Azaborine Versus Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Azaborine Chromophores,
2022
Kennesaw State University
Azaborine Versus Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Azaborine Chromophores, Kaia Ellis, Janiyah Riley, Lyric Gordon, Janiyah Riley
Symposium of Student Scholars
Azaborines are fascinating compounds because of their valuable and interesting optical properties making them suitable to be utilized in many optoelectronic devices. We have designed, synthesized, and investigated a series of novel conjugated thermally stable azaborine chromophores by incorporating a phenyl ring as a spacer linking the chromophore to different electronic moieties as easily tunable high-luminescent organic materials. We investigated the effect of the phenyl spacer on the azaborine unit. The substituent effects of different electronic moieties were investigated by the insertion of electron –withdrawing and –donating moieties to the phenyl spacer. We examined the role of the electron –donating …
Computer Simulation Of Raman Spectra And Mode Assignment: Application To Methane,
2022
Kennesaw State University
Computer Simulation Of Raman Spectra And Mode Assignment: Application To Methane, Oluwaseun Omodemi, Ciara Tyler, Martina Kaledin
Symposium of Student Scholars
This work uses driven molecular dynamics (DMD) method, in conjunction with an analytic PES calculated using MP2/aug-cc-pVDZ energies to identify and assign Raman vibrational modes of methane. Recently, a new linearized approach was proposed for the Polarizability Tensor Surfaces (PTS) that yields a unique solution to the least-squares fitting problem and provides a competitive level of accuracy compared to the non-linear PTS model. We used the previously reported B3LYP/6-31+G(d) molecular geometries for CH4 and generated a new PTS at the MP2/aug-cc-pVDZ level of theory. The performance of the linearly parametrized functional form for the CH4 PTS is examined. …
Relative Energy Comparison For Various Water Clusters Using Mp2, Df-Mp2, And Ccsd(T):Mp2 Methods,
2022
University of Mississippi
Relative Energy Comparison For Various Water Clusters Using Mp2, Df-Mp2, And Ccsd(T):Mp2 Methods, Qihang Wang
Honors Theses
The study of water clusters is an important area of research in many disciplines, such as biology, physical chemistry, and environmental studies. However, due to the difficulty in studying larger water clusters, such as clathrate hydrates, it is beneficial to obtain accurate descriptions of smaller water clusters to use as models for larger systems via computational methods. By starting with small water clusters, such as (H2O)6, and moving into larger systems it is possible to build up data on various water structures that can determine the energetics of the various geometries within a certain number of water molecules. …
Unraveling Molecular Mechanisms Of Antibiotic Resistance Through Multiscale Simulations And Explainable Machine Learning,
2022
Southern Methodist University
Unraveling Molecular Mechanisms Of Antibiotic Resistance Through Multiscale Simulations And Explainable Machine Learning, Zilin Song
Chemistry Theses and Dissertations
Pathogen resistance to β-lactam antibiotics compromises effective treatments of superbug infections. One major source of β-lactam resistance is the bacterial production of β-lactamases, which could effectively hydrolyze β-lactam drugs. In this thesis, the hydrolysis of various β-lactam antibiotics by class A serine-based β-lactamases (ASβLs) were investigated using hybrid Quantum Mechanical / Molecular Mechanical (QM/MM) minimum energy pathway (MEP) calculations and explainable machine learning (ML) approaches. The TEM-1/benzylpenicillin acylation reaction with QM/MM chain-of-states reaction pathways was firstly revisited. I proposed two decomposition methods for energy contribution analysis based on perturbing ML regression models. Both methods were shown to be model implementation …
A Proposed Treatment Of Mixed Connective Tissue Disease By Competitive Inhibition Of Autoantibodies,
2022
Liberty University
A Proposed Treatment Of Mixed Connective Tissue Disease By Competitive Inhibition Of Autoantibodies, Thomas Russell
Senior Honors Theses
Mixed Connective Tissue Disease is an autoimmune disease characterized by Raynaud’s phenomenon and arthritis among other symptoms. It is primarily caused by antibodies that target the U1-RNP 70K peptide. The treatment proposed in this paper uses competitive inhibition to prevent the binding of the anti-U1-RNP 70K antibodies with the U1-RNP 70K peptide. A method for testing the designed treatment in silico is proposed using AutoDock Vina docking software.
The Effect Of Fluorinated Substitution Of Meso Phenyl Porphyrins On Porphyrin Basicity,
2022
Nova Southeastern University
The Effect Of Fluorinated Substitution Of Meso Phenyl Porphyrins On Porphyrin Basicity, Harsh Chheda, Rushi Patel, Maria Ballester Ph.D., Victor Castro Ph.D.
Chemistry and Physics Faculty Proceedings, Presentations, Speeches, Lectures
The protonation of meso-Tetra(2,3,4-trifluoromethylphenyl) porphyrin (TF) and meso-Tetra(pentafluorophenyl) porphyrin (PF) will be studied through UV vis spectroscopy. Protonation is achieved by titration of each porphyrin in toluene with trifluoroacetic acid (TFA). The presence of a wavelength shift from the free base Soret to the protonated Soret will indicate the formation of a dication. The data from the UV spectra will be used to calculate the pKa values associated with each porphyrin. Based on the results, the average pKa for TF upon protonation was 2.07, while the average pKa for PF was 1.36 over four trials. A greater acidic value for …
Recent Advances In Electrochemical Kinetics Simulations And Their Applications In Pt-Based Fuel Cells,
2022
1. Collaborative Innovation Center of Chemistry for Energy Material, Key Laboratory of Computational Physical Science (Ministry of Education), Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China;
Recent Advances In Electrochemical Kinetics Simulations And Their Applications In Pt-Based Fuel Cells, Ji-Li Li, Ye-Fei Li, Zhi-Pan Liu
Journal of Electrochemistry
Theoretical simulations of electrocatalysis are vital for understanding the mechanism of the electrochemical process at the atomic level. It can help to reveal the in-situ structures of electrode surfaces and establish the microscopic mechanism of electrocatalysis, thereby solving the problems such as electrode oxidation and corrosion. However, there are still many problems in the theoretical electrochemical simulations, including the solvation effects, the electric double layer, and the structural transformation of electrodes. Here we review recent advances of theoretical methods in electrochemical modeling, in particular, the double reference approach, the periodic continuum solvation model based on the modified Poisson-Boltzmann …
A Beginners’ Guide To Modelling Of Electric Double Layer Under Equilibrium, Nonequilibrium And Ac Conditions,
2022
1. School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, Anhui, People’s Republic of China;
A Beginners’ Guide To Modelling Of Electric Double Layer Under Equilibrium, Nonequilibrium And Ac Conditions, Lu-Lu Zhang, Chen-Kun Li, Jun Huang
Journal of Electrochemistry
In electrochemistry, perhaps also in other time-honored scientific disciplines, knowledge labelled classical usually attracts less attention from beginners, especially those pressured or tempted to quickly jam into research fronts that are labelled, not always aptly, modern. In fact, it is a normal reaction to the burden of history and the stress of today. Against this context, accessible tutorials on classical knowledge are useful, should some realize that taking a step back could be the best way forward. This is the driving force of this article themed at physicochemical modelling of the electric (electrochemical) double layer (EDL). We begin the exposition …
Phenanthrene: Establishing Lower And Upper Bounds To The Binding Energy Of A Very Weakly Bound Anion,
2022
University of Innsbruck
Phenanthrene: Establishing Lower And Upper Bounds To The Binding Energy Of A Very Weakly Bound Anion, Elisabeth Gruber, Siegfried Kollotzek, Stefan Bergmeister, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt
Faculty Publications
Quite a few molecules do not form stable anions that survive the time needed for their detection; their electron affinities (EA) are either very small or negative. How does one measure the EA if the anion cannot be observed? Or, at least, can one establish lower and upper bounds to their EA? We propose two approaches that provide lower and upper bounds. We choose the phenanthrene (Ph) molecule whose EA is controversial. Through competition between helium evaporation and electron detachment in HenPh- clusters, formed in helium nanodroplets, we estimate the lower bound of the vertical detachment energy …
The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry,
2022
Roanoke College
The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry, Kelly Anderson, Sarah Arradondo, K Aurelia Ball, Chrystal D. Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer Mcdonald, Maria C. Nagan, Carol Parish, Caitlin E. Scott, Patricia Soto, Aime'e Tomlinson, Mychel Varner
2022 Faculty Bibliography
The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% women) at 34 different institutions, who have trained nearly 900 undergraduate students, more than two-thirds of whom identify as women and one-quarter identify as students of color. MERCURY provides a model for the support necessary for faculty to achieve professional advancement and career satisfaction. The range of experiences and expertise of the consortium members provides excellent networking opportunities …
Nonhematopoietic Erythropoietin: A Study Of Signaling, Structure, And Behavior,
2022
University of South Dakota
Nonhematopoietic Erythropoietin: A Study Of Signaling, Structure, And Behavior, Nicholas John Pekas
Dissertations and Theses
Erythropoietin (EPO) is a cytokine hormone known for initiating red blood cell proliferation by binding to its homodimer receptor (EPOR)2 in the bone marrow. Recent progress in neurobiology has shown that EPO also exerts robust neurotrophic and neuroprotective activity in the CNS. It is widely thought that EPO’s neurotrophic activity is centrally involved in its antidepressant and cognitive enhancing effects. However, EPO’s potent erythropoietic effects prevent it from being used in the clinic to treat psychiatric disorders. A chemically engineered non-erythropoietic derivative of EPO, carbamoylated EPO (CEPO), produces psychoactive effects without activating hematopoiesis. However, CEPO is expensive to produce and …
Analyzing The Free Energy Of Ions Sampling A Voltage Gated Sodium Ion Channel,
2022
Colby College
Analyzing The Free Energy Of Ions Sampling A Voltage Gated Sodium Ion Channel, Isabel Varghese
Honors Theses
Voltage gated sodium ion channels are implicated in cardiac diseases, seizures, etc., and they play a role in maintaining ionic homeostasis in cells. Computational studies use prokaryotic model because they are simpler but function similarly to human voltage gated sodium ion channels. This study uses molecular dynamics (MD) to study three specific questions regarding voltage gated sodium ion channels of Magnetococcus marinus. The first question in this study is how the free energy of sodium diffusion compares to that of calcium ion diffusion. We were not able to find any physically significant information due to poor sampling and a lack …
Development Of Accurate And Efficient Computational Methodologies For Predicting Protein-Ligand And Protein-Protein Binding Free Energies,
2022
University of Kentucky
Development Of Accurate And Efficient Computational Methodologies For Predicting Protein-Ligand And Protein-Protein Binding Free Energies, Alexander Hamilton Williams
Theses and Dissertations--Pharmacy
Computational modeling is an invaluable tool in the drug discovery process either for small ligand or protein therapeutics. The widespread availability of protein X-Ray Crystal and Cryo-Electron Microscopy (Cryo-EM) structures has allowed for more accurate molecular dynamics (MD) simulations that are not reliant on methods such as homology modeling, which may produce structures that require significant computational time to demonstrate their stability. In this thesis we describe several novel methodologies for the computationally efficient modeling of protein/ligand and protein/protein complexes that may be employed within both large-scale virtual screenings and lead compound optimization. These methodologies may also be utilized in …
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes,
2022
Michigan Technological University
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi
Dissertations, Master's Theses and Master's Reports
Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter …
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level,
2022
Michigan Technological University
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level, Geeta Sachdeva
Dissertations, Master's Theses and Master's Reports
The field of two-dimensional (2D) layered materials provides a new platform for studying diverse physical phenomena that are scientifically interesting and relevant for technological applications. Theoretical predictions from atomically resolved computational simulations of 2D materials play a pivotal role in designing and advancing these developments. The focus of this thesis is 2D materials especially graphene and BN studied using density functional theory (DFT) and molecular dynamics (MD) simulations. In the first half of the thesis, the electronic structure and optical properties are discussed for graphene, antimonene, and borophene. It is found that the absorbance in (atomically flat) multilayer antimonene (group …
Density Functional Theory Of Samarium(Ii) Reactivity In Thf And Water,
2022
University of South Dakota
Density Functional Theory Of Samarium(Ii) Reactivity In Thf And Water, Parisa Fasihianifard
Dissertations and Theses
Sm(II) diiodide is widely used in organic synthesis for the reduction of functional groups such as esters, anhydrides, amides, carbonyls, and arenes. Moreover, in aqueous systems and in mixtures of water and THF, the addition of Sm(II) diiodide can reduce water directly resulting in the formation of hydrogen gas. However, the mechanism of these reactions is not completely understood, making it difficult to improve experimental design. The reaction can proceed either through subsequent electron-transfer proton-transfer (ET-PT), subsequent proton transfer electron-transfer (PT-ET), or via proton coupled electron transfer (PCET). Density functional theory (DFT) calculations were performed to understand the speciation of …
Heterogeneous Oxidation Of Multi-Component Aqueous Organic Aerosols: The Effect Of Transport Phenomena And Reaction Compartment On Reaction Kinetics.,
2022
West Virginia University
Heterogeneous Oxidation Of Multi-Component Aqueous Organic Aerosols: The Effect Of Transport Phenomena And Reaction Compartment On Reaction Kinetics., Tadini Wenyika Masaya
Graduate Theses, Dissertations, and Problem Reports (ETD)
The surface-bulk partitioning of small organic molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80-Å cubic water box containing series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water-bulk were examined at a molecular-level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars …
From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design,
2022
West Virginia University
From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design, Pedram Tavazohi
Graduate Theses, Dissertations, and Problem Reports (ETD)
Density-functional theory (DFT) has gained popularity because of its ability to predict the properties of a large group of materials a priori. Even though DFT is exact, there are inaccuracies introduced into the theory due to the approximations in the exchange-correlation (XC) functionals. Over the 50 years of its existence, scientists have tried to improve the design of the XC functionals. The errors introduced by these functionals are not consistent across all types of solid-state materials. In this project, a high throughput framework was utilized to compare the theoretical DFT predictions with the experimental results available in the Inorganic Crystal …
Fluorescence Probes For Bioimaging: Synthesis, Photophysical Properties And Applications,
2021
New Jersey Institute of Technology
Fluorescence Probes For Bioimaging: Synthesis, Photophysical Properties And Applications, Mehrun Nahar Uddin
Dissertations
Fluorescent probes are a vital tool in the study of cell imaging. There are many types of fluorescent probes ranging from inorganic and organic nanoparticles to organic molecules. When used judiciously, they can help provide essential information on cellular structure and function. The introduction of two-photon microscopy has expanded the need for new probes, in particular near-infrared (NIR) absorbing and emitting fluorescent probes. The photochemical and photophysical properties of NIR probes play a crucial role in their effectiveness in cell imaging by both conventional and two-photon excitation (2PE) microscopy. In this research, the synthesis, photophysical properties, and two-photon absorption (2PA) …
Cyclic Voltammetric Simulations On Batteries With Porous Electrodes,
2021
Materials Genome Institute, Shanghai University, Shanghai 200444, China;
Cyclic Voltammetric Simulations On Batteries With Porous Electrodes, Xue-Fan Cai, Sheng Sun
Journal of Electrochemistry
Lithium-ion batteries (LIBs) are among the most widely used energy storage devices. Whole-cell modeling and simulations of LIBs can optimize the design of batteries with lower costs and higher speeds. The Pseudo-Two-Dimensional (P2D) electrochemical model is among the most famous whole-cell models and widely applied in LIB simulations. P2D model consists of a series of kinetic equations to model Li+/Li diffusion in working/counter electrodes and electrolytes, which are filled in the porous electrodes and separator, and reactions at the interface of electrolyte and active particles. The traditional applications of P2D model, however, are limited to the cases where …
