Physical Sciences and Mathematics Commons^™

Bandwidth Tuning Triggers Interplay Of Charge Order And Superconductivity In Two-Dimensional Organic Materials, S. Kaiser, M. Dressel, Y. Sun, A. Greco, J. A. Schlueter, Gary L. Gard, N. Drichko

Chemistry Faculty Publications and Presentations

We observe charge-order fluctuations in the quasi-two-dimensional organic superconductor β″-(BEDT-TTF)₂SF₅CH₂CF₂SO₃, both by means of vibrational spectroscopy, locally probing the fluctuating charge order, and by investigating the in-plane dynamical response by infrared reflectance spectroscopy. The decrease of the effective electronic interaction in an isostructural metal suppresses both charge-order fluctuations and superconductivity, pointing to their interplay. We compare the results of our experiments with calculations on the extended Hubbard model.

Scoring Function To Predict Solubility Mutagenesis, Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Chemistry Faculty Publications and Presentations

Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to …

Structure Of The Cholera Toxin Secretion Channel In Its Closed State, Steve Reichow, Konstantin V. Korotkov, Wim Gj Hol, Tamir Gonen

Chemistry Faculty Publications and Presentations

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins including multimeric assemblies like cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the “secretin” GspD. Electron cryomicroscopy reconstruction of the V. cholerae secretin at 19 Å resolution reveals a dodecameric structure reminiscent of a barrel with a large channel at its center that appears to contain a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and binds …

Cooperative Interaction Of Transcription Termination Factors With The Rna Polymerase Ii C-Terminal Domain, Bradley M. Lunde, Steve Reichow, Minkyu Kim, Hyunsuk Suh, Thomas C. Leeper, Fan Yang, Hannes Mutschler, Stephen Buratowski, Anton Meinhart, Gabriele Varani

Chemistry Faculty Publications and Presentations

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that …

Extensive Aerosol Optical Properties And Aerosol Mass Related Measurements During Tramp/Texaqs 2006 – Implications For Pm Compliance And Planning, Monica Elizabeth Wright, Dean B. Atkinson, Luke Ziemba, Robert Griffin, Naruki Hiranuma, Sarah D. Brooks, James Flynn, Ryan Perna, Bernhard Rappenglück, Winston Luke, Paul Kelley

Chemistry Faculty Publications and Presentations

Extensive aerosol optical properties, particle size distributions, and Aerodyne quadrupole aerosol mass spectrometer measurements collected during TRAMP/TexAQS 2006 were examined in light of collocated meteorological and chemical measurements. Much of the evident variability in the observed aerosol-related air quality is due to changing synoptic meteorological situations that direct emissions from various sources to the TRAMP site near the center of the Houston-Galveston-Brazoria (HGB) metropolitan area. In this study, five distinct long-term periods have been identified. During each of these periods, observed aerosol properties have implications that are of interest to environmental quality management agencies. During three of the periods, long …

Facile Pyrolytic Synthesis Of Silicon Nanowires, Joo C. Chan, Hoang Tran, James W. Pattison, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

One-dimensional nanostructures such as silicon nanowires (SiNW) are attractive candidates for low power density electronic and optoelectronic devices including sensors. A new simple method for SiNW bulk synthesis[1, 2] is demonstrated in this work, which is inexpensive and uses low toxicity materials, thereby offering a safe, energy efficient and green approach. The method uses low flammability liquid phenylsilanes, offering a safer avenue for SiNW growth compared with using silane gas. A novel, duo-chamber glass vessel is used to create a low-pressure environment where SiNWs are grown through vapor-liquid-solid mechanism using gold nanoparticles as a catalyst. The catalyst decomposes silicon precursor …

Biosynthesis Of Salinosporamides From Α,Β-Unsaturated Fatty Acids: Implications For Extending Polyketide Synthase Diversity, Yuan Liu, Christopher Hazzard, Alessandra S. Eustáquio, Kevin A. Reynolds, Bradley S. Moore

Chemistry Faculty Publications and Presentations

A new series of coenzyme A-tethered polyketide synthase extender units were discovered in relation to the biosynthesis of the salinosporamide family of anticancer agents from the marine bacterium Salinispora tropica. In vivo and in vitro experiments revealed that the crotonyl-CoA reductase/carboxylase SalG has broad substrate tolerance toward 2-alkenyl-CoAs that give rise to the salinosporamide C-2 substitution pattern.

C - Reactive Protein Induced Rearrangement Of Phosphatidylcholine On Nanoparticle Mimics Of Lipoprotein Particles, Marilyn R. Mackiewicz, Heather L. Hodges, Scott M. Reed

Chemistry Faculty Publications and Presentations

Lipid-coated metal nanoparticles are developed here as a mimic of low-density lipoprotein (LDL) particles and used to study C-reactive protein (CRP) binding to highly curved lipid membranes. A 12 nm shift in the localized surface plasmon resonance (LSPR) was observed when CRP was added to the lipid-coated gold nanoparticles. Transmission electron microscopy (TEM) revealed that CRP induced a structural change to the lipids, resulting in clusters of nanoparticles. This clustering provides a visualization of how CRP could cause the aggregation of LDL particles, which is a key step in atherosclerosis. The cluster formation and resultant LSPR shift requires the presence …

Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.

Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen …

Microscopic Formulation Of The Zimm-Bragg Model For The Helix-Coil Transition, A. V. Badasyan, A. Giacometti, Y. S. Mamasakhlisov, V. F. Morozov, Albert S. Benight

Chemistry Faculty Publications and Presentations

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field. However, the dependence on temperature of the reduced external field turns out to differ from the standard one-dimensional Ising model and hence it gives rise to different thermophysical properties, despite the exact mapping connecting them. …

Homocystamides Promote Free-Radical And Oxidative Damage To Proteins, Martha Sibrian-Vazquez, Jorge O. Escobedo, Soojin Lim, George K. Samoei, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Elevated levels of homocysteine are associated with several major diseases. However, it is not clear whether homocysteine is a marker or a causative agent. The majority (ca. 80%) of the homocysteine present in humans is protein bound. The study of the posttranslational modification of proteins by homocysteine and its cyclic congener, homocysteine thiolactone, is emerging as an area of great current interest for unraveling the ongoing “mediator/marker controversy” [Jacobsen DW (2009) Clin Chem 55:1–2]. Interestingly, many of the pathologies associated with homocysteine are also linked to oxidative stress. In the current study, chemical evidence for a causal relationship between homocysteine-bound …

S-Nitrosothiols: Formation, Decomposition, Reactivity And Possible Physiological Effects, Moshood Kayode Morakinyo

Dissertations and Theses

Three biologically-active aminothiols cysteamine (CA), DL-cysteine (CYSH) and DL-homocysteine, were studied in this thesis. These aminothiols react with nitrous acid (HNO₂), prepared in situ, to produce S-nitrosothiols (RSNOs): S-nitrosocyteamine (CANO), S-nitrosocysteine (CYSNO) and S-nitrosohomocysteine (HCYSNO). They also react with S-nitrosoglutathione (GSNO) and S-nitroso-N-acetylpenicillamine (SNAP) through a transnitrosation reaction to produce their corresponding RSNOs. A detailed kinetics and mechanistic study on the formation of these RSNOs and their subsequent decomposition to release nitric oxide (NO) were studied.

For all three aminothiols the stoichiometry of their reaction with nitrous acid is strictly 1:1 with the formation of one mole …

Cest And Paracest Mr Contrast Agents, Ileana Hancu, W. Thomas Dixon, Mark Woods, Elena Vinogradov, A. Dean Sherry, Robert E. Lenkinski

Chemistry Faculty Publications and Presentations

In this review we describe the status of development for a new class of magnetic resonance (MR) contrast agents, based on chemical exchange saturation transfer (CEST). The mathematics and physics relevant to the description of the CEST effect in MR are presented in an appendix published in the online version only. We discuss the issues arising when translating in vitro results obtained with CEST agents to using these MR agents in in vivo model studies and in humans. Examples are given on how these agents are imaged in vivo. We summarize the status of development of these CEST agents, and …

Investigation Of The Sources And Sinks Of Atmospheric Methane, Christopher Lee Butenhoff

Dissertations and Theses

The work presented here represents a number of independent studies that investigated various components of the CH₄ budget, namely the sources and sinks. We used a chemical-tracer model and created unique long-term time series of atmospheric CH₄, carbon monoxide (CO), molecular hydrogen (H₂), and methylchloroform (CH₃CCl₃) measurements at marine background air to derive histories of atmospheric hydroxyl radical (OH) - the main chemical oxidant of CH₄, biomass burning - an important source of CH₄ in the tropics, and emissions of CH₄ from rice paddies - one of …

Nir Dyes For Bioimaging Applications, Jorge O. Escobedo, Oleksandr Rusin, Soojin Lim, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Fluorescent dyes based on small organic molecules that function in the near infra red (NIR) region are of great current interest in chemical biology. They allow for imaging with minimal autofluorescence from biological samples, reduced light scattering and high tissue penetration. Herein, examples of ongoing NIR fluorophore design strategies as well as their properties and anticipated applications relevant to the bioimaging are presented.

Corrosion Behavior Of Copper Thin Films In Organic Hf-Containing Cleaning Solution For Semiconductor Applications, Nabil George Mistkawi, Makarem A. Hussein, Malgorzata Ziomek-Moroz, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

The corrosion behavior of electrochemically deposited copper thin films in deaerated and non-deaerated commercial cleaning solutions containing HF was investigated. Potentiodynamic polarization experiments were carried out to determine active, active–passive, passive, and transpassive regions. Corrosion rates were calculated from Tafel slopes. The addition of hydrogen peroxide to the solution and its influence on corrosion was also investigated by employing inductively coupled plasma-mass spectroscopy (ICP-MS) and X-ray photoelectron spectroscopy (XPS). The ICP-MS and potentiodynamic methods yielded comparable Cu dissolution rates. Surface analysis using atomic force microscopy and scanning electron microscopy, performed before and after the cleaning solution treatment, did not reveal …

Comparison Of In Situ And Columnar Aerosol Spectral Measurements During Texaqs-Gomaccs 2006: Testing Parameterizations For Estimating Aerosol Fine Mode Properties, Dean B. Atkinson, Paola Massoli, Norman T. O'Neill, Patricia K. Quinn, Sarah D. Brooks, Barry Lefer

Chemistry Faculty Publications and Presentations

During the 2006 Texas Air Quality Study and Gulf of Mexico Atmospheric Composition and Climate Study (TexAQS-GoMACCS 2006), the optical, chemical and microphysical properties of atmospheric aerosols were measured on multiple mobile platforms and at ground based stations. In situ measurements of the aerosol light extinction coefficient (σep) were performed by two multi-wavelength cavity ring-down (CRD) instruments, one located on board the NOAA R/V Ronald H. Brown (RHB) and the other located at the University of Houston, Moody Tower (UHMT). An AERONET sunphotometer was also located at the UHMT to measure the columnar aerosol optical depth (AOD). The σep data …

Selective Fluorescence Detection Of Cysteine And N-Terminal Cysteine Peptide Residues, Soojin Lim, Jorge O. Escobedo, Mark Lowry, Xiangyang Xu, Robert M. Strongin

Chemistry Faculty Publications and Presentations

A new fluorogenic fluorescein derivative containing an α,β-unsaturated aldehyde moiety produces a selective fluorescent signal enhancement in the presence of cysteine or peptides containing N-terminal cysteine residues. The mechanism is based on synergistic covalent and supramolecular interactions.

Copper Thin-Film Dissolution/Precipitation Kinetics In Organic Hf Containing Cleaning Solution, Nabil George Mistkawi, Makarem A. Hussein, Malgorzata Ziomek-Moroz, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

The corrosion behavior of electrochemically deposited copper thin films in deaerated and non-deaerated commercial cleaning solution containing HF has been investigated. Thin-film copper dissolution and reaction kinetics were investigated by monitoring Cu²⁺ , employing inductively coupled plasma–mass spectroscopy, and the oxidation states of copper on Si wafer surface, employing X-ray photoelectron spectroscopy. It was determined that the reaction kinetics is first order with respect to both HF and oxygen concentrations. A kinetic scheme involving reduction of oxygen and oxidation of Cu⁰ and Cu¹⁺ is proposed, which is consistent with the experimentally determined reaction kinetic orders and the …

The Population Of Sap And Tsap Isomers In Cyclen-Based Lanthanide(Iii) Chelates Is Substantially Affected By Solvent, Kyle J. Miller, Ali A. Saherwala, Benjamin C. Webber, Yunkou Wu, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

The square antiprism/twisted square antiprism ratio in LnDOTA-tetraamide chelates is a critical parameter in governing water-exchange kinetics and ultimately the utility of a chelate as a PARACEST MRI contrast agent. In LnDOTA-tetraamide chelates with tertiary amides, this ratio and the rate of interconversion between these two structural isomers are found to be dramatically dependent upon the solvent and possibly other local environmental factors.

Polymeric Paracest Mri Contrast Agents As Potential Reporters For Gene Therapy, Yunkou Wu, Christiane E. Carney, Michael Denton, Elaine Hart, Piyu Zhao, Daniel N. Streblow, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

Gene therapy is a potentially powerful treatment approach that targets molecular remedies for disease. Among other challenges it remains difficult to monitor gene delivery and its downstream metabolic consequences. Approaches to MRI gene reporters have been reported but few have the potential for translation beyond isolated cell systems. Herein, we report a polycationic polymer MRI contrast agent that binds to DNA in a ratio of one monomer unit per phosphate group of DNA. Significantly, this binding event diminishes the MR contrast signal from the agent itself potentially providing a platform for imaging delivery and release of a gene into cells …