Computational Chemistry Commons^™

Transient Diode Laser Absorption Spectroscopy For Measuring Collisional Quenching Rates Of Co And Its Potential For Studying H2o, Jordan M. Polvere

Master’s Theses

Motivated by the necessity of non-LTE models that account for species that are not in Local Thermodynamic Equilibrium (LTE) in Titan’s and Earth’s atmospheres, collisional quenching rates of CO and H2O_(g) have been studied. Providing more accurate and precise values of collisional quenching rate coefficients is crucial in the development of more advanced atmospheric models, which are important to fields of science such as meteorology and astronomy. Rates of collisional quenching of CO(v=1,2) by CO and CO(v=2) by N₂ at approximately 301-321 K were measured by transient diode laser absorption spectroscopy. The rate coefficients of CO(v=1)-CO, CO(v=2)-CO, and …

Assessing Fixed-Node Diffusion Monte Carlo For Radical Polymerization Reaction Energetics, Timothy Brian Huber

Graduate Research Theses & Dissertations

The art of quantum chemistry is grounded to the discovery of a time efficient computational method that can capture the essential physics. Historically, the Hartree-Fock method, where an electron moves in the mean field of the other electrons, has provided the orbitals used to construct a single-reference Slater determinant and thus formed the basis for molecular orbital calculations. Kohn-Sham density functionals have become overwhelmingly popular among the chemistry community due to their low computational cost. However, their prediction of thermodynamic properties important in free radical polymerization has shown difficulty due to an artificial delocalization of electron density and spin contamination …

Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust

Graduate Theses/Dissertations

The world today relies on hydrocarbon combustion for many reasons, including its high energy density that provides ease of transportation. However, hydrocarbons sourced from fossil fuels are not expected to last forever. Biodiesel, a renewable alternative, has many attractive benefits but comes with other downsides. Biodiesel can gel in cold environments and may leave residue in an engine. Pyrolysis of biodiesel has shown promise in addressing these common detriments. Inducing pyrolysis on biodiesel feedstock (commonly soybean oil in the USA) would be an attractive option presuming it continues to produce fossil fuel analogs similar to biodiesel pyrolysis. Herein, Langevin molecular …

Intelligent Control Based On Bp Artificial Neural Network For Electrochemical Nitrate Removal, Xin-Wan Zhang, Guang-Yuan Meng, Li-Qiang Fang, Ding-Ming Chang, Tong Li, Jin-Wen Hu, Peng Chen, Yong-Di Liu, Le-Hua Zhang

Journal of Electrochemistry

Achieving effective control of parameters in the process of nitrate wastewater treatment is critical to electrochemical water treatment. The powerful nonlinear mapping ability, self-adaptation and self-learning ability of neural network technology can optimize the electrochemical processing. However, there are few researches in this direction. Hence, based on the test data of the electrochemical reduction of nitrate, an electrochemical prediction model was established by using the BP neural network algorithm. Considering the correlation of various parameters in the electrochemical process, the reaction time, initial nitrate nitrogen concentration, pH and current density were determined as the input layer of the BP neural …

Computational Investigations Of Bond Breaking Processes Using Dft And Td-Dft Approaches., Saurav Parmar

Electronic Theses and Dissertations

The efficient application of DFT and TD-DFT has been harnessed to study bond-breaking processes in some molecules which play a prominent role in enzymatic reactions. The first application includes Radical S-adenosyl methionine (SAM) enzymes which are fundamentally important sources of organic radicals to initiate diverse radical reactions. Recently a bio-organometallic intermediate (Ω) that contains an Fe‒C bond has been characterized and shown to be a common feature of radical SAM enzymes. The strength of Fe‒C bond in Ω has been computed using broken-symmetry density functional theory (BS‒DFT). Additionally, Fe‒C bond dissociation energy (BDE) in Ω has been compared to that …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Charge-Dependence Of Dissolution/Deposition Energy Barrier On Cu(111) Electrode Surface By Multiscale Simulations, Hang Qiao, Yong Zhu, Sheng Sun, Tong-Yi Zhang

Journal of Electrochemistry

Behaviors of electrified interface under different applied potentials/charges play the central role in electroplating process and electrochemical corrosion. The mechanism, however, is unclear yet for a surface atom dissolving/depositing from/on an electrode surface under an applied potential. The energy barrier along the reaction path is the key variable. The present work conductes hybrid first-principle/hybrid calculations to study the direct and indirect dissolution/deposition of a Cu atom on perfect/stepped Cu(111) planar electrodes in an electrolyte under different excess charges. Energy profiles present a linear relationship between the energies of the initial/final state and the activation state of different reaction paths under …

Deciphering The Role Of Molecular Interactions On The Interfacial Structure Of Aqueous And Non-Aqueous Interfaces, Dodangodage Ishara Indunil Senadheera, D I. Senadheera

LSU Doctoral Dissertations

The study focused on "Deciphering the role of molecular interactions on the interfacial structure of aqueous and non-aqueous interfaces" holds immense significance in diverse scientific and industrial domains. Our primary objective is to unravel the intricate web of molecular interactions occurring at the boundaries between aqueous and non-aqueous phases. The research presented here spans a wide scope, encompassing applications in microelectromechanical systems in the semiconductor industry, energy-efficient membranes for electrochemical separations, and renewable energy storage systems. Molecular dynamics simulations were conducted in collaboration with experimental studies, specifically atomic force microscopy, to achieve insights at the molecular level.The first project centered …

Three-Dimensional Two-Phase Cfd Simulation Of Alkaline Electrolyzers, Ling-Yu Gao, Lin Yang, Chen-Hui Wang, Gui-Xuan Shan, Xin-Yi Huo, Meng-Fei Zhang, Wei Li, Jin-Li Zhang

Journal of Electrochemistry

The structural and operation parameters of the electrolyzer play important roles in the efficiency of alkaline water electrolysis. In this article, a three-dimensional numerical model coupled with the electric field and the Euler-Eulerian k-ε turbulence flow field was first established to simulate accurately the performance of alkaline electrolyzers, based on a compact assembly structure of the industrial alkaline water electrolyzers, especially at current densities higher than 5000 A·m^–2. The simulation results are compared with the experimental data to verify the accuracy of the model. Suitable operating conditions for concentration, flow rate and the optimal design method of the …

Quantifying Temperature-, Pressure-, And Nuclear Quantum Effects On Hydrophobic And Hydrophilic Water-Mediated Interactions, Justin T. Engstler

Dissertations, Theses, and Capstone Projects

Water-mediated interactions (WMIs) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure, and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic–hydrophilic) interactions have been mostly overlooked. Here, we study the role of T and P on the WMI between nanoscale (i) hydrophobic–hydrophobic, (ii) hydrophilic–hydrophilic, and (iii) hydrophilic–hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic, and hybrid interactions are all sensitive to …

Advances In One-Electron Self-Interaction-Correction Methods For Accurate And Efficient Self-Interaction-Free Density Functional Calculations, Selim Romero

Open Access Theses & Dissertations

Density functional theory (DFT) is a widely used computational method for studying electronic structures of atoms, molecules, and solids. It provides an exact theory for obtaining ground state energy from the ground state density. However, since the exact exchange-correlation functional remains unknown, approximate exchange-correlation functionals called approximate density approximations (DFAs) are used. The foundation of many DFAs is the local spin density approximation (LSDA). It serves as the starting point for constructing various DFAs. However, DFAs are prone to self-interaction errors (SIE) due to the improper cancellation of the approximate exchange energy and the Coulomb energy. This issue impacts the …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

All Dissertations

The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

The Investigation Of Singlet Fission From The Perspective Of Hierarchy Of Pure States (Hops), Tao (James) Chen

Chemistry Theses and Dissertations

This thesis provides a preliminary investigation of singlet fission from the perspective of Hierarchy of pure states (HOPS), which provides a numerical exact solution for the investigation of a series of open quantum systems. Since the inception of the concept of singlet fission about half a century ago, this photo-physical process has attracted the attention of a multitude of researchers and has been extensively studied theoretically and experimentally. However, these previous methods for the investigation of singlet fission focus more or less on tackling the underlying mechanisms of singlet fission from the perspective of perturbation. So far, the HOPS method …

The Investigation Of Singlet Fission From The Perspective Of Hierarchy Of Pure States (Hops), Tao (James) Chen

Chemistry Theses and Dissertations

This thesis provides a preliminary investigation of singlet fission from the perspective of Hierarchy of pure states (HOPS), which provides a numerical exact solution for the investigation of a series of open quantum systems. Since the inception of the concept of singlet fission about half a century ago, this photo-physical process has attracted the attention of a multitude of researchers and has been extensively studied theoretically and experimentally. However, these previous methods for the investigation of singlet fission focus more or less on tackling the underlying mechanisms of singlet fission from the perspective of perturbation. So far, the HOPS method …

First-Principles Simulations Of Attosecond Transient X-Ray Absorption, Min Chen

LSU Doctoral Dissertations

The first part of this dissertation presents calculations of the extinction spec- tra of gold-silver/silver-gold core-shell nanospheres. The goal of this projectsis to get a deeper understanding of surface plasmonic resonance in metal nanospheres with core-shell geometry. Here, we used the finite-difference time-domain (FDTD) method and total-field/scattered-field (TFSF) framework to compute the extinction spectra of nanoparticles to determine the geometry of gold-silver/silver-gold core-shell nanoparticles. This supported experimental work on monitoring the growth dynamics of colloidal gold- silver/silver-gold core-shell nanoparticles using in situ second harmonic generation (SHG) and extinction spectroscopy.

The second and main project involved simulating attosecond transient spectra for …

The Decomposition Of Normal Vibrational Modes In Different Chemistry Problems, Mateus Macedo Quintano

Chemistry Theses and Dissertations

The least action principle yields the Euler-Lagrange equations, which explain molecular vibrations in minimizing action. Subsequently, the Lagrangian gives rise to the equations of motion using the Euler-Lagrange equations. We can then solve the characteristic value problem to obtain normal vibrational modes. Ultimately, the vibrational spectrum of a molecule can be extracted from the characteristic values. Normal coordinates are linear combinations of internal or Cartesian coordinates. However, the delocalization of normal vibrational modes across the molecule restricts the direct use of normal mode frequencies and force constants for measuring bond strength. From the force constant matrix and the normal mode …

Modeling Exciton Migration In Two-Dimensional Space, Christian D. Etnyre

DePaul Discoveries

Computational analysis through density matrix quantum mechanics was performed to model exciton migration in two-dimensional space for a zinc-substituted tetraazaphthalocyanine. The model produced resembles a two-dimensional sheet of molecules. Energy transport mechanisms, controlled by point dipole couplings, were evaluated while altering the size of the crystal lattice. It was determined that energy transport was much more significant with a decreasing size of the crystal lattice. Likewise, the result of increasing the size of the crystal lattice had the effect of dampening the rate of energy transport. It was of interest to determine, with varying crystal lattice dimensions, the time that …

N–((2–Acetylphenyl)Carbamothioyl)Benzamide: Synthesis, Crystal Structure Analysis, And Theoretical Studies, Akin Oztaslar, Hakan Arslan

Karbala International Journal of Modern Science

N–((2–Acetylphenyl)carbamothioyl)benzamide has been synthesized and characterized. The molecular conformation of the investigated compound is stabilized by C16–H16B⋅⋅⋅O2ⁱ (i: 1+x, y, z) intermolecular and C14–H14⋅⋅⋅S1, N2–H2⋅⋅⋅O2, and N2–H2⋅⋅⋅O1 intramolecular H–bonds. All DFT calculations have been implemented at the B3LYP level with the 6–311G(d,p) basis set. The optimized molecular structure parameters have been compared with the experimental one in the solid phase. The energy gap, global chemical reactivity descriptor parameters, MEP, Fukui functions, DoS, NLO, and NBO analysis were also computed and investigated. The intermolecular interactions and their energies are evaluated using Hirshfeld surface and energy framework analyses. To determine …

Isolating The Electronic Effects Of Systematic Twist In Highly Substituted Aromatic Hydrocarbons Using Density Functional Theory, Grace Tully, Emily A. Jarvis

Honors Thesis

Density functional theory (DFT) was employed to investigate dodecaphenyltetracene as well as similar molecules containing differing backbone lengths and electron withdrawing groups with interest in manipulating the twist to lower the LUMO level for increased electron mobility. Optimization and frequency time-independent calculations followed by time-dependent (TD-DFT) energy calculations were performed at the B3LYP/G-311G level of theory to analyze electronic trends as a result of increased backbone length and consequently distorted end-to-end molecular twist. These calculations demonstrate a linear relationship with negative slope between the estimated HOMO-LUMO, fundamental, and optical gaps as a function of the number of fused rings along …

Probing The Effect Of Nitrogen And Boron Doping On Structures, Properties, And Stability Of C20 Clusters, Ramsay Revennaugh, Martina Kaledin

Symposium of Student Scholars

Fullerenes are carbon molecules arranged in a closed hollow shell to form spherical-like structures. These clusters exist in various sizes, C_n, with the smallest being C₂₀. C₂₀, often when doped with other elements, has shown promise in creating new materials as a catalyst and as energy storage material. Here, we look at the existence of C₂₀ doped with nitrogen or boron atoms using density functional theory (DFT). C₂₀ is doped with one to three boron or nitrogen atoms, respectively, including the five different C₁₈N₂ / C₁₈B_{2 …}

Ab Initio Calculations Of Vibrational Spectra Of Model Peptides, Katheryn Foust, Martina Kaledin

Symposium of Student Scholars

The function of biological molecules is closely related to their spatial structure and conformational dynamics. Therefore, understanding the structure and functions of small peptides contributes to gaining insight into the behavior of more complex systems. The peptide bond (-CO-NH-) is among the very important binding patterns in biochemistry. It links amino acids together, specifies rigidity to the protein backbone, and includes the two essential docking sites for hydrogen-bond-mediated protein folding and protein aggregation, namely, the C=O acceptor and the N-H donor parts. Therefore, the C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of …

A Comparative Study Of Specific Enthalpy Of Aromatic Hydrocarbons With Simple Carbohydrates, Kohl D. Kervin, Subha Pratihar

ATU Scholars Symposium

Calorimetry is an aspect of chemistry primarily focused on determining the enthalpy of reactions (∆Hrxn). In the bomb calorimetry technique, the heat of combustion of chemical compounds can be measured experimentally. From this data and the application of Hess’s Law, ∆the Hrxn of several chemical reactions can be determined. The technique of bomb calorimetry can be applied to food, fuels, pharmaceuticals, and many other fields. The objective of the present project is to determine the specific enthalpy of various simple carbohydrates (naturally occurring sugars) through bomb calorimetry and compare it with that of aromatic hydrocarbons.

By performing benzoic acid standardization …

Additivity Of Diene Substituent Gibbs Free Energy Contributions For Diels–Alder Reactions Between Me2c=Cme2 And Substituted Cyclopentadienes, Thomas M. Gilbert, Austin S. Flemming, Brendan C. Dutmer

Faculty Articles, Papers, and Other Scholarship

Systematic computational studies of pericyclic Diels–Alder reactions between (H3C)2C═C(CH3)2, 1, and all permutations of substituted cyclopentadienes c-C5R1R2R3R4R5aR5b (R = H, CH3, CF3, F) allowed isolation of substitutional effects on Gibbs free energy barrier heights and reaction Gibbs free energies. “Average Substitution Gibbs Free Energy Correction” ΔGASC#‡/ΔGASC# values for each substituent in each position appeared to be additive. Substituent effects on barriers showed interesting contrasts. Methyl substitution at positions 5a and 5b increased barriers significantly, while substitution at all other positions had essentially no impact. In contrast, fluoro substitution at positions 5a and 5b lowered barriers more than substitution at other …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Minimal Auxiliary Basis Set Approach For The Electronic Excitation Spectra Of Organic Molecules, Zehao Zhou, Shane M. Parker

Faculty Scholarship

We report a minimal auxiliary basis model for time-dependent density functional theory (TDDFT) with hybrid density functionals that can accurately reproduce excitation energies and absorption spectra from TDDFT while reducing cost by about \change{two} orders of magnitude. Our method, dubbed TDDFT-ris, employs the resolution-of-the-identity technique with just one $s$-type auxiliary basis function per atom for the linear response operator, where the Gaussian exponents are parametrized across the periodic table using %using tabulated atomic radii with a single global scaling factor. By tuning on a small test set, we determine a single functional-independent scale factor that balances errors in excitation energies …

Investigation Of Ch4 Adsorption And Activation On Modified Metalloporphyrin Graphene Sheets, Brianna Haase

Masters Theses

Finding a good catalyst for C-H bond breaking is important due to the rise of natural gas and crude oil emissions. From 2000-2006, CH4 emission concentrations stabilized, but in 2007, it sharply started increasing again. For example, atmospheric CH₄ levels were 1886.37 ppb in July 2021 but this rose to 1904.52 ppb in just one year. Precious metal catalysts, such as Ir systems, have been used for C-H bond breaking, but are not sustainability ideal as they are costly to produce and have a significant carbon footprint. Because of this, less expensive 3d metal catalysts have risen in investigative …

Using Superatomic Clusters And Charge Transfer Ligands To Control Electronic Characteristics Of Phosphorene Nanoribbons And Phosphorene Monolayer, Ryan Lambert

Theses and Dissertations

Phosphorene is a two-dimensional electron poor p-type semiconductor with high carrier mobility and great promise for applications in electronics and optoelectronics. As the main theme in this dissertation, the following work represents different investigations of various electronic properties associated with phosphorene. Most notable are the findings on charge transfer doping with metal-chalcogenide superatoms which displays novel control of the two most important properties of a semiconductor – the band gap energy and the nature of carriers. By tuning the width of the gap and p-/n-type character of conduction, we gain control over a material’s capacity to play a certain role …

Computational Investigation Of The Ionization Potential Of Lead Sulfide Quantum Dots, Jessica Beyer

Scripps Senior Theses

The purpose of this work was to determine the impact of quantum dot size on ionization potential and to determine how the presence of carbonyl-based ligands affect the ionization potential of lead sulfide quantum dot systems. Ionization potential (IP) is defined as the energy required to remove an electron from an atom, molecule, or material. IP helps scientists determine how reactive the material of interest is, which is crucial information when manufacturing nanomaterials. Accurate quantum chemical calculations of ionization potential are challenging due to the computational cost associated with the numerical solution of the Dyson equation. In this work, the …

Developing Novel Femtosecond Time-Resolved Mass Spectrometry Techniques For Analysis Of Energetic Materials, Shane L. Mcpherson

Theses and Dissertations

Energetic materials and the unimolecular dissociation dynamics attributed to their initiation and subsequent bimolecular detonation have been a subject of interest for defense agencies such as the Department of Defense (DoD) for decades. The timescale in which these initial dynamics exist ranges from several picoseconds to dozens of femtoseconds, necessitating equally fast time-resolved experiments to capture and characterize these events. Our lab specializes in one such laser-based technique: femtosecond time-resolved mass spectrometry (FTRMS). FTRMS is an essentially nondiscriminatory pump-probe laser technique with nearly infinite modifications via pulse shaping, intensity, and wavelength modulation that can readily examine previously undefined dissociation pathways …

Electronic Structure And Molecular Geometries Of Metal Complexes With Dft And Multireference Method, Rina Bhowmick

Dissertations and Theses

Metal complexes are ubiquitous for their diverse applications including catalysis, sensing, medicine, and environmental applications. For effective use of metal complexes, understanding their electronic structure is essential. In most cases, molecules can be represented as a single electron configuration. However, in some cases, especially transition metal and actinide complexes, multireference electronic structures are observed. This is because the valence d (and f) orbitals in metals are often nearly degenerate, leading to close-lying energy states and the subsequently more frequent presence of multiconfigurational electronic structures. The traditional approach to modeling these systems is to use density functional theory to optimize the …