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Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter 2024 Western Kentucky University

Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter

Masters Theses & Specialist Projects

Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …


Micropatterning And Functionalization Of Single Layer Graphene: Tuning Its Electron Transport Properties, Miao-Miao Cui, Lian-Huan Han, Lan-Ping Zeng, Jia-Yao Guo, Wei-Ying Song, Chuan Liu, Yuan-Fei Wu, Shi-Yi Luo, Yun-Hua Liu, Dong-Ping Zhan 2024 Department of Chemistry, College of Chemistry and Chemical Engineering; State Key Laboratory of Physical Chemistry of Solid Surfaces (PCOSS); Engineering Research Center of Electrochemical Technologies of Ministry of Education; Xiamen University; Xiamen 361005, China

Micropatterning And Functionalization Of Single Layer Graphene: Tuning Its Electron Transport Properties, Miao-Miao Cui, Lian-Huan Han, Lan-Ping Zeng, Jia-Yao Guo, Wei-Ying Song, Chuan Liu, Yuan-Fei Wu, Shi-Yi Luo, Yun-Hua Liu, Dong-Ping Zhan

Journal of Electrochemistry

As a promising 2D material, graphene exhibits excellent physical properties including single-atom-scale thickness and remarkably high charge carrier mobility. However, its semi-metallic nature with a zero bandgap poses challenges for its application in high-performance field-effect transistors (FETs). In order to overcome these limitations, various approaches have been explored to modulate graphene's bandgap, including nanoscale confinement, external field induction, doping, and chemical micropatterning. Nevertheless, the stability and controllability still need to be improved. In this study, we propose a feasible method that combines electrochemical bromination and photolithography to precisely tune the electron transport properties of single layer graphene (SLG). Through this …


Recent Advances In Solar Photo(Electro)Catalytic Nitrogen Fixation, Jun-Bo Ma, Sheng Lin, Zhiqun Lin, Lan Sun, Chang-Jian Lin 2024 State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China

Recent Advances In Solar Photo(Electro)Catalytic Nitrogen Fixation, Jun-Bo Ma, Sheng Lin, Zhiqun Lin, Lan Sun, Chang-Jian Lin

Journal of Electrochemistry

Ammonia (NH3) is an essential chemical in modern society. It is currently produced in industry by the Haber-Bosch process using H2 and N2 as reactants in the presence of iron-based catalysts at high-temperature (400–600 oC) and extremely highpressure (20–40 MPa) conditions. However, its efficiency is limited to 10% to 15%. At the same time, a large amount of energy is consumed, and CO2 emission is inevitably. The development of a sustainable, clean, and environmentally friendly energy system represents a key strategy to address energy crisis and environmental pollution, ultimately aiming to achieve carbon neutrality. …


The Determination Of Pzc And Differential Capacitance Curve Of Platinum-Alkaline Polymer Electrolyte Interfaces, Chen-Xi Liu, Ze-Ping Zou, Mei-Xue Hu, Yu Ding, Yu Gu, Shuai Liu, Wen-Jing Nan, Yi-Chang Ma, Zhao-Bin Chen, Dong-Ping Zhan, Qiu-Gen Zhang, Lin Zhuang, Jia-Wei Yan, Bing-Wei Mao 2024 College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China

The Determination Of Pzc And Differential Capacitance Curve Of Platinum-Alkaline Polymer Electrolyte Interfaces, Chen-Xi Liu, Ze-Ping Zou, Mei-Xue Hu, Yu Ding, Yu Gu, Shuai Liu, Wen-Jing Nan, Yi-Chang Ma, Zhao-Bin Chen, Dong-Ping Zhan, Qiu-Gen Zhang, Lin Zhuang, Jia-Wei Yan, Bing-Wei Mao

Journal of Electrochemistry

Alkaline polymer electrolyte (APE) is the core component of modern alkaline hydrogen and oxygen fuel cells, and its single ion conductor nature makes the "electrode/APE" interfaces different from the conventional "electrode/solution" interfaces in terms of ion distribution, electrical double layer structure and polarization behavior. Due to the complexity of the APE and the associated solid-solid interfaces, fundamental investigations are challenging and deeper understanding of the structures and properties of such interfaces is in the infant stage. In this work, we aim to investigate the double layer structure from the aspects of differential capacitance curve and potential of zero charge (PZC) …


Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin 2024 The University of Texas Rio Grande Valley

Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin

Research Symposium

Carbon–carbon (C–C) bond activation has gained increased attention as a direct method for the synthesis of pharmaceuticals. Due to the thermodynamic stability and kinetic inaccessibility of the C–C bonds, however, activation of C–C bonds by homogeneous transition-metal catalysts under mild homogeneous conditions is still a challenge. Most of the systems in which the activation occurs either have aromatization or relief of ring strain as the primary driving force. The activation of unstrained C–C bonds of phosphaalkynes does not have this advantage. This study employs Density Functional Theory (DFT) calculations to elucidate Pt(0)-mediated C–CP bond activation mechanisms in phosphaalkynes. Investigating the …


Role Of Electronegativity In Environmentally Persistent Free Radicals (Epfrs) Formation On Zno, Syed Monjur Ahmed, Reuben Oumnov, Orhan Kizilkaya, Randall W. Hall, Philip T. Sprunger, Robert L. Cook 2024 Louisiana State University at Baton Rouge

Role Of Electronegativity In Environmentally Persistent Free Radicals (Epfrs) Formation On Zno, Syed Monjur Ahmed, Reuben Oumnov, Orhan Kizilkaya, Randall W. Hall, Philip T. Sprunger, Robert L. Cook

Natural Sciences and Mathematics | Faculty Scholarship

Environmentally persistent free radicals (EPFRs), a group of emerging pollutants, have significantly longer lifetimes than typical free radicals. EPFRs form by the adsorption of organic precursors on a transition metal oxide (TMO) surface involving electron charge transfer between the organic and TMO. In this paper, dihalogenated benzenes were incorporated to study the role of electronegativity in the electron transfer process to obtain a fundamental knowledge of EPFR formation mechanism on ZnO. Upon chemisorption on ZnO nanoparticles at 250 °C, electron paramagnetic resonance (EPR) confirms the formation of oxygen adjacent carbon-centered organic free radicals with concentrations between 1016 and 1017 spins/g. …


Confirmation Of Anomalous-Heat Report, Steven B. Krivit, Melvin H. Miles 2024 New Energy Times 369-B 3rd St. #556, San Rafael, CA, 94901

Confirmation Of Anomalous-Heat Report, Steven B. Krivit, Melvin H. Miles

Journal of Electrochemistry

This study identifies, for the first time, critical calculation errors made by Nathan Lewis and his co-authors, in their study presented on May 1, 1989, at the American Physical Society meeting in Baltimore, Maryland. Lewis et al. analysed calorimetrically measured heat results in nine experiments reported by Martin Fleischmann and his co-authors. According to the Lewis et al. analysis, each of the experiments, where calculated for no recombination, showed anomalous power losses. When we used the same raw data, our corrected calculations indicate that each experiment showed anomalous power gains. As such, these data suggest the possibility of a new, …


Joint Time-Frequency Analysis: Taking Charge Penetration Depth And Current Spatial Distribution In The Single Pore As An Example, Nan Wang, Qiu-An Huang, Wei-Heng Li, Yu-Xuan Bai, Jiu-Jun Zhang 2024 Institute for Sustainable Energy/College of Science, Shanghai University, Shanghai 201800, China

Joint Time-Frequency Analysis: Taking Charge Penetration Depth And Current Spatial Distribution In The Single Pore As An Example, Nan Wang, Qiu-An Huang, Wei-Heng Li, Yu-Xuan Bai, Jiu-Jun Zhang

Journal of Electrochemistry

In recent years, joint time-frequency analysis has once again become a research hotspot. Supercapacitors have high power density and long service life, however, in order to balance between power density and energy density, two key factors need to be considered: (i) the specific surface area of the porous matrix; (ii) the electrolyte accessibility to the intra-pore space of porous carbon matrix. Electrochemical impedance spectra are extensively used to investigate charge penetration ratio and charge storage mechanism in the porous electrode for capacitance energy storage. Furthermore, similar results could be obtained by different methods such as stable-state analysis in the frequency …


Measurements Of Rate Constant For Electrode Reactions, Lian-Huan Han, Jia-Yao Guo, Miao-Miao Cui 2024 Department of Mechanical and Electrical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, Fujian, China

Measurements Of Rate Constant For Electrode Reactions, Lian-Huan Han, Jia-Yao Guo, Miao-Miao Cui

Journal of Electrochemistry

Standard electron-transfer rate constant is one of the intrinsic properties for an electrochemical reaction, which is significant in the study of electrode kinetics. It is a key criterion for one to clarify the mechanism and pathway of a specific electrochemical reaction, and to screening and design the electrocatalysts and battery materials. Herein, we will introduce the measuring methods of rate constant for electrode reactions, including polarization curve, rotating disk electrode, ultramicroelectrode, scanning electrochemical microscopy, electrochemical impedance spectroscopy, current step, potential step and cyclic voltammetry, etc., to provide a guide to investigate electrode kinetics for graduate students and researchers in the …


Automated Workflow For Redox Potentials And Acidity Constants Calculations From Machine Learning Molecular Dynamics, Feng Wang, Jun Cheng 2024 aState Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen 361005, Fujian, China

Automated Workflow For Redox Potentials And Acidity Constants Calculations From Machine Learning Molecular Dynamics, Feng Wang, Jun Cheng

Journal of Electrochemistry

Redox potentials and acidity constants are key properties for evaluating the performance of energy materials. To achieve computational design of new generation of energy materials with higher performances, computing redox potentials and acidity constants with computational chemistry have attracted lots of attention. However, many works are done by using implicit solvation models, which is difficult to be applied to complex solvation environments due to hard parameterization. Recently, ab initio molecular dynamics (AIMD) has been applied to investigate real electrolytes with complex solvation. Furthermore, AIMD based free energy calculation methods have been established to calculate these physical chemical properties accurately. However, …


Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave 2024 The Graduate Center, City University of New York

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 …


On The Exact Helium Wave Function Expansion, Ii, An Exponential Modulated Form, Carl W. David 2024 University of Connecticut

On The Exact Helium Wave Function Expansion, Ii, An Exponential Modulated Form, Carl W. David

Chemistry Education Materials

A 11S wave function’s expansion for 2 electron atoms and ions is proposed employing an appropriate exponential factor and Fock’s logarithmic terms. The leading coefficient’s are presented.


The Top Ten Scientific Questions In Electrochemistry, Chinese Society of Electrochemistry 2024 Chinese Chemical Society | Xiamen University

The Top Ten Scientific Questions In Electrochemistry, Chinese Society Of Electrochemistry

Journal of Electrochemistry

No abstract provided.


Rational Design Of Heterostructured Nanomaterials For Accelerating Electrocatalytic Hydrogen Evolution Reaction Kinetics In Alkaline Media, Hai-Bin Ma, Xiao-Yan Zhou, Jia-Yi Li, Hong-Fei Cheng, Ji-Wei Ma 2024 Shanghai Key Laboratory for R&D and Application of Metallic Functional Materials, Institute of New Energy for Vehicles, School of Materials Science and Engineering, Tongji University, Shanghai 201804, China

Rational Design Of Heterostructured Nanomaterials For Accelerating Electrocatalytic Hydrogen Evolution Reaction Kinetics In Alkaline Media, Hai-Bin Ma, Xiao-Yan Zhou, Jia-Yi Li, Hong-Fei Cheng, Ji-Wei Ma

Journal of Electrochemistry

Owing to the merits of high energy density, as well as clean and sustainable properties, hydrogen has been deemed to be a prominent alternative energy to traditional fossil fuels. Electrocatalytic hydrogen evolution reaction (HER) has been considered to be mostly promising for achieving green hydrogen production, and has been widely studied in acidic and alkaline solutions. In particular, HER in alkaline media has high potential to achieve large-scale hydrogen production because of the increased durability of electrode materials. However, for the currently most prominent catalyst Pt, its HER kinetics in an alkaline solution is generally 2–3 orders lower than that …


Stability Of A Solid Oxide Cell Stack Under Direct Internal-Reforming Of Hydrogen-Blended Methane, Ya-Fei Tang, An-Qi Wu, Bei-Bei Han, Hua Liu, Shan-Jun Bao, Wang-Lin Lin, Ming Chen, Wan-Bing Guan, Subhash C. Singhal 2024 Key Laboratory of Advanced Fuel Cells and Electrolyzers cell Technology of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, Zhejiang, China

Stability Of A Solid Oxide Cell Stack Under Direct Internal-Reforming Of Hydrogen-Blended Methane, Ya-Fei Tang, An-Qi Wu, Bei-Bei Han, Hua Liu, Shan-Jun Bao, Wang-Lin Lin, Ming Chen, Wan-Bing Guan, Subhash C. Singhal

Journal of Electrochemistry

In this work, the long-term stability and degradation mechanism of a direct internal-reforming solid oxide fuel cell stack (IR-SOFC stack) using hydrogen-blended methane steam reforming were investigated. An overall degradation rate of 2.3%·kh–1 was found after the stack was operated for 3000 hours, indicating a good long-term stability. However, the voltages of the two cells in the stack were increased at the rates of 3.38 mV·kh–1 and 3.78 mV·kh–1, while the area specific resistances of the three metal interconnects in the stack were increased to 0.276 Ω·cm2, 0.254 Ω·cm2 and 0.249 Ω·cm2 …


Monodispersed Cu-Tcpp/Cu2O Hybrid Microspheres: A Superior Cascade Electrocatalyst Toward Co2 Reduction To C2 Products, Zi-Xuan Wan, Aidar Kuchkaev, Dmitry Yakhvarov, Xiong-Wu Kang 2024 New Energy Research Institute, School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, Guangdong, China

Monodispersed Cu-Tcpp/Cu2O Hybrid Microspheres: A Superior Cascade Electrocatalyst Toward Co2 Reduction To C2 Products, Zi-Xuan Wan, Aidar Kuchkaev, Dmitry Yakhvarov, Xiong-Wu Kang

Journal of Electrochemistry

The electrochemical conversion of carbon dioxide (CO2) into valuable chemicals is a feasible way to mitigate the negative impacts of overmuch CO2 emissions. Porphyrin-based metal organic frameworks (MOFs) are expected to be used for selective and efficient electrochemical CO2 reduction (ECR) with porous structure and ordered active sites. Herein, we report the synthesis of a monodispersed and spherical organic/inorganic hybrid Cu-TCPP@Cu2O electrocatalyst composed of Cu-TCPP (TCPP=tetrakis (4-carboxyphenyl) porphyrin) and Cu2O, where TCPP plays significant roles in regulating the morphology. In-situ formed Cu during ECR process in combination with Cu-TCPP (Cu-TCPP@Cu) can suppress …


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 2024 Morehead State University

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 …


Group 14 Metallocene Catalysts For Carbonyl Hydroboration And Cyanosilylation, Haley J. Robertson, Mallory N. Fujiwara, Allegra L. Liberman-Martin 2024 Chapman University

Group 14 Metallocene Catalysts For Carbonyl Hydroboration And Cyanosilylation, Haley J. Robertson, Mallory N. Fujiwara, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of six Group 14 metallocene compounds (M = Ge, Sn, Pb) were studied as catalysts for carbonyl hydroboration and cyanosilylation reactions at room temperature. Both bis(pentamethylcyclopentadienyl) and tetramethyldisiloxa[3]metallocenophane compounds were compared. The tin and lead metallocenophanes exhibited the highest reactivity in hydroboration and cyanosilylation reactions. Hammett analysis of aldehyde hydroboration provided a ρ value of 0.73, suggesting a buildup of negative charge during the turnover-limiting step, consistent with the transition state for hydride transfer to the carbonyl center. NMR studies of Lewis acidity indicate that the Ge, Sn, and Pb tetramethyldisiloxa[3]metallocenophane compounds are weak Lewis acids.


Probing Charge Transport Mechanisms In 2d Semiconductive Metal Organic Framewoks, James Nyakuchena 2024 Marquette University

Probing Charge Transport Mechanisms In 2d Semiconductive Metal Organic Framewoks, James Nyakuchena

Dissertations (1934 -)

Metal organic frameworks (MOFs) are a class of highly porous crystalline materials constructed from metal nodes connected by multitopic organic ligands. Due to their unique properties such as large surface area, tunable pore structure, and structural diversity, they have demonstrated potential in a wide array of applications including gas storage and separation, sensing, catalysis, and drug delivery. However, there are only a handful of MOFs reported that have electrical conductivity, which prevents their applications in photoelectronic and photocatalytic applications. This is because hard metals and redox inactive ligands with terminal hard linking bases such as carboxylates are often used in …


Assessing The Performance Of Newly Developed Silica Nanoparticles Against Lead And Phosphate Ion Removal From Contaminated Solutions Using Adsorption Isotherm, Hasan Shamseddine, Nour Abi Aad, Rami Oweini, Ghassan Younes 2023 Faculty of Science, Beirut Arab University, Debbieh, Lebanon

Assessing The Performance Of Newly Developed Silica Nanoparticles Against Lead And Phosphate Ion Removal From Contaminated Solutions Using Adsorption Isotherm, Hasan Shamseddine, Nour Abi Aad, Rami Oweini, Ghassan Younes

BAU Journal - Science and Technology

This study investigates the removal of Lead and Phosphate ion from aqueous solution using new silica nanoparticles doped with europium (H1) which was characterized using Scanning Electron Microscopy (SEM), Dynamic Light Scattering (DLS), Fourier-transform Infrared Spectroscopy (FTIR). The aim of this research is to develop a novel adsorbent material that can efficiently remove contaminated ions from wastewater or aqueous solutions. The adsorption of lead and phosphate ion onto the silica nanoparticles is investigated, and the efficiency of this removal is evaluated. Equilibrium data analysis reveals linear fitting with Langmuir isotherm with 24.76 mg/g Lead ion uptake, while for phosphate the …


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