Computational Chemistry Commons^™

Evaluating The Reliability And Accuracy Of Alchemical Binding Free Energy Methods And Calculations, Fnu Sheenam

Dissertations, Theses, and Capstone Projects

Molecular recognition plays a crucial role in various biological processes, such as enzymatic reactions, signal transduction, and genetic information processing. Investigating how proteins selectively bind to their partners is an active research area, but there is a lack of experimental details on protein structures and interactions in molecular complexes. Computational techniques based on macromolecular structures offer a way to predict protein-ligand interactions and explore their recognition mechanisms. Estimating binding affinities, particularly through alchemical binding free energy calculations, has become valuable in supporting drug discovery. This work introduces new methodologies, utilizing the Alchemical Transfer Method, to address issues like poor convergence …

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

De Novo Drug Design Using Transformer-Based Machine Translation And Reinforcement Learning Of An Adaptive Monte Carlo Tree Search, Dony Ang, Cyril Rakovski, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The discovery of novel therapeutic compounds through de novo drug design represents a critical challenge in the field of pharmaceutical research. Traditional drug discovery approaches are often resource intensive and time consuming, leading researchers to explore innovative methods that harness the power of deep learning and reinforcement learning techniques. Here, we introduce a novel drug design approach called drugAI that leverages the Encoder–Decoder Transformer architecture in tandem with Reinforcement Learning via a Monte Carlo Tree Search (RL-MCTS) to expedite the process of drug discovery while ensuring the production of valid small molecules with drug-like characteristics and strong binding affinities towards …

Analyzing Novel Metal Alloys For Glucose Sensing And Electrocatalysis, Anna Grace Boddy

Theses and Dissertations

In pharmaceutical and medicinal chemistry, metals and metal alloys often receive less attention compared to biological or organic compounds due to many factors including toxicity in the body for drug development or the cost of these metals. However, metals can play an important role in pharmaceuticals, having an impact on original cancer drugs, such as platinum used for head and neck tumors. Electrocatalysis is also another topic that receives less attention over topics such as chromatography in pharmaceuticals due to its potential toxic catalysts and voltages that could be harmful to the body. Electrocatalytic sensors can play an important role …

Development Of Stochastic And Time-Dependent Quantum Chemical Methods For Accurate Description Of Light-Matter Interactions With Applications In Photoionization And Inverse Photoemission In Nanomaterials, Nicole Spanedda

Dissertations - ALL

There are three main focuses of this work. First, the theoretical details of the Stratified Stochastic Enumeration of Molecular Orbitals (SSE-MO) method is presented, along with its application for calculating ionization potentials (IPs) of quantum dots. The SSE-MO method can readily be applied for the purpose of efficiently and accurately calculating ionization potentials, by constructing the frequency-dependent self-energy operator and then subsequently, solving the associated Dyson equation. Constructing the frequency-dependent self-energy operator is challenging because the scaling of the computational cost with respect to system size, becomes prohibitive for large systems, such as quantum dots. This is due to the …

Predicting The Reactions Of Cs2, Ocs, And Co2 With Group Iv And Group Vi Transition Metal Oxides, Marissa Shea Blair, Zachary Ryan Lee Phd, David A. Dixon Phd

Posters-at-the-Capitol

Building on a recent serious of high level electronic structure studies of Lewis acid gas reactions with metal oxide sorbents, DFT (B3LYP and ωB97X-D) and CCSD(T) methods are being used to predict the Lewis acid-base addition (physisorption) and formation of metal oxide carbonate/thiocarbonate formation (chemisorption) reactions of CS2, OCS, and CO2 of CS2, OCS, and CO2 with Group IV (MO2)n and Group VI (MO3)n (n = 1 - 3) nanoclusters. For the Group IV oxides, chemisorption to form terminal carbonates and thiocarbonates is predicted to be the most favored, with thiocarbonate ligand binding energies slightly more exothermic than their carbonate …

Attochemistry Regulation Of Charge Migration, Aderonke Folorunso

LSU Doctoral Dissertations

Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. This phenomenon is potentially useful to understand the fundamental principles of photochemistry, such as light harvesting. The first part of this dissertation discusses the molecular modes of attosecond charge migration. In this work, we used first-principles calculations to investigate the modes of charge migration (CM) in halogenated hydrocarbon chains at attosecond timescales. We have simulated the creation of a localized hole on the halogen atom using constrained density functional theory (DFT) and then tracked its subsequent dynamics with time-dependent DFT (TDDFT). Our …

Phenanthrene Jamboree, Alexander D. Roth

Honors Theses

Using cyclopropanated and cyclobutanated phenanthrene precursors, our hero embarks on a mission to find as many reactive intermediates as possible. Fraught with danger, romance, and mangosteens, Anderson calls this work 'monstrous' and 'alarming.'

Experimental And Chemical Modeling Of Applied Dc Electric Field Induced H2 – Air Axisymmetric Laminar Co-Flow Diffusion Flames With Low Carbon Impurities, Susith Dilshan Pathmasiri Gunamuni Halowitage

Graduate Theses, Dissertations, and Problem Reports (ETD)

The effect of externally applied DC electric fields on flame structure was investigated in a stationary atmospheric axisymmetric laminar H₂–Air flame with less than 100 ppm carbon equivalent impurities. Flame OH chemiluminescence signals were recorded using a UV-sensitive CCD array as a function of voltage (+10 to -10 kV) applied to a stainless-steel ring electrode placed around the burner nozzle. Changes in chemiluminescence signal are reported as a function of electrode height above the burner, airflow, and fuel composition. Significant changes in OH* distributions were observed for voltages below -5 kV. Under optimum conditions, the height of the …

Computational Study Of Proton Transfer At Transition Metal Hydrides, Megan Ford

Honors Theses

Energy storage in the bonds of common chemical feedstocks is an attractive solution to the unreliability of wind and solar power due to its long term efficiency and easy recoverability. Energy is stored by reducing chemicals like ammonia, formic acid, and hydrogen, the reaction of which is dependent on a catalyst. To catalyze the reaction, the catalyst undergoes a slow proton transfer (PT) step to form what is known as a metal hydride. The sluggish kinetics of this step lower the effectiveness of the catalyst, and therefore must be better understood in order to improve the efficiency of energy storage …

Spiral Wave Teleportation And Multiplex Network Synchronization In Light Sensitive Belousov-Zhabotinsky Systems, Shannyn Alicia Tyler

Graduate Theses, Dissertations, and Problem Reports (ETD)

We experimentally and computationally investigate dynamical behaviors in excitable and oscillatory media using light sensitive Belousov-Zhabotinsky (BZ) systems. These systems are not in a state of thermodynamic equilibrium, and have been proven to show various interesting phenomena including spatiotemporal patterns, self-organization, and chaos. We utilize the BZ reaction, a nonlinear chemical reaction, known for its relaxation-type oscillations, to explore the dynamics of these systems.

We examine spiral wave teleportation in an excitable media as an effective alternate defibrillation method. Spiral waves have emerged as a key phenomenon associated with the initiation and persistence of cardiac arrhythmias. Using a light sensitive …

Transient Diode Laser Absorption Spectroscopy For Measuring Collisional Quenching Rates Of Co And Its Potential For Studying H2o, Jordan M. Polvere

Master’s Theses

Motivated by the necessity of non-LTE models that account for species that are not in Local Thermodynamic Equilibrium (LTE) in Titan’s and Earth’s atmospheres, collisional quenching rates of CO and H2O_(g) have been studied. Providing more accurate and precise values of collisional quenching rate coefficients is crucial in the development of more advanced atmospheric models, which are important to fields of science such as meteorology and astronomy. Rates of collisional quenching of CO(v=1,2) by CO and CO(v=2) by N₂ at approximately 301-321 K were measured by transient diode laser absorption spectroscopy. The rate coefficients of CO(v=1)-CO, CO(v=2)-CO, and …

Corrosion Inhibitors: Mitigating The Degradation Of Rebar, Jake R. Hughes

Williams Honors College, Honors Research Projects

Our conjecture was twofold: first, that two compounds historically used as food preservatives could act as environmentally friendly inhibitors against rebar corrosion, and second, that molecular properties have a quantifiable influence on inhibition efficiency (%IE). To evaluate the two compounds, cyclic potentiodynamic polarization was used to determine corrosion current density (i_corr) and %IE. The “green” inhibitor candidates included sodium metabisulfite and ascorbic acid, which yielded maximum %IE values of -123900% and 91%, respectively. Results indicated that sodium metabisulfite is not a suitable inhibitor, while ascorbic acid showed potential to extend reinforced concrete’s design life without posing health or …

Assessing Fixed-Node Diffusion Monte Carlo For Radical Polymerization Reaction Energetics, Timothy Brian Huber

Graduate Research Theses & Dissertations

The art of quantum chemistry is grounded to the discovery of a time efficient computational method that can capture the essential physics. Historically, the Hartree-Fock method, where an electron moves in the mean field of the other electrons, has provided the orbitals used to construct a single-reference Slater determinant and thus formed the basis for molecular orbital calculations. Kohn-Sham density functionals have become overwhelmingly popular among the chemistry community due to their low computational cost. However, their prediction of thermodynamic properties important in free radical polymerization has shown difficulty due to an artificial delocalization of electron density and spin contamination …

Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust

Graduate Theses/Dissertations

The world today relies on hydrocarbon combustion for many reasons, including its high energy density that provides ease of transportation. However, hydrocarbons sourced from fossil fuels are not expected to last forever. Biodiesel, a renewable alternative, has many attractive benefits but comes with other downsides. Biodiesel can gel in cold environments and may leave residue in an engine. Pyrolysis of biodiesel has shown promise in addressing these common detriments. Inducing pyrolysis on biodiesel feedstock (commonly soybean oil in the USA) would be an attractive option presuming it continues to produce fossil fuel analogs similar to biodiesel pyrolysis. Herein, Langevin molecular …

Molecular Understanding And Design Of Deep Eutectic Solvents And Proteins Using Computer Simulations And Machine Learning, Usman Lame Abbas

Theses and Dissertations--Chemical and Materials Engineering

Hydrophobic deep eutectic solvents (DESs) have emerged as excellent extractants. A major challenge is the lack of an efficient tool to discover DES candidates. Currently, the search relies heavily on the researchers’ intuition or a trial-and-error process, which leads to a low success rate or bypassing of promising candidates. DES performance depends on the heterogeneous hydrogen bond environment formed by multiple hydrogen bond donors and acceptors. Understanding this heterogeneous hydrogen bond environment can help develop principles for designing high performance DESs for extraction and other separation applications. This work investigates the structure and dynamics of hydrogen bonds in hydrophobic DESs …

Recovering Relativistic Effects In Electronic Structure Calculations Of F-Element Single Molecule Magnets, Nathan Roy Loutsch

Dissertations and Theses

There has been a great interest in developing new information technologies. Single molecule magnets (SMMs) are emerging as materials for high density data storage, qubits, and molecular spintronics. SMMs containing lanthanide or actinide centers are of interest due to their potentially high magnetic anisotropy. This would enable the use of SMMs at higher temperatures. Accurately modelling the electronic structure of f-element complexes can be quite challenging. Density Functional Theory (DFT) is a popular choice for optimizing geometry and studying the electronic structure due to its relatively low cost. In certain cases, more accuracy is desired or necessary to predict experimental …

Intelligent Control Based On Bp Artificial Neural Network For Electrochemical Nitrate Removal, Xin-Wan Zhang, Guang-Yuan Meng, Li-Qiang Fang, Ding-Ming Chang, Tong Li, Jin-Wen Hu, Peng Chen, Yong-Di Liu, Le-Hua Zhang

Journal of Electrochemistry

Achieving effective control of parameters in the process of nitrate wastewater treatment is critical to electrochemical water treatment. The powerful nonlinear mapping ability, self-adaptation and self-learning ability of neural network technology can optimize the electrochemical processing. However, there are few researches in this direction. Hence, based on the test data of the electrochemical reduction of nitrate, an electrochemical prediction model was established by using the BP neural network algorithm. Considering the correlation of various parameters in the electrochemical process, the reaction time, initial nitrate nitrogen concentration, pH and current density were determined as the input layer of the BP neural …

Search For Osme Bonds With Π Systems As Electron Donors, Xin Wang, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO₄ (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C₂H₂ , C₂H₄ , C₆H₆ , C₄H₅N, C₄H₄O, and C₄H₄S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, …

The Effects Of Aggregation Of Tetrafluoro(Trifluoromethyl-Λ6-Sulfanyl) Ethanes On The Secondary Structure Stabilization Of Melittin: A Molecular Dynamics Simulation Study, Samadrita Biswas

Legacy Theses & Dissertations (2009 - 2024)

Introduction of novel tetrafluoro(trifluoromethyl-λ6-sulfanyl) (CF3SF4) functional group has garnered substantial interest because of its increased hydrophobicity. This super fluorinated group attributed to increased lipophilicity, decreased heat of vaporization, and lowered dielectric constants. The highly electronegative nature of this group can profoundly influence the reactivity of compounds containing the CF3SF4 moiety. The hypervalency associated with this new group presents an exciting platform to explore the fundamental understanding of molecular interactions, reactivity patterns, and electronic behaviors. This dissertation investigates the molecular properties and behaviors of tetrafluoro(trifluoromethyl-λ6-sulfanyl) ethanes (CF3SF4-ethanes), with a specific emphasis on 2-tetrafluoro(trifluoromethyl)-λ6-sulfanylethan-1-ol (CF3SF4-ethanol) and 2-tetrafluoro(trifluoromethyl)-λ6-sulfanylethanamine (CF3SF4-ethanamine). Utilizing ab initio calculations …

Computational Investigations Of Bond Breaking Processes Using Dft And Td-Dft Approaches., Saurav Parmar

Electronic Theses and Dissertations

The efficient application of DFT and TD-DFT has been harnessed to study bond-breaking processes in some molecules which play a prominent role in enzymatic reactions. The first application includes Radical S-adenosyl methionine (SAM) enzymes which are fundamentally important sources of organic radicals to initiate diverse radical reactions. Recently a bio-organometallic intermediate (Ω) that contains an Fe‒C bond has been characterized and shown to be a common feature of radical SAM enzymes. The strength of Fe‒C bond in Ω has been computed using broken-symmetry density functional theory (BS‒DFT). Additionally, Fe‒C bond dissociation energy (BDE) in Ω has been compared to that …

Computation-Assisted Molecular Discovery For Biomedical Applications: Seeking Small Molecules And Dna Sequences With High Affinity Target Binding, Payam Kelich

Open Access Theses & Dissertations

Binding affinity between two molecules is an essential property in drug and sensor discovery. Several computational and experimental methods exist to find molecules with high binding affinities to desired target molecules. These methods are often complementary, where fast computational methods can be used for the initial screening of molecules, and experimental methods can then screen and determine the molecules of interest and sometimes define the structures of bound complexes. After these steps, computational methods, like molecular dynamics (MD) simulations, can provide detailed insights into atomic interactions and binding, and machine learning approaches can analyze experiment-derived data to discern patterns and …

Computational Quantum Chemistry Studies Of The Stabilities Of Radical Adducts Formed During The Oxidation Of Melatonin Derivatives, James Horne

Electronic Theses and Dissertations

Melatonin is a natural antioxidant that has been investigated for properties as a potential spin trap to identify short-lived free radicals. Computational quantum chemistry studies have been performed for the oxidation of melatonin to N¹-acetyl-N²-formyl-5-methoxykynuramine. This research focused on modification of melatonin into derivatives and analyzing the change in total molecular energy from melatonin to its oxidation product, as well as the corresponding derivatives. Each of the molecular geometries were optimized at the DFT/B3LYP/6-31G(d), DFT/B3LYP/cc-pVXZ (X = D, T), HF/6-31G(d), HF/cc-PVXZ (X = D, T), MP2/6-31G(d), and MP2/cc-PVXZ (X = D, T) levels of theory. …

Investigating The Diffusion Of Solid Yttria Into Solid Zirconia For The Formation Of Yttria Stabilized Zirconia, Logan Thomas Ockershausen

Seton Hall University Dissertations and Theses (ETDs)

A molecular dynamics simulation of yttria-stabilized zirconia (YSZ) is reported in order to analyze the diffusion of the oxygen atoms from the yttria into the zirconia from an initial structure containing a layer of yttria on zirconia. The simulation was performed starting from a pure zirconia slab which was amorphized at the surface followed by placing a slab of yttria on top and a vacuum layer above that. The yttria/zirconia system was simulated at increasing temperatures to 1500K under canonical (NVT) constraints for 6.98 ns until the yttrium atom diffusion was found to occur. The final run was analyzed for …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

An Insight Into The Physicochemical, Drug-Likeness, Pharmacokinetics And Toxicity Profile Of Kigelia Africana (Lam) Bioactive Compounds, Sulyman Olalekan Ibrahim, Halimat Yusuf Lukman, Marili Funmilayo Zubair, Oluwagbemiga Tayo Amusan, Fatimah Ronke Abdulkadri, Bashir Lawal, Lateefat Bello Abdulfatah, Olubunmi Atolani

Al-Bahir

Kigelia africana plant is multipurpose plant whose therapeutic potential has been thoroughly investigated. The physicochemical, solubilities, ADMET, pharmacological, and drug-like properties of this plant have not been reported in details. This study makes use of the information that is currently known on the chemical make-up of the plant to forecast its overall toxicity as well as the potential for the phytochemicals it contains to be employed in medication discovery. The study also employed free web servers for the lipophilicity, water solubility, drug-likness, bioavailability score, medicinal chemistry and toxicological profiling of the compounds of K. africana. Artemether, a known antimalaria …

Biomimetic Modifications On The Bridging Cys Residue Ligand Of An Feni Hydrogenase, Madeline Kesner

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Charge-Dependence Of Dissolution/Deposition Energy Barrier On Cu(111) Electrode Surface By Multiscale Simulations, Hang Qiao, Yong Zhu, Sheng Sun, Tong-Yi Zhang

Journal of Electrochemistry

Behaviors of electrified interface under different applied potentials/charges play the central role in electroplating process and electrochemical corrosion. The mechanism, however, is unclear yet for a surface atom dissolving/depositing from/on an electrode surface under an applied potential. The energy barrier along the reaction path is the key variable. The present work conductes hybrid first-principle/hybrid calculations to study the direct and indirect dissolution/deposition of a Cu atom on perfect/stepped Cu(111) planar electrodes in an electrolyte under different excess charges. Energy profiles present a linear relationship between the energies of the initial/final state and the activation state of different reaction paths under …

Computational Investigations Of Polymer Electrolytes In Aqueous Solutions, Hishara Keshani Gallage Dona

LSU Doctoral Dissertations

Polymer electrolyte membranes, an intriguing category of soft materials, are characterized by polymer backbones tethered with negatively or positively charged functional groups, finding applications from biological macromolecules to electrochemical separations in fuel cells. This dissertation focuses on computational investigations of polymer electrolytes in aqueous solutions using polypeptoids and ion exchange membranes. Polypeptoids, highly tailorable peptidomimetic polymers lacking backbone hydrogen bonding or chirality, were used as model systems. Micelles formed from these polypeptoid polymers exhibited electrostatic repulsion, which competes with charge-sodium interactions, adding complexity to predicting micelle shapes. This research refined the design strategy, enhancing micelle shape and structure through precise …

Computational Chemistry At Bethel, Rollin King

Day of Scholarship

In the 21st century, computational methods play a significant role in all areas of chemistry, ranging from small-molecule spectroscopy to drug design. Research in computational chemistry is multidisciplinary, involving the application of physics, math, and computer science to address questions and challenges in chemistry. This poster will survey the field, highlight the outstanding work of Bethel students, and present a couple of ongoing projects.