Chemistry Commons^™

Optical And Electrochemical Molecular And Nanoscale Sensors For The Selective Detection Of Organophosphorus Based Pesticides, Chandrima De

Masters Theses

Organophosphorus based pesticides are highly toxic and represent serious environmental concerns. These compounds tend to easily enter ground water and cause drastic pollution. The toxicity levels of the organophosphorus pesticides however are based on their structures, and hence methods for their selective detection are in high demand. The creation of new materials for sensing and actuation requires careful manipulation of the responsive units required to control analyte selectivity. We have successfully designed and synthesized a molecular sensor based on the family of stilbenes that not only can detect organophosphorus pesticides, but also distinguish between them. Four different pesticides have been …

A Fluorescent Photoinduced Electron Transfer (Pet) Sensor For Cations With A Separate Pet Channel To Suppress Proton Signals, Supun Pathirana

Theses, Dissertations and Culminating Projects

This thesis presents A-((10-((2-methoxy-4-methylphenoxy)methyl)anthracen-9- yl)methyl)(pyridin-2-yl)-A-((pyridin-2-yl)methyl)methanamine, 1, a photoinduced electron transfer (PET) sensor that acts as a fluorescent ‘Off-On’ switch in the presence of Zn ions and not sensitive to protons.

Isotope Effect In Quasi-Two-Dimensional Metal-Organic Antiferromagnets, P A. Goddard, J Singleton, C Maitland, S J. Blundell, T Lancaster, P J. Baker, R D. Mcdonald, S Cox, P Sengupta, J L. Manson, K A. Funk, J A. Schlueter

Chemistry and Biochemistry Faculty Publications

Although the isotope effect in superconducting materials is well documented, changes in the magnetic properties of antiferromagnets due to isotopic substitution are seldom discussed and remain poorly understood. This is perhaps surprising given the possible link between the quasi-two-dimensional (Q2D) anti ferromagnetic and superconducting phases of the layered cuprates. Here we report the experimental observation of shifts in the Neel temperature and critical magnetic fields (Delta T(N)/T(N)approximate to 4%; Delta B(c)/B(c)approximate to 4%) in a Q2D organic molecular antiferromagnet on substitution of hydrogen for deuterium. These compounds are characterized by strong hydrogen bonds through which the dominant superexchange is mediated. …

Photolithographically Patterned Covalently Bonded Polythiophene Films Using In Tandem Sol-Gel, Surface Initiated Free Radical And Redox Polymerization Methods, Anand Ghanashyam Sedekar, Naveen Chandrasekaran, Sudhir Mulik, Chariklia Sotiriou-Leventis, Nicholas Leventis

Chemistry Faculty Research & Creative Works

A bifunctional monomer, 3,4-bis(vinyloxy)thiophene (BVOT), that can be polymerized both by radical as well as by redox chemistry was utilized in the fabrication of lithographic patterns of conducting polymer films via a sol-gel method. The judicious use of several chemistries yields polythiophene patterns covalently bonded to substrate showing superior adhesion relative to physically bonded counterparts. The films were characterized electrically and mechanically. Surface confinement starts with a bidentate free radical initiator (Si-AIBN) synthesized via condensation reaction between 3-aminopropyltriethoxysilane (APTES) and azobiscyano-valeric acid. Si-AIBN is attached to the surface of glass by hydrolysis of the ethoxy groups and reaction with the …

Preparation Of Macroporous Conductive Carbon Cerogels From Pyrolysis Of Isocyanate-Crosslinked Resorcinol Formaldehyde Aerogels, Sudhir Mulik, Nicholas Leventis, Chariklia Sotiriou-Leventis

Chemistry Faculty Research & Creative Works

Carbon aerogels combine typical aerogal properties such as high surface area and low density with electrical conductivity. They are prepared by pyrolysis under N2 or Ar at 600-2100 degrees C of resorcinol formaldehyde (RF) aerogels, which in turn are prepared via aqueous sol-gel chemistry. Carbon aerogels are considered for numerous applications such as separation media in HPLC, as supercapacitors, as materials for hydrogen storage, as non-reflective materials, and as anodes in lithium-ion batteries. Meanwhile, porous carbons with high hydrophobic surface areas and large pore volumes are used as industrial adsorbents. In addition, macropores enhance mass transport for applicatoins in energy …

Rational Design Of A Minimal Size Sensor Array For Metal Ion Detection, Manuel A. Palacios, Zhuo Wang, Victor A. Montes, Grigory V. Zyryanov, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

The focus of this study was to demonstrate that, in the luminescent sensors, the signal transduction may possibly be the most important part in the sensing process. Rational design of fluorescent sensor arrays for cations utilizing extended conjugated chromophores attached to 8-hydroxyquinoline is reported. All of the optical sensors utilized in the arrays comprise the same 8-hydroxyquinoline (8-HQ) receptor and various conjugated chromophores to yield a different response to various metal cations. This is because the conjugated chromophores attached to the receptor are partially quenched in their resting state, and upon the cation coordination by the 8-HQ, the resulting metalloquinolinolate …

Characterization Of P62, Hah1 And Their Interaction With The Wilson Disease Protein, Paul Sifuna Oshule

Masters Theses

Wilson disease is an autosomal recessive disorder resulting in the accumulation of copper in the body primarily in the liver and brain. In order to understand the pathogenesis of Wilson disease, our laboratory is studying several different proteins. Wilson disease protein (ATP7B) is a P-type ATPase which acts to remove excess copper from the cells. The p62 subunit of the dynactin complex is a protein whose function is still unknown but it has been proposed to have a copperdependent interaction with ATP7B. HAH1 is a human metallochaperone that binds copper as it comes into the cells from CTR1, a permease. …

High-Definition Self-Assemblies Driven By The Hydrophobic Effect: Synthesis And Properties Of A Supramolecular Nanocapsule, Bruce C. Gibb

Chemistry Faculty Publications

High definition self-assemblies, those that possess order at the molecular level, are most commonly made from subunits possessing metals and metal coordination sites, or groups capable of partaking in hydrogen bonding. In other words, enthalpy is the driving force behind the free energy of assembly. The hydrophobic effect engenders the possibility of (nominally) relying not on enthalpy but entropy to drive assembly. Towards this idea, we describe how template molecules can trigger the dimerization of a cavitand in aqueous solution, and in doing so are encapsulated within the resulting capsule. Although not held together by (enthalpically) strong and directional non-covalent …

Ligand Effects In Homogeneous Au Catalysis, David J. Gorin, Benjamin D. Sherry, F. Dean Toste

Chemistry: Faculty Publications

The solutions with the problems regarding the ligand effects in homogeneous catalysis through December 2007 has been given. Specifically, the problems with the obvious differences in reactivity and selectivity that comes from changing neutral or anionic ligands will be addressed with a focus on ligands and complexes that enables enantioselective catalysis. There are at times when catalyst choice gives off better improvement within the reaction yields or efficiencies. Meanwhile, an emphasis will be given on the privileged ligands and catalysts for a given class of reactions. Finally, the Hayashi/Ito asymmetric aldol reaction will be dealt with.

The Photooxidation Of Hexabromorhenate(Iv) In Ethyl Bromide, Jessica L. Cohen, Patrick Hoggard

Chemistry and Biochemistry

Irradiation at 254 or 313 nm of solutions of (Bu4N)2[ReBr6] in ethyl bromide exposed to air causes complete conversion of the hexabromorhenate(IV) to perrhenate ion. The rate of the reaction is linearly dependent on the incident light intensity and on a combination of the fraction of light absorbed by the rhenium complex and the fraction absorbed by the ethyl bromide. The experimental results are consistent with a mechanism in which the peroxy radical CH3CH(Br)OO, produced in both the solvent-initiated and metal-initiated pathways, oxidizes [ReBr6]2− by electron transfer.

Identification Of Two Distinct Glutaminyl Cyclase Isoforms In Drosophila Melanogaster, Amanda Thigpen Parker

Dissertations

Sequence analyses revealed two putative glutaminyl cyclase genes in Drosophila melanogaster with greater than 60% amino acid sequence identity to previously identified glutaminyl cyclase in humans. Expression, purification, and characterization of both putative proteins revealed two enzymatically active glutaminyl cyclase enzymes. Comparison of the Drosophila melanogaster glutaminyl cyclase enzymes to the published human glutaminyl cyclase revealed the enzymes were very similar. The Km values obtained were identical to those of human glutaminyl cyclase for three different substrates tested. However, the Drosophila glutaminyl cyclases demonstrated lower turnover numbers. Both Drosophila glutaminyl cyclase isoforms were inhibited by imidazole, imidazole derivatives, and metal …

Reactions Of Rhenium And Manganese Carbonyl Complexes With 1,8-Bis(Diphenylphosphino)Naphthalene: Ligand Chelation, C–H And C–P Bond-Cleavage Reactions, Shariff E. Kabir, Faruque Ahmed, Shishir Ghosh, Mohammad R. Hassan, Muhammad S. Islam, Ayesha Sharmin, Derek A. Tocher, Daniel T. Haworth, Sergey V. Lindeman, Tasneem Siddiquee, Dennis W. Bennett, Kenneth I. Hardcastle

Chemistry Faculty Research and Publications

Reaction of [Re₂(CO)₈(MeCN)₂] with 1,8-bis(diphenylphosphino)naphthalene (dppn) afforded three mono-rhenium complexes fac-[Re(CO)₃(κ¹:η¹-PPh₂C₁₀H₆)(PPh₂H)] (1), fac-[Re(CO)₃{κ¹:κ¹:η¹-(O)PPh₂C₁₀H₆(O)PPh(C₆H₄)}] (2) and fac-[ReCl(CO)₃(κ²-PPh₂C₁₀H₆PPh₂)] (3). Compounds 1–3 are formed by Re–Re bond cleavage and P–C and C–H bond activation of the dppn ligand. Each of these three …

Spectroscopic Study Of Compressible Mobile Phase And Stationary Phase Behavior In Chromatography, Lawrence R. Baker

Theses and Dissertations

Raman spectroscopy, laser-induced fluorescence, and sum-frequency generation (SFG) spectroscopy are used to investigate the behavior of compressible mobile phases and stationary phases under a variety of chromatographic conditions. Efforts to understand and optimize separations employing compressible mobile phases have been limited by a lack of understanding of the mobile phase density gradient. Mobile phase compressibility leads to gradients in linear velocity and solute retention and affects separation speed and efficiency, especially in packed columns. This work describes on-column density measurement of CO2, a common carrier fluid for SFC and SGC, in packed capillary columns using Raman microspectroscopy. On-column detection by …

Towards Development Of A Fully Synthetic Conjugate Vaccine: Investigation Of Structural Analogs Of Streptococcus Pneumoniae Serogroup 6, Archana R. Parameswar

Dissertations

Involvement of complex glycostructures in a variety of damaging and healing processes has already been acknowledged by development of carbohydrate-based vaccines and therapeutics. The bacteria Streptococcus pneumoniae (SPn) have become one of the most frequent causes of pneumonia, bacteremia, and meningitis in the elderly, immunocompromised, and, especially, in young children. SPn has one of the largest public health and economic impacts amongst all bacterial infectious diseases. Over 2 million children die annually worldwide due to pneumonia, accounting for almost 20% of deaths under age five with more than half of these deaths attributed to SPn. Amongst over ninety elucidated SPn …

Synthesis Of Α-Hydroxy And Fluoro Phosphonates And Cyclic Ether-Containing Natural Products, Nongnuch Sutivisedsak

Dissertations

A number of important classes of natural product (eg. amphidinolide C, (-)-centrolobine, etc) contain common structural features of tetrahydrofurans and tetrahydropyrans. This study involved the development of stereoselective mothods for the synthesis of tetrahydrofurans and tetrahydropyrans including the application of allylic hydroxy phosphonates and their derivatives as chiral, non racemic building blocks for the synthesis of biological active molecules. The enantiomeric excess of non racemic α-hydroxy phosphonates and carbonate derivatives prepared via the asymmetric Pudovik reaction can be improved by kinetic resolution. Both chemical and enzyme catalysts were utilized in the kinetic resolution of phosphonates. Enantioselective acylation of a variety …

An Extended Multireference Study Of The Electronic States Of Para-Benzyne, Carol A. Parish, Evan B. Wang, Hans Lischka

Chemistry Faculty Publications

A state-averaged, multireference complete active space (CAS) approach was used for the determination of the vertical excitation energies of valence and Rydberg states of para-benzyne. Orbitals were generated with a 10- and 32-state averaged multiconfigurational self-consistent field approach. Electron correlation was included using multireference configuration interaction with singles and doubles, including the Pople correction for size extensivity, multireference averaged quadratic coupled cluster (MR-AQCC) and MR-AQCC based on linear response theory. There is a very high density of electronic states in this diradical system—there are more than 17 states within 7 eV of the ground state including two 3s …

50th Rocky Mountain Conference On Analytical Chemistry

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 50th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Breckenridge, Colorado, July 27-31, 2008.

A Study On The Protein Interaction With Different Platinum Compounds, Nayna Kotadia

Masters Theses & Specialist Projects

Since the discovery of anti-tumor activity of cisplatin in 1960, significant progress has been made in treating metastatic or advanced cancer with cisplatin and platinum compounds. Platinum compounds covalently bind to DNA and disrupt DNA function. They are also known to bind with amino acids like methionine, histidine and cysteine to form cisplatin-protein adducts which are responsible for most of its cytotoxicity and side effects. Recent articles on cisplatin-protein have shown that adding bulky adjuncts to cisplatin or using different platinum compounds varies the degree and extent of reaction thus possibly reducing cisplatin resistance and side effects.

One of the …

The Effect Of Active Site Mutations On The Homodimeric Behavior Of The Pvuii Restriction Endonuclease, Grigorios A. Papadakos

Dissertations

The PvuII restriction endonuclease, a homodimer of two 18 kDa subunits, belongs to the type II family of restriction enzymes. Located in the active site of PvuII, Tyrosine 94 has previously been shown to be involved in the metal ion binding by the enzyme. The profile of the Ca2+ dependence of the DNA binding to the Y94F variant is shown to be clearly biphasic. The application of a sequential binding model yielded a coupling energy (ΔGcoop) at -0.54 for the upper phase and -1.15 kcal/mole for the lower phase. The similar metal binding pattern between the Y94F and the WT …

Capillary Electrophoresis Used As An Alternative To Hplc For Pharmaceutical Analysis Of Antifungal Agents, Christopher N. Lechnou

Full-Text Theses & Dissertations

HPLC is a commonly used analytical tool in the pharmaceutical industry for the characterization of drug potency and purity. However, HPLC analysis can be very time consuming, use large quantities of organics, and thus costly and not environmentally friendly. In this study, we describe an alternative to HPLC that can be used for pharmaceutical analysis. Capillary electrophoresis is being utilized increasingly for biochemistry and analytical chemistry applications. With advances in auto samplers and improvements in injection precision, the potential for this instrumentation to be used in conjunction or as an alternative to HPLC is currently being evaluated in analytical laboratories. …

Mechanistic Studies Of Specific Dna Cleavage By Pvuii Restriction Endonuclease, Xie Fuqian

Dissertations

PvuII restriction endonuclease is a homodimeric protein which recognizes and cleaves the palindromic sequence (CAG?CTG) in the presence of Mg(II) ions. Starting with PvuII as a model system, pKa calculations with crystallographically defined metal ligated water are applied to PD?D/ExK motif metallonucleases in order to investigate the activation of nucleophile in metal dependent DNA hydrolysis. These results establish the electrostatic contributions of the metal ions and the conserved Lys in lowering water pKa. The calculated pKa values of metal ligands have been used to simulate the pH dependence of Mg(II) binding to PvuII. The bell shaped pH-rate profile is dissected …

Differences In A Conformational Equilibrium Distinguish Catalysis By The Endothelial And Neuronal Nitric-Oxide Synthase Flavoproteins, Robielyn P. Ilagan, Mauro Tiso, David Konas, Craig Hemann, Deborah Durra, Russ Hille, Dennis J. Stuehr

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Nitric oxide (NO) is a physiological mediator synthesized by NO synthases (NOS). Despite their structural similarity, endothelial NOS (eNOS) has a 6-fold lower NO synthesis activity and 6-16-fold lower cytochrome c reductase activity than neuronal NOS (nNOS), implying significantly different electron transfer capacities. We utilized purified reductase domain constructs of either enzyme (bovine eNOSr and rat nNOSr) to investigate the following three mechanisms that may control their electron transfer: (i) the set point and control of a two-state conformational equilibrium of their FMN subdomains; (ii) the flavin midpoint reduction potentials; and (iii) the kinetics of NOSr-NADP+ interactions. Although eNOSr and …

Genetic Analysis Of The Role Of Smpb In Establishing The Reading Frame On Tmrna, Talina Christensen Watts

Theses and Dissertations

Ribosomes translate the genetic information encoded by mRNA into proteins. Defective mRNAs can cause stalling of translating ribosomes. The molecule tmRNA (transfer-messenger RNA) rescues stalled ribosomes in eubacteria. Together with its protein partner SmpB, tmRNA mimics a tRNA by entering the ribosomal A site and linking an alanine residue to the growing polypeptide chain. The ribosome then abandons the defective mRNA template and resumes translation on tmRNA, adding ten more amino acids to the nascent polypeptide. As a result of tmRNA action, stalled ribosomes are released and recycled, the defective mRNA is destroyed, and the aborted protein product is tagged …

The Work Function Of Submonolayer Cesium-Covered Gold: A Photoelectron Spectroscopy Study, Jerry L. Larue, J. D. White, N. H. Nahler, Z. Liu, Y. Sun, P. A. Pianetta, Daniel J. Auerbach, Alec M. Wodtke

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Using visible and x-ray photoelectron spectroscopy, we measured the work function of a Au(111) surface at a well-defined submonolayer coverage of Cs. For a Cs coverage producing a photoemission maximum with a He–Ne laser, the work function is , consistent with previous assumptions used to analyze vibrationally promoted electron emission. A discussion of possible Cs layer structures is also presented.

Design And Synthesis Of Antimalarial Drugs Based On A Chloroquine Scaffold, Steven James Burgess

Dissertations and Theses

There are between 350 and 500 million clinical cases of malaria each year, and over 1 million deaths, with pregnant women and children under the age of 5 being most at risk. Chloroquine (CQ) became the preferred drug to treat malaria in the late 1940s, but is now rendered mostly ineffective in many parts of the world, due to widespread CQ resistance by the malaria parasite. All other malaria treatments suffer from some drawbacks, which include development of resistance, side effects including toxicity, risk for pregnant women and young children, and high cost. Some existing, non-antimalarial, drugs have been found …

Ion Permeation Through Membrane Channels: Molecular Dynamics Simulations Studies, Morad Mustafa

Theses and Dissertations

Molecular dynamics simulation was used to study ion permeation through different membrane proteins embedded in a lipid bilayer (DMPC) with different saline solutions. The potential of mean force (PMF) for ion transport was obtained by umbrella sampling simulations. A revised MacKerell force field for tryptophan residues was studied using gramicidin A (gA) channel as a test model. The revised force field contribution to the Na+ PMF was consonant with the prediction from the experimental results, but in stark contrast to the prediction of the CHARMM force field, version 22, for the tryptophan side-chain. A new grid-based correction map algorithm by …

Stable Long-Time Semiclassical Description Of Zero-Point Energy In High-Dimensional Molecular Systems, Sophya Garashchuk, Vitaly A. Rassolov

Faculty Publications

Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181 (2004)] is further developed to give a stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the linearization errors are added into the time-evolution equations for the classical and nonclassical components of the momentum operator. The wave function normalization and energy are rigorously conserved. Numerical tests are performed for model systems of up to 40 degrees of freedom.

Surface Charge Effects Involved In The Control Of Stability Of Sols Comprising Uniform Cholesterol Particles, Vuk Uskoković

Pharmacy Faculty Articles and Research

The reported is a method for the preparation of stable dispersions of narrowly dispersed cholesterol crystals, which may provide an excellent model for the aggregation studies thereof. The effects of experimental parameters that include concentration, pH, ionic strength, temperature, and aging on the resulting morphologies are acknowledged. Regardless of the cause of destabilization, the multilayered aggregates of cholesterol particles are formed by “face-to-face” stacking of the original platelets, as promoted by higher surface charge density on particle sides comparing to their faces. In accordance with the crucial involvement of surface charge effects in stabilization of cholesterol dispersions produced hereby, aggregation …

Inversion Symmetry And Local Vs. Dispersive Interactions In The Nucleation Of Hydrogen Bonded Cyclic N-Mer And Tape Of Imidazolecarboxamidines, Sihui Long, Venkatraj Muthusamy, Peter G. Willis, Sean Parkin, Arthur Cammers

Chemistry Faculty Publications

Substitutional changes to imidazolecarboxamidine that preserved intermolecular hydrogen bonding in the solid state were used to study the relationship between packing and the hydrogen bond motif. Various motifs competed, but the most common imidazolecarboxamidine crystalline phase was a C_i symmetric dimer that established inversion centers by associating enantiomeric tautomers. Counter to intuition, the calculated gas-phase energies per molecule of the solid state atomic coordinates of the C_i dimer motifs were higher than those of the C₁ dimer, trimer, tetramer and tape motifs, while the packing densities of C_i dimers were found to be higher. This result …

A Novel Approach To The Synthesis Of Silicon Nanowires, Joo Chick Chan

Dissertations and Theses

Contemporary VLS-SiNW synthetic methods employ CVD and laser ablation methods that produce single crystalline SiNW; which can be doped by co-flowing appropriate dopants, such as diborane (p-type) and phosphine (n-type). Not only are these gases toxic (non-green), but also the synthetic methods used are costly requiring elaborate instrumental assembly. This thesis presents a low-cost and "green" method in synthesizing and doping of SiNW in a glass tube. It was found that by selecting the appropriate metal catalyst, precursor reactants, and the reaction conditions both SiNW and carbon nanotube (CNT) can be synthesized on metallic (aluminum and copper), semiconducting (silicon) and …