractive option presuming it continues to produce fossil fuel analogs similar to biodiesel pyrolysis. Herein, Langevin molecular …

Microhydration Of Hexachlorophosphate Anion, Anna Robertson

Honors Theses

The microhydration of the hexafluorophosphate anion has been the focus of many previous experimental and computational studies, due to its use in room temperature ionic liquids.This preliminary study examines the analogous hexachlorophosphate anion and its interactions with one to two water molecules (PCl₆⁻(H₂O)_n, n = 1-2), identifying the structural and energetic differences in the microhydration of PCl₆⁻ versus PF₆⁻. A systematic investigation of the possible orientations of one to two water molecules around PCl₆⁻ was done. Full geometry optimizations were performed using the ab initio method …

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 …

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 …

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 …

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 …

Exploring Structure-Function Relationship In Small-Molecular Catalysts Using Computational And Experimental Methodologies, Avik Bhattacharjee

Dissertations and Theses

Molecular modeling is a useful tool in the field of catalyst design for various processes. The use of Density Functional Theory (DFT) is routine in almost every discipline of chemistry. This allows for a deeper understanding of a molecular system even in situations where implementation of an experimental technique is unfeasible. However, without the right choice of theory and insufficient description, the model becomes susceptible to produce ambiguous results. This often leads to poor correlation with experimental findings hence an incomplete understanding of the system under study. Hence, to acquire a thorough knowledge of the intricacies involved in a system, …

Calcium Bistriflimide-Mediated Sulfur (Vi)–Fluoride Exchange (Sufex): Mechanistic Insights Toward Instigating Catalysis, Nicholas Ball, Brian Han, Samuel R. Khasnavis, Matthew Nwerem, Michael Bertagna, O Maduka Ogba

Pomona Faculty Publications and Research

We report a mechanistic investigation of calcium bistriflimide-mediated sulfur(VI)–fluoride exchange (SuFEx) between sulfonyl fluorides and amines. We determine the likely pre-activation resting state─a calcium bistriflimide complex with ligated amines─thus allowing for corroborated calculation of the SuFEx activation barrier at ∼21 kcal/mol, compared to 21.5 ± 0.14 kcal/mol derived via kinetics experiments. Transition state analysis revealed: (1) a two-point calcium-substrate contact that activates the sulfur(VI) center and stabilizes the leaving fluoride and (2) a 1,4-diazabicyclo[2.2.2]octane additive that provides Brønsted-base activation of the nucleophilic amine. Stable Ca–F complexes upon sulfonamide formation are likely contributors to inhibited catalytic turnover, and a proof-of-principle redesign …

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 …

Theoretical Studies Of Benzoquinone Reactivity In Acidic And Basic Environments, Natali Majoras

Honors Theses

Quinones are a class of organic compounds containing a six-membered unsaturated ring with two carbonyl groups. They are biologically relevant mostly due to their ability to participate in redox reactions. Prior experiments in our lab showed that quinones can induce protein modifications that are pH dependent. In an acidic environment the modifications were less significant than in a basic environment. Previous computational studies have also been carried out to model, in neutral solutions, the reaction between various quinones and various amines. Various amine groups are used as a model for the amino group of lysine to represent protein modification. The …

The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry, Kelly Anderson, Sarah Arradondo, K Aurelia Ball, Chrystal D. Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer Mcdonald, Maria C. Nagan, Carol Parish, Caitlin E. Scott, Patricia Soto, Aime'e Tomlinson, Mychel Varner

2022 Faculty Bibliography

The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% women) at 34 different institutions, who have trained nearly 900 undergraduate students, more than two-thirds of whom identify as women and one-quarter identify as students of color. MERCURY provides a model for the support necessary for faculty to achieve professional advancement and career satisfaction. The range of experiences and expertise of the consortium members provides excellent networking opportunities …

Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan

Legacy Theses & Dissertations (2009 - 2024)

Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …