Chemistry Commons^™

Density Functional Theory Based Electrolyte Design Formulation For Lithium-Sulfur Batteries, Cynthia Ly, Carolyn Sturges, Vijay Murugesan

STAR Program Research Presentations

Lithium-ion (Li-ion) batteries are commonly used in portable electronics such as cellphones and laptops. Most Li-ion batteries operate on intercalation principle with typical theoretical specific energy of 400-600 (Wh/Kg). There is great scientific interest in lithium-sulfur (Li-S) batteries as a possible successor of traditional Li-ion batteries because Li-S holds the potential of being a very powerful (1550 Wh/kg theoretical specific energy) yet very cost-efficient battery (due the abundance and inexpensiveness of sulfur). However, one major problem in Li-S battery research is the polysulfide “shuttle phenomenon”, which is the shuttling of polysulfide species due to the dissolution of sulfide from the …

The First Potential Energy Surfaces For The C₆Hˉ-H₂ And C₆Hˉ-He Collisional Systems And Their Corresponding Inelastic Cross Sections, Kyle M. Walker, Fabien Dumouchel, François Lique, Richard Dawes

Chemistry Faculty Research & Creative Works

Molecular anions have recently been detected in the interstellar and circumstellar media. Accurate modeling of their abundance requires calculations of collisional data with the most abundant species that are usually He atoms and H₂ molecules. In this paper, we focus on the collisional excitation of the first observed molecular anion, C₆H^-, by He and H₂. Theoretical calculations of collisional cross sections rely generally on ab initio interaction potential energy surfaces (PESs). Hence, we present here the first PESs for the C₆H^--H₂ and C₆H^--He van …

A New Set Of Potential Energy Surfaces For Hco: Influence Of Renner-Teller Coupling On The Bound And Resonance Vibrational States, Steve Alexandre Ndengué, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

It is commonly understood that the Renner-Teller effect can strongly influence the spectroscopy of molecules through coupling of electronic states. Here we investigate the vibrational bound states and low-lying resonances of the formyl radical treating the Renner-Teller coupled X2A' and Ã2A" states using the MultiConfiguration Time Dependent Hartree (MCTDH) method. The calculations were performed using the improved relaxation method for the bound states and a recently published extension to compute resonances. A new set of accurate global potential energy surfaces were computed at the explicitly correlated multireference configuration interaction (MRCI-F12) level and yielded remarkably close agreement with experiment in this …

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

Alignment For Comprehensive Two-Dimensional Gas Chromatography (Gcxgc) With Global, Low-Order Polynomial Transformations, Davis Rempe, Stephen Reichenbach, Stephen Scott

UCARE: Research Products

As columns age and differ between systems, retention times for GC x GC may vary between runs. In order to properly analyze chromatograms, it is often desirable to align chromatographic features between chromatograms. This alignment can be characterized by a mapping of retention times from one chromatogram to the retention times of another chromatogram. Alignment methods can be classified as global or local, i.e., whether the geometric differences between chromatograms are characterized by a single function for the entire chromatogram or by a combination of many functions for different regions of the chromatogram. Previous work has shown that global, low-degree …

Volume 08, Meghan Enzinna, Casey Dawn Gailey, Raven Collins, Chiara Enriquez, Amelia Mcconnell, Alexander Morton, Emma Beckett, Leah G. Parr, Briana Adhikusuma, Taylor Embrey, Rowan Davis, Danielle Sisson, Bianca Cherry, Melissa Cacho, Chloe Woodward, Catherine Rollins, Carson Reeher, Landon Cooper, Haley Vasquez, Marlisha Stewart, Eric Whitehead, Sabrina Walker, James Bates

Incite: The Journal of Undergraduate Scholarship

Introduction from Interim Dean Dr. Jennifer Apperson

Indigenous Peoples and the Modern Era by Meghan Enzinna

"Who Says": How Selena Gomez and the Scene Attempt to Subvert the Popular Standards of Beauty by Casey Dawn Gailey

Art by Raven Collins

Meltdown on Social Media: Amy's Baking Company Meets Kitchen Nightmares by Nathena Haddrill

Art by Chiara Enriquez

Design by Amelia Mcconnell

Worth More Than a Thousand Words: A Visual Rhetorical Discussion of Virtual Reality by Examining "Clouds Over Sidra" by Alexander Morton

Design by Emma Beckett

The Sonata: An Analysis of Piano Sonata No. 14 in C Minor, K. …

Calculated Vibrational States Of Ozone Up To Dissociation, Steve Alexandre Ndengué, Richard Dawes, Xiaogang Wang, Tucker Carrington Jr., Zhigang Sun, Hua Guo

Chemistry Faculty Research & Creative Works

A new accurate global potential energy surface for the ground electronic state of ozone [R. Dawes et al., J. Chem. Phys. 139, 201103 (2013)] was published fairly recently. The topography near dissociation differs significantly from previous surfaces, without spurious submerged reefs and corresponding van der Waals wells. This has enabled significantly improved descriptions of scattering processes, capturing the negative temperature dependence and large kinetic isotope effects in exchange reaction rates. The exchange reactivity was found to depend on the character of near-threshold resonances and their overlap with reactant and product wavefunctions, which in turn are sensitive to the potential. Here …

Calculating Potential Energy Curves With Fixed-Node Diffusion Monte Carlo: Co And N₂, Andrew D. Powell, Richard Dawes

Chemistry Faculty Research & Creative Works

This study reports on the prospect for the routine use of Quantum Monte Carlo (QMC) for the electronic structure problem, applying fixed-node Diffusion Monte Carlo (DMC) to generate highly accurate Born-Oppenheimer potential energy curves (PECs) for small molecular systems. The singlet ground electronic states of CO and N₂ were used as test cases. The PECs obtained by DMC employing multiconfigurational trial wavefunctions were compared with those obtained by conventional high-accuracy electronic structure methods such as multireference configuration interaction and/or the best available empirical spectroscopic curves. The goal was to test whether a straightforward procedure using available QMC codes could …

Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón

Computer Science Faculty Publications

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop …

Applying Bayesian Machine Learning Methods To Theoretical Surface Science, Shane Carr

McKelvey School of Engineering Graduate Student Theses & Dissertations

Machine learning is a rapidly evolving field in computer science with increasingly many applications to other domains. In this thesis, I present a Bayesian machine learning approach to solving a problem in theoretical surface science: calculating the preferred active site on a catalyst surface for a given adsorbate molecule. I formulate the problem as a low-dimensional objective function. I show how the objective function can be approximated into a certain confidence interval using just one iteration of the self-consistent field (SCF) loop in density functional theory (DFT). I then use Bayesian optimization to perform a global search for the solution. …

Functionalized Nanodiamond Reinforced Biopolymers, Gongyao Zhou, Peter I. Lelkes, Yury Gogotsi, Vadym Mochalin

Chemistry Faculty Research & Creative Works

The present invention includes a composition for implantation in a patient, comprising surface-functionalized nanodiamonds and at least one biodegradable biocompatible polymer. The present invention also includes a surgical fixation device for use in a patient.

Chemometric And Bioinformatic Analyses Of Cellular Biochemistry, Bradley Worley

Department of Chemistry: Dissertations, Theses, and Student Research

The amount of information collected and analyzed in biochemical and bioanalytical research has exploded over the last few decades, due in large part to the increasing availability of analytical instrumentation that yields information-rich spectra. Datasets from Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), infrared (IR) or Raman spectroscopy may easily carry tens to hundreds of thousands of potentially correlated variables observed from only a few samples, making the application of classical statistical methods inappropriate, if not impossible. Drawing useful biochemical conclusions from these unique sources of data requires the use of specialized multivariate data handling techniques.

Unfortunately, proper implementation of …

Distributed Approach For Peptide Identification, Naga V K Abhinav Vedanbhatla

Masters Theses & Specialist Projects

A crucial step in protein identification is peptide identification. The Peptide Spectrum Match (PSM) information set is enormous. Hence, it is a time-consuming procedure to work on a single machine. PSMs are situated by a cross connection, a factual score, or a probability that the match between the trial and speculative is right and original. This procedure takes quite a while to execute. So, there is demand for enhancement of the performance to handle extensive peptide information sets. Development of appropriate distributed frameworks are expected to lessen the processing time.

The designed framework uses a peptide handling algorithm named C-Ranker, …

Vibrational Energy Levels Of The Simplest Criegee Intermediate (Ch₂Oo) From Full-Dimensional Lanczos, Mctdh, And Multimode Calculations, Hua-Gen Yu, Steve Alexandre Ndengué, Jun Li, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

Accurate vibrational energy levels of the simplest Criegee intermediate (CH₂OO) were determined on a recently developed ab initio based nine-dimensional potential energy surface using three quantum mechanical methods. the first is the iterative Lanczos method using a conventional basis expansion with an exact Hamiltonian. the second and more efficient method is the multi-configurational time-dependent Hartree (MCTDH) method in which the potential energy surface is refit to conform to the sums-of-products requirement of MCTDH. Finally, the energy levels were computed with a vibrational self-consistent field/virtual configuration interaction method in MULTIMODE. the low-lying levels obtained from the three methods are …

Towards A Global Model Of Spin-Orbit Coupling In The Halocarbenes, Silver Nyambo, Cyrus Karshenas, Scott A. Reid, Phalgun Lolur, Richard Dawes

Chemistry Faculty Research & Creative Works

We report a global analysis of spin-orbit coupling in the mono-halocarbenes, CH(D)X, where X = Cl, Br, and I. These are model systems for examining carbene singlet-triplet energy gaps and spin-orbit coupling. Over the past decade, rich data sets collected using single vibronic level emission spectroscopy and stimulated emission pumping spectroscopy have yielded much information on the ground vibrational level structure and clearly demonstrated the presence of perturbations involving the low-lying triplet state. To model these interactions globally, we compare two approaches. First, we employ a diabatic treatment of the spin-orbit coupling, where the coupling matrix elements are written in …

Kinetic Isotope Effect Of The ¹⁶O+³⁶O₂ And ¹⁸O+³²O₂ Isotope Exchange Reactions: Dominant Role Of Reactive Resonances Revealed By An Accurate Time-Dependent Quantum Wavepacket Study, Zhigang Sun, Dequan Yu, Wenbo Xie, Jiayi Hou, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

The O + O₂ isotope exchange reactions play an important role in determining the oxygen isotopic composition of a number of trace gases in the atmosphere, and their temperature dependence and kinetic isotope effects (KIEs) provide important constraints on our understanding of the origin and mechanism of these and other unusual oxygen KIEs important in the atmosphere. This work reports a quantum dynamics study of the title reactions on the newly constructed Dawes-Lolur-Li-Jiang-Guo (DLLJG) potential energy surface (PES). The thermal reaction rate coefficients of both the 18O + 32O₂ and 16O + 36O₂ reactions obtained using the …

Simulation In Algorithmic Self-Assembly, Jacob Hendricks

Graduate Theses and Dissertations

Winfree introduced a model of self-assembling systems called the abstract Tile Assembly Model (aTAM) where square tiles with glues on their edges attach spontaneously via matching glues to form complex structures. A generalization of the aTAM called the 2HAM (two-handed aTAM) not only allows for single tiles to bind, but also for "supertile" assemblies consisting of any number of tiles to attach. We consider a variety of models based on either the aTAM or the 2HAM. The underlying commonality of the work presented here is simulation. We introduce the polyTAM, where a tile system consists of a collection of polyomino …

Volume 07, Rachel C. Lombardi, Ben Osterhout, Lindsay Graybill, Rebecca E. Dey, Skyler T. Carpenter, Emma Beckett, Jason Ware, Mollie Andrews, James Bates, Landon Cooper, Tiffani Jeffries, Maria Wheaton, Dallas Price, Laura Kahler, Sarah Charlton, Anna Bultrowicz, Emily Spittle, Erin Godwin, Eamon Brokenbrough

Incite: The Journal of Undergraduate Scholarship

Introduction from Interim Dean Dr. Jennifer Apperson

Spatial Analysis of Potential Risk Factors Associated with Addition of Atlantic Coast Pipeline Through Virginia by Rachel C. Lombardi

"Delicate Matters with No Speaking," "Hope and Nothing," "Mono Duality" by Ben Osterhout

"Connect" Graphic Design Senior Project by Lindsay Graybill

Phenolic Acids in Brassicaceae Plants: Ovipositional Stimulants or Deterrents for Cabbage White Butterfly, Pieris Rapae? by Rebecca E. Dey And Skyler T. Carpenter

"Abecedarian Cards" by Emma Beckett, Jason Ware, And Mollie Andrews

Helvetica: A Type Specimen Book by James Bates, Landon Cooper, Tiffani Jeffries, And Maria Wheaton

“Things Left Behind” by Dallas …

Delay Line As A Chemical Reaction Network, Josh Moles, Peter Banda, Christof Teuscher

Computer Science Faculty Publications and Presentations

Chemistry as an unconventional computing medium presently lacks a systematic approach to gather, store, and sort data over time. To build more complicated systems in chemistries, the ability to look at data in the past would be a valuable tool to perform complex calculations. In this paper we present the first implementation of a chemical delay line providing information storage in a chemistry that can reliably capture information over an extended period of time. The delay line is capable of parallel operations in a single instruction, multiple data (SIMD) fashion.

Using Michaelis-Menten kinetics, we describe the chemical delay line implementation …

State-To-State Reaction Dynamics Of ¹⁸O+³²O₂ Studied By A Time-Dependent Quantum Wavepacket Method, Wenbo Xie, Lan Liu, Zhigang Sun, Hua Guo, Richard Dawes

Chemistry Faculty Research & Creative Works

The title isotope exchange reaction was studied by converged time-dependent wave packet calculations, where an efficient 4th order split operator was applied to propagate the initial wave packet. State-to-state differential and integral cross sections up to the collision energy of 0.35 eV were obtained with ³²O₂ in the hypothetical j₀ = 0 state. It is discovered that the differential cross sections are largely forward biased in the studied collision energy range, due to the fact that there is a considerable part of the reaction occurring with large impact parameter and short lifetime relative to the rotational period …

Boron Nitride Colloidal Solutions, Ultralight Aerogels And Freestanding Membranes Through One-Step Exfoliation And Functionalization, Weiwei Lei, Vadym Mochalin, Dan Liu, Si Qin, Yury G. Gogotsi, Ying Chen

Chemistry Faculty Research & Creative Works

Manufacturing of aerogels and membranes from hexagonal boron nitride (h-BN) is much more difficult than from graphene or graphene oxides because of the poor dispersibility of h-BN in water, which limits its exfoliation and preparation of colloidal solutions. Here, a simple, one-step mechano-chemical process to exfoliate and functionalize h-BN into highly water-dispersible, few-layer h-BN containing amino groups is presented. The colloidal solutions of few-layer h-BN can have unprecedentedly high concentrations, up to 30 mg ml^-1, and are stable for up to several months. They can be used to produce ultralight aerogels with a density of 1.4 mg cm …

Ranking Methods For Global Optimization Of Molecular Structures, John Norman Mcmeen Jr

Electronic Theses and Dissertations

This work presents heuristics for searching large sets of molecular structures for low-energy, stable systems. The goal is to find the globally optimal structures in less time or by consuming less computational resources. The strategies intermittently evaluate and rank structures during molecular dynamics optimizations, culling possible weaker solutions from evaluations earlier, leaving better solutions to receive more simulation time. Although some imprecision was introduced from not allowing all structures to fully optimize before ranking, the strategies identify metrics that can be used to make these searches more efficient when computational resources are limited.

Quantum Crystallography Of Hydronium Cations, Sonjae Sycoria Wallace

Dissertations, Theses, and Capstone Projects

Cationic hydronium clusters of the form [HaOb]^c,(c>0), have been investigated. After investigating over 2000 crystal structures containing hydronium cations found in the Cambridge Structural Database. The hydronium cationic compounds that were most unusual, mischaracterized, or those of apparent aggregates, were investigated further by geometry optimization and in some cases with the Quantum Theory of Atoms in Molecules (QTAIM). The results of our investigations yielded the first reports of stable conformations of cyclic dihydronium cationic clusters. In a second investigation we reported the first theoretically confirmed transition state of a H7O3+conformer captured within a crystal. A third product from our …

Theoretical/Experimental Comparison Of Deep Tunneling Decay Of Quasi-Bound H(D)Oco To H(D) + Co₂, Albert F. Wagner, Richard Dawes, Robert Continetti, Hua Guo

Chemistry Faculty Research & Creative Works

The measured H(D)OCO survival fractions of the photoelectron-photofragment coincidence experiments by the Continetti group are qualitatively reproduced by tunneling calculations to H(D) + CO₂ on several recent ab initio potential energy surfaces for the HOCO system. the tunneling calculations involve effective one-dimensional barriers based on steepest descent paths computed on each potential energy surface. the resulting tunneling probabilities are converted into H(D)OCO survival fractions using a model developed by the Continetti group in which every oscillation of the H(D)-OCO stretch provides an opportunity to tunnel. Four different potential energy surfaces are examined with the best qualitative agreement with experiment …

Communication: Rigorous Quantum Dynamics Of O + O₂ Exchange Reactions On An Ab Initio Potential Energy Surface Substantiate The Negative Temperature Dependence Of Rate Coefficients, Yaqin Li, Zhigang Sun, Bin Jiang, Daiqian Xie, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

The kinetics and dynamics of several O + O₂ isotope exchange reactions have been investigated on a recently determined accurate global O₃ potential energy surface using a time-dependent wave packet method. The agreement between calculated and measured rate coefficients is significantly improved over previous work. More importantly, the experimentally observed negative temperature dependence of the rate coefficients is for the first time rigorously reproduced theoretically. This negative temperature dependence can be attributed to the absence in the new potential energy surface of a submerged "reef" structure, which was present in all previous potential energy surfaces. In addition, contributions …

Volume 06, Kristen Gains, Amanda Willis, Holly Backer, Monika Gutierrez, Cara O'Neal, Sara Nelson, Sasha Silberman, Jessica Beardsley, Jamie Gardner, Edward Peeples, Matthew Sakach, Tess Lione, Emily Wilkins, Kelsey Holt, Jessica Page, Jamie Clift, Charles Vancampen, Gilbert Hall, Jenny Nehrt, Kasey Dye, Amanda Tharp, Jamie Leeuwrik, Ashley Mcgee, Emily Poulin, Michael Kropf, Nick Pastore, Austin Polasky, Morgan Glasco, Laura L. Kahler, Melinda L. Edwards, Brandon C. Smith, Mariah Asbell, Cabell Edmunds, Amelia D. Perry, Alyssa Hayes, Irina Boothe, Perry Bason, James Early

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Caught Between Folklore and the Cold War: The Americanization of Russian Children's Literature by Kristen Gains

Graphic Design by Amanda Willis

Graphic Design by Holly Backer

Prejudices in Swiss German Accents by Monika Gutierrez

Photography by Cara O'Neal

Photography by Sara Nelson

Edmund Tyrone's Long Journey through Night by Sasha Silberman

Photography by Jessica Beardsley

Photography by Jamie Gardner and Edward Peeples

The Republican Razor: The Guillotine as a Symbol of Equality by Jamie Clift

Graphic Design by Matthew Sakach

Genocide: The Lasting Effects of Gender Stratification in Rwanda By Tess Lione and Emily …

Computational Study Of The Rovibrational Spectrum Of Co₂-Cs₂, James Corgan Brown, Xiao-Gang Wang, Tucker Carrington Jr., Garry S. Grubbs, Richard Dawes

Chemistry Faculty Research & Creative Works

A new intermolecular potential energy surface, rovibrational transition frequencies, and line strengths are computed for CO₂-CS₂. the potential is made by fitting energies obtained from explicitly correlated coupled-cluster calculations using an interpolating moving least squares method. the rovibrational Schrödinger equation is solved with a symmetry-adapted Lanczos algorithm and an uncoupled product basis set. All four intermolecular coordinates are included in the calculation. in agreement with previous experiments, the global minimum of the potential energy surface (PES) is cross shaped. the PES also has slipped-parallel minima. Rovibrational wavefunctions are localized in the cross minima and the slipped-parallel …

06. Computer Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

04. Botany, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

09. Environmental Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.