Computational Chemistry Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

Computer-Aided Molecular Design To Identify More Environmentally Friendly Pfas, Melvin M. Keita

Williams Honors College, Honors Research Projects

The goal of this project is to inversely design alternatives to per- and polyfluoroalkyl substances (PFAS) using Computer-Aided Molecular Design (CAMD). PFAS, also described as “forever chemicals”, have been used in industry and consumer products since the 1940s. PFAS can be found in drinking water, food, food packaging, waste sites, and other sources. Exposure to different PFAS can lead to increased risks of some cancers, immune effects, and reproductive effects. Pulling from existing data, this project will use quantitative structure-property relationships (QSPRs) to design PFAS alternatives that possess optimal properties to prevent adsorption into drinking water and other potential sources …

Additional Information For Fully Anharmonic Ir Spectra Of Neutral Polycyclic Aromatic Hydrocarbons With Up To 38 Carbons, Nolan J. H. White, Vincent J. Esposito, Christiaan Boersma, Louis J. Allamandola, Jesse D. Bregman, Alexandros Maragkoudakis, Pasquale Temi, Ryan C. Fortenberry

Faculty and Student Publications

Interstellar aromatic infrared band (AIB) spectra are showing strong agreement with presently-computed, anharmonic spectra for various types of polycyclic aromatic hydrocarbons (PAH) determined using a novel semi-empirical quantum chemical method. Since the AIB spectrum is a blend of emission spectra from a vast number of different PAHs, likely with an array of different molecular structures, the spectra for a sample set of 31 PAHs ranging in size from naphthalene (C$_{10}$H$_8$) up to circumbiphenyl (C$_{38}$H$_{16}$) are combined giving consideration to almost all PAH structural motifs. The computed, numerical quartic force fields coupled to second-order vibrational perturbation theory clearly confirm that PAH …

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 …

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 …

Data-Driven Analysis And Atomistic Simulations Of Next-Generation Materials For Energy Conversion And Storage, Yuliang Shi

Dissertations

Metal-organic frameworks (MOFs), with their modular architectures and tunable properties, represent an especially rich domain for accelerated material design and discovery for a range of diverse applications. Within this class of multifunctional materials, two-dimensional (2D) electrically conductive MOFs (EC MOFs) are of particular interest, as their 7r-stacked layered structures combine permanent porosity with electronic conductivity, enabling potential breakthroughs in energy storage, energy conversion, and quantum sensing. But the discovery and design of new EC MOFs based on expensive experimental screening is increasingly impractical due to the infinite chemical space. Furthermore, the practical implementation of EC MOFs for specific tasks depends …

Two Members Of The Editorial Board Of Journal Electrochemistry, Kai Wu Elected As An Academician Of The Chinese Academy Of Engineering And Yi Cui A Foreign Academician Of The Chinese Academy Of Sciences, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Electrochemical Characterization And Modulation Of Biological Processes, Yue-Qi Li, Wei-Hua Huang, De-Chen Jiang, Bao-Hong Liu, Bin Su, Yang Tian, Jing-Juan Xu, Ping Yu, Feng Zhao, Huang-Xian Ju, Jing-Hong Li

Journal of Electrochemistry

Electrochemical processes lie at the core of biological function, governing energy transduction, metabolic flux, and molecular signaling. Recent advances in electrochemical science now allow these processes to be probed and controlled with unprecedented spatial, temporal, and chemical resolution. In this review, we present an integrated framework that progresses from fundamental mechanisms to analytical technologies and functional modulation. We begin by outlining electron transfer pathways in mitochondrial respiration, microbial extracellular electron transfer, and DNA- and protein-based charge conduction, followed by the principles of photon-electron conversion in photosynthesis and the central role of redox equilibrium in coordinating cellular responses. We then highlight …