Physical Chemistry Commons^™

Quantum Effects In Collisional Energy Transfer Simulated Using Mixed Quantum/Classical Theory, Dulat Bostan

Dissertations (1934 -)

Mixed quantum/classical theory (MQCT) was used to study collisional energy transfer between the rotational states of molecules with the focus on reproducing quantum effects related to this process. Namely, rotational energy transfer in the N₂ + O system was studied to replicate quantum interference effects observed as oscillations of scattering cross section as a function of collision energy. Both MQCT code and the full-quantum code MOLSCAT were used for calculations, and results were in excellent agreement with the experiment and the full-quantum infinite-order sudden method from literature. The CO + CO system was used as a case study for …

Experimental And Computational Investigation Of Ethylene Oxide Hydrate And Its Mixed Hydrates With Propane And Isobutane, Adebayo Paul Adeleye

Master's Theses (2009 -)

Gas hydrates represent an important class of crystalline solids, where water molecules form cage-like frameworks that encapsulate gas molecules. They have garnered significant attention for their unique properties and diverse applications in energy and environmental science. This study investigates the formation and vibrational properties of the ethylene oxide (EO) hydrate (structure I, sI) and EO-seeded hydrates of propane and isobutane (structure II, sII) using matrix isolation Fourier-transform infrared (FTIR) spectroscopy, supported by Density Functional Theory (DFT) calculations at the B3LYP/6-311++G(d,p) level of theory. Under low-temperature and low-pressure conditions, EO hydrate was formed by co-depositing a premix of EO and argon …

Elucidating The Effect Of Surface Modifications On Nanomaterial Function, Nicholas Langer

Dissertations (1934 -)

Nanoparticles (NPs) are an exciting class of materials with unique properties that inspire their use in sensing, catalysis, optoelectronic devices, and more. NPs are frequently coated in organic molecules, termed ligands, to increase their stability, but ligands also influence NP catalytic activity and their interactions with neighboring molecules. To fully realize the potential of nanomaterials as key components in novel complex systems, a more nuanced understanding of the relationships between NPs, ligands, and their surrounding microenvironment is critical. After a brief review of the NP field in Chapter 1, Chapter 2 begins the investigation of structure-function relationships with a cross-class …

Probing Charge Transport Mechanisms In 2d Semiconductive Metal Organic Framewoks, James Nyakuchena

Dissertations (1934 -)

Metal organic frameworks (MOFs) are a class of highly porous crystalline materials constructed from metal nodes connected by multitopic organic ligands. Due to their unique properties such as large surface area, tunable pore structure, and structural diversity, they have demonstrated potential in a wide array of applications including gas storage and separation, sensing, catalysis, and drug delivery. However, there are only a handful of MOFs reported that have electrical conductivity, which prevents their applications in photoelectronic and photocatalytic applications. This is because hard metals and redox inactive ligands with terminal hard linking bases such as carboxylates are often used in …

The Photodynamic And Structural Analyses Of Advanced Materials For Solar Fuel Conversion, Brian Pattengale

Dissertations (1934 -)

Mitigating the current and future climate and pollution issues that have been brought on by the combustion of fossil fuels is of utmost importance and will rely on, in part, the availability of renewable fuel sources. Of the possible sources of energy, solar is abundant, but must be harnessed efficiently and stored as a solar fuel to overcome the current storage issues that limit photovoltaic cells. One such fuel, H2(g), represents a carbon-neutral source of energy if it can be efficiently liberated from water via the water splitting reaction. Thus, much attention is focused on designing materials to perform the …

Nucleotide-Dependent Preferential Localization Of Ras In Model Membranes With Lipid Raft Nanodomains, Anna Shishina

Dissertations (1934 -)

Membrane proteins constitute a third of all proteins in the cell and more than 50% of drug targets. However, the analysis of membrane proteins has many challenges owing to their partially hydrophobic surfaces, flexibility and lack of stability. One example of an essential membrane protein is Ras superfamily. Ras is a small monomeric GTPase involved in regulation of cell growth, proliferation and differentiation. Therefore, Ras and its effectors are among the most important targets for cancer therapy. A detailed knowledge of the processes occurring during signal propagation via Ras might help to elucidate the mechanisms of the involved signal cascades. …

Mixed Quantum/Classical Theory (Mqct) For Rotationally And Vibrationally Inelastic Scattering And Its Application To The Molecules Of Astrochemical Importance, Alexander Semenov

Dissertations (1934 -)

This thesis presents developments and applications of the mixed quantum/classical theory (MQCT) for inelastic scattering. In this approach, translational motion of collision partners is treated classically, while the internal degrees of freedom – rotational and/or vibrational motion – are treated quantum mechanically. Within this framework calculations of rotationally inelastic cross sections are carried out in a broad range of collision energies and results are compared against the exact full quantum data for several real systems. For CO +He, N2 + Na and H2 + He the agreement is excellent through six orders of magnitude range of cross sections values and …

Functional And Structural Studies Of Cytochromes P450 By Resonance Raman Spectroscopy, Yilin Liu

Dissertations (1934 -)

Cytochrome P450 is a broad class of heme monooxygenase enzymes which catalyze various oxidative transformations. There are two main kinds of mammalian P450s: steroidogenic and drug metabolizing P450s. The first project involves a steroidogenic P450, CYP17A1, occupying a central role in the biosynthesis of steroid hormones. It catalyzes hydroxylation reaction on pregnenolone and progesterone, generating 17OH-pregnenolone and 17OH-progesterone, presumably utilizing a “Compound I” species. However, these hydroxylated products can be further processed in a second oxidative cycle to cleave the C17–C20 bond to form dehydroepiandrosterone or androstenedione, respectively, a crucial step in androgen production. Interestingly, it is well known that …

Theoretical Study Of Ozone Forming Recombination Reaction And Anomalous Isotope Effect Associated With It, Alexander Teplukhin

Dissertations (1934 -)

The ozone forming recombination reaction stands out among many chemical processes that take place in the atmosphere. This reaction is responsible for the reconstruction of ozone layer, which protects life on Earth from harmful ultra-violate radiation and is a source of so-called anomalous isotope effect in ozone. The reaction was intensively studied, but at a very basic level. There were only couple of papers where the recombination rate coefficient was computed and found to roughly agree with the experimental data. In this dissertation, the recombination process in ozone is approached using new and efficient method, which includes several modern techniques. …

On The Structure And Properties Of S-Nitrosated Cysteine Models: A Computational Study, Dmitry Khomyakov

Dissertations (1934 -)

S-Nitrosation of cysteine (Cys) residues, a covalent modification of its S atom by NO group, is a major post-translational modification of proteins. Despite the importance of S-nitrosoproteins in numerous physiological processes, lability of the S-nitrosothiol (-SNO) group hinders the research progress. In this work, computational chemistry methods were applied to S-nitrosated cysteine (CysNO) models to gain a deeper insight into its structure and properties. First, we obtained the most accurate at the moment computational estimation of the molecular structure and properties of CH3SNO model molecule using Feller-Peterson-Dixon (FPD) ab initio protocol. The S–N bond length in cis- CH3SNO is calculated …

Computational Modeling Of S-Thiolation Reaction: Toward Discovering The Enzymatic Mechanisms Of Endogenous Hno Formation, Elena Ivanova

Dissertations (1934 -)

S-nitrosothiols (RSNOs) have long been proposed as potential sources of the elusive endogenous nitroxyl (HNO) via S-thiolation reaction with thiols. It is however not clear how S-thiolation can compete with the trans-S-nitrosation pathway commonly observed in vitro. Based on the insights into the highly unusual, antagonistic chemical nature of RSNO molecules, we hypothesize that, while difficult in vitro, S-thiolation could easily lend itself to enzymatic catalysis. To explore this possibility, we adopted a bottom-up computational approach that aims to identify possible catalytic mechanisms able to steer the RSNO + thiol reaction toward HNO production. Inspired by recent discovery of small …

An Investigation Of The Requirements For Excimer Formation And Charge Stabilization In Model Pi-Stacked Assemblies, Brandon Uhler

Dissertations (1934 -)

Formation of -stacked excimers plays an important role in many systems, ranging from biological phenomena and polymer formation and function to photovoltaic devices and organic molecular electronics. In these systems, the geometrical reorganization of the ground state upon photoexcitation is still a subject of debate. In this work, we compare the dynamics of excimer formation and hole (charge) stabilization in fluorene and fluorene-based model systems. We use a variety of gas-phase methods to examine the spectroscopy and dynamics of these systems, including Two-Color Resonant Two-Photon Ionization (2CR2PI), Hole-Burning (HB), Laser Induced Fluorescence (LIF), and Dispersed Fluorescence (DF). In order to …

Resonance Raman Studies Of Oxygenated Forms Of Myoglobin And Cyp2b4 And Their Mutants, Ying Wang

Dissertations (1934 -)

Important oxidative heme enzymes use hydrogen peroxide or activate molecular oxygen to generate highly reactive peroxo-, hydroperoxo- and feryl intermediates resulting from heterolytic O-O bond cleavage. Members of the cytochrome P450 superfamily catalyze difficult chemical transformations, including hydroxylations and C-C bond cleavage reactions. In mammals, these enzymes function to reliably produce important steroids with the required high degree of structural precision. On the other hand, certain other mammalian P450s serve a different role, efficiently metabolizing xenobiotics, including pharmaceuticals and environmental pollutants. Though so important, the precise mechanisms involved in such transformations are incompletely understood, because of difficulties in structurally characterizing …

Novel Numerical Models Of Electrostatic Interactions And Their Application To S-Nitrosothiol Simulations, Maxim Vadimovich Ivanov

Dissertations (1934 -)

Atom-centered point charge model of the molecular electrostatics remains a major workhorse in the atomistic biomolecular simulations. However, this approximation fails to reproduce anisotropic features of the molecular electrostatic potential (MEP), and the existing methods of the charge derivation are often associated with the numerical instabilities. This work provides an in-depth analysis of these limitations and offers a novel approach to describe electrostatic interactions that paves the way toward efficient next-generation force fields. By analyzing the charge fitting problem from first principles, as an example of the mathematical inverse problem, we show that the numerical instabilities of the charge-fitting problem …

Mixed Valent Metal Pincer Complexes And Reactivity Of Metal Complexes Of Extended Pincer Ligands, Jeewantha Sampath Hewage

Dissertations (1934 -)

Historically, the study of mixed valence complexes has been critical for advancing our understanding of electron transfer processes in biological and abiological systems. The recent use of mixed valence complexes in electrochromic materials, and the promise of their use in future technological or molecular electronic applications, has spurred further interest in this class of compound. Previous studies by our research group have shown that gallium(III) or tricarbonylrhenium(I) complexes of pincer-type ligands with diarylamido anchors and either pyrazol-1-yl (pz) or diarylphosphino (PAr2) flanking donors are electroactive species with quasi reversible ligand-centered oxidations. Moreover, the one-electron oxidized derivative with pz flankers, [Ga(L)(L+)]2+ …

S-Nitrosothiols: Electronic Structure And Substituent Effects, Matthew Flister

Dissertations (1934 -)

S-nitrosothiols (RSNOs) are biologically important molecules involved in the storage and transport of nitric oxide (NO) and account for much of its signaling activity in living organisms. RSNOs have significant impact on NO signaling through, S-nitrosation, a major post-translational modification of proteins. These unstable thiol derivatives readily undergo homolytic dissociation of the S–N bond to release NO. RSNOs have potential therapeutic applications as NO donors, although the development of novel RSNOs has been slow due to the complex electronic structure of the –SNO group. A specific focus on the impact of the –R group on RSNO properties via substituent effect …

With Vibrationally Excited Thiophosgene Molecule And Double-Well Ion Traps, Dmytro Shyshlov

Dissertations (1934 -)

For practical realization of quantum information processing we need a quantum system that provides reliable preparation of the initial state, high-fidelity quantum gate operations, error tolerance, readout of the result of quantum computation and scalability of the system to increase the number of qubits. In this dissertation we show how these requirements can be addressed for molecular quantum computer. For computational study of quantum information processing with molecules we employ thiophosgene (SCCl2) molecule that has been used as a test system for quantum control experiments [Mol. Phys. 105, 1999 (2007)]. We investigate the gateway scheme of control in which transitions …

Resonant Two-Photon Ionization Studies Of Non Covalent Interactions In Halo Aromatic Clusters And Spin-Orbit Coupling Modeling In Mono-Halocarbenes, Silver Nyambo

Dissertations (1934 -)

Non-covalent interactions in halobenzenes (PhX) (X=F, Cl, Br) and phenylamine (C₆ H₅ NH₂ ) have been studied here using resonance two-photon ionization (R2PI) spectroscopy combined with a linear TOF-mass spectrometer. Their interaction with polar molecules in form of ammonia (NH ₃ ) and trifluorohalomethanes (CF₃ X) has also been studied. DFT and TD-DFT calculations using M06-2X functionals were carried out on different cluster conformations to compliment experimental results. A general trend of broadness in homogenous dimers (PhX)₂ , has been attributed to mainly the presence of multiple cluster isomers and Frank-Condon activity in the low …

Determination Of Saponification Rate By Change In Hydrogen Ion Concentration Measured With Quinhydrone And Glass Electrodes, Richard Porter

Bachelors’ Theses

The measurement or hydrogen ion concentration is becoming more important in all the fields of chemistry since the states or many chemical systems can to some extent be defined by their hydrogen ion concentration. If the hydrogen ion concentration or a particular solution can be measured accurately, in many cases other important relations and quantities may be determined. Methods or measurement are therefore important instruments or investigation.

When an ester is saponified by an alkali, the hydrogen ion concentration increases as the reaction proceeds. Thus, it the hydrogen ion concentration can be calculated at different intervals of time, some knowledge …

A Study Of The Transparency Of Paraffin Wax, Gordon B. Smith

Bachelors’ Theses

The problem of wax transparency with which this thesis is concerned interested the author as a result of past experience with a bakery firm. The practical application of a positive solution to this problem would be as a competitor of cellophane, that is, transparent paraffin used for commercial wax paper would combine the quality of keeping bakery goods fresh with the display value of cellophane.

The Throwing Power In Chromium Plating, Samuel F. Gerstein

Bachelors’ Theses

In chromium plating, it is very difficult to get a continuous deposit of chromium of uniform properties upon irregularly shaped articles and especially upon those having deep recesses. the nature, cause, and methods on improvement of this poor throwing power will be treated.

The Effect Of Various Waxes On The Rate Of Evaporation Of Light Naphtha, Juel Osmund Severson

Bachelors’ Theses

Solids dissolved in a liquid produce a general decrease in the evaporation rate of the solvent. Experiments were performed, using light naphtha as the solvent and Paraffin, Japan, Carnauba, Candelilla, Ozokerite, Montan, and Bees waxes as solutes. These waxes were selected since they are the waxes most commonly used in the manufacture of floor waxes and work of the kind presented in this thesis finds its greatest application in connection with that industry.