Physical Chemistry Commons^™

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⁺.

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 …

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. …

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 …

Co-Ordination Driven Heteroleptic Self-Assembly Of Naphthalene Diimide And Aromatic Dicarboxylate, Rosanna Jees, Kennedy Kuchta, Joshua Do, Erendra Manandhar

Posters - 2026

Co-ordination driven self-assembly is a powerful tool to construct supramolecular co-ordination complexes (SCCs) with predictable and well-defined molecular structures. Fujita, Stang, Newkome, & others have developed novel methodology to synthesize 2D & 3D Metallo-supramolecular structures, such as triangles, cubes, and octahedrons. These have potential applications for optical materials, sensing, catalysis, light harvesting & emissions due to the structures’ well-defined cavity and easy functionalization at the periphery position of ligands.1–4 SCCs with various functional groups, fluorophores, and chromophores, like crown ethers, carbazoles, fullerenes, and dendrimers, have been reported through self-assembly, yet naphthalene-diimide (NDI)-based macrocycles and cages are limited. This project focuses …

Steric And Electronic Considerations Of Ester Hydrolysis: Updating A Longstanding Physical Organic Kinetics Experiment, Mara J. Aucoin

Chemistry Theses

A current, longstanding undergraduate physical chemistry kinetics experiment uses UV-Vis spectrophotometry to follow the hydrolysis of para-nitrophenyl acetate (NPA) with an imidazole (Im) catalyst. The catalyzed and uncatalyzed reaction paths can be studied simultaneously under pseudo first order conditions ([Im]>>>[NPA]). To obtain the rate constants for the catalyzed and uncatalyzed reactions, the concentration of imidazole is varied between reactions and then plotted against the observed rate constant (k_obs).This produces a linear line where the slope is equal to the rate constant of the catalyzed reaction (k_cat) and the intercept is equal to …

Competitive Reaction Pathways In The Fully Green Synthesis And Surface Modification Of Silver Nanowires Under L-Ascorbic Acid-Limited Conditions, Finley Neal

Honors Theses

Silver nanowires (AgNWs) are critical building blocks for transparent conductive films (TCFs) in flexible electronics, yet their commercial viability is hindered by environmentally hazardous, energy-intensive synthesis methods and limited intrinsic chemical stability. This study investigated a fully green, room-temperature (25℃) batch synthesis of pristine AgNWs using tannic acid as a biodegradable dual reducing and capping agent under strict kinetic pH control (pH 1.25). To enhance oxidative resistance, a subsequent surface modification protocol was evaluated to deposit a protective palladium (Pd) shell using L-ascorbic acid (LAA) as a secondary reducing agent. The pristine green synthesis yielded one-dimensional Ag nanostructures with a …

2026 Research Day Program, Lincoln Memorial University

Research Day

This program contains abstracts and presentation summaries from LMU's 2026 Annual Research Day conference.

Observations Of An Oscillatory Mechanochemical Reaction Between Tetrathiafulvalene And Chloranilic Acid, Alastair Deans

Physics Theses & Dissertations

Mechanochemistry is the study of chemical reactions driven by the input of mechanical en ergy in addition to thermal activation. Mechanochemical reactions from powders are carried out by manual grinding or milling using various types of ball mills, or in twin extruders. While mechanochemistry has great potential affording economically and environmentally advantageous “green” synthetic methods, a drawback is that its chemical mechanisms are not well understood. One example of such a reaction currently under study involves tetrathiafulvalene, an organic elec tron donor with two polymorphs (orange and brown), and chloranilic acid, an electron acceptor. Previous results show that neat grinding …

Anthrone-Based Dummy Molecularly Imprinted Polymer For The Selective Detection Of Fluorene And Phenanthrene In Simulated River Water, Aria Pinandita, Nurrahmi Handayani, Muhammad Iqbal, Untung Triadhi, Rusnadi Rusnadi, Samitha Dewi Djajanti, Muhammad Bachri Amran, Muhammad Ali Zulfikar

Makara Journal of Science

A dummy-template molecularly imprinted polymer (DMIP) was synthesized via precipitation polymerization using anthrone as a template analog for the selective analysis of low-molecular-weight polycyclic aromatic hydrocarbons (PAHs), specifically fluorene and phenanthrene. Styrene, benzoyl peroxide, and ethylene glycol dimethacrylate were employed as the functional monomer, radical initiator, and crosslinking agent, respectively. The synthesized polymers were characterized by Fourier-transform infrared spectroscopy, scanning electron microscopy, and particle size analysis. The imprinting factors were 1.16 and 1.09 for fluorene and phenanthrene, respectively, indicating enhanced affinity of the imprinted sites. High-performance liquid chromatography analysis following DMIP-based solid-phase extraction yielded recoveries of 91.49% ± 3.87% for …

Axial Sulfur-Coordination Engineering Boosting Fe–N–C Catalysts For High-Performance Proton Exchange Membrane Fuel Cells, Lin Lin, Xiu-Xuan Hou, Zhe-Chen Fan, Yi-Xuan Yin, Wei-Yi Zhao, Kai Wei, Yu-Die Zhou, Li-Na Hou, Ying Wang, Hao Wan, Jun-Jie Ge

Journal of Electrochemistry

Fe-N-C catalysts have long suffered from kinetically sluggish oxygen reduction reaction (ORR) due to excessive adsorption strength toward oxygen intermediates and low site utilization. Heteroatom doping effectively accelerates ORR reaction kinetics through electronic structure modulation of metal sites for optimal intermediate adsorption, while chemical vapor deposition (CVD) enhances the turnover frequency (TOF) of active sites. Herein, we developed an FeSNC catalyst featuring abundant FeS₁N₄ sites via a dual-precursor CVD strategy. Experimental and theoretical analyses revealed that S incorporation disrupts the symmetric coordination of active sites, which optimizes OH* adsorption energies from 0.212 eV to 1.194 eV. Moreover, …

Deciphering The Role Of Binder Reaction Exothermicity In Thermal Runaway Of Lithium-Ion Cells, Wen Wen, Jing-Hong Zhou, Hao-Tian Lu, Xing-Gui Zhou

Journal of Electrochemistry

Thermal safety associated with lithium-ion cells as power sources remains a critical industry concern. A comprehensive understanding of how internal exothermic side reactions contribute to temperature rise is fundamental for accurately analyzing thermal runaway processes and predicting the thermal safety of lithium-ion cells. While various side-reactions, such as decomposition of solid electrolyte interphase layer, reaction between anode materials and electrolyte, reaction between cathode materials and electrolyte, and electrolyte decomposition, have been identified as heat generation sources in previous studies, the quantification of these reactions remains insufficiently standardized. Particularly, the impact of heat generation from binder decomposition (most commonly polyvinylidene difluoride) …

Entropy Of Metal/Solution Interfaces: Thermodynamic Framework, Theoretical Models, And Roles Of Interfacial Water, Zeng-Ming Zhang, Zi-Xi Liang, Jun Huang

Journal of Electrochemistry

Entropy is a basic thermodynamic property of the electrical double layer (EDL) at metal/solution interfaces, yet, its definition, measurement, and theoretical treatment are dispersed in the literature, and, in some cases, ambiguous. In this paper, we revisit the thermodynamic theory of EDL, from which two variants of entropy, excess entropy and formation entropy, are obtained and compared. In terms of the formation entropy, two calculation routes are validated in the context of a primitive EDL model, namely, the Gouy-Chapman (GC) model. After clarifying the concepts and calculation routes, we investigate interfacial water effects on the EDL entropy, using a refined …

Extension Of The Local Vibrational Mode Theory To Periodic Systems, Filippo Bodo

Chemistry Theses and Dissertations

Over the years, vibrational spectroscopy was used to gain a deeper understanding of the electronic structure and the chemical bond in both molecular and periodic systems. In this framework, the Local Vibrational Mode Theory (LVMT), as first introduced by Konkoli and Cremer in 1998, provides a unique tool to quantify the strength of a chemical bond, and better interpret the molecular vibrational spectra, thanks to the adiabatic force constants ($k^a$) and the composition of normal modes (CNM). While LVMT was originally developed for molecular systems, its application to periodic solids has remained limited. This thesis presents a complete and systematic …

Physical And Chemical Study Of Interaction In The Urea–Valine System For The Creation Of Modified Liquid Nitrogen Fertilizers, Suvonkul Erkhanovich Nurmonov, Saydullo Khamidovich Azimov

Chemical Technology, Control and Management

This study reports the results of a comprehensive physicochemical investigation of the urea–L-valine binary system, conducted to validate its potential as a modified base for liquid nitrogen fertilizers.

By utilizing the methods of isomolar series, visual-polythermal analysis, X-ray phase (XRD) and single-crystal X-ray diffraction (SC-XRD), synchronous thermal analysis (TGA/DTA), and FT-IR spectroscopy, it was determined that the interaction between components in both aqueous solutions and the solid phase results in the formation of molecular associates stabilized by hydrogen bonds, without the formation of new stoichiometric compounds.

The concentration and temperature limits of the system's stability were defined, revealing a reduction …

Intramolecular Nonbonding Interactions And Geared Phenyl Twisting In Para-Disubstituted 1,4-Diphenylazines: Electron Correlation Effects On Molecular Conformations And Enantiomerization, Kaidi Yang, Harmeet Bhoday, Rainer Glaser

Chemistry Faculty Research & Creative Works

The results are reported of potential energy surface (PES) analyses of six symmetrical azines Y_p − Ph − RC=N − N=CR − Ph − Y_p, namely, the benzaldehyde azines 1H, 2H, and 8H with R = H and the acetophenone azines 1M, 2M, and 8M with R = Me. The Y substituents Cl (1), Br (2), and Me (8) were studied because sets of polymorphs I (C2-symmetry, azine twist τ ≈ 135 ± 10°, disrotatory phenyl twists ϕi ≠ 0°) and II (Ci-symmetry, τ = 180°, conrotatory ϕi ≠ 0°) were crystallized for these three azines. The …