Chemistry Commons^™

Dual-Functional-Tag-Facilitated Protein Labeling And Immobilization, Xinyi Zhang, Wei Lu, Kevin Kwan, Dibakar Bhattacharyya, Yinan Wei

Chemistry Faculty Publications

An important strategy in the construction of biomimetic membranes and devices is to use natural proteins as the functional components for incorporation in a polymeric or nanocomposite matrix. Toward this goal, an important step is to immobilize proteins with high efficiency and precision without disrupting the protein function. Here, we developed a dual-functional tag containing histidine and the non-natural amino acid azidohomoalanine (AHA). AHA is metabolically incorporated into the protein, taking advantage of the Met-tRNA and Met-tRNA synthetase. Histidine in the tag can facilitate metal-affinity purification, whereas AHA can react with an alkyne-functionalized probe or surface via well-established click chemistry. …

Controlled Microfabrication Of High-Aspect-Ratio Structures In Silicon At The Highest Etching Rates: The Role Of H2o2 In The Anodic Dissolution Of Silicon In Acidic Electrolytes, Chiara Cozzi, Giovanni Polito, Kurt W. Kolasinski, Giuseppe Barillaro

Chemistry Faculty Publications

In this work the authors report on the controlled electrochemical etching of high-aspect-ratio (from 5 to 100) structures in silicon at the highest etching rates (from 3 to 10 µm min−1) at room temperature. This allows silicon microfabrication entering a previously unattainable region where etching of high-aspect-ratio structures (beyond 10) at high etching rate (over 3 µm min−1) was prohibited for both commercial and research technologies. Addition of an oxidant, namely H2O2, to a standard aqueous hydrofluoric (HF) acid electrolyte is used to dramatically change the stoichiometry of the silicon dissolution process under anodic biasing without loss of etching control …

Isolation Of A Chiral Anthracene Cation Radical: X-Ray Crystallography And Computational Interrogation Of Its Racemization, Mikhail V. Ivanov, Khushabu Thakur, Anshul Bhatnagar, Rajendra Rathore

Chemistry Faculty Research and Publications

Chiral cation-radical salts hold significant promise as charge-transfer materials, chiroptical switches, and electron-transfer catalysts for enantioselective synthesis. Herein we demonstrate that the readily-available chiral 9,10-diphenyleanthracene derivative (i.e.^SANT) forms a robust cation radical, whose structure was elucidated by X-ray crystallography and DFT calculations. While ^SANT was observed to racemize on a timescale (t_1/2) of 1.1 hours, a computational conformational search and kinetic analysis of the racemization pathway led us to identify a simple methyl substituted ^SANT derivative, which does not racemize (racemization t_1/2 10¹³–10¹⁷ years).

Modeling Of S‐Nitrosothiol–Thiol Reactions Of Biological Significance: Hno Production By S‐Thiolation Requires A Proton Shuttle And Stabilization Of Polar Intermediates, Lena V. Ivanova, Daniel Cibich, Gregory Deye, Marat R. Talipov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S‐thiolation reaction between thiols and S‐nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S‐thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge‐separated zwitterionic intermediate structure RSS⁺(R)N(H)O⁻ (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S−S …

Implicating The Contributions Of Surface And Bulk States On Carrier Trapping And Photocurrent Performance Of Bivo4 Photoanodes, Brian Pattengale, Jier Huang

Chemistry Faculty Research and Publications

Monoclinic-scheelite BiVO₄ has been widely studied as a promising oxygen evolution reaction (OER) catalyst in artificial photosynthesis. Though significant progress to improve or augment its catalysis performance has been made, fundamental understanding of its relatively poor performance as a bare material is lacking. In this paper, we report the correlation of the surface structure and trap states with charge separation efficiency and OER performance of bare BiVO₄ photoanodes viavarying the sample thickness. Using X-ray absorption spectroscopy (XAS), we observed a more compacted, symmetric Bi center in the surface state. Using transient absorption (TA) spectroscopy, we show that the …

Phosphonium-Functionalized Polymer Micelles With Intrinsic Antibacterial Activity, Benjamin Hisey, Paul J. Ragogna, Elizabeth Gillies

Chemistry Publications

New approaches to treat bacterial infections are badly needed to address the increasing problem of antibiotic resistance. This study explores phosphonium-functionalized block copolymer micelles as intrinsically antibacterial polymer assemblies. Phosphonium cations with varying alkyl lengths were conjugated to the terminus of a poly(ethylene oxide)− polycaprolactone block copolymer, and the phosphonium-functionalized block copolymers were self-assembled to form micelles in aqueous solution. The size, morphology, and ζ -potential of the assemblies were studied, and their abilities to kill Escherichia coli and Staphylococcus aureus were evaluated. It was found that the minimum bactericidal concentration depended on the phosphonium alkyl chain length, and different …

Enzyme–Free Uric Acid Electrochemical Sensors Using Β–Cyclodextrin Modified Carboxylic Acid Functionalized Carbon Nanotubes, Mulugeta B. Wayu, Margaret A. Schwarzmann, Samuel D. Gillespie, Michael C. Leopold

Chemistry Faculty Publications

Carboxylic acid-functionalized multi-walled carbon nanotubes (COOH-MWCNT) were modified via ultrasonication with β-cyclodextrin (β-CD) to obtain a COOH-MWCNT:β-CD nanocomposite material for the purpose of developing an enzyme-free electrochemical sensor for uric acid—a clinically relevant molecule implemented in pregnancy-induced hypertension diagnosis. The nanocomposite material is deposited onto glassy carbon electrodes and subsequently capped with layers of Nafion and Hydrothane polyurethane. The surface morphology and electronic structure of the nanocomposite material were characterized using UV–Vis, TEM, and FTIR. The performance of the electrochemical sensor was measured through direct injection of UA during amperometry. With the high surface area of the COOH-MWCNT in concert …

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.

Effect Of Zinc Cations On The Kinetics Of Supramolecular Assembly And The Chirality Of Porphyrin J-Aggregates, A. Romeo, M. A. Castriciano, R. Zagami, G. Pollicino, L Monsù Scolaro, Robert F. Pasternack

Chemistry & Biochemistry Faculty Works

Dilute aqueous solutions of anionic meso-4-sulfonatophenyl-porphyrin (TPPS) extract zinc(ii) ions from glass or quartz surfaces at room temperature and efficiently form the corresponding metal complex (ZnTPPS). The partial or complete formation of ZnTPPS has been probed by UV/Vis spectroscopy and both static and time-resolved fluorescence. The source of zinc(ii) ions has been clearly identified through inductively coupled plasma optical emission spectrometry. The presence of increasing amounts of ZnTPPS slows down the rate of TPPS J-aggregate formation in acid solution. This influences the nucleation step and has a profound impact on the onset of chirality in these species. This evidence indicates …

Strong Metal-Support Interactions: An Extra Layer Of Complexity, Bert D. Chandler

Chemistry Faculty Research

Strong interactions between oxide supports and catalytic metal particles can lead to inhibitive oxide layers forming over the active metal catalyst. Now, adsorbate-induced metal–support interactions have been shown to lead to a porous overlayer in the Rh/TiO₂ system that tunes catalyst activity, improving its selectivity for the partial reduction of CO₂.

Hmba Is A Putative Hsp70 Activator Stimulating Hexim1 Expression That Is Down-Regulated By Estrogen, Rati Lama, Chunfang Gan, Nethrie Idippily, Viharika Bobba, David Danielpour, Monica Montano, Bin Su Ph.D.

Chemistry Faculty Publications

Hexamethylene bis-acetamide inducible protein 1 (HEXIM1) is identified as a novel inhibitor of estrogen stimulated breast cell growth, and it suppresses estrogen receptor-a transcriptional activity. HEXIM1 protein level has been found to be downregulated by estrogens. Recently, HEXIM1 has been found to inhibit androgen receptor transcriptional activity as well. Researchers have used Hexamethylene bisacetamide (HMBA) for decades to stimulate HEXIM1 expression, which also inhibit estrogen stimulated breast cancer cell gene activation and androgen stimulated prostate cancer gene activation. However, the direct molecular targets of HMBA that modulate the induction of HEXIM1 expression in mammalian cells have not been identified. Based …

Novel Trifluoromethylated 9-Amino-3,4-Dihydroacridin-1(2h)-Ones Act As Covalent Poisons Of Human Topoisomerase Iiα, Lorena Infante Lara, Alexis Sledge, Amine Laradji, Cosmas O. Okoro, Neil Osheroff

Chemistry Faculty Research

A number of topoisomerase II-targeted anticancer drugs, including amsacrine, utilize an acridine or related aromatic core as a scaffold. Therefore, to further explore the potential of acridine-related compounds to act as topoisomerase II poisons, we synthesized a series of novel trifluoromethylated 9-amino-3,4-dihydroacridin-1(2H)-one derivatives and examined their ability to enhance DNA cleavage mediated by human topoisomerase IIα. Derivatives containing a H, Cl, F, and Br at C7 enhanced enzyme-mediated double-stranded DNA cleavage ∼5.5- to 8.5-fold over baseline, but were less potent than amsacrine. The inclusion of an amino group at C9 was critical for activity. The compounds lost their activity against …

Design Of Collagen-Mimetic Peptides, Parminder Jeet Kaur

Dissertations, Theses, and Capstone Projects

Collagen is the major component of the extracellular matrix and is involved in a wide range of cellular functions during tissue development and action. At the core of the diverse functions of this versatile protein is its remarkable ability to form supramolecular structures through self-assembly and/or through interactions with other biomolecules. One typical example of such supramolecular structure is the fibrils of collagen types I, II and III of the connective tissues. These fibrils have staggered arrangement of the laterally associated collagen triple helices – the structural unit of collagen – to form long, smooth fibrils with a characteristic 67 …

Iterative Non-Proteinogenic Residue Incorporation Yields Α/Β-Peptides With A Helix-Loop-Helix Tertiary Structure And High Affinity For Vegf, James W. Checco, Samuel H. Gellman

Department of Chemistry: Faculty Publications

Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues (“α/β-peptides”) that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure. We show how a two-helix “mini-Z-domain” can be modified to contain β and other non-proteinogenic residues while retaining the target-binding epitope using iterative non-natural residue incorporation. …

Synthesis Of Complex/Multifunctional Metal (Hydr)Oxide/Graphite Oxide/Aunps Or Agnps Adsorbents And Analysis Of Their Interactions With Chemical Warfare Agents, Dimitrios A. Giannakoudakis

Dissertations, Theses, and Capstone Projects

One of the most widely used chemical warfare agent (CWA) is mustard gas, which is a highly toxic blistering agent. In this study we investigated the interactions of mustard gas surrogates’ vapors on zinc and zirconium hydroxides and their composites with graphite oxide (GO) and/or Au or Ag nanoparticles. Even though a small quantity of reports about the detoxification of CWAs on metal oxides is reported in the literature, almost all of these studies are performed in the liquid phase. Both herein reported Zn(OH)₂ and Zr(OH)₄ showed a good adsorption performance, with the former being photoactive under visible …

Ozone Depletion, A Big Threat To Climate Change: What Can Be Done?, Sumera Aziz Ali, Savera Aziz Ali, Nadir Suhail

Community Health Sciences

Ozone in the stratosphere is very important as it acts as a safeguard for the earth and protects life from harmful ultraviolet radiations coming from the sun. Depletion of stratospheric ozone, resulting from atmospheric pollution has led to increased ultraviolet radiation at the earth’s surface as well as spectral shifts to the more biologically damaging shorter wavelengths. A decrease in the concentration of stratospheric ozone enhances the solar ultraviolet (UV) radiation, which is harmful to the growth of the plant and various other metabolic processes of the organisms and might cause changes in pigment concentrations, nucleic acids, and proteins. Multiple …

Effects Of Molecular Structure And Packing Order On The Stretchability Of Semicrystalline Conjugated Poly(Tetrathienoacene-Diketopyrrolopyrrole) Polymers, Chien Lu, Wen-Ya Lee, Xiaodon Gu, Jie Xu, Ho-Hsiu Chou, Hongping Yan, Yu-Cheng Chiu, Mingqian He, James R. Matthews, Weijun Niu, Jeffery B.-H. Tok, Michael F. Toney, Wen-Chang Chen, Zhenan Bao

Faculty Publications

The design of polymer semiconductors possessing high charge transport performance, coupled with good ductility, remains a challenge. Understanding the distribution and behavior of both crystalline domains and amorphous regions in conjugated polymer films, upon an applied stress, shall provide general guiding principles to design stretchable organic semiconductors. Structure–property relationships (especially in both side chain and backbone engineering) are investigated for a series of poly(tetrathienoacene-diketopyrrolopyrrole) polymers. It is observed that the fused thiophene diketopyrrolopyrrole-based polymer, when incorporated with branched side chains and an additional thiophene spacer in the backbone, exhibits improved mechanical endurance and, in addition, does not show crack propagation …

Multi-Instrument Comparison And Compilation Of Non-Methane Organic Gas Emissions From Biomass Burning And Implications For Smoke-Derived Secondary Organic Aerosol Precursors, Lindsay E. Hatch, Robert J. Yokelson, Chelsea E. Stockwell, Patrick R. Veres, Isobel J. Simpson, Donald R. Blake, John J. Orlando, Kelley C. Barsanti

Chemistry and Biochemistry Faculty Publications

Multiple trace-gas instruments were deployed during the fourth Fire Lab at Missoula Experiment (FLAME- 4), including the first application of proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOFMS) and comprehensive two-dimensional gas chromatography-time-offlight mass spectrometry (GC×GC-TOFMS) for laboratory biomass burning (BB) measurements. Open-path Fourier transform infrared spectroscopy (OP-FTIR) was also deployed, as well as whole-air sampling (WAS) with onedimensional gas chromatography-mass spectrometry (GCMS) analysis. This combination of instruments provided an unprecedented level of detection and chemical speciation. The chemical composition and emission factors (EFs) determined by these four analytical techniques were compared for four representative fuels. The results demonstrate that the instruments are …

Comparison Of Tetrel Bonds In Neutral And Protonated Complexes Of Pyridinetf3 And Furantf3 (T = C, Si, And Ge) With Nh3, Mingxiu Liu, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio calculations have been performed for the complexes H+–PyTX3⋯NH3 and H+–furanTF3⋯NH3 (T = C, Si, and Ge; X = F and Cl) with focus on geometries, energies, orbital interactions, and electron densities to study the influence of protonation on the strength of tetrel bonding. The primary interaction mode between α/β-furanCF3/p-PyCF3 and NH3 changes from an F⋯H hydrogen bond to a C⋯N tetrel bond as a result of protonation. Importantly, the protonation has a prominent enhancing effect on the strength of tetrel bonding with an increase in binding energy from 14 to 30 kcal mol−1. The tetrel bonding becomes stronger …

Evolution Of Complex Target Selex To Identify Aptamers Against Mammalian Cell-Surface Antigens, Prabodhika R. Mallikaratchy

Publications and Research

The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This …

Application Of Electrochemical Sensors For Nanomolar Detection Of Chromium (Vi) In Drinking Water And Development Of Graphene Based Ionophore-Doped Polymeric Membrane Electrode, Fatma Ali Al-Amoody

Student Theses and Dissertations

Toxic chemicals like chromium (VI) pose a great risk to humans and environment. In this study, we used ion-selective electrode like glassy carbon (GC) to detect trace analysis of chromium in the form of hydrogen chromate ion (HCrO4-) in drinking water. The surfaces of GC electrodes were electrochemically modified by polymerizing with poly 3-octylthiophene (POT) using cyclic voltammetry followed by plasticized polyvinyl chloride (PVC) to form a double polymer membrane. They were then used in the stripping voltammetry technique whereby current showed a linear response of hydrogen chromate ion between 30 nM to 1300 nM in drinking water. Graphene is …

Assessment Of The Link Between In Utero Exposure To 2-Aminoanthracene (2aa) And Type-1 Diabetes (T1d), Christopher A. Mays, Daniel A. Hunter, Wilson Yau, Worlanyo E. Gato

Chemistry: Faculty Publications (1990-2023)

Background: A recent diabetes report revealed an increased incidence in diabetes including type 1-diabetes (T1D). The increase in the numbers of T1D incidences are thought to be related to environmental reasons such as the exposure to environmental chemicals including arylamine 2-aminoanthracene (2AA). T1D is an autoimmune disease of the pancreatic islet in which insulin-producing beta cells are destroyed by auto-reactive T-cells and monocytic cells.

Methods: The purpose of this study is to examine the extent to which 2AA exposure contributes to T1D. Three groups of pregnant Sprague Dawley dams ingested various concentrations of dietary 2AA from gestation through …

Monofluorophosphate Blocks Internal Polysaccharide Synthesis In Streptococcus Mutans, Miguel Ballicora, Ana M. Demonte, Conrad Naleway, Matias D. Asencion Diez, Alberto A. Iglesias

Chemistry: Faculty Publications and Other Works

Streptococcus mutans is the leading cause of dental caries worldwide by accumulating a glycogen-like internal polysaccharide (IPS) that contributes to cariogenicity when sugars are in excess. Sodium monofluorophosphate (MFP) is an active anticariogenic compound in toothpastes. Herein, we show that MFP inhibits (with an I_0.5 of 1.5 mM) the S. mutans ADP-glucose pyrophosphorylase (EC 2.7.7.27), which catalyzes the key step in IPS biosynthesis. Enzyme inhibition by MFP is similar to orthophosphate (Pi), except that the effect caused by MFP is not reverted by fructose-1,6-bisP, as occurs with Pi. Inhibition was correlated with a decrease in acidogenesis and IPS …

The Subject Librarian Newsletter, Chemistry, Spring 2017, Sandy Avila

Libraries' Newsletters

No abstract provided.

One Ion To Rule Them All: Combined Antibacterial, Osteoinductive And Anticancer Properties Of Selenite-Incorporated Hydroxyapatite, Vuk Uskoković, Maheshwar Adiraj Iyer, Victoria M. Wu

Pharmacy Faculty Articles and Research

Although hydroxyapatite (HAp) has been doped with dozens of different ions, the quest for an ion imparting a combination of properties conducive to bone healing is still ongoing. Because of its protean potency and the similarity in size and shape to the phosphate tetrahedron, the selenite ion presents a natural ionic substitute in HAp. The incorporation of selenite into synthetic HAp using two different methods – co-precipitation and ion-exchange sorption – was studied for its effect on crystal properties and on a triad of biological responses: antibacterial, anticancer and osteoinductive. Co-precipitation yielded HAp with a higher selenite content than sorption …

Inelastic Neutron Scattering Cross Section Measurements For 134,136Xe Of Relevance To Neutrinoless Double-Β Decay Searches, Erin E. Peters, T. J. Ross, S. H. Liu, Marcus T. Mcellistrem, Steven W. Yates

Chemistry Faculty Publications

Neutrinoless double-β decay (0νββ) searches typically involve large-scale experiments for which backgrounds can be complex. One possible source of background near the 0νββ signature in the observed spectra is γ rays arising from inelastic neutron scattering from the materials composing or surrounding the detector. In relation to searches for the 0νββ of ¹³⁶Xe to ¹³⁶Ba, such as the EXO-200 and KamLAND-Zen projects, inelastic neutron scattering γ-ray production cross sections for ¹³⁶Xe and ¹³⁴Xe are of importance for characterizing such γ rays that may inhibit the unambiguous identification of this yet-to-be-observed …

Time Evolution, Ronald Lovett

Topics in Quantum Mechanics

No abstract provided.

Far-Red And Near-Infrared Seminaphthofluorophores For Targeted Pancreatic Cancer Imaging, Lei Wang, Connor W. Barth, Martha Sibrian-Vazquez, Jorge O. Escodedo, Mark Lowry, John Muschler, Haiyan Li, Summer L. Gibbs, Robert Strongin

Chemistry Faculty Publications and Presentations

Molecular probes that selectively highlight pancreatic cancer (PC) tissue have the potential to improve pancreatic ductal adenocarcinoma (PDAC) margin assessment through the selective highlighting of individual PC cells. Herein, we report a simple and unique family of systematically modified red and near-infrared fluorescent probes that exhibit a field-effect-derived redshift. Two of thirteen probes distributed to the normal mouse pancreas following systemic administration. One selectively accumulated in genetically modified mouse models of PDAC. The probe exhibited intracellular accumulation and enabled visualization of four levels of the structure, including the whole organ, resected tissue, individual cells, and subcellular organelles. In contrast to …

Thermal Conductivity Performance Of Polypropylene Composites Filled With Polydopamine-Functionalized Hexagonal Boron Nitride, Lin Chen, Hong-Fei Xu, Shao-Jian He, Yi-Hang Du, Nan-Jie Yu, Jun Lin, Sergei I. Nazarenko

Faculty Publications

Mussel-inspired approach was attempted to non-covalently functionalize the surfaces of boron nitride (BN) with self-polymerized dopamine coatings in order to reduce the interfacial thermal barrier and enhance the thermal conductivity of BN-containing composites. Compared to the polypropylene (PP) composites filled with pristine BN at the same filler content, thermal conductivity was much higher for those filled with both functionalized BN (f-BN) and maleic anhydride grafted PP (PP-g-ma) due to the improved filler dispersion and better interfacial filler-matrix compatibility, which facilitated the development of more thermal paths. Theoretical models were also applied to predict the composite thermal conductivity in which the …

Safer Chemicals Design Diagrams, Longzhu Shen, Fjodor Melnikov, John Roethle, Aditya Gudibanda, Richard Judson, Julie Zimmerman, Paul Anastas

Yale Day of Data

The NRF2-ARE antioxidant pathway is an important biological sensing and regulating system that responds to chemical insults. At minute level, it protects a living species to go through hard environmental conditions. However, when the external disruption exceeds the inherent resilience, cellular damage can occur, eventually leading to cytotoxicity. Therefore, studying the likelihood of a chemical activating the NRF2-ARE pathway is interesting to discovering therapeutic agents and designing safer chemicals. In this research, we engaged a combination of computational chemistry, statistical learning and mechanistic toxicology to estimate the likelihood of a chemical to perturb this critical toxicological pathway and derive a …