Chemistry Commons^™

Applied Molecular Dynamics: From Targeting Viral Helicases, To Understanding The Interactions Of Cucurbituril Complexes In Ionic Solutions, Bryan Raubenolt

LSU New Orleans Theses and Dissertations

Molecular Dynamics simulations are a highly useful tool in helping understand the fundamental interactions present in a variety of chemical systems. The work discussed here illustrates it’s use in determining the conformational dynamics of the Zika and SARS-Cov-2 helicase in a physiological environment, largely in an effort to discover inhibitors capable of rendering the protein inert. Additionally, we show how it can be used to understand paradoxical trends in the anion-induced precipitation of Cucurbituril cavitands.

Viral helicases are motor proteins tasked with unwinding the viral dsRNA, a crucial step in preparing the strand to be translatable by host cells. By …

Understanding The Role Of Atom Trapping In The Evolution Of Hydrocarbon Transformation Catalyst Morphology, Griffin Alexander Canning

Chemistry and Chemical Biology ETDs

Converting alkanes to other, more chemically and economically valuable molecules requires catalysts that can survive elevated temperatures and highly reducing environments. These environments can cause many metal-nanoparticle based catalysts to sinter rapidly, causing a loss of activity. They must also tolerate the coke formation, as well, since coke can restrict access to active sites by gas phase molecules, thus lowering catalytic activity. While there are routes to improve both the sinter and coke resistance of catalysts, an alternative strategy is to develop a protocol for regenerating the activity of the catalyst in question when coke formation or sintering becomes problematic. …

Predicting The Hydration Free Energy Of Small Alkanes And Alcohols From Custom, Electronic Structure-Based Force Fields, T. Ryan Rogers

Graduate Theses and Dissertations

Mathematical theories reveal the fundamental physics involved in experimentalphenomena. Computer models of such theories are routinely used to corroborate or explain experiments and predict properties of chemical systems. Therefore, an important effort in computational chemistry is the development of more accurate and efficient chemical models. Current-generation models are only beginning to approach experimental-quality predictions of hydration free energies (HFEs).Using computations of quantum mechanical (QM) forces and classical simulations based on these forces, I investigate models to predict several properties of solutes and solutions. This dissertation is a collection of projects exemplifying methods used to gain insight into chemical systems.

Simulations …

Developments Of Machine Learning Potentials For Atomistic Simulations, Howard Yanxon

UNLV Theses, Dissertations, Professional Papers, and Capstones

Atomistic modeling methods such as molecular dynamics play important roles in investigating time-dependent physical and chemical processes at the microscopic level. In the simulations, energy and forces, sometimes including stress tensor, need to be recalculated iteratively as the atomic configuration evolves. Consequently, atomistic simulations crucially depend on the accuracy of the underlying potential energy surface. Modern quantum mechanical modeling based on density functional theory can consistently generate an accurate description of the potential energy surface. In most cases, molecular dynamics simulations based on density functional theory suffer from highly demanding computational costs. On the other hand, atomistic simulations based on …

Unspecified Verticality Of Franck-Condon Transitions, Absorption And Emission Spectra Of Cyanine Dyes, And A Classically Inspired Approximation, Joseph D. Alia, Joseph A. Flack

Chemistry Publications

The computed vertical energy, Ev,a/f, from the equilibrium geometry of the initial electronic state is frequently considered as representative of the experimental excitation/emission energy, Eabs/fl = hc/λmax. Application of the quantum mechanical version of the Franck–Condon principle does not involve precise specification of nuclear positions before, after, or during an electronic transition. Moreover, the duration of an electronic transition is not experimentally accessible in spectra with resolved vibrational structure. It is shown that computed vibronic spectra based on TDDFT methods and application of quantum mechanical FC analysis predict Eabs = hc/λmax …

Structure And Dynamics Of Phospholipid Vesicles And The Dependence On Nanoscale Interactions With Molecules Of Varying Complexity, Lakshapathy Widanelage Judith Upeka De Mel

LSU Doctoral Dissertations

In this dissertation, molecular interactions and changes imposed by nano-scale structures on phospholipid vesicles were investigated. 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) large unilamellar vesicles (LUVs) were used as the model system. Understanding changes of the bilayer structure, interfacial properties, lipid dynamics, and self-assembly, allows bridging relationships between biological cell membrane structure and dynamics to cellular functionalities. For example, membrane curvature changes are linked to membrane protein functions, although the exact mechanisms of control are not yet understood. Moreover, the knowledge gained from vesicle models allows exploring novel strategies for drug delivery applications. To achieve this, DOPC LUVs were synthesized and characterized by a …

Computational Investigations Of Battery Electrolytes, Ke Li

LSU Doctoral Dissertations

In this dissertation, the structure and dynamics of battery electrolytes were investigated using atomistic molecular dynamics (MD) simulations. Battery electrolytes play a key role in transporting ions between the cathode and anode. The chemical stability and ionic conductivity of electrolytes influence battery performance. In order to design better electrolytes, one needs an understanding of the relationship between electrolyte structure, dynamics, and bulk properties. To bridge the gap between the macroscopic phenomenon and the hidden molecular physics, in the first project we focused on probing an ether-based electrolyte, chosen for its relevance in sodium-based batteries. Through studying the impact of concentration …

Radial Basis Densities And The Density Functional-Based Atom-In-Molecule: Designing Charge-Transfer Potentials, Godwin Amo-Kwao

Nanoscience and Microsystems ETDs

Classical potentials that are capable of describing charge transfer and charge polarization in complex systems are of central importance for classical atomistic simulation of biomolecules and materials. Current potentials—regardless of the system—do not generalize well, and, with the exception of highly-specialized empirical potentials tuned for specific systems, cannot describe chemical bond formation and breaking. The charge-transfer embedded atom method (CT-EAM), a formal, DFT-based extension to the original EAM for metals, has been developed to address these issues by modeling charge distortion and charge transfer in interacting systems using pseudoatom building blocks instead of the electron densities of isolated atoms. CT-EAM …

New Metal Based Saturable Absorber For Ultrashort Pulse Generation, Muhammad Taufiq Ahmad

Student Works (2020-2029)

Cost-efficient, robust and flexible laser systems are vital for a wide-range of applications ranging from high-precision material processing to biomedicine. This thesis aims to explore pure silver and gold based saturable absorbers (SAs) as Q-switcher and mode-locker in various fibre laser cavities. The generations of Q-switched pulses in 1-,1.55-, and 2-micron regions have been successfully demonstrated using a pure gold, which was deposited using electron beam deposition onto a PVA thin-film as SA. For instance, a stable Q-switched thulium-doped fibre laser (TDFL) operating at 1949 nm was successfully demonstrated with the gold SA. The proposed laser generates Q switched pulses …

Adsorption And Reconfiguration Of Amphiphiles At Silica-Water Interfaces: Role Of Electrostatic Interactions, Van Der Waals Forces And Hydrogen Bonds, Yao Wu

LSU Doctoral Dissertations

The ability to explore and predict metastable structures of hybrid self-assemblies is of central importance for the next generation of advanced materials with novel properties. As compared to their thermodynamically stable forms, the kinetically stabilized materials show improved functionality potentially over their stable counterparts. The self-assembly processes usually originate from weak intermolecular interactions, involving a dynamic competition between attractive and repulsive interactions. These weak forces, including van der Waals (vdW), electrostatic interaction and the hydrogen bonding (H-bonding), can be tuned by external stimuli, e.g., confinement, temperature and ionization, and consequently driving hybrid materials into different configurations. It is challenging to …

High Level Ab Initio Study Of The Energetic And Spectroscopic Properties Of [Al,S,O]X (X=0,+1) And Its Potential For Detection In Space, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Highly reliable molecular properties have been computed for the [Al, S, O]^x (x = 0, +1) molecular system. Spectroscopic parameters are predicted from analysis of each isomer’s 3D potential energy surface calculated using the explicitly correlated multireference configuration interaction method, including the Davidson correction (MRCI-F12+Q). These parameters provide an accurate prediction of spectroscopic data that can be used in laboratory and observational studies of these molecules. Linear-SAlO is expected to have a large permanent dipole moment suitable for detection in the circumstellar envelopes of large, evolved, oxygen-rich stars such as VY Canis Majoris, IK Tauri, and R Doradus. …

Cycling Performance And Solid-Electrolyte-Interphase Synergic Formation Of Silicon Nanoparticles In The Concentrated Electrolyte With Additives, Zeng-Hua Chang, Fu-Juan Han, Xi-Xin Yang, Jian-Tao Wang, Shi-Gang Lu

Journal of Electrochemistry

In this paper, the effects of additives on the cycling performance of silicon nanoparticles in LiFSI-(PC)₃ based concentrated electrolytes were systematically studied. The structures of silicon nanoparticle electrodes and the evolution of solid-electrolyte-interphase were characterized by scanning electron microscopy (SEM), attenuated total reflection Flourier transformed infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS). The results indicated that the additives can efficiently improve the cycling performance of silicon nanoparticle electrodes. In LiFSI-(PC)₃ concentrated electrolyte, the capacity became 574.8 mAh·g^-1 after 300 cycles with the initial capacity of 3296.1 mAh·g^-1. In contrast, the 3% LiDFOB, 3% FEC …

Facile Synthesis Of Nitrogen-Doped Graphene-Like Active Carbon Materials For High Performance Lithium-Sulfur Battery, Quan-Hua Meng, Wen-Wen Deng, Chang-Ming Li

Journal of Electrochemistry

Lithium-sulphur (Li-S) battery is regarded as a promising energy storage device because of its high theoretical capacity. However, the low S utilization and short cycling life limit the commercial applications. In this work, nitrogen-doped graphene-like carbon (NGC) materials were synthesized by simply pyrolyzing and carbonizing the mixture of melamine (C₃H₆N₆) and L-cysteine (C₃H₇NO₂S). The graphene-like structure in NGC effectively buffered the volume change of S during the discharge/charge process and improved the cycling stability. Meanwhile, nitrogen-containing functional groups in NGC facilitated the transportation of ions and suppressed the …

Highly Efficient Co2 Utilization Via Molten Salt Co2 Capture And Electrochemical Transformation Technology, Bo-Wen Deng, Hua-Yi Yin, Di-Hua Wang

Journal of Electrochemistry

The molten electrolytes exhibit high CO₂ absorption capacities, wide electrochemical windows and excellent reaction kinetics, which are promising electrolyte candidates for efficient capture and electrochemical conversion of high-flux CO₂ driven by renewable and clean electricity sources. This short review introduces the recent advancements of CO₂ electroreduction achieved by the authors using molten salt CO₂ capture and electrochemical transformation (MSCC-ET) technology, involving CO₂ absorption kinetics, cathodic kinetics, controllable synthesis of carbon products with unique nanostructures, development of inert oxygen evolution anodes and CO₂ conversion efficiency as well as energy efficiency. The challenges and prospects are …

Electrochemical Engineering Of Carbon Nanodots, Lei Bao, Dai-Wen Pang

Journal of Electrochemistry

Aqueous batteries have been considered to be a competitive candidate for large-scale energy storage. However, most of aqueous batteries adopt inorganic electrode materials with metallic elements, which are based on the reversible insertion of metal ions, making their application being highly hindered by limited cycle life, environmental issue, high cost and low reserves. On the other hand, organic electrode materials offer the advantages of abundant reserves, tunable structures, renewability and environmental benignity. Furthermore, the wide internal space enables these organics to flexibly store various charge carriers. Organics have been investigated as the alternative to inorganic electrode materials. Herein, we review …

Research Progress Of Sulfur Cathode Catalytic Conversions For Lithium-Sulfur Batteries, Qin-Jun Shao, Jian Chen

Journal of Electrochemistry

The electrochemical reduction of sulfur (S) takes place through multistep reactions when S is used as a cathode material. The complete discharge of S to form final product lithium sulfide (Li₂S) is a two-electron reaction. The formation of low-order lithium polysulfides (LiPS) needs to overcome certain energy barriers. And the reduction of Li₂S₂ to Li₂S is the rate-limited step. The reaction kinetic of sulfur cathode is the critical key to determine the electrochemical performance of Li-S batteries, such as specific energy, specific power and low temperature performance, etc. Accelerating the rate-limited step kinetics …

Liquid Metal Electrodes For Electrochemical Energy Storage Technologies, Hao-Miao Li, Hao Zhou, Kang-Li Wang, Kai Jiang

Journal of Electrochemistry

Electrochemical energy storage technologies (ESTs) with low cost, long lifespan and high safety are of great importance for efficient integration of renewable energy into the grid. Liquid metal electrodes (LMEs) possessing the merits of high electronic conductivity, easy manufacture and amorphous structure is of great application value in the field of energy storage batteries. During charge-discharge processing, the LMEs could avoid the issues of structural deformation and dendrite growth in solid metal electrodes, which could effectively extend the cycle life of the LME based batteries. Moreover, LME based batteries are easy to be scaled up and less expensive, which are …

A Model For The Anodic Carbonization Of Alkaline Polymer Electrolyte Fuel Cells, Qi-Hao Li, Ying-Ming Wang, Hua-Long Ma, Li Xiao, Gong-Wei Wang, Jun-Tao Lu, Lin Zhuang

Journal of Electrochemistry

The alkaline polymer electrolyte fuel cell (APEFC) has made appreciable progress in recent years but is still suffering performance loss during discharge with air as the oxidant. Several theories have been suggested to interpret the loss. However, efforts are still needed to reach a clear quantitative understanding. Based on the major experimental findings in combination with thermodynamics and kinetics of the reactions involved in the anode, this paper presents a model featuring layered carbonization in the anode and relevant grouped equations. The simulation results generated from the latter are compared with experiments, and possible principles to suppress the performance loss …

Porous-Electrode Theory Of Lithium Ion Battery: Old Paradigm And New Challenge, Xiao-Xiao Wang, Zi-Rui Zhou, Qiang Shan, Zeng-Ming Zhang, Jun Huang, Yu-Wen Liu, Sheng-Li Chen

Journal of Electrochemistry

A critical review on the porous electrode theory developed by Newman and his colleagues is presented. We propose several ideas for further development of this theory by analyzing its limitations. The classical Newman theory does not consider ion steric effect in describing ion transport in electrolyte solutions, which can be amended by a newly developed ion-vacancy coupled charge transfer model for ion transport in concentrated solutions. Ion transport in solid particles of active materials is essentially an ion-electron coupled transport process, and its rationality is verified by comparing the calculated and experimental diffusion coefficients of Li ⁺ ion in intercalation …

Research Progress Of High-Safety Phosphorus-Based Electrolyte, Zi-Qi Zeng, Xin-Ping Ai, Han-Xi Yang, Yu-Liang Cao

Journal of Electrochemistry

Lithium-ion batteries (LIBs) have emerged as the most widely used energy storage devices owing to their high energy density and excellent cycling stability. However, safety issues have become a critical obstacle for the large-scale applications of LIBs in the energy storage systems and electric vehicles (EVs). Currently, LIBs use a low flash- and boiling-point organic carbonate as the electrolyte, which is extremely likely to cause firing or explosion. Although some flame-retardant additives can inhibit the combustion of electrolyte to a certain extent, it brings little effect in practical application. Therefore, the development of nonflammable electrolytes is an essential solution to …

Porous Electrodes In Electrochemical Energy Storage Systems, Wei-Xiao Ji, Gong-Wei Wang, Qiang Wang, Li-Jun Bai, De-Yang Qu

Journal of Electrochemistry

Professor C.S. Cha was among the pioneers who have introduced modern electrochemistry to China. Under his leadership, the electrochemical research group in Wuhan University became one of the global powerhouses in fundamental and applied electrochemical researches. During the past many decades, Professor Cha and his colleagues in the university have educated and trained many students who have become part of the backbone of electrochemistry worldwide. In this review, we demonstrate the solid foundation laid by Professor Cha and his colleagues in Wuhan University, and the advancements made in the area of porous electrodes by the authors. All the authors in …

Progress And Prospects On Multifunctional Coating Separators For Lithium-Sulfur Battery, Zhuang-Zhuang Wei, Nan-Xiang Zhang, Feng Wu, Ren-Jie Chen

Journal of Electrochemistry

The development of advanced energy storage systems is crucial to meet the growing demand for electric vehicles, portable devices and renewable energy storage. Lithium-sulfur (Li-S) batteries, with their advantages of high specific energy, low cost of raw materials and environmental friendliness, are hotspots in the research field of new high performance batteries. However, there are still many problems which hinder the practical applications of lithium-sulfur batteries, such as the shuttle effect of soluble polysulfide intermediates, the growth of lithium dendrites, and the thermal stability and safety of lithium-sulfur batteries during use. The design of multifunctional coating separator is one of …

Licoo2 As Sulfur Host To Enhance Cathode Volumetric Capacity For Lithium-Sulfur Battery, Lu Wang, Xue-Ping Gao

Journal of Electrochemistry

Lithium-sulfur battery is one of the most promising secondary battery systems due to its super high theoretical gravimetric and volumetric energy densities (2600 Wh·kg^-1 and 2800 Wh·L^-1, respectively). However, the practical volumetric capacity of sulfur cathode is still unsatisfied due to the overuse of low-density host materials, such as carbon nanomaterials. Herein, commercial LiCoO₂ with the high tap density of 2.94 g·cm^-3 was used as the host material to build high density sulfur-based composite and compact electrode for increasing the volumetric capacity. Obviously, the tap density of the as-prepared S/LiCoO₂ composite was 1.90 g·cm …

Research Progress Of Key Components In Lithium-Sulfur Batteries, Jia-Jia Chen, Quan-Feng Dong

Journal of Electrochemistry

Due to the much higher theoretical specific capacity and energy density than the ones of traditional lithium ion battery, Li-S batteries have long been at the pinnacle in the realms of high-energy Li-metal batteries. However, the complicated electrochemical reactions on the sulfur cathode and Li anode, induced by the thermodynamic and kinetic behaviors of lithium polysulfides, are the intrinsic bottleneck to realize the full potential of Li-S batteries for practical application. In this review, we firstly discuss the roles, and thermodynamic and kinetic behaviors of polysulfides in the charging and discharging processes of Li-S batteries. Then, the functional design and …

Preface To The Memorial Special Issue For Professor Chuansin Cha, Xin-Ping Ai, Han-Xi Yang, Lin Zhuang, Sheng-Li Chen

Journal of Electrochemistry

No abstract provided.

Fundamentals Of Distribution Of Relaxation Times For Electrochemical Impedance Spectroscopy, Jia Wang, Qiu-An Huang, Wei-Heng Li, Juan Wang, Quan-Chao Zhuang, Jiu-Jun Zhang

Journal of Electrochemistry

Electrochemical impedance spectroscopy (EIS) is a powerful electrochemical characterization technology, which has been widely used in the field of electrochemical energy, such as lithium-ion batteries, supercapacitors, fuel cells, etc. Distribution of relaxation time (DRT) is an EIS deconvolution technique which does not depend on the prior knowledge of the targeted research object. Furthermore, DRT can serve to separate and analyze physical and chemical processes which are highly overlapped in their EIS data. In order to encourage the application and popularization of DRT deconvolution technology, several core questions are addressed in this paper: (1) DRT deconvolution principle, implementation steps and important …

Oxidation Of Phenolic Aldehydes By Ozone And Hydroxyl Radicals At The Air-Water Interface, Md Sohel Rana, Marcelo I. Guzman

Chemistry Faculty Publications

Biomass burning releases highly reactive methoxyphenols into the atmosphere, which can undergo heterogeneous oxidation and act as precursors for secondary organic aerosol (SOA) formation. Understanding the reactivity of such methoxyphenols at the air–water interface is a matter of major atmospheric interest. Online electrospray ionization mass spectrometry (OESI-MS) is used here to study the oxidation of two methoxyphenols among three phenolic aldehydes, 4-hydroxybenzaldehyde, vanillin, and syringaldehyde, on the surface of water. The OESI-MS results together with cyclic voltammetry measurements at variable pH are integrated into a mechanism describing the heterogeneous oxidative processing of methoxyphenols by gaseous ozone (O₃) and …

Single‐Molecule 3d Orientation Imaging Reveals Nanoscale Compositional Heterogeneity In Lipid Membranes, Jin Lu, Hesam Mazidi, Tianben Ding, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm⁻²) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single‐molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus “wobble”) of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve …

Surface Modification Of Biomaterials To Reduce Polyethylene Wear In Metal-Polymer Contact / Tan Mean Yee, Tan Mean Yee

Student Works (2020-2029)

This research focus on studying different surface modification (Texturing and DLC coating) on the metal part of TKR (Total knee replacement) in improving UHMWPE (Ultra-high molecular weight polyethylene) wear. TKR was widely being used to relieve knee pain due to osteoarthritis and further restore knee function of patients. Generally, TKR consists of metal femoral component, metal tibial component, and UHMWPE tibial insert. TKR will fail due to various factors over time, however, this study will be focusing on failure cause by loosening. Loosening failure of TKR was mainly caused by wear debris generated during articulation motion, where UHMWPE wear was …

Effect Of Oxidation Level On The Interfacial Water At The Graphene Oxide-Water Interface: From Spectroscopic Signatures To Hydrogen-Bonding Environment, Rolf David, Aashish Tuladhar, Le Zhang, Christopher Arges, Revati Kumar

Faculty Publications

The interfacial region of the graphene oxide (GO)-water system is nonhomogenous due to the presence of two distinct domains: an oxygen-rich surface and a graphene-like region. The experimental vibrational sum-frequency generation (vSFG) spectra are distinctly different for the fully oxidized GO-water interface as compared to the reduced GO-water case. Computational investigations using ab initio molecular dynamics were performed to determine the molecular origins of the different spectroscopic features. The simulations were first validated by comparing the simulated vSFG spectra to those from the experiment, and the contributions to the spectra from different hydrogen bonding environments and interfacial water orientations were …