Physical Sciences and Mathematics Commons^™

The Rna World: 4,000,000,050 Years Old, Niles Lehman

Chemistry Faculty Publications and Presentations

The notion that molecular systems such as RNA can display a wide range of evolutionary processes in the absence of fully formed cellular life continues to gain support. Understanding how RNA can behave in an abiotic context is a key piece of our picture of how life developed and expanded on the Earth, and by proxy, elsewhere. We can study how RNA behaves in this regard through a combination of in vivo work (with small regulatory RNAs and larger catalytic RNAs alike), experimental work in the laboratory, and through powerful analytical and simulation studies. These efforts will not only grant …

Design Of A Vlp-Nanovehicle For Cyp450 Enzymatic Activity Delivery, Lorena Sanchez-Sanchez, Alejandro Tapia-Moreno, Karla Juarez-Moreno, Dustin P. Patterson, R. D. Cadena-Nava, T. Douglas, R. Vazquez-Duhalt

Chemistry Faculty Publications and Presentations

Background: The intracellular delivery of enzymes for therapeutic use has a promising future for the treatment of several diseases such as genetic disorders and cancer. Virus-like particles offer an interesting platform for enzymatic delivery to targeted cells because of their great cargo capacity and the enhancement of the biocatalyst stability towards several factors important in the practical application of these nanoparticles. Results: We have designed a nano-bioreactor based on the encapsulation of a cytochrome P450 (CYP) inside the capsid derived from the bacteriophage P22. An enhanced peroxigenase, CYPBM3, was selected as a model enzyme because of its potential in enzyme …

Phase Considerations In The Gas/Particle Partitioning Of Organic Amines In The Atmosphere, James F. Pankow

Chemistry Faculty Publications and Presentations

Amines in the atmosphere are of interest because of their likely role in new particle formation, and because of anthropogenic emissions of amines at post-combustion carbon capture (PCCC) facilities. A conceptual framework for considering the partitioning of a monobasic amine (Am = unprotonated "free-base form) from the gas phase to atmospheric particulate matter (PM) is presented for cases when the PM may be composed of multiple liquid phases. Three types of liquid phases are considered as being individually or simultaneously possible for absorptive uptake of atmospheric amines: w) a mostly water phase; α ) a mostly (by mass) organic phase …

Microwave Spectra And Structure Of The Cyclopropanecarboxylic Acid-Formic Acid Dimer, Aaron M. Pejlovas, Wei Lin, Stephen G. Kukolich

Chemistry Faculty Publications and Presentations

The rotational spectrum of the cyclopropanecarboxylic acid-formic acid doubly hydrogen bonded dimer has been measured in the 4-11 GHz region using a Flygare-Balle type pulsed-beam Fourier transform microwave spectrometer. Rotational transitions were measured for the parent, four unique singly substituted ¹³C isotopologues, and a singly deuterated isotopologue. Splittings due to a possible concerted double proton tunneling motion were not observed. Rotational constants (A, B, and C) and centrifugal distortion constants (DJ and DJK) were determined from the measured transitions for the dimer. The values of the rotational (in MHz) and centrifugal distortion constants (in kHz) for the parent isotopologue …

Formaldehyde From E-Cigarettes - It's Not As Simple As Some Suggest, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

The Authors address critics of a previously published letter to the Editor in The New England Journal of Medicine, pertaining to hidden formaldehyde in E-Cigarette aerosols and the need for future testing of their safety.

A Comparative Study Of Polyurethane Nanofibers With Different Patterns And Its Analogous Nanofibers Containing Mwcnts, Javier Macossay-Torres, Faheem A. Sheikh, Hassan Ahmad, Hern Kim, Gary L. Bowlin

Chemistry Faculty Publications and Presentations

Tissue engineering is a multidisciplinary field that has evolved in various dimensions in recent years. One of the main aspects in this field is the proper adjustment and final compatibility of implants at the target site of surgery. For this purpose, it is desired to have the materials fabricated at the nanometer scale, since these dimensions will ultimately accelerate the fixation of implants at the cellular level. In this study, electrospun polyurethane nanofibers and their analogous nanofibers containing MWCNTs are introduced for tissue engineering applications. Since MWCNTs agglomerate to form bundles, a high intensity sonication procedure was used to disperse …

Molecular View Modeling Of Atmospheric Organic Particulate Matter: Incorporating Molecular Structure And Co-Condensation Of Water, James F. Pankow, Marguerite Colasurdo Marks, Kelley C. Barsanti, Abdullah Mahmud, William E. Asher, Jingyi Li, Qi Ying, Shantanu H. Jathar, Michael J. Kleeman

Chemistry Faculty Publications and Presentations

Most urban and regional models used to predict levels of organic particulate matter (OPM) are based on fundamental equations for gas/particle partitioning, but make the highly simplifying, anonymized-view (AV) assumptions that OPM levels are not affected by either: a) the molecular. characteristics of the condensing organic compounds (other than simple volatility); or b) co-condensation of water as driven by non-zero relative humidity (RH) values. The simplifying assumptions have allowed parameterized chamber results for formation of secondary organic aerosol (SOA) (e.g., “two-product” (2p) coefficients) to be incorporated in chemical transport models. However, a return towards a less simplistic (and more computationally …

Synthesis And Structure−Activity Relationships Of Tambjamines And B‑Ring Functionalized Prodiginines As Potent Antimalarials, Papireddy Kancharla, Jane Xu Kelly, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

Synthesis and antimalarial activity of 94 novel bipyrrole tambjamines (TAs) and a library of B-ring functionalized tripyrrole prodiginines (PGs) against a panel of Plasmodium falciparum strains are described. The activity and structure–activity relationships demonstrate that the ring-C of PGs can be replaced by an alkylamine, providing for TAs with retained/enhanced potency. Furthermore, ring-B of PGs/TAs can be substituted with short alkyl substitutions at either 4-position (replacement of OMe) or 3- and 4-positions without impacting potency. Eight representative TAs and two PGs have been evaluated for antimalarial activity against multidrug-resistant P. yoelii in mice in the dose range of 5–100 mg/kg …

Nmr-Based Structural Analysis Of Threonylcarbamoyl-Amp Synthase And Its Substrate Interactions, Kimberly A. Harris, Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, Paul F. Agris

Chemistry Faculty Publications and Presentations

The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in …

Dft Analysis Into The Intermediates Of Nickel Pyridenthiolate Catalysed Proton Reduction, Carolyn N. Virca, Theresa M. Mccormick

Chemistry Faculty Publications and Presentations

Nickel pyridine 2-thiolate (Ni(PyS)₃ −) has shown good stability and activity as a H₂ generation catalyst for use in solar energy storage. The experimentally proposed catalytic pathway is explored using DFT calculations. Free energy changes along the reaction coordinate, spin states, localization of charge and geometry of the intermediates were explored. Calculations were performed using Gaussian 09 with a B3P86/ 6-31+G(d) basis set and a CPCM water solvation model. Of particular interest were our findings that the first reduction occurs at the nickel rather than through non-innocent ligands and that water coordination is not favourable although protonation of …

Hydrophobic Surfactant Proteins Strongly Induce Negative Curvature, Mariya Chavarha, Ryan W. Loney, Shankar B. Rananavare, Stephen B. Hall

Chemistry Faculty Publications and Presentations

The hydrophobic surfactant proteins SP-B and SP-C greatly accelerate the adsorption of vesicles containing the surfactant lipids to form a film that lowers the surface tension of the air/water interface in the lungs. Pulmonary surfactant enters the interface by a process analogous to the fusion of two vesicles. As with fusion, several factors affect adsorption according to how they alter the curvature of lipid leaflets, suggesting that adsorption proceeds via a rate-limiting structure with negative curvature, in which the hydrophilic face of the phospholipid leaflets is concave. In the studies reported here, we tested whether the surfactant proteins might promote …

Internal Dynamics In The Molecular Complex Of Cf3cn And H2o, Wei Lin, Anan Wu, Xin Lu, Xiao Tang, Daniel A. Obenchain, Stewart E. Novick

Chemistry Faculty Publications and Presentations

The rotational spectrum of trifluoroacetonitrile–water complex has been studied by pulsed-nozzle, Fourier transform microwave spectroscopy. Both a-type and b-type transitions have been observed. The rotational constants, centrifugal distortion constants, and the 14N nuclear quadrupole coupling constants have been determined. The complex is T-shaped, with the oxygen atom from the water located 3.135 Å from the carbon atom of CF3 of the trifluoroacetonitrile molecule.

Tio 2 Fibers: Tunable Polymorphic Phase Transformation And Electrochemical Properties, Edna Garcia, Qiang Li, Xing Sun, Karen Lozano, Yuanbing Mao

Chemistry Faculty Publications and Presentations

A series of one-dimensional (1D) nanoparticle-assembled TiO2 fibers with tunable polymorphs were prepared via a novel and large scale ForceSpinning® process of titanium tetraisopropoxide (TTIP)/polyvinylpyrrolidone (PVP) precursor fibers followed with a thermal treatment at various calcinations temperatures. The thermal and structural transformations were characterized by thermogravimetric analysis/differential scanning calorimetry, scanning electron microscopy, and X-ray diffraction. The influence of polymorphic phase of the TiO2 fibers on the electrochemical performance in neutral aqueous 1 M Na2SO4 electrolyte was investigated. The polymorphic amorphous/anatase/rutile TiO2 fibers prepared at 450 °C achieved a highest capacitance of 21.2 F g−1 (6.61 mF cm−2) at a current …

The Requisite Electronic Structure Theory To Describe Photoexcited Nonadiabatic Dynamics: Nonadiabatic Derivative Couplings And Diabatic Electronic Couplings, Joseph E. Subotnik, Ethan Alguire, Qi Ou, Brian R. Landry, Shervin Fatehi

Chemistry Faculty Publications and Presentations

Conspectus

Electronically photoexcited dynamics are complicated because there are so many different relaxation pathways: fluorescence, phosphorescence, radiationless decay, electon transfer, etc. In practice, to model photoexcited systems is a very difficult enterprise, requiring accurate and very efficient tools in both electronic structure theory and nonadiabatic chemical dynamics. Moreover, these theoretical tools are not traditional tools. On the one hand, the electronic structure tools involve couplings between electonic states (rather than typical single state energies and gradients). On the other hand, the dynamics tools involve propagating nuclei on multiple potential energy surfaces (rather than the usual ground state dynamics).

In this …

Flavour Chemicals In Electronic Cigarette Fluids, Peyton A. Tierney, Clarissa D. Karpinski, Jessica E. Brown, Wentai Luo, James F. Pankow

Chemistry Faculty Publications and Presentations

Background: Most e-cigarette liquids contain flavour chemicals. Flavour chemicals certified as safe for ingestion by the Flavor Extracts Manufacturers Association may not be safe for use in e-cigarettes. This study identified and measured flavour chemicals in 30 e-cigarette fluids.

Methods: Two brands of single-use e-cigarettes were selected and their fluids in multiple flavour types analysed by gas chromatography/mass spectrometry. For the same flavour types, and for selected confectionary flavours (eg, bubble gum and cotton candy), also analysed were convenience samples of e-cigarette fluids in refill bottles from local ‘vape’ shops and online retailers.

Results: In many liquids, total flavour chemicals …

Aerosol Optical Hygroscopicity Measurements During The 2010 Cares Campaign, Dean B. Atkinson, James Gregory Radney, Janel Lum, Katheryn R. Kolesar, Daniel J. Cziczo, Mikhail Pekour, Qi Zhang, Ari Setyan, Alla Zelenyuk, Christopher D. Cappa

Chemistry Faculty Publications and Presentations

Measurements of the effect of water uptake on particulate light extinction or scattering made at two locations during the 2010 CARES study around Sacramento, CA are reported. The observed influence of water uptake, characterized through the dimensionless optical hygroscopicity parameter γ, is compared with calculations constrained by observed particle size distributions and size-dependent particle composition. A closure assessment has been carried out that allowed for determination of the average hygroscopic growth factors (GF) at 85% relative humidity and the dimensionless hygroscopicity parameter κ for oxygenated organic aerosol (OA) and for supermicron particles, yielding κ = 0.1–0.15 and 0.9–1.0, respectively. The …

Analysis Of The Surface Density And Reactivity Of Perfluorophenylazide And The Impact On Ligand Immobilization, Gilad Zorn, David G. Castner, Anuradha Tyagi, Xin Wang, Hui Wang, Mingdi Yan

Chemistry Faculty Publications and Presentations

Perfluorophenylazide (PFPA) chemistry is a novel method for tailoring the surface properties of solid surfaces and nanoparticles. It is general and versatile, and has proven to be an efficient way to immobilize graphene, proteins, carbohydrates, and synthetic polymers. The main thrust of this work is to provide a detailed investigation on the chemical composition and surface density of the PFPA tailored surface. Specifically, gold surfaces were treated with PFPA-derivatized (11-mercaptoundecyl) tetra(ethylene glycol) (PFPA-MUTEG) mixed with 2-[2-(2-mercaptoethoxy)ethoxy]ethanol (MDEG) at varying solution mole ratios. Complementary analytical techniques were employed to characterize the resulting films including Fourier transform infrared spectroscopy to detect fingerprints …

Hidden Formaldehyde In E-Cigarette Aerosols, R. Paul Jensen, Wentai Luo, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

This letter reports a chemical analysis of vapor from electronic cigarettes that shows high levels of formaldehyde, a known carcinogen. The authors project that the associated incremental lifetime risk of cancer could be higher than that from long-term smoking.

Long-Range Pcr Amplification Of Dna By Dna Polymerase Iii Holoenzyme From Thermus Thermophilus, Wendy Ribble, Shawn D. Kane, James M. Bullard

Chemistry Faculty Publications and Presentations

DNA replication in bacteria is accomplished by a multicomponent replicase, the DNA polymerase III holoenzyme (pol III HE). The three essential components of the pol III HE are the α polymerase, the β sliding clamp processivity factor, and the DnaX clamp-loader complex. We report here the assembly of the functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme capable of DNA synthesis consists of α, β and DnaX ( and γ), and components of the clamp-loader complex. The proteins were each cloned and expressed in a native form. Each component of the system was purified extensively. The …

Multiple-Time Step Ab Initio Molecular Dynamics Based On Two-Electron Integral Screening, Shervin Fatehi, Ryan P. Steele

Chemistry Faculty Publications and Presentations

A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree–Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and …

Palladium-Catalyzed C8-Selective C-H Arylation Of Quinoline N-Oxides: Insights Into The Electronic, Steric And Solvation Effects On The Site-Selectivity By Mechanistic And Dft Computational Studies, David E. Stephens, Johant Lakey-Beitia, Abdurrahman Atesin, Tülay A. Ateşin, Gabriel Chavez, Hadi D. Arman, Oleg V. Larionov

Chemistry Faculty Publications and Presentations

We report herein a palladium-catalyzed C-H arylation of quinoline N-oxides that proceeds with high selectivity in favor of the C8-isomer. This site-selectivity is unusual for palladium, since all of the hitherto described methods of palladium-catalyzed C-H functionalization of quinoline N-oxides are highly C2-selective. The reaction exhibits a broad synthetic scope with respect to quinoline N-oxides and iodoarenes and can be significantly accelerated to sub-hour reaction times under microwave irradiation. The C8-arylation method can be carried out on gram scale and has excellent functional group tolerance. Mechanistic and Density Functional Theory (DFT) computational studies provide evidence for the …

An Acid-Bath Technique To Break Seed Dormancy In Common Sunflower, Helianthus L. Annuus (Asteraceae), Yuridia Patricia Gandy, Michael W. Persans, Kenneth R. Summy

Chemistry Faculty Publications and Presentations

The phenomenon of seed dormancy is widespread in plants and serves to prevent all or most of a given population from germinating at the “wrong” time, e.g., during an unusually mild fall in an area subject to typically harsh winters. Seed dormancy is an effective survival strategy in many plant populations, but may greatly complicate efforts to establish large cohorts of seedlings (groups of similar age or developmental stage) needed for re-search and other purposes. In an effort to break seed dormancy in common sunflower, Helianthus annuus L. (Asteraceae), we conducted experiments designed to compare germination times and overall germination …

Controlled Deposition Of Tin Oxide And Silver Nanoparticles Using Microcontact Printing, Joo C. Chan, Nicole Hannah-Moore, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

This report describes extensive studies of deposition processes involving tin oxide (SnO_x) nanoparticles on smooth glass surfaces. We demonstrate the use of smooth films of these nanoparticles as a platform for spatially-selective electroless deposition of silver by soft lithographic stamping. The edge and height roughness of the depositing metallic films are 100 nm and 20 nm, respectively, controlled by the intrinsic size of the nanoparticles. Mixtures of alcohols as capping agents provide further control over the size and shape of nanoparticles clusters. The distribution of cluster heights obtained by atomic force microscopy (AFM) is modeled through a modified …

Curcumin: A Folklore Remedy From Kitchen On The Way To Clinic As Cancer Drug, Debasish Bandyopadhyay

Chemistry Faculty Publications and Presentations

Numerous compounds are widely distributed in nature and many of these possess medicinal/biological/pharmacological activity. Curcumin, a polyphenol derived from the rhizomes (underground stems) of Curcuma longa Linn (a member of the ginger family, commonly known as turmeric) is a culinary spice and therapeutic used in India for thousands of years to induce color and flavor in food as well as to treat a wide array of diseases. The origin of turmeric as spice and folklore medicine is so old that it is lost in legend. Curcumin has many beneficial pharmacological effects which includes, but are not limited with, antimicrobial, anti-inflammatory, …

Imaging, Spectroscopy, Mechanical, Alignment And Biocompatibility Studies Of Electrospun Medical Grade Polyurethane (Carbothane™ 3575a) Nanofibers And Composite Nanofibers Containing Multiwalled Carbon Nanotubes, Faheem A. Sheikh, Javier Macossay-Torres, Travis Cantu, Xujun Zhang, M. Shamshi Hassan, M. Esther Salinas, Chakavak S. Farhangi, Hassan Ahmad, Hern Kim, Gary L. Bowlin

Chemistry Faculty Publications and Presentations

In the present study, we discuss the electrospinning of medical grade polyurethane (Carbothane™ 3575A) nanofibers containing multi-walled-carbon-nanotubes (MWCNTs). A simple method that does not depend on additional foreign chemicals has been employed to disperse MWCNTs through high intensity sonication. Typically, a polymer solution consisting of polymer/MWCNTs has been electrospun to form nanofibers. Physiochemical aspects of prepared nanofibers were evaluated by SEM, TEM, FT-IR and Raman spectroscopy, confirming nanofibers containing MWCNTs. The biocompatibility and cell attachment of the produced nanofiber mats were investigated while culturing them in the presence of NIH 3T3 fibroblasts. The results from these tests indicated non-toxic behavior …

Phthalimide-Based Π-Conjugated Small Molecules With Tailored Electronic Energy Levels For Use As Acceptors In Organic Solar Cells, Arthur D. Hendsbee, Seth M. Mcafee, Jon-Paul Sun, Theresa M. Mccormick, Ian G. Hill, Gregory C. Welch

Chemistry Faculty Publications and Presentations

The design, synthesis, and characterization of seven phthalimide-based organic π-conjugated small molecules are reported. The new materials are based on a phthalimide–thiophene–CORE–thiophene–phthalimide architecture. The CORE units utilized were phthalimide (M2), diketopyrrolopyrrole (M3), isoindigo (M4), naphthalene diimide (M5), perylene diimide (M6), and difluorobenzothiadiazole (M7); they were specifically selected to progressively increase the electron affinity of the resulting compound. A small molecule with no core (M1) was synthesized for comparison. Each material was synthesized through optimized direct heteroarylation cross-coupling procedures using bench top solvents in air. Combinations of …