Chemistry Faculty Research and Publications Copyright (c) 2013 Marquette University All rights reserved. http://epublications.marquette.edu/chem_fac Recent documents in Chemistry Faculty Research and Publications en-us Wed, 08 May 2013 07:43:14 PDT 3600 Analysis of Binding Site Hot Spots on the Surface of Ras GTPase http://epublications.marquette.edu/chem_fac/224 http://epublications.marquette.edu/chem_fac/224 Wed, 01 May 2013 08:46:48 PDT We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the “off” and “on” allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the active site. Comparison of FTMaps for the H and K isoforms reveals essentially identical hot spots. Furthermore, using NMR measurements of spin relaxation, we determined that K-Ras exhibits global conformational dynamics very similar to those we previously reported for H-Ras. We thus hypothesize that the global conformational rearrangement serves as a mechanism for allosteric coupling between the effector interface and remote hot spots in all Ras isoforms. At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well. Ras has so far been elusive as a target for drug design. The present work identifies various unexplored hot spots throughout the entire surface of Ras, extending the focus from the disordered active site to well-ordered locations that should be easier to target.

]]> Greg Buhrman et al. Potential Energy and Dipole Moment Surfaces of HCO- for the Search of H- in the Interstellar Medium http://epublications.marquette.edu/chem_fac/223 http://epublications.marquette.edu/chem_fac/223 Fri, 12 Apr 2013 14:21:05 PDT Potential energy and permanent dipole moment surfaces of the electronic ground state of formyl negative ion HCO− are determined for a large number of geometries using the coupled-cluster theory with single and double and perturbative treatment of triple excitations ab initio method with a large basis set. The obtained data are used to construct interpolated surfaces, which are extended analytically to the region of large separations between CO and H− with the multipole expansion approach. We have calculated the energy of the lowest rovibrational levels of HCO− that should guide the spectroscopic characterization of HCO− in laboratory experiments. The study can also help to detect HCO− in the cold and dense regions of the interstellar medium where the anion could be formed through the association of abundant CO with still unobserved H−.

]]> M. Ayouz et al. Polysaccharide Ecocomposite Materials: Materials: Synthesis, Characterization and Application for Removal of Pollutants and Bacteria http://epublications.marquette.edu/chem_fac/222 http://epublications.marquette.edu/chem_fac/222 Thu, 04 Apr 2013 11:29:38 PDT A novel, simple and totally recyclable method has been developed for the synthesis of nontoxic, biocompatible and biodegradable composite materials from cellulose and chitosan. In this method, [BMIm+Cl-], an ionic liquid (IL), was used as a solvent to dissolve and synthesize the [CEL+CS] composite materials. Since the IL can be removed from the materials by washing them with water, and recovered from the washed solution, the method is totally recyclable. XRD, FTIR, NIR and SEM were used to characterize the materials and to confirm that CEL and CS were successfully regenerated by the method without any chemical transformation. More importantly, we have successfully demonstrated that [CEL+CS] material can serve as an effective adsorbent for removal of various endocrine disruptors including polychlorophenols and bisphenol A. This is because the composites have combined advantages of their components, namely superior chemical stability and mechanical stability (from CEL) and excellent adsorption capability for pollutants (from CS).

]]> Simon Duri et al. NMR Line Shapes and Multi-State Binding Equilibria http://epublications.marquette.edu/chem_fac/221 http://epublications.marquette.edu/chem_fac/221 Fri, 25 Jan 2013 10:34:48 PST Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes—NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule is coupled to binding of a ligand. Through an extensive analysis of multiple exchange regimes for a family of three-state models, I identified signature features to guide an NMR experimentalist in recognizing specific interaction mechanisms. Results also show that distinct multistate models may produce very similar spectral patterns. I also discussed aggregation of a receptor as a possible source of spurious three-state line shapes and provided specific suggestions for complementary experiments that can ensure reliable mechanistic insight.

]]> Evgeni Kovrigin On Pi-Stacking, CH/Pi, and Halogen Bonding in Halobenzene Clusters: Resonant 2-Photon Ionization Studies of Chlorobenzene http://epublications.marquette.edu/chem_fac/220 http://epublications.marquette.edu/chem_fac/220 Fri, 18 Jan 2013 10:46:11 PST Noncovalent interactions such as hydrogen bonding, π-π stacking, CH/π interactions, and halogen bonding play crucial roles in a broad spectrum of chemical and biochemical processes, and can exist in cooperation or competition. Here we report studies of the homoclusters of chlorobenzene, a prototypical system where π-π stacking, CH/π interactions, and halogen bonding interactions may all be present. The electronic spectra of chlorobenzene monomer and clusters (Clbz)n with n = 1-4 were obtained using resonant 2-photon ionization in the origin region of the S0–S1 (ππ*) state of the monomer. The cluster spectra show in all cases a broad spectrum whose center is redshifted from the monomer absorption. Electronic structure calculations aid in showing that the spectral broadening arises in large part from inhomogeneous sources, including the presence of multiple isomers and Franck-Condon (FC) activity associated with geometrical changes induced by electronic excitation. Calculations at the M06-2x/aug-cc-pVDZ level find in total five minimum energy structures for the dimer, four π-stacked structures, and one T-shaped, and six representative minimum energy structures were found for the trimer. The calculated time-dependent density functional theory spectra using range-separated and meta-GGA hybrid functionals show that these isomers absorb over a range that is roughly consistent with the breadth of the experimental spectra, and the calculated absorptions are redshifted with respect to the monomer transition, in agreement with experiment. Due to the significant geometry change in the electronic transition, where for the dimer a transition from a parallel displaced to sandwich structure occurs with a reduced separation of the two monomers, significant FC activity is predicted in low frequency intermolecular modes.

]]> Lloyd Muzangwa et al. On the Electronic Spectroscopy of the Iso-Polyhalomethanes http://epublications.marquette.edu/chem_fac/219 http://epublications.marquette.edu/chem_fac/219 Fri, 18 Jan 2013 10:30:12 PST The iso-polyhalomethanes are important reactive intermediates, displaying intense near-UV absorption bands that have been assigned to the S0 → S3 transition on the basis of Time-Dependent Density Functional Theory (TDDFT) calculations. In this work, theory and multi-dimensional Franck–Condon (FC) analysis are used to model the electronic spectra of selected iso-polyhalomethanes. The S0 → S3 transition approximately corresponds to a π–π∗ transition on the halocarbocation subunit, which induces significant geometry changes. The calculated multimode FC profiles capture features of the experimental spectra of the matrix-isolated species, and are compared with the results of previous Resonance Raman studies of the isomers in solution.

]]> Aimable Kalume et al. Chemical Physics Letters http://epublications.marquette.edu/chem_fac/218 http://epublications.marquette.edu/chem_fac/218 Fri, 18 Jan 2013 10:08:34 PST We examine radical mediated pathways in electrophilic addition to the simplest alkene, ethylene, where the structure of the radical intermediate has been extensively debated. Starting from the π-complex with a dihalogen, C2H4⋯I2, isolated in an inert matrix, we initiate reaction by photolytically cleaving the I2 bond. We succeed in trapping and spectroscopically interrogating the symmetrically bridged radical complex, which calculations confirm is the global minimum on the C2H5I Potential Energy Surface (PES). Consistent with the participation of a bridged intermediate, radical addition preferentially but not exclusively yields the anti-stereoisomer of the 1,2-diiodoethane product.

]]> Lisa George et al. Spectroscopic and Computational Studies of Matrix-Isolated iso-CXBr3 (X=F,Cl,Br): Structure, Properties, and Photochemistry of Substituted Iso-Tribromomethanes http://epublications.marquette.edu/chem_fac/217 http://epublications.marquette.edu/chem_fac/217 Fri, 18 Jan 2013 09:40:28 PST Iso-polyhalomethanes are important reactive intermediates in the condensed and gas-phase chemistry of halomethanes. Building upon our recent study of iso-bromoform, in this work the substituted iso-tribromomethanes (iso-CXBr3; X = F, Cl, Br) were characterized by matrix isolation infrared and UV/Vis spectroscopy, supported by ab initio calculations, to further probe the structure, spectroscopy, properties, and photochemistry of these important intermediates. Selected wavelength laser irradiation of CXBr3 samples in an inert rare gas (typically Ar; mixing ratio 1:500) held at ∼5 K yielded iso-CXBr3 (XBrC–Br–Br or Br2C–Br–X). The observed infrared and UV/Vis absorptions are in excellent agreement with computational predictions, and the energies of various stationary points on the CXBr3 Potential Energy Surfaces (PESs) were characterized computationally using DFT, MP2, and CCSD (T) methods in combination with triple-zeta quality basis sets. These calculations show that the isomers are minima on the PESs that lie ∼200 kJ/mol above the global CXBr3 minimum, yet are bound by some 50–70 kJ/mol in the gas-phase with respect to the CXBr2 + Br asymptote. Laser irradiation of the isomers resulted in back photoisomerization to CXBr3, and intrinsic reaction coordinate (IRC) calculations confirmed the existence of a first order saddle point connecting the two isomers. Calculations of important stationary points on the CXBr3 PESs show that in the gas-phase the isomerization barrier lies energetically near the threshold for simple bond fission. The iso-CXBr3 species are significantly stabilized in the condensed phase, due to the high degree of ion-pair character, as revealed by Natural Resonance Theory analysis.

]]> Lisa George et al. Spectroscopy and Dynamics of the Predissociated, Quasi-linear S2 State of Chlorocarbene http://epublications.marquette.edu/chem_fac/216 http://epublications.marquette.edu/chem_fac/216 Fri, 18 Jan 2013 08:58:04 PST In this work, we report on the spectroscopy and dynamics of the quasi-linear S2 state of chlorocarbene, CHCl, and its deuterated isotopologue using optical-optical double resonance (OODR) spectroscopy through selected rovibronic levels of the S1 state. This study, which represents the first observation of the S2 state in CHCl, builds upon our recent examination of the corresponding state in CHF, where pronounced mode specificity was observed in the dynamics, with predissociation rates larger for levels containing bending excitation. In the present work, a total of 14 S2 state vibrational levels with angular momentum ℓ = 1 were observed for CHCl, and 34 levels for CDCl. The range of ℓ in this case was restricted by the pronounced Renner-Teller effect in the low-lying S1 levels, which severely reduces the fluorescence lifetime for levels with Ka > 0. Nonetheless, by exploiting different intermediate S1 levels, we observed progressions involving all three fundamental vibrations. For levels with long predissociation lifetimes, rotational constants were determined by measuring spectra through different intermediate J levels of the S1 state. Plots of the predissociation linewidth (lifetime) vs. energy for various S2 levels show an abrupt onset, which lies near the calculated threshold for elimination to form C(3P) + HCl on the triplet surface. Our experimental results are compared with a series of high level ab initio calculations, which included the use of a dynamically weighted full-valence CASSCF procedure, focusing maximum weight on the state of interest (the singlet and triplet states were computed separately). This was used as the reference for subsequent Davidson-corrected MRCI(+Q) calculations. These calculations reveal the presence of multiple conical intersections in the singlet manifold.

]]> Chong Tao et al. On the Electronic Spectroscopy of Closed Shell Cations Derived From Resonance Stabilized Radicals: Insights From Theory and Franck-Condon Analysis http://epublications.marquette.edu/chem_fac/215 http://epublications.marquette.edu/chem_fac/215 Fri, 18 Jan 2013 08:32:46 PST Context. Recent attention has been directed on closed-shell aromatic cations as potential carriers of the diffuse interstellar bands. The spectra of mass-selected, matrix-isolated benzylium, and tropylium cations were recently reported. The visible spectrum of benzylium exhibits a large Franck-Condon (FC) envelope, inconsistent with diffuse interstellar band carriers.

Aims. We perform a computational analysis of the experimentally studied benzylium spectrum before extending the methods to a range of larger, closed-shell aromatic cations to determine the potential for this class of systems as diffuse interstellar band carriers.

Methods. Density functional theory (DFT), time-dependant ((TD)DFT), and multi-configurational self-consistent field second-order perturbation theory (MRPT2) methods in concert with multidimensional FC analysis is used to model the benzylium spectrum. These methods are extended to larger closed-shell aromatic hydrocarbon cations derived from resonance-stabilized radicals, which are predicted to show strong S0 → Sn transitions in the visible region. The ionization energies of a range of these systems are also calculated by DFT.

Results. The simulated benzylium spectrum was found to yield excellent agreement with the experimental spectrum showing an extended progression in a low frequency (510 cm-1) ring distortion mode. The FC progression was found to be significantly quenched in the larger species: 1-indanylium, 1-naphthylmethylium, and fluorenium. Excitation and ionization energies of the closed-shell cations were found to be consistent with diffuse interstellar band carriers, with the former lying in the visible range and the latter straddling the Lyman limit in the 13−14 eV range.

Conclusions. Large closed-shell polycyclic aromatic hydrocarbon cations remain viable candidate carriers of the diffuse interstellar bands.

]]> T. P. Troy et al. Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues http://epublications.marquette.edu/chem_fac/214 http://epublications.marquette.edu/chem_fac/214 Tue, 15 Jan 2013 14:49:24 PST Conformational flexibility between structural ensembles is an essential component of enzyme function. Although the broad dynamical landscape of proteins is known to promote a number of functional events on multiple time scales, it is yet unknown whether structural and functional enzyme homologues rely on the same concerted residue motions to perform their catalytic function. It is hypothesized that networks of contiguous and flexible residue motions occurring on the biologically relevant millisecond time scale evolved to promote and/or preserve optimal enzyme catalysis. In this study, we use a combination of NMR relaxation dispersion, model-free analysis, and ligand titration experiments to successfully capture and compare the role of conformational flexibility between two structural homologues of the pancreatic ribonuclease family: RNase A and eosinophil cationic protein (or RNase 3). In addition to conserving the same catalytic residues and structural fold, both homologues show similar yet functionally distinct clusters of millisecond dynamics, suggesting that conformational flexibility can be conserved among analogous protein folds displaying low sequence identity. Our work shows that the reduced conformational flexibility of eosinophil cationic protein can be dynamically and functionally reproduced in the RNase A scaffold upon creation of a chimeric hybrid between the two proteins. These results support the hypothesis that conformational flexibility is partly required for catalytic function in homologous enzyme folds, further highlighting the importance of dynamic residue sectors in the structural organization of proteins.

]]> Donald Gagné et al. Photochemistry of Furyl- and Thienyldiazomethanes: Spectroscopic Characterization of Triplet 3-Thienylcarbene http://epublications.marquette.edu/chem_fac/213 http://epublications.marquette.edu/chem_fac/213 Mon, 07 Jan 2013 13:19:33 PST Photolysis (λ > 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N2 at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm–1, |E/hc| = 0.0554 cm–1; |D/hc| = 0.579 cm–1, |E/hc| = 0.0315 cm–1). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon—an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λmax = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C5H4S or C5H4O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively).

]]> Caroline R. Pharr et al. Surface Modification of Polyamide-6: Graft Copolymerization of Vinyl Monomers onto Polyamide-6 and Thermal Analysis of the Graft Copolymers http://epublications.marquette.edu/chem_fac/212 http://epublications.marquette.edu/chem_fac/212 Fri, 04 Jan 2013 10:25:15 PST Graft copolymerization of vinyl monomers onto polyamide-6 using radical initiation has been investigated. Two monomers were used: methacrylic acid and acrylic acid. The initiators selected included hydrogen peroxide, benzoyl peroxide and azobisisobutyronitrile. The extent of graft copolymerization depends on the concentrations and identity of the initiator and monomer and the time and temperature of the reaction. The graft copolymers were not soluble in solvents that will dissolve the starting material; definitive proof for the formation of the graft copolymers was obtained from infrared spectroscopy. Thermogravimetric analysis was performed on the graft copolymers and it was found that the presence of the acid invariably accelerated the degradation of the polyamide. © 1998 John Wiley & Sons, Ltd.

]]> Nicole M. Langer et al. The influence of α-zirconium phosphate on fire performance of EVA and PS composites http://epublications.marquette.edu/chem_fac/211 http://epublications.marquette.edu/chem_fac/211 Fri, 04 Jan 2013 10:12:00 PST Composites of polystyrene (PS) and poly(ethylene-co-vinyl acetate) (EVA) with organically modified zirconium phosphate (OZrP) were prepared by melt blending. Their morphologies were assessed by X-ray diffraction and transmission electron microscopy, while the thermal stability and flammability properties were characterized by thermogravimetric analysis and cone calorimetry. Increasing the OZrP content was not conducive to the formation of a nanostructure in EVA and poor dispersion of zirconium phosphate layers in PS at the nanometer level was observed. Increased thermal stability at high temperature and a slight reduction in peak heat release rate were found when OZrP was added to PS, while in EVA, deteriorated thermal stability and flame retardancy were observed. Unlike montmorillonite, the partial replacement of intumescent flame retardants (IFR) by 2% OZrP imparted a negative effect on the flammability of the EVA/IFR (23%)/OZrP (2%) composite, increasing the peak heat release rate of EVA/IFR (25%). The PS/IFR (18%)/OZrP (2%) composite with poly(styrene-co-maleic anhydride) (SMA) as compatibilizer exhibited better flame retardancy than PS/SMA/IFR (20%), prolonging the combustion process and increasing the time to peak heat release rate significantly. Copyright © 2011 John Wiley & Sons, Ltd.

]]> Hongdian Lu et al. Fire Properties of Polymer Nanocomposites http://epublications.marquette.edu/chem_fac/210 http://epublications.marquette.edu/chem_fac/210 Tue, 24 Apr 2012 10:26:08 PDT Charles Wilkie Char Formation http://epublications.marquette.edu/chem_fac/209 http://epublications.marquette.edu/chem_fac/209 Fri, 13 Apr 2012 12:13:25 PDT Sergei V. Levchik et al. Recent Studies on Thermal Stability and Flame Retardancy of Polystyrene-Nanocomposites http://epublications.marquette.edu/chem_fac/208 http://epublications.marquette.edu/chem_fac/208 Thu, 12 Apr 2012 10:50:26 PDT Nanocomposites of polystyrene with both organically-modified clays and with graphite have been prepared. For both of these materials, which will impart nanometer dimension to the polymer, the thermal stability of the polymer, as measured by thermogravimetric analysis and Cone calorimetry, is enhanced. A synergistic combination of a clay nanocomposite with resorcinol diphosphate has also been studied.

]]> Jin Zhu et al. Cross-Linking of Polystyrene by Friedel-Crafts Chemistry: A Review http://epublications.marquette.edu/chem_fac/207 http://epublications.marquette.edu/chem_fac/207 Tue, 10 Apr 2012 11:38:48 PDT The cross-linking of polystyrene by Friedel-Crafts chemistry is briefly reviewed. The focus has been on producing a cross-linked structure which will char and provide thermal protection to the underlying polymer. The mechanism and kinetics of cross-linking along with the identity and activity of the functional groups have been of interest. The key parameter is the cross-linking temperature, control of which could be achieved through the choice of functional groups, catalysts, and inhibitors. The utilization of Friedel-Crafts chemistry to promote thermal stabilization and flame retardancy for styrenic polymers has been the intent of this study.

]]> Hongyang Yao et al. Practical Issues and Future Trends in Polymer Nanocomposite Flammability Research http://epublications.marquette.edu/chem_fac/206 http://epublications.marquette.edu/chem_fac/206 Wed, 14 Mar 2012 14:38:03 PDT This chapter will focus on practical issues associated with flame retardant polymer nanocomposite research and fabrication and discuss future trends for this field of research. The topics of polymer nanocomposite design, synthesis, characterization, and commercialization will be covered. This will include known issues that directly affect polymer nanocomposite design as well as ancillary issues, such as regulatory factors, that can have effects on the practical success of a polymer nanocomposite for flammability applications. For future trends the gaps of fundamental knowledge are indicated so that researchers will know how to focus their efforts. Finally, we will give our opinions on where the field of polymer nanocomposite flammability is most likely headed in the next 10 years, including efforts towards true multi-functional materials.

]]> Alexander B. Morgan et al. Intercalation Compounds and Clay Nanocomposites http://epublications.marquette.edu/chem_fac/205 http://epublications.marquette.edu/chem_fac/205 Mon, 05 Mar 2012 11:32:21 PST This chapter contains sections titled:

  • Introduction

  • Polymer Lamellar Material Nanocomposites

    • Types of Lamellar Nano-additives

    • Montmorillonite Layer Structure

    • Modification of Clay

  • Nanostructures and Characterization

    • X-ray Diffraction and Transmission Electron Microscopy to Probe Morphology

    • Other Techniques to Probe Morphology

  • Preparation of Polymer-clay Nanocomposites

    • Solution Mixing

    • Polymerization

    • Melt Compounding

  • Polymer-graphite and Polymer Layered Double Hydroxide Nanocomposites

    • Nanocomposites Based on Layered Double Hydroxides and Salts

  • Properties of Polymer Nanocomposites

  • Potential Applications

  • Conclusion and Prospects for the Future

]]> Jin Zhu et al.