Physical Chemistry Commons^™

Computational-Experimental Synergy As A Predictive And Interpretive Tool Through Metal-Organic Framework Investigations, Cristian Sayers

Graduate Student Theses and Dissertations

In the search for tunable materials platforms capable of addressing both clean energy conversion and viable post-combustion carbon capture, metal-organic frameworks (MOFs) have emerged as a uniquely versatile class of porous solids offering high specific surface area, structural tunability, and chemically addressable metal nodes and organic linkers. Realizing their potential requires understanding behavior that spans atomic-scale electronic structure and bulk-scale property response, a regime in which neither computation nor experiment alone is sufficient. This work attempts to develop a tighter integration between density functional theory (DFT) and laboratory investigation, treating the two modalities as mutually informing probes of the same …

Applications For The Quasi-Atomic Orbital And Constrained Density Functional Theory Methods On Catalytic Reactions, Alvaro David Loaiza Orduz

LSU Doctoral Dissertations

Selective activation of C–O, C–H, and C–C bonds underpins biomass upgrading, alkane functionalization, and CO₂ conversion. Despite their importance, the electronic factors governing catalytic performance remain incompletely understood, and many industrial processes still rely on empirical trends or material-specific observations. This dissertation addresses this gap by applying density functional theory (DFT), thermodynamic decomposition, and electronic-structure analysis to identify unifying principles of reactivity across transition-metal phosphides, vanadate oxides, copper-based electrocatalysts, and mixed IrO₂–RuO₂ layers. This work examines how charge transfer, orbital localization, and ligand-induced perturbations control reaction pathways in diverse catalytic systems. C–O bond scission in 2-methyltetrahydrofuran (MTHF) and methanol was …

Novel Chiral Interstellar Molecules: Quantum Anharmonic Ir And Vcd Predictions, Meredith Paik

Dissertations, Master's Theses and Master's Reports

The 2016 discovery of the chiral molecule propylene oxide (C₃H₆O) in the interstellar medium (ISM) has opened new avenues into explaining the origin of biomolecular homochirality on Earth. Thus, studies of chiral molecules in the ISM may be able to reveal more about the mechanism behind homochirality. However, while the search for chiral molecules in space has become an active field of study, astrochemical researchers have yet to detect other chiral molecules in the ISM. For this purpose, numerous characteristics for detectability have been outlined that may facilitate the discovery of other interstellar chiral molecules. With …

Elucidating The Impacts Of Non-Covalent Interactions In Organic Materials Through A Multiscale Computational Approach, Sashen A. Ruhunage

Theses and Dissertations--Chemistry

Noncovalent interactions (NCIs) in π-conjugated organic materials serve as tunable levers that influence molecular structure and intermolecular interactions in the condensed phase and, in turn, impact the electronic, optical, and mechanical properties of these materials. NCIs include attractive dispersion, electrostatic, and induction interactions, as well as repulsive exchange interactions. However, how to design materials with NCI considerations remains an open question across many fields. Here, we seek to provide an electronic and atomistic perspective on these interactions through multiscale simulations to aid materials design, processing, and performance optimization. In this study, we investigate NCIs and their effects across various systems …

Effect Of Electronegativity On Environmentally Persistent Free Radical (Epfr) Formation, Persistence, And Toxicity On Transition Metal Oxides, Syed Monjur Ahmed

LSU Doctoral Dissertations

Environmentally persistent free radicals (EPFRs) are a group of emerging environmental pollutants. Owing to their resonance structures, EPFRs have significantly higher lifetimes than typical free radicals, and can induce the formation of reactive oxygen species (ROS) known to cause pulmonary and cardiovascular dysfunction. EPFRs form by the adsorption of organic precursors on a transition metal oxide (TMO) surface and exhibit enough stability to cause negative health and environmental effects. While aromatic and substituted aromatic precursors form EPFRs on TMO surface at elevated temperatures and numerous substituted organics are ubiquitous in various industrial processes and household products, studies have largely overlooked …

Use Of Computational Methods To Determine The Relative Thermodynamic Stability Of Myricetin, Quercetin And 4-Methylesculetin For Use As Spin Traps, Cole Walker

Electronic Theses and Dissertations

The research conducted focused on the oxidative intermediates of antioxidants known as Myricetin, Quercetin, and 4-Methylesutin by calculating the reaction mechanism. During this research, computational quantum chemistry on selected parts for the 3 antioxidants previously mentioned were performed to find the most stable intermediate to act as a spin trap. The hypothesis is that the intermediates found can act as spin traps which will allow longer preservation of a free radical to be identified using Electron Paramagnetic Resonance (EPR) spectroscopy. This may be because the buildup of excess free radicals in a system leads them to cause damage down to …

Theoretical Spectroscopic Predictions Of Electronically Excited States, Noah R. Garrett

Honors Theses

The quest for faster computation of anharmonic vibrational frequencies of both ground and excited electronic states has led to combining coupled cluster theory harmonic force constants with density functional theory (DFT) cubic and quartic force constants for defining a quartic force field (QFF) utilized in conjunction with vibrational perturbation theory at second order (VPT2). This work shows that explicitly correlated coupled cluster theory at the singles, doubles, and perturbative triples level [CCSD(T)-F12] provides accurate anharmonic vibrational frequencies and rotational constants when conjoined with any of B3LYP, CAM-B3LYP, BHandHLYP, PBE0, and ωB97XD for roughly one-quarter of the computational time of the …

Transient Diode Laser Absorption Spectroscopy For Measuring Collisional Quenching Rates Of Co And Its Potential For Studying H2o, Jordan M. Polvere

Master’s Theses

Motivated by the necessity of non-LTE models that account for species that are not in Local Thermodynamic Equilibrium (LTE) in Titan’s and Earth’s atmospheres, collisional quenching rates of CO and H2O_(g) have been studied. Providing more accurate and precise values of collisional quenching rate coefficients is crucial in the development of more advanced atmospheric models, which are important to fields of science such as meteorology and astronomy. Rates of collisional quenching of CO(v=1,2) by CO and CO(v=2) by N₂ at approximately 301-321 K were measured by transient diode laser absorption spectroscopy. The rate coefficients of CO(v=1)-CO, CO(v=2)-CO, and …

Electronic Structure And Molecular Geometries Of Metal Complexes With Dft And Multireference Method, Rina Bhowmick

Dissertations and Theses

Metal complexes are ubiquitous for their diverse applications including catalysis, sensing, medicine, and environmental applications. For effective use of metal complexes, understanding their electronic structure is essential. In most cases, molecules can be represented as a single electron configuration. However, in some cases, especially transition metal and actinide complexes, multireference electronic structures are observed. This is because the valence d (and f) orbitals in metals are often nearly degenerate, leading to close-lying energy states and the subsequently more frequent presence of multiconfigurational electronic structures. The traditional approach to modeling these systems is to use density functional theory to optimize the …

Insights Into Molecular Recognition And Reactivity From Molecular Simulations Of Protein-Ligand Interactions Using Md And Qm/Mm, Jerrano L. Bowleg

Theses and Dissertations

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is …

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 …

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 …

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 …

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

Graduate Theses/Dissertations

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 …

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 …

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 …

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 …

Water-Mediated Peptide Bond Formation In The Gas Phase: A Model Prebiotic Reaction, George C. Shields, Ariel Gale, Tuguldur T. Odbadrakh, Tyler Ball

Chemistry Publications

The emergence of life on the prebiotic Earth must have involved the formation of polypeptides, yet the polymerization of amino acids is thermodynamically unfavorable under biologically relevant aqueous conditions because amino acids are zwitterions in solution and because of the production of a water molecule through a condensation reaction. Many mechanisms for overcoming this thermodynamic unfavorability have been proposed, but the role of gas phase water clusters has not been investigated. We present the thermodynamics of the water-mediated gas phase dimerization reaction of glycine as a model for the atmospheric polymerization of amino acids prior to the emergence of biological …

Nmr Spectroscopic Properties Of Nucleotides, And A New Method Of Numeric Calculation Of Raman Intensities For Organic Molecules, William R. Ehrhardt

Graduate Theses/Dissertations

General and accurate computational methodologies are currently lacking for large chemical systems. This is primarily due to the computational expense required to perform calculations on systems with one hundred or more atoms. Calculated spectroscopic properties could aid in the process of elucidating structural features of large biologically relevant molecules if accurate and inexpensive methods are developed. Towards this end the first steps were taken to design a general methodology for predicting NMR chemical shifts of large nucleic acid systems. It was found that HF and semi-empirical methods were not sufficient for optimization of nucleobases, and therefore larger nucleotide or nucleic …

Computational Modeling Of Electronically Excited States In Cobalamin-Dependent Reactions., Brady D. Garabato

Electronic Theses and Dissertations

The current understanding of the photolytic properties of Vitamin B12 derivatives or cobalamins are summarized from a computational point of view. The focus is on two non-alkylcobalamins, cyanocobalamin (CNCbl) and hydroxocobalamin (HOCbl), two alkylcobalamins, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), as well as the stable cob(II)alamin radical. Photolysis of alkylcobalamins involves low-lying singlet excited states where photo-dissociation of the Co-C bond forms singlet-born alkyl/cob(II)alamin radical pairs (RPs). Potential energy surfaces (PESs) of low-lying excited states as functions of both axial bonds provide the most reliable tool for analysis of photochemical and photophysical properties. Due to the size limitations associated with the …

Computational Study Of Lawesson’S Reagent Mediated Fluorenone Dimerization Forming 9,9’-Bifluorenylidene, Andrew Jourdan Eckelmann

Graduate Theses/Dissertations

The ambition of this work is to start a path to the a priori rational design of high yield production for electron acceptors with finely tuned band gaps, from the comfort of an armchair. To this end, organic photovoltaics offer a cheap and sustainable means of manufacture using readily available materials and avoids the toxicity of some of the heavy metals used in first and second-generation solar cells such as cadmium. The microwave assisted Lawesson’s reagent mediated one-pot one-step solventless synthesis takes less than 3 minutes and results in an 84% yield of 9,9’-bifluorenylidene from two equivalents of fluorenone. While …

Physicochemical, Spectroscopic Properties, And Diffusion Mechanisms Of Small Hydrocarbon Molecules In Mof-74-Mg/Zn: A Quantum Chemical Investigation, Gemechis Degaga

Dissertations, Master's Theses and Master's Reports

In petroleum refining industries, the fracturing process allows for the cracking of long-chain hydrocarbons into a mixture of small olefin and paraffin molecules that are then separated via the energetically and monetarily demanding cryogenic distillation process. In an attempt to mitigate both energetic and capital consumptions, selective sorption of light hydrocarbons by tunable sorbents, such as metal-organic frameworks (MOFs), appears to be the most promising alternative for a more efficient gas separation process. MOFs are novel porous materials assembled from inorganic bricks connected by organic linkers. From a crystal engineering stand point, MOFs are advantageous in creating a range …

Electronic Structure Evaluation Of Competing Pathways In The Gold(Iii)-Catalyzed Ohloff-Rautenstrauch Cyclosimerization Converting Propargylic Acetates To Carene-Like Natural Products, Jeremy M. Hines

Graduate Theses/Dissertations

Propargylic acetates can lead to complex transformations upon exposure to a gold catalyst. Gold catalyzed transformations also allow for simple synthesis of a number of natural products. Gold (III)-cycloisomerization of a 5-acetoxy-1,6-enyne is reported to proceed through two pathways that differ in the order of major events: cyclization followed by ester migration (“cyclization first”) or the reverse (“migration first”). Both pathways could theoretically proceed in either order. This rearrangement is called the Ohloff-Rautenstrauch rearrangement and has high regio- and stereocontrol affording a bicylo[4.1.0]heptane carbon substructure. This rearrangement allows for the synthesis of the carene class of natural products. Computational modeling …

Homogeneous Ligand-Centered Hydrogen Evolution And Hydrogen Oxidation : Exploiting Redox Non-Innocence To Drive Catalysis., Andrew Z. Haddad

Electronic Theses and Dissertations

Hydrogen is a promising carbon-free fuel / energy carrier and is an essential building block for many industrial and agricultural processes. Rising energy demands have ignited interest in the development of carbon-free and carbon neutral energy sources. In this context, hydrogen is an attractive candidate—being energy-dense, carbon-free—and easily accessible through a two-electron reduction of water. Accordingly, many electrochemical homogeneous catalyst systems have been studied, with a focus on understanding the mechanism of hydrogen evolution proceeding through metal-hydride intermediates. However, there has been a renaissance in hydrogen evolution reaction (HER) catalyst design, with many groups implicating ligand redox non-innocence as a …

Computational Quantum Chemistry Studies Of The Stabilities Of Radical Intermediates Formed During The Oxidation Of Melatonin, Constance E. Warden

Electronic Theses and Dissertations

Melatonin, a nontoxic natural antioxidant, is of interest as a possible spin trap for use in spectroscopic methods to observe and identify short-lived free radicals, which have been linked to oxidative stress that may result in serious health problems. However, the reaction mechanisms for the oxidation of melatonin to form the product N¹-acetyl-N²-formyl-5-methoxykynuramine are still not well understood. Computational quantum chemistry studies have been done on four proposed reaction mechanisms, involving the following major intermediate structures: a dioxetane, an epoxide, a melatonin radical cation, and a spin radical adduct. Molecular geometries were optimized at the …

From Dye Sensitized Solar Cells To Organic Field Effect Transistors: A Computational Investigation Into The Structural And Electronic Properties Of Novel Phthalocyanines, Patrick J. Dwyer

Seton Hall University Dissertations and Theses (ETDs)

Phthalocyanines (Pc) have gained intense research attention in many diverse application areas due to their highly tunable electronic and structural properties through modification of the molecular periphery and metal center. Throughout this work a series of novel perfluoro-isopropyl substituted MPc have been investigated through theoretical methods. First, the synthetic mechanisms of these Pcs will be explored to gain insight into the experimentally observed Pc product distribution. By examining the electronic structure and formation energies of the various Pc precursors, we explain the product distribution as well as propose the formation of additional Pcs, which were not currently believed to form. …

First-Principles Study Of The Electric Field Effect On The Water-Adsorbed Rutile Titanium Dioxide Surface, Abraham L. Hmiel

Legacy Theses & Dissertations (2009 - 2024)

TiO₂ is a semiconducting material that has been used extensively in many industrial applications, and recently has become a candidate for photocatalytic water splitting, fuel cell anode support materials, sensors, and other novel nanodevices. The interface of TiO2 with water, historically well-studied but still poorly understood, presents a ubiquitous environmental challenge towards the ultimate practical usefulness of these technologies. Ground-state density functional theory (DFT) calculations studying the characteristics of molecular adsorption on model surfaces have been studied for decades, showing constant improvement in the description of the energetics and electronic structure at interfaces. These simulations are invaluable in the …

A Proposed Palladium-Catalyzed Cycle For The Epoxidation Of Alkenes, Marie Vernell Parkes

Chemistry and Chemical Biology ETDs

Epoxides are an important chemical functional group, used in a wide variety of processes, from the small-scale production of pharmaceuticals to the large-scale production of propylene oxide. Current methods for production of epoxides require costly multi-step syntheses that use toxic or explosive reagents, result in low yields, and produce co-products that must be removed and often disposed. The development of an atom-efficient general method, preferably catalytic, for converting alkenes to epoxides using safe, cheap, and readily available molecular oxygen as the stoichiometric oxidant would be a great advance in both industrial and academic chemistry. Presented here is a proposed catalytic …

Applications Of Density Functional Theory In Materials Science And Engineering, Manuel Alvarado

Open Access Theses & Dissertations

Density Functional Theory (DFT) is a powerful tool that can be used to model various systems in materials science. Our research applies DFT to two problems of interest. First, an organic/inorganic complex dye system known as a Mayan pigment is modeled to determine chemical binding sites, verifying each model with physical data such as UV/Vis spectra. Preliminary studies on palygorskite-based mayan pigments (mayacrom blue, mayacrom purple) show excellent agreement with experimental studies when using a dimer dye geometry binding with tetrahedrally-coordinated aluminum impurity sites in palygorksite. This approach is applied to a sepiolite-based organic/inorganic dye system using thioindigo attached to …

Density Functional Theory Calculations On Hydrated Dimethylarsinic Acid And Iron Oxide Clusters, Adrian Adamescu

Theses and Dissertations (Comprehensive)

Dimethylarsinic Acid (DMA) or (CH₃)₂AsO₂H is an important organoarsenical compound detected in arsenic speciation studies of environmental samples and synthesized during pyrolysis of oil shale. DMA was used historically as a herbicide on large agricultural fields and can be detected in the leachates of landfills rich in waste containing arsenic such as glass, alloys, and semiconductors, as well as biologically pre-treated municipal solid waste. Under certain soil conditions DMA can become bio-available and has the potential to be recycled to more toxic inorganic forms of arsenic. Bioavailability of DMA is largely controlled by the …