Computational Chemistry Commons^™

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.

Deciphering The Role Of Molecular Interactions On The Interfacial Structure Of Aqueous And Non-Aqueous Interfaces, Dodangodage Ishara Indunil Senadheera, D I. Senadheera

LSU Doctoral Dissertations

The study focused on "Deciphering the role of molecular interactions on the interfacial structure of aqueous and non-aqueous interfaces" holds immense significance in diverse scientific and industrial domains. Our primary objective is to unravel the intricate web of molecular interactions occurring at the boundaries between aqueous and non-aqueous phases. The research presented here spans a wide scope, encompassing applications in microelectromechanical systems in the semiconductor industry, energy-efficient membranes for electrochemical separations, and renewable energy storage systems. Molecular dynamics simulations were conducted in collaboration with experimental studies, specifically atomic force microscopy, to achieve insights at the molecular level.The first project centered …

Three-Dimensional Two-Phase Cfd Simulation Of Alkaline Electrolyzers, Ling-Yu Gao, Lin Yang, Chen-Hui Wang, Gui-Xuan Shan, Xin-Yi Huo, Meng-Fei Zhang, Wei Li, Jin-Li Zhang

Journal of Electrochemistry

The structural and operation parameters of the electrolyzer play important roles in the efficiency of alkaline water electrolysis. In this article, a three-dimensional numerical model coupled with the electric field and the Euler-Eulerian k-ε turbulence flow field was first established to simulate accurately the performance of alkaline electrolyzers, based on a compact assembly structure of the industrial alkaline water electrolyzers, especially at current densities higher than 5000 A·m^–2. The simulation results are compared with the experimental data to verify the accuracy of the model. Suitable operating conditions for concentration, flow rate and the optimal design method of the …

Optimizing Mn-Al Permanent Magnet Performance Through Control Of The Phase Transformation, Ternary Element Addition, And Advanced Processing, Thomas R. Keller

Dartmouth College Ph.D Dissertations

The growing need for electrical power in machines and vehicles brings with it a growing need for critical materials. The current high-performance permanent magnets (PMs) based on rare-earth (RE) elements Nd and Sm cannot escape the problem of raw material cost, geographic scarcity in the earth’s crust, and lack of circular global supply chains. This poses a problem of industrial ecology: can PMs be made from inexpensive, more abundant materials while still meeting sufficient performance criteria? PMs based on the magnetic τ phase of Mn-Al offer a possible alternative to REPMs. However, years of innovation have not yet achieved real-world …

Quantifying Temperature-, Pressure-, And Nuclear Quantum Effects On Hydrophobic And Hydrophilic Water-Mediated Interactions, Justin T. Engstler

Dissertations, Theses, and Capstone Projects

Water-mediated interactions (WMIs) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure, and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic–hydrophilic) interactions have been mostly overlooked. Here, we study the role of T and P on the WMI between nanoscale (i) hydrophobic–hydrophobic, (ii) hydrophilic–hydrophilic, and (iii) hydrophilic–hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic, and hybrid interactions are all sensitive to …

Singlet Oxygen-Mediated Conformational Flexibility, Antioxidant, And Isomerization Studies In Chemistry And Biochemistry, Oliver Turque

Dissertations, Theses, and Capstone Projects

Three chapters are included in this dissertation, each of which describes non-oxidative reactions, with peroxy intermediates formed between singlet oxygen (¹O₂) and substrate. (1) Novel discoveries related to the intermediate formed by ¹O₂ and dimethyl disulfane are explored. (2) A new mechanism is proposed, wherein the dihedral angle CS–SC (θ) determines the pro- or antioxidant activity of an organic disulfide. (3) A review of ¹O₂'s ability to facilitate the geometric isomerization of alkenes and polyenes is presented in Chapter 3.

Chapter 1 investigates the role of singlet oxygen potentially …

Data-Driven 2d Materials Discovery For Next-Generation Electronics, Zeyu Zhang

Dissertations

The development of material discovery and design has lasted centuries in human history. After the concept of modern chemistry and material science was established, the strategy of material discovery relies on the experiments. Such a strategy becomes expensive and time-consuming with the increasing number of materials nowadays. Therefore, a novel strategy that is faster and more comprehensive is urgently needed. In this dissertation, an experiment-guided material discovery strategy is developed and explained using metal-organic frameworks (MOFs) as instances. The advent of 7r-stacked layered MOFs, which offer electrical conductivity on top of permanent porosity and high surface area, opened up new …

Computational And Experimental Investigation Of Elemental Sulfur And Polysulfide, Jyoti Sharma

Dissertations

Petroleum processing results in the generation of significant quantities of elemental sulfur (S₈), leading to a surplus of sulfur worldwide. Despite its abundance and low cost, the use of sulfur in value-added organic compound synthesis is limited due to its unpredictable and misunderstood reactivity. This dissertation aims to address this issue by tackling it from two angles. Firstly, by utilizing Density Functional Theory (DFT) calculations, the reactivity of sulfur in the presence of nucleophiles is studied. This facilitates the identification of organic polysulfide intermediates that can be generated under different conditions, as well as the corresponding reactivity for …

A Dft Analysis And Simple Hamiltonian Modeling Of A Molecular System Employed For Experimental Evidence Of Quantum Teleportation, Pedro Ulises Medina Gonzalez

Open Access Theses & Dissertations

Radical ion pairs (RIPs) have been used to demonstrate quantum teleportation in molecular systems for applications in quantum information science. Covalent organic donor-acceptor (D-A) molecules can produce RIPs through photo-induced charge transfer and an additional radical (R) molecule makes quantum teleportation possible. We present the electronic structure and analyze charge transfer excited states of a recently studied [1] D-A-R molecular system using density functional theory. The distances between donor-acceptor and donor-radical are about 12.9 \AA $\,$ and 21.9 \AA, respectively. The excitation energies are calculated using the perturbative delta-SCF method and agree with other conventional excited-state methods and experimental reference …

Advances In One-Electron Self-Interaction-Correction Methods For Accurate And Efficient Self-Interaction-Free Density Functional Calculations, Selim Romero

Open Access Theses & Dissertations

Density functional theory (DFT) is a widely used computational method for studying electronic structures of atoms, molecules, and solids. It provides an exact theory for obtaining ground state energy from the ground state density. However, since the exact exchange-correlation functional remains unknown, approximate exchange-correlation functionals called approximate density approximations (DFAs) are used. The foundation of many DFAs is the local spin density approximation (LSDA). It serves as the starting point for constructing various DFAs. However, DFAs are prone to self-interaction errors (SIE) due to the improper cancellation of the approximate exchange energy and the Coulomb energy. This issue impacts the …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

All Dissertations

The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

The Investigation Of Singlet Fission From The Perspective Of Hierarchy Of Pure States (Hops), Tao (James) Chen

Chemistry Theses and Dissertations

This thesis provides a preliminary investigation of singlet fission from the perspective of Hierarchy of pure states (HOPS), which provides a numerical exact solution for the investigation of a series of open quantum systems. Since the inception of the concept of singlet fission about half a century ago, this photo-physical process has attracted the attention of a multitude of researchers and has been extensively studied theoretically and experimentally. However, these previous methods for the investigation of singlet fission focus more or less on tackling the underlying mechanisms of singlet fission from the perspective of perturbation. So far, the HOPS method …

The Investigation Of Singlet Fission From The Perspective Of Hierarchy Of Pure States (Hops), Tao (James) Chen

Chemistry Theses and Dissertations

This thesis provides a preliminary investigation of singlet fission from the perspective of Hierarchy of pure states (HOPS), which provides a numerical exact solution for the investigation of a series of open quantum systems. Since the inception of the concept of singlet fission about half a century ago, this photo-physical process has attracted the attention of a multitude of researchers and has been extensively studied theoretically and experimentally. However, these previous methods for the investigation of singlet fission focus more or less on tackling the underlying mechanisms of singlet fission from the perspective of perturbation. So far, the HOPS method …

C···O And Si···O Tetrel Bonds: Substituent Effects And Transfer Of The Sif3 Group, Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF₃-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO₂, CN, F, CH₃, OH, OCH₃, NH₂, and Li) is examined by quantum chemical means. The Si···O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C···O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite …

Enhanced Quantum Chemistry With Machine Learning, Brock Dyer

Physics and Astronomy Summer Fellows

This file is a catalogue of the relevant quantum mechanical and computer programming topics that I learned during the summer which will be helping me to generate an artificial intelligence that will be able to perform computational chemical calculations at a much faster rate and comparable or better accuracy than current methods.

First-Principles Simulations Of Attosecond Transient X-Ray Absorption, Min Chen

LSU Doctoral Dissertations

The first part of this dissertation presents calculations of the extinction spec- tra of gold-silver/silver-gold core-shell nanospheres. The goal of this projectsis to get a deeper understanding of surface plasmonic resonance in metal nanospheres with core-shell geometry. Here, we used the finite-difference time-domain (FDTD) method and total-field/scattered-field (TFSF) framework to compute the extinction spectra of nanoparticles to determine the geometry of gold-silver/silver-gold core-shell nanoparticles. This supported experimental work on monitoring the growth dynamics of colloidal gold- silver/silver-gold core-shell nanoparticles using in situ second harmonic generation (SHG) and extinction spectroscopy.

The second and main project involved simulating attosecond transient spectra for …

The Decomposition Of Normal Vibrational Modes In Different Chemistry Problems, Mateus Macedo Quintano

Chemistry Theses and Dissertations

The least action principle yields the Euler-Lagrange equations, which explain molecular vibrations in minimizing action. Subsequently, the Lagrangian gives rise to the equations of motion using the Euler-Lagrange equations. We can then solve the characteristic value problem to obtain normal vibrational modes. Ultimately, the vibrational spectrum of a molecule can be extracted from the characteristic values. Normal coordinates are linear combinations of internal or Cartesian coordinates. However, the delocalization of normal vibrational modes across the molecule restricts the direct use of normal mode frequencies and force constants for measuring bond strength. From the force constant matrix and the normal mode …

Modeling Exciton Migration In Two-Dimensional Space, Christian D. Etnyre

DePaul Discoveries

Computational analysis through density matrix quantum mechanics was performed to model exciton migration in two-dimensional space for a zinc-substituted tetraazaphthalocyanine. The model produced resembles a two-dimensional sheet of molecules. Energy transport mechanisms, controlled by point dipole couplings, were evaluated while altering the size of the crystal lattice. It was determined that energy transport was much more significant with a decreasing size of the crystal lattice. Likewise, the result of increasing the size of the crystal lattice had the effect of dampening the rate of energy transport. It was of interest to determine, with varying crystal lattice dimensions, the time that …