Physical Sciences and Mathematics Commons^™

Leveraging Non-Covalent Interactions Between Small Organic Molecules And Inorganic Scaffolds In The Design Of Advanced Materials, Jonathan Lefton

Chemistry Theses and Dissertations

Powder diffraction is a powerful tool for studying crystal structures, especially as it relates to interactions of small organic molecules with inorganic compounds. The first part of this dissertation involves small organic ligands interacting with metal-organic framework, MOF-74. The first and simplest iteration involves the crystal structure solution of a neat, liquid loading of n-propylmercaptan to the open metal sites within the MOF-74 pores. Later studies investigate the leveraging of a similarly sized bitopic ligand in the solution loading of 1,2-ethanedithiol, which results in the amorphization of MOF-74. Having no crystallinity, amorphous or severely defected materials can be a …

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 …

New Methods For Core-Hole Spectroscopy Based On Coupled Cluster Theory, Megan Simons

Chemistry Theses and Dissertations

X-ray absorption spectra (XAS) is a method used to investigate atomic local structure and electronic states. Coupled cluster method is a numerical method used for describing many-body systems and electron correlation in a wavefunction. When equation-of-motion coupled cluster is used in XAS calculations, the ground state is applied to the excitation operator, which excites or ionizes the electron. This causes a large orbital relaxation error, normally ~5 eV, which leads to the need for triple excitations in order to obtain accurate results.

This dissertation introduces a coupled cluster method that uses "transition potential" reference orbitals to reduce the orbital relaxation …

Microscale Chemical Manipulation And Imaging Using Photoactive Molecules And Light, Uroob Haris

Chemistry Theses and Dissertations

Chemical manipulation with light has been an active and growing area of research with important implications in materials science, biotechnology, and environmental science. From early investigations of light sensitive materials for photography in the 19^th century, to printing billions of transistors on a semiconductor chip in present day, scientists have gained a deep understanding of photochemistry and the processes that allow us to harness light for everyday applications. In this work, we explore microscale fabrication and molecular imaging using light and photoactive molecules as foundational tools. We develop a visible-light mediated technique for high resolution microscale chemical lithography comprising …

Exploring Protein Conformations And Functions Through Molecular Dynamics Simulations And Machine Learning, Hao Tian

Chemistry Theses and Dissertations

Proteins are essential biomacromolecules that perform a variety of critical functions in living organisms. The tertiary structure of a protein plays a crucial role in its biological activity as it determines how the protein interacts with other molecules. Consequently, understanding protein conformation and function is an important area of research with implications in medicine, biotechnology, and other fields.

The first part of this dissertation focuses on protein allostery, a process by which proteins transmit perturbations caused by binding at one site to a distal site, thereby regulating activity. With the development of computational methods like molecular dynamics simulations and machine …

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 …

Sulfur Behavior In The 1257 Ce Samalas Magma (Lombok, Indonesia) As Revealed By Volcanic Apatite, Yasmin Jackson

Earth Sciences Theses and Dissertations

Explosive volcanic eruptions can inject massive amounts of volatiles, including SO₂ and H₂S, into the stratosphere, inducing drastic tropospheric cooling via sulfate aerosols. Greenland and Antarctic ice cores record evidence of these substantial releases of SO₂ and H₂S, including the massive release during the ultraplinian 1257 CE Samalas eruption. The 1257 CE Samalas eruption is estimated to have released ~158 Tg of SO₂, making it the largest volcanogenic release of SO₂ within the last 2000 years. Vidal et al. (2016) propose that most of this sulfur (S) was hosted in a …

Unraveling Molecular Mechanisms Of Antibiotic Resistance Through Multiscale Simulations And Explainable Machine Learning, Zilin Song

Chemistry Theses and Dissertations

Pathogen resistance to β-lactam antibiotics compromises effective treatments of superbug infections. One major source of β-lactam resistance is the bacterial production of β-lactamases, which could effectively hydrolyze β-lactam drugs. In this thesis, the hydrolysis of various β-lactam antibiotics by class A serine-based β-lactamases (ASβLs) were investigated using hybrid Quantum Mechanical / Molecular Mechanical (QM/MM) minimum energy pathway (MEP) calculations and explainable machine learning (ML) approaches. The TEM-1/benzylpenicillin acylation reaction with QM/MM chain-of-states reaction pathways was firstly revisited. I proposed two decomposition methods for energy contribution analysis based on perturbing ML regression models. Both methods were shown to be model implementation …

The Role Of Hydrogen Bonding And Hydrogen Migration In Different Environments, Nassim Beiranvand

Chemistry Theses and Dissertations

Hydrogen bonding is one of the most important topics in chemistry and has been a subject of many studies for years, using both experimental techniques and computational methods. My dissertation focuses on mechanistic studies of various types of intermolecu-lar and intramolecular hydrogen bonding in di˙erent systems based on quantum chemical calculations. In my work, I investigated the interplay of ring puckering and hydrogen bonding in DNA building blocks; hydrogen bonding in natural and unnatural base pairs and the nature of dihydrogen bonding by applying the Ring Puckering Analysis and the Local Vibrational Mode Theory (LVM). An additional aim of my …

From Small Molecules To Infinite Crystals: Probing Noncovalent Interactions Through Vibrational Spectroscopy, Sadisha Nanayakkara

Chemistry Theses and Dissertations

During my four years in the CATCO group supervised by Dr. Kraka, I have been exposed to various topics targeted to address a multitude of chemical problems, broadening our knowledge of modern chemistry research as we know it. In undertaking the age-old problem of understanding the nature of chemical bonding, I could modestly contribute with my work, using in-house tools based on vibrational spectroscopy.

First part of my dissertation is focused on inventing new methods and tools to efficiently investigate chemical bonding, followed by the study of some non-covalent interactions, imperative in catalysis and solid-state chemistry. This includes analysis of …

Quantum Chemical Investigation Of Novel Noncovalent Interactions Utilizing Vibrational Spectroscopy, Seth Francis Yannacone

Chemistry Theses and Dissertations

Theoretical/computational methods have been utilized to investigate a diverse array of questions currently at the forefront of modern chemistry research. The focus of this work is Local Vibrational Mode (LVM) Theory, originally formulated by Konkoli and Cremer, and under continuous development by the CaTcO research group. Derived from LVM theory, local stretching force constants (ka) represent physically meaningful measurements of chem- ical bond strength. Decomposition of normal vibrational modes into LVM contributions, also called characterization of normal modes (CNM), is another powerful manifestation of LVM theory; most notably when applied to the analysis of theoretical/experimental IR/Ra- man spectra. Recent developments …

Structure And Reactivity Of The First Row Transition Metals Bearing Redox-Active Ligands And Tunable H-Bonding Interactions, Khashayar Rajabimoghadam

Chemistry Theses and Dissertations

Metalloenzymes, as natural catalysts, can break a reaction with high activation energy to multiple small reactions with lower activation energies; in these small reactions, multiple bonds form and dissociate rapidly, some metalloenzymes use redox-active ligands in their active site to provide the needed electrons for these multiple small reactions. Additionally, in the secondary coordination sphere in the vicinity of the metalloenzymes, the hydrogen bonding interactions facilitate the transfer and interaction of the substrates and the stabilization of the active intermediates. These unique features in metalloenzymes inspired chemists to design molecular models that can partially mimic the structure and reactivity of …

Cu-Promoted C-H Bond Hydroxylation Inspired By Cu-Dependent Metalloenzymes, Rachel Trammell

Chemistry Theses and Dissertations

From 2003 to 2015, Schӧnecker and Baran proposed a dinuclear Cu/O₂ species in their mechanistic proposal for the hydroxylation of sp³ C-H bonds within their systems (proposed based on yields). Inspired from the site selectivity of this methodology and poor analysis of the mechanism, the first project was inspired to re-examine the sp³ C-H bond hydroxylation by Schrӧnecker and Baran and perform an intensive investigation into understanding how Cu/O₂ interact which led us to propose a new mechanism based on the evidence collected (i.e., LCu^II-hydroperoxide species that undergoes homolytic O-O bond cleavage). From there …

Hypervalent Iodine Compounds With Halogen-Containing And Phosphinate Ligands, Yakun Cao

Chemistry Theses and Dissertations

In modern organic chemistry, hypervalent (HV) iodine(III) compounds have been used widely as oxidizing agents but applications of λ³-iodanes in polymer and material chemistry is still underexplored. In the first project, a new series of heterocyclic HV iodine(III) compounds with I–Cl bonds and various substituents at the N atom were synthesized and successfully employed in the synthesis of highly branched polymers when added to mixtures of styrene and 1,4-divinylbenzene containing 10–80 mol% of the divinyl crosslinker, or even pure crosslinker. HV iodine(III) also can be utilized for polymer modification. HV iodine(III) compounds with fluorine-containing ligands (F, CF_{3 …}

I. Non-Degradable Polysiloxane Networks For Controlled Release Applications, And Ii. Additive Free, Degradable Silyl-Ether Furyl-Maleimide Networks, Caleb M. Bunton

Chemistry Theses and Dissertations

I. Two different series of non–degradable polysiloxane networks were prepared for the encapsulation and controlled release of a small molecule agent. For the first series, hydrosilylation was utilized to prepare networks of varying crosslink densities, as determined from swelling studies, from vinyl terminated and silylhydride functional poly(dimethyl)siloxanes. For the second series, the thiol-ene reaction was utilized to prepare networks of varying crosslink densities, as determined from swelling studies, from vinyl terminated and mercaptopropyl functional poly(dimethyl)siloxanes. Nile red dye was used as an encapsulated agent and dye release from each series of networks was measured using UV–vis spectroscopy to determine controllability …

Hypervalent Iodine Compounds With Carboxylate And Tetrazolate Ligands, Avichal Vaish

Chemistry Theses and Dissertations

In modern organic chemistry, hypervalent (HV) iodine(III) compounds are frequently used as oxidizing agents but application of λ³-iodanes in polymer and material chemistry is still underexplored. This dissertation describes the preparation of dynamic and self-healing materials by employing ligand exchange reactions involving HV iodine(III) compounds of the type ArIL₂ (Ar = Aryl, L = ligand, e.g., carboxylate or (pseudo)halide). These compounds can undergo ligand exchange reactions in presence of nucleophiles (Nu^-) to form ArINu₂. Diacetoxyiodo benzene was successfully employed as a crosslinker to prepare dynamic and self-healing gels derived from carboxylate-containing polymers. Furthermore, …

Cell-Trappable Chemiluminescent Probes For Monitoring Hydrogen Sulfide In Living Cells, Briley Bezner

Chemistry Theses and Dissertations

Hydrogen sulfide (H2S) is an important biological signaling molecule that has been recognized alongside nitric oxide and carbon monoxide as being a small gasotransmitter that is enzymatically produced and impacts multiple physiological functions. To detect hydrogen sulfide, there has been a focus on developing fluorescent probes to target particular analytes; however, fluorescent probes lack sensitivity and depth penetration due to background autofluorescence and light scattering. Chemiluminescence does not require light excitation, which greatly reduces the amount of autofluorescence and photoactivation.

In order to detect hydrogen sulfide in living systems with high sensitivity, a series of sterically stabilized 1,2-dioxetane chemiluminescent reduction-reaction …

Evaluation Of The Mechanisms And Effectiveness Of Nano-Hydroxides, Wood And Dairy Manure-Derived Biochars To Remove Fluoride And Heavy Metals From Water, Anna Rose Wallace, Wenjie Sun Dr, Chunming Su Dr

Civil and Environmental Engineering Theses and Dissertations

The development of effective treatment processes for the removal contaminants, such as fluoride and heavy metals, from polluted water have been urgently needed due to serious environmental health and safety concerns. In this dissertation, a variety of materials including various (hydro)oxide nanomaterials, biochars and surface modified biochar were studied to evaluate their effectiveness and mechanism on removing fluoride or mixed heavy metals from water.

In the Chapter 2, this study investigated the adsorptive removal of fluoride from water using various (hydro)oxide nanomaterials, focusing on ferrihydrite, hydroxyapatite (HAP) and brucite, which have the potential to be used as sorbents for surface …

Polyarylenes: Synthesis And Characterization Towards Advanced Applications, Stephen Budy

Chemistry Theses and Dissertations

A series of semi-fluorinated and non-fluorinated Diels−Alder step-growth polyarylene polymers and co-polymers were synthesized via typical oil bath heating (days/weeks) and more rapid microwave-assisted polymerization (hours). The polymers were characterized by multi-nuclear (¹H, ¹³C, and ¹⁹F) NMR and ATR−FTIR spectroscopy, thermal analysis (TGA, DSC, and DMA), GPC, XRD, water contact analysis (WCA), and refractive index (RI) measurements. The NMR spectra indicated a mixture of para and meta conformations through the polymer backbone increasing to more para with greater fluorine content. Thermal gravimetric analysis revealed the fluorine-containing polyarylenes possessed the highest char yields at almost 80% at …

Hypervalent Iodine(Iii) Compounds With (Pseudo)Halide And Tetrazole Ligands In The Synthesis Of Functional Polymers, Rajesh Kumar

Chemistry Theses and Dissertations

The organic compounds of iodine(III) with the general formula ArIL₂ (Ar = aryl, L = (pseudo) halides) degrade homolytically upon irradiation or heating to the corresponding monovalent iodine compound (ArI) and the radicals L^• . If the latter contains a functional group, they can be used to initiate the polymerization of vinyl monomers to afford chain end-functionalized linear polymers. When "conventional" monovinyl monomers are copolymerized with di- or multivinyl monomers (crosslinkers) in the presence of relatively high concentrations of rapidly decomposing ArIL₂ compounds, highly branched polymers are formed that contain multiple chain-end functionalities derived from the radicals …

Unravel Allostery Mechanism Through Molecular Dynamic Simulations With Machine Learning Approaches, Hongyu Zhou

Chemistry Theses and Dissertations

Allostery is referred to as protein function changes due to external perturbations, and ubiquitous in the living cells. Investigation of the allosteric mechanism is essential for developing drugs or assisting protein engineering. Recently, the population shift model has been proposed to explain the allosteric mechanism. This model emphasizes the importance of conformational distribution in the allostery. In the past several years, I have been continuously working on developing computational methods to explore and quantify protein allostery mechanism. By fully utilizing protein simulation results, several machine learning related methods have been applied to protein systems to investigate the underlying conformational changes …

Design And Synthesis Of Circadian Clock Modulators And The Study Of Lov Domain Protein Lkp2 In Arabidosis Thaliana And Brassica Rapa, Aditi Nagar

Chemistry Theses and Dissertations

Circadian rhythms are self-autonomous endogenous clocks synchronized with the rotation of the Earth. With the Earth’s rotation and revolution on its axis, the internal clock undergoes oscillation in the period of ~24 hour and governs day to day activities in most organisms. In humans, it regulates the day to day physiological activities. Today’s modern lifestyle has an impact on health: shift work, jet lag, and irregular eating habits contribute to the misalignment of the endogenous circadian oscillator, thereby, increasing the risk of many metabolic disorders including diabetes, irregular blood pressure, sleep disorders, obesity, depression, and cancer. The primary goal of …

Advances In Local Vibrational Mode Theory And Unified Reaction Valley Approach (Urva), Yunwen Tao

Chemistry Theses and Dissertations

Since the establishment of the Local Vibrational Mode Theory and the Unified Reaction Valley Approach (URVA), these two research pillars have been pushed forward in the CATCO group and played an important role in (i) characterizing the chemical bonds in molecules and (ii) molecular chemical reactions. This dissertation elaborates my contributions to the Local Vibrational Mode Theory and the Unified Reaction Valley Approach (URVA).

We have applied the Local Vibrational Mode Theory to hydrogen bonding in liquid water and proposed an explanation for the Mpemba effect. We explored and discovered new directions of applying local vibrational modes majorly in characterizing …

Multi-Reference Systems In Chemistry; Unconventional Bonding In Organic Chemistry; Covalent Bonding In Transition Metal Clusters, Alan Wilfred Humason

Chemistry Theses and Dissertations

The geometries, chemical properties, and reactivities of molecules are determined by their electronic structure. The field of ab initio computational chemistry works to calculate the kinetic and potential energies between the nuclei and electrons of a molecule. These calculations usually begin with the determination the electronic ground state.

Molecules that cannot be adequately described with a single, ground state configuration are called \textit{multi-reference systems}, which require the calculation of a linear combination of all pertinent electronic configurations, with a corresponding increase in computational cost. This is not `black box' methodology, because solving these systems requires a good understanding of the …

Quantum Chemical Studies Of Noncovalent Interactions And Multicenter Bonds Utilizing Local Vibrational Modes, Vytor Oliveira

Chemistry Theses and Dissertations

Noncovalent interactions play an important role for the design of novel drugs, better catalysts, synthesis of complex supramolecular structures, and so on. To develop new materials, a well-founded knowledge of how to control the strength of these interactions is desirable. Despite the many investigations done so far, a quantitative assessment of the intrinsic strength of most types of noncovalent interactions is still missing. Recently and for the first time, the Konkoli-Cremer local modes analysis was successfully used to probe the intrinsic strength of hydrogen and pnicogen bonds. We extended these investigations to more than 300 halogen and chalcogen bonds. A …