Scientific Publications 2006
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2006. "Homonuclear and Heteronuclear NMR Studies of a Statherin Fragment Bound toHydroxyapatite Crystals." Journal of Physical Chemistry B 110(18):9324-9332. doi:10.1021/jp056644g Abstract Acidic proteins found in mineralized tissues act as nature’s crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), Ca10(PO4)6(OH)2, the main mineral component of bone and teeth. Key to understanding the structural basis of protein-crystal recognition and protein control of hard tissue growth is the nature of interactions between the protein side chains and the crystal surface. In an earlier work we have measured the proximity of the lysine (K6) side chain in an SN-15 peptide fragment of the salivary protein statherin adsorbed to the Phosphorus-rich surface of HAP using solid-state NMR recoupling experiments. 15N{31P} rotational echo double resonance (REDOR) NMR data on the side-chain nitrogen in K6 gave rise to three different models of protein-surface interaction to explain the experimental data acquired. In this work we extend the analysis of the REDOR data by examining the contribution of interactions between surface phosphorus atoms to the observed 15N REDOR decay. We performed 31P-31P recoupling experiments in HAP and (NH4)2HPO4 (DHP) to explore the nature of dipolar coupled 31P spin networks. These studies indicate that extensive networks of dipolar coupled 31P spins can be represented as stronger effective dipolar couplings, the existence of which must be included in the analysis of REDOR data. We carried out 15N{31P} REDOR in the case of DHP to determine how the size of the dephasing spin network influences the interpretation of the REDOR data. Although use of an extended 31P coupled spin network simulates the REDOR data well, a simplified 31P dephasing system composed of two spins with a larger dipolar coupling also simulates the REDOR data and only perturbs the heteronuclear couplings very slightly. The 31P-31P dipolar couplings between phosphorus nuclei in HAP can be replaced by an effective dipolar interaction of 600 Hz between two 31P spins. We incorporated this coupling and applied the above approach to reanalyze the 15N{31P} REDOR of the lysine side chain approaching the HAP surface and have refined the binding models proposed earlier. We obtain 15N-31P distances between 3.3 and 5 Å from these models that are indicative of the possibility of a lysine-phosphate hydrogen bond.
2006. "New Experimental and Theoretical Approach to the Heterogeneous Hydrolysis of NO2: Key Role of Molecular Nitric Acid and Its Complexes." Journal of Physical Chemistry A 110(21):6886-6897. doi:10.1021/jp056426n Abstract Although heterogeneous chemistry on surfaces in the troposphere is known to be important, there currently only a few techniques available for studying the nature of surface-adsorbed species as well as their chemistry and photochemistry under atmospheric conditions of 1 atm pressure and in the presence of water vapor. We report here a new laboratory approach using a combination of long path FTIR to identify gases and attenuated total reflectance (ATR)-FTIR that allows the simultaneous observation and quantification of gases and surface species. Theory is used to identify the surface-adsorbed intermediates and products, and to quantify their relative concentrations. At intermediate relative humidities typical of the tropospheric boundary layer, the nitric acid formed in the NO2 heterogeneous hydrolysis is shown to exist as both nitrate ions from the dissociation of nitric acid formed on the surface, and as molecular nitric acid. In both cases, the ions and HNO3 are complexed to water molecules. Upon pumping, water is selectively removed, shifting the NO3- - HNO3(H2O)y equilibria towards more dehydrated forms of HNO3. Photolysis of the nitric acid-water film using 300 - 400 nm radiation generates gaseous NO, while photolysis at 254 nm generates both NO and HONO, resulting in conversion of surface-adsorbed nitrogen oxides into photochemically active NOx. This suggests that the assumption that deposition or formation of nitric acid provides a permanent removal mechanism from the atmosphere may not be correct. Furthermore, a potential role of surface-adsorbed nitric acid and other species formed during the heterogeneous hydrolysis of NO2 on the oxidation of organics on surfaces, and on the generation of gas phase HONO on local to global scales, should be considered.
2006. "Electrostatics of DNA-DNA Juxtapositions: Consequences for Type II Topoisomerase Function ." Journal of Physics: Conference Series 18(14):S173-S185. doi:10.1088/0953-8984/18/14/S03 Abstract An abstract for this journal article is not available at this time.
2006. "Quantum Tunneling in the Midrange Vibrational Fundamentals of Tropolone." Journal of Physical Chemistry A 110(31):9633-9642. Abstract The Fourier transform infrared spectrum of tropolone(OH) vapor in the 1175-1700 cm-1 region is reported at 0.0025 and 0.10 cm-1 spectral resolutions. The 12 vibrational fundamentals in this region of rapidly rising vibrational state density are dominated by mixtures of the CC, CO, CCH, and COH internal coordinates. Estimates based on the measurement of sharp Q branch peaks are reported for 11 of the spectral doublet component separations DSv =|∆v ± ∆0|, ∆0 = 0.974 cm-1 is the known zero-point splitting, and three a1 modes show tunneling splittings ∆v ≈ ∆0, four b2 modes show splittings ∆v ≈ 0.90∆0, and the remaining four modes show splittings ∆v falling 5-14% from ∆0. Significantly, the splitting for the nominal COH bending mode v8 (a1) is small, that is, 10% from ∆0. Many of the vibrational excited states demonstrate strong anharmonic behavior, but there are only mild perturbations on the tautomerization mechanism driving ∆0. The data suggests, especially for the higher frequency a1 fundamentals, the onset of selective intramolecular vibrational energy redistribution processes that are fast on the time scale of the tautomerization process. These appear to delocalize and smooth out the topographical modifications of the zero-point potential energy surface that are anticipated to follow absorption of the vv photon. Further, the spectra show the propensity for the ∆v splittings of b2 and other complex vibrations to be damped relative to ∆0.
2006. "Pressure-temperature dependence of nanowire formation in the arsenic-sulfur system." Physics and Chemistry of Glasses 47(6):675-680. Abstract Nanowire Formation in Arsenic Trisulfide Brian J. Riley, S.K. Sundaram*, Bradley R. Johnson, Mark Engelhard Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352 * Corresponding author: Phone: 509-373-6665; Fax: 509-376-3108, E-mail: sk.Sundaram@pnl.gov Abstract: Arsenic trisulfide (As2S3) nanowires, nano-droplets, and micro-islands were synthesized on fused silica substrates, using a sublimation-condensation process at reduced pressures (70 mtorr – 70 torr) in a sealed ampoule. Microstructural control of the deposited thin film was achieved by controlling initial pressure, substrate temperature and substrate surface treatment. Microstructures were characterized using scanning electron microscopy (SEM), and energy dispersive spectrometry (EDS). Surface topography and chemistry of the substrates were characterized using x-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). Semi-quantitative image analysis and basic curve-fitting were used to develop empirical models to mathematically describe the variation of microstructure as a function of initial pressure and substrate temperature and map out the regions of different microstructures in P-T space. Thermodyamic properties (available from literature) of this system are also incorporated in this map. Nanowires of an amorphous, transparent in visible-LWIR region, semi-conducting material, like As2S3, provide new opportunities for the development of novel nano-photonic and electronic devices. Additionally, this system provides an excellent opportunity to model (and control) microstructure development from nanometer to micron scales in a physical vapor deposition process, which is of great value to nanoscience and nanotechnology in general.
2006. "The Partial Oxidation of Isobutene and Propene on TiO2(110)." Journal of Catalysis 238(1):111-121. doi:10.1016/j.jcat.2005.11.041 Abstract General techniques for the partial oxidation of alkenes by molecular oxygen are a goal for surface science and catalysis research as they may lead to more efficient and environmentallyfriendly industrial processes. In order to better understand the thermal surface chemistry of metal oxides toward alkene partial oxidation, the interactions of isobutene and propene on TiO2(110) were studied using temperature programmed desorption (TPD). Isobutene was found to adsorb and desorb molecularly below 250 K on the clean surface. With exposure to oxygen (>1000 L) and unknown quantities of water (< 10 L), isobutene monolayers on TiO2(110) react to form products that include methacrolein and isobutanal, as well as a third product that possesses a C4H8O stoichiometry. We tentatively assign this species to 2,2-dimethyloxirane (isobutene oxide). Structural conservation within this family of products points to a common surface intermediate which we propose to result from addition of O from a hydrogen peroxo (HOO) species to the C=C bond of isobutene. This hydrogen peroxo (HOO) species forms from the reaction of physisorbed water and oxygen assisted by partial charge transfer from the TiO2(110) substrate. Initial studies reveal a similar reaction pathway for the partial oxidation of propene on TiO2(110), yielding acetone and propanal. This work suggests that TiO2 surface sites on supported Au/TiO2 catalysts are active for partial oxidation of alkenes.
2006. "NMR Studies of Ligand Binding to P450eryF Provides Insight into the Mechanism of Cooperativity." Biochemistry 45(6):1673-1684. Abstract Cytochrome P450’s (P450’s) catalyze the oxidative metabolism of most drugs and toxins. Although extensive studies have proven that some P450’s demonstrate both homotropic and heterotropic cooperativity toward a number of substrates, the mechanistic and molecular details of P450 allostery are still not well-established. Here, we use UV/vis and heteronuclear nuclear magnetic resonance (NMR) spectroscopic techniques to study the mechanism and thermodynamics of the binding of two 9-aminophenanthrene (9-AP) and testosterone (TST) molecules to the erythromycin-metabolizing bacterial P450eryF. UV/vis absorbance spectra of P450eryF demonstrated that binding occurs with apparent negative homotropic cooperativity for TST and positive homotropic cooperativity for 9-AP with Hill-equation-derived dissociation constants of KS ) 4 and 200 íM, respectively. The broadening and shifting observed in the 2D-{1H,15N}-HSQC-monitored titrations of 15N-Phe-labeled P450eryF with 9-AP and TST indicated binding on intermediate and fast chemical exhange time scales, respectively, which was consistent with the Hillequation- derived KS values for these two ligands. Regardless of the type of spectral perturbation observed (broadening for 9-AP and shifting for TST), the 15N-Phe NMR resonances most affected were the same in each titration, suggesting that the two ligands “contact” the same phenylalanines within the active site of P450eryF. This finding is in agreement with X-ray crystal structures of bound P450eryF showing different ligands occupying similar active-site niches. Complex spectral behavior was additionally observed for a small collection of resonances in the TST titration, interpreted as multiple binding modes for the lowaffinity TST molecule or multiple TST-bound P450eryF conformational substates. A structural and energetic model is presented that combines the energetics and structural aspects of 9-AP and TST binding derived from these observations.
2006. "Coherent Anti-Stokes Raman Scattering Microscopy: A Biological Review." Cytometry. Part A 69(8):779-791. doi:10.1002/cyto.a.20299 Abstract Microscopic imaging of cells and tissues are generated by the interaction of light with either the sample itself or contrast agents that label the sample. Most contrast agents, however, alter the cell in order to introduce molecular labels, complicating live cell imaging. The interaction of light from multiple laser sources has given rise to microscopy, based on Raman scattering or vibrational resonance, which demonstrates selectivity to specific chemical bonds while cell imaging unmodified live cells. Here, we discuss the nonlinear optical technique of coherent anti-Stokes Raman scattering (CARS) microscopy, its instrumentation, and its status in live cell imaging.
2006. "Catalyst Deactivation and Regeneration in Low Temperature Ethanol Steam Reforming with Rh/CeO2-ZrO2 Catalysts." Catalysis Letters 110(1-2):1-6. Abstract Rh/CeO2-ZrO2 catalysts with various CeO2/ZrO2 ratios have been applied to H2 production from ethanol steam reforming at low temperatures. The catalysts all deactivated with time on stream (TOS) at 350°C. The addition of 0.5% K has a beneficial effect on catalyst stability, while 5% K has a negative effect on catalytic activity. The catalyst could be regenerated considerably even at ambient temperature and could recover its initial activity after regeneration above 200°C with 1% O2. The results are most consistent with catalyst deactivation due to carbonaceous deposition on the catalyst.
2006. "Low Temperature and H2 Selective Catalysts for Ethanol Steam Reforming." Catalysis Letters 108(1-2):15-19. doi:10.1007/s10562-006-0021-2 Abstract Supported Rh catalysts have been developed for selective H2 production at low temperatures. Ethanol dehydration is favorable over either acidic or basic supports such as γ-Al2O3 and MgAl2O4, while ethanol dehydrogenation is more favorable over neutral supports. A series of CeO2-ZrO2 supports with various CeO2/ZrO2 ratios were prepared by a co-precipitation method and Rh was impregnated on the as-synthesized support to achieve a strong metal to support interaction (SMSI). 2%Rh/Ce0.8Zr0.2O2 catalyst exhibited the highest H2 yield at 450oC among the various supported Rh catalysts evaluated in this study. This is mainly due to a favored reaction pathway via ethanol dehydrogenation to form the acetaldehyde intermediate, and both the strong interaction between Rh and Ce0.8Zr0.2O2 and the high oxygen storage capacity of Ce0.8Zr0.2O2 which favors oxidation of acetaldehyde decomposition products
2006. "Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4." Applied and Environmental Microbiology 72(5):3236-3244. doi:10.1128/AEM.72.5.3236-3244.2006 Abstract A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation.
2006. "A Molecular Dynamics Investigation of Hydrolytic Polymerization in a Metal-Hydroxide Gel." Journal of Physical Chemistry B 110(14):7107-7112. doi:10.1021/jp054379t Abstract The early stages of the spontaneous hydrolytic polymerization of an active hydroxide in the anti-bayerite structure are followed by using molecular dynamics simulations. The polymer populations are calculated as a function of reaction progress and compared with a model governed by purely random bonding. In agreement with experimental observations in aqueous solutions, the transformation of singly bridged to doubly bridged metal ions is shown to have a significant autocatalytic component. The overall polymer populations, however, are very close to the predictions of the random bonding model, indicating that local autocatalytic behavior is decoupled from multimer populations at the larger scales. The calculations show that solid-state transformation processes do not preferentially give rise to higher order multimers, and suggest that interfacial processes, involving bulk solution, are required to facilitate rapid transformation to higher order oligomers. Two reaction pathways are identified for the dewatering of u-H3O2 bridges into u-OH bridges. Both are activated primarily by undercoordination of one of the metals centers involved in the bridge.
2006. "A Molecular Dynamics Investigation of the Titration of a TrivalentAqueous Ion." Theoretical Chemistry Accounts 115(2):136-144. doi:10.1007/s00214-005-0048-2 Abstract We carried out a series of molecular dynamics simulations of the hydrolysis of a model trivalent metal ion in aqueous solution. We use a dissociative model for water and examine the spontaneous speciation of M3+ into M(OH)n(3−n)+(n = 1, 4) both in neutral solution and as a function of added protons and hydroxide ions. The species distributions in neutral solution correspond reasonably well with those expected for real trivalent metal ions at neutral pH. However, the change in the species distributions as a function of either added protons or hydroxide ions is much less than expected with very large concentrations of protons or hydroxide ions required to shift the species equilibria in either direction. The influence of added protons and hydroxide ions on the species distributions appears to be proportional to the average charge of the hydrolysis couples, being highest for the 3+/2+ couple and lowest for the 1+/0 and 0/1- couples. Proton exchange rates varywith proton/hydroxide ion concentration giving a minimum at intermediate values ([H+]≈ 0.166) with increasing rates at both lower and higher pH
