Translating Chemistry, Structure, And Processing To The Solid-State Morphology And Function Of Organic Semiconductors Through Computational Modeling And Simulations,
2023
University of Kentucky
Translating Chemistry, Structure, And Processing To The Solid-State Morphology And Function Of Organic Semiconductors Through Computational Modeling And Simulations, Chamikara D. Karunasena
Theses and Dissertations--Chemistry
The immense synthetic design space and material versatility have driven the exploration and development of organic semiconductors (OSC) over several decades. While many OSC designs focus on the chemistries of the molecular or polymer building blocks, a priori, multiscale control over the solid-state morphology is required for effective application of the active layer in a given technology. However, molecular assembly during solid-state formation is a complex function interconnecting the building block chemistry and the processing environment. Insufficient knowledge as to how these aspects engage, especially at the atomistic and molecular scales, has so far limited the ability to predict …
Developing And Deploying Data-Driven Tools For Accelerated Design Of Organic Semiconductors,
2023
University of Kentucky
Developing And Deploying Data-Driven Tools For Accelerated Design Of Organic Semiconductors, Vinayak Bhat
Theses and Dissertations--Chemistry
Organic semiconductors have gained widespread attention due to their potential applications in flexible, low-cost, lightweight electronics, energy storage and generation technologies, and sensing applications. However, developing new organic semiconductors with improved performance remains a significant challenge due to the vast chemical space of possible molecular and materials structures. Furthermore, the high cost and time-consuming nature of experimental synthesis and characterization hinder the rapid discovery of new materials. To overcome these challenges, this dissertation presents a data-driven approach to organic semiconductor discovery. The primary focus of this work is the development of data-driven tools, namely machine learning models, to predict critical …
Water-Soluble Palladium, Copper, And Nickel Catalysts And Their Formation In Ligand-Free Suzuki-Miyaura Cross-Coupling Reactions,
2023
University of Kentucky
Water-Soluble Palladium, Copper, And Nickel Catalysts And Their Formation In Ligand-Free Suzuki-Miyaura Cross-Coupling Reactions, Priya Karna
Theses and Dissertations--Chemistry
Transition-metal catalyzed Suzuki-Miyaura (SM) cross coupling is a powerful synthetic method for constructing carbon-carbon and carbon-heteroatom bonds in designing organic compounds, agrochemicals, pharmaceuticals, and precursors for materials. However, the nature of catalysis and identity of the transition metal catalysts used in these reactions remain under debate or unknown. This dissertation reports the studies of three metals: Pd, Cu, and Ni. Pd-nanocluster catalysts and their formation in ligand-free SM reactions with Pd(II) nitrate as a precatalyst was investigated. The catalysts are water-soluble neutral Pd tetramer and trimer in their singlet electronic states as identified by UV-Vis absorption spectroscopy and are formed …
First Principles Calculations To Investigate Surface And Catalytic Properties Of Materials For Green Energy Generation,
2023
University of Kentucky
First Principles Calculations To Investigate Surface And Catalytic Properties Of Materials For Green Energy Generation, Keerthan Raghavendra Rao
Theses and Dissertations--Chemistry
Climate change due to greenhouse gas build up in the earth’s atmosphere is an existential threat to humanity. To mitigate climate change, a significant shift from fossil fuels is necessary. Over the years, several renewable energy sources like solar, wind, geothermal etc. have been explored with the aim providing carbon-free energy. In this work, we focus on using density functional theory (DFT) methods to investigate key functional properties of materials of interest for applications in solar cells and catalytic conversion for energy generation. We show geometric effects of carboxylic acid binding on a transition metal surface to impact the deoxygenation …
Computational Studies On Molecular Mechanisms For Dysregulation Of Monoamine Transporters By Hiv-1 Tat And Drug Discovery Of Novel Phosphodiesterase-2 Inhibitors,
2023
University of Kentucky
Computational Studies On Molecular Mechanisms For Dysregulation Of Monoamine Transporters By Hiv-1 Tat And Drug Discovery Of Novel Phosphodiesterase-2 Inhibitors, Charles A. Adeniran
Theses and Dissertations--Chemistry
Computational chemistry methods have been greatly used and has great potential in drug discovery and understanding the detailed molecular mechanism of biological processes. Scientific questions can initially be addressed using computational modeling and simulation studies. The common feature in this work is to understand intermolecular interactions related to protein targets in the brain, as it relates to HIV infection and Alzheimer’s Disease. HIV is among the world’s most deadly infectious diseases. Recent therapeutic advancements have begun to increase the life expectancy of people living with this virus. The mechanisms that lead to neurobiological complications known as HIV- associated neurocognitive disorders …
Structural Analysis Of Polar Aggregates And Inter-Ionic Distances In Room Temperature Ionic Liquids,
2023
Northern Illinois University
Structural Analysis Of Polar Aggregates And Inter-Ionic Distances In Room Temperature Ionic Liquids, Emily Elizabeth Dalbey
Graduate Research Theses & Dissertations
Ionic liquids have a wide variety of applications in chemistry due to their unique properties such as low flammability, low volatility, and high thermal and chemical stability. These properties make them great solvents, electrolytes for lithium-ion batteries, and more. Ionic liquids are salts whose components are mis-matched in size and shape leading to low melting points. To design an ionic liquid with a desired property it is key to first understand their structure. Lineshape analysis of the charge alternation peak from the experimentally measured or computationally calculated X-ray scattering data can give information about the size of the polar aggregates …
The Design And Characterization Of Gold Nanoclusters As Elementary Building Blocks,
2023
Wilfrid Laurier University
The Design And Characterization Of Gold Nanoclusters As Elementary Building Blocks, Heather Gaebler
Theses and Dissertations (Comprehensive)
Gold nanoclusters with diameters in the quantum size regime (< ~2 nm) are promising building blocks for the design of novel nanomaterials as they exhibit unique size-dependent properties that can be altered and fine-tuned. The research outlined in this PhD thesis employs density functional theory to construct and analyze small ligand-protected cage and rod-shaped nanoclusters. Chapter 2 reports stable halide-protected gold nanocages that were engineered to have a closed-shell valence electron count of 18. This study finds that nanocages comprised of 19 and 20 gold atoms can be converted into stable magic number species containing 18 valence electrons by modifying their charged states via adsorption of halide ligands to the cage’s surface. Chapter 3 reports stable ligand-protected gold nanoclusters with a tetrahedral Au4 core that were engineered to have a closed-shell valence electron count of 2. This study investigates the structural and electronic effects of halide and alkoxy ligands on the tetrahedral nanocluster and concludes that the results support the broader conclusion that it’s possible to fine-tune the stability and electronic properties of small gold nanoclusters using appropriate ligands. Chapter 4 reports stable gold nanorods that have diameters in the quantum regime that were constructed from elementary building blocks that contain “halide-staples”. This study presents different orientations of the “halide-staple” motifs on …
Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes,
2023
Michigan Technological University
Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed
Dissertations, Master's Theses and Master's Reports
Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps …
Multilevel Computational Investigation Into The Catalytic Mechanisms Of Matrix Metalloproteinase-1 And Fat Mass And Obesity-Associated Enzyme,
2023
Michigan Technological University
Multilevel Computational Investigation Into The Catalytic Mechanisms Of Matrix Metalloproteinase-1 And Fat Mass And Obesity-Associated Enzyme, Ann Varghese
Dissertations, Master's Theses and Master's Reports
Enzymes are biological macromolecules, typically proteins, that efficiently accelerate the rate of chemical reactions. Their remarkable catalytic power plays a vital role in essential processes across all kingdoms of life. Nowadays, computational chemistry methods provide valuable insights into enzymatic functions aiding our understanding of biological processes and providing advancements in fields such as biomedical sciences, biomimetic catalysis, drug design and biotechnology. This dissertation employs multilevel computational chemistry methods to investigate the structure-function relationships and the catalytic mechanisms of two metalloenzymes -Zn(II)-dependent matrix metalloproteinase-1 (MMP-1) and non-heme Fe(II)/2-oxoglutarate (2OG) dependent fat-mass and obesity-associated (FTO) enzyme. Chapter 2 explores the role of …
Molecular Dynamics Modeling Of Polymers For Aerospace Composites,
2023
Michigan Technological University
Molecular Dynamics Modeling Of Polymers For Aerospace Composites, Swapnil Sambhaji Bamane
Dissertations, Master's Theses and Master's Reports
Polymer matrix composite materials are widely used as structural materials in aerospace and aeronautical vehicles. Resin/reinforcement wetting and the effect of polymerization on the thermo-mechanical properties of the resin are key parameters in the manufacturing of aerospace composite materials. Determining the contact angle between combinations of liquid resin and reinforcement surfaces is a common method for quantifying wettability. It is challenging to determine contact angle values experimentally of high-performance resins on CNT materials such as CNT, graphene, bundles or yarns, and BNNT surfaces. It is also experimentally difficult to determine the effect of polymerization reaction on material properties of a …
Predicting The Reactivities And Reaction Mechanisms Of Photochemically Produced Reactive Intermediates,
2023
Michigan Technological University
Predicting The Reactivities And Reaction Mechanisms Of Photochemically Produced Reactive Intermediates, Benjamin Barrios Cerda
Dissertations, Master's Theses and Master's Reports
Photochemically produced reactive intermediates (PPRIs) such as the hydroxyl radical, carbonate radical (CO3•-) singlet oxygen (1O2) and triplet state of chromophoric dissolved organic matter (3CDOM*) are formed in sunlit natural waters upon photoexcitation of chromophoric dissolved organic matter (CDOM). PPRIs react with the organic compounds involved in key environmental processes, resulting in transformation products of smaller molecular weight than their parent compounds. Photochemical transformation of these key water constituents due to their reactions with PPRIs may pose potential effects on human and aquatic ecosystems. Consequently, there is a need …
Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases,
2022
Duquesne University
Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases, Angel Tamez
Electronic Theses and Dissertations
Biophysical phenomena are modeled using a combination of quantum and classical methods to interpret and supplement three distinct and diverse problems in this dissertation. In the first project, decarboxylation reactions are ubiquitous across chemical and biological disciplines, yet the origin of non-catalytic solvent effects remains elusive. Specific solvent structure and energetics have not been well described for the monoanion of malonate, nor corrected from the gas-phase charge-assisted intramolecular hydrogen bond model known as “pseudochair”. In the aqueous phase, a low-lying energy conformer known as the “orthogonal conformation” is computed to be preferred by a three-water cluster of hydrogen bonding over …
Computer Simulation Of The Light Absorption Band Of The Jumping Spider Isorhodopsin,
2022
Bowling Green State University
Computer Simulation Of The Light Absorption Band Of The Jumping Spider Isorhodopsin, Noah Zoldak
Honors Projects
In order to simulate the photoisomerization of the 9-cis Jumping Spider Isorhodopsin (JSiR-1) it is necessary to first simulate its light-absorption band. Here we report on the absorption band simulated using protein models constructed using the advanced Automatic Rhodopsin Modeling (a-ARM) program. A population of S0 models was created and the corresponding S0 to S1 transitions were determined for each member of the resulting population. The calculation resulted in a Gaussian plot showing that the wavelength of the absorption maximum of 560 nm (a violet color) that is consistent, but red-shifted, with respect the experimentally observed value.
Hydrogen Bonding In Small Model Peptides; The Dft And Mp2 Study,
2022
Kennesaw State University
Hydrogen Bonding In Small Model Peptides; The Dft And Mp2 Study, Gracie Smith, Martina Kaledin
Symposium of Student Scholars
Formamide is a small model compound for the study of the peptide bond. The peptide bond links amino acids together, specifies rigidity to the protein backbone, and includes the 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 infrared C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. This computational chemistry work, we study hydrogen bonds in formamide dimer isomers. We evaluate the accuracy of the density functional theory (DFT) and many-body perturbation theory to the 2nd order (MP2) …
Turning Ligands On Their Side: Computational Investigation Into The Binding Of N2o And N2 In Transition Metal Complexes,
2022
Stephen F Austin State University
Turning Ligands On Their Side: Computational Investigation Into The Binding Of N2o And N2 In Transition Metal Complexes, Cole Donald
Electronic Theses and Dissertations
Common greenhouse gas nitrous oxide (N2O) is a thermodynamically potent and environmentally benign oxidant, making it a desirable target for metal center activation. Unfortunately, N2O is a poor ligand for transition metals due to its weak sigma-donating and pi-accepting properties; as a result, few transition metal complexes capable of interacting with N2O have been found. As the primary source of all nitrogen in organisms, abundant gas dinitrogen (N2) is a crucially important tiny molecule and an essential part of daily existence. However, due to its inertness, it has limited practical uses in …
Elucidation Of Active Site And Mechanism Of Metal Catalysts Supported In Nu-1000,
2022
Clemson University
Elucidation Of Active Site And Mechanism Of Metal Catalysts Supported In Nu-1000, Hafeera Shabbir
All Dissertations
Advances in extraction of shale oil and gas has increased the production of geographically stranded natural gas (primarily consisting of methane (C1) and ethane (C2)) that is burned on site. A potential utilization strategy for shale gas is to convert it into fuel range hydrocarbons by catalytic dehydrogenation followed by oligomerization by direct efficient catalysts. This work focuses on understanding metal cation catalysts supported on metal-organic framework (MOF) NU-1000 that will actively and selectively do this transformation under mild reaction conditions, while remaining stable to deactivation (via metal agglomeration or sintering). I built computational models validated by experimental methods to …
Perfect Polar Alignment Of Parallel Beloamphiphile Monolayers: Synthesis, Characterization, And Crystal Architectures Of Unsymmetrical Phenoxy-Substituted Acetophenone Azines,
2022
Missouri University of Science and Technology
Perfect Polar Alignment Of Parallel Beloamphiphile Monolayers: Synthesis, Characterization, And Crystal Architectures Of Unsymmetrical Phenoxy-Substituted Acetophenone Azines, Harmeet Bhoday, Michael Lewis, Steven P. Kelley, Rainer Glaser
Chemistry Faculty Research & Creative Works
It remains a great challenge to achieve polar order in organic molecular crystals because anti-parallel alignment of side-by-side molecules is intrinsically preferred. We have addressed this problem with a rational design that focuses on the polar stacking of parallel beloamphiphile monolayers (PBAMs) with strong lateral quadrupole-quadrupole attractions. We employ arene-arene interactions as lateral synthons. The first successes were achieved with unsymmetrical donor (X), acceptor (Y) substituted acetophenone azines which form polar PBAMs with double T-contacts between the azines. Near-perfect alignment was achieved with the methoxy series of (MeO, Y)-azines with Y=Cl, Br, I. Here, we report on the synthesis, the …
Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases,
2022
University at Albany, State University of New York
Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers
Legacy Theses & Dissertations (2009 - 2024)
Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …
First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting,
2022
University of Arkansas, Fayetteville
First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting, Zegnet Yimer Muhammed
Graduate Theses and Dissertations
In this dissertation, we have thoroughly studied the effect of chemical and charge dopingon ferroelectrics (PbTiO3 and BaTiO3) and Rashba type semiconductor (BiTeI). In the first project, We investigate the polar instability and soft modes in electron-doped PbTiO3 using linear-response density functional calculations. Because, metallicity and ferroelectric-like polar distortion are mutually non-compatible, and their coexistence in the same system is an intriguing subject of fundamental interest in the field of structure phase transition. However, it is unclear what mechanism may extend the limit of metallicity that allows polar distortion. We find that ferroelectric instability can remarkably sustain up to an …
Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications,
2022
University of Arkansas, Fayetteville
Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications, Adithya Polasa
Graduate Theses and Dissertations
Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were …
