Chemistry Commons^™

A Practical, Quantitative Electrostatics Experiment, Bryan K. Armentrout, Diego Castano

Chemistry and Physics Faculty Articles

An electrostatics experiment is presented that is practical, affordable, and quantitative. The equipment required is readily available and relatively inexpensive. The experiment relies on the electrostatic induction that results from a charged insulative plate in proximity to a conductive sphere. The experiment yields accessible results (a) under a variety of environmental conditions and results that (b) allow for quantitative analyses. These two characteristics distinguish it from most other simple electrostatics experiments. It is intended for college introductory physics students.

Method Of Increasing Mass Transfer Rate Of Acid Gas Scrubbing Solvents, Joseph E. Remias, Cameron A. Lippert, Kunlei Liu

Center for Applied Energy Research Faculty Patents

A method of increasing the overall mass transfer rate of acid gas scrubbing solids is disclosed. Various catalyst compounds for that purpose are also disclosed.

Molecular Dynamics Simulations Of Substrate Release From Trypanosoma Cruzi Udp-Galactopyranose Mutase, Rodrigo Cossio-Pérez, Gustavo Pierdominici-Sottile, Pablo Sobrado, Juliana Palma

Chemistry Faculty Research & Creative Works

The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes that both substrate and enzyme undergo during the process. It was determined that the galactopyranose portion of the substrate is highly mobile and that the opening/closing of the active site occurs in stages. Previously uncharacterized interactions with highly conserved residues were also identified. These findings provide new pieces of information that contribute to the rational design of …

Micro-Raman Imaging Of Isomeric Segregation In Small-Molecule Organic Semiconductors, Chiung-Wei Huang, Xiao You, Peter J. Diemer, Anthony Joseph Petty Ii, John E. Anthony, Oana D. Jurchescu, Joanna M. Atkin

Chemistry Faculty Publications

Charge transport in organic semiconductors is highly sensitive to film heterogeneity and intermolecular interactions, but probing these properties on the length scales of disorder is often difficult. Here we use micro-Raman spectroscopy to assign vibrational modes of isomerically pure syn and anti 2,8-difluoro-5,11-bis(triethylsilylethynyl)anthradithiophene (diF-TES ADT) by comparing to density functional theory calculations. With polarization-dependent measurements, we determine the orientation of crystallites in pure isomers. In mixed-isomer samples, we observe narrow linewidths and superposition spectra, indicating coexistence of isomerically pure sub-domains on length scales smaller than the probe area. Using the ring breathing modes close to 1300 cm⁻¹ as indicators …

Biosensor Applications Of Electrodeposited Nanostructures, Keith Stine

Chemistry & Biochemistry Faculty Works

The development of biosensors for a range of analytes from small molecules to proteins to oligonucleotides is an intensely active field. Detection methods based on electrochemistry or on localized surface plasmon responses have advanced through using nanostructured electrodes prepared by electrodeposition, which is capable of preparing a wide range of different structures. Supported nanoparticles can be prepared by electrodeposition through applying fixed potentials, cycling potentials, and fixed current methods. Nanoparticle sizes, shapes, and surface densities can be controlled, and regular structures can be prepared by electrodeposition through templates. The incorporation of multiple nanomaterials into composite films can take advantage of …

Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Various methods exist for measuring molecular orientation, thereby providing insight into biochemical activities at nanoscale. Since fluorescence intensity and not electric field is detected, these methods are limited to measuring even-order moments of molecular orientation. However, any measurement noise, for example photon shot noise, will result in nonzero measurements of any of these even-order moments, thereby causing rotationally-free molecules to appear to be partially constrained. Here, we build a model to quantify measurement errors in rotational mobility. Our theoretical framework enables scientists to choose the optimal single-molecule orientation measurement technique for any desired measurement accuracy and photon budget.

Large Fatty Acid-Derived Aβ42 Oligomers Form Ring-Like Assemblies, Wenhui Xu, Dexter N. Dean, Kelli A. Stockmal, Sarah E. Morgan, Ulrich H.E. Hansmann, Vijayaraghavan Rangachari

Faculty Publications

As the primary toxic species in the etiology of Alzheimer disease (AD) are low molecular weight oligomers of Aβ, it is crucial to understand the structure of Aβ oligomers for gaining molecular insights into AD pathology. We have earlier demonstrated that in the presence of fatty acids, Aβ42 peptides assemble as 12-24mer oligomers. These Large Fatty Acid-derived Oligomers (LFAOs) exist predominantly as 12mers at low and as 24mers at high concentrations. The 12mers are more neurotoxic than the 24mers and undergo self-replication, while the latter propagate to morphologically distinct fibrils with succinct pathological consequences. In order to glean into their …

Effect Of Drug Loading On The Properties Of Temperature-Responsive Polyester-Poly(Ethylene Glycol)-Polyester Hydrogels, D. Andrew Prince, Ian J. Villamagna, Cameron C. Hopkins, John R. De Bruyn, Elizabeth R. Gillies

Chemistry Publications

Hydrogels that can undergo gelation upon injection in vivo are promising systems for the site-specific delivery of drugs. In particular, some thermo-responsive gels require no chemical additives but simply gel in response to a change from a lower temperature to physiological temperature (37 °C). The gelation mechanism does not involve covalent bonds, and it is possible that incorporation of drugs into the hydrogel could disrupt gelation. We investigated the incorporation of drugs into thermo-responsive hydrogels based on poly(ϵ-caprolactone-co-lactide)-block-poly(ethylene glycol)-block-poly(ϵ-caprolactone-co-lactide) (PCLA–PEG–PCLA). Significant differences in properties and in the response …

Realization Of A Type-Ii Nodal-Line Semimetal In Mg3bi2, Weiwei Xie

Faculty Publications

Nodal-line semimetals (NLSs) represent a new type of topological semimetallic phase beyond Weyl and Dirac semimetals in the sense that they host closed loops or open curves of band degeneracies in the Brillouin zone. Parallel to the classification of type-I and type-II Weyl semimetals, there are two types of NLSs. The type-I NLS phase has been proposed and realized in many compounds, whereas the exotic type-II NLS phase that strongly violates Lorentz symmetry has remained elusive. First-principles calculations show that Mg3Bi2 is a material candidate for the type-II NLS. The band crossing is close to the Fermi level and exhibits …

Metal-Assisted Hydrolysis Reactions Involving Lipids: A Review, Dominique E. Williams, Kathryn B. Grant

Chemistry Faculty Publications

This report covers major advances in the use of metal ions and complexes to hydrolyze ester and phosphate ester lipid bonds. These metal-based Lewis acids have been investigated as catalysts to isolate fatty acids from biological sources, as probes to study phospholipid bilayer properties, as tools to examine signal transduction pathways, and as lead compounds toward the discovery of therapeutic agents. Metal ions that accelerate phosphate ester hydrolysis under mild conditions of temperature and pH may have the potential to mimic phospholipase activity in biochemical applications.

Student-Faculty Collaborative Research Grant Report, Megan Bestwick

Post-Grant Reports

Mitochondria are essential organelles in most eukaryotic cells because of their role in metabolism and the production of ATP by the oxidative phosphorylation (OXPHOS) pathway, as well as other key cellular processes. Metal cofactors, such as copper (Cu) and iron (Fe), are incorporated into OXPHOS protein complexes of yeast located within the inner membrane of the mitochondria. Misincorporation or modulation of these available metals in mitochondrial enzymes leads to the production of reactive oxygen species (ROS). ROS are reactive molecules containing oxygen such as peroxides, superoxide, and hydroxyl radicals. Yeast are a good model for studying aging and the effect …

X-Ray Fluorescence And Emission | Total Reflection X-Ray Fluorescence, Martina Schmeling

Chemistry: Faculty Publications and Other Works

Total reflection X-ray fluorescence spectrometry (TXRF) is a trace elemental micro analysis technique based on conventional energy dispersive X-ray fluorescence. It has become increasingly popular in the last few decades and is applied in almost every field of trace elemental analysis where low detection limits and multi element capabilities are required. Like all X-ray techniques TXRF is non-destructive making it highly useful and important in areas where samples are precious and/or need to be available for further characterization. The ability of probing extremely small sample amounts makes TXRF a superior analytical technique for samples of limited amount. New table top …

Substrate-Dependent Photoconductivity Dynamics In A High-Efficiency Hybrid Perovskite Alloy, Ali Moeed Tirmzi, Jeffrey A. Christians, Ryan P. Dwyer, David T. Moore, John A. Marohn

Faculty Publications

Films of (FA_0.79MA_0.16Cs_0.05)_0.97Pb(I_0.84Br_0.16)_2.97 were grown over TiO₂, SnO₂, indium tin oxide (ITO), and NiO. Film conductivity was interrogated by measuring the in-phase and out-of-phase forces acting between the film and a charged microcantilever. We followed the films’ conductivity versus time, frequency, light intensity, and temperature (233−312 K). Perovskite conductivity was high and light-independent over ITO and NiO. Over TiO₂ and SnO₂, the conductivity was low in the dark,increased with light intensity, and persisted for 10’s of seconds after the light …

Slips-Teng: Robust Triboelectric Nanogenerator With Optical And Charge Transparency Using A Slippery Interface, Wanghuai Xu, Xiaofeng Zhou, Chonglei Hao, Huanxi Zheng, Yuan Liu, Xiantong Yan, Zhengbao Yang, Michael Leung, Xiao Cheng Zeng, Ronald X. Xu, Zuankai Wang

Xiao Cheng Zeng Publications

Energy harvesting devices that prosper in harsh environments are highly demanded in a wide range of applications ranging from wearable and biomedical devices to self-powered and intelligent systems. Particularly, over the past several years, the innovation of triboelectric nanogenerators (TENGs) that efficiently convert ambient kinetic energy of water droplets or wave power to electricity has received growing attention. One of the main bottlenecks for the practical implications of such devices originates from the fast degradation of the physiochemical properties of interfacial materials under harsh environments. To overcome these challenges, here we report the design of a novel slippery lubricant-impregnated porous …

Metrics And Methods Used To Compare Student Performance Data In Chemistry Education Research Articles, Michael R. Mack, Cory Hensen, Jack Barbera

Chemistry Faculty Publications and Presentations

Quasi-experiments are common in studies that estimate the effect of instructional interventions on student performance outcomes. In this type of research, the nature of the experimental design, the choice in assessment, the selection of comparison groups, and the statistical methods used to analyze the comparison data dictate the validity of causal inferences. Therefore, gathering and reporting validity evidence in causal studies is of utmost importance, especially when conclusions have real policy implications for students and faculty, among other stakeholders. This review examines 24 articles that reported quantitative investigations of the effect of instructional interventions on performance-based outcomes conducted within undergraduate …

Comparison Of Σ-Hole And Π-Hole Tetrel Bonds In Complexes Of Borazine With Th3f And F2to/H2to (T=C,Si,Ge), Jingru Zhang, Qingze Hu, Qing-Zhong Li, Steve Scheiner, Shufeng Liu

Chemistry and Biochemistry Faculty Publications

The complexes between borazine and TH3F/F2TO/H2TO (T=C, Si, Ge) are investigated with high-level quantum chemical calculations. Borazine has three sites of negative electrostatic potential: the N atom, the ring center, and the H atom of the B-H bond, while TH3F and F2TO/H2TO provide the σ-hole and π-hole, respectively, for the tetrel bond. The N atom of borazine is the favored site for both the σ and π-hole tetrel bonds. Less stable dimers include a σ-tetrel bond to the borazine ring center and to the BH proton. The π-hole tetrel-bonded complexes are more strongly bound than aretheirσ-hole counterparts. Due to the …

A New Multivariate Optical Computing Microelement And Miniature Sensor For Spectroscopic Chemical Sensing In Harsh Environments: Design, Fabrication, And Testing, Christopher M. Jones, Bin Dai, Jimmy Price, Jian Li, Megan Pearl, Bill Soltmann, Michael L. Myrick

Faculty Publications

Multivariate optical computing (MOC) is a compressed sensing technique with the ability to provide accurate spectroscopic compositional analysis in a variety of different applications to multiple industries. Indeed, recent developments have demonstrated the successful deployment of MOC sensors in downhole/well-logging environments to interrogate the composition of hydrocarbon and other chemical constituents in oil and gas reservoirs. However, new challenges have necessitated sensors that operate at high temperatures and pressures (up to 230 °C and 138 MPa) as well as even smaller areas that require the miniaturization of their physical footprint. To this end, this paper details the design, fabrication, and …

Exposure Characterization Of Haloacetic Acids In Humans For Exposure And Risk Assessment Applications: An Exploratory Study, Shahid Parvez, Jeffrey L. Ashby, Susana Y. Kimura, Susan D. Richardson

Faculty Publications

Disinfected water is the major source of haloacetic acids (HAAs) in humans, but their inter- and intra-individual variability for exposure and risk assessment applications is under-researched. Thus, we measured HAAs in cross-sectional and longitudinal urine and water specimens from 17 individuals. Five regulated HAAs—mono-, di-, and trichloroacetic acid (MCAA, DCAA, and TCAA) and mono- and dibromoacetic acid (MBAA and DBAA)—and one unregulated HAA—bromochloroacetic acid (BCAA)—were measured. Urinary DCAA, MBAA, DBAA, and BCAA levels were always below the limits of detection (LOD). Measured levels and interindividual variability of urinary MCAA were higher than urinary TCAA. Longitudinal urinary specimens showed MCAA levels …

Thermally Induced Disorder-Order Phase Transition Of Gd 2 Hf 2 O 7 :Eu 3+ Nanoparticles And Its Implication On Photo-And Radioluminescence, Santosh K. Gupta, Maya Abdou, Partha Sarathi Ghosh, Jose P. Zuniga, Yuanbing Mao

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Crystal structure has a strong influence on the luminescence properties of lanthanide-doped materials. In this work, we have investigated the thermally induced structural transition in Gd 2 Hf 2 O 7 (GHO) using Eu 3+ ions as the spectroscopic probe. It was found that complete phase transition from the disordered fluorite phase (DFP) to the ordered pyrochlore phase (OPP) can be achieved in GHO with the increase of annealing temperature from 650 ? 1100 ? 1300 °C. OPP is the more stable structural form for the GHOE nanoparticles (NPs) annealed at a higher temperature based on the energy calculation by …

Switchable Aromaticity In An Isostructural Mn Phthalocyanine Series Isolated In Five Separate Redox States, Camden Hunt, Madeline Peterson, Cassidy Anderson, Tieyan Chang, Guang Wu, Steve Scheiner, Gabriel Ménard

Chemistry and Biochemistry Faculty Publications

The synthesis and characterization of a new phthalocyanine(Pc) Mn-nitride complex, (OEtPc)MnN (2; OEtPc= 1,4,8,11,15,18,22,25-octaethoxy-Pc), as well as its stable, readily accessible oxidized (2+ and 22+) and reduced (2-, 22-) congeners is reported. This unique isostructural series displays switchable aromatic character spanning the aromatic (2), non-aromatic (22+), and antiaromatic (22-) triad, in addition to the open-shell radical states (2+, 2-). All complexes were structurally characterized and displayed significant structural distortions at the redox extrema (22+, 22-) consistent with proposed [16 or 18]annulene π ring circuit models. Spectroscopic and computational studies further support these models. This isolated, fully characterized, isostructural series spanning …

Toward Unraveling The Mechanisms Of “Green” Mechanochemical Reactions, Richard Chen, Mehmet Kerem Gokus

Undergraduate Research Symposium

The mechanical processing of solids, such as milling or grinding powders, often leads to mechanochemical reactions. Mechanochemistry affords “green” synthetic routes avoiding or reducing the use of solvents, thus providing environmentally friendly and cost-effective synthetic alternatives for many materials. The solid-state reactants are usually ground together with small quantities of organic solvents, called “liquid assisted grinding” (LAG). LAG increases the reaction rates, it can yield products from otherwise unreactive mixtures, it increases the products crystallinity, and it selectively leads to crystal structures (polymorphs) of the products, depending on the quantities and physicochemical properties of the liquids used in LAG.

Mechanochemistry …

Viscosities, Diffusion Coefficients, And Mixing Times Of Intrinsic Fluorescent Organic Molecules In Brown Limonene Secondary Organic Aerosol And Tests Of The Stokes–Einstein Equation, Dagny A. Ullmann, Mallory L. Hinks, Adrian M. Maclean, Christopher Butenhoff, James W. Grayson, Kelley Barsanti, Jose L. Jimenez, Sergey A. Nizkorodov, Saeid Kamal, Allan K. Bertram

Physics Faculty Publications and Presentations

Viscosities and diffusion rates of organics within secondary organic aerosol (SOA) remain uncertain. Using the bead-mobility technique, we measured viscosities as a function of water activity (a_w) of SOA generated by the ozonolysis of limonene followed by browning by exposure to NH₃ (referred to as brown limonene SOA or brown LSOA). These measurements together with viscosity measurements reported in the literature show that the viscosity of brown LSOA increases by 3–5 orders of magnitude as the aw decreases from 0.9 to approximately 0.05. In addition, we measured diffusion coefficients of intrinsic fluorescent organic molecules within brown …

Ring Expansion Of Alkylidenecarbenes Derived From Lactams, Lactones, And Thiolactones Into Strained Heterocyclic Alkynes: A Theoretical Study, N. N. Thu Le, J. Just, J. M. Pankauski, Paul R. Rablen, D. M. Thamattoor

Chemistry & Biochemistry Faculty Works

Strained cycloalkynes are of considerable interest to theoreticians and experimentalists, and possess much synthetic value as well. Herein, a series of cyclic alkylidenecarbenes—formally obtained by replacing the carbonyl oxygen of four-, five-, and six-membered lactams, lactones, and thiolactones with a divalent carbon—were modeled at the CCSD(T)/cc-pVTZ//B3LYP/6-311+G** and CCSD(T)/cc-pVTZ//CCSD/6-311+G** levels of theory. The singlet carbenes were found to be more stable than the triplets. The strained heterocyclic alkynes formed by ring expansion of these singlet carbenes were also modeled. Interestingly, the C≡C bonds in the five-membered heterocycles, obtained from the rearrangement of β-lactam- and β-lactone-derived alkylidenecarbenes, displayed lengths intermediate between formal …

Mutagenesis Of Α-Conotoxins For Enhancing Activity And Selectivity For Nicotinic Acetylcholine Receptors, Matthew W. Turner, Leanna A. Marquart, Paul D. Phillips, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Nicotinic acetylcholine receptors (nAChRs) are found throughout the mammalian body and have been studied extensively because of their implication in a myriad of diseases. α-Conotoxins (α-CTxs) are peptide neurotoxins found in the venom of marine snails of genus Conus. α-CTxs are potent and selective antagonists for a variety of nAChR isoforms. Over the past 40 years, α-CTxs have proven to be valuable molecular probes capable of differentiating between closely related nAChR subtypes and have contributed greatly to understanding the physiological role of nAChRs in the mammalian nervous system. Here, we review the amino acid composition and structure of several …

Synthesis, Biological Evaluation And Molecular Modeling Studies Of Novel Chromone/Aza-Chromone Fused Α-Aminophosphonates As Src Kinase Inhibitors, S. Bapat, N. Viswanadh, M. Mujahid, Amir Nasrolahi Shirazi, Rakesh Tiwari, Keykavous Parang, M. Karthikeyan, M. Muthukrishnan, Renu Vyas

Pharmacy Faculty Articles and Research

A series of novel chromone/aza-chromone fused α-aminophosphonate derivatives were synthesized in good yields using silica chloride as the catalyst. All the synthesized compounds were tested for their c-Src kinase inhibitory activity. Aza-chromone compound showed Src kinase inhibition with an IC50 value of 15.8 µM. The compounds were subjected to molecular docking and dynamics simulations to study the atomic level interactions with an unphosphorylated proto-oncogenic tyrosine protein kinase Src (PDB code 1Y57) as well as phosphorylated tyrosine protein kinase Src (PDB code 2H8H). Docking and molecular dynamic results revealed phosphorylated Src tyrosine kinase protein better results than unphosphorylated tyrosine Src kinase …

Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey

Dissertations, Theses, and Capstone Projects

The displacement of water from surfaces upon biomolecular recognition and association makes a significant contribution to the free energy changes of these processes. We therefore posit that accurate characterization of local structural and thermodynamic molecular water properties can improve computational model accuracy and predictivity of recognition and association processes. In this thesis, we discuss Solvation Thermodynamic Mapping (STM) methods that we have developed using inhomogeneous fluid solvation theory (IST) to better characterize active site water structural and thermodynamic properties on protein surfaces and the open source tools that we have developed, GIST-CPPTRAJ and SSTMap, which implement these methods which we …

Pretargeted Radioimmunotherapy Utilizing The Inverse Electron Demand Diels-Alder Reaction, Rosemery Membreno

Dissertations, Theses, and Capstone Projects

Radioimmunotherapy capitalizes on the specificity and affinity of antibodies for their antigens to localize radioactivity at the tumor site. One limitation in using antibodies is their long circulation time, which can take days to weeks to fully clear from blood circulation. When a radioisotope is directly conjugated to this immunoglobulin vector, the red marrow and other healthy organs are receiving a constant radiation dose while it is in blood circulation. This not only harms healthy organs, but limits the dose of radioactivity that can be administered thus prolonging treatment. A promising alternative to limit the radiation dose to non-tumor tissue …

Potential Degradation Of Hexabromocyclododecane (Hbcdd) In Sediments: Stereoisomer Specific Reaction Of Hbcdd With Reduced Sulfur Species Or Fe(Ii) Bound To Iron Oxides, Xianmiao Zhang

Dissertations, Theses, and Capstone Projects

The individual degradation rates of the three dominant stereoisomers (alpha, beta, gamma) of hexabromocyclododecane (HBCDD) with bisulfide and polysulfides were investigated at pH 9-10 in methanol/water solutions at two different temperatures (25 °C and 40 °C). alpha-HBCDD reacts significantly slower than beta-HBCDD and gamma-HBCDD. It was also observed that the reaction of HBCDD with polysulfides is faster than with bisulfide. For the reaction of HBCDD with bisulfide, the experiments were performed in 20% water/80% methanol, 50% water/50% methanol and 80% water/20% methanol at 40 °C. It was determined that the solvent polarity affects the reaction and the second-order rate constants …

Bisthioether Stapled Peptides Targeting Polycomb Repressive Complex 2 Gene Repression, Gan Zhang

Dissertations, Theses, and Capstone Projects

Interactions between proteins play a key role in nearly all cellular process, and therefore, disruption of such interactions may lead to many different types of cellular dysfunctions. Hence, pathologic protein-protein interactions (PPIs) constitute highly attractive drug targets and hold great potential for developing novel therapeutic agents for the treatment of incurable human diseases. Unfortunately, the identification of PPI inhibitors is an extremely challenging task, since traditionally used small molecule ligands are mostly unable to cover and anchor on the extensive flat surfaces that define those binary protein complexes. In contrast, large biomolecules such as proteins or peptides are ideal fits …

Development Of Palladium(0)-Catalyzed Suzuki Cross-Coupling Polymerizations, Wei Peng

Dissertations, Theses, and Capstone Projects

The synthesis of well-defined and high molecular weight π-conjugated polymers under mild condition within short reaction time is a challenging and important task in both organic chemistry and polymer chemistry. As one of the most efficient and high tolerance to solvents and reaction conditions, palladium(0)-catalyzed cross-coupling reactions would give us a good chance to achieve the goal. Thus, my Ph. D dissertation research projects focused on developing Pd(0)-catalyzed Suzuki cross-coupling polymerization reactions including controlled ones.

My research first studied t-Bu₃P-coordinated 2-phenylaniline-based palladacycle complex catalyzed Suzuki cross-coupling polymerization of aryl dibromides with aryldiboronic acids at room temperature. Based …