Other Chemistry Commons^™

Computational Investigation Of Stellar Cooling, Noble Gas Nucleation, And Organic Molecular Spectra, Jax Dallas

Honors Theses

Since the advent and optimization of the Hartree-Fock method, quantum chemistry has been utilized to investigate systems operating on timeframes and environments traditionally unavailable to bench-top chemistry. As computational methods have grown more robust and less time consuming, quantum chemistry has been utilized to investigate a range of fields, including the steadily growing discipline of computational astrochemistry. Through the lens of computational astrochemistry, chemistry that occurred billions of years ago can be explored with equal clarity to that which is currently happening in the cosmos. The work presented throughout this thesis is a series of investigations into different timeframes of ...

Dibenzophosphole Synthesis From 4-4’-Ditertbutyl-1,1’-Biphenyl By Double C-P Bond Formation, Annette Echevarria

Campus Research Day

No abstract provided.

Products Of An Acid-Catalyzed 1-Methylcyclopentene Reaction, Erin Burke

Campus Research Day

The poster presents research on the alternate products produced from 1-methylcyclopentene across different concentrations of sulfuric acid catalyst.

Cown Sustains Nitrogenase Turnover In The Presence Of The Inhibitor Carbon Monoxide, Michael S. Medina, Kevin O. Bretzing, Richard A. Aviles, Kiersten M. Chong, Alejandro Espinoza, Chloe Nicole G. Garcia, Benjamin B. Katz, Ruchita N. Kharwa, Andrea Hernandez, Justin L. Lee, Terrence M. Lee, Christine Lo Verde, Max W. Strul, Emily Y. Wong, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N₂) to ammonia (NH₃). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN ...

Sulfur Anions: Comments Upon Structure, Charles A. Kingsbury

Faculty Publications -- Chemistry Department

This work emphasizes the need for solvent simulation as well as a counterion in calculations concerning anions, although optimization may be difficult. Solvent and counterion both play a large role in conformation of the ion. Part of the reason for the success of sulfur anions in chemical reactions may be the ability of sulfone oxygen(s) to coordinate with the counterion (usually lithium). The “solvent” partially dissociates lithium from the carbanion center.

The Mechanism Of Β-N-Methylamino-L-Alanine Inhibition Of Trna Aminoacylation And Its Impact On Misincorporation, Nien-Ching Han, Tammy J. Bullwinkle, Kaeli F. Loeb, Kym F. Faull, Kyle Mohler, Jesse Rinehart, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

β-N-methylamino-l-alanine (BMAA) is a nonproteinogenic amino acid that has been associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD). BMAA has been found in human protein extracts; however, the mechanism by which it enters the proteome is still unclear. It has been suggested that BMAA is misincorporated at serine codons during protein synthesis, but direct evidence of its cotranslational incorporation is currently lacking. Here, using LC-MS–purified BMAA and several biochemical assays, we sought to determine whether any aminoacyl-tRNA synthetase (aaRS) utilizes BMAA as a substrate for aminoacylation. Despite BMAA's previously predicted ...

Transcriptional Repressor Protein Based Macrolide Biosensor Development With Improved Sensitivity, Jayani A. Christopher

Graduate Research Posters

Macrolide antibiotics are in high demand for clinical applications. Macrolides are biosynthesized via giant assembly line polyketide synthases (PKS) which are arranged in a modular fashion. Combinatorial biosynthetic methods have been used to produce diversified macrolides by reprograming these modules and modifying tailoring enzymes required for post synthetic modifications. However it is challenging due to the size and complexity of PKSs. To overcome this challenge, new enzymes for macrolide diversification could be obtained by directed evolution where a large number of enzyme variants need to be screened. Therefore it is important to develop high throughput screening methods to identify the ...

Elucidating The Role Of Hydrogen Bond Donor And Acceptor On Solvation In Deep Eutectic Solvents Formed By Ammonium/Phosphonium Salts And Carboxylic Acids, Muhammad Qamar Farooq, Gabriel A. Odugbesi, Nabeel Mujtaba Abbasi, Jared L. Anderson

Chemistry Publications

Deep eutectic solvents (DESs) constitute a rapidly emerging class of sustainable liquids that have been widely studied and employed in chemical separations, catalysis, and electrochemistry. The unique physicochemical and solvation properties of DESs can be highly tailored by choosing the appropriate hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD). Understanding the role of the HBA and HBD on the multiple solvation interactions in DESs is important to enable their judicious selection for particular applications. This work constitutes the first study to exploit chromatography to measure solute–solvent interactions of DESs using a wide array of known probe molecules. The ...

Predicting The Hydration Free Energy Of Small Alkanes And Alcohols From Custom, Electronic Structure-Based Force Fields, T. Ryan Rogers

Theses and Dissertations

Mathematical theories reveal the fundamental physics involved in experimentalphenomena. Computer models of such theories are routinely used to corroborate or explain experiments and predict properties of chemical systems. Therefore, an important effort in computational chemistry is the development of more accurate and efficient chemical models. Current-generation models are only beginning to approach experimental-quality predictions of hydration free energies (HFEs).Using computations of quantum mechanical (QM) forces and classical simulations based on these forces, I investigate models to predict several properties of solutes and solutions. This dissertation is a collection of projects exemplifying methods used to gain insight into chemical systems ...

Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of ...

Efficient Step-Merged Quantum Imaginary Time Evolution Algorithm For Quantum Chemistry, Niladri Gomes, Feng Zhang, Noah F. Berthusen, Cai-Zhuang Wang, Kai-Ming Ho, Peter P. Orth, Yongxin Yao

Physics and Astronomy Publications

We develop a resource-efficient step-merged quantum imaginary time evolution approach (smQITE) to solve for the ground state of a Hamiltonian on quantum computers. This heuristic method features a fixed shallow quantum circuit depth along the state evolution path. We use this algorithm to determine the binding energy curves of a set of molecules, including H2, H4, H6, LiH, HF, H2O, and BeH2, and find highly accurate results. The required quantum resources of smQITE calculations can be further reduced by adopting the circuit form of the variational quantum eigensolver (VQE) technique, such as the unitary coupled cluster ansatz. We demonstrate that ...

Modification Of Chm20 Lab: Synthesis Of Aspirin, Nicole Diaz, Amy Musselman Prof.

KU Inspires! Undergraduate Research Day

No abstract provided.

Resource-Saving Technologies For The Production Of Elastic Leather Materials: Collective Monograph, Olena Korotych, Anatolii Danylkovych, Serhii Bilinskyi, Serhii Bondarenko, Slava Branovitska, Vasyl Chervinskyi, Nataliia Khliebnikova, Alona Kudzieva, Viktor Lishchuk, Nataliia Lysenko, Olena Mokrousova, Nataliia Omelchenko, Vera Palamar, Yuliia Potakh, Oksana Romanyuk, Olga Sanginova, Oleksandr Zhyhotsky

Chemistry Publications and Other Works

This monograph contains a collection of recent research papers focusing on advancing existing technologies and developing new technologies to improve the environmentally friendliness and save resources during the production of elastic leather materials. The papers are organized based on the type of technological process used to preserve raw hides. A lot of attention is devoted to mathematical planning, simulations, and multicriteria optimization of the technological processes using newly developed chemical reagents. The monograph contains a complex study of physicochemical properties and characteristics of the resulting leather materials. The developed technologies were tested by the private joint-stock company Chinbar (Kyiv, Ukraine ...

Novel Antibacterial Compounds And Methods Of Making And Using Same, Amit Basu, Christopher W. Reid, Michael Saladino

Science and Technology Faculty Journal Articles

The invention provides novel antibacterial diamide compounds, pharmaceutical compositions comprising the compounds and methods for treating or preventing an infection in a subject using the compounds.

Capsaicin Is A Negative Allosteric Modulator Of The 5-Ht3 Receptor, Eslam El Nebrisi, Tatiana Prytkova, Dietrich Ernst Lorke, Luke Howarth, Asma Hassan Alzaabi, Keun-Hang Susan Yang, Frank Christopher Howarth, Murat Oz

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this study, effects of capsaicin, an active ingredient of the capsicum plant, were investigated on human 5-hydroxytryptamine type 3 (5-HT₃) receptors. Capsaicin reversibly inhibited serotonin (5-HT)-induced currents recorded by two-electrode voltage clamp method in Xenopus oocytes. The inhibition was time- and concentration-dependent with an IC₅₀ = 62 μM. The effect of capsaicin was not altered in the presence of capsazepine, and by intracellular BAPTA injections or trans-membrane potential changes. In radio-ligand binding studies, capsaicin did not change the specific binding of the 5-HT₃ antagonist [³H]GR65630, indicating that it is a noncompetitive inhibitor of 5-HT ...

Highly Swelling Ph-Responsive Microgels For Dual Mode Near Infra-Red Fluorescence Reporting And Imaging, Mingning Zhu, Dongdong Lu, Qing Lian, Shanglin Wu, Wenkai Wang, L. Andrew Lyon, Weiguang Wan, Paulo Bártolo, Mark Dickinson, Brian R. Saunders

Engineering Faculty Articles and Research

Near infra-red (NIR) fluorescence is a desirable property for probe particles because such deeply penetrating light enables remote reporting of the local environment in complex surroundings and imaging. Here, two NIR non-radiative energy transfer (NRET) fluorophores (Cy5 and Cy5.5) are coupled to preformed pH-responsive poly(ethylacrylate-methacrylic acid-divinylbenzene) microgel particles (PEA-MAA-5/5.5 MGs) to obtain new NIR fluorescent probes that are cytocompatible and swell strongly. NIR ratiometric photoluminescence (PL) intensity analysis enables reporting of pH-triggered PEA-MAA-5/5.5 MG particle swelling ratios over a very wide range (from 1–90). The dispersions have greatly improved colloidal stability compared to ...

Electrostatic Denaturation Of Dna-Cisplatin Adducts, Eddie Madrigal

Master's Theses

In this thesis, electrochemical approaches are used to determine the properties of deoxyribonucleic acid (DNA) by electrostatic denaturation. The electrochemical routine involves an application of a destabilization potential, an equilibration potential, and a square wave voltammogram (SWV) to monitor the extent of melting. Our method uses a monolayer consisting of thiol modified DNA and mercaptohexanol on a gold electrode. These electrodes are then incubated in a complementary sequence tagged with methylene blue. By using our electrostatic denaturation technique, different parameters are explored, such as surface densities, surface coverages, and ionic strengths. As proof of concept, these techniques were applied toward ...

Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the “second secret of life.” The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of ...

The Development Of A Surface Enhanced Raman Spectroscopy Method For The Detection Of Synthetic Cannabinoids In Urine, Thaddeus Mostowtt

FIU Electronic Theses and Dissertations

The use and abuse of synthetic cannabinoids has increased significantly in recent years due to their easy access and growing popularity. Despite having more known drugs become illegal, new synthetic versions of these drugs are being made that have not yet been recognized or classified as illegal substances. Therefore, standard methods may not be able to detect these drugs.

The most common method of screening detection for drugs of abuse in biological samples is the immunoassay. However, the immunoassay method presents some disadvantages, particularly for newly synthesized compounds. More advanced methods have also been used, such as LC-MS; however, these ...

Systematic Comparison Of Pre-Treatment Parameters In Forensic Hair Analysis And Investigating Hair-Drug Interactions, Jennett Chenevert Aijala

FIU Electronic Theses and Dissertations

Forensic toxicological analysis for the purposes of protecting human health and supporting criminal justice activities can be achieved, in part, by means of analysis of human head hair for detection of abused substances. Hair is considered an alternative sample matrix (compared to blood and urine) because of persistent interpretive challenges caused by a lack of standardization in analytical approaches and poor understanding of the biases resulting from physicochemical interactions between major hair components (e.g., melanin) and drugs of abuse. Some of the uncertainty regarding optimal techniques for the pre-treatment of hair specimens results from the unknown nature of the ...