Computational Chemistry Commons^™

Exploring The Effects Of Polymer-Graphene Interactions On Bulk Composite Properties Using Finite Element Analysis, Bryant Grove

Dissertations

As a filler in high performance materials, graphene significantly enhances the mechanical properties of polymer composites. Experimental characterization of graphene composite enhancements is limited by labor-intensive processes in both synthesizing composites for different purposes and in characterizing the interactions between graphene and polymer composites that lead to these enhancements. Computational approaches such as finite element analysis (FEA) are suitable alternatives that go beyond experimental analysis. This dissertation demonstrates the utility of FEA in analyzing polymer graphene composites with an emphasis on modeling the interaction between graphene fillers and the matrix within the interphase formed between them. The accessible design framework …

Computational Studies Of Alpha-Lactalbumin Binding To Perfluorodecanoic Acid, Randhal Smith Ramirez Orozco

Open Access Theses & Dissertations

This thesis investigates the structural and thermodynamic interactions between Perfluorodecanoic acid (PFDA) and bovine alpha-lactalbumin (ALAC), a critical milk protein essential for infant nutrition. The primary objectives were to computationally determine the most probable binding sites of PFDA to ALAC and to quantify the strength of these interactions alongside the structural changes they induce. This study addresses a critical gap in understanding how persistent environmental contaminants like PFDA are recruited and transported by nutritional proteins within the milk matrix. The methodology integrated high-throughput molecular docking with long-range, molecular dynamics (MD) simulations to provide a dynamic characterization of the ALAC-PFDA complex. …

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 …

Exploring Ancestral Enzymes Through Sequence Reconstruction And Stability Prediction, Jeyun Park, Masakatsu Watanabe

SACAD: Scholarly Activities

Proteins evolve through sequence changes that shape structure, stability,

and function. Ancestral sequence reconstruction (ASR) infers ancestral

proteins from modern homologs, but many studies focus on sequence

inference without evaluating structural or energetic feasibility.

β-lactamases provide an ideal model due to their evolutionary diversity and

clinical relevance in antibiotic resistance.

Here, we present an integrated ASR workflow combining phylogenetic

inference (IQ-TREE), ancestral reconstruction, and structural and stability

validation using AlphaFold and FoldX. By reanalyzing a curated β-

lactamase dataset and comparing with a recent study (Risso et al., 2013),

we provide a controlled comparison of ancestral sequences, predicted

structures, and …

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⁺.

The Hartree-Fock Method: Quantum Theory To Python Code, Joshua Lohr

Campus Research Month

This poster presents a Restricted Hartree-Fock (RHF) program that solves the Roothaan-Hall equations within a finite basis set. Starting from an initial guess density, the Fock matrix is constructed via Coulomb and Exchange contributions. The resulting pseudo-eigenvalue problem is solved iteratively until self consistency. The electronic energy of water was calculated using the STO-3G basis set and validated against PySCF as a reference.

Design And In Silico Modeling Of Heterocyclic-Based Xanthone Derivatives As Potential Anticancer Agents Through Tyrosine Kinase Inhibition, Yehezkiel Steven Kurniawan, Ervan Yudha, Nela Fatmasari, Radite Yogaswara, Harno Dwi Pranowo, Eti Nurwening Sholikhah, Jumina Jumina

Makara Journal of Science

Cancer is one of the deadliest diseases nowadays, and tyrosine kinase receptors play crucial roles in cancer cell survival, differentiation, proliferation, and migration. This study designed and developed a new inhibitor from heterocyclic-based xanthone derivatives to target two tyrosine kinase receptors, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), through in silico screening. Eighteen heterocyclic-based xanthones were evaluated through molecular docking for both receptors. All heterocyclic-based xanthones gave the root mean square deviation (RMSD) value lower than 2.00 Å. Xanthone with isobenzothiazole substituent (iBzThio) was found as the most potent inhibitor with binding energies of -10.60 and …

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 …

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) …

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 …

Spectroscopy And Photochemistry Of The Astrochemical Molecules Sicp And Alcp, Vincent J. Esposito, Tarek Trabelsi, Rebecca Firth, Ryan C. Fortenberry, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Through characterization of the electronic excited-state topology, linear-SiCP is predicted to be photostable in the UV region, whereas linear-AlCP is predicted to undergo photodissociation to form Al+CP products after absorption of light in the 200–250 nm range, representing a catalytic process for freeing aluminum molecules from a solid dust grain. Both SiCP and AlCP are predicted to have electronic transitions with large absorption cross sections (∼10^–17 cm²) and to undergo fluorescence from bound excited states. The total electronic absorption spectrum is provided to inform electronic spectroscopy experiments. Silicon (SiC) and aluminum (Al₂O₃) dust …

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 …

Triphenylmethane-Derived Levelers For High-Speed Redistribution Layer Copper Electroplating Of Tailored Surface Morphologies, Zi-Hao Song, Wei-Bin Wang, Xiao-Hui Liu, Xiao-Min Han, Yi Zhou, Rui Huang, Yan-Xia Jiang, Zhe Li, Xiao-Wei Liu, Mei-Ling Xiao, Hong-Gang Liao, Wei-Lin Xu, Rong Sun

Journal of Electrochemistry

Redistribution Layer (RDL), composed of layered dielectrics and electroplated copper materials, is a basic structure to rearrange numerous I/O pads on the chip surface in wafer-level advanced packaging. As the key chemicals in electrolyte baths, electroplating additives have undergone continuous development to meet the industrial needs for high-speed and fine-line/fine-pitch applications. Meanwhile, the intricate relationships between additive chemical structures and electroplated copper properties are yet to be well understood. In this work, a pair of triphenylmethane-based dye molecules, i.e., gentian violet (GV) and methyl green (MG), was comparatively investigated as levelers for high-speed RDL copper electroplating. Compared to GV, significantly …

A Computational Study Of The Chemomechanics Of Paracetamol Polymorphs: Towards Improving Drug Tabletability, Karim Nader Samra

Theses and Dissertations

The mechanical properties of pharmaceutical crystals are of great importance in tablet manufacturing. Also, knowing the mechanical properties of different polymorphs of the same crystal can reduce the overall production cost. In this study, computational work was done via performing density functional theory calculations on 3 paracetamol crystal polymorphs Form I, II, and III. Understanding the chemical bonding helps in predicting the key elastic properties for different crystallographic directions. In Form II, lattice vector C is dominated with the intermolecular hydrogen bond OH…O giving it the stiffest Young Modulus and the least Poisson’s ratio. Then comes the A-Axis which contains …

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 …

Probing Feni Alloys With Atomic Precision, Scipio Han, Kaushik Rajkumar Jayaprabha, Xin Qi

Wetterhahn Science Symposium Posters

We compared EAM and MEAM atomic potentials for modeling FeNi (tetrataenite), a rare 50/50 alloy found in meteorites. Picking 4 potentials, we calculated minimum lattice constants and order-disorder transition temperatures. MEAM potentials accurately predicted the experimental transition temperature, confirming that MEAM better captures FeNi's directional bonding.

Microwave Synthesis And Characterization Of Fe2ptge Nanoparticles, Ally T. Fennell, David Carnevale

Chemistry Theses

Magnetic, semiconductor, and spintronic materials are vital to the functionality of devices from household appliances and sensors to medical and computing systems. This study discusses a novel synthesis and characterization of nanoscale Fe₂PtGe nanoparticles. The material was synthesized using microwave irradiation (175oC, 5 minutes) and characterized using XRD, XRF, TEM, and VSM. XRD of the synthesized particles correlates to a cubic crystal structured, indicating a face-centered cubic (fcc) platinum structure with iron and germanium incorporated in a disordered manner. XRF confirms the presence and relative ratios of iron, platinum, and germanium species. TEM imagery shows spherical nanoparticles with an average …

Investigating The In Vitro Antimicrobial Potential And Comprehensive Computational Studies Of New Schiff Base Derivatives, Abrar Hussain, Shahzaib Akhter, Hammad Nasir, Khurram Shahzad, Muhammad Arfan, Sand Hyun Park

Chemistry & Biochemistry Faculty Publications

Antimicrobial resistance (AMR) is a growing global health threat driven by multidrug-resistant bacteria (Staphylococcus aureus, Pseudomonas aeruginosa), and fungi (Candida albicans, and C. parapsilosis). This study evaluated six novel Schiff base derivatives (HSB-1 to HSB-6) through integrated in vitro antimicrobial activity and comprehensive computational studies. In vitro disk diffusion assay demonstrated the largest zones of inhibition against S. aureus for HSB-6 and HSB-1 (15–17 mm), activity against P. aeruginosa for HSB-5 and HSB-6 (12 mm), and moderate antifungal activity for HSB-4 (8–11 mm). Molecular docking results correlated with the in vitro findings with the binding energy ΔG = −12.3 kcal/mol …

Basis Design For Electronic Structure And Beyond, Weishi Wang

Dartmouth College Ph.D Dissertations

At the intersection of quantum physics, quantum chemistry, and materials science, electronic structure is the study of electrons in solid-state and molecular systems. Electronic-structure computation relies on discretizing the many-electron Hamiltonian with a finite single-particle basis set. However, basis-set construction is conventionally treated as an ad hoc preprocessing step. This thesis develops an expressive and flexible framework for active, system-oriented basis-set design and numerical modeling strategies that treat basis functions as tunable representations to encode electronic ground-state information.

We first introduce a multi-layered, differentiable basis-construction framework that embeds a set of primitive parameters into mixed-contracted Gaussian-type orbitals. We then develop …