Chemistry Commons^™

Analytic Derivative Couplings Between Configuration-Interaction-Singles States With Built-In Electron-Translation Factors For Translational Invariance, Shervin Fatehi, Ethan Alguire, Yihan Shao, Joseph Subotnik

Chemistry Faculty Publications and Presentations

We present a method for analytically calculating the derivative couplings between a pair of configuration-interaction-singles (CIS) excited states obtained in an atom-centered basis. Our theory is exact and has been derived using two completely independent approaches: one inspired by the Hellmann-Feynman theorem and the other following from direct differentiation. (The former is new, while the latter is in the spirit of existing approaches in the literature.) Our expression for the derivative couplings incorporates all Pulay effects associated with the use of an atom-centered basis, and the computational cost is minimal, roughly comparable to that of a single CIS energy gradient. …

Reactions With Platinum (Ll) Complexes And Selenium-Containing Amino Acids, Stephanie Robey

Mahurin Honors College Capstone Experience/Thesis Projects

We have reacted [Pt(Me₄en)(D₂O)₂]²⁺ [Me₄En=N,N,N’N’-tetramethylethylenediamine] with Selenomethionine (SeMet), Methionine (Met), and Methylselenocysteine (MeSeCys). When MeSeCys was reacted with [Pt(Me₄en)(D₂O)₂]²⁺, we observed both stereoisomers of Se,N chelates, as well as [Pt(Me₄en)(MeSeCys)Cl]⁺ from ­¹­H NMR Spectroscopy; the latter formed due to the presence of Cl^- in the solution. Both isomers of the chelate seemed to form proportionally to one another, not favoring a specific stereoisomer. Eventually the [Pt(Me₄en)(MeSeCys)Cl]⁺ products became Se,N chelates. We incubated SeMet with …

Relating Dynamic Protein Interactions Of Metallochaperones With Metal Transfer At The Single-Molecule Level, J. J. Benítez, A. M. Keller, D. L. Huffman, Liliya A. Yatsunyk, A. C. Rosenzweig, P. Chen

Chemistry & Biochemistry Faculty Works

Metallochaperones undertake specific interactions with their target proteins to deliver metal ions inside cells. Understanding how these protein interactions are coupled with the underlying metal transfer process is important, but challenging because they are weak and dynamic. Here we use a nanovesicle trapping scheme to enable single-molecule FRET measurements of the weak, dynamic interactions between the copper chaperone Hahl and the fourth metal binding domain (MBD4) of WDP. By monitoring the behaviors of single interacting pairs, we visualize their interactions in real time in both the absence and the presence of various equivalents of Cu(1+). Regardless of the proteins' metallation …

Affinity Chromatography In Environmental Analysis And Drug-Protein Interaction Studies, Efthimia Papastavros

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation will examine the use of novel affinity sorbents to extract emerging contaminants from water. These contaminants include carbamazepine, an anti-epileptic drug which is resistant to natural degradation in the environmental and to drinking water treatment procedures. This drug has been found in fish, drinking water, estuarine and coastal waters, and river sediment and has been used as a general marker of contaminants in wastewater. Carbamazepine was one of the most commonly detected compounds in surface-water and groundwater samples in a recent reconnaissance study of untreated drinking water sources in the U.S. Besides using this drug as a representative …

Acrb Trimer Stability And Efflux Activity, Insight From Mutagenesis Studies, Linliang Yu, Wei Lu, Yinan Wei

Chemistry Faculty Publications

The multidrug transporter AcrB in Escherichia coli exists and functions as a homo-trimer. The assembly process of obligate membrane protein oligomers, including AcrB, remains poorly understood. In a previous study, we have shown that individual AcrB subunit is capable of folding independently, suggesting that trimerization of AcrB follows a three-stage pathway in which monomers first fold, and then assemble. Here we destabilized the AcrB trimer through mutating a single Pro (P223) in the protruding loop of AcrB, which drastically reduced the protein activity. We replaced P223 separately with five residues, including Ala, Val, Tyr, Asn, and Gly, and found that …

Development And Optimization Of Organic Based Monoliths For Use In Affinity Chromatography, Erika L. Pfaunmiller

Department of Chemistry: Dissertations, Theses, and Student Research

Affinity chromatography is an important and useful tool for studying biological interactions, such as the binding of an antibody with an antigen. Monolithic supports offer many advantages over traditional packed bed supports in affinity chromatography, including their ease of preparation, low back pressures and good mass transfer properties. Monoliths can be broken down into two basic categories: organic (polymer) and inorganic (silica) monoliths. There are many varieties of polymer based monoliths; however, a large focus has been on co-polymers of glycidyl methacrylate (a functional monomer) and ethylene dimethacrylate (a cross-linking agent). The solvents of choice for making this type of …

Organ-Distribution Of The Metabolite 2-Aminothiazoline-4-Carboxylic Acid In A Rat Model Following Cyanide Exposure, Ilona Petrikovics, David E. Thompson, Gary A. Rockwood, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

The reaction of cyanide (CN⁻) with cystine to produce 2-aminothiazoline-4-carboxylic acid (ATCA) is one of the independent detoxification pathways of cyanide in biological systems. In this report, in vivo production of ATCA and its distributions in plasma and organs were studied after a subcutaneous sublethal dose of 4 mg/kg body weight potassium cyanide (KCN) administration to rats. At this sublethal dose of KCN, ATCA concentration was not significantly increased in the plasma samples, however, it was found significantly increased in liver samples. These results suggested that ATCA might not be a good diagnostic biomarker in plasma for sublethal …

The Tetrafluoroborate Salt Of 4-Methoxybenzyl N-2-(Dimethylamino)Ethyl-N-Nitrosocarbamate: Synthesis, Crystal Structure And Dft Calculations, Helene Hedian, Vladimir Benin

Chemistry Faculty Publications

The tetrafluoroborate salt of 4-methoxybenzyl N-2-(dimethylamino)ethyl-N-nitrosocarbamate was prepared in two steps, via the corresponding carbamate. Its crystal structure is monoclinic, space group P21/c. The unit cell dimensions are: a = 19.499(8) Å, b = 5.877(3) Å, c = 15.757(7) Å, α = 90°, β = 110.019(7)°, γ = 90°, V = 1696.5(12) Å3, Z = 4. The structure exhibits an unexpected, pseudo-gauche conformation with respect to the C2–C3 bond, due to a stabilizing hydrogen bond between the carbonyl oxygen (O1) and the hydrogen atom at the trialkylammonium center (H3n), with a distance between them of …

Maxwell's Equations, Part Iv, David W. Ball

Chemistry Faculty Publications

In this column, we continue our explanation of Maxwell’s equations, the seminal classical explanation of electricity and magnetism (and, ultimately, light). For those of you new to the series, consider finding the last few appearances of this column to get caught up. Alternately, you should be able to find past columns on our website, www.spectroscopymag.com and look for “The Baseline” link. Words of warning: for my own reasons, the figures are being numbered sequentially through this series of columns, which is why the first figure in this column is numbered 26. Also, we’re going to get a bit mathematical. Unfortunately …

Fabrication Of Mineralized Collagen From Bovine Waste Materials By Hydrothermal Method As Promised Biomaterials, Faheem A. Sheikh, M. A. Kanjwal, Javier Macossay-Torres, Muneeb A. Muhammad, Travis Cantu, Ioannis S. Chronakis, N. A. M. Barakat, Hak Yong Kim

Chemistry Faculty Publications and Presentations

In the present study, we aimed to produce mineralized-collagen by hydrothermal process. A simple method not depending on additional foreign chemicals has been employed to isolate the mineralized-collagen fibers from bovine waste. The process of extraction involves the use of hydrothermal method from available bovine bones. The structural and morphological properties of the collagen fibers were characterized by using scanning electron microscopy and transmission electron microscopy. These results indicated well received collagen fibers, having a diameter less than 1 μm and with established mineral content in the individual fibers. The X-ray diffraction showed the crystalline feature of the obtained nano-compounds. …

Chemical Modification On Gold Slides To Gain Better Control Of Patterning Techniques, Ragini Vuppalapati

Masters Theses & Specialist Projects

Nanolithography is a rapidly evolving field that requires new combinations of techniques to improve patterning and to assist in fabricating electromechanical devices. An increasing number of applications require surfaces with defined regions of different chemical functionality. In our previous project optimum conditions for lithographic patterning were determined and potential blockers were identified to reduce force on the tip.

This work is focused on identifying good chemical modifications that will allow better control of basic patterning and to investigate the minimum force of patterning required while using each chemical system. The primary aim is to gain better control of basic pattern …

Activity Of Analogs Of Anticancer Drugs On The Serine Protease Enzymes Subtilisin And Chymotrypsin, Dhatri Ravipati

Masters Theses & Specialist Projects

The anticancer activity of several platinum compounds is due to the formation of complexes with DNA. We hypothesize that the size and shape of the platinum compounds would impact interaction with proteins, and these interactions may be partly responsible for the anticancer activity. Chymotrypsin and subtilisin are serine proteases that have a histidine residue in the active site. We are investigating the inhibition of the digestive enzymes chymotrypsin and subtilisin by analogs of the anticancer drug cisplatin and trying to discern trends in the inhibition as the active site residues vary. In our research, we found that the enzyme subtilisin …

Inhibition Of Cysteine Protease By Platinum (Ii) Diamine Complexes, Chaitanya Rapolu

Masters Theses & Specialist Projects

Chemotherapy is the first line of treatment used in cancer. Chemotherapy drugs such as cisplatin, carboplatin and oxaliplatin are used in treatment. Cisplatin enters the cell through copper transporter CTR1 by passive diffusion and bind to DNA and proteins. Cisplatin is found to inhibit several enzymes targeting cysteine, histidine and methionine residues, which are expected to be responsible for its anticancer activity. A better understanding of how the size and shape and leaving ligands of platinum complexes affect cysteine protease, papain enzyme are studied. This could give new ways to optimize anticancer activity. The activity of papain enzyme was measured …

Analysis Of Volatile Organic Compounds In Virgin Coconut Oil And Their Sensory Attibutes, Fabian M. Dayrit, Jaclyn Elizabeth R. Santos, Bianca J. Villarino, Anthony R. Zosa

Chemistry Faculty Publications

The volatile compounds in the headspace of twenty-four commercial virgin coconut oil (VCO) samples prepared by different methods (i.e. expeller, centrifugation, and fermentation with and without heat) were analyzed by solid phase microextraction-gas chromatography mass spectrometry (SPME-GCMS). The following volatile organic compounds (VOCs) were identified: ethyl acetate, acetic acid, 2-pentanone, hexanal, n-octane, 2-heptanone, limonene, nonanal, octanoic acid, ethyl octanoate, δ-octalactone, ethyl decanoate, δ-decalactone, and dodecanoic acid. Fermentation-produced samples were found to have higher levels of acetic acid and free fatty acids in the headspace compared to VCO produced using the centrifuge and expeller methods. Descriptive sensory analysis of the VCO …

Preparation And Characterization Of Biomimetic Hydroxyapatite-Resorbable Polymer Composites For Hard Tissue Repair, Kristopher R. Hiebner

Department of Chemistry: Dissertations, Theses, and Student Research

Autografts are the orthopedic “gold standard” for repairing bone voids. Autografts are osteoconductive and do not elicit an immune response, but they are in short supply and require a second surgery to harvest the bone graft. Allografts are currently the most common materials used for the repair of segmental defects in hard tissue. Unlike autografts, allografts can cause an undesirable immune response and the possibility of disease transmission is a major concern. As an alternative to the above approaches, recent research efforts have focused on the use of composite materials made from hydroxyapatite (HA) and bioresorbable polymers, such as poly-L-lactide …

Opacity Of P(Mma-Maa)-Pmma Composite Latex System With Varying Maa Concentration, Gilbert U. Yu, Jerry T. Dy, Erwin P. Enriquez

Chemistry Faculty Publications

Polymer composites of core-shell morphology are commonly used in the paint industry as opacity enhancer. These are usually made of block copolymer systems wherein the core is formed from a polymer that swells in the presence of a solvent and surrounded by a high glass transition polymeric shell. Thus, upon drying, the swollen regions turn into voids while leaving a hard shell. Here, composites based on poly(methyl methacrylate-butyl acrylate) [P(MMA-BuA)] (seed stage), poly(methyl methacrylate-methacrylic acid) [P(MMA-MAA)] (second stage), and poly(methyl methacrylate) [PMMA] (third stage) were synthesized through a multistage sequential emulsion polymerization and their opacity was investigated. The second stage …

Quantum Mechanical And Molecular Mechanical Study Of Solvent Effects, Dejun Si

Department of Chemistry: Dissertations, Theses, and Student Research

Intermolecular interaction and solvent effects play important roles in determining physical and chemical properties of molecular systems, and must be considered in relevant quantum mechanical (QM) calculations. Due to the high computational cost, full and rigorous QM treatment of both solute and solvent molecules is impractical. Computationally efficient molecular mechanical (MM) methods can be used to describe solvent effects, and combined into QM methods to formulate QM/MM methods. Classical force field method and reaction-field method are the two most popular MM methods. However, the issue of effectively combining MM methods with high-level QM methods remains unsolved. This thesis presents several …

First-Principles Studies On Physical And Chemical Properties Of Nanostructures, Menghao Wu

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

The physical and chemical properties of decorated graphene and graphene ribbons, single-layer III-V systems, three-dimensional carbon and BN foam, and transition-metal-molecular sandwich nanowires have been investigated by first-principle calculations and their potential applications have been predicted. First, it is shown that zigzag graphene nanoribbons (ZGNRs) can be converted into half metal when their edges are decorated by some chemical functional groups, and the half-metalicity is induced by chemical potential difference between two edges when one edge is decorated by electron-donating group like –OH and the other edge is decorated by electron-accepting group like –F, -NH₂, -N(CH₃) …

Using Lectinmicroarrays To Identify Regulatory Mechanisms For Mammalian Glycosylation, John F. Rakus

Chemistry Faculty Research

Glycosylation involves the post-translational addition of carbohydrates to protein molecules and is an intricate and indispensable biochemical process. Study of this complicated network of interactions is hindered by the lack of a coding template analogous to the genetic code, and by the vast structural complexity inherent to carbohydrate polymers. We use lectins (non-enzymatic carbohydrate-binding proteins of non-immunological origin) as microarray probes to identify carbohydrate features expressed on cellular surfaces. Specifically, we utilized lectin microarray technology to investigate the differences in carbohydrates expressed by the cell lines of the Nation Cancer Institute’s NCI-60 panel. Our investigation identified tissue-specific expression differences in …

Sweep, Step, Pulse, And Frequency-Based Techniques Applied To Protein Monolayer Electrochemistry At Nanoparticle Interfaces, Debbie S. Campbell-Rance, Tran T. Doan, Michael C. Leopold

Chemistry Faculty Publications

Protein monolayer electrochemistry (PME), a strategy using synthetic platforms to study the electron transfer (ET) properties of adsorbed proteins, has been successfully applied to proteins adsorbed at monolayer-protected gold cluster (MPCs) assembled films, an adsorption interface shown to be an effective alternative, compared to traditional self-assembled monolayer (SAM) films, for the immobilization and study of ET proteins. Within PME studies, cyclic voltammetry (CV) remains the most commonly applied electrochemical technique in spite of several limitations that occur when the sweep technique is used at either platform. In particular, CV for PME at MPC films results in analysis complications stemming from …

Preparation, Properties, And Reactivity Of Carbonylrhodium(I) Complexes Of Di(2-Pyrazolylaryl)Amido-Pincer Ligands, Sarath Wanniarachchi, Brendan J. Liddle, Sergey V. Lindeman, James R. Gardinier

Chemistry Faculty Research and Publications

A series of six carbonylrhodium(I) complexes of three new and three previously reported di(2-3R-pyrazolyl)-p-Z/X-aryl)amido pincer ligands, (^RZX)Rh(CO), (R is the substituent at the 3-pyrazolyl position proximal to the metal; Z and X are the aryl substituents para- to the arylamido nitrogen) were prepared. The metal complexes were studied to assess how their properties and reactivities can be tuned by varying the groups along the ligand periphery and how they compared to other known carbonylrhodium(I) pincer derivatives. This study was facilitated by the discovery of a new CuI-catalyzed coupling reaction between 2-(pyrazolyl)-4-X-anilines (X = Me or …

Reflections On The Journey: Six Short Stories, Sharon L. Haynie, Amber S. Hinkle, Nancy L. Jones, Cheryl A. Martin, Paula J. Olsiewski, Mary F. Roberts

Integrated Science and Business Technology Faculty Work

One of the goals of the 2011 International Year of Chemistry is to celebrate the contributions of women to science. A question that has been frequently asked in this regard is... Why is it necessary to highlight women in the "age of equality"? The reasons are varied but the facts are that many women scientists worked in obscurity throughout the 19th and even well into the 20th century, sometimes publishing anonymously to be heard. This celebration of Women in Science is one way to recognize both the resiliency and passion of these women. As part of this celebration, Chemistry Central …

Field-Induced Xy And Ising Ground States In A Quasi-Two-Dimensional S=1/2 Heisenberg Antiferromagnet, Yoshimitsu Kohama, Marcelo Jaime, Oscar E. Ayala-Valenzuela, Ross D. Mcdonald, Eun Deok Mun, Jordan F. Corbey, Jamie L. Manson

Chemistry and Biochemistry Faculty Publications

High field specific heat up to 35 T, C-p, and magnetic susceptibility, chi, measurements were performed on the quasi-two-dimensional (2D) Heisenberg antiferromagnet [Cu(pyz)(2)(pyO)(2)](PF6)(2). While no C-p anomaly is observed down to 0.5 K in zero magnetic field, the application of field parallel to the crystallographic ab-plane induces a lambda-like anomaly in C-p, suggesting Ising-type magnetic order. On the other hand when the field is parallel to the c-axis, C-p and chi show evidence of XY-type antiferromagnetism. This dependence upon the field orientation occurs because the extreme two-dimensionality allows the intrinsic (zero field) spin anisotropy to dominate the interlayer coupling, which …

Density Functional Theory Study On The Electronic Structure Of N- And P-Type Doped Srtio3 At Anodic Solid Oxide Fuel Cell Conditions, Suwit Suthirakun, Salai Cheettu Ammal, Guoliang Xiao, Fanglin Chen, Andreas Heyden, Hans-Conrad Zur Loye

Faculty Publications

The electronic conductivity and thermodynamic stability of mixed n-type and p-type doped SrTiO₃ have been investigated at anodic solid oxide fuel cell (SOFC) conditions using density functional theory (DFT) calculations. In particular, constrained ab initio thermodynamic calculations have been performed to evaluate the phase stability and reducibility of various Nb- and Ga-doped SrTiO₃ at synthesized and anodic SOFC conditions. The density of states (DOS) of these materials was analyzed to study the effects of n- and p-doping on the electronic conductivity. In agreement with experimental observations, we find that the transformation from 20% Nb-doped Sr-deficient SrTiO …

The Evolution Of Function In Strictosidine Synthase-Like Proteins, Michael A. Hicks, Alan E. Barber, Lesley Ann Giddings, Jenna Caldwell, Sarah E. O'Connor, Patricia C. Babbitt

Chemistry: Faculty Publications

The exponential growth of sequence data provides abundant information for the discovery of new enzyme reactions. Correctly annotating the functions of highly diverse proteins can be difficult, however, hindering use of this information. Global analysis of large superfamilies of related proteins is a powerful strategy for understanding the evolution of reactions by identifying catalytic commonalities and differences in reaction and substrate specificity, even when only a few members have been biochemically or structurally characterized. A comparison of >2500 sequences sharing the six-bladed β-propeller fold establishes sequence, structural, and functional links among the three subgroups of the functionally diverse N6P superfamily: …

Heavy Metal Analysis Of Sabine River And Toledo Bend Reservoir Bed Sediments, Michael A. Janusa

Faculty Posters

Core samples were collected from the Sabine River and Toledo Bend Reservoir beds, digested, and analyzed using atomic absorption spectroscopy for several heavy metals. The magnitude of heavy metal concentrations in the bed sediments and the pattern of deposition can help determine which heavy metals are present, the source of heavy metals found in the fish (bed sediment or water), and the source of the heavy metal pollution, if any: industrial, geologic, or atmospheric.

A Mild One-Pot Conversion Of Alkenes Into Amines Through Tandem Ozonolysis And Reductive Amination, Shivakumar Kyasa, Thomas J. Fisher, Patrick Dussault

Patrick Dussault Publications

The selective reduction of hydroperoxyacetals to aldehydes by sodium triacetoxyborohydride provides the basis for a mild one-pot synthesis of amines from alkenes.

Includes Supplementary Materials.

Templated Synthesis Of Glycoluril Hexamer And Monofunctionalized Cucurbit[6]Uril Derivatives, Derick Lucas, Tsuyoshi Minami, Greg Iannuzzi, Liping Cao, James B. Wittenberg, Pavel Anzenbacher Jr., Lyle Isaacs

Chemistry Faculty Publications

We report that the p-xylylenediammonium ion (11) acts as a template in the cucurbit[n]uril forming reaction that biases the reaction toward the production of methylene bridged glycoluril hexamer (6C) and bis-nor-seco-CB [10]. Hexamer 6C is readily available on the gram scale by a one step synthetic procedure that avoids chromatography. Hexamer 6C undergoes macrocylization. with (substituted) phthalaldehydes 12,14,.15, and 18-in 9 M H2SO4 or concd HCl at room temperature to deliver monofunctionalized CB[6] derivatives 13,16,17, and 19 that are poised for further functionalization reactions: The kinetics of the macrocyclization reaction between hexamer and formaldehyde or phthalaldehyde depends on the presence …

Valine Sulfonamidecinnamic Acid Asymmetric Crystal Reactions, Kraig A. Wheeler, Steven H. Malehorn, Annie E. Egan

Faculty Research and Creative Activity

Racemic and homochiral valine sulfonamidecinnamic acidscrystallize with components aligned by use of thecomplementary features of hydrogen bonds and moleculartopology to give supramolecular dimers. These discretemotifs effectively organize adjacent olefins for UV initiated10 single-crystal-to-single-crystal [2+2] photodimerizationreactions. The racemic crystals produce inversion relatedcyclobutane products, while the desymmetrized crystallinearchitectures of the homochiral phase promote asymmetricphotodimerization with 90% conversion.

Statistical Thermodynamics Of Material Transport In Non-Isothermal Mixtures, Semen Semenov, Martin Schimpf

Chemistry and Biochemistry Faculty Publications and Presentations

This chapter outlines a theoretical framework for the microscopic approach to material transport in liquid mixtures, and applies that framework to binary one-phase systems. The material transport in this approach includes no hydrodynamic processes related to the macroscopic transfer of momenta. In analyzing the current state of thermodynamic theory, we indicate critically important refinements necessary to use non-equilibrium thermodynamics and statistical mechanics in the application to material transport in nonisothermal mixtures.