Computational Chemistry Commons^™

Multiscale Computational Chemistry Studies Of The Catalytic Mechanisms Of Non-Heme Fe(Ii)/2-Oxoglutarate-Dependent Oxygenases, Simahudeen Bathir Jaber Sathik Rifayee

Dissertations, Master's Theses and Master's Reports

Enzymes catalyze complex biological transformations. Non-heme Fe(II)/2-oxoglutarate (2OG)–dependent enzymes are highly versatile catalysts capable of selective C–H oxidation, enabling transformations such as hydroxylation, halogenation, desaturation, demethylation, ring rearrangements, epoxidation, and electrophilic aromatic substitution. These enzymes are involved in various biological processes, including fatty acid metabolism, hypoxic signaling, collagen maturation, and transcriptional regulation. Computational Modeling provides detailed knowledge of the enzymes including atomistic details of the important catalytic species, conformational and electronic effects, which are crucial to enzyme engineering and drug design efforts. This dissertation implements advanced multi-scale molecular modelling techniques including Molecular dynamics and Quantum Mechanic / Molecular Mechanics calculations …

Towards Developing Glut2 Specific Probes For Biochemical And Biomedical Applications, Abdelrahman Ismail

Dissertations, Master's Theses and Master's Reports

Facilitated Glucose transporters (GLUTs) are membrane proteins responsible for the uptake of simple sugars and other structurally similar metabolites in all mammalian cells. One of the hallmarks of cancer is dysfunctional sugar metabolism, known as the Warburg effect, and one of the manifestations of that effect is abnormal GLUT expression. There are 14 known GLUT proteins with different expression patterns in different tissues, and tumors tend to express certain GLUTs that are not present in surrounding healthy tissue. Therefore, selective targeting of GLUTs presents a potentially powerful tool for diagnostics and treatment of cancer and other diseases. This has been …

Contributions To Journal Of Electrochemistry, The Flagship Journal Of Chinese Chemical Society Electrochemical Committee, Will Be Listed As A New Recommendation Policy For China Youth Awards Of Electrochemist, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Intrinsic Gas-Phase Behavior Of Uranium Species: A Comprehensive Reactivity Study Of [O=U≡Ch]+ And [Uh]+, Justin Terhorst

Electronic Theses and Dissertations

The intrinsic chemistry of actinide elements, particularly uranium, remains a key challenge in understanding f-block reactivity due to the complexity introduced by solvent interactions, counter-ions, and complex equilibria in the condensed phase. In this dissertation, a systematic gas-phase study utilizing preparative tandem ion-trap mass spectrometry (PTMSⁿ) is presented, focusing on the reactivity of uranium-centered species, specifically [OUCH]⁺, an oxy uranium methylidyne species, and [UH]⁺ ions. By stripping away solvent effects and isolating the ions, PTMSⁿ provides a powerful platform to probe the fundamental chemical behavior of uranium species in their intrinsic state.

The …

Rna Structural-Dynamical Hierarchy: Sars-Cov, Sars-Cov-2, And Delta/Omicron Variant S2m Monomers, Kissing Complexes, And Extended Duplexes, Adam Kensinger

Electronic Theses and Dissertations

The power and promise of ribonucleic acid (RNA) molecules are only beginning to be realized in living organisms and pharmaceutical intervention. Specifically, defining the chemical physics of RNA’s heterogenous structural ensemble and dynamics, which has experienced expansive growth over the last few years, is central to a complete understanding, yet continues to be a significant challenge. A 41-nucleotide hairpin called the stem-loop II motif (s2m), present in the viral genomes of severe acute respiratory syndrome (SARS), SARS-coronavirus-2 (SARS-CoV-2), and the Delta and Omicron variants responsible for the COVID-19 pandemic, is a potential antiviral target due to its high sequence conservation …

Assembly Of Ppsu-Oligomers, Mariam Nesterov

Student Theses and Dissertations

The development of nanostructures for delivering multiple proteins to targeted antibodies has become a promising avenue in biotechnology, driven by advancements in synthetic polymers like poly(propylene sulfone), PPSU. However, the PPSU polymer faces a major limitation - its high insolubility. To address this challenge, this study investigates whether PPSU oligomers can enhance both the solubility and stability of lysozyme, a model protein that is cost-effective and widely accessible. Using dimer, trimer, tetramer, and hexamer configurations, we analyzed the interactions between PPSU oligomer and lysozyme under varying conditions. Our results show that the dimer and trimer are water soluble (no aggregate …

Computational Logp Calculations And Determination Of Lipophilicity Values Of Fluorinated Morphine Derivatives, Mirabella Romano, Allison Vu, Emily Chen

Student Scholar Symposium Abstracts and Posters

The addictive effect of opioids impacted 60 million people globally in 2023. This opioid crisis necessitates the development of opioid derivatives that maintain analgesic efficacy while minimizing addictive effects from opioid use. The present work focuses on morphine, a commonly prescribed opioid with high affinity to the mu-opioid receptor (MOR). Morphine binds non-selectively within both healthy and inflamed tissue. By modifying morphine’s structure through fluorination to counteract its non-selective binding, the drug’s pharmacological ability to provide effective pain relief comes with a lower risk of addiction. Specifically, the addition of fluorine to differing beta positions of the main binding site …

Theoretical Investigation Of Hydrogen Abstraction From Fluorinated Propanones And Fluorinated Propanals, Laurel Washburn

Honors Theses

Per- and polyfluoroalkyl substances (PFAS) are a class of thousands of industrially used compounds often called “forever” chemicals because of their slow degradation process that leads to accumulation in soil, dust, drinking water, and the body. PFAS are used for their grease and water resistance properties but some of these compounds are toxic at extremely low levels. To better understand the effects of these types of compounds, the main pathways of their degradation need to be further investigated. This study analyzes computationally the hydrogen abstraction reactions by both hydroxyl radical and triplet oxygen atom for all possible fluorinated propanones and …

Nuclear Fuel Cycle Chemistry: A Density Functional Study, Eduardo Montoya

UNLV Theses, Dissertations, Professional Papers, and Capstones

The nuclear fuel cycle aptly describes the life cycle of nuclear fuel sources such as uranium. From its early forms in naturally bearing ores, to its high-temperature sintering into a fuel pellet, the chemistry uranium experiences throughout the fuel cycle is diverse, driving many experimental efforts towards understanding its chemistry to both improve nuclear technologies and advance the safety and handling of nuclear materials. Computing techniques and methodologies can be used to supplement experimental research and are readily available to researchers interested in utilizing computing-based data to support experimental findings. Density functional theory (DFT) is commonly practiced, reliably predicting the …

Chemical And Structural Design Of Single Molecule Switches, Elaina Grogg

Longwood Senior Thesis Proposal

No abstract provided.

The Adviser Of Journal Of Electrochemistry Professor Christian Amatore Received The Chinese Government Friendship Award, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Goodbye With Tears! Deep Condolences To Academician Zhao-Wu Tian!, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Journal Of Electrochemistry Is Selected To Entering Ici Journals Master List, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Air-Stable Palladium N-Heterocyclic Carbene Based Ccc-Nhc Pincer Complexes: Synthesis, Characterization, Photophysical And Raman Vibrational Studies, And Dft Studies, Plus Observation Of An Abnormal Carbene Pincer, Jason A. Denny, Georgette M. Lang, Shane Autry, Vivek Dixit, Tyler L. Woodby, Annie Mcclellan, Jaclyn M. Trate, Nathan I. Hammer, Charles Edwin Webster, Thedford K. Hollis

CAS Publications

A series of CCC-NHC pincer Pd(II)X complexes, where X = Cl, Br, or I, were synthesized by a metalation/transmetalation reaction sequence and characterized by NMR and Raman spectroscopy, photophysical studies, X-ray crystallography, and DFT computational studies. This is the first detailed report of the CCC-NHC pincer Pd complexes analogous the previously reported Pt analogs. Photophysical measurements show that by varying the X ligand, the emission wavelength can be tuned. The chloride complex is a water and air stable blue emitter with a quantum yield of 46% and all three complexes have photostabilities >90%. A combined DFT and TD-DFT study has …

Zhong-Qun Tian, Academician And Honorary Member Of Electrochemistry Committee Chinese Chemical Society, Achieved "Raman Lifetime Award", Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Optimization Of Channel Structure Of Alkaline Water Electrolyzer By Using An Expanded Mesh As A Bipolar Plate, Hai-Yan Xiong, Zhen-Xiao Zhu, Xin Gao, Chen-Ming Fan, Hui-Bao Luan, Bing Li

Journal of Electrochemistry

Alkaline water electrolysis (AWE) is the most mature technology for hydrogen production by water electrolysis. Alkaline water electrolyzer consists of multiple electrolysis cells, and a single cell consists of a diaphragm, electrodes, bipolar plates and end plates, etc. The existing industrial bipolar plate channel is concave-convex structure, which is manufactured by complicated and high-cost mold punching. This structure still results in uneven electrolyte flow and low current density in the electrolytic cell, further increasing in energy consumption and cost of AWE. Thereby, in this article, the electrochemical and flow model is firstly constructed, based on the existing industrial concave and …

Aging Characteristics Of Lithium-Ion Battery Under Fast Charging Based On Electrochemical-Thermal-Mechanical Coupling Model, Dong-Xu Zuo, Pei-Chao Li

Journal of Electrochemistry

The aging characteristics of lithium-ion battery (LIB) under fast charging is investigated based on an electrochemical-thermal-mechanical (ETM) coupling model. Firstly, the ETM coupling model is established by COMSOL Multiphysics. Subsequently, a long cycle test was conducted to explore the aging characteristics of LIB. Specifically, the effects of charging (C) rate and cycle number on battery aging are analyzed in terms of nonuniform distribution of solid electrolyte interface (SEI), SEI formation, thermal stability and stress characteristics. The results indicate that the increases in C rate and cycling led to an increase in the degree of nonuniform distribution of SEI, and thus …

Preliminary Molecular Study Of Chloramphenicol Anchoring On Laccase Enzyme From Trametes Hirsuta, Hanzhola Gusman Riyanto, Afiten Rahmin Sanjaya

Makara Journal of Science

Antibiotics are one of emerging pollutants generally emitted from livestock production and the food industry to the environment. The presence of this pollutant could initiate the development of resistant bacteria that can be fatal to human health. The degradation of antibiotics using enzymes or microbe could be an alternative because the residue or intermediate product is less harmful than of the conventional method. This research aims to support a preliminary study of the degradation of antibiotics using enzyme through molecular docking via Molecular Operating Environment software and molecular dynamics (MD) study via CABSFLEX 2.0 and WebGro macromolecular simulations. The molecular …

Development And Benchmark Of Polarizable Models For Ions, Luke Landry

Dissertations

Metalloproteins are ubiquitous in biology, playing crucial roles in diverse processes. Meanwhile, molecular simulations have become an important tool in scientific research. To accurately simulate metalloprotein systems, accounting for polarization and charge transfer effects is required. The fluctuating charge (FQ) model can effectively simulate the charge transfer effect, but the existing models often lack specificity for metalloproteins. In our research, a tailored FQ model for zinc-containing metalloproteins, leveraging the extended charge equilibration (EQeq) scheme, was introduced. CM5 charges were used as the target in our model parameterization, which offers advantages over RESP/CHELPG charges. Most notably, CM5 charges hold independence over …

Incorporating Solvation Thermodynamic Mapping In Computer-Aided Drug Design, Yeonji Ji

Dissertations, Theses, and Capstone Projects

Advancements in computational techniques have revolutionized structure-based drug design, substantially improving the efficiency and effectiveness of the drug discovery process by reducing time, costs, and labor requirements. These advancements include various methods, such as investigating small molecule ligands binding to proteins, exploring alternative protein conformations, and solvation mapping on the protein surfaces. Among these methods, understanding the correlation between protein-ligand binding and the role of solvation is important.

A fundamental concept in protein-ligand binding is shape and electrostatic complementarity, which is complicated by the inherent flexibility of proteins. In the absence of small molecule ligands, proteins are complementary to surface …