Scientific Publications 2007
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H
2007. "First Observation of Charge Reduction and Desorption Kinetics of Multiply Protonated Peptides Soft Landed onto Self-Assembled Monolayer Surfaces." Journal of Physical Chemistry C 111(49):18220-18225. doi:10.1021/jp075293y Abstract The kinetics of charge reduction and desorption of different species produced by soft-landing of mass-selected ions was studied using in situ secondary ion mass spectrometry (SIMS) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). The improved SIMS capability described in this work utilizes an in-line 8 keV Cs+ ion gun and allows us to interrogate the surface both during the ion deposition and after the deposition is terminated. As a model system doubly protonated ions of Gramicidin S were deposited onto a fluorinated self-assembled monolayer (FSAM) surface. Our results demonstrate for the first time that various peptide-related peaks in FT-ICR SIMS spectra follow very different kinetics. We obtained unique kinetics signatures for doubly protonated, singly protonated and neutral peptides retained on the surface and followed their evolution as a function of time. The experimental results are in excellent agreement with a kinetic model that takes into account charge reduction and thermal desorption of different species from the surface.
2007. "Design and Performance of a Novel Instrument for Soft-Landing of Biomolecular Ions on Surfaces." Analytical Chemistry 79(17):6566-6574. doi:10.1021/ac070600h Abstract A new ion deposition apparatus was designed and constructed in our laboratory. Our research objectives were to investigate interactions of biomolecules with hydrophilic and hydrophobic surfaces and to carry out exploratory experiments aimed at highly-selective deposition of spatially defined and uniquely selected biological molecules on surfaces. The apparatus includes a high-transmission electrospray ion source, quadrupole mass filter, bending quadrupole that deflects the ion beam and prevents neutral molecules originating in the ion source from impacting the surface, an ultrahigh vacuum (UHV) chamber for ion deposition by soft landing, and a vacuum-lock system for introducing surfaces into the UHV chamber without breaking vacuum. Ex situ analysis of surfaces following soft-landing of mass-selected peptide ions was performed using 15 keV Ga+ time-of-flight secondary ion mass spectrometry (TOF-SIMS) and grazing incidence infrared reflection-absorption spectroscopy (IRRAS). It will be shown that these two techniques are highly complementary methods for characterization of surfaces prepared with a range of doses of mass-selected biomolecular ions.
2007. "Dynamic Polarizabilities of Polyaromatic Hydrocarbons Using Coupled-Cluster Linear Response Theory." Journal of Chemical Physics 127:Art. No. 144105. doi:10.1063/1.2772853 Abstract Coupled-cluster theory with single and double excitations (CCSD) is applied to the calculation of optical properties of large polyaromatic hydrocarbons. Dipole polarizabilities are reported for benzene, pyrene, and the oligoacenes sequence n=2-6. Dynamic polarizabilities were calculated on polyacences as large asa pentacene for a single frequency and for benzene and pyrene at many frequencies. The basis set effect was studied for benzene using a variety of basis sets in the Pople and Dunning families up to aug-cc-pVQZ and the Sadlej p VTZ basis, which was used exclusively for the largest molecules. Optimized geometries were evaluated for some of the compounds using HF, B3LYP, PBE0, MP2 and CCSD to understand the role of bond-length-alteration (BLA). Finally, the polarizability results ere compared to four common density-functionals (B3LYP, BLYP, PBE0, PBE).
2007. "Calculations of Molecular Properties in Hybrid Coupled-Cluster and Molecular Mechanics Approach." Journal of Physical Chemistry A 111(25):5492-5498. doi:10.1021/jp070553x Abstract The ability to describe properties of molecular system in realistic environment is important for many applications. To address this issue we recently combined [M. Valiev, K. Kowalski, J. Chem. Phys. 2006, 125, 211101] classical molecular mechanics (MM) and ab initio coupled-cluster (CC) modules of NWChem. This paper reports the results of calculations of dipole moments and static polarizabilities for the C1₂0 system in the CC1₄ solution using the CCSD (CC with singles and doubles) linear response approach. We also discuss the application of the asymptotic extrapolation scheme (AES) [K. Kowalski, M. Valiev, J. Phys. Chem. A 2006, 110, 13106] in reducing the numerical cost of ab initio methods in the quantum region.
2007. "Atomic-Scale Assembly of a Heterogeneous Catalytic Site." Journal of the American Chemical Society 129(46):14355-14361. doi:10.1021/ja074891n Abstract The (100) surface of a AuPd bulk alloy was imaged by scanning tunneling microscopy. Chemical-contrast revealed structures with short-range order involving surface Pd atoms at c(2x2) sites with respect to the surface lattice—a first time observation of a known active heterogeneous catalytic site with atomic resolution. Comparison of the Pd distribution in a AuPd(100) surface with that in a Au3Pd(100) surface shows the unique thermodynamic properties of the 50 : 50 alloy are decisive in controlling the formation of isolated Pd sites.
2007. "Differences in Electrostatic Potential Around DNA Fragments Containing Guanine and 8-oxo-Guanine." Theoretical Chemistry Accounts 117(2):291-296. doi:10.1007/s00214-006-0133-1 Abstract hanges of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotoides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The “intact” DNA fragment contained guanine in the middle layer, while the “damaged” fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps.
2007. "Quantum Mechanical Energy-based Screening of Combinatorially Generated Library of Tautomers. TauTGen: A Tautomer Generator Program." Journal of Chemical Information and Modeling 47(2):686-694. doi:10.1021/ci6002703 Abstract Many computational methods have been derived from quantum mechanics for molecular and extended systems. We advocate that these methods will soon become indispensable research tools of combinatorial chemistry. Although applications of these combinatorial methods driven by quantum-mechanics-derived computational engines seem to be distant, our recent experience suggests the opposite. We developed algorithms and codes to search for the most stable tautomers of molecules. In our approach, we: (i) create large libraries of molecular tautomers using combinatorial methods, and (ii) prescreen these libraries using quantum chemical electronic structure methods. We have identified many adiabatically bound and previously unknown tautomers of anionic nucleic acid bases. Our results unraveled that ordering of nucleic acid bases according to their affinity to an excess electron is: G > U > T > C > A , when all biologically relevant tautomers are considered. Acknowledgements This work was supported by the: (i) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.) and (ii) Polish State Committee for Scientific Research (KBN) Grant DS/8221-4-0140-4 (M.H.). M.H. thanks for financial support from the European Union Social Funds ZPORR/2.22/II/2.6/ARP/U/2/O5. M.H. is a holder of the award from the Fundation for Polish Science (FNP). R.A.B. acknowledges the financial support from Nanoquant EC Marie Curie Research Training Network, contract number: MRTN-506842. Computing resources were available through: (i) the Academic Computer Center in Gdańsk (TASK) (ii) a Computational Grand Challenge Application grant from the Molecular Sciences Computing Facility (MSCF) in the Environmental Molecular Sciences Laboratory located at the Pacific Northwest National Laboratory, and (iii) the National Energy Research Scientific Computing Center (NERSC). The MSCF is funded by DOE’s Office of Biological and Environmental Research. PNNL is operated by Battelle for the U.S. DOE under Contract DE-AC06-76RLO 1830.
2007. "Structure and Singly Occupied Molecular Orbital Analysis of Anionic Tautomers of Guanine." Journal of Computational Chemistry 29(8):1277-1291. doi:10.1002/jcc.20886 Abstract In the current study, we analyze the adiabatically bound anions of guanine in two aspects: (1) the geometries and excess electron distributions are analyzed and compared with anions of the most stable neutrals to identify the sources of stability; (2) the chemical space of guanine tautomers is explored to verify if these new tautomers are contained in a particular subspace of the tautomeric space.
2007. "Differences in Electrostatic Potential Around DNA Fragments Containing Adenine and 8-oxo-Adenine. An Analysis Based on Regular Cylindrical Projection ." Journal of Molecular Graphics and Modelling 26(1):282-289. Abstract Changes of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The “intact” DNA fragment contained adenine in the middle layer, while the “damaged” fragment had the adenine replaced with 8-oxo-adenine. The electrostatic potential around these DNA fragments was projected on a cylindrical surface around the double helix. The two-dimensional maps of EP of the intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-adenine (8oA). It was found that distortions of a phosphate group neighboring 8oA and displacements of the accompanying countercation are clearly reflected in the EP maps. Helpful discussions Michel Dupuis are gratefully acknowledged. Authors wish to thank Marcel Swart for directing us to a compilation of van der Waals radii. This work was supported by the: (i) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G. and M.H.), (ii) the Office of Science (BER), U. S. Department of Energy, Grant No. DE-FG03-02ER63470 (JHM), (iii) Polish State Committee for Scientific Research (KBN) Grant DS/8221-4-0140-6 (MG), (iv) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic Computer Center in Gdańsk (TASK) and at the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at the Pacific Northwest National Laboratory, which is operated by Battelle for the US Department of Energy. The MSCF resources were available through a pilot project.
2007. "Adiabatically Bound Valence Anions of Guanine." Journal of Physical Chemistry B 111(51):14073-14076. doi:10.1021/jp077439z 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. It is believed that guanine, a basic component of DNA and RNA, has the smallest affinity to an excess electron among all nucleic acid bases. Our experimental and computational findings indicate, however, that many so far neglected tautomers of guanine support adiabatically bound anionic states in the gas phase. The computed values of electron vertical detachment energy for the most stable anionic tautomers are within a broad range of the dominant feature of the photoelectron spectrum. We suggest that guanine might be the strongest excess electron acceptor among nucleic acid bases. Thus it might be critical to radiobiological damage of DNA and it might contribute to those chemical transformations of DNA that proceed through bound anionic states.
2007. "Bound Anionic States of Aadenine." Proceedings of the National Academy of Sciences of the United States of America 104(12):4804-4807. doi:10.1073/pnas.0609982104 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 are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases are thought to be adiabatically unbound. Contrary to this expectation,wehave demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the newfound anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike the dipole-bound state, could exist in condensed phases and might be relevant to radiobiological damage. The discovery of these valence anionic states of adenine was facilitated by the development of (i) an experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a combinatorial/quantum chemical approach for identification of the most stable tautomers of organic molecules.
2007. "Bound Anionic States of Adenine ." Proceedings of the National Academy of Sciences of the United States of America 104(12):4804-4807. doi:10.1073/pnas.0609982104 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 are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the newfound anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike the dipole-bound state, could exist in condensed phases and might be relevant to radiobiological damage. The discovery of these valence anionic states of adenine was facilitated by the development of (i) an experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (it) a combinatorial/quantum chemical approach for identification of the most stable tautomers of organic molecules.
2007. "Effect of Co Doping on the Structural, Optical and Magnetic Properties of ZnO Nanoparticles." Journal of Physics. Condensed matter 19(26):Art. No. 266203. doi:10.1088/0953-8984/19/26/266203 Abstract We report the results of a detailed investigation of sol-gel synthesized nanoscale Zn1-xCoxO powders processed at 350 °C with 0 @ x @ 0.12 to understand how the structural, morphological, optical and magnetic properties of ZnO are modified by Co doping, in addition to searching for the theoretically predicated ferromagnetism. With x increasing to 0.03, both lattice parameters a and c of the hexagonal ZnO decreased suggesting substitutional doping of Co at the tetrahedral Zn2+ sites. For x > 0.03, these trends reversed and the lattice showed a gradual expansion as x approached 0.12, probably due to additional interstitial incorporation of Co. Raman spectroscopy measurements showed a rapid change in the ZnO peak positions for x > 0.03 suggesting significant disorder and changes in the ZnO structure, in support of additional interstitial Co doping possibility. Combined x-ray photoelectron spectroscopy (XPS), electron paramagnetic resonance spectroscopy, photoluminescence spectroscopy and diffuse reflectance spectroscopy showed clear evidence for tetrahedrally coordinated high spin Co2+ ions occupying the lattice sites of ZnO host system, which became saturated for x > 0.03. Magnetic measurements showed a paramagnetic behavior in Zn1-xCoxO with increasing antiferromagnetic interactions as x increased to 0.10. Surprisingly, a weak ferromagnetic behavior was observed for the sample with x = 0.12 with a characteristic hysteresis loop showing a coercivity Hc ~ 350 Oe, 25% remanence Mr, a low saturation magnetization Ms ~ 0.04 emu/g and with a Curie temperature Tc ~ 540 K. The XPS data collected from Zn1-xCoxO samples showed a gradual increase in the oxygen concentration, changing the oxygen deficient undoped ZnO to an excess oxygen state for x = 0.12. This indicates that such high Co concentrations and appropriate oxygen stoichiometry may be needed to achieve adequate ferromagnetic exchange coupling between the incorporated Co2+ ions.
2007. "Physisorption of CO2 on non-ice materials relevant to icy satellites." Icarus 191(1):371-380. doi:10.1016/j.icarus.2007.04.012 Abstract CO2 is known to adsorb onto clay and other minerals when a significant atmospheric pressure is present. We have found that CO2 can also adsorb onto some clays when the CO2 partial pressure is effectively zero under ultra-high vacuum (UHV) if cooled to the surface temperatures of the icy satellites of Jupiter and Saturn. The strength of adsorption and the spectral characteristics of the adsorbed CO2 infrared (IR) ν3 absorption band near 4.25 μm depend on the composition and temperature of the adsorbent. CO2 remains adsorbed onto the clay mineral montmorillonite for >10 s of min when exposed to a vacuum of ∼1×10−8 Torr at ∼125 K. CO2 does not adsorb onto serpentine, goethite, or palagonite under these conditions. A small amount may adsorb onto kaolinite. When heated above 150 K under vacuum, the CO2 desorbs from the montmorillonite within a few minutes. The ν3 absorption band of CO2 adsorbed onto montmorillonite at 125 K is similar to that of the CO2 detected on the saturnian and Galilean satellites and is markedly different from CO2 adsorbed onto montmorillonite at room temperature. We infer the adsorption process is physisorption and postulate that this mechanism may explain the presence and spectral characteristics of the CO2 detected in the surfaces of these outer satellites.
2007. "Effect of Divalent Cations on the Structure of the Antibiotic Daptomycin." European Biophysics Journal:EBJ 37(4):421-433. doi:10.1007/s00249-007-0227-2 Abstract Abstract Daptomycin, a cyclic anionic lipopeptide antibiotic, whose three-dimensional structure was recently solved using solution state NMR (Ball et al. 2004; Jung et al. 2004; Rotondi and Gierasch 2005), requires calcium for function. To date, the exact nature of the interaction between divalent cations, such as Ca2+ or Mg2+, has not been fully characterized. It has, however, been suggested that addition of Ca2+ to daptomycin in a 1:1 molar ratio induces aggregation. Moreover, it has been suggested that certain residues, e.g. Asp3 and Asp7, which are essential for activity (Grunewald et al. 2004; Kopp et al. 2006), may also be important for Ca2+ binding (Jung et al. 2004).
2007. "Microreactor Development for Martian In-Situ Propellant Production ." Catalysis Today 120(1):35-44. doi:doi:10.1016/j.cattod.2006.07.019 Abstract The second part of the Martian In-situ Propellant Production (MIPPS) system reviews the development of the Sabatier Reactor (SR). The microchannel SR had integrated cooling channels as well as reaction channels. It was <100cc in volume. The reactor utilized a proprietary catalyst. When operated at 400oC 70-80% CO2 conversion was achieved which enabled ~0.0125 kg CH4/hr production, or 1/8th the target mission. The modular design of the microchannel reactors would enable simple scale up to full scale production for the proposed mission.
2007. "Methods for Mapping of Interaction Networks Involving Membrane Proteins." Biochemical and Biophysical Research Communications 363(3):457-461. Abstract Numerous approaches have been taken to study protein interactions, such as tagged protein complex isolation followed by mass spectrometry, yeast two-hybrid methods, fluorescence resonance energy transfer, surface plasmon resonance, site-directed mutagenesis, and crystallography. Membrane protein interactions pose significant challenges due to the need to solubilize membranes without disrupting protein-protein interactions. Traditionally, analysis of isolated protein complexes by high-resolution 2D gel electrophoresis has been the main method used to obtain an overall picture of proteome constituents and interactions. However, this method is time consuming, labor intensive, detects only abundant proteins and is not suitable for the coverage required to elucidate large interaction networks. In this review, we discuss the application of various methods to elucidate interactions involving membrane proteins. These techniques include methods for the direct isolation of single complexes or interactors as well as methods for characterization of entire subcellular and cellular interactomes.
2007. "Correlations Between Optical, Chemical and Physical Properties of Biomass Burn Aerosols." Geophysical Research Letters 34:Art. No. L18806. doi:10.1029/2007GL030502 Abstract Single scattering albedo (ω) and Angstrom absorption coefficient (αap) values are measured at 405, 532 and 870 nm for aerosols generated during controlled laboratory combustion of twelve wildland fuels. Considerable fuel dependent variation in these optical properties is observed at these wavelengths. Complementary microspectroscopy techniques are used to elucidate spatially resolved local chemical bonding, carbon-to-oxygen atomic ratios, percent of sp2 hybridization (graphitic nature), elemental composition, particle size and morphology. These parameters are compared directly with the corresponding optical properties for each combustion product, facilitating an understanding of the fuel dependent variability observed. Results indicate that combustion products can be divided into three categories based on chemical, physical and optical properties. Only materials displaying a high degree of sp2 hybridization, with chemical and physical properties characteristic of ‘soot’ or black carbon, exhibit ω and αap values that indicate a high light absorbing capacity.
2007. "Increased Reactivity of Single Wall Carbon Nanotubes at Carbonad-dimer Defect Sites." Chemical Physics Letters 450(1):71-75. doi:10.1016/j.cplett.2007.10.079 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. A quantum chemical study of the reactivity of the 7-5-5-7 topological defect, corresponding to a carbon ad-dimer, on a (5, 5) armchair nanotube is reported. The energies indicate that the defect is more reactive by 46–70 kcal/mol towards adsorbates containing p-bonds, such as C₂H4, O₂, and O₃, than are pristine nanotubes or the Stone–Wales 5-7-7-5 defect. The enhanced reactivity of this defect was also obtained for other sizes and types of carbon nanotubes.
2007. "Conversion of Biomass-Derived Syngas to Alcohols and C2 Oxygenates Using Supported Rh Catalysts in a Microchannel Reactor." Catalysis Today 120(1):90-95. doi:10.1016/j.cattod.2006.07.006 Abstract Conversion of Biomass-Derived Syngas to Alcohols and C2 Oxygenates Using Supported Rh Catalysts in a Microchannel Reactor
