Chemistry Commons^™

Blind Prediction Of Host-Guest Binding Affinities: A New Sampl3 Challenge, H. S. Muddana, C. D. Varnado, C. W. Bielawski, Adam R. Urbach, L. Isaacs, M. T. Geballe, M. K. Gilson

Chemistry Faculty Research

The computational prediction of protein–ligand binding affinities is of central interest in early-stage drug-discovery, and there is a widely recognized need for improved methods. Low molecular weight receptors and their ligands—i.e., host–guest systems—represent valuable test-beds for such affinity prediction methods, because their small size makes for fast calculations and relatively facile numerical convergence. The SAMPL3 community exercise included the first ever blind prediction challenge for host–guest binding affinities, through the incorporation of 11 new host–guest complexes. Ten participating research groups addressed this challenge with a variety of approaches. Statistical assessment indicates that, although most methods performed well at predicting some …

Résonance Dans Alliages Des Couches Supraconductrices Refroidi Rapidement: (Bi1.7pb0.3sr2can‐1cuno2n+4+Δ)2, N=1 To 9détecté Par Local Renforcée Atomique Xrd, Juana Acrivos, J. Chigvinadze, D. Gulamova

Faculty Publications, Chemistry

Lien résonance dans alliages supraconductrice à haute température (HTLSC): (Bi1.7Pb0.3Sr2Can-1CunO2n+4+δ)2,n=1-9 appelé (2s:2:n-1:n) préparé en Ouzbékistan à partir de oxide fondu par flux concentré du Soleil, suivi d'un refroidissement rapide, technologie SFQA préserve fondre carrelage. Tc,n est mesurée en Tbilissi, et atomique local renforcée synchrotron diffraction des rayons X, (XRD) à proximité de la Cu-K bord est effectuée à DOE National Laboratoire SLAC-SSRL. La structure indexé dans le groupe D17 4h démontre qui (n-1) unîtes: (CuO2)1/2/Ca/(CuO2)1/2 sont intercalés à chaque extrémité de la phase n=1: [(CuO2)1/2/SrO/Bi1.7Pb0.3O/Bi1.7Pb0.3O/SrO/(CuO2)1/2]2. Les effets de surface conduit à intercalations des different n-phase, et à des distorsions réseau …

Synthesis, Structure, And Characterization Of Hybrid Solids Containing Polyoxometalates And Ruthenium Polypyridyl Complexes, Yanfen Ll

Masters Theses & Specialist Projects

Polyoxometalates (POMs), which are inorganic metal oxide cluster anions with discrete structures, have been extensively studied in recent years due to their large variety of applications such as medicine, biology, catalysis, material sciences and chemical analysis. Ruthenium polypyridyl complexes have been extensively studied for their applications as photosensitizers in solar energy conversion and photoelectronic materials. Recently, ruthenium heterocyclic ligand complex-based building blocks have been used for the synthesis of hybrid organic-inorganic solids through the self-assembly. We are interested in the synthesis of ruthenium polypyridyl complexes and polyoxometalate anions through different ways such as coordination bonds, hydrogen bonds and ionic bonds …

Sprectral Data For "Generation Of Molecular Complexity From Cyclooctatetraene Using Dienyliron And Olefin Metathesis", Mohamed F. El-Mansy, Anobick Sar, Subhabrata Chaudhury, Nathaniel J. Wallock, William A. Donaldson

Natural Products Synthesis via Organoiron Methodology

Spectral data used in the course of researching "Generation of molecular complexity from cyclooctatetraene using dienyliron and olefin metathesis methodology".

Transformation of the simple hydrocarbon cyclooctatetraene into a variety of polycyclic skeletons was achieved by sequential coordination to iron, reaction with electrophiles followed by allylated nucleophiles, decomplexation and olefin metathesis.

The Reaction Of Methionine With A Non-C2-Symmetrical Platinum (Ii) Diamine Compound, Nilesh Sahi

Mahurin Honors College Capstone Experience/Thesis Projects

The research that we have conducted has allowed us to discover that the amino acids, methionine (Met) and N-acetyl methionine (N-AcMet), will react in a 1:1 and 1:2 molar ratio with platinum complexes containing bulky diamine ligands. Previous research has allowed us to gain a plethora of information on the experimentation and results of specific bulky diamine ligands such as N,N,N',N'-tetramethylethylenediamine and N,N-diethylethylenediamine. In the current study, we have investigated the bulky diamine ligand of N,N-dimethylethylenediamine, or Me₂en. With our focus on the bulk of the Me₂en ligand, we have been able to synthesize a platinum …

Time-Dependent Density-Functional-Theory Calculation Of High-Order-Harmonic Generation Of H-2, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

The observation of the isotope effect in the high-order-harmonic generation (HHG) of H-2 presents a challenge for time-dependent density-functional-theory (TDDFT) methods, since this effect is related to the dynamics of the ion created in the tunneling ionization step of HHG and it depends on the harmonic order. As an initial step toward describing this effect within current computational capacity, we benchmark a method in which the nuclear and electronic degrees of freedom are separated and both treated quantum mechanically. For the electrons two TDDFT formalisms are adopted. Although the ion-dynamics effect is not described in our method, it reproduces the …

Cross-Linked Pdms Expansion Due To Submersion In Liquid And Supercritical Co2, Teng Yang

Graduate Theses and Dissertations

Characterization of micro/nano-copper particles impregnated Polydimethylsiloxane (PDMS) submersed in supercritical carbon dioxide (scCO2) was studied. The purpose of this investigation was to advance micro-corrosion sensor technology utilizing PDMS and micro-metal particle composite as the sensing element currently under-development. One of the key challenges encountered was the removal of the native oxides inherently existing on the metal particles. Numerous techniques were experimented with to counter this problem at the UA Engineered Micro/Nano Systems Laboratory (EMNSL), with swell-based protocols being identified as the most promising solution. In terms of compatibility to Micro-electro-mechanical Systems (MEMS) fabrication, CO2 is often used in the release …

Oxaliplatin And Oxaliplatin Derivatives: Synthesis, Characterization, And Reactivity With Biologically Relevant Ligands, Amy Poynter

Mahurin Honors College Capstone Experience/Thesis Projects

Oxaliplatin is a third generation anticancer drug that has proven to be successful in fighting ovarian and testicular cancer. We are interested in determining how oxaliplatin and oxaliplatin derivatives interact with proteins, as well as how that interaction is affected by the size and shape of these platinum compounds. We have synthesized oxaliplatin as it is used in cancer treatment, as well as similar platinum compounds with the same diaminocyclohexane ligand as oxaliplatin but with additional bulk added to the nitrogen atoms. We are reacting oxaliplatin with key amino acids, including methionine, and will be comparing the kinetics of this …

Benzo[1,2-B:4,5-B′]Dithio­Phene-4,8-Dione, Amanda L. Ramirez, Benny C. Chan, Daniel T. De Lill

Chemistry and Physics Faculty Articles

The title mol­ecule, C₁₀H₄O₂S₂, is situated on a crystallographic center of inversion. In the crystal, weak hydrogen bonding contributes to the packing of the mol­ecules.

Tuning Photophysics And Nonlinear Absorption Of Bipyridyl Platinum(Ii) Bisstilbenylacetylide Complexes By Auxiliary Substituents, Zhongjing Li, Ekaterina Badaeva, Dapeng Zhou, Josiah Bjorgaard, Ksenija D. Glusac, Svetlana Killina, Wenfang Sun

Chemistry Faculty Publications

The photophysics of six bipyridyl platinum(II) bisstilbenylacetylide complexes with different auxiliary substituents are reported. These photophysical properties have been investigated in detail by UV-vis, photoluminescence (both at room temperature and at 77 K) and transient absorption (nanosecond and femtosecond) spectroscopies, as well as by linear response time-dependent density functional theory (TD-DFT) calculations. The photophysics of the complexes are found to be dominated by the singlet and triplet pi,pi* transitions localized at the stilbenylacetylide ligands with strong admixture of the metal-to-ligand (MLCT) and ligand-to-ligand (LLCT) charge-transfer characters. The interplay between the pi,pi* and MLCT/LLCT states depends on the electron-withdrawing or -donating …

Hydrodynamic Evaluation And Characterization Of Capillary Channeled Polymer (C-Cp) Fibers As A Stationary Phase In Hplc Of Macromolecules, Kelum Randunu Pathirannahalage

All Theses

High Performance Liquid Chromatography (HPLC) is the most used analytical technique for the separation of samples in solution. HPLC of has progressed with successive use of new supports such as silica, polysaccharides, monoliths, and organic polymers. Although porous silica phases are very effective in small molecule separations, they suffer from certain drawbacks including pH stability, chemical robustness, high backpressure, and slow mass transfer for macromolecule separations. Thus, the most protein separations are carried out using nonporous, partially porous, and superficially porous phases to overcome mass transfer limitations. As a competing methodology, fiber based polymer support/stationary phases are also developed for …

Racemization Of Amino Acids In Teeth For The Determination Of Age, Andrea Lee Toll

Masters Theses & Specialist Projects

Instrumental to forensic investigations is the ability to identify unknown human remains providing key evidence to criminal cases, resolution to missing persons, and assistance in mass or natural disasters. Identification of remains in an effort to determine age is an area of forensics that has received considerable attention. Traditional methods in age determination such as morphology are often biased, antiquated, and frequently result in a large margin of error. Conversely, the emergence of new forensic techniques provide promise to reduce the margin of error in determining age. One such technique has focused on relating the extent of amino acid racemization …

Hydro/Solvothermal Synthesis, Structures And Properties Of Metal-Organic Frameworks Based On S-Block Metals, Raj Kishore Vakiti

Masters Theses & Specialist Projects

Carbon dioxide removal from flue gases of power plants is critical for reduction of greenhouse gas emissions implicated in global warming. Metal Organic Frameworks (MOFs) promising potential applications in carbon dioxide capture due to their unique structural properties such as high porosity and high thermal stability. These MOFs have application in separation processes and gas storage. By the assembly of the organic ligands and metal oxide clusters, porous MOFs can be synthesized. The use of s-block metals such as calcium, magnesium and rubidium in porous materials is appealing because their ionic binding characters with organic ligands will general flexible MOFs. …

Removal Of Heavy Metals Using Modified Limestone Media: Zinc And Cadmium, Keerthy Mandadi

Masters Theses & Specialist Projects

Heavy metal contamination is a serious concern throughout the world. Increased concentrations in drinking water have many negative impacts on human health. Limestone is an inexpensive and simple media for removing high concentrations of heavy metals from drinking water supplies. Ferric based media is commonly used to remove zinc, cadmium, lead, arsenic and other heavy metals. The drinking water standards set by the US EPA for cadmium, zinc and arsenic are 0.005 mg/L, 5 mg/L and 0.010 mg/L respectively. Bangladesh, parts of India, China and the United States have high concentrations of arsenic in drinking water. Although many technologies exist …

Reducing Lead And Selenium From Drinking Water Using Limestone-Based Material, Sindhu Tumati

Masters Theses & Specialist Projects

Contamination of drinking water with metals is a major problem facing many areas of United States and the World. There is a need for an inexpensive remediation technology for the removal of metals in drinking water that can be applied to small rural water systems. This research will focus on the development of a process for removal of select metals from drinking water by limestone-based material. Metals in drinking water considered for this research include lead and selenium. Limestone-based material has demonstrated the potential to reduce select metals (lead, cadmium and arsenic) in drinking water, with the additional benefit of …

Synthesis, Characterization And Applications Of Different Nanostructures, Whitney Snyder

All Theses

There has been a growing interest in the field of nanoscience for the last several decades including the use in optical, electrical, biological and medicinal applications. This thesis focuses on the synthesis of different nanoparticles for their potential uses in drug delivery and antimicrobial agents as well as porous alumina membranes as surface enhanced Raman scattering or SERS substrates.
The synthesis of nanocomposites (NCs) composed of silica and poly(4-vinyl pyridine) (P4VP) in a basic ethanol solution is presented in chapter 2. The composition of the NCs appears to be homogenous after synthesis and is greatly affected by heat and pH …

Insufficient Radiofrequency Ablation Promotes Angiogenesis Of Residual Hepatocellular Carcinoma Via Hif-1Α/Vegfa, Jian Kong, Jinge Kong, Bing Pan, Shan Ke, Shuying Dong, Xiuli Li, Aimin Zhou, Lemin Zheng, Wen Bing Sun

Chemistry Faculty Publications

Background: The mechanism of rapid growth of the residual tumor after radiofrequency (RF) ablation is poorly understood. In this study, we investigated the effect of hyperthermia on HepG2 cells and generated a subline with enhanced viability and dys-regulated angiogenesis in vivo, which was used as a model to further determine the molecular mechanism of the rapid growth of residual HCC after RF ablation. Methodology/Principal Findings: Heat treatment was used to establish sublines of HepG2 cells. A subline (HepG2 k) with a relatively higher viability and significant heat tolerance was selected. The cellular protein levels of VEGFA, HIF-1α and p-Akt, VEGFA …

Accessible High-Throughput Virtual Screening Molecular Docking Software For Students And Educators, Reed B. Jacob, Tim Andersen, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK …

Synthesis Of A 2,2'-Bipyridyl Functionalized Oligovinylene- Phenylene Using Heck And Horner-Wadsworth-Emmons Reactions And X-Ray Crystal Structure Of E-(4-(4-Bromostyryl)Phenyl)(Methyl)Sulfane, Orsolya Karácsony, Jeffrey R. Deschamps, Scott A. Trammell, Rafaela Nita, D. Andrew Knight

Chemistry and Chemical Engineering Faculty Publications

The synthesis of a new 2,2'-bipyridyl functionalized oligovinylenephenylene (OVP-5) containing a methyl protected thiol using Heck coupling and the Horner-Wadsworth- Emmons reaction and is described. A key step involving a diisopropylcarbodiimide promoted dehydration of a stable ?-hydroxyphosphonate intermediate was identified. The structure of precursor E-(4-(4-bromostyryl) phenyl)(methyl)sulfane (1) was determined using X-ray crystallography. © 2012 by the authors.

Conformational Motions Associated With Ligand Binding In Dihydrofolate Reductase From Bacillus Stearothermophilus, Mayam Tobilola Alapa

Theses, Dissertations and Culminating Projects

A fluorescently-labeled, conformationally-sensitive Bacillus stearothermophilus (Bs) dihydrofolate reductase (DHFR) (C73A/S131C_MDCC DHFR) was developed and used to investigate kinetics and protein conformational motions associated with methotrexate (MTX) binding. This construct bears a covalently attached fluorophore, N-[2-(lmaleimidyl) ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC) attached at a distal cysteine, introduced by mutagenesis. The probe is sensitive to the local molecular environment, reporting on changes in the protein structure associated with ligand binding. Intrinsic tryptophan fluorescence of the unlabeled Bs DHFR construct (C73A/S131C DHFR) also showed changes upon MTX association. Stopped-flow analysis of all data can be understood by invoking the presence of two native state DHFR …

Characterization Of A C-Jun N-Terminal Kinase Pathway In The Parasitic Nematode, Brugia Malayi, Agnieszka N. Chojnowski

Theses, Dissertations and Culminating Projects

Lymphatic filariasis (elephantiasis) is a major neglected disease caused by filarial nematodes including; Wuchereria bancrofti, Brugia malayi {B. malayi) and Brugia timori. Over 120 million individuals are infected and more than 1.3 billion people are at risk of infection in 81 endemic countries. Current treatments are limited, toxic and fail to kill adult parasites. There is a need for new target and treatments. One potential novel drug target for this disease is stress-activated protein kinases. It has been previously demonstrated in our laboratory that a B. malayi stress-activated protein kinase, Bm- MPK1, an ortholog of the human p38/Caenorhabditis elegans (C. …

Investigation Of Autoregulation Of Icer And Electrochemical Properties Of Tryptophan, Mark Demilio

Theses, Dissertations and Culminating Projects

A relatively new development in the field of research-based chemistry is to study biomolecules, their interactions, and a biochemical mechanisms by examination of their physical properties and application of laboratory techniques rooted in concepts of physical chemistry. Both projects that are encompassed within this master's thesis indeed fall under the umbrella of biophysical chemistry, as they apply physical chemical techniques study particular biomolecular interactions.

The first of these two projects is the study of a leucine zipper protein, Inducible cAMP Early Repressor [ICER], which is a product of the cAMP Responsive Element Modulator [CREM] gene. ICER functions as a transcriptional …

A Leishmania Mitogen Activated Protein Kinase As A Potential Anti-Parasitic Drug Target : Purification, Characterization And Inhibitor Interactions, Aysenur Sayakci

Theses, Dissertations and Culminating Projects

The disease, Leishmaniasis, is caused by the protozoal parasite Leishmania, which is transmitted by the bite of an infected Phlebotomine female sandfly. It is a significant health problem in tropical regions of the world and new therapeutic approaches for treating this disease are urgently needed.

Protozoal MAPKs (Mitogen Activated Protein Kinases) play important roles in parasite viability and infectivity and as such, represent viable drug targets. It has been demonstrated that LmxMPKl is an essential MAPK required for the parasite to establish infection and for proliferation of the amastigote stage (the mammalian stage of the parasite) of the parasite. In …

Introducing Nob-Nobs: Nitrogen-Oxygen-Boron Cycles With Potential High-Energy Properties, Aloysus K. Lawong, David W. Ball

Chemistry Faculty Publications

As a follow-up on a study of a family of boron-oxygen-nitrogen compounds composed of two datively bonded B–O–N backbones, we investigate a similar series of compounds that have similar fragments but are covalently bonded. B3LYP/6-31G(d,p) quantum mechanical calculations have been performed to determine the minimum-energy geometries, vibrational frequencies, and thermochemical properties of the parent compound and a series of nitro-substituted derivatives. Our results indicate that some of the derivatives have at least appropriate thermodynamics for possible high-energy materials, in some cases being favorable over similar dimeric compounds with coordinate covalent B–N bonds

Synthesis Of Novel Alkaline Earth Tosylate Complexes Through Donor Studies, Adam J. Brooks

Renée Crown University Honors Thesis Projects - All

Salt metathesis has become a critical reaction pathway in organometallic chemistry; however, for alkaline earth metals this process is hindered by the need of highly pure and expensive metal iodides as starting materials. This contribution highlights recent attempts to identify inexpensive reagents for salt metathesis. Alkaline earth-tosylates can be prepared cost effectively using p-toluenesulfonic acid in one-pot reactions in water. The coordinated water molecules can be removed by gentle heating under vacuum. The anhydrous tosylates, however, have major solubility limitations as the result of extensive aggregation networks. The goal of this study was to increase the solubility of the tosylates …

Synthesis, Modification, And Characterization Of Spherical Sba-15 Ordered Mesoporous Silica And Evaluation In High Performance Liquid Chromatography, Alexander P. Giaquinto

Seton Hall University Dissertations and Theses (ETDs)

.

Analysis Of Street Drugs Using Comprehensive Two Dimensional Gas Chromatography Coupled With Time Of Flight Mass-Spectrometry, Brian B. Barnes

Seton Hall University Dissertations and Theses (ETDs)

.

Human Sperm Dna Oxidation, Motility And Viability In The Presence Of L-Carnitine During In Vitro Incubation And Centrifugation, S. Banihani, R. Sharma, Mekki Bayachou, E. Sabanegh, A. Agarwal

Chemistry Faculty Publications

In vitro incubation and centrifugation is known to decrease human sperm quality. In the human body, besides its antioxidant effects, l-carnitine (LC) facilitates the transport of activated fatty acids from the cytosol to the mitochondrial matrix. In this study, we investigated the effect of LC on human sperm motility, viability and DNA oxidation after incubation and centrifugation, following the sperm preparation protocols of assisted reproduction. Normozoospermic semen samples (n = 55) were analysed according to the World Health Organization (WHO) guidelines. LC concentrations that are not toxic to spermatozoa as determined by sperm motility and viability were standardised after 2 …

Nmr Characterization Of Parathion: Properties, Transport, And Reaction Kinetics, Emma Catherine Baker

Boise State University Theses and Dissertations

The hydrolysis reaction of parathion (PTH) to produce para-nitrophenolate (pNP) and O,O-diethylthiophosphate (DETP) was examined in a minimally disturbed liquid-liquid biphasic reaction system by proton and phosphorous nuclear magnetic resonance spectroscopy. The effect of the micellar cationic surfactant, cetyltrimethylammonium chloride (CTAC), on PTH transport, hydrolysis, and system characteristics including reactant-product concentrations, pNP partition coefficients, pNP surface activity, ultraviolet degradation of pNP, oxidation of pNP, and impurities in PTH are reported. Surfactant reaction systems resulted in a 2.5 order of magnitude increase in the amount of PTH transported into the aqueous layer as compared to the control system at 2100 …

Biomass Assisted Synthesis Of Antibacterial Gold Nanoparticles And Commentary On Its Future Potential And Applications In Medicine, Chad Willis

Mahurin Honors College Capstone Experience/Thesis Projects

Xylose is a natural monosaccharide found in biomass such as straw, pecan shells, cottonseed hulls, and corncobs. Using this monosaccharide, we report the green synthesis and characterization of biocompatible, biodegradable xylose encapsulated gold nanoparticles (Xyl-GNPs) with potential antibacterial activity. GNPs were synthesized using the bioreduction property of xylose on the chloroaurate anions in an aqueous solution at room temperature and at atmospheric pressure. The characterization of synthesized GNPs was examined by UV-vis spectroscopy; transmission electron microscopy (TEM), energy-dispersive x-ray spectroscopy (EDS) and fourier transform infrared spectroscopy (FTIR). Results indicate that the particles were stable; near spherical in shape with an …