Scientific Publications 2007
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
L
2007. "Electron-Stimulated Oxidation of Thin Water Films Adsorbed on TiO2(110)." Journal of Physical Chemistry C 111(44):16319-16329. doi:10.1021/jp072479o Abstract Electron-stimulated reactions in thin (< 3 monolayer, ML) water films adsorbed on TiO2(110) are investigated. For electron fluences less than ~1×1016 e-/cm2, irradiation with 100 eV electrons results in electron-stimulated desorption (ESD) of atomic and molecular hydrogen, but no measurable O2. The ESD leaves adsorbed hydroxyls which oxidize the TiO2(110) surface and change the post-irradiation TPD spectra of the remaining water in characteristic ways. The species remaining on the TiO2(110) after irradiation of adsorbed water films are apparently similar to those produced without irradiation by co-dosing water and O2. Annealing above ~600 K reduces the oxidized surfaces, and water TPD spectra characteristic of ion sputtered and annealed TiO2(110) are recovered. The rate of electron-stimulated “oxidation” of the water films is proportional to the coverage of water in the first layer for coverages less than 1 ML. However, higher coverages suppress this reaction. When thin water films are irradiated, the rate of electron-stimulated oxidation is independent of the initial oxygen vacancy concentration, as is the final oxidized state achieved at high electron fluences. To explain the results, we propose that electron excitation of water molecules adsorbed on Ti4+ sites leads to desorption of hydrogen atoms and leaves an OH adsorbed at the site. If hydroxyls are present in the bridging oxygen rows, these react with the OH’s on the Ti4+ sites to reform water and heal the oxygen vacancy associated with the bridging OH. Once the bridge bonded hydroxyls have been eliminated, further irradiation increases the concentration of OH’s in the Ti4+ rows leading to the creation of species which block sites in the Ti4+ rows, perhaps H2O2 and/or HO2.
2007. "Site-Dependent Electron-Stimulated Reactions in Water Films on TiO2(110)." Journal of Chemical Physics 127(22):Art. No. 224706. Abstract Electron-stimulated reactions in thin (<3 monolayer, ML) water films adsorbed on TiO2(110) are investigated. Irradiation with 100 eV electrons results in electron-stimulated dissociation and electron-stimulated desorption (ESD) of adsorbed water molecules. The ESD yield for water molecules adsorbed on the bridging oxygen rows, H2OBBO, is 4-5 times greater than the ESD yield for water adsorbed on Ti4+ sites, H2OTi. In contrast, the probability for electron-stimulated dissociation of adsorbed water is comparable for both H2OTi and H2OBBO. The total electron-stimulated sputtering rate is larger for coverages greater than 1 ML due to the increased water ESD for those coverages. The water ESD yields versus electron energy (for 5 – 50 eV) are qualitatively similar for 1, 2 and 40 ML water films. In each case, the observed ESD threshold is at ~10 eV and the yield increases monotonically with increasing electron energy. The results indicate that excitations in the adsorbed water layer are primarily responsible for the ESD in thin water films on TiO2(110). Experiments on “isotopically layered” films with D2OTi and H2OBBO demonstrate that increasing the water coverage above 1 ML rapidly suppresses the electron-stimulated desorption of D2OTi and D atoms, despite the fact that the total water ESD and atomic hydrogen ESD yields increase with increasing coverage. The coverage dependence of the electron-stimulated reactions is probably related to the different bonding geometries for H2OTi and H2OBBO and its influence on the desorption probability of the reaction products.
2007. "Is Dissociation of Peptide Radical Cations an Ergodic Process?" Journal of the American Chemical Society 129(31):9598-9599. Abstract Achieving a fundamental understanding of the mechanism of unimolecular dissociation of internally excited complex molecules is one of the most important challenges in modern mass spectrometry. One of the central questions is whether the dissociation of large molecules is properly described by statistical theories—RRKM/QET or Phase Space Theories —that have proved to be remarkably successful both for small molecules and a number of small and medium size peptides. The concept question is whether the ergodic assumption that the internal excitation of the ion is randomly redistributed among the vibrational degrees of freedom prior to fragmentation is satisfied for large molecules. The validity of the ergodic hypothesis for dissociation of gas-phase biomolecules has been recently reviewed and will be only briefly discussed here.
2007. "Charge Retention by Peptide Ions Soft-Landed onto Self-Assembled Monolayer Surfaces." International Journal of Mass Spectrometry 265(1):237-243. Abstract Soft-landing of singly and doubly protonated peptide ions onto three self-assembled monolayer surfaces (SAMs) was performed using a novel ion deposition instrument constructed in our laboratory and a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially designed for studying collisions of large ions with surfaces.. Modified surfaces were analyzed using in situ 2 keV Cs+ secondary ion mass spectrometry or ex situ 15 keV Ga+ time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results demonstrate that a fraction of multiply protonated peptide ions retain more than one proton following soft-landing on the FSAM surface. [M+2H]2+ ions observed in FT-ICR SIMS spectra are produced by desorption of multiply charged ions from the surface, while re-ionization of singly protonated ions or neutral peptides is a source of [M+2H]2+ ions in Tof-SIMS spectra. Differences in neutralization efficiency of soft-landed ions following exposure of surfaces to laboratory air has a measurable effect on the results of ex situ ToF-SIMS analysis of soft-landed ions on SAM surfaces.
2007. "Charge-Remote Fragmentation of Odd-Electron Peptide Ions." Analytical Chemistry 79(17):6607-6614. doi:10.1021/ac070777b Abstract Comparison between gas-phase fragmentation of odd-electron M+• and [M-2H]-• ions of model peptides reported in this study demonstrates that charge-remote radical-driven fragmentation pathways play an important role in dissociation of odd-electron peptide ions. We found that charge-remote processes are responsible for a variety of side chain losses from the precursor ion and some backbone fragmentation. These fragmentation pathways most likely involve hydrogen abstraction from the β-carbon of the side chain by the radical site that initiates subsequent cleavages. The results reported in this work are generally relevant for understanding of fragmentation patterns of odd-electron peptide ions produced by different approaches including capture of low-energy electrons, electron detachment and electron transfer.
2007. "Theoretical Prediction of the Ionization Energies of the C₄H₇ Radicals:1-Methylallyl, 2-Methylallyl, Cyclopropylmethyl, and Cyclobutyl Radicals." Journal of Chemical Physics 127:154302 1-12. doi:10.1063/1.2774972 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The ionization energies (IEs) for the 1-methylallyl, 2-methylallyl, cyclopropylmethyl, and cyclobutyl radicals have been calculated by the wave function based ab initio CCSD(T)/CBS approach, which involves the approximation to the complete basis set (CBS) limit at the coupled cluster level with single and double excitations plus quasiperturbative triple excitation [CCSD(T)]. The zero-point vibrational energy correction, the core-valence electronic correction, and the scalar relativistic effect correction are included in these calculations. The present CCSD(T)/CBS results are then compared with the IEs determined in the photoelectron experiment by Schultz et al. [J. Am. Chem. Soc. 106, 7336 (1984)] The predicted IE value (7.881 eV) of 2-methylallyl radical is found to compare very favorably with the experimental value of 7.90±0.02 eV. Two ionization transitions for cis-1-methylallyl and trans-1-methylallyl radicals have been considered here. The comparison between the predicted IE values and the previous measurements shows that the photoelectron peak observed by Schultz et al. likely corresponds to the adiabatic ionization transition for the trans-1-methylallyl radical to form trans-1-methylallyl cation. Although a precise IE value for the cyclopropylmethyl radical has not been directly determined, the experimental value deduced indirectly using other known energetic data is found to be in good accord with the present CCSD(T)/ CBS prediction. We expect that the Franck-Condon factor for ionization transition of c-C₄H₇ →bicyclobutonium is much less favorable than that for ionization transition of c-C₄H₇ →planar-C₄H₇ +, and the observed IE in the previous photoelectron experiment is likely due to the ionization transition for c-C₄H₇→planar-C₄H₇ +. Based on our CCSD(T)/CBS prediction, the ionization transition of c-C₄H₇→bicyclobutonium with an IE value around 6.92 eV should be taken as the adiabatic ionization transition for the cyclobutyl radical. The present study provides support for the conclusion that the CCSD(T)/CBS approach with high-level energetic corrections can be used to provide reliable IE predictions for C4 hydrocarbon radicals with an uncertainty of ±22 meV. The CCSD(T)/CBS predictions to the heats of formation for the aforementioned radicals and cations are also presented.
2007. "Biogenic mineral production by a novel arsenic-metabolizing thermophilic bacterium from the Alvord Basin, OR." Applied and Environmental Microbiology 73(18):5928-5936. doi:10.1128/AEM.00371-07 Abstract The Alvord Basin in southeast Oregon, USA contains a variety of hydrothermal features, which have never been microbiologically characterized. Murky Pot (61°C, pH 7.1) was selected for this study. Sampling of Murky Pot led to the isolation of a novel arsenic-metabolizing organism (YeAs), which produces an arsenic sulfide mineral known as beta-realgar, a mineral that has not previously been observed as a product of bacterial arsenic metabolism. Our goal was to characterize and identify YeAs based on its phylogenetic, physiological, and morphological characteristics. 16S rRNA gene analysis revealed that YeAs has 98.9% sequence similarity to that of Thermobrachium celere. YeAs was grown on a freshwater medium and could utilize a variety of organic substrates, particularly carbohydrates and organic acids. Optimum growth of the organism was seen at 55ºC, but showed growth at a range of 37° to 75°C. No growth was observed when YeAs was grown under aerobic conditions. Microscopic examination revealed Gram-indeterminate, non-spore forming, rod shaped cells. Electron microscopy and elemental analysis revealed significant arsenic sulfide mineralization of cell walls, and extracellular particulate deposition of arsenic sulfide minerals. YeAs showed no detectable respiratory arsenate reductase; however, the organism did display significant detoxification arsenate reductase activity. The phylogenetic, physiological, and morphological characteristics of YeAs demonstrate that it is an anaerobic, moderately thermophilic, arsenic-reducing bacterium. This organism and its associated metabolism could have major implications in the search for innovative methods for arsenic waste management and in the search for novel biogenic signatures.
2007. "Pressure Behaviour of the UV and Green Emission Bands in ZnO Micro-rods." Physica Status Solidi B, Basic Research 244(1):87-92. doi:10.1002/pssb.200672545 Abstract The pressure behavior of the ultraviolet (UV) and green emission bands in ZnO tetrapod-like micro-rods has been investigated at 300 and 70 K, respectively. The pressure coefficient of the UV band at 300 K is 24.5 meV/GPa, consistent with that of the band gap of bulk ZnO. However, the pressure coefficient of the green band is 25 meV/GPa, far larger than previous literature reports. The green band in this work comes originates from Cu-related emission, as confirmed by the fine structure observed in the spectra at 10 K. The pressure coefficients of four pho-non replicas of the free exciton emission (FX) at 70 K are 21.0, 20.2, 19.8, and 19.3 meV/GPa, respectively. The energy shift rate of the FX emission and the LO phonon energies is then determined to be 21.4 and 0.55 meV/GPa. The pressure coefficient of the neutral donor bound exciton (D0X) transition is 20.5 meV/GPa, only 4% smaller than that of FX. This confirms that the D0X emission corresponds to excitons bound to neutral shallow donors.
2007. "Combined Vacuum Ultraviolet Laser and Synchrotron Pulsed Field IonizationStudy of CH₂BrCl." Journal of Chemical Physics 126:184304 1-10. doi:10.1063/1.2730829 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The pulsed field ionization-photoelectron (PFI-PE) spectrum of bromochloromethane (CH₂BrCl) in the region of 85 320–88 200 cm−1 has been measured using vacuum ultraviolet laser. The vibrational structure resolved in the PFI-PE spectrum was assigned based on ab initio quantum chemical calculations and Franck-Condon factor predictions. At energies 0–1400 cm⁻1 above the adiabatic ionization energy (IE) of CH₂BrCl, the Br–C–Cl bending vibration progression (Ʋ₁⁺=0–8) of CH₂BrCl⁺ is well resolved and constitutes the major structure in the PFI-PE spectrum, whereas the spectrum at energies 1400–2600 cm−1 above the IE(CH₂BrCl) is found to exhibit complex vibrational features, suggesting perturbation by the low lying excited CH₂BrCl⁺(A²A") state. The assignment of the PFI-PE vibrational bands gives the IE(CH₂BrCl) =85 612.4±2.0 cm−1 (10.6146±0.0003 eV) and the bending frequencies Ʋ₁⁺(a₁')=209.7±2.0 cm−1 for CH₂BrCl⁺(X²A'). We have also examined the dissociative photoionization process, CH₂BrCl+hƲ→CH₂Cl++Br+e−, in the energy range of 11.36–11.57 eV using the synchrotron based PFI-PE-photoion coincidence method, yielding the 0 K threshold or appearance energy AE(CH₂Cl⁺)=11.509±0.002 eV. Combining the 0 K AE(CH₂Cl⁺) and IE(CH₂BrCl) values obtained in this study, together with the known IE(CH₂Cl), we have determined the 0 K bond dissociation energies (D0) for CH₂Cl+–Br (0.894±0.002 eV) and CH₂Cl–Br (2.76±0.01 eV). We have also performed CCSD(T, full)/complete basis set (CBS) calculations with high-level corrections for the predictions of the IE(CH₂BrCl), AE(CH₂Cl+), IE(CH₂Cl), D0(CH₂Cl+–Br), and D0(CH₂Cl–Br). The comparison between the theoretical predictions and experimental determinations indicates that the CCSD(T, full)/CBS calculations with high-level corrections are highly reliable with estimated error limits of <17 meV.
2007. "Isomers and Conformers of H(NH₂BH₂)(n)H Oligomers: Understanding the Geometries and Electronic Structure of Boron-Nitrogen-Hydrogen Compounds as Potential Hydrogen Storage Materials." Journal of Physical Chemistry C 111(8):3294-3299. doi:10.1021/jp066360b Abstract Boron-nitrogen-hydrogen (BNHx) materials are polar analogs of hydrocarbons with potential applications as media for hydrogen storage. As H(NH₂BH₂)nH oligomers result from dehydrogenation of NH₃BH₃ and NH₄BH₄ materials, understanding the geometries, stabilities, and electronic structure of these oligomers is essential for developing chemical methods of hydrogen release and regeneration of the BNHx-based hydrogen storage materials. In this work we have performed computational modeling on the H(NH₂BH₂)nH (n = 1 – 6) oligomers using density functional theory (DFT). We have investigated linear chain structures and the stabilizing effects of coiling, biradicalization, and branching through Car-Parrinello molecular dynamics simulations and geometry optimizations. We find that the zig-zag linear oligomers are unstable with respect to the coiled, square-wave chain, and branched structures, with the coiled structures being the most stable. Dihydrogen bonding in oligomers, where protic Hδ⁺(N) hydrogens interact with hydridic Hδ⁻(B) hydrogens, plays a crucial role in stabilizing different isomers and conformers. The results are consistent with structures of products that are seen in experimental NMR studies of dehydrogenated ammonia borane.
2007. "First-principles study of electronic properties of La2Hf2O7 and Gd2Hf2O7." Journal of Applied Physics 102(6):paper #063704. doi:10.1063/1.2779262 Abstract The structural and electronic properties of A2Hf2O7 (A=La and Gd) pyrochlore compounds are investigated by means of first-principles total energy calculations. Also, the formation energies of defects are calculated, and the results can be used to explain the stability of pyrochlores. Hybridizations between A 5p and O 2s and between A 5d and O 2p states are observed, but the interaction between A 5p and O 2s orbitals is much stronger in Gd2Hf2O7 than that in La2Hf2O7. Gd2Hf2O7 compound shows much different density of state distribution from that of La2Hf2O7. Mulliken overlap population analysis shows that the A-O48f and A-O8b bonds in Gd2Hf2O7 are more ionic than the corresponding bonds in La2Hf2O7, while the Hf-O48f bond in Gd2Hf2O7 is more covalent. These calculations suggest that A-O48f and A-O8b bonds may play important roles in their responses to irradiation-induced amorphization observed experimentally.
2007. "Benchmark Calculations on the Electron Detachment Energies of MO₃⁻ and M₂O₆⁻(M = Cr, Mo, W)." Journal of Physical Chemistry A 111(46):11908-11921. doi:10.1021/jp074768i Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Neutral and anionic molecules of the monomers and dimers of the group VIB transition metal oxides (MO₃ and M₂O₆) were studied with density functional theory (DFT) and coupled cluster CCSD(T) theory. Franck- Condon simulations of the photoelectron spectra were carried out for the transition from the ground state of the anion to that of the neutral molecule. Molecular structures from the DFT and CCSD(T) methods are compared. Electron detachment energies reported in the literature were evaluated. The calculated adiabatic and vertical electron detachment energies (ADEs and VDEs) were compared with the experimental results. CCSD(T) gives results within 0.12 eV for the ADEs. CCSD(T) predicts VDEs that are in error by as much as 0.3 eV for M = Cr. DFT hybrid functionals were found to give poor results for the ADEs and VDEs for M = Cr due to the substantial amount of multireference character in the wavefunction, whereas the pure DFT functionals give superior results. For M = Mo and W, excellent agreement was found for both CCSD(T) and many DFT fucntionals. The BP86 functional yields the best overall results for the VDEs of all the metal oxide clusters considered. Heats of formation calculated at the CCSD(T) level extrapolated to the complete basis set limit are also in good agreement with available experimental data.
2007. "Low-Lying Electronic States of M₃O₉- and M₃O₉²- (M = Mo, W)." Journal of Physical Chemistry 111(38):11093-11099. doi:10.1021/jp074187t Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Multiple low-lying electronic states of M₃O₉- and M₃O₉²- (M = Mo, W) arise from the occupation of the near-degenerate low-lying virtual orbitals in the neutral clusters. We used density functional theory (DFT) and coupled cluster theory (CCSD(T)) with correlation consistent basis sets to study the structures and energetics of the electronic states of these anions. The adiabatic and vertical electron detachment energies (ADEs and VDEs) of the anionic clusters were calculated with 27 exchange-correlation functionals including one local spin density approximation functional, 13 generalized gradient approximation (GGA) functionals, and 13 hybrid GGA functionals, as well as the CCSD(T) method. For Mo₃O₉-, CCSD(T) and nearly all of the DFT exchange-correlation functionals studied predict the 2A1 state arising from the Jahn-Teller distortion due to singly occupying the degenerate e' orbital to be lower in energy than the ²A₁' state arising from singly occupying the nondegenerate a₁' orbital. For W₃O₉-, the ²A₁' state was predicted to have essentially the same energy as the ²A₁' state at the CCSD(T) level with core-valence correlation corrections included and to be higher in energy or essentially isoenergetic with most DFT methods. The calculated VDEs from the CCSD(T) method are in reasonable agreement with the experimental values for both electronic states if estimates for the corrections due to basis set incompleteness are included. For M₃O₉²-, the singlet state arising from doubly occupying the nondegenerate a₁' orbital was predicted to be the most stable state for both M ) Mo and W. However, whereas Mo₃O₉²- was predicted to be less stable than Mo₃O₉-, W₃O₉²- was predicted to be more stable than W₃O₉-.
2007. "Photoelectron Spectroscopy of Adiabatically Bound Valence Anions of RareTautomers of the Nucleic Acid Bases." Journal of Chemical Physics 127(17):Art. 174309. doi:10.1063/1.2795719 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Anionic states of nucleic acid bases (NABs) are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated NAB parent anions probed mostly dipole-bound states, which are not present in condensed phase environments. Recently, we demonstrated that very rare tautomers of uracil (U), cytosine (C), adenine (A), and guanine (G), which are obtained from canonical tautomers through N-to-C proton transfers, support valence anionic states. Here we report the photoelectron spectrum of the final member of the NABs series: the valence state of the thymine (T) anion. Additionally, we summarized the work of all five NABs. All of the newfound anionic tautomers of the NABs may be formed via dissociative electron attachment followed by hydrogen atom reattachment to a carbon atom. Furthermore, these unusual tautomers may affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike dipole bound states, could exist in condensed phases and may be relevant to radiobiological damage.
2007. "Templating Mesoporous Hierarchies in Silica Thin Films Using the Thermal Degradation of Cellulose Nitrate." Microporous and Mesoporous Materials 99(3):308-318. Abstract Materials containing a hierarchical pore structure (i.e. large pores leading to small pores) are highly desirable because they combine the advantages of high surface area with the rapid mass transport. Mesoporous SiO2 with hierarchical pore structure was prepared by a novel dual templating approach using a combination of cellulose nitrate and surfactants as the templates. Both ionic and nonionic surfactants, or mixtures of surfactants, in conjunction with cellulose nitrate were used as the pore templates. Low angle XRD patterns show well-defined pore structures and BET shows surface areas from 500 to over 800m2/g, with tunable bimodal or trimodal pore-size distributions from 18Å to 0.3µm. The hierarchical pore structure can be controlled by manipulating the template composition.
2007. "The Synthesis of Cadmium Doped Mesoporous TiO2." Inorganic Chemistry Communications 10(6):639-641. doi:10.1016/j.inoche.2007.02.018 Abstract Cd doped mesoporous titanium oxide was prepared using non-ionic surfactants and easily handled titanium precursors. The Cd doping was found to be able to significantly inhibit the growth of anatase crystal size, stabilize the mesoporous structure, and retard the densification of nanoporous TiO2 at elevated temperatures.
2007. "Gas-phase Acidities of Aspartic Acid, Glutamic Acid,and their Amino Acid Amides." International Journal of Mass Spectrometry 265(2-3):213-223. doi:10.1016/j.ijms.2007.02.009 Abstract Gas-phase acidities (GA or ∆Gacid) for the two most acidic common amino acids, aspartic acid and glutamic acid, have been determined for the first time. Because of the amide linkage’s importance in peptides and as an aid in studying side chain versus main chain deprotonation, aspartic acid amide and glutamic acid amide were also studied. Experimental GA values were measured by proton transfer reactions in an electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by density functional and molecular orbital theory approaches. The best agreement with experiment was found at the G3MP2 level; the MP2/CBS and B3LYP/aug-cc-pVDZ results are 3–4 kcal/mol more acidic than the G3MP2 results. Experiment shows that aspartic acid is more acidic than glutamic acid by ca. 3 kcal/mol whereas the G3MP2 results show a smaller acidity difference of 0.2 kcal/mol. Similarly, aspartic acid amide is experimentally observed to be ca. 2 kcal/mol more acidic than glutamic acid amide whereas the G3MP2 results show a correspondingly smaller energy difference of 0.7 kcal/mol. The computational results clearly show that the anions are all ring-like structures with strong hydrogen bonds between the OH or NH2 groups and the CO2− group from which the proton is removed. The two amino acids are main-chain deprotonated. In addition, use of the COSMO model for the prediction of the free energy differences in aqueous solution gave values in excellent agreement with the most recent experimental values for pKa. Glutamic acid is predicted to be more acidic than aspartic acid in aqueous solution due to differential solvation effects.
2007. "Effects of Microstructure of Carbon Nanofibers for Amperometric Detection of Hydrogen Peroxide." Analytica Chimica Acta 597(2):238-244. doi:10.1016/j.aca.2007.06.046 Abstract Carbon nanofibers (CNFs) with different microstructures, including platelet-carbon nanofibers (PCNFs), fish-bone-carbon nanofibers (FCNFs), and tube-carbon nanofibers (TCNFs), were synthesized, characterized, and evaluated for electrochemical sensing of hydrogen peroxide. The CNFs studied here can show several microstructures in which various stacked morphologies and their sizes and graphite-layer ordering can be well controlled. Glassy carbon (GC) electrodes modified by CNFs were fabricated and compared for amperometric detection of hydrogen peroxide. Sensors of PCNFs/GC, FCNFs/GC, and TCNFs/GC were used in the amperometric detection of H2O2 in a solution of 0.05 M phosphate buffered saline solution (pH 7.4).
2007. "Dissociation of water buried under ice on Pt(111) ." Physical Review Letters 98(1):Art. No. 016105 . Abstract Water on Pt(111) is generally thought to be non-dissociative. However, by adsorbing a thick ice film (>150 monolayers (ML)), substantial (~0.16 to 1 ML) dissociation of the "buried water" occurs for T > 151K . New temperature-programmed desorption peaks signal the dissociation (after careful isothermal pre-desorption of the overlying ice films). The buried water likely dissociates via the elevated temperatures and/or solvation changes experienced under the ice. Dissociation also creates large work function changes (up to +9V!) due the trapping of ~0.007ML H3O+ at the vacuum-ice interface of the growing ice.
2007. "Reply to Comment on Dissociation of Water Buried Under Ice on Pt(111)." Physical Review Letters 99(10):109602. Abstract [1] on our Letter ‘‘Dissociation of Water Buried under Ice on Pt(111)’’ [2] raises some interesting points. In the original Letter, we made two sets of observations: (1) that thick water films ( > 150 monolayers) absorbed at temperatures higher than usually used in ultrahigh vacuum studies ( > 153 K for H2O) on Pt(111) showed a positive charging that behaved much as would be expected for positive ions trapped on the ice surface during the film growth, and (2) that the thick ice films, when desorbed carefully in a two-step process, showed a consistent pattern of high temperature programmed desorption (TPD) features spanning 170 to 200 K. Based on this, we concluded that water was dissociating at the Pt(111) surface under the thick ice film and in amounts greater than a few tenths of a monolayer. Zimbitas et al. [1] argue that the high temperature peaks can be explained by a nonwetting phenomena that they see for adsorption above 152 K (for H2O), that leads to large water clusters sitting upon a single monolayer of water. Thus, they conclude that our evidence for dissociation of water is weak.
2007. "Magnetic Beads-based Bioelectrochemical Immunoassay of Polycyclic Aromatic Hydrocarbons." Electrochemistry Communications 9(7):1547-1552. doi:10.1016/j.elecom.2007.02.007 Abstract A simple, rapid, and sensitive bioelectrochemical immunoassay method based on magnetic beads (MBs) has been developed to detect polycyclic aromatic hydrocarbons (PAHs). The principle of this bioassay is based on a direct competitive enzyme-linked immunosorbent assay using PAH-antibody-coated MBs and horseradish peroxidase (HRP)-labeled PAH (HRP-PAH). A magnetic process platform was used to mix and shake the samples during the immunoreactions and to separate free and unbound reagents after the liquid-phase competitive immunoreaction among PAH-antibody-coated MBs, PAH analyte, and HRP-PAH. After a complete immunoassay, the HRP tracers attached to MBs were transferred to a substrate solution containing 3, 3´, 5, 5´- tetramethylbenzidine (TMB) and hydrogen peroxide (H2O2) for electrochemical detection. The voltammetric characteristics of the substrate were investigated, and the reduction peak current of TMB was used to quantify the concentration of PAH. The different parameters, including the amount of HRP-PAH conjugates, the enzyme catalytic reaction time, and the pH of the supporting electrolyte that governs the analytical performance of the immunoassay have been studied in detail and optimized. The detection limit of 50 pg mL-1 was obtained under optimum experimental conditions. The performance of this bioelectrochemical magnetic immunoassay was successfully evaluated with tap water spiked with PAHs, indicating that this convenient and sensitive technique offers great promise for decentralized environmental applications.
2007. "Energetics and Dynamics of the Fragmentation Reactions of Protonated Peptides Containing Methionine Sulfoxide or Aspartic Acid via Energy- and Time-Resolved Surface Induced Dissociation." Journal of Physical Chemistry A 111(42):10580-10588. doi:10.1021/jp073040z Abstract The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility on these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (non-mobile proton conditions) to lysine (partially-mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFEC) reveals that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1–2 orders of magnitude lower than non-selective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to non-selective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes are much slower compared to amide bond cleavage, explaining why these selective bond cleavages are not observed if fragmentation is performed under mobile proton conditions. This study further affirms that fragmentation of peptide ions in the gas phase are predominantly governed by entropic effects.
2007. "Modeling the Metal Center of Cys4 Zinc Proteins." Journal of the American Chemical Society 129(29):9192-9200. doi:10.1021/ja071430t Abstract We present here a ⁶⁷Zn solid-state NMR investigation of several model complexes of zinc coordinated by four sulfurs. The lineshapes were obtained at a variety of magnetic fields from 500 to 900 MHz for protons and at ambient temperature down to 10 K. The Cզ’s ranged from 3.25 to 16.7 MHz throughout the series while the average bond distances only spanned 2.34 to 2.36 Å. Reasonable agreement with experiment was achieved in the molecular orbital calculations using DFT methods and the local density approximation to predict electric field gradients.
2007. "An Ion Diffusion Model in Semi-Permeable Clay Materials." Environmental Science and Technology 41(15):5403-5409. doi:10.1021/es0624117 Abstract Ion diffusion in semi-impermeable clay materials dynamically interacts with electrostatic fields (or diffuse double layers) associated with clay particles. Current theory of ion transport in porous media containing fixed charges on solid materials, however, cannot explicitly account for the dynamic interactions. Here we proposed a model by coupling electrodynamics and nonequilibrium thermodynamics to describe ion diffusion in the clay materials. The developed model was validated by comparing the calculated and measured apparent ion diffusion coefficients in clay materials as a function of ionic strength, which affects the overlap extent of the electrostatic double layers associated with adjacent clay particles. The model shows that ion diffusion in clay materials is a complex function of factors including surface charge density, tortuosity, porosity, chemico-osmotic coefficient, and ion self-diffusivity. At transitional states, ion diffusive fluxes are dynamically related to the electrostatic fields, which shrink or expand as ion diffusion. At steady states, the electrostatic fields are time-invariant and ion diffusive fluxes conform to flux and concentration gradient relationships; and apparent diffusivity can be expressed by the ion diffusivity in bulk electrolytes corrected by a tortuosity factor and concentration gradient variations at the interfaces between clay materials and bulk solutions.
2007. "Influence of Calcium on Microbial Reduction of Solid Phase Uranium (VI)." Biotechnology and Bioengineering 97(6):1415-1422. doi:10.1002/bit.21357 Abstract The effect of calcium on microbial reduction of a solid phase U(VI), sodium boltwoodite (NaUO2SiO3OH ∙1.5H2O), was evaluated in a culture of a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. Batch experiments were performed in a non-growth bicarbonate medium with lactate as electron donor at pH 7 buffered with PIPES. Calcium increased both the rate and extent of Na-boltwoodite dissolution by increasing its solubility through the formation of a ternary aqueous calcium-uranyl-carbonate species. The ternary species, however, decreased the rates of microbial reduction of aqueous U(VI). Laser-induced fluorescence spectroscopy (LIFS) and transmission electron microscopy (TEM) revealed that microbial reduction of solid phase U(VI) is a sequentially coupled process of Na-boltwoodite dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) to U(IV) that accumulated on bacterial surfaces/periplasm. The overall rates of microbial reduction of solid phase U(VI) can be described by the coupled rates of dissolution and microbial reduction that were both influenced by calcium. The results demonstrated that dissolved U(VI) concentration during microbial reduction was a complex function of solid phase U(VI) dissolution kinetics, aqueous U(VI) speciation, and microbial activity.
2007. "Electrochemical Quantification of Single Nucleotide Polymorphisms Using Nanoparticle Probes." Journal of the American Chemical Society 129(34):10394-10401. doi:10.1021/ja070429r Abstract We report a new approach for electrochemical quantification of single-nucleotide polymorphisms (SNPs) using nanoparticle probes. The principle is based on DNA polymerase I (klenow fragment)-induced coupling of the nucleotide-modified nanoparticle probe to the mutant sites of duplex DNA under the Watson-Crick base pairing rule. After liquid hybridization events occurred among biotinylated DNA probes, mutant DNA, and complementary DNA, the resulting duplex DNA helixes were captured to the surface of magnetic beads through a biotin-avidin affinity reaction and magnetic separation. A cadmium phosphate-loaded apoferritin nanoparticle probe, which is modified with nucleotides and is complementary to the mutant site, is coupled to the mutant sites of the formed duplex DNA in the presence of DNA polymerase. Subsequent electrochemical stripping analysis of the cadmium component of coupled nanoparticle probes provides a means to quantify the concentration of mutant DNA. The method is sensitive enough to detect 21.5 attomol mutant DNA, which will enable the quantitative analysis of nucleic acid without polymerase chain reaction pre-amplification. The approach was challenged with constructed samples containing mutant and complementary DNA. The results indicated that it was possible to accurately determine SNPs with frequencies as low 0.01. The proposed approach has a great potential for realizing an accurate, sensitive, rapid, and low-cost method of SNP detection.
2007. "Nanomaterial Labels in Electrochemical Immunosensors and Immunoassays." Talanta 74(3):308-317. doi:10.1016/j.talanta.2007.10.014 Abstract This article reviews recent advances in nanomaterial labels in electrochemical immunosensors and immunoassays. Various nanomaterial labels are discussed, including colloidal gold/silver, semiconductor nanoparticles, and markers loaded nanocarriers (carbon nanotubes, apoferritin, silica nanoparticles, and liposome beads). The enormous signal enhancement associated with the use of nanomaterial labels and with the formation of nanomaterial–antibody-antigen assemblies provides the basis for ultrasensitive electrochemical detection of disease-related protein biomarkers, biothreat agents, or infectious agents. In general, all endeavors cited here are geared to achieve one or more of the following goals: signal amplification by several orders of magnitude, lower detection limits, and detecting multiple targets.
2007. "Apoferritin-Templated Synthesis of Encoded Metallic Phosphate Nanoparticle Tags." Analytical Chemistry 79(15):5614-5619. doi:10.1021/ac070086f Abstract Encoded metallic-phosphate nanoparticle tags, with distinct encoding patterns, have been prepared using an apoferritin template. A center-cavity structure as well as the disassociation and reconstructive characteristics of apoferritin at different pH environments provide a facile route for preparing such encoded nanoparticle tags. Encapsulation and diffusion approaches have been investigated during the preparation. The encapsulation approach, which is based on the dissociation and reconstruction of apoferritin at different pHs, exhibits an effective route to prepare such encoded metallic-phosphate nanoparticle tags. The compositionally encoded nanoparticle tag leads to a high coding capacity with a large number of distinguishable voltammetric signals, reflecting the predetermined composition of the metal mixture solution (and hence the nanoparticle composition). Releasing the metal components from the nanoparticle tags at pH 4.6 acetate buffer avoids harsh dissolution conditions, such as strong acids. Such a synthesis of encoded nanoparticle tags, including single-component and compositionally encoded nanoparticle tags, is substantially simple, fast, and convenient compared to that of encoded metal nanowires and semiconductor nanoparticle (CdS, PbS, and ZnS) incorporated polystyrene beads. The encoded metallic-phosphate nanoparticle tags thus show great promise for bioanalytical or product-tracking/identification/protection applications.
2007. "Nanovehicles based Bioassay Labels." Electroanalysis 19(7-8):777-785. doi:10.1002/elan.200603787 Abstract In this article, we review recent advances of our group in nanoparticle labels based bioassay. Apoferritin and silica nanoparticles have been used as nanovehicles to load large amount of markers for highly sensitive bioassay. Markers loaded apoferritin, apoferritin-templated metallic phosphate nanoparticles, and poly [guanine] coated silica nanoparticles have been prepared, characterized and used as labels for highly sensitive bioassay of protein and DNA. Dissociation and reconstitution characteristics at different pH as well as the special cavity structure of apoferritin nanovehicle provides a simple and convenient route to prepare versatile nanoparticle labels and avoid the complicated and tedious synthesis process of conventional nanoparticle labels. The optical and electrochemical characteristics of the prepared nanoparticle labels are easily controlled by loading different optical or electrochemical markers. Additionally, the use of apoferritin nanovehicle as template for synthesis of metallic phosphate nanoparticle labels offers fast route to prepare uniform-size metallic nanoparticle labels for electrochemical bioassay and avoids the traditional harsh dissolution conditions to dissolve metallic nanoparticle tags (that is, the strong-acid dissolution of quantum dots and gold nanoparticles) during the stripping analysis step. Silica nanoparticle has also been used as nanovehicle to carry thousands of poly [guanine] tracers, which was used to enhance the oxidation current of Ru(bpy)32+, resulting in enhanced sensitivity of electrochemical immunoassay. The new nanovehicle-based labels have been used for highly sensitive electrochemical detection of DNA and protein biomarkers, such as tumor necrosis factor-alpha (TNF-a). The high sensitivity and selectivity make these labels a useful addition to the armory of nanoparticle-based bioassay. The new nanovehicles based labels hold great promise for multiplex protein and DNA detection and for enhancing the sensitivity of other bioassays.
2007. "Disposable Electrochemical Immunosensor Diagnosis Device Based on Nanoparticle Probe and Immunochromatographic Strip." Analytical Chemistry 79(20):7644-7653. doi:10.1021/ac070691i Abstract We describe a disposable electrochemical immunosensor diagnosis device that is based on the immunochromatographic strip technique and an electrochemical immunoassay based on quantum dot (QD, CdS@ZnS) labels. The device takes advantage of the speed and low-cost of the conventional immunochromatographic strip test and the high-sensitivity of the nanoparticle-based electrochemical immunoassay. A sandwich immunoreaction was performed on the immunochromatographic strip, and the captured QD labels in the test zone were determined by highly sensitive stripping voltammetric measurement of the dissolved metallic component (cadmium) with a disposable-screen-printed electrode, which is embedded underneath the membrane on the test zone. The new device coupled with a portable electrochemical analyzer shows great promise for in-field and point-of-care quantitative testing of disease-related protein biomarkers. The parameters (e.g., voltammetric measurement of QD labels, antibody immobilization, the loading amount of QD-antibody, and the immunoreaction time) that govern the sensitivity and reproducibility of the device were optimized with IgG model analyte. The voltammetric response of the optimized device is highly linear over the range of 0.1 to 10 ng mL-1 IgG, and the limit of detection is estimated to be 30 pg mL-1 in association with a 7-min immunoreaction time. The detection limit was improved to 10 pg mL-1 using a 20-min immunoreaction time. The new disposable electrochemical diagnosis device thus provides a more user-friendly, rapid, clinically accurate, less expensive, and quantitative tool for protein detection.
2007. "Accurate Mass Measurements in Proteomics." Chemical Reviews 107(8):3621-3653. doi:10.1021/cr068288j Abstract To understand different aspects of life at the molecular level, one would think that ideally all components of specific processes should be individually isolated and studied in details. Reductionist approaches, i.e., studying one biological event at a one-gene or one-protein-at-a-time basis, indeed have made significant contributions to our understanding of many basic facts of biology. However, these individual “building blocks” can not be visualized as a comprehensive “model” of the life of cells, tissues, and organisms, without using more integrative approaches.1,2 For example, the emerging field of “systems biology” aims to quantify all of the components of a biological system to assess their interactions and to integrate diverse types of information obtainable from this system into models that could explain and predict behaviors.3-6 Recent breakthroughs in genomics, proteomics, and bioinformatics are making this daunting task a reality.7-14 Proteomics, the systematic study of the entire complement of proteins expressed by an organism, tissue, or cell under a specific set of conditions at a specific time (i.e., the proteome), has become an essential enabling component of systems biology. While the genome of an organism may be considered static over short timescales, the expression of that genome as the actual gene products (i.e., mRNAs and proteins) is a dynamic event that is constantly changing due to the influence of environmental and physiological conditions. Exclusive monitoring of the transcriptomes can be carried out using high-throughput cDNA microarray analysis,15-17 however the measured mRNA levels do not necessarily correlate strongly with the corresponding abundances of proteins,18-20 The actual amount of functional proteins can be altered significantly and become independent of mRNA levels as a result of post-translational modifications (PTMs),21 alternative splicing,22,23 and protein turnover.24,25 Moreover, the functions of expressed proteins can also be extensively modified by PTMs26-31 or by their interactions with other biomolecules or small molecules.32,33 Thus, it is highly desirable that proteins, the primary functional macromolecules involved in almost all biological activities, can be studied directly and systematically to determine their diverse properties and interplay. Such proteome-wide analysis is expected to provide a wealth of biological information, such as sequence, quantity, PTMs, interactions, activities, subcellular distribution and structure of proteins, which is critical to the comprehensive understanding of the biological systems. However, the de novo analysis of proteins isolated from cells, tissues or bodily fluids poses significant challenges due to the tremendous complexity and depth of the proteome, which necessitates high-throughput and highly sensitive analytical techniques. It is therefore not surprising that mass spectrometry (MS) has become an indispensable technology for proteome analysis.
2007. "Kinetic Study of Heterogeneous Reaction of Deliquesced NaCI Particles with Gaseous HNO3 Using Particle-on-Substrate Stagnation Flow Reactor Approach." Journal of Physical Chemistry A 111(40):10026-10043. doi:10.1021/jp072005p Abstract Heterogeneous reaction kinetics of gaseous nitric acid with deliquesced sodium chloride particles were investigated with a novel Particle-on-Substrate Stagnation Flow Reactor (PS-SFR) approach under conditions, including particle size, relative humidity and reaction time, directly relevant to the atmospheric chemistry of sea salt particles. Particles deposited onto an electron microscopy grid substrate were exposed to the reacting gas at atmospheric pressure and room temperature by impingement via a stagnation flow inside the reactor. The reactor design and choice of flow parameters were guided by computational fluid dynamics results to ensure uniformity of the diffusion flux to all particles undergoing reaction. The chloride depletion in the particles was followed by computer-controlled scanning electron microscopy with energy-dispersive X-ray analysis (CCSEM/EDX). The validity of the current approach was examined first by conducting experiments with median dry particle diameter = 0.82 μm, 80% relative humidity, particle loading densities 4×104 ≤ Ns ≤ 7×106 cm–2 and free stream HNO3 concentrations 2, 7 and 22 ppb. Upon deliquescence the droplet diameter approximately doubles. The apparent, pseudo first-order rate constant determined in these experiments varied with particle loading and HNO3 concentration in a manner consistent with a diffusion-kinetic analysis reported earlier (Laskin, A.; Wang, H.; Robertson, W. H.; Cowin, J. P.; Ezell, M. J.; Finlayson-Pitts, B. J. J. Phys. Chem. A 2006, 110, 10619). The intrinsic, second-order rate constant was obtained as kII = 5.7×10–15 cm3molecule–1s–1 in the limit of zero particle loading and by assuming that the substrate is inert to HNO3. Under this loading condition the experimental, net reaction uptake coefficient was found to be γnet = 0.11 with an uncertainty factor of 3. Additional experiments examined the variations of HNO3 uptake on pure NaCl, a sea salt-like mixture of NaCl and MgCl2 (Mg-to-Cl molar ratio of 0.114) and real sea salt particles as a function of relative humidity. Results show behavior of the uptake coefficient to be similar for all three types of salt particles with ~ 0.9 μm over the relative humidity range of 20-80%. Well over 0.2 for sea salt. Below the efflorescence relative humidity the uptake coefficient rapidly declines with decreasing RH for all three sea salt types, and it does so without exhibiting a sudden shutoff of reactivity. The uptake of HNO, and uptake on both sea salt and sea salt-like mixture was faster than on pure NaCl. The uptake of HNOon pure NaCl particles was also examined over the particle size range of 0.57 ≤ ≤ 1.7 μm (1.1 ≤ Gaseous HNO3 uptake coefficient peaks around a relative humidity of 55%, with γnet 3 on sea salt particles was more rapid than that on the mixture of NaCl and MgCl23 ≤ 3.4 μm) under a constant relative humidity of 80%. The uptake coefficient decreases monotonically with an increase in particle size. Application of a resistance model of reaction kinetics and reactant diffusion over a single particle suggests that, over the range of particle size studied, the uptake is largely controlled by gaseous reactant diffusion from the free stream to the particle surface. In addition, a combined consideration of uptake coefficients obtained in the present study and those previously reported for substantially smaller droplets (~ 0.1 μm) (Saul, T. D.; Tolocka, M. P.; Johnston, M. V. J. Phys. Chem. A 2006, 110, 7614) suggests that the peak reactivity occurs at a droplet diameter of ~0.7 μm, which is immediately below the size at which sea salt aerosols begin to notably contribute to light scattering.
2007. "Direct Dynamics Trajectory Study of F− + CH3OOH Reactive Collisions Reveals a Major Non-IRC Reaction Path." Journal of the American Chemical Society 129(32):9976-9985. Abstract A direct dynamics simulation at the B3LYP/6-311+G(d,p) level of theory was used to study the reaction dynamics of F− + CH3OOH collisions. The results of the simulations are in excellent agreement with a previous experimental study (J. Am. Chem. Soc. 2002, 124, 3196). Two product channels, HF + CH2O + OH− and HF + CH3 OO−, are observed. The former dominates and occurs via an ECO2 mechanism in which F− attacks the CH3− group, abstracting a proton. Concertedly, a carbon-oxygen double bond is formed and OH− eliminated. Somewhat surprisingly this is not the reaction path, predicted by the intrinsic reaction coordinate (IRC), following F− attack of the CH3− group. The IRC leads to a deep potential energy minimum for the CH2(OH)2 · · · F− complex which dissociates to F− + CH2(OH)2. None of the direct dynamics trajectories followed the IRC, leading to this minimum and product channel. This channel has an exothermicity of 60 kcal/mol, much lower than the 27 kcal/mol exothermicity for the observed channel. Other channels not observed and which have lower exothermicities are F−+CO+H2+H2O (43 kcal/mol) and F− + CH2O + H2O (51 kcal/mol). Formation of a CH3OOH· · ·F− complex, with randomization of its internal energy, is important. This complex dissociates via the ECO2 mechanism forming HF + CH2O + OH−. Trajectories which form HF + CH3OO− are non-statistical events and, for the 4 ps direct dynamics simulation, are not mediated by a CH3OOH· · · F− complex. Dissociation of this complex to form HF + CH3OO− may occur on longer time scales.
2007. "Direct Dynamics Simulations using Hessian-based Predictor-correctorIntegration Algorithms." Journal of Chemical Physics 126:044105 1-11. doi:10.1063/1.2437214 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. In previous research (J. Chem. Phys. 111, 3800 (1999)) a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H₂CO→H₂+CO, O₃+C₃H₆, and F−+CH₃OOH chemical reactions.
2007. "Specific Bonds between an Iron Oxide Surface and Outer Membrane Cytochromes MtrC and OmcA from Shewanella oneidensis MR-1." Journal of Bacteriology 189(13):4944-4952. doi:10.1128/JB.01518-06 Abstract Shewanella oneidensis MR-1 is purported to express outer membrane cytochromes (e.g., MtrC and OmcA) that transfer electrons directly to Fe(III) in a mineral during anaerobic respiration. A prerequisite for this type of reaction would be the formation of a stable bond between a cytochrome and an iron oxide surface. Atomic force microscopy (AFM) was used to detect whether a specific bond forms between a hematite (Fe2O3) thin film, created with oxygen plasma assisted molecular beam epitaxy (MBE), and recombinant MtrC or OmcA molecules coupled to gold substrates. Force spectra displayed a unique force signature indicative of a specific bond between each cytochrome and the hematite surface. The strength of the OmcA-hematite bond was approximately twice as strong as the MtrC-hematite bond, but direct binding to hematite was twice as favorable for MtrC. Reversible folding/unfolding reactions were observed for mechanically denatured MtrC molecules bound to hematite. The force measurements for the hematite-cytochrome pairs were compared to spectra collected between an iron oxide and S. oneidensis under anaerobic conditions. There is a strong correlation between the whole cell and pure protein force spectra suggesting that the unique binding attributes of each cytochrome complement one another and allow both MtrC and OmcA to play a prominent role in the transfer of electrons to Fe(III) in minerals. Finally, by comparing the magnitude of binding force for the whole cell vs. pure protein data, we were able to estimate that a single bacterium of S. oneidensis (2 x 0.5 μm) expresses ~104 cytochromes on its outer surface.
2007. "Structure and Reaction of Oxametallacycles Derived from StyreneOxide on Ag(110)." Surface Science 601(16):3372-3382. doi:10.1016/j.susc.2007.06.015 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Styrene oxide forms a strongly bound oxametallacycle intermediate via activated adsorption on the Ag(110) surface. The oxametallacycle species derived from styrene oxide on Ag(110) fits well with the family of oxametallacycles identified previously in studies of nonallylic epoxides with unsaturated substituent groups on silver. Temperature-programmed reaction experiments demonstrate that styrene oxide ring opens at the substituted carbon, and Density Functional Theory calculations indicate that the phenyl ring of the resulting oxametallacycle is oriented nearly parallel to the Ag(110) surface. Interaction of the phenyl group with the silver surface stabilizes this intermediate relative to that derived from the mono-olefin epoxide, ethylene oxide. During temperature-programmed reaction, the oxametallacycle undergoes ring-closure to reform styrene oxide and isomerization to phenylacetaldehyde at 505 K on Ag(11 0). Styrene oxide-derived oxametallacycles exhibit similar ring-closure behavior on the Ag(111) surface.
2007. "Direct Observation of Adsorption Evolution and Bonding Configuration of TMAA on TiO2(110)." Journal of Physical Chemistry C 111(11):4342-4346. doi:10.1021/jp067264d Abstract Trimethyl acetic acid (TMAA) adsorption evolution on the rutile TiO2(110) surface from submonolayer to saturation coverages was examined at the atomic level by scanning tunneling microscopy using the same area analysis approach. Upon TMAA deprotonation, no evidence of terminal OH group formation has been found. It has been suggested that uncommon geometry associated with detached hydrogen atom takes place instead, with proton bonding to pair bridging oxygen atoms. Such a configuration is likely to be stabilized by adjacent adsorbed TMA groups and, in turn, be a factor in the formation of TMA (2x1) reconstruction at saturation coverage. Our results indicate that TMAA adsorption on reduced TiO2 is virtually not affected by bridging oxygen vacancies or other surface defects.
