Physical Chemistry Commons^™

Allosteric Mechanism On Dream Dimerization And Impact On Its Interactions With Divalent Metal Zn2+, Maria D. Santiago Estevez

FIU Electronic Theses and Dissertations

DREAM belongs to the NCS family, and it is involved in several physiological processes mediated by Ca²⁺ association, which produces changes in its oligomerization state. The mechanism of how Ca²⁺ binds to DREAM remains unknown. A kinetic study of the binding of Ca²⁺ to DREAM suggested that DREAM dimerization is a two-step process, the first step( τ₁= 8±0.1ms) is associated with the binding of Ca²⁺ to the monomer, while the second step (τ₂ = 3.6 ±0.4 s ) corresponds to a conformation relaxation that leads to the dimerization. Furthermore, by analyzing the fast …

Exonuclease Digestion Assay For Streamlining Aptamer Characterization, Engineering, And Sensor Development, Juan Canoura

FIU Electronic Theses and Dissertations

Aptamers are DNA or RNA oligonucleotide-based bioreceptors isolated in vitro through the Systematic Evolution of Ligands by Exponential Enrichment. Given the ease with which a selection can be customized, aptamers can be evolved to function in nearly any chemical environment, making them tailormade for their final application. However, the post-SELEX characterization of the 100-1000’s aptamer candidates remains a significant bottleneck as there are no suitable techniques for high-throughput characterization of each candidate’s affinity/specificity. Moreover, the final aptamer must be engineered to possess signal reporting functionality; this is often done via trail-and-error truncation to yield a structure-switching aptamer. This dissertation describes …

Purine Nucleosides Modified At C8 Or C2 Position With (Β-Halo)Vinylsulfone And Β-Ketosulfone Reactive Groups And Their Incorporation Into Dna: Synthesis Of The Organoarsenical Antibiotic Arsinothricin And Polyaromatic Hydrocarbons, Md Abu Hasan Howlader

FIU Electronic Theses and Dissertations

Modified nucleosides gained great attention as potential anticancer and antiviral therapeutics. In this dissertation, synthesis and reactivity of (β-iodovinyl)sulfone and β-ketosulfone groups incorporated into purine nucleosides at C8 or C2 positions and DNA incorporation of their 5' triphosphates have been developed. Moreover, synthesis of novel antibiotic arsinothricin (AST) as well as polycyclic aromatic hydrocarbons (PAHs) have been discussed. The 8-(1-iodo-2-tosylvinyl)-2'-deoxyadenosine and 8-(1-Iodo-2-tosylvinyl)adenosine were synthesized employing iodovinylsulfonation of 8-ethynyl precursors with TsNa/I₂/NaOAc. The 8-(β-iodovinyl)sulfonyl-2'-deoxyguanosine was prepared via radical mediated iodovinylsulfonation of 8-ethynyl-2'-deoxyguanosine with TsNHNH₂/KI/(BzO)₂. Conformationally different C2 substituted isomeric adenosine analogues were prepared by iodovinylsulfonation …

Surface Enhanced Raman Spectroscopy (Sers) As A Nanoscale Adsorption Phenomenon: Development Of Tailored Nanomaterials For Applications In Drug Detection, Chiara Deriu

FIU Electronic Theses and Dissertations

Surface Enhanced Raman Spectroscopy (SERS) is an analytical technique in which nanostructured substrates amplify the inherently weak Raman signal of an adsorbed species by several orders of magnitude, enabling the detection of trace compounds, up to the single molecule level. While this may be an exceptional tool for any analytical scientist, SERS is at present relegated to the role of academic sensation, and is underutilized in everyday analytical practice. The SERS community is increasingly attributing this setback to a poor understanding of nanoscale surfaces and their chemical environment; since molecular adsorption at the nanostructured surface enables SERS detection, uncertainty about …

The Cyclodextrin-Perfluorinated Surfactant Host-Guest Complex: Fundamental Studies For Potential Environmental Remediation And Therapeutic Applications, Mary J. Errico

FIU Electronic Theses and Dissertations

Perfluoroalkyl substances (PFASs) are contaminants of emerging concern, and have been detected in drinking water, wildlife, humans, and the environment. Cyclodextrins (CDs), cyclic sugars composed of glucose monomers, are proposed as a potential remediation strategy. CDs can form host-guest complexes with hydrophobic molecules; this complexation could be capitalized on for PFAS removal and sequestration. These dissertation projects aim to study the fundamental host-guest interactions between a variety of PFASs and CDs for eventual applications in environmental and biological remediation. 1D and 2D Nuclear magnetic resonance (NMR) spectroscopic methods were employed to determine the strength, dynamics, and structure of the CD:PFAS …

Pyrolysis Of Jet Propellants And Oxidation Of Polycyclic Aromatic Radicals With Molecular Oxygen: Theoretical Study Of Potential Energy Surfaces, Mechanisms, And Kinetics, Daniel E. Belisario-Lara

FIU Electronic Theses and Dissertations

Two reaction classes have been studied computationally including the pyrolysis of various components of airplane fuels, such as decane, dodecane, butylbenzene isomers, and JP-10 (exo-tetrahydrodicyclopentadiene), and oxidation of a group of molecules belonging to the class of Polycyclic Aromatic Hydrocarbons (PAHs). Investigation of both reaction classes have been performed using ab initio quantum chemistry methods with the Gaussian 09 and MOLPRO programs at various levels of theory. Initially, Potential Energy Surfaces (PES) were generated at the G3(MP2,CC)/B3LYP/6-311G** level of theory for various radicals involved in the reactions as reactants, intermediates, transition states, and products. The next step was …

Hybrid Electrochemical Capacitors: Materials, Optimization, And Miniaturization, Richa Agrawal

FIU Electronic Theses and Dissertations

With the ever-advancing technology, there is an incessant need for reliable electrochemical energy storage (EES) components that can provide desired energy and power. At the forefront of EES systems are electrochemical capacitors (ECs), also known as supercapacitors that typically have higher power and superior cycle longevity but lower energy densities than their battery counterparts. One of the routes to achieve higher energy density for ECs is using the hybrid EC configuration, which typically utilizes a redox electrode coupled with a counter double-layer type electrode.

In this dissertation, both scale-up (coin-cell type) as well as scale-down (on-chip miniaturized) hybrid ECs were …

Hybrid Polymer Electrolyte For Lithium-Oxygen Battery Application, Amir Chamaani

FIU Electronic Theses and Dissertations

The transition from fossil fuels to renewable resources has created more demand for energy storage devices. Lithium-oxygen (Li-O₂) batteries have attracted much attention due to their high theoretical energy densities. They, however, are still in their infancy and several fundamental challenges remain to be addressed. Advanced analytical techniques have revealed that all components of a Li-O₂ battery undergo undesirable degradation during discharge/charge cycling, contributing to reduced cyclability. Despite many attempts to minimize the anode and cathode degradation, the electrolyte remains as the leading cause for rapid capacity fading and poor cyclability in Li-O₂ batteries. In this …

Capture And Densification Of Floating Hydrophobic Liquids By Natural Granular Materials, Daria Boglaienko

FIU Electronic Theses and Dissertations

Densification and submergence of floating crude oil is proposed as a novel oil spills treatment method. Surface application of dry granular materials (e.g., quartz sand, limestone) on top of a floating oil layer increases the density of the floating oil phase/granule mixture and leads to formation of relatively large and stable aggregates with significant amounts of captured oil. The aggregates separate from the floating hydrophobic phase and settle by gravity. Implementation of this method will reduce the impact radius of a spill and its mobility, preventing direct contamination of beaches, coastal flora and fauna.

The major objective of this research …

Kinetics And Reaction Mechanisms For Methylidyne Radical Reactions With Small Hydrocarbons, Joao Marcelo Lamim Ribeiro

FIU Electronic Theses and Dissertations

The chemical evolution with respect to time of complex macroscopic mixtures such as interstellar clouds and Titan’s atmosphere is governed via a mutual competition between thousands of simultaneous processes, including thousands of chemical reactions. Chemical kinetic modeling, which attempts to understand their macroscopic observables as well as their overall reaction mechanism through a detailed understanding of their microscopic reactions and processes, thus require thousands of rate coefficients and product distributions. At present, however, just a small fraction of these have been well-studied and measured; in addition, at the relevant low temperatures, such information becomes even more scarce. Due to the …

Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham

FIU Electronic Theses and Dissertations

Downstream regulatory element antagonist modulator (DREAM) is involved in various interactions with targets both inside and outside of the nucleus. In the cytoplasm, DREAM interacts with the C-terminal fragments of presenilins to facilitate the production of β-amyloid plaques in Alzheimer’s disease. In the nucleus, Ca²⁺ free DREAM directly binds to specific downstream regulatory elements of prodynorphin/c-fos gene to repress the gene transcription in pain modulation. These interactions are regulated by Ca²⁺ and/or Mg²⁺ association at the EF-hands in DREAM. Therefore, understanding the conformational dynamics and stability associated with Ca²⁺ and/or Mg²⁺ binding to DREAM …

Development Of A Two-Fluid Drag Law For Clustered Particles Using Direct Numerical Simulation And Validation Through Experiments, Ahmadreza Abbasi Baharanchi

FIU Electronic Theses and Dissertations

This dissertation focused on development and utilization of numerical and experimental approaches to improve the CFD modeling of fluidization flow of cohesive micron size particles. The specific objectives of this research were: (1) Developing a cluster prediction mechanism applicable to Two-Fluid Modeling (TFM) of gas-solid systems (2) Developing more accurate drag models for Two-Fluid Modeling (TFM) of gas-solid fluidization flow with the presence of cohesive interparticle forces (3) using the developed model to explore the improvement of accuracy of TFM in simulation of fluidization flow of cohesive powders (4) Understanding the causes and influential factor which led to improvements and …

The Influence Of The Proximal Amide Hydrogen Bonds And The Proximal Helix Dipole On The Catalytic Activity Of Chloroperoxidase, Armando D. Pardillo

FIU Electronic Theses and Dissertations

Chloroperoxidase (CPO) is a heme-thiolate protein with exceptional versatility and great potential as a biocatalyst. The CPO reactive species, Compound I ( Cpd I) is of particular interest, as well as the Cytochrome P450 (P450) -type monoxygenase catalytic activity, which has significant biotechnological potential. Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH•••S) is a conserved feature of heme-thiolate enzymes. In CPO, the effect of NH•••S bonds is amplified by the dipole moment of the proximal helix. The role of the proximal region has been disputed as to whether it simply protects the axial sulfur, or whether …

Formation Of Polycyclic Aromatic Hydrocarbons And Nitrogen Containing Polcyclic Aromatic Compounds In Titan's Atmosphere, The Interstellar Medium And Combustion, Alexander Landera

FIU Electronic Theses and Dissertations

Several different mechanisms leading to the formation of (substituted) naphthalene and azanaphthalenes were examined using theoretical quantum chemical calculations. As a result, a series of novel synthetic routes to Polycyclic Aromatic Hydrocarbons (PAHs) and Nitrogen Containing Polycyclic Aromatic Compounds (N-PACs) have been proposed. On Earth, these aromatic compounds originate from incomplete combustion and are released into our environment, where they are known to be major pollutants, often with carcinogenic properties. In the atmosphere of a Saturn’s moon Titan, these PAH and N-PACs are believed to play a critical role in organic haze formation, as well as acting as chemical precursors …