Chemistry Commons^™

Rapid And Convenient Method For Preparing Masters For Microcontact Printing With 1–12 Μm Features, Lloyd W. Zilch, Ghaleb A. Husseini, Yit-Yian Lua, Michael V. Lee, Kevin R. Gertsch, Bennion R. Cannon, Robert M. Perry, Eric T. Sevy, Matthew C. Asplund, Adam T. Woolley, Matthew R. Linford

Faculty Publications

Mechanical scribing can be employed to create surfaces with recessed features. Through replica molding elastomeric copies of these scribed surfaces are created that function as stamps for microcontact printing. It is shown that this new method for creating masters for microcontact printing can be performed with a computer-controlled milling machine (CNC), making this method particularly straightforward and accessible to a large technical community that does not need to work in a particle free environment. Thus, no clean room, or other specialized equipment is required, as is commonly needed to prepare masters. Time-of-flight secondary ion mass spectrometry confirms surface pattering by …

Evidence Of Linear Lattice Expansion And Covalency Enhancement In Rutile Tio2 Nanocrystals, Guangshe Li, Juliana Boerio-Goates, Brian F. Woodfield, Liping Li

Faculty Publications

Lattice variations and bonding characteristics in rutile TiO2 nanocrystals were examined by x-ray diffraction and x-ray photoelectron spectroscopy. With a reduction in the physical dimensions, rutile TiO2 nanocrystals show a linear lattice expansion and an anomalous covalency enhancement in apparent contradiction to the ionicity increase in BaTiO3 and CuO nanocrystals as reported recently by S. Tsunekawa et al. [Phys. Rev. Lett. 2000, 85, 3440] and V. R. Palkar et al. [Phys. Rev. B 1996, 53, 2167]. A surface defect dipole model is proposed to explain these physical phenomena in terms of the strong interactions among the surface dipoles that produce …

An Evening To Remember, Desmond H. Murray

Faculty Publications

No abstract provided.

Radical Initiated Polymerization In A Bifunctional Mixture Via Computer Simulation, Keri L. Diamond, Ras B. Pandey, Shelby F. Thames

Faculty Publications

Computer simulations are performed to study the polymerization behavior in a mixture of bifunctional groups such as olefins (A) and acrylates (B) in an effective solvent (a coarse description for vegetable oil derived macromonomers (VOMMs) in solution) on a cubic lattice. A set of interactions between these units and solvent (S) constituents and their relative concentrations (p(A), p(B), and p(S)) are considered. Samples are equilibrated with Metropolis algorithm to model the perceived behavior of VOMMs. The covalent bonding between monomeric units is then implemented via reaction pathways initiated by stochastic motion of free radicals (a very small fraction). The rate …

Geminal Model Chemistry Ii. Perturbative Corrections, Vitaly A. Rassolov, Feng Xu, Sophya Garashchuk

Faculty Publications

We introduce and investigate a chemical model based on perturbative corrections to the product of singlet-type strongly orthogonal geminals wave function. Two specific points are addressed (i) Overall chemical accuracy of such a model with perturbative corrections at a leading order; (ii) Quality of strong orthogonality approximation of geminals in diverse chemical systems. We use the Epstein–Nesbet form of perturbation theory and show that its known shortcomings disappear when it is used with the reference Hamiltonian based on strongly orthogonal geminals. Application of this model to various chemical systems reveals that strongly orthogonal geminals are well suited for chemical models, …

Identification Of An Il-17-Producing Nk1.1neg Inkt Cell Population Involved In Airway Neutrophilia, Paul B. Savage, Marie-Laure Michel, Alexandre Castro Keller, Christophe Paget, Masakazu Fujio, Francois Trottein, Chi-Huey Wong, Elke Schneider, Michael Dy, Maria C. Leite-De-Moraes

Faculty Publications

Invariant natural killer T (iNKT) cells are an important source of both T helper type 1 (Th1) and Th2 cytokines, through which they can exert beneficial, as well as deleterious, effects in a variety of inflammatory diseases. This functional heterogeneity raises the question of how far phenotypically distinct subpopulations are responsible for such contrasting activities. In this study, we identify a particular set of iNKT cells that lack the NK1.1 marker (NK1.1neg) and secrete high amounts of interleukin (IL)-17 and low levels of interferon (IFN)-{gamma} and IL-4. NK1.1neg iNKT cells produce IL-17 upon synthetic ({alpha}-galactosylceramide [{alpha}-GalCer] or PBS-57), as well …

Bohmian Dynamics On Subspaces Using Linearized Quantum Force, Vitaly A. Rassolov, Sophya Garashchuk

Faculty Publications

In the de Broglie–Bohm formulation of quantum mechanics the time-dependent Schrödinger equation is solved in terms of quantum trajectories evolving under the influence of quantum and classical potentials. For a practical implementation that scales favorably with system size and is accurate for semiclassical systems, we use approximate quantum potentials. Recently, we have shown that optimization of the nonclassical component of the momentum operator in terms of fitting functions leads to the energy-conserving approximate quantum potential. In particular, linear fitting functions give the exact time evolution of a Gaussian wave packet in a locally quadratic potential and can describe the dominant …

Binary Frontal Polymerization: Velocity Dependence On Initial Composition, John A. Pojman, Jerry A. Griffith, H. Archie Nichols

Faculty Publications

Frontal polymerization is a mode of polymerization in which a localized zone of reaction propagates through the coupling of thermal diffusion and the Arrhenius dependence of the reaction rate. The dependence of the front propagation velocity on the initial composition has been determined in initially miscible binary systems of a free-radically cured diacrylate and an amine- or cationically cured epoxy resin. A minimum of the velocity as a function of the monomer mole fraction is observed if the two polymerizations occur independently. Excellent agreement with an analytical description was found with the diacrylate and an amine-cured epoxy but not for …

Human Glutaminyl Cyclase And Bacterial Zinc Aminopeptidase Share A Common Fold And Active Site, Rachell E. Booth, Simon C. Lovell, Stephanie A. Misquitta, Robert C. Bateman Jr.

Faculty Publications

Background: Glutaminyl cyclase (QC) forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP) and mutated the apparent active site residues to assess their role in QC catalysis.

Results: The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence …

Energy Conserving Approximations To The Quantum Potential: Dynamics With Linearized Quantum Force, Sophya Garashchuk, Vitaly A. Rassolov

Faculty Publications

Solution of the Schrödinger equation within the de Broglie–Bohm formulation is based on propagation of trajectories in the presence of a nonlocal quantum potential. We present a new strategy for defining approximate quantum potentials within a restricted trial function by performing the optimal fit to the log-derivatives of the wave function density. This procedure results in the energy-conserving dynamics for a closed system. For one particular form of the trial function leading to the linear quantum force, the optimization problem is solved analytically in terms of the first and second moments of the weighted trajectory distribution. This approach gives exact …

"A New Phase Of The Complex Trinitratotris(Triphenylphosphineoxide)Neodymium(Lll), J. Brannon Gary

Faculty Publications

There has been considerable interest in the complexes formed by the lanthanides with various monodentate neutral ligands with O as the donor atom. Phosphine oxides, in particular, have proven useful in complexing to lanthanide metal ions and have found practical application in the solvent extraction and separation of lanthanides.1 Several lanthanide(III) nitrate complexes with triphenylphosphine oxide (OPPh3) have been prepared resulting in complexes having as few as two and as many as four OPPh3 groups per lanthanide center.2−4 An earlier study by Cousins and Hart5 identified the complex [Nd(OPPh3)3(NO3)3]. Two crystal phases of this same complex were briefly reported later …

Superior 5' Homogeneity Of Rna From Atp-Initiated Transcription Under The T7 Φ2.5 Promoter, Tricia M. Coleman, Guocan Wang, Faqing Huang

Faculty Publications

Transcription from the commonly used GTP- initiating T7 class III promoter phi6.5 frequently produces heterogeneous RNA at both 3' and 5' ends. We demonstrate here that RNA transcripts from the T7 class II promoter phi2.5 have superior 5' homogeneity over those from the phi6.5 promoter, with comparable total RNA yields. The overall homogeneity of RNA transcripts is improved to different degrees depending on RNA sequences, although transcription under phi2.5 does not affect the 3' heterogeneity of RNA. In combination with 3' RNA trimming by DNAzymes or ribozymes, this ATP- initiated transcription system based on the T7 phi2.5 promoter can provide …

Self-Aligned Mechanical Attachment Of Carbon Nanotubes To Silicon Dioxide Structures By Selective Silicon Dioxide Chemical-Vapor Deposition, Jed D. Whittaker, Ghaleb A. Husseini, Matthew A. Linford, Robert C. Davis, Markus Brink

Faculty Publications

A self-aligned thin-film deposition technique was developed to mechanically attach carbon nanotubes to surfaces for the fabrication of structurally robust nanotube-based nanomechanical devices. Single-walled carbon nanotubes were grown by thermal chemical-vapor deposition (CVD) across 150-nm-wide SiO2 trenches. The nanotubes were mechanically attached to the trench tops by selective silicon tetraacetate-based SiO2 CVD. No film was deposited on the nanotubes where they were suspended across the trenches.

Synthesis Of Adenosine Derivatives As Transcription Initiators And Preparation Of 5 ' Fluorescein- And Biotin-Labeled Rna Through One-Step In Vitro Transcription, Faqing Huang, Guocan Wang, Tricia Coleman, Na Li

Faculty Publications

Expanding our previous finding of an adenosine-initiated transcription system, we now demonstrate that either the 5' site or the N6 site of adenosine nucleotides can be modified extensively without abolishing their ability to initiate transcription under the T7 phi2.5 promoter. Two series of amino derivatives of adenosine nucleotides were synthesized. Fluorescein and biotin groups were coupled to AMP derivatives through linkers of different sizes and hydrophobicities. Both fluorescein- and biotin-conjugated (at either the 5' or N6 site) adenosine nucleotides can act as efficient transcription initiators, producing fluorescein- and biotin-labeled RNA at the specific 5' end by a one-step transcription procedure, …

Pyridoxamine Traps Intermediates In Lipid Peroxidation Reactions In Vivo: Evidence On The Role Of Lipids In Chemical Modification Of Protein And Development Of Diabetic Complications, Thomas O. Metz, Nathan L. Alderson, Mark E. Chachich, Suzanne R. Thorpe, John W. Baynes

Faculty Publications

Maillard or browning reactions between reducing sugars and protein lead to formation of advanced glycation end products (AGEs) and are thought to contribute to the pathogenesis of diabetic complications. AGE inhibitors such as aminoguanidine and pyridoxamine (PM) inhibit both the formation of AGEs and development of complications in animal models of diabetes. PM also inhibits the chemical modification of protein by advanced lipoxidation end products (ALEs) during lipid peroxidation reactions in vitro. We show here that several PM adducts, formed in incubations of PM with linoleate and arachidonate in vitro, are also excreted in the urine of PM-treated animals. The …

Markov Chains And Dynamic Geometry Of Polygons, Jiu Ding, L. Richard Hitt, Xin-Min Zhang

Faculty Publications

In this paper we construct sequences of polygons from a given n-sided cyclic polygon by iterated procedures and study the limiting behaviors of these sequences in terms of non-negative matrices and Markov chains. (C) 2003 Elsevier Science Inc. All rights reserved.

Bis[Μ-1,2-Bis(2-Pyridyl)Ethyne-K2N:N']Bis[Aquadinitratocadmium(Ii)], Badruz Zaman Md., Matthew J. Davis, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Two twisted 1,2-bis(2-pyridyl)ethyne ligands bridge two Cd²⁺ centers in the C₂-symmetric title complex, [Cd₂(NO₃)₄(-C₁₂H₈N₂)₂(H₂O)₂]. The bridging ligands arch across one another creating a `zigzag loop' molecular geometry. Two nitrate ions and a water molecule complete the irregular seven-coordinate Cd-atom environment. The dihedral angles between the equivalent pyridyl ring planes of the two independent ligands are 67.2 (1)°. O_water-HO_nitrate hydrogen bonding creates two-dimensional layers parallel to the ab plane.

Formula: [Cd₂(NO₃)₄(C …

Sr3Mgpto6, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Single crystals of the mixed alkaline earth platinate, tristrontium magnesium platinum hexaoxide, Sr₃MgPtO₆, were grown from a KOH flux at 1273 K. The compound adopts the rhombohedral K₄CdCl₆ structure type, featuring chains of face-shared, distorted MgO₆ trigonal prisms (Mg site symmetry 32) and PtO₆ octahedra (Pt site symmetry ) surrounded by columns of Sr²⁺ ions (Sr site symmetry 2).

Density Of States Simulations Of Proteins, Nitin Rathore, Thomas A. Knotts Iv, Juan J. De Pablo

Faculty Publications

A modified version of a recently introduced algorithm that calculates density of states by performing a random walk in energy space has been proposed and implemented to study protein folding in a continuum. A united atom representation and the CHARMM19 [B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983)] force field are employed for these simulations. This method permits estimation of the density of states of a protein via a random walk in the energy space, thereby allowing the system to escape from local free-energy minima …

Review Of The Final Frontier, Michael F. Russo

Faculty Publications

No abstract provided.

Semiclassical Dynamics With Quantum Trajectories: Formulation And Comparison With The Semiclassical Initial Value Representation Propagator, Sophya Garashchuk, Vitaly A. Rassolov

Faculty Publications

We present a time-dependent semiclassical method based on quantum trajectories. Quantum-mechanical effects are described via the quantum potential computed from the wave function density approximated as a linear combination of Gaussian fitting functions. The number of the fitting functions determines the accuracy of the approximate quantum potential (AQP). One Gaussian fit reproduces time-evolution of a Gaussian wave packet in a parabolic potential. The limit of the large number of fitting Gaussians and trajectories gives the full quantum-mechanical result. The method is systematically improvable from classical to fully quantum. The fitting procedure is implemented as a gradient minimization. We also compare …

Efficient Incorporation Of Coa, Nad And Fad Into Rna By In Vitro Transcription, Faqing Huang

Faculty Publications

Protein enzymes frequently recruit small molecule coenzymes to perform a variety of biochemical reactions. While the catalytic activities of RNA have been expanding rapidly, a similar strategy for RNA to utilize coenzymes and to increase its functional capabilities has yet to be demonstrated. A general in vitro transcription procedure has been developed to efficiently prepare RNA with coenzymes CoA, NAD and FAD covalently attached to the 5' end. These adenosine-containing coenzymes initiate transcription under the T7 class II promoter by T7 RNA polymerase. In addition to the three coenzymes, other adenosine-containing molecules may be incorporated into the first nucleotide position …

Tetratricopeptide Repeat Motif-Mediated Hsc70-Msti1 Interaction Molecular Characterization Of The Critical Contacts For Successful Binding And Specificity*, Odutayo O. Odunuge, Judith A. Hornby, Chrisiane Bies, Richard Zimmermann, David J. Pugh, Gregory L. Blatch

Faculty Publications

Murine stress-inducible protein 1 (mSTI1) is a cochaperone that is homologous with the human Hsp70/ Hsp90-organizing protein (Hop). Guided by Hop structural data and sequence alignment analyses, we have used site-directed mutagenesis, co-precipitation assays, circular dichroism spectroscopy, steady-state fluorescence, and surface plasmon resonance spectroscopy to both qualitatively and quantitatively characterize the contacts necessary for the N-terminal tetratricopeptide repeat domain (TPR1) of mSTI1 to bind to heat shock cognate protein 70 (Hsc70) and to discriminate between Hsc70 and Hsp90. We have shown that substitutions in the first TPR motif of Lys8 or Asn12 did not affect binding of mSTI1 to Hsc70, …

Dendritic Surfactants Show Evidence For Frustrated Intercalation: A New Organoclay Morphology, Erick J. Acosta, Youjun Deng, G. Norman White, Joe B. Dixon, Kevin J. Mcinnes, Scott A. Senseman, Alyx S. Frantzen, Eric E. Simanek

Faculty Publications

Mixing a smectite clay with some dendritic surfactants shows that despite the large size of some of these molecules, a property that frustrates complete intercalation into the gallery of the clay, organoclay materials are obtained. X-ray powder diffraction (XPD) reveals no significant increases in lattice spacing as these surfactants are added. Infrared (IR) spectroscopy and thermal gravimetric analysis (TGA) show that interlayer water is preserved. Consistent with an undisturbed interlayer, the amount of organic material in organoclays derived from frustrated surfactants does not exceed 15% of the cationic exchange capacity (CEC) of the composite. Smaller dendritic surfactants do not display …

Crystal Structure Of Boc-Trp(Cho)-Dphe-Ile-Dphe-Leu-Och3, C48h59n6o10, Vijayaraghavan Rangachari, J. Makker, P. Kumar, S. Dey, Tej P. Singh

Faculty Publications

No abstract provided.

Nitroalkane Anomaly: Computational Study With Cluster And Continuum Modeling, H. Yamataka, Salai Cheettu Ammal

Faculty Publications

The origin of anomalous relation between rates and equilibria for the proton-transfer reactions of nitroalkanes, known as nitroalkane anomaly, was investigated by theoretical calculations with a cluster model, in which three water molecules are explicitly considered in the system, as well as the PCM solvent continuum model. For the CH3NO2/CH3CH2NO2 system, B3LYP and MP2 computations reproduced the anomaly, and the imbalance in the charge distribution at the transition state (TS) was observed. In contrast, although the TS imbalance was detected for the substituted phenylnitromethane system, the Brønsted plots did not show any anomaly. The experimentally observed abnormally large Brønsted coefficient …

Seasonality Of Dissolved Rare Earth Elements In The Lower Mississippi River, Alan M. Shiller

Faculty Publications

[1] Dissolved rare earth element (REE) concentrations were determined in a 27-month time series of the lower Mississippi River. Overall, the results agree with limited previous investigations; that is, the river shows enrichment of heavy REEs relative to light REEs and also has a significant Ce anomaly. However, the previous investigations relied on only single samples from the river. This seasonal investigation reveals significant temporal variations in the river's REE chemistry. In particular, large ( approximately fivefold) variations in light REE concentrations are observed. The light REEs follow a seasonality similar to particle-reactive trace elements. Also, the Ce anomaly shows …

Distributions Of Nobel Metal Pd And Pt In Mesoporous Silica, J. Arbiol, A. Cabot, J. R. Morante, Fanglin Chen, Meilin Liu

Faculty Publications

Mesoporous silicananostructures have been synthesized and loaded with Pd and Pt catalytic noble metals. It is found that Pd forms small nanoclusters (3–5 nm) on the surface of the mesoporous structure whereas Pt impregnation results in the inclusion of Pt nanostructures within the silica hexagonal pores (from nanoclusters to nanowires). It is observed that these materials have high catalyticproperties for CO–CH₄CO–CH₄CO–CH₄ combustion, even in a thick film form. In particular, results indicate that the Pt and Pd dispersed in mesoporous silica are catalytically active as a selective filter for gas sensors.

The Effect Of Reactor Geometry On Frontal Polymerization Spin Modes, John A. Pojman, Jonathan Masere, Enrico Petretto, Mauro Rustici, Do-Sung Huh, Min Suk Kim, Vladimir Volpert

Faculty Publications

Using reactors of different sizes and geometries the dynamics of the frontal polymerization of 1,6-hexanediol diacrylate (HDDA) and pentaerythritol tetraacrylate (PETAC), with ammonium persulfate as the initiator were studied. For this system, the frontal polymerization exhibits complex behavior that depends on the ratio of the monomers. For a particular range of monomers concentration, the polymerization front becomes nonplanar, and spin modes appear. By varying the reactor diameter, we experimentally confirmed the expected shift of the system to a greater number of "hot spots" for larger diameters. For square test tubes a "zig-zag" mode was observed for the first time in …

A Post-Amadori Inhibitor Pyridoxamine Also Inhibits Chemical Modification Of Proteins By Scavenging Carbonyl Intermediates Of Carbohydrate And Lipid Degradation, Paul A. Voziyan, Thomas O. Metz, John W. Baynes, Billy G. Hudson

Faculty Publications

Reactive carbonyl compounds are formed during autoxidation of carbohydrates and peroxidation of lipids. These compounds are intermediates in the formation of advanced glycation end products (AGE) and advanced lipoxidation end products (ALE) in tissue proteins during aging and in chronic disease. We studied the reaction of carbonyl compounds glyoxal (GO) and glycolaldehyde (GLA) with pyridoxamine (PM), a potent post-Amadori inhibitor of AGE formation in vitro and of development of renal and retinal pathology in diabetic animals. PM reacted rapidly with GO and GLA in neutral, aqueous buffer, forming a Schiff base intermediate that cyclized to a hemiaminal adduct by intramolecular …