Other Chemistry Commons^™

Parallelization Of Molecular Docking Algorithms Using Cuda For Use In Drug Discovery, Brandon Stewart, Jonathan Fine, Gaurav Chopra Phd

The Summer Undergraduate Research Fellowship (SURF) Symposium

Traditional drug discovery methodology uses a multitude of software packages to design and evaluate new drug-like compounds. While software packages implement a wide variety of methods, the serial (i.e. single core) implementation for many of these algorithms, prohibit large scale docking, such as proteome-wide docking (i.e. thousands of compounds with thousands of proteins). Several docking algorithms can be parallelized, significantly reducing the runtime of the calculations, thus enabling large-scale docking. Implementing algorithms that take advantage of the distributed nature of graphical processing units (GPUs) via the Compute Unified Device Architecture (CUDA) enables us to efficiently implement massively parallel ...

Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury

Mathematics, Physics, and Computer Science Faculty Articles and Research

Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at ...

Oligo(Ethylene Glycol)-Sidechain Microgels Prepared In Absence Of Cross-Linking Agent: Polymerization, Characterization And Variation Of Particle Deformability, Nicole Welsch, L. Andrew Lyon

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present a systematic study of self-cross-linked microgels formed by precipitation polymerization of oligo ethylene glycol methacrylates. The cross-linking density of these microgels and, thus, the network flexibility can be easily tuned through the modulation of the reaction temperature during polymerization. Microgels prepared in absence of any difunctional monomer, i.e. cross-linker, show enhanced deformability and particle spreading on solid surfaces as compared to microgels cross-linked with varying amounts of poly(ethylene glycol diacrylate) (PEG-DA) in addition to self-crosslinking. Particles prepared at low reaction temperatures exhibit the highest degree of spreading due to the lightly cross-linked and flexible polymer network ...

The Quantification Of Cocaine From The Erythroxylum Coca Plant And The Comparison On High Performance Liquid Chromatography And Gas Chromatography Mass Spectroscopy As An Analytical Method., Tuesday James

Student Theses

Cocaine is derived from the Erythroxylum coca plant, is a highly addictive stimulant abused all over the world. There are two types of Erythroxylum coca plants that produce cocaine; the E. Coca and E. Novogranatense. Cocaine exists as the salt, and the freebase which is typically referred to as “crack” due to the crackling sound it makes when heated. It is popular because it is inexpensive and easily available on the streets, mainly in poor urban areas. The purpose of this project was to determine the amount of cocaine that can be extracted from E.coca and to assess which ...

Catalytic Conversion Reactions In Nanoporous Systems With Concentration-Dependent Selectivity: Statistical Mechanical Modeling, Andrés García, Jing Wang, Theresa L. Windus, Aaron D. Sadow, James W. Evans

Theresa Windus

Statistical mechanical modeling is developed to describe a catalytic conversion reaction A→Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Furthermore, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.

Catalytic Conversion Reactions In Nanoporous Systems With Concentration-Dependent Selectivity: Statistical Mechanical Modeling, Andrés García, Jing Wang, Theresa L. Windus, Aaron D. Sadow, James W. Evans

James W. Evans

Statistical mechanical modeling is developed to describe a catalytic conversion reaction A→Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Furthermore, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.

Mesoporous Silica Nanoparticles: Structural Design And Applications, Igor I. Slowing, Juan Luis Vivero-Escoto, Brian G. Trewyn, Victor S.Y. Lin

Igor I. Slowing

The structural properties of mesoporous silica nanoparticles are reviewed. Different strategies for the introduction of functional groups are considered. Based on the architectural features of the material, the functionalization at defined regions of the particles is described, along with the properties emerging from the corresponding site-specific modifications of their chemistry. Many applications derived from the unique architecture and chemistry of these nanostructured composite materials are shown.

Role Of Co2 As A Soft Oxidant For Dehydrogenation Of Ethylbenzene To Styrene Over A High-Surface-Area Ceria Catalyst, Li Zhang, Zili Wu, Nicholas C. Nelson, Aaron D. Sadow, Igor I. Slowing

Igor I. Slowing

Catalytic performance and the nature of surface adsorbates were investigated for high-surface-area ceria during the ethylbenzene oxidative dehydrogenation (ODH) reaction using CO2 as a soft oxidant. The high surface area ceria material was synthesized using a template-assisted method. The interactions among ethylbenzene, styrene, and CO2 on the surface of ceria and the role of CO2 for the ethylbenzene ODH reaction have been investigated in detail by using activity test, in situ diffuse reflectance infrared and Raman spectroscopy. CO2 as an oxidant not only favored the higher yield of styrene but also inhibited the deposition of coke during the ethylbenzene ODH ...

Heterogeneous Multicatalytic System For Single-Pot Oxidation And C–C Coupling Reaction Sequences, Nicholas C. Nelson, Umesh Chaudhary, Kapil Kandel, Igor I. Slowing

Igor I. Slowing

A system comprising two catalysts supported on mesoporous silica nanoparticles (MSNs) was employed to perform a sequence of two reactions in a single pot. Palladium nanoparticles catalyzed the oxidation of furfuryl alcohol with molecular oxygen at atmospheric pressure. The oxidation product, furfural, was then reacted with acetone via an aldol condensation catalyzed by amines supported on MSNs. Each reaction was first tested individually to establish optimal conditions. Both catalysts were then introduced into the same reactor under the proven conditions, and the entire reaction sequence was performed giving the desired product with high selectivity. The overall yield of the reaction ...

Supported Iron Nanoparticles For The Hydrodeoxygenation Of Microalgal Oil To Green Diesel, Kapil Kandel, James W. Anderegg, Nicholas C. Nelson, Umesh Chaudhary, Igor I. Slowing

Igor I. Slowing

Iron nanoparticles supported on mesoporous silica nanoparticles (Fe-MSN) catalyze the hydrotreatment of fatty acids with high selectivity for hydrodeoxygenation over decarbonylation and hydrocracking. The catalysis is likely to involve a reverse Mars–Van Krevelen mechanism, in which the surface of iron is partially oxidized by the carboxylic groups of the substrate during the reaction. The strength of the metal–oxygen bonds that are formed affects the residence time of the reactants facilitating the successive conversion of carboxyl first into carbonyl and then into alcohol intermediates, thus dictating the selectivity of the process. The selectivity is also affected by the pretreatment ...

Substrate Inhibition In The Heterogeneous Catalyzed Aldol Condensation: A Mechanistic Study Of Supported Organocatalysts, Kapil Kandel, Stacey Marie Althaus, Chorthip Peeraphatdit, Takeshi Kobayashi, Brian G. Trewyn, Marek Pruski, Igor I. Slowing

Igor I. Slowing

In this study, we demonstrate how materials science can be combined with the established methods of organic chemistry to find mechanistic bottlenecks and redesign heterogeneous catalysts for improved performance. By using solid-state NMR, infrared spectroscopy, surface and kinetic analysis, we prove the existence of a substrate inhibition in the aldol condensation catalyzed by heterogeneous amines. We show that modifying the structure of the supported amines according to the proposed mechanism dramatically enhances the activity of the heterogeneous catalyst. We also provide evidence that the reaction benefits significantly from the surface chemistry of the silica support, which plays the role of ...

Exocytosis Of Mesoporous Silica Nanoparticles From Mammalian Cells: From Asymmetric Cell-To-Cell Transfer To Protein Harvesting, Igor I. Slowing, Juan L. Vivero-Escoto, Yannan Zhao, Kapil Kandel, Chorthip Peeraphatdit, Brian G. Trewyn, Victor S.Y. Lin

Igor I. Slowing

The exocytosis of mesoporous silica nanoparticles (MSNs) from mammalian cells is demonstrated for the first time. The differences in the degree of exocytosis of MSNs between healthy and cancer cells are shown to be responsible for the asymmetric transfer of the particles between both cell types. The exo­cytosis of highly adsorbent magnetic MSNs proves to be useful as a means for harvesting biomolecules from living cells.

Silanol-Assisted Carbinolamine Formation In An Amine-Functionalized Mesoporous Silica Surface: Theoretical Investigation By Fragmentation Methods, Ana P. De Lima Batista, Federico Zahariev, Igor I. Slowing, Ataualpa A. C. Braga, Fernando R. Ornellas, Mark S. Gordon

Igor I. Slowing

The aldol reaction catalyzed by an amine-substituted mesoporous silica nanoparticle (amine-MSN) surface was investigated using a large molecular cluster model (Si392O958C6NH361) combined with the surface integrated molecular orbital/molecular mechanics (SIMOMM) and fragment molecular orbital (FMO) methods. Three distinct pathways for the carbinolamine formation, the first step of the amine-catalyzed aldol reaction, are proposed and investigated in order to elucidate the role of the silanol environment on the catalytic capability of the amine-MSN material. The computational study reveals that the most likely mechanism involves the silanol groups actively participating in the reaction, forming and breaking covalent bonds in the carbinolamine ...

The Physical And Chemical Characteristics Of Lards And Other Fats In Relation To Their Culinary Value Ii. Use In Plain Cake, Belle Lowe, P. Mabel Nelson

Research Bulletin (Iowa Agriculture and Home Economics Experiment Station)

These studies on the use of lards in plain cake were initiated in the fall of 1932 and completed during the summer of 1936. The major results of these investigations with cake have been included in a series of four theses by Martin (11), Buel (2), Minard (13) and Myers (15) .

Cakes containing fat may be divided into two types:

1. The pound cake, named from the proportions formerly used by our great-grandmothers, consists of a pound each of fat, sugar, flour and eggs, with no baking powder or soda. The volume of the cake depends upon the expansion of ...

The Advanced Spectroscopic Analysis Of Organic Gunshot Residue And Explosives, Jennifer M. Leonard

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

With the prevalence of shooting cases and terrorist attacks/or threats that plague the current state of the criminal justice system, it is of paramount importance to be able to detect, identify and interpret the presence of gunshot residue or explosives material. This concern is seen in law enforcement agencies and the media throughout the United States and abroad.

Currently, the typical method of analyzing gunshot residue in most crime laboratories serves to identify the inorganic constituents of the primer residue, namely lead, barium and antimony. However, it is possible that the organic matter from the propellant could provide different ...

Fluorine Toxicosis In The Albino Rat, J. A. Schultz

Research Bulletin (Iowa Agriculture and Home Economics Experiment Station)

The toxicity of fluorine compounds once considered of little general importance is no longer so regarded. The increasing use of fluorides as insecticides, the discovery that fluorine may be a component of many foodstuffs and the work of Dr. Margaret Cammack Smith and associates (77·88) in proving that potable waters containing as little as 0.9 parts per million of fluorine may produce mottled teeth in growing children when regularly ingested over periods of several years, has excited much popular as well as scientific interest in fluorine toxicoses. Ostrem, Nelson, Greenwood and Wilhelm (55) have shown that this mottling ...

The Physical And Chemical Characteristics Of Lards And Other Fats In Relation To Their Culinary Value I. Shortening Value In Pastry And Cookies, Belle Lowe, P. Mabel Nelson, J. H. Buchanan

Research Bulletin (Iowa Agriculture and Home Economics Experiment Station)

These studies on the relationship of the physical and chemical characteristics and constants of lards and other fats to their culinary value were started during the fall of 1932 and completed during the summer of 1937.

The culinary tests were divided into three groups as follows: 1. The shortening power of lards and other fats in pastry and cookies. 2. the use of lards and other fats in plain cake, 3. the frying life of lards compared with other fats.

This section of the report presents the studies relating to the shortening value of lards as compared with other fats ...

A Computational Approach To Studying The Properties Of Photosensitizers In Photodynamic Therapy, Keenan Komoto

Graduate Student Conference

Cancer has long been a significant problem that has affected our world’s population for years and continues to this day. With the number of cases expected to increase annually there is a societal pressure to find effective treatment methods for eliminating cancer. Current forms of cancer treatment tend to cause detrimental effects to the human body and are usually quite expensive and long lasting, some costing upwards of $30,000 over an 8 week period. A more recently established form of cancer treatment known as photodynamic therapy is an effective treatment option for ridding cancers that lie on or ...

Fluorescently-Labeled Glutathiones To Quantify Cysteine Reactivity, Saloni H. Patolia

Undergraduate Honors Theses

The purpose of this study was to quantify cysteine reactivity with fluorescently-labeled glutathiones. Previous work on fluorescein-labeled glutathiones had established that they undergo S-glutathionylation with GAPDH and tubulin cysteines. In the current study, the proteins GAPDH and LDH were reacted with fluorescein-labeled and dansyl-labeled glutathiones under different reaction conditions identical to steric, salt, and pH environments in a cell. These reactions were monitored via UV/Vis spectroscopy to obtain quantitative data on reactivity of GAPDH and LDH cysteines. Reactions were determined qualitatively through nitrocellulose membrane dot blots and SDS-PAGE gels. Cysteine reactivity with fluorescently- labeled glutathiones was shown to be ...

Analyzing The Kinetics Of A Bromophenol Blue Fading Reaction In Basic Conditions For An Undergraduate Lab, Zeljka Popovic

Georgia College Student Research Events

Bromophenol blue is a common pH indicator and dye used in many different industries. Once a solution of bromophenol blue is placed in a concentrated basic solution, the color fades from a blue/violet color to clear solution with a pH of 4.6 or greater. The rate law of the reaction is analyzed through the use of a small footprint visible-near-infrared spectrometer (Vis-NIR) with a diode array detector. An absorbance wavelength of 590 nm as a function of time was collected using Ocean Optics OceanView software. The results contained in the data collection file are exported to a spreadsheet ...