Physical Chemistry Commons^™

Divergence Of Thioesterase Function: Human Bfit2, Escherichia Coli Enth, And Ydii, Danqi Chen

Chemistry and Chemical Biology ETDs

My doctoral research primarily focuses on two hotdog-fold thioesterases, EntH (also known as YbdB) from E. coli, and BFIT2 from Homo sapiens. The EntH (YbdB) gene is included in a large gene cluster that encodes the enzymes of the biosynthetic pathway leading to enterobactin. Building on the hypothesis that EntH might function in a house-keeping' role by liberating misacylated EntB, two potential pathways to EntB misacylation were identified, one involving the phosphopantetheinyl transferase EntD and the other involving 2,3-DHB-AMP ligase EntE. EntH displays thioesterase activity towards a variety of acyl and aryl-holo EntB adducts. Lastly, It was shown that EntF …

The Nature And Kinetic Analysis Of Carbon-Carbon Bond Fragmentation Reactions Of Cation Radicals Derived From Set-Oxidation Of Lignin Model Compounds, Adam S. Pimentel

Chemistry and Chemical Biology ETDs

The lignin peroxidase promoted α-carbon β-carbon bond cleavage of two diastereomeric pairs of dimeric lignin model compounds were investigated to determine which structural units are more readily cleaved. These model compounds, β-1 (1,2-diaryl-1,3-propanediol) and β-O-4 (1-diaryl-2-aryloxy-1,3-propanediol), represent the most common structural units present in the plant cell wall polymer lignin. The lignin peroxidase catalyzed reaction mechanism was shown to parallel two mechanistically well understood systems, the cerric (IV) ammonium nitrate promoted chemical reacton, and the dicyannoanthracene promoted photochemical reaction, both of which proceed by a SET mechanism. Product profiles and kinetic rate constants were determined and compared for all four …

Laser-Assisted Single-Molecule Refolding, Rui Zhao

Wayne State University Dissertations

Non-coding RNAs must fold into precise secondary and tertiary structures in order to perform the biological functions. Due to the flexibility of RNA, the RNA folding energy landscape can be rugged and full of local minimum (kinetic trap). To provide a means to study kinetically trapped RNAs, we have developed a new technique combining single-molecule FRET detection with laser induced temperature jump. We have calibrated the magnitude of the temperature jump with 1˚C accuracy using gold micro-size sensor. The accuracy of temperature calibration was confirmed by close agreement between single-molecule and bulk DNA duplex melting experiments.

HIV 1 DIS RNAs …

Astrochemical Dynamics: Fundamental Studies Relevant To Titan's Atmosphere, Wilson Kamundia Gichuhi

Wayne State University Dissertations

This work presents results of primary fundamental photodissociation and state-specific ion-molecule dynamical studies that are relevant to understanding the formation and growth mechanisms of unsaturated hydrocarbon molecules, haze layers and aerosols in Titan's upper atmosphere. In the diacetylene dimer, it is shown, via laboratory studies combined with electronic structure calculations that the photodissociation of the dimer readily initiates atomic hydrogen (H) loss and atomic H transfer reactions forming two prototypes of resonantly stabilized free radicals, C8H3 and C4H3, respectively. In ethylamine cation, high-level ab initio calculations identify the complex dissociation pathways for the ground state CH3CH2NH2+ radical cation at 233.3 …

Electronic Excitations In Branched Conjugated Oligomers: A Quasiparticle View And Tight-Binding Models, Hao Li

Wayne State University Dissertations

This dissertation focuses on the theoretical understanding and simulation of the excited state electronic structures of organic conjugated molecules. The exciton scattering (ES) approach has been extended for efficient calculation of optical spectra of large branched conjugated oligomers. The methodology of tight-binding (lattice) model, originally developed in condensed matter theory, has been extended to the building block structure of conjugated molecules for explicit description of the electronic excitations.

Within the ES approach, the electronic excitations in quasi-1D molecular structures are attributed to standing waves that represent quantum quasiparticles (excitons) scattered at the molecular vertices. Excitation energies can be found by …

Dynamic Light Scattering And Zeta Potential Of Colloidal Mixtures Of Amelogenin And Hydroxyapatite In Calcium And Phosphate Rich Ionic Milieus, Vuk Uskoković, Roselyn Odsinada, Sonia Djordjevic, Stefan Habelitz

Pharmacy Faculty Articles and Research

The concept of zeta-potential has been used for more than a century as a basic parameter in controlling the stability of colloidal suspensions, irrespective of the nature of their particulate ingredients – organic or inorganic. There are prospects that self-assembly of peptide species and the protein-mineral interactions related to biomineralization may be controlled using this fundamental physicochemical parameter. In this study, we have analyzed the particle size and zeta-potential of the full-length recombinant human amelogenin (rH174), the main protein of the developing enamel matrix, in the presence of calcium and phosphate ions and hydroxyapatite (HAP) particles. As calcium and phosphate …

The Impact Of Driving Conditions On Phev Battery Performance, Nathan Christensen, John Patten, Steven Srivastava, Gary P. Nola

Green Manufacturing Research Journal

The battery performance of a modified Prius with a 5 kWh plug-in battery was documented for a year to determine the impact of environmental conditions and user attributes on vehicle performance.  Both fuel economy and pure electrical efficiency were compared to ambient temperature.  The fuel economy has a positive relationship with ambient temperature until approximately 70˚F where the efficiency begins to drop.  Electrical performance has a positive linear relationship with ambient temperature.  With the emergence of electric vehicles (EVs) and PHEVs from a variety of automotive manufacturers, information on EV and PHEV performance for consumers will become more important.

Application Of Niobium Enriched Ormosils As Thermally Stable Coatings For Aerospace Aluminium Coatings, P.C. Rajath Varma, Mohamed Oubaha, Pradeepan Periyat, Colette Mcdonagh, Brendan Duffy

Articles

The aim of this experimental research is to study the ability of niobium rich sol-gel coatings to withstand thermal stress, while remaining impermeable to corrosive agents for the protection of aerospace alloys. The coating material is developed via polymeric sol-gel synthesis employing 3-(trimethoxysilyl)propylmethacrylate (MAPTMS) and niobium ethoxide precursors as a source of silicon and niobium, respectively. The beneficial effect of niobium inclusion within coating was characterised spectroscopically, calorimetrically and electrochemically. The thermal cycling effects of the coating were studied using microscopic and accelerated test methods. Electrochemical tests showed that corrosion current of the material was 2 orders lower in magnitude …

Investigation Of Titanium Nitride As Catalyst Support Material And Development Of Durable Electrocatalysts For Proton Exchange Membrane Fuel Cells, Bharat Avasarala

Legacy Theses & Dissertations (2009 - 2024)

The impending energy and climatic crisis makes it imperative for human society to seek non-fossil based alternative sources for our energy needs. Although many alternative energy technologies are currently being developed, fuel cell technology provides energy solutions, which satisfy a wide range of applications. But the current fuel cell technology is far from its target of large scale commercialization mainly because of its high cost and poor durability. Considerable work has been done in reducing the cost but its durability still needs significant improvement. Of the various materials in a PEM fuel cell, the degradation of electrocatalyst affects its durability …

Band Structures Of Layered Carbon/Boron Nitride Materials With Commensurate Lattices, Christopher C. Wells

Legacy Theses & Dissertations (2009 - 2024)

The electronic structures of systems consisting of hexagonal boron nitride layers and graphite sheets have been investigated in detail using density functional theory methods with two exchange correlation functions (local density approximation and generalized gradient approximation). The experimental data of graphene, graphite, monolayer hexagonal BN, and hexagonal BN were reproduced well with computational models. The commensurate models used in the investigation were generated by taking the averages of the lattice constants for graphite and h-BN.

Fourier Transform Emission Spectroscopy Of Yh And Yd: Observation Of New A¹Δ And B¹Π Electronic States, R. S. Ram, G. Li, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

The emission spectra of YH and YD molecules have been investigated in the 3600–12 000 cm⁻¹ region using a Fourier transform spectrometer. Molecules were formed in an yttrium hollow cathode lamp operated with a continuous flow of a mixture of Ne and Ar gases, and YH and YD were observed together in the same spectra. A group of bands observed near 1 μm have been identified as 0-0 and 1-1 bands of the A¹Δ-X¹Σ⁺ and B¹Π-X¹Σ⁺ transitions of YH and the 0-0 bands of the same two transitions …

Nonuniformity In Lattice Contraction Of Bismuth Nanoclusters Heated Near Its Melting Point, A. Esmail, M. Abdel-Fattah, Hani E. Elsayed-Ali

Electrical & Computer Engineering Faculty Publications

The structural properties of bismuth nanoclusters were investigated with transmission high-energy electron diffraction from room temperature up to 525 ± 6 K. The Bi nanoclusters were fabricated by thermal evaporation at room temperature on transmission electron microscope grids coated with an ultrathin carbon film, followed by thermal and femtosecond laser annealing. The annealed sample had an average cluster size of ∼14 nm along the minor axis and ∼16 nm along the major axis. The Debye temperature of the annealed nanoclusters was found to be 53 ± 6 K along the [012] direction and 86 ± 9 K along the [110] …

Theoretical Characterization Of Non-Covalent Weakly Bound Clusters Through The Application Of Sophisticated Computational Quantum Chemistry Methodologies And The Development Of Integrated Fragmentation Techniques, Desiree Bates

Electronic Theses and Dissertations

Non-covalent, weakly bound clusters have been and remain of significant interest to many researchers. However, with computational studies, accurate description of these interactions requires sophisticated electronic structure methods employing large basis sets. This methodology becomes extremely computationally demanding as the size of the system increases. This work presents benchmark data and explores methods for obtaining highly accurate ab initio results for larger systems at greatly reduced computational costs. CCSD(T) complete basis set limit interaction energies are presented for a variety of parallel-slipped π...π dimers and low-lying isomers of (h₂o)₆. The calibration of a 2-body:Many-body fragmentation method …

Characterization Of Intermolecular Pi-Type Interactions Using Sophisticated Quantum Mechanical, Electronic Structure Computations, Emily Joy Carrell

Electronic Theses and Dissertations

Much like the instrumentation in an experimental lab, computational chemists use computers to solve the mathematical equations that describe the physics of electrons to understand the chemistry involved. The combination of the two main components of computational chemistry, the basis set and method, determines the ``cost'' (disk, memory, and CPU time) of a computation. A variety of basis sets and methods have been developed in the past century. The focus of this report is to accurately describe non-covalent interactions with the use of various quantum computational techniques. In Chapter 1 a brief discussion on the theory behind computational chemistry is …

Ultrafast Rempi In Benzene And The Monohalobenzenes Without The Focal Volume Effect, Timothy D. Scarborough, James Strohaber, David B. Foote, Collin J. Mcacy, Cornelis J. Uiterwaal

C.J.G.J. Uiterwaal Publications

We report on the photoionization and photofragmentation of benzene (C₆H₆) and of the monohalobenzenes C₆H₅–X (X = F, Cl, Br, I) under intense-field, single-molecule conditions. We focus 50-fs, 804-nm pulses from a Ti:sapphire laser source, and record ion mass spectra as a function of intensity in the range ~10¹³ W/cm² to ~10¹⁵ W/cm². We count ions that were created in the central, most intense part of the focal area; ions from other regions are rejected. For all targets, stable parent ions (C₆H₅X+) are …

Elastic Properties Of Poly(Vinyldene Fluoride) (Pvdf) Crystals: A Density Functional Theory Study, Yong Pei, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We computed structural and elastic properties of totally nine phases of poly(vinyldene fluoride) (PVDF) crystals using the density-functional theory (DFT) method with and without inclusion of the dispersion corrections. In addition to the four known crystalline forms, mechanic properties of five theoretically predicted crystalline forms of PVDF are also investigated. The all-trans form I_p exhibits the largest cohesive energy, bulk, and Young’s modulus among the nine crystalline forms. The DFT calculations suggest that the δ crystalline forms (III_au, III_pu, III_pd, and III_ad) possess poor chain rigidity among the nine PVDF …

Structure Evolution Of Gold Cluster Anions Between The Planar And Cage Structures By Isoelectronic Substitution: AuN− (N = 13–15) And MauN− (N = 12–14; M = Ag, Cu), Rhitankar Pal, Lei-Ming Wang, Wei Huang, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The structural and electronic effects of isoelectronic substitution by Ag and Cu atoms on gold cluster anions in the size range between 13 and 15 atoms are studied using a combination of photoelectron spectroscopy and first-principles density functional calculations. The most stable structures of the doped clusters are compared with those of the undoped Au clusters in the same size range. The joint experimental and theoretical study reveals a new C_3v symmetric isomer for Au₁₃ ⁻, which is present in the experiment, but has hitherto not been recognized. The global minima of Au₁₄ ⁻ and Au …

Studies On Silicon Nmr Characterization And Kinetic Modeling Of The Structural Evolution Of Siloxane-Based Materials And Their Applications In Drug Delivery And Adsorption, Jyotrhirmai Ambati

University of Kentucky Doctoral Dissertations

This dissertation presents studies of the synthetic processes and applications of siloxane-based materials. Kinetic investigations of bridged organoalkoxysilanes that are precursors to organic-inorganic hybrid polysilsesquioxanes are a primary focus. Quick gelation despite extensive cyclization is found during the polymerization of bridged silane precursors except for silanes with certain short bridges. This work is an attempt to characterize and understand some of the distinct features of bridged silanes using experimental characterization, kinetic modeling and simulation. In addition to this, the dissertation shows how the properties of siloxane- materials can be engineered for drug delivery and adsorption.

The phase behavior of polymerizing …

Evaluation Of The Physicochemical Properties And Stability Of Solid Lipid Nanoparticles Designed For The Delivery Of Dexamethasone To Tumors, Melissa Howard

University of Kentucky Doctoral Dissertations

Pre-clinical and clinical trials suggest that pre-treatment with dexamethasone (Dex) may facilitate enhanced uptake of subsequently administered chemotherapeutic agents. To reduce the side effects associated with systemic administration of Dex, solid lipid nanoparticles (SLNs) containing dexamethasone palmitate (Dex-P) were prepared as a means of achieving tumor-targeted drug delivery. These studies were aimed at evaluating the physicochemical properties and both the physiological and storage stability of the SLNs.

SLNs were prepared using nanotemplate engineering technology. Stearyl alcohol (SA) was used as the lipid phase with Brij^® 78 and Polysorbate 60 as surfactants and PEG6000 monostearate as a long-chain PEGylating agent. …

Precise Control Of Highly Ordered Arrays Of Nested Semiconductor/Metal Nanotubes, Diefeng Gu, Helmut Baumgart, Kandabara Tapily, Pragya Shrestha, Gon Namkoong, Xianyu Ao, Frank Müller

Electrical & Computer Engineering Faculty Publications

Lithographically defined microporous templates in conjunction with the atomic layer deposition (ALD) technique enable remarkable control of complex novel nested nanotube structures. So far three-dimensional control of physical process parameters has not been fully realized with high precision resolution, and requires optimization in order to achieve a wider range of potential applications. Furthermore, the combination of composite insulating oxide layers alternating with semiconducting layers and metals can provide various types of novel applications and eventually provide unique and advanced levels of multifunctional nanoscale devices. Semiconducting TiO₂ nanotubes have potential applications in photovoltaic devices. The combination of nanostructured semiconducting materials …