Chemistry Commons^™

Ultrafast Hole Trapping And Relaxation Dynamics In P-Type Cus Nanodisks, John Ludwig, Li An, Brian Pattengale, Qingyu Kong, Xiaoyi Zhang, Pinxian Xi, Jier Huang

Chemistry Faculty Research and Publications

CuS nanocrystals are potential materials for developing low-cost solar energy conversion devices. Understanding the underlying dynamics of photoinduced carriers in CuS nanocrystals is essential to improve their performance in these devices. In this work, we investigated the photoinduced hole dynamics in CuS nanodisks (NDs) using the combination of transient optical (OTA) and X-ray (XTA) absorption spectroscopy. OTA results show that the broad transient absorption in the visible region is attributed to the photoinduced hot and trapped holes. The hole trapping process occurs on a subpicosecond time scale, followed by carrier recombination (~100 ps). The nature of the hole trapping sites, …

Genetic Algorithm Optimization Of Point Charges In Force Field Development: Challenges And Insights, Maxim Vadimovich Ivanov, Marat R. Talipov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA …

Structural Classification Of Metal Complexes With Three-Coordinate Centres, Timothy L. Davis, Joshua A. Watts, Kenneth J. Brown, Jeewantha S. Hewage, Alexander Richard Treleven, Sergey V. Lindeman, James R. Gardinier

Chemistry Faculty Research and Publications

Attempts to describe the geometry about three-coordinate silver(I) complexes have proven difficult because interatomic angles generally vary wildly and there is no adequate or readily available classification system found in the literature. A search of the Cambridge Structural Database shows that complexes formed between any metal centre and three non-metal donors (18001 examples) usually adopt geometries that are quite different than ideal ‘textbook’ extremes of either trigonal planar (∼4% with α = β = γ = 120 ± 2°), T-shaped (∼0.05% with α = 180 ± 2°, β = γ = 90 ± 2°), or trigonal pyramidal (∼0.3% with α …

Indolinyl-Thiazole Based Inhibitors Of Scavenger Receptor-Bi (Sr-Bi)-Mediated Lipid Transport, Chris Dockendorff, Patrick W. Faloon, Miao Yu, Willmen Youngsaye, Marsha Penman, Thomas J.F. Nieland, Partha P. Nag, Timothy A. Lewis, Jun Pu, Melissa Bennion, Joseph Negri, Conor Paterson, Garrett Lam, Sivaraman Dandapani, José R. Perez, Benito Munoz, Michelle A. Palmer, Stuart L. Schreiber, Monty Krieger

Chemistry Faculty Research and Publications

A potent class of indolinyl-thiazole based inhibitors of cellular lipid uptake mediated by scavenger receptor, class B, type I (SR-BI) was identified via a high-throughput screen of the National Institutes of Health Molecular Libraries Small Molecule Repository (NIH MLSMR) in an assay measuring the uptake of the fluorescent lipid DiI from HDL particles. This class of compounds is represented by ML278 (17–11), a potent (average IC₅₀ = 6 nM) and reversible inhibitor of lipid uptake via SR-BI. ML278 is a plasma-stable, noncytotoxic probe that exhibits moderate metabolic stability, thus displaying improved properties for in vitro …

Electrostatic Point Charge Fitting As An Inverse Problem: Revealing The Underlying Ill-Conditioning, Maxim Vadimovich Ivanov, Marat R. Talipov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Atom-centered point charge (PC) model of the molecular electrostatics-a major workhorse of the atomistic biomolecular simulations-is usually parameterized by least-squares (LS) fitting of the point charge values to a reference electrostatic potential, a procedure that suffers from numerical instabilities due to the ill-conditioned nature of the LS problem. To reveal the origins of this ill-conditioning, we start with a general treatment of the point charge fitting problem as an inverse problem and construct an analytical model with the point charges spherically arranged according to Lebedev quadrature which is naturally suited for the inverse electrostatic problem. This analytical model is contrasted …

Boron Functionalization Of Bodipy Dyes, And Their Evaluation As Bioimaging Agents, Alex Long Nguyen

LSU Doctoral Dissertations

BODIPY, also known as “porphyrin’s little sister,” belongs to a class of fluorescent dyes. It contains a dipyrromethene π-system with a disubstituted boron atom. The basic 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) is known for its numerous useful applications in the fields of biology and materials. Modification of this well-known fluorophore has been shown to change its photophysical and chemical properties. There has been great interest in the modification at the boron center in recent years for synthesizing new dyads and cascade-type dyes. This work focuses on functionalization at the boron center with carbon and oxygen nucleophiles for further investigation as bioimaging agents. Chapter …

Impact Of Size, Secondary Structure, And Counterions On The Binding Of Small Ribonucleic Acids To Layered Double Hydroxide Nanoparticles, B. V. Rodriguez, J. Pescador, N. Pollok, G. W. Beall, Corina Maeder, L. K. Lewis

Chemistry Faculty Research

Use of ribonucleic acid (RNA) interference to regulate protein expression has become an important research topic and gene therapy tool, and therefore, finding suitable vehicles for delivery of small RNAs into cells is of crucial importance. Layered double metal hydroxides such as hydrotalcite (HT) have shown great promise as nonviral vectors for transport of deoxyribose nucleic acid (DNA), proteins, and drugs into cells, but the adsorption of RNAs to these materials has been little explored. In this study, the binding of small RNAs with different lengths and levels of secondary structure to HT nanoparticles has been analyzed and compared to …

On The Development Of Analytical Methodologies To Interrogate The Lipid Dynamics And Phase Transition Resulting From The Reduction Of Stimuli-Responsive Vesicles, James Edward Winter

LSU Doctoral Dissertations

The potential is great for liposome drug delivery systems that provide specific contents release at diseased tissue sites upon activation by upregulated enzymes; however, this potential will only come to fruition with mechanistic knowledge of the contents release process. NAD(P)H:quinone oxidoreductase type 1 (NQO1) is a target for reductively-responsive liposomes, as it is an enzyme upregulated in numerous cancer tissues and is capable of reducing quinone propionic acid (QPA) trigger groups to hydroquinones that self-cleave from dioleolylphosphatidylethanolamine (DOPE) liposome surfaces, thereby initiating contents release. This research targets the development of analytical methodologies to observe and characterize the dynamics and resulting …

Computational Investigations Of Potential Energy Function Development For Metal-Organic Framework Simulations, Metal Carbenes, And Chemical Warfare Agents, Christian R. Cioce

USF Tampa Graduate Theses and Dissertations

Metal-Organic Frameworks (MOFs) are three-dimensional porous nanomaterials with a variety of applications, including catalysis, gas storage and separation, and sustainable energy. Their potential as air filtration systems is of interest for designer carbon capture materials. The chemical constituents (i.e. organic ligands) can be functionalized to create rationally designed CO2 sequestration platforms, for example. Hardware and software alike at the bleeding edge of supercomputing are utilized for designing first principles-based molecular models for the simulation of gas sorption in these frameworks. The classical potentials developed herein are named PHAST -- Potentials with High Accuracy, Speed, and Transferability, and thus are designed …

Fabrication Of Tissue Precursors Induced By Shape-Changing Hydrogels, Olukemi O. Akintewe

USF Tampa Graduate Theses and Dissertations

Scaffold based tissue reconstruction inherently limits regenerative capacity due to inflammatory response and limited cell migration. In contrast, scaffold-free methods promise formation of functional tissues with both reduced adverse host reactions and enhanced integration. Cell-sheet engineering is a well-known bottom-up tissue engineering approach that allows the release of intact cell sheet from a temperature responsive polymer such as poly-N-isopropylacrylamide (pNIPAAm). pNIPAAm is an ideal template for culturing cell sheets because it undergoes a sharp volume-phase transition owing to the hydrophilic and hydrophobic interaction around its lower critical solution temperature (LCST) of 32°C, a temperature close to physiological temperature. Compared to …

Theoretical Investigations Of Gas Sorption And Separation In Metal-Organic Materials, Tony Pham

USF Tampa Graduate Theses and Dissertations

Metal--organic frameworks (MOFs) are porous crystalline materials that are synthesized from rigid organic ligands and metal-containing clusters. They are highly tunable as a number of different structures can be made by simply changing the organic ligand and/or metal ion. MOFs are a promising class of materials for many energy-related applications, including H₂ storage and CO₂ capture and sequestration. Computational studies can provide insights into MOFs and the mechanism of gas sorption and separation. Theoretical studies on existing MOFs are performed to determine what structural characteristics leads to favorable gas sorption mechanisms. The results from these studies can provide …

Organic-Inorganic Hybrid Materials Based On Oxyanion Linkers For Selective Adsorption Of Polarizable Gases, Mona Hanafy Mohamed

USF Tampa Graduate Theses and Dissertations

The separation of industrially important gases into pure supplies that can be used for many practical applications is based mainly on energy intensive methods such as the cryogenic distillation which is costly and energy intensive. Therefore other routes have been introduced to industrial separation of gases such as the selective adsorption using porous solid materials. Zeolites and activated carbon are the most widely used recyclable energy-efficient porous solid materials for industrial gas separations, however the low uptake and selectivity hurdles their commercialization in some separation applications. Metal organic frameworks (MOFs) have been extensively studied as solid porous materials in term …

2,4-Disubstituted Quinazolines With Antileishmanial Or Antibacterial Activity, Megan Marie Barber

USF Tampa Graduate Theses and Dissertations

Herein 47 2,4-disubstituted quinazolines were synthesized and tested against Leishmania donovani intracellular amastigotes. A structure-activity relationship was conducted and lead to the identification of quinazolines with EC50s in the single digit and high nanomolar range with favorable antileishmanial selectivity indexes. Quinazoline 2.6 and 2.31 underwent in vivo efficacy studies in murine models of visceral leishmaniasis, reducing liver parasitemia by 12 % and 24 %, respectively, when given by the intraperitoneal route at 15 mg/kg/day x 5 days. The antileishmanial efficacy and easy of synthesis make the 2,4-disubstituted quinazoline compound series a suitable platform for the future development of antileishmanial agents. …

Biosynthesis Of Long-Chain Fatty Acid Amides, Kristen A. Jeffries

USF Tampa Graduate Theses and Dissertations

The vast variety of long-chain fatty acid amides identified in biological systems is intriguing. The general structure of a fatty acid amide is R-CO-NH-X, where R is an alkyl group and X is derived from an immense variety of biogenic amines. Although structurally simple, the bioactivities of these molecules as signaling lipids are very diverse and have just recently begun to emerge in the literature. Interest in the long-chain fatty acid amides dramatically increased following the identification and characterization of one specific N-acylethanolamine, N-arachidonoylethanolamine (anandamide), as the endogenous ligand for the cannabinoid receptors in the mammalian brain. Since …

Metal Organic Frameworks (Mofs) And Porous Organic Polymers (Pops) For Heterogeneous Asymmetric Catalysis, Youngran Ji

USF Tampa Graduate Theses and Dissertations

The administration of enantiopure drugs brings advantages such as improved efficacy, more predictable pharmacokinetics and reduced toxicity from the point of view of the pharmaceutical area.[1] For this reason, a tremendous amount of supply and demand for enantiomeric pure compounds has been shown not only in market, but industry and academia.[^2-4] According to the industry publication Genetic Engineering and Biotechnology News (GEN) in 2014, 22 billion dollars were accounted for enantiopure form of drugs such as Sovaldi® (Sofosbuvir), Crestor® (Rosuvastatin), and Advair® (fluticasone/salmeterol).

The fact that one enantiomer can be pharmacologically effective whereas the other enantiomer can be …

Development Of Orally Bioavailable 4(1H)-Quinolones And 1,2,3,4-Tetrahydroacridin-9(10H)-Ones With Potent Anti-Malarial Activity, Jordany Richarlson Maignan

USF Tampa Graduate Theses and Dissertations

Although Malaria rates are on the decline due to the efforts of the World Health Organization and other organizations dedicated to the eradication of this disease, a relaxed attitude towards the development of new antimalarial entities would be flawed. Due to the emergence of resistance in the parasite, the almost 50% world-wide reduction in malarial death rates that have been produced over the past 15 years are threatening to be lost

New drugs are urgently needed and our approach focuses on the re-evaluation and optimization of the historic antimalarial ICI 56,780. Due to its causal prophylactic activity, along with its …

Regional-Scale Simulations Of Fungal Spore Aerosols Using An Emission Parameterization Adapted To Local Measurements Of Fluorescent Biological Aerosol Particles, Matthias Hummel, Corinna Hoose, M. Gallagher, D. A. Healy, J. Alex Huffman, D. O'Connor, U. Pöschl, C. Pöhlker, N. H. Robinson, M. Schnaiter, J. R. Sodeau, M. Stengel, E. Toprak, H. Vogel

Chemistry and Biochemistry: Faculty Scholarship

Fungal spores as a prominent type of primary biological aerosol particles (PBAP) have been incorporated into the COSMO-ART (Consortium for Small-scale Modelling- Aerosols and Reactive Trace gases) regional atmospheric model. Two literature-based emission rates for fungal spores derived from fungal spore colony counts and chemical tracer measurements were used as a parameterization baseline for this study. A third, new emission parameterization for fluorescent biological aerosol particles (FBAP) was adapted to field measurements from four locations across Europe. FBAP concentrations can be regarded as a lower estimate of total PBAP concentrations. Size distributions of FBAP often show a distinct mode at …

The Micro-Orifice Uniform Deposit Impactor–Droplet Freezing Technique (Moudi-Dft) For Measuring Concentrations Of Ice Nucleating Particles As A Function Of Size: Improvements And Initial Validation, R. H. Mason, C. Chou, C. S. Mccluskey, E. J. T. Levin, C. L. Schiller, T. C. J. Hill, J. Alex Huffman, P. J. Demott, A. K. Bertram

Chemistry and Biochemistry: Faculty Scholarship

The micro-orifice uniform deposit impactor– droplet freezing technique (MOUDI-DFT) combines particle collection by inertial impaction (via the MOUDI) and a microscope-based immersion freezing apparatus (the DFT) to measure atmospheric concentrations of ice nucleating particles (INPs) as a function of size and temperature. In the first part of this study we improved upon this recently introduced technique. Using optical microscopy, we investigated the non-uniformity of MOUDI aerosol deposits at spatial resolutions of 1, 0.25 mm, and for some stages when necessary 0.10 mm. The results from these measurements show that at a spatial resolution of 1mm and less, the concentration of …