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 …

Ab Initio Method Development For Electronic Structure Response And Symmetry Quantification, Duc Anh Lai

Chemistry Theses and Dissertations

Electronic structure provides a fundamental framework for understanding molecular properties and reactivity, as it encodes the spatial distribution of electrons and their response to external and internal perturbations. This dissertation develops theoretical and computational frameworks to characterize and manipulate electronic structure through two complementary directions: the response to oriented external electric fields and the quantification of symmetry regulation in electron density.

First, a rigorous theoretical and computational framework is established for treating electric fields with arbitrary orientations relative to molecular structure. The concept of the rotational potential energy surface is introduced to characterize the dependence of molecular energy on field …

Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix

Chemistry and Chemical Biology ETDs

Advancements in machine learning have emerged as a pivotal tool in computational biochemistry, offering new advancements to address challenges in protein structure and function. However, current machine-learning approaches offer limited insight in understanding protein dynamics. The purpose of this work is to combine traditional physics-based computational tools, such as molecular dynamics and coarse-grained simulations, with recently developed AI-driven computational tools to bridge gaps and advance the understanding of proteins in both structural and dynamic aspects. I investigated several approaches such as (i) traditional physics-based methods to study protein conformation and ensembles; (ii) identifying a peptide inhibitor for the PICK1 PDZ …

Nanoscale Structure And Spontaneous Self-Assembly Of Hydrothermal Organic Products, Glorianne P. Dorce

Chemistry and Chemical Biology ETDs

Carbon nanomaterials derived from citric acid and urea exhibit behaviors that challenge conventional structure–property models based on static bulk descriptions. This study examines how precursor pairing and reaction duration, post‑synthetic thermal history, and time‑dependent aging govern nanoscale organization and optical response. Through controlled synthesis and processing, distinct nanostructures with tunable structural and spectroscopic profiles are generated.

A multiscale framework integrating nano‑FTIR, atomic force microscopy, and thermal analysis reveals chemical heterogeneity and continuous structural reorganization across length scales. By correlating local chemical environments with optical behavior, we show that fluorescence efficiency and photostability depend on specific nanoscale architectures rather than average …

Urea-Based Boronium Salts As Antimicrobial Agents, Gabriel Allen Merchant

Honors Theses

Quaternary ammonium compounds (QACs) are widely used in disinfectants due to their ability to inhibit the growth of and eliminate microbes. The potency, broad-spectrum activity, and low cost of QACs have made them a cornerstone of modem hygiene. In recent years, QACs have garnered many health and safety concerns due to their overuse and subsequent accumulation in the environment. The increased use of QACs has further led to an increase in antimicrobial-resistant bacteria, making the synthesis of novel antibacterial compounds vital to combat this growing threat. Recent advances in boronium salts offer a unique alternative to address these adverse effects. …

Mechanism Of Formation Of Guanine-Guanine Crosslinks As Products Of One-Electron Oxidation Of 1-Methylguanosine In Acidic Medium, Ibrahim Braimah Mr

Electronic Theses and Dissertations

Reactive oxygen species (ROS) from normal metabolism and environmental exposure may cause oxidative DNA damage. Guanine (G) is the most oxidizable nucleobase. One-electron oxidation (OEO) of G in produces guanine radical cation (G•⁺), which deprotonates to form guanyl radical G(-H)•.This radical exists in two tautomeric forms: G(N1-H)• and G(N2-H)•. Dimerization of guanyl radical yields G-G cross-links (D1/D2); a tautomeric form for dimer formation remains elusive. This study presents the first characterization of G• dimerization products from the OEO of 1-MeGuo in acidic medium. Photolysis at 470 nm in the presence of S₂O₈²⁻ and Ru(II)(bpy)₃²⁺ generates two major stereoisomers (D1AW* and …

Hollow Nickel-Iron Nanoshells As Electrocatalysts For The Oxygen Evolution Reaction, Jonathan Batey

Chemistry & Biochemistry Undergraduate Honors Theses

The development of highly active and affordable catalysts for the oxygen evolution reaction is crucial to achieve a future where hydrogen is generated cleanly using renewable methods. Ni-Fe nanocatalysts show great promise in this area, as they are affordable and highly active. However, to overcome the industrial dominance of steam methane reforming, their activity needs improvement. This work aims to increase the activity of Ni-Fe nanocatalysts by making hollow nanostructures. Hollow Ni-Fe nanostructures were synthesized by coating a Cu template with Ni and Fe, followed by the etching of the Cu template. This left hollow Ni-Fe nanoshells, which were used …

Fret Studies On The Binding Of Fibroblast Growth Factor (Fgf) Proteins To The Hard Corona Of Cuins2-Based Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

Fibroblast Growth Factor (FGF) has been shown to be an important protein in angiogenesis, which is critical in developmental biology and wound healing but has also been implicated in cancer metastasis. FGF interacts with an FGF Receptor (FGFR) to signal the onset of angiogenesis but the detailed mechanism of angiogenesis, and particularly its regulation, is still largely unknown. Imaging the interaction of FGF with FGFR in biologically-relevant environments, such as directly in cells, is key towards furthering this understanding and may eventually aid in the development of better cancer treatments. CuInS2/ZnS quantum dots (QDs) are an attractive fluorescent probe to …

Molecular Catalysts For Electrochemical Nitrogen Activation Toward Sustainable Ammonia Synthesis, Jin-Xiu Han, Hao Xue, Xian-Biao Fu

Journal of Electrochemistry

Homogeneous electrocatalytic nitrogen reduction reaction (NRR) provides a powerful framework to interrogate molecular nitrogen-fixation pathways under mild conditions. By tuning the metal center, ligand architecture, and reaction medium, these systems enable capturing key intermediates and delivering mechanistic insight at the molecular-level resolution. Nevertheless, advances remain constrained by highly reduced operating potentials, intense competition from the hydrogen evolution reaction (HER), limited durability in turnover, and inadequate long-term stability.

In this review, we take electron delivery to the molecular active site as the guiding principle for organizing homogeneous electrochemical N₂ activation and transformation. We classify reported systems into direct electron transfer …

Water-Driven Solid Electrolyte Interphase Governs Continuous-Flow Ammonia Electrosynthesis, Peng-Bo Liu, Sheng-Liang Zhai, Ji Huang, Zhong-Shuo Zhang, Jie Zeng, Shao-Feng Li

Journal of Electrochemistry

Flow-cell architectures have emerged as a powerful platform for continuous and stable lithium-mediated nitrogen reduction (Li-NRR), enabling ambient-condition electrochemical ammonia synthesis and offering a promising alternative to Haber-Bosch processes. However, Li-NRR is exceptionally sensitive to trace water, and even minor variations in water content can profoundly alter interfacial chemistry. Here, we systematically investigate how initial water concentration affects Li-NRR performance in a continuous-flow cell. Excess water drives the formation of a thick solid electrolyte interphase (SEI) layer, which may impede nitrogen access to metallic lithium and hinder lithium-ion transport. As a result, the ammonia Faradaic efficiency collapses from ~61% to …

Insertion Of Noble Metal Free Cathodic Catalyst Layer With Fe-N-C Catalyst For Boosted Performance Of Pemfc, Shi Zhou, Muhammad Tariq, Asif Nadeem Tabish, Muhammad Salman, Fan-Di Ning, Muhammad Rayyan Tayyab, Ran-Ran Peng, Meng-Geng Hao, Wen-Mu Li, Xiao-Chun Zhou

Journal of Electrochemistry

Economical Fe-N-C catalysts are considered as promising alternatives to platinum group metal catalysts for proton exchange membrane fuel cells (PEMFCs). Despite exhibiting robust activity on rotating disk electrodes, their performance within membrane electrode assemblies often experiences limitations, such as decreased O₂ diffusion, high H₂O₂ formation, low proton conduction, and a lower electron transfer number. In this study, key factors, including proton transport, electron conduction, and gas diffusion within air-breathing PEMFCs, have been investigated by adjusting cathode catalyst layer (CCL) compositions. From the experimental results, the optimal peak power density was obtained when the loading of Fe-N-C …

Evaluating The Applicability Of Gamess For Determining Bond Lengths And Bond Dissociation Energies Through Constructing Potential Energy Curves For H2, N2, F2, Cl2, And Br2, Iaroslavna Kovalenko, Jillian Pabalan

Research and Creativity Symposium

The applicability and limitations of the GAMESS dihydrogen potential energy curve computational tool were evaluated for the following diatomic molecules: H₂, N₂, F₂, Cl₂, and Br₂. The aug-cc-pVDZ basis set and the B3LYP density functional theory (DFT) functional were employed to ensure more accurate electronic energy results for each calculation. Potential energy curves were generated for each molecule by plotting the electronic energy as a function of interatomic distance, and the bond dissociation energies (BDEs) and radii of diatomic molecules were determined. The radii were determined to be 76 pm …

Robust Thermodynamic Analysis Of Flexible Protein-Ligand Binding Using Statistical Mechanics, Mitchell Dulaney

Create@State

Understanding how proteins bind small molecules is essential for accurate computational modeling of biological systems. However, calculating binding free energy (delta G), enthalpy (delta H), and entropy (delta S) becomes unreliable when proteins are flexible, and ligands are between multiple binding positions. This motion causes traditional computational methods to produce inconsistent thermodynamic values.

A computational workflow was implemented that included docking to predict likely binding positions, molecular dynamics simulations to sample how the protein and ligand move over time, and statistical mechanics analysis to calculate thermodynamic quantities. A new theoretical framework was developed and implemented in a custom program to …

Kinetic Analysis Of 2-Methylpentan-2-Ol*, Nicole Seheult

Campus Research Month

This experiment investigated the kinetics of 2-methylpentan-2-ol using UV-visible spectroscopy under strongly acidic conditions (96% sulfuric acid). The dehydration of the tert-amyl alcohol produced a carbocation intermediate whose absorbance at 300 nm was evaluated at various temperatures. An Arrhenius plot of ln(k) versus 1/T produced a linear relationship with a calculated activation energy of 90.0 kJ/mol. This value is consistent with literature expectations for tertiary carbocation formation and supports the acid-catalyzed dehydration mechanism predicted for this molecule.

Calculating Potential Energy Curves Of Molecular Hydrogen And Its Ion Using Psi4 For Blinc Fusion Applications*, Angelina Castillo, Oscar Coral, Canaan Hercules, Blake Laing, Vola Andrianarijaona

Campus Research Month

Southern Adventist University’s Beamline for Ionic and Neutral Collisions (BLINC) is investigating the interactions between hydrogen molecules and fusion particles. To perform in-house theoretical calculations, the BLINC Theory and Analysis Group is testing Psi4 as a viable computational method for BLINC fusion research. Successful calculations of the potential energy curves and dissociation energies of H₂ and H₂⁺ have been completed and compared to known values. Preliminary results align with known values, demonstrating Psi4’s potential for BLINC research. Future work will focus on the vibrational energies, wavefunctions, and transition probabilities of H₂ and H₂⁺.

An Efficient Approximation To The Vibrational Coupled Cluster Method For Large Molecules, Nivedhitha P Ms

Theses and Dissertations

The Watson Hamiltonian is a widely used model for describing anharmonic vibrational motion in polyatomic molecules. It expresses the kinetic energy in separable dimensionless normal coordinates and represents the potential energy as a Taylor series expansion around the equilibrium geometry, usually up to the quartic approximation. Several computational methods have been developed to solve the corresponding vibrational Schrödinger equation for predicting infrared (IR), Raman, and vibrational circular dichroism (VCD) spectra. These include the Vibrational Self-Consistent Field (VSCF) method, Vibrational Configuration Interaction (VCI) and its approximations, and Vibrational Second-Order Perturbation Theory (VPT2), each providing different balances between computational cost and accuracy. …

Elucidating The Structure And Binding Nature Of Thianaphthene Dimers Using Gas-Phase Infrared Spectroscopy, Gaia Zucali, Vincent J. Esposito, Sandra Brünken, Piero Ferrari

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Crucial for many biological systems, in astrochemistry, and for fundamental chemistry in general, the conformations adopted by weakly bound complexes of polycyclic aromatic hydrocarbons (PAHs) have been the focus of debate for decades. Still, there are great challenges in forming such complexes in the laboratory, measuring accurate spectroscopic information sensitive to structure, and computing molecular properties for systems subtly bound by dispersive interactions. Here, we employ a combination of gas-phase infrared spectroscopy with extensive density functional theory (DFT) calculations to unambiguously determine the preferred conformation adopted by dimers of neutral thianaphthene, a PAH composed of one six- and one five-membered …

Eco-Assisted Ultrasonic Synthesis, Characterization, And Electrical Conductivity Study Of Polyaniline/ Silica@Fe3o4 Q1 Nanocomposites, Ali Salim Shaway, Kholoud Dham Khamkheem, Jawad Kadhim Abaies, Athra G. Sager

Karbala International Journal of Modern Science

وفي هذه الدراسة الصوتية، أصبحت السيليكا المُنتجة بأكسيد الحديد (Fe₃O₄) ومركبات نانوية قائمة على البولي أنيلين مُطعّم بنسبة 5-15% من السيليكا المُعزز للحديد (Fe₃O₄). وأكملت نهائيا ماء أنيلين والمركبات العلمية المتنوعة الارتباط باستخدام تقنيات FT-IR وUV-Vis وXRD وSEM وTEM. وأحدثت نتائج XRD أن حجم جسيمات البولينج أنيلين الناي (PANI) يبلغ 55.5. مكثف هذا الحجم إلى 45.2 عند تطعيم بولي أنيلين بنسبة 15% وزناً من السيليكا المُغلفة بأكسيد الحديد (Fe₃O₄) مُحضّرة بطريقة جيدة بشكل جيد، مما يميل إلى التمدد بشكل ثابت في تشكيل المركب المتباين المنظم. ضاقت النطاق البصري من 3.2 إلى 2.5 إلكترون فولت مع زيادة نسبة المطعّم، مما يشير …

Asphalt Pavement Rejuvenation Investigated By Nuclear Magnetic Resonance Relaxometry, Catherine Skaggs

Miners Solving for Tomorrow Research Conference

Asphalt is a relatively inexpensive material commonly used for road pavements; however, asphalt ages from exposure to oxygen and UV radiation, leading to loss of elasticity, which leads to cracks and potholes. To slow or reverse asphalt aging, pavement preservation treatments are in use. It’s unclear whether these treatments truly rejuvenate the pavement structure or merely offer a short-term benefit. Nuclear Magnetic Resonance (NMR) relaxometry is an analytical technique that uses the recovery of excited nuclear magnetization as a parameter to gain insights into molecular environments. Recovery-time distributions gathered from asphalt materials show differences between regular and rejuvenated asphalt samples, …

Non-Redundant Rovibrational Hamiltonians By Molien Generating Functions And Gröbner-Basis Reduction, Leandro Ajo

University Libraries Undergraduate Research Award

High-resolution molecular spectroscopy requires an effective Hamiltonian whose operator content is both complete, containing every term allowed by molecular symmetry and nonredundant, free of any algebraically dependent operators that would cause ill-conditioned parameter fits. Traditional derivations based on Van Vleck contact transformations satisfy neither criterion automatically. This paper develops a rigorous, algorithmic pipeline that guarantees both properties simultaneously. Starting from the permutation– inversion (PI) group GPI of a molecule (Longuet-Higgins, 1963), we apply Molien’s theorem (Molien, 1897) to the symplectic normal-coordinate representation to obtain the vibrational generating function Φvib(t); integrate over the Haar measure of SO(3) (Weyl, 1946) to obtain …