Computational Chemistry Commons^™

Development Trends And Priority Research Fields Of Electrochemical Discipline In The 15th Five Year Plan Period, Lin Zhuang, Wen-Bin Cai, Heng-Xing Ji, Qing Li, Gong-Wei Wang, Sen Xin, Qing Zhao, Fang-Yi Cheng, Yu-Guo Guo, Lan-Qun Mao, Yang Tian, Fei Wu, Li-Min Zhang, Yan Xiang, Jin-Song Hu, Rui Cao, Li Xiao, Hua-Bing Tao, Wei Xing, Dong-Ping Zhan, Hong-Gang Liao, Mei-Ling Xiao, Bin Ren, Zhang-Quan Peng, Rui Wen, Xiang Wang, Yue-Feng Song, Hou-Fu Lv, Bao-Yu Xia, Guo-Xiong Wang, Jun Cheng, Zhi-Pan Liu, Min Zhou, Bing Huang, Cun-Pu Li, Yu-Qin Zou, Shuang-Yin Wang, Hai-Bo Lin, Zi-Dong Wei

Journal of Electrochemistry

In fulfillment of the national science-and-technology development agenda, the Department of Chemical Sciences of the National Natural Science Foundation of China (NSFC) convened the Strategic Symposium on the Fifteenth Five-Year (2026–2030) Development Plan for Electrochemistry held in Xiamen on 29 August, 2025—the culminating year of the Fourteenth Five-Year (2021–2025) Development Plan. More than forty leading experts in the field of electrochemistry participated with spanning nine thematic fronts: Interfacial Electrocatalysis, Interfacial Electrochemistry for Energy Storage, Bioelectrochemistry, Electrochemistry of Hydrogen Energy, Electrochemical Micro-/Nano-Manufacturing, Operando Electrochemical Characterization, Electro-Thermal Coupling Catalysis, Theoretical and Computational Electrochemistry, and Electrochemical Synthesis. The forum assembled China’s foremost electrochemical …

First Principles Molecular Dynamics Simulations Of Infrared And Raman Vibrational Spectra Of H5o2 +, D5o2 +, Dh4o2 +, And D4ho2 + From 50 To 300 K, Oluwaseun Omodemi, Martina Kaledin

Faculty Articles

We report molecular dynamics simulations of infrared (IR) and Raman spectra of H5O2+ and its deuterium-substituted analogs. We use the well-tested HBB potential and dipole surfaces along with a recently fitted polarizability surface of CCSD(T)/aug-cc-pVTZ quality. The focus of the present work is to provide new insights into the O···O stretch region, located in the [500–700] cm–1 spectral range, by means of analyzing the spectra over a broad range of temperatures: from 50 to 300 K. Also, rovibrational thermal averaging was performed to untangle the unusually complex spectra of partially deuterated isotopologues DH4O2+ and D4HO2+ with H and D minority …

Investigating The Redox Properties Of Photoredox Catalysts And Organic Compounds Through Quantum Chemistry, Peter Girnt

Open Access Theses & Dissertations

This dissertation explores the redox behavior of organic and organometallic systems using density functional theory (DFT), focusing on electron transfer mechanisms and structur –property relationships. The first study investigates the two-electron reduction of bianthrone isomers, revealing a potential-inverted ECE mechanism driven by isomerization and electronic destabilization. The second study examines ruthenium photoredox catalysts, showing that ligand fusion positions significantly affect redox potentials due to backbone dearomatization, while p extension has minimal impact. Together, these findings provide insight into redox tuning strategies and support the rational design of advanced catalysts and electroactive materials.

Series Reports From Professor Wei’S Group Of Chongqing University: Advancements In Electrochemical Energy Conversions (2/4): Report 2: High-Performance Water Splitting Electrocatalysts, Ling Zhang, Wang-Yang Wu, Qiu-Yue Hu, Shi-Dan Yang, Li Li, Rui-Jin Liao, Zi-Dong Wei

Journal of Electrochemistry

The unavailability of high-performance and cost-effective electrocatalysts has impeded the large-scale deployment of alkaline water electrolyzers. Professor Zidong Wei’s group has focused on resolving critical challenges in industrial alkaline electrolysis, particularly elucidating hydrogen and oxygen evolution reaction (HER/OER) mechanisms while addressing the persistent activity-stability trade-off. This review summarizes their decade-long progress in developing advanced electrodes, analyzing the origins of sluggish alkaline HER kinetics and OER stability limitations. Professor Wei proposes a unifying “12345 Principle” as an optimization framework. For HER electrocatalysts, they have identified that metal/metal oxide interfaces create synergistic “chimney effect” and “local electric field enhancement effect”, enhancing selective …

Local Electric Fields Coupled With Cl− Fixation Strategy For Improving Seawater Oxygen Reduction Reaction Performance, Yu-Rong Liu, Miao Zhang, Yan-Hui Yu, Ya-Lin Liu, Jing Li, Xiao-Dong Shi, Zhen-Ye Kang, Dao-Xiong Wu, Peng Rao, Ying Liang, Xin-Long Tian

Journal of Electrochemistry

Development of robust electrocatalyst for oxygen reduction reaction (ORR) in a seawater electrolyte is the key to realize seawater electrolyte-based zinc-air batteries (SZABs). Herein, constructing a local electric field coupled with chloride ions (Cl⁻) fixation strategy in dual single-atom catalysts (DSACs) was proposed, and the resultant catalyst delivered considerable ORR performance in a seawater electrolyte, with a high half-wave potential (E_1/2) of 0.868 V and a good maximum power density (Pmax) of 182 mW·cm⁻² in the assembled SZABs, much higher than those of the Pt/C catalyst (E_1/2: 0.846 V; Pmax: 150 mW·cm^{−2 …}

Allosteric Control Overcomes Steric Limitations For Neutralizing Antibodies Targeting Conserved Binding Epitopes Of The Sars-Cov-2 Spike Protein: Exploring The Intersection Of Binding, Allostery, And Immune Escape With A Multimodal Computational Approach, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Understanding the atomistic basis of multi-layer mechanisms employed by broadly reactive neutralizing antibodies of the SARS-CoV-2 spike protein without directly blocking receptor engagement remains an important challenge in coronavirus immunology. Class 4 antibodies represent an intriguing case: they target a deeply conserved, cryptic epitope on the receptor-binding domain yet exhibit variable neutralization potency across subgroups F1 (CR3022, EY6A, COVA1-16), F2 (DH1047), and F3 (S2X259). The molecular basis for this variability is not fully understood. Here, we employed a multi-modal computational approach integrating atomistic and coarse-grained molecular dynamics simulations, binding free energy calculations, mutational scanning, and dynamic network analysis to elucidate …

The Role Of Water In Peptide Behavior And Peptide-Based Water-Responsive Crystals, Janel Jannette Rivera Cancel

Dissertations, Theses, and Capstone Projects

Water plays a crucial role in shaping the behavior and function of biomolecules across the liquid, supercooled, and glassy states. This thesis presents a dual approach combining computational simulations and experimental investigations to explore the influence of water on biomolecular systems, particularly peptide-based materials. We employ molecular dynamics simulations to study the hydration-dependent structural dynamics of homopolymer peptides. Simulations were carried out across a range of temperatures and pressures to analyze changes in hydration and structural stability, shedding light on the behavior of peptides under supercooled and glassy conditions. These studies are especially relevant for understanding biomolecular stability in cryopreservation. …

Effect Of Saccharin On Crystallization Behavior Of Electroless Cobalt Plating, Yu-Xin Luo, Jing-Jing Wang, Lu Wang, Zi-Yi Yan, Yi Ma, Xin Bo, Jing-Shuang Dang, Zeng-Lin Wang

Journal of Electrochemistry

In the process of electroless cobalt plating, the saccharin additive can significantly change the surface morphology, texture orientation, and conductivity of the cobalt coating layer. When the amount of saccharin was 3 mg·L^–1, the cobalt coating transformed from disordered large grains to a honeycomb structure, with a preferred orientation of (002) facet on hexagonal close-packed (HCP) cobalt crystals. The resistivity of the cobalt film decreased to 14.4 μΩ·cm, and further decreased to 10.7 μΩ·cm after the annealing treatment. When the concentration of saccharin was increased, the grain size was gradually refined and a “stone forest” structure was observed, …

Simulating Chemiluminescence Spectra Of Oh Radical Using Quantum Dynamical Simulations, Triet M. Cao

Research from the Berry Summer Thesis Institute, 2025

Chemiluminescence is a phenomenon of light emission that occurs when molecules transition from an excited state to the ground state. This phenomenon is widely utilized in applications ranging from quantifying product yields in chemical reactions to biological imaging and atmospheric chemistry studies. It has also been used in many crucial applications in the scarce conditions of heat and electricity, such as light sources for astronomy discovery or deep-sea diving. A notable example of such reactions is combustion, where highly reactive hydroxyl radicals (OH) are products. These radicals exhibit a chemiluminescence spectrum because of the interaction between their ground state and …

Designing A Data Collection And Visualization Toolkit For Scalable Tensor Algebra In Quantum Chemistry Applications, Epiya J. Ebiapia

LSU Master's Theses

Large-scale quantum chemistry computations, such as those executed with the Tensor Algebra for Many-body Methods (TAMM) framework, require careful configuration of runtime parameters to achieve high performance and cost efficiency in high-performance computing (HPC) and cloud environments. Without effective performance analysis tools, researchers risk inefficient use of computational resources, leading to longer runtimes and higher costs.

To address this challenge, this thesis presents the design and implementation of a performance profiling and visualization toolkit for TAMM, developed as part of the DOE TEC4 project in collaboration with Pacific Northwest National Laboratory, Microsoft, and Louisiana State University. The toolkit collects detailed …

Mechanistic Study Of The Evan's Anti-Aldol Reaction, Aidan Hau

Summer Research Showcase

The Evans Aldol reaction can make a syn product with a boron, lithium, or titanium catalyst. The anti product is catalyzed by magnesium instead. Our goal is to understand the mechanism behind the formation of the anti product. We used WebMO to model what the lowest energy reaction pathways would be with a magnesium catalyst. We played with coordination to the magnesium and electron geometry to see if that would generate a low energy pathway that is likely to occur. We can use our information gathered to help determine the anti mechanism.

Effect Of Bond Strength Variation And Ionizing Radiation On Mutations In Cytosine-Guanine Islands, Joshua Robert Bedwell, Yan Poniatovskyi, Vola Andrianarijaona

Achieve

Ionizing radiation produces free electrons within cells which then ionizes DNA and has the potential to cause carcinogenic mutations. Cytosine-Guanine (CpG) islands are regions that are rich in cytosine and guanine bases and are common sites of single point mutations and strand breaks. In this study, density function theory (DFT) is used to calculate the potential energy of DNA nucleotide dimers varying bond lengths in five different ionized states. Crossing between two ionized states can be seen in the potential energy curves, indicating the possibility of natural transition between the two states. Potential energy curves are used to determine bond …

Analyzing The Strength Of The Amine Bond Of Guanine Via Potential Curve Analysis: A Computational Approach, Yan Poniatovskyi, Joshua Robert Bedwell, Vola Andrianarijaona

Achieve

The deamination of guanine can be a cause of single point DNA mutations. In this study, the strength of the amine bond was examined using DFT and B3LYP to map out the bond’s potential curves under conditions of various charges being imposed on the molecule. Such an approach yielded a few potential curves that do not exhibit the expected behavior and rather, show crossings in potential energy curves. Discussions regarding the suspected causes of these unexpected behaviors are included in the poster presentation. The Mulliken charge analysis of guanine under these conditions is coherent with the proposition that the deamination …

Melts To Solutions: Structure, Dynamics, And Response Of Polyelectrolytes, Shalika Meedin

All Dissertations

The current research elucidates the changes in the structure and motion of polyelectrolytes as they are perturbed by solvents and shear flows. Polyelectrolytes are macromolecules whose backbone consists of long, predominantly hydrocarbon chains, substituted by ionizable groups, which tend to dissociate into ions in polar solvents. Their properties result from a delicate balance of elastic energy that arises from the polymeric backbone and electrostatic forces, which stem from the ionizable groups. Though polyelectrolytes have an immense potential to propel numerous technologies, from clean energy to drug delivery systems, understanding the delicate balance between the properties of the polymer backbone and …

A Systematic Approach To The Characterization Of Liquid-Vapor Coexistence In Platinum, Meghan K. Lentz

Physics & Astronomy ETDs

Platinum is a material standard used in high pressure and shock compression experiments at Sandia National Laboratories. During experiments, materials are subjected to a very large range of thermodynamic conditions, during which materials regularly enter the liquid-vapor coexistence region. Despite its status as a standard, the region around the liquid-vapor critical point is poorly understood for platinum, with reported critical temperatures spanning approximately 7000 K. In this dissertation we conduct density functional theory based molecular dynamics (DFTMD) simulations for platinum for a range of temperatures and densities near liquid-vapor coexistence. The phase diagram for platinum is refined near the critical …

Numerical Simulation Of The Pitting Corrosion Behavior Of Stainless Steel Bellows Influenced By Varying Liquid Film Thicknesses, Lu-Jun Ren, Guo-Min Li, Zhen-Xiao Zhu, Hai-Yan Xiong, Bing Li

Journal of Electrochemistry

To advance the understanding of the corrosion behavior of stainless steel bellows in marine atmospheric environments and enhance the precision of service life predictions, this study employs finite element simulations to investigate the pitting corrosion rates and pit morphologies of bellows peaks and troughs under varying electrolyte film thicknesses. The model incorporates localized electrochemical reactions, oxygen concentration, and homogeneous solution reactions. For improved computational accuracy, the fitted polarization curve data were directly applied as nonlinear boundary conditions on the electrode surface via interpolation functions. Simulation results reveal that the peak regions exhibit faster corrosion rates than the trough regions. With …

Ionic Liquid Enhanced Proton Transfer For Neutral Oxygen Evolution Reaction, Ming-Xing Chen, Nian Liu, Zi-He Dua, Jing Qi, Rui Cao

Journal of Electrochemistry

The development of highly active catalyst in pH-neutral media for oxygen evolution reaction (OER) is critical in the field of renewable energy storage and conversion. Nevertheless, the slow kinetics of proton-coupled electron transfer (PCET) hinders the overall OER efficiency. Herein, we report an ionic liquid (IL) modified CoSn(OH)₆ nanocubes (denoted as CoSn(OH)₆-IL), which could be prepared through a facile strategy. The modified IL would not change the structural characteristics of CoSn(OH)₆, but could effectively regulate the local proton activity near the active sites. The CoSn(OH)₆-IL exhibited higher intrinsic OER performances than the pristine …

Development Of Novel Force Fields For Metal Ions, Madelyn Smith

Dissertations

Many biological proteins require the presence of a metal ion in order to properly function. However, metal ions’ complex nature charge poses several challenges to accurately and efficiently simulate computationally. For example, metal ions can exhibit multiple oxidation states, electronic state degeneracy, flexible coordination numbers, and significant polarization effects. To address these problems, this dissertation aims to enhance force fields for modeling metal ions in molecular dynamics simulations. First, a comprehensive set of van der Waals radii for metal ions is derived, demonstrating the importance of using physically meaningful parameters in force fields. Second, a comprehensive set of atomic and …

Ensemble-Based Binding Free Energy Profiling And Network Analysis Of The Kras Interactions With Darpin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants And Universal Architecture Of Regulatory Hotspots And Allosteric Binding, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conformational restriction and allosteric modulation. Mutational scanning across all four DARPin systems identifies a core set of evolutionarily constrained residues …

Molecular Insights Into The Role Of Estrogen Receptor Beta In Ecdysterone Mediated Anabolic Activity, Syeda Sumayya Tariq, Madiha Sardar, Muhammad Shafiq, Hendrick Heinz, Mohammad Nur-E-Alam, Aftab Ahmad, Zaheer Ul-Haq

Pharmacy Faculty Articles and Research

Ecdysterone, often dubbed a “natural steroid,” has garnered significant attention among athletes for its reputed growth-promoting and anabolic properties. Unlike synthetic anabolic steroids, which are classified as controlled substances, ecdysteroids remain largely unregulated in many countries and are widely marketed as dietary supplements. Notably, ecdysterone has been included in the World Anti-Doping Agency (WADA) monitoring program, highlighting its potential impact on athletic performance and raising questions about its regulation. Emerging evidence indicates that, unlike traditional anabolic steroids that act primarily via the Androgen Receptor (AR), ecdysterone’s anabolic effects may be mediated through Estrogen Receptors (ERs), particularly Estrogen Receptor beta (ERβ). …