Copyright (c) 2013 Boise State University All rights reserved. http://scholarworks.boisestate.edu/chem_facpubs Recent documents in Chemistry Faculty Publications and Presentations en-us Sun, 31 Mar 2013 01:33:30 PDT 3600 http://scholarworks.boisestate.edu/chem_facpubs/82 http://scholarworks.boisestate.edu/chem_facpubs/82 Fri, 29 Mar 2013 14:40:37 PDT The compound 2,4-dichlorophenylcyanoxime (later H(2,4-diCl-PhCO)) has significance in its possible application in cancer chemotherapy treatments since it acts as an inhibitor of the human carbonic reductase. This enzyme decreases the effectiveness of anthracycline drug treatment of some types of cancer. The compound was synthesized in high yield at ambient conditions from 2,4-dichlorophenylacetonitrile, using gaseous methylnitrite. The compound was characterized by means of UV–visible, IR, ¹H, ¹³C NMR spectroscopy and X-ray analysis. The cyanoxime crystallizes in a monoclinic space group P2₁/c (#14) with unit cell constants: a = 3.7587(9) Å, b = 30.087(7) Å, c = 7.6874(17) Å, β = 96.163(3)°; V = 864.3(3) ų, Z = 4. The structure was solved, using direct methods, to final R indices [I > 2σ (I)] R1 = 0.0551 (wR2 = 0.1217). The compound adopts a non-planar, trans-anti configuration with the value of the dihedral angle between the cyanoxime and dichlorophenyl planes equal to 50.61°.

]]> Michael Hilton et al. http://scholarworks.boisestate.edu/chem_facpubs/81 http://scholarworks.boisestate.edu/chem_facpubs/81 Thu, 28 Mar 2013 09:04:23 PDT α-Conotoxin MII (α-CTxMII) is a potent and selective peptide antagonist of neuronal nicotinic acetylcholine receptors (nAChR’s). Studies have shown that His9 and His12 are significant determinants of toxin binding affinity for nAChR, while Glu11 may dictate differential toxin affinity between nAChR isoforms. The protonation state of these histidine residues and therefore the charge on the α-CTx may contribute to the observed differences in binding affinity and selectivity. In this study, we assess the pH dependence of the protonation state of His9 and His12 by ¹H NMR spectroscopy and constant pH molecular dynamics (CpHMD) in α-CTxMII, α-CTxMII[E11A], and the triple mutant, α-CTxMII- [N5R:E11A:H12K]. The E11A mutation does not significantly perturb the pK_a of His9 or His12, while N5R:E11A:H12K results in a significant decrease in the pK_a value of His9. The pK_a values predicted by CpHMD simulations are in good agreement with ¹H NMR spectroscopy, with a mean absolute deviation from experiment of 0.3 pK_a units. These results support the use of CpHMD as an efficient and inexpensive predictive tool to determine pK_a values and structural features of small peptides critical to their function.

]]> Owen M. McDougal et al. http://scholarworks.boisestate.edu/chem_facpubs/80 http://scholarworks.boisestate.edu/chem_facpubs/80 Thu, 15 Nov 2012 17:20:14 PST We analyze the material transport equations (MTE) derived by Eslamian and co-authors and address the criticism expressed regarding the approach formulated in our previous work. In doing so, we show that the MTE formulated by Eslamian and co-authors are valid only in closed stationary non-isothermal systems in combination with the restrictions on the Onsager coefficients formulated in our work which is criticized, and that for nonstationary systems the approach we took can be used.

]]> Semen N. Semenov et al. http://scholarworks.boisestate.edu/chem_facpubs/79 http://scholarworks.boisestate.edu/chem_facpubs/79 Wed, 24 Oct 2012 11:44:32 PDT The increasing use of low temperature co-fired ceramic (LTCC) for the fabrication of biological microfluidic devices necessitates further research on LTCC biocompatibility. In this study we explore the inhibitory effect of DuPont's 951 LTCC on Polymerase Chain Reaction (PCR), and demonstrate a novel mechanism to increase biocompatibility between LTCC and PCR with the addition of a common passivation substance, bovine serum albumin (BSA). We show that DuPont's 951 LTCC binds negatively charged proteins including BSA and ovalbumin (OVA). This is a significant discovery as proteins (enzymes) are an essential component of most biological reactions, and a frequent addition to microfluidic devices. A proposed model for LTCC inhibition of PCR by enzyme adsorption is presented.

]]> Jason Besecker et al. http://scholarworks.boisestate.edu/chem_facpubs/78 http://scholarworks.boisestate.edu/chem_facpubs/78 Wed, 03 Oct 2012 12:15:31 PDT The amino propeptide of collagen a1(XI) (NPP) has been shown to bind glycosaminoglycans and to form a dimer. While these are independent biochemical events, it is likely that dimerization facilitates the interaction with glycosaminoglycans or alternatively, that glycosaminoglycan interaction facilitates the formation of an NPP:NPP dimer. The computer program MODELLER was used to generate a homology model of the collagen a1(XI) NPP monomer using the crystal structure of the closely related noncollagenous-4 (NC4) domain of collagen a1(IX) (PDB:2UUR) as the template. Additionally, a dimer model of collagen a1(XI) NPP domain was created based upon the thrombospondin dimer template (PDB:1Z78). The structure of the dimer created in MODELLER was validated by comparison to a dimer model generated by docking two monomers of PDB:2UUR using ClusPro. Calculations of relative binding energy for the interaction between each collagen 1(XI) NPP model and glycosaminoglycans as ligands was performed using AutoDock4. Computational results support a higher affinity between heparan sulfate and a dimer compared to a monomer. These findings are supported by affinity chromatography experiments in which distinct monomer and dimer peaks were observed. Sequentialvpoint mutation studies of the putative binding site (147-KKKITK-152) indicated the importance of the basic lysine residue for binding to heparan sulfate. Two orders of magnitude change in binding affinity was predicted when comparing wild type to the mutation K152A. Experimental data supports the predicted change in affinity.

]]> Julia Oxford et al. http://scholarworks.boisestate.edu/chem_facpubs/77 http://scholarworks.boisestate.edu/chem_facpubs/77 Thu, 27 Sep 2012 11:49:56 PDT The material transport equations derived in the article by Leroyer and Würger [J. Chem. Phys. 135, 054102 (2011)10.1063/1.3615954] do not adequately provide a description of material transport in liquid binary systems. An alternate approach based on non-equilibrium thermodynamics is presented.

]]> Semen N. Semenov et al. http://scholarworks.boisestate.edu/chem_facpubs/76 http://scholarworks.boisestate.edu/chem_facpubs/76 Fri, 27 Jul 2012 11:47:04 PDT We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.

]]> Reed B. Jacob et al. http://scholarworks.boisestate.edu/chem_facpubs/75 http://scholarworks.boisestate.edu/chem_facpubs/75 Wed, 13 Jun 2012 12:07:42 PDT The use of susceptibility matching to minimize spectral distortion of biphasic samples layered in a standard 5 mm NMR tube is described. The approach uses magic angle spinning (MAS) to first extract chemical shift differences by suppressing bulk magnetization. Then, using biphasic coaxial samples, magnetic susceptibilities are matched by titration with a paramagnetic salt. The matched phases are then layered in a standard NMR tube where they can be shimmed and examined. Linewidths of two distinct spectral lines, selected to characterize homogeneity in each phase, are simultaneously optimized. Two-dimensional distortion-free, slice-resolved spectra of an octanol/water system illustrate the method. These data are obtained using a 2D stepped-gradient pulse sequence devised for this application. Advantages of this sequence over slice-selective methods are that acquisition efficiency is increased and processing requires only conventional software.

]]> Bryan T. Martin et al. http://scholarworks.boisestate.edu/chem_facpubs/74 http://scholarworks.boisestate.edu/chem_facpubs/74 Wed, 06 Jun 2012 12:27:28 PDT Treatment of Zn(II) and Cd(II) hydroxide complexes of the tris(2-pyridylmethyl)amine (TPA) ligand with COS or CS₂ in protic solvents (MeOH or EtOH) resulted in [(TPA)Zn–SC(S)OCH₃]ClO₄ (1), [(TPA)Zn–SC(O)OCH₃]BF₄ (2), [(TPA)Zn–SC(O)OCH₃]ClO₄ (3), [(TPA)Zn–SC(O)OCH₂CH₃]BF₄ (4), [(TPA)Cd–SC(S)OCH₃]ClO₄ (5) and [(TPA)Cd–SC(O)OCH₃]ClO₄ (6). The molecular structures of 1, 2, 5 and 6 were determined by X-ray crystallography. Complexes 2, 3 and 4, unlike 1, 5 and 6, are easily hydrolyzed upon treatment with water in CH₃CN to give zinc hydrosulfide complexes of the form [(TPA)Zn–SH]X (X = BF₄⁻ (7) and ClO₄⁻ (8)), as evidenced by spectroscopic methods and the crystal structure of 7. These complexes may be prepared more directly by (a) reacting equimolar amounts of TPA, Zn(ClO₄)₂·6H₂O and Me₄NOH·5H₂O with COS in CH₃CN or (b) treating [((TPA)Zn)₂(μ-OH)₂](ClO₄)₂ with H₂S. Moreover, reactivity and density functional theory computational studies comparing the cationic hydrosulfide complexes 7 and 8 with the neutral zinc hydrosulfide complexes supported by tris(pyrazolyl)borate ligands have been conducted and subtle differences between the two types of hydrosulfide complexes have been determined.

]]> Nicholas G. Spiropulos et al. http://scholarworks.boisestate.edu/chem_facpubs/73 http://scholarworks.boisestate.edu/chem_facpubs/73 Thu, 15 Mar 2012 14:02:53 PDT The ability to couple problem solving both to the understanding of chemical concepts and to laboratory practices is an essential skill for undergraduate chemistry programs to foster in our students. Therefore, chemistry programs must offer opportunities to answer real problems that require use of problem-solving processes used by practicing chemists, including those of experimental design. Additionally, programs should assess the extent to which these skills are mastered by students and use the results to inform curricular development. This manuscript describes a rubric for experimental problem solving in chemistry that seeks to assess the extent to which students can both understand a chemical problem and design an instrument-based strategy to address it. The rubric effectively differentiates responses to practicum questions answered by students at different stages of the undergraduate chemistry curriculum. The data show that students improve in their ability to problem solve as they progress through the program. On average, students are able to provide a "correct" answer before they are able to articulate a complete understanding of the problem or to justify their choices. The rubric will be useful to others seeking to study or assess student problem-solving skills at both the course and curricular levels.

]]> Susan E. Shadle et al. http://scholarworks.boisestate.edu/chem_facpubs/72 http://scholarworks.boisestate.edu/chem_facpubs/72 Thu, 15 Mar 2012 13:58:06 PDT A concerted effort has been made to increase the opportunities for undergraduate students to address scientific problems employing the processes used by practicing chemists. As part of this effort, an infrared (IR) spectroscopy and molecular modeling experiment was developed for the first-year general chemistry laboratory course. In the experiment, students explore the dynamic nature of the covalent bond in a hands-on, inquiry-based approach by experimenting with mass and spring systems, using molecular modeling software, and performing IR spectroscopy on a series of structurally related compounds. Students see the effect of bond order, atomic size, and molecular weight on bond strength, bond length, and vibrational frequency. As an added benefit, students are introduced to scientific instrumentation and tools that can then be expanded upon in later laboratory classes.

]]> Clifford M. Csizmar et al. http://scholarworks.boisestate.edu/chem_facpubs/66 http://scholarworks.boisestate.edu/chem_facpubs/66 Fri, 09 Dec 2011 12:28:33 PST The retention of both underivatized and carboxylated polystyrene latex beads by electrical field-flow fractionation (EIFFF) was investigated using a 2 mM aqueous solution of quinonehydroquinone as the carrier liquid. The quninone-hydroquinone redox couple passes current with less polarization of the electrodes than carrier liquids previously employed. Underivatized beads, ranging in diameter from 0.15 to 0.74 μm eluted in the normal mode, while carboxylated beads larger than 1 μm eluted in the steric mode. Normal mode retention increases with flow rate, probably due to shearing of the polarization layer, which increases the working field. At a constant field and flow rate, normal-mode retention is inversely related to the product of a particle's size and electrophoretic mobility, in accordance with retention theory. Thus, ElFFF can be used to obtain both the size and electrophoretic mobility of particle suspensions.

]]> Martin E. Schimpf et al. http://scholarworks.boisestate.edu/chem_facpubs/64 http://scholarworks.boisestate.edu/chem_facpubs/64 Fri, 09 Dec 2011 11:13:31 PST Martin E. Schimpf et al. http://scholarworks.boisestate.edu/chem_facpubs/63 http://scholarworks.boisestate.edu/chem_facpubs/63 Fri, 09 Dec 2011 11:09:31 PST Thermal field-flow fractionation (ThFFF) is a useful technique for separating complex polymer mixtures. The unique features of ThFFF make it applicable to many polymers that are difficult to characterized by conventional methods. Advances in channel design, spearheaded by work at the University of Utah's Field-Flow Fractionation Research Center, have recently culminated in the introduction of a commercially available instrument. Motivated by this progress, ThFFF is reviewed in this paper with an emphasis on implementation. Theories governing retention, zone dispersion and optimization are summarized. Procedures for obtaining accurate molecular-weight distributions on polymers are reviewed along with sample handling techniques. Also discussed is the application of ThFFF to studies of thermal diffusion in polymer solutions. The paper concludes with a discussion of current trends in the field.

]]> Martin E. Schimpf http://scholarworks.boisestate.edu/chem_facpubs/62 http://scholarworks.boisestate.edu/chem_facpubs/62 Fri, 09 Dec 2011 11:06:42 PST Martin E. Schimpf http://scholarworks.boisestate.edu/chem_facpubs/61 http://scholarworks.boisestate.edu/chem_facpubs/61 Fri, 09 Dec 2011 11:04:48 PST Martin E. Schimpf http://scholarworks.boisestate.edu/chem_facpubs/60 http://scholarworks.boisestate.edu/chem_facpubs/60 Fri, 09 Dec 2011 11:01:26 PST Polymer retention in thermal field-flow fractionation (ThFFF) is enhanced by the use of certain carrier-liquid mixtures. The origin of enhanced retention is explored with a focus on thermal diffusion, which is the driving force behind ThFFF. First, we examine thermal diffusion in several binary liquid mixtures; here, the relative tendency of a component to concentrate at the cold wall is correlated to its density and viscous activation energy. Next, we measure polymer retention in several binary carrier liquids. Retention is affected by thermal diffusion of the liquid components if the components have different solvating powers for the polymer. When the better solvent partitions to the cold wall, polymer retention is enhanced; when the better solvent partitions to the hot wall, retention is diminished. These results indicate that a solvent gradient constitutes a significant driving force on the polymer, which may act either in concert or in opposition to thermal diffusion of the polymer, thereby enhancing or diminishing polymer retention, respectively. Thermodynamic arguments confirm the significance of this additional force, and the phenomenon is used to fractionate several polystyrene standards ranging in molecular weight from 2500 to 160 000.

]]> Chad A. Rue et al. http://scholarworks.boisestate.edu/chem_facpubs/58 http://scholarworks.boisestate.edu/chem_facpubs/58 Fri, 09 Dec 2011 10:51:32 PST Earlier studies of copolymer thermal diffusion are extended here to include several new random and block copolymers of polystyrene and polyisoprene. Thermal diffusion coefficients for these polymers in tetrahydrofuran and cyclohexane were obtained by thermal field-flow fractionation (ThFFF). The results confirm the dependence of thermal diffusion (and therefore ThFFF retention) on the radial distribution of monomeric units in the solvated macromolecule. For random copolymers and block copolymers that assume a random configuration, the thermal diffusion coefficient DT is a linear function of copolymer composition. This relationship provides a basis for obtaining compositional information on such copolymers by ThFFF.

]]> Martin Schimpf et al. http://scholarworks.boisestate.edu/chem_facpubs/57 http://scholarworks.boisestate.edu/chem_facpubs/57 Fri, 09 Dec 2011 10:36:02 PST Martin Schimpf http://scholarworks.boisestate.edu/chem_facpubs/56 http://scholarworks.boisestate.edu/chem_facpubs/56 Fri, 09 Dec 2011 10:32:22 PST Martin E. Schimpf