Computational Chemistry Commons^™

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 …

Singlet Oxygen-Mediated Conformational Flexibility, Antioxidant, And Isomerization Studies In Chemistry And Biochemistry, Oliver Turque

Dissertations, Theses, and Capstone Projects

Three chapters are included in this dissertation, each of which describes non-oxidative reactions, with peroxy intermediates formed between singlet oxygen (¹O₂) and substrate. (1) Novel discoveries related to the intermediate formed by ¹O₂ and dimethyl disulfane are explored. (2) A new mechanism is proposed, wherein the dihedral angle CS–SC (θ) determines the pro- or antioxidant activity of an organic disulfide. (3) A review of ¹O₂'s ability to facilitate the geometric isomerization of alkenes and polyenes is presented in Chapter 3.

Chapter 1 investigates the role of singlet oxygen potentially …

Optimizing Mn-Al Permanent Magnet Performance Through Control Of The Phase Transformation, Ternary Element Addition, And Advanced Processing, Thomas R. Keller

Dartmouth College Ph.D Dissertations

The growing need for electrical power in machines and vehicles brings with it a growing need for critical materials. The current high-performance permanent magnets (PMs) based on rare-earth (RE) elements Nd and Sm cannot escape the problem of raw material cost, geographic scarcity in the earth’s crust, and lack of circular global supply chains. This poses a problem of industrial ecology: can PMs be made from inexpensive, more abundant materials while still meeting sufficient performance criteria? PMs based on the magnetic τ phase of Mn-Al offer a possible alternative to REPMs. However, years of innovation have not yet achieved real-world …

Data-Driven 2d Materials Discovery For Next-Generation Electronics, Zeyu Zhang

Dissertations

The development of material discovery and design has lasted centuries in human history. After the concept of modern chemistry and material science was established, the strategy of material discovery relies on the experiments. Such a strategy becomes expensive and time-consuming with the increasing number of materials nowadays. Therefore, a novel strategy that is faster and more comprehensive is urgently needed. In this dissertation, an experiment-guided material discovery strategy is developed and explained using metal-organic frameworks (MOFs) as instances. The advent of 7r-stacked layered MOFs, which offer electrical conductivity on top of permanent porosity and high surface area, opened up new …

Computational And Experimental Investigation Of Elemental Sulfur And Polysulfide, Jyoti Sharma

Dissertations

Petroleum processing results in the generation of significant quantities of elemental sulfur (S₈), leading to a surplus of sulfur worldwide. Despite its abundance and low cost, the use of sulfur in value-added organic compound synthesis is limited due to its unpredictable and misunderstood reactivity. This dissertation aims to address this issue by tackling it from two angles. Firstly, by utilizing Density Functional Theory (DFT) calculations, the reactivity of sulfur in the presence of nucleophiles is studied. This facilitates the identification of organic polysulfide intermediates that can be generated under different conditions, as well as the corresponding reactivity for …

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 …

A Dft Analysis And Simple Hamiltonian Modeling Of A Molecular System Employed For Experimental Evidence Of Quantum Teleportation, Pedro Ulises Medina Gonzalez

Open Access Theses & Dissertations

Radical ion pairs (RIPs) have been used to demonstrate quantum teleportation in molecular systems for applications in quantum information science. Covalent organic donor-acceptor (D-A) molecules can produce RIPs through photo-induced charge transfer and an additional radical (R) molecule makes quantum teleportation possible. We present the electronic structure and analyze charge transfer excited states of a recently studied [1] D-A-R molecular system using density functional theory. The distances between donor-acceptor and donor-radical are about 12.9 \AA $\,$ and 21.9 \AA, respectively. The excitation energies are calculated using the perturbative delta-SCF method and agree with other conventional excited-state methods and experimental reference …

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 …

C···O And Si···O Tetrel Bonds: Substituent Effects And Transfer Of The Sif3 Group, Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF₃-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO₂, CN, F, CH₃, OH, OCH₃, NH₂, and Li) is examined by quantum chemical means. The Si···O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C···O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite …

Enhanced Quantum Chemistry With Machine Learning, Brock Dyer

Physics and Astronomy Summer Fellows

This file is a catalogue of the relevant quantum mechanical and computer programming topics that I learned during the summer which will be helping me to generate an artificial intelligence that will be able to perform computational chemical calculations at a much faster rate and comparable or better accuracy than current methods.

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 …

Computational Qsar & Molecular Docking Of Anti- Inflammatory Asthma Drugs Against Human Serum Albumin: A Computational Approach Towards Drug Design & Drug Discovery, Sara Alkarimy

Theses and Dissertations

There is a growing need for medications to fight deep-rooted and new diseases because of their socioeconomic consequences, as evidenced by the COVID-19 epidemic which slowed down the economy and affected the social life of mankind globally. This work is a step among many other steps undertaken by research around the world in order to achieve this objective. Asthma is one of the diseases that causes the death of thousands of lives every year. This work aims at the development of novel anti-inflammatory asthma drugs where the quantum chemical descriptors of eleven anti-inflammatory asthma drugs including Ambroxol, Amoxicillin, Budesonide, Fluticasone, …

Atomistic Assessment Of Drug-Phospholipid Interactions Consequent To Cancer Treatment: A Study Of Anthracycline Cardiotoxicity, Yara Elsayed Ahmed

Theses and Dissertations

Despite being one of the most effective chemotherapeutic agents developed to date, Anthracyclines are notorious for their cardiotoxicity. Their clinical use is frequently limited both in dosage and in prescription due to the severe cardiac damage they cause. The mechanism of anthracycline-induced cardiotoxicity is not yet fully understood. However, it is hypothesized that interactions with the myocardial membrane play an important role in imparting cardiotoxicity. In this study, we use molecular dynamics simulations and density functional theory calculations to study the anthracycline drug molecules and the interactions that they have with the myocardial membrane. We construct a myocardial membrane model …

Simulations Of Intruder-Free X-Ray Transient Absorption And Time-Resolved X-Ray Scattering For Probing Attosecond Electron Dynamics, Mengqi Yang

LSU Doctoral Dissertations

The motion of electrons plays a fundamental role in both physics and chemistry, and capturing such dynamics requires the ability to resolve changes at the attosecond timescale, which is enabled by the advent of ultrashort laser pulses. This dissertation aims to facilitate the interpretation of ultrafast electron dynamics and attosecond spectroscopy by real-time time-dependent density functional theory (RT-TDDFT) simulations. The first part of this dissertation focuses on improving the simulation of X-ray transient absorption spectra (XTAS) with Gaussian basis sets in RT-TDDFT by applying a filter to the transition dipole matrix. Due to the spatial limitation of atom-centered Gaussian functions, …

Cpsrp43 Is Both Highly Flexible And Stable: Structural Insights Using A Combined Experimental And Computational Approach, Mitchell Benton, Mercede Furr, Vivek Govind Kumar, Adithya Polasa, Feng Gao, Colin David Heyes, Thallapuranam Krishnaswamy Suresh Kumar, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 …