Scientific Publications 2006
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2006. "Active-Space Coupled-Cluster Methods Through Connected Quadruple Excitations." Journal of Chemical Physics 124(10): Art No. 104108-104117. Abstract This abstract is currently not available for viewing at this time.
2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725. doi:10.1074/mcp.M500301-MCP200 Abstract We describe the application of liquid chromatography coupled to mass spectrometry (LC/MS) without the use of stable isotope labeling for differential quantitative proteomics analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and sub-oxic conditions. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used to initially identify peptide sequences, and LC coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) was used to confirm these identifications, as well as measure relative peptide abundances. 2343 peptides, covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as SAM, while another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis is transitioned from aerobic to sub-oxic conditions.
2006. "A General Simulator for Reaction-Based Biogeochemical Processes." Computers & Geosciences 32(1):64-72. doi:10.1016/j.cageo.2005.05.003 Abstract Abstract: As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, passivation of reactive surfaces, dissolution of sorbates), there is a growing need for biogeochemical simulators to flexibly and facilely address new reaction forms and rate laws. This paper presents an approach that accommodates this need to efficiently simulate general biogeochemical processes, while insulating the user from additional code development. The approach allows for the automatic extraction of fundamental reaction stoichiometry and thermodynamics from a standard chemistry database, and the symbolic entry of arbitrarily complex user-specified reaction forms, rate laws, and equilibria. The user-specified equilibrium and kinetic reactions (i.e., reactions not defined in the format of the standardized database) are interpreted by the Maple symbolic mathematical software package. FORTRAN 90 code is then generated by Maple for 1) the analytical Jacobian matrix (if preferred over the numerical Jacobian matrix) used in the Newton-Raphson solution procedure, and 2) the residual functions for user-specified equilibrium expressions and rate laws. Matrix diagonalization eliminates the need to conceptualize the system of reactions as a tableau, while identifying a minimum rank set of basis species with enhanced numerical convergence properties. The newly generated code, which is designed to operate in the BIOGEOCHEM biogeochemical simulator, is then compiled and linked into the BIOGEOCHEM executable. With these features, users can avoid recoding the simulator to accept new equilibrium expressions or kinetic rate laws, while still taking full advantage of the stoichiometry and thermodynamics provided by an existing chemical database. Thus, the approach introduces efficiencies in the specification of biogeochemical reaction networks and eliminates opportunities for mistakes in preparing input files and coding errors. Test problems are used to demonstrate the features of the procedure.
2006. "A quantitative account of quantum effects in liquid water." Journal of Chemical Physics 125(14 ):Art. No. 141102. Abstract We report quantum statistical mechanical simulations of liquid water with the TTM2.1-F flexible, polarizable interaction potential for water. The potential is the first representation of the molecular interaction that reproduces the converged Born-Oppenheimer potential energy surface obtained from systematically improvable electronic structure analysis of binding energies of water clusters. Proper quantum statistical simulation of properties allows for a quantitative account of the magnitude of quantum effects in liquid water. We report path integral quantum dynamical simulations of total length of 600 ps with a 0.05 fs time step for a periodic system of 256 molecules. The representation of the quantum effects was achieved using up to 32 replicas per atom. These allow for a quantitative description of the broadening of the radial distribution functions and the corresponding energy shifts in the heat of vaporization. Our best estimate for the enthalpy of the liquid from the results of the quantum simulations is in the range 10.4 – 10.6 kcal/mol, in agreement with the experimental value of 10.51 kcal/mol. 1Battelle operates PNNL for the USDOE
2006. "The bend angle of water in ice Ih and liquid water: The significance of implementing the nonlinear monomer Dipole Moment Surface in classical interaction potentials." Journal of Chemical Physics 124(17):Art. no. 174504. Abstract The implementation of the physically accurate non-linear dipole moment surface of the water monomer in the context of an interaction potential results in the only classical potential, which reproduces the experimentally observed increase of the monomer bend angle in ice Ih from its value in the gas phase. This is in contrast to all other classical potentials, which predict a decrease of the monomer bend angle in ice Ih from the gas phase value. Our approach suggests a new paradigm in the development of classical potential models of water that are used to describe condensed aqueous environments and the local structure of water around biomolecules. Battelle operates PNNL for the US DOE.
2006. "The flexible, polarizable, thole-type interaction potential for water (TTM2-F) Revisited." Journal of Physical Chemistry A 110(11):4100-4106. doi:10.1021/jp056477k Abstract We report classical molecular dynamics simulations of liquid water with a flexible, polarizable, Thole-type interaction potential. We report the radial distribution functions, average energy, internal geometry and dipole moment in the liquid as well as the density, dielectric constant and self-diffusion coefficient at T=300 K from (NVT) and (NPT) classical molecular dynamics simulations. In order to facilitate these simulations we have found it necessary to modify the original version of the TTM2-F potential [J. Chem. Phys. 116, 5115 (2002)] in order to consistently describe the fragment molecular dipole moment and alleviate problems arising at small intermolecular separations. Furthermore, the parallel implementation of the revised version (TTM2.1-F) under periodic boundary conditions enables for the efficient calculation of the macroscopic structural and thermodynamic properties of liquid water as its performance scales superlinearly with number of processors for a 256 molecule periodic simulation box.
2006. "The Aqueous Complexation of Thorium with Citrate under Neutral to Basic Conditions." Radiochimica Acta 94(4):205-212. doi:10.1524/ract.2006.94.4.205 Abstract The aqueous complexation of thorium with citrate was investigated under neutral to basic conditions and over a broad range of ionic strengths. The solubility data for ThO2(am) as a function of citrate concentration indicate the presence of stable species with citrate-to-metal ratios of between two to three. The dependence of the ThO2(am) solubilities on hydrogen ion concentration can also be readily explained by the classical assumption of hydrolysis of the central Th(IV) ion to form mixed thorium-hydroxide-citrate complexes. 13C NMR spectra of the species in solution confirm that the citrate-to-metal ratio of the species in solution is between two and three and show that the citrate attaches to the metal in a bidentate fashion through oxygens on the -carboxylate and -alkoxyl groups, rather than through the carboxylate groups. The 13C NMR spectra, as well as a density functional theory (DFT) electronic structure study of the presumptive complexes, suggests that the associated α-hydroxyl proton can be displaced during complex formation. These findings indicate an alternative explanation for the observed changes in solubility as a function of hydrogen ion concentration, the displacement of protons from the citrate alkoxyl groups via metal binding. Removal of protons from the alkoxyl groups or hydrolysis of the central Th(IV) cannot be distinguished by thermodynamic measurements, however the species with the α-hydroxyl proton removed (i.e., ThOH(Cit)25- and Th(Cit)38-) would appear to better represent the microscopic binding. Apparent equilibrium constants for the solution phase reactions of these species and the hydrous thorium oxide have been calculated as a function of ionic strength.
2006. "Protein Identification Via Surface-Induced Dissociation in an FT-ICR Mass Spectrometer and a Patchwork Sequencing Approach." Journal of the American Society for Mass Spectrometry 17(5):700-709. Abstract Surface-induced dissociation (SID) and collision-induced dissociation (CID) are ion activation techniques based on energetic collisions with a surface or gas molecules, respectively. One noticeable difference between CID and SID is that SID does not require a collision gas for ion activation and is therefore directly compatible with the high vacuum requirement of Fourier Transform Ion Cyclotron Resonance mass spectrometers (FT-ICR MS). Eliminating the introduction of collision gas into the ICR cell for collisional activation dramatically shortens the acquisition time for MS/MS experiments, suggesting that SID could be utilized for high-throughput MS/MS studies in FT-ICR MS. We demonstrate for the first time the utility of SID combined with FT-ICR MS for protein identification. Tryptic digests of standard proteins were analyzed using a hybrid 6-Tesla FT-ICR MS with SID and CID capabilities. SID spectra of mass-selected singly and doubly charged peptides were obtained using a diamond-coated target mounted at the rear trapping plate of the ICR cell. The broad internal energy distribution deposited into the precursor ion following collision with the diamond surface allowed a variety of fragmentation channels to be accessed by SID. Composition and sequence qualifiers produced by SID of tryptic peptides were used to improve the statistical significance of database searches. Protein identification MASCOT scores obtained using SID were comparable or better than scores obtained using sustained off-resonance irradiation collision-induced dissociation (SORI-CID) –the conventional ion activation technique in FT-ICR MS.
2006. "High Resolution Spectroscopy of H212C16O in the 1.9 to 2.56 um Spectral Range." Molecular Physics 104(12):1891-1903. Abstract Infrared spectra of H2CO covering the 1.9 – 2.5 μm spectral domain have been recorded at very high resolution (0.005 cm-1) using Fourier transform spectroscopy. A thorough analysis of this spectral region has led to the observation and analysis of the v1+v6, v2+v4+v6, 2v3+ v6, v3+v5, v1+v2, v2+v5, 2v2+ v6 and 3v2 bands. The line frequencies were calculated using effective (empirical) Hamiltonian models which account for the main Coriolis and vibrational interactions. Using an interactive scheme it was then possible to least-squares fit the observed energy levels to within a few thousandths of a wavenumber. The Obs. – Calc. differences do not match the spectral precision (~0.0008 cm-1), but given the congestion in the spectrum resulting from the density of the vibrational states as well as the large centrifugal distortion and Coriolis and anharmonic coupling effects, we believe that a reasonable agreement was obtained.
2006. "Identification of Isotopically Primitive Interplanetary Dust Particles: A NanoSIMS Isotopic Imaging Study." Geochimica et Cosmochimica Acta 70(9):2371-2399. doi:10.1016/j.gca.2006.01.023 Abstract We have carried out a comprehensive survey of the isotopic compositions (H, B, C, N, O,S) of a suite of interplanetary dust particles (IDPs), including both cluster and individual particles. Isotopic imaging with the NanoSIMS shows the presence of numerous discrete hotspots that are strongly enriched in 15N, including the largest 15N enrichments (~1300 ‰) observed in IDPs to date. A number of the IDPs also contain larger regions with more modest enrichments in 15N, leading to average bulk N isotopic compositions that are 15N-enriched in these IDPs. Although C isotopic compositions are normal in most of the IDPs, two 15N-rich hotspots have correlated 13C anomalies. CN–/C– ratios suggest that most of the 15N-rich hotspots are associated with relatively N-poor carbonaceous matter, although specific carriers have not been determined. H isotopic distributions are similar to those of N: D anomalies are present both as distinct very D-rich hotspots and as larger regions with more modest enrichments. Nevertheless, H and N isotopic anomalies are not directly correlated, consistent with results from previous studies. Oxygen isotopic imaging shows the presence of abundant presolar silicate grains in the IDPs. The O isotopic compositions of the grains are similar to those found in presolar oxide and silicate grains from primitive meteorites. Most of the silicate grains in the IDPs have isotopic ratios consistent with meteoritic Group 1 oxide grains, indicating origins in oxygen-rich red giant and asymptotic giant branch stars, but several presolar silicates exhibit the 17O and 18O enrichments of Group 4 oxide grains, whose origin is less well understood. Based on their N isotopic compositions, the IDPs studied here can be divided into two groups. One group is characterized as being “isotopically primitive” and consists of those IDPs that have anomalous bulk N isotopic compositions. These particles typically also contain numerous 15N-rich hotspots, occasional C isotopic anomalies, and abundant presolar silicate grains. In contrast, the other “isotopically normal” IDPs have normal bulk N isotopic compositions and, although some contain 15N-rich hotspots, none exhibit C isotopic anomalies and none contain presolar silicate or oxide grains. Thus, isotopically interesting IDPs can be identified and selected on the basis of their N isotopic compositions for further study. However, this distinction does not extend to H isotopic compositions. Although both H and N anomalies 2 are frequently attributed to the survival of molecular cloud material in IDPs and, thus, should be more common in IDPs with anomalous bulk N compositions, D anomalies are as common in normal IDPs as they are in those characterized as isotopically primitive, based on their N isotopes. This may be due to different effects of secondary processing on the isotopic systems involved.
2006. "A Solid-State 95Mo NMR and Computational Investigation of Dodecahedral and Square Antiprismatic Octacyanomolybdate(IV) Anions: Is the Point-Charge Approximation an Accurate Probe of Local Symmetry?" Journal of the American Chemical Society 128(24):7817-7827. Abstract Solid-state 95Mo NMR spectroscopy is shown to be an efficient and effective tool for analyzing the diamagnetic octacyanomolybdate(IV) anions, Mo(CN)8 4-, of approximate dodecahedral, D2d, and square antiprismatic, D4d, symmetry. The sensitivity of the Mo magnetic shielding (ó) and electric field gradient (EFG) tensors to small changes in the local structure of these anions allows the approximate D2d and D4d Mo(CN)8 4- anions to be readily distinguished. The use of high applied magnetic fields, 11.75, 17.63 and 21.1 T, amplifies the overall sensitivity of the NMR experiment and enables more accurate characterization of the Mo ó and EFG tensors. Although the magnitudes of the Mo ó and EFG interactions are comparable for the D2d and D4d Mo(CN)8 4- anions, the relative values and orientations of the principal components of the Mo ó and EFG tensors give rise to 95Mo NMR line shapes that are significantly different at the fields utilized here. Quantum chemical calculations of the Mo ó and EFG tensors, using zeroth-order regular approximation density functional theory (ZORA DFT) and restricted Hartree-Fock (RHF) methods, have also been carried out and are in good agreement with experiment. The most significant and surprising result from the DFT and RHF calculations is a significant EFG at Mo for an isolated Mo(CN)8 4- anion possessing an ideal square antiprismatic structure; this is contrary to the point-charge approximation, PCA, which predicts a zero EFG at Mo for this structure.
2006. "Similar Transition States Mediate the Q-cycle and Superoxide Production by the Cytochrome bc1 Complex." Journal of Biological Chemistry 281(50):38459-38465. doi:10.1074/jbc.M605119200 Abstract The cytochrome bc complexes found in mitochondria, chloroplasts and many bacteria catalyze a critical reaction in their respective electron transport chains. The quinol oxidase (Qo) site in this complex oxidizes a hydroquinone (quinol), reducing two one-electron carriers, a low-potential cytochrome b heme and a ‘Rieske’ iron-sulfur cluster. The overall electron transfer reactions are coupled to transmembrane translocation of protons via a ‘Q-cycle’ mechanism, which generates proton motive force for ATP synthesis. Since semiquinone intermediates of quinol oxidation are generally highly reactive, one of the key questions in this field is: how does the Qo site oxidize quinol without the production of deleterious side reactions including superoxide production? We attempt to test three possible general models to account for this behavior: 1) The Qo site semiquinone (or quinol:imidazolate complex) is unstable and thus occurs at a very low steady-state concentration, limiting O2 reduction; 2) the Qo site semiquinone is highly stabilized making it unreactive towards oxygen; and 3) the Qo site catalyzes a quantum mechanically-coupled two-electron/two proton transfer without a semiquinone intermediate. Enthalpies of activation were found to be almost identical between the uninhibited Q-cycle and superoxide production in the presence of Antimycin A in wild type. This behavior was also preserved in a series of mutants with altered driving forces for quinol oxidation. Overall, the data supports models where the rate-limiting step for both Q-cycle and superoxide production are essentially identical, consistent with model 1 but requiring modifications to models 2 and 3.
2006. "The Synthesis of Functional Mesoporous Materials." Inorganic Chemistry Communications 9(11):1141-1150. Abstract The ability to decorate a silica surface with specific ligand fields and/or metal complexes creates powerful new capabilities for catalysis, chemical separations and sensor development. Integrating this with the ability to control the spacing of these complexes across the surface, as well as the symmetry and size of the pore structure, allows the synthetic chemist to hierarchically tailor these structured nanomaterials to specific needs. The next step up the “scale ladder” is provided by the ability to coat these mesoporous materials onto complex shapes, allowing for the intimate integration of these tailored materials into device interfaces. The ability to tailor the pore structure of these mesoporous supports is derived from the surfactant templated synthesis of mesoporous materials, an area which has seen an explosion of activity over the last decade.[1,2] The ability to decorate the surface with the desired functionality requires chemical modification of the oxide interface, most commonly achieved using organosilane self-assembly.[3-6] This manuscript describes recent results from the confluence of these two research areas, with a focus on synthetic manipulation of the morphology and chemistry of the interface, with the ultimate goal of binding metal centers in a chemically useful manner.
2006. "Collision Induced Dissociation of [4Fe-4S] Cubane Cluster Complexes: [Fe4S4C14-x(SC2H5)x]2-/1- (x=0-4)." International Journal of Mass Spectrometry 255-256:102-110. doi:10.1016/j.ijms.2005.12.009 Abstract Collision-induced dissociation (CID) experiments on a series of [4Fe-4S] cluster ions, [Fe4S4Cl4-x(SC2H5)x]2-/1- (x = 0 - 4), revealed that their fragmentation channels change with the coordination environment. Among the three Coulomb repulsion related channels for the doubly charged species, the collision induced electron detachment channel was found to become more significant from x = 0 to 4 due to the decreasing electron binding energies and the magnitude of the repulsion Coulomb barrier, while both the ligand detachment of Cl- and the fission of the [Fe4S4]2+ core became more and more significant with the increase of the Cl- coordination, and eventually became the dominant channel at x = 0. From the parents containing the -SC2H5 ligand, neutral losses of HSC2H5 (62) and/or HSCH=CH2 (60) were observed. It was proposed that interand intra-ligand proton transfer could happen during the CID process, resulting in hydrogen coordination to the [4Fe-4S] cluster. In the presence of O2, [Fe4S4Cl3(SC2H5)]2- and [Fe4S4Cl4]2- can form the O2-substituted products [Fe4S4Cl2(SC2H5)O2]- and [Fe4S4Cl3O2]-, respectively. It was shown that the O2 complexation occurs by coordination to the empty iron site of the [4Fe-4S] cubane core after dissociation of one Cl- ligand.
2006. "Reactions associated with ionization in water: a direct ab initio dynamics study of ionization in (H2O)17." Journal of Chemical Physics 124:164310. doi:10.1063/1.2194904 Abstract A quasi-classical ab initio dynamics calculation of the (H2O)17 cluster, which is the first water cluster that includes a four-fold coordinated water molecule, has been carried out to obtain a detailed picture of the elementary processes and energy redistribution induced by ionization in a model of aqueous water. Well within 100 fs after ionization, a proton is seen to have transferred from the “ionized molecule” to a neighboring molecule, forming a hydronium ion and a hydroxyl radical. Two neighboring water molecules to the ionized water molecule play an important role in the reaction, in what we term a “reactive trimer”. The reaction time is gated by the encounter of the “ionized” water molecule with these two neighboring molecules and this occurs at ~ 35 fs after ionization. We find that the distance of approach between the “ionized” molecule and the neighboring molecule reflects best the time characteristics of the transfer of a proton, and thus of the formation of a hydronium ion and an OH radical. These findings are consistent with those for smaller cyclic clusters, albeit the dynamics of the transferring proton is much damped in our simulation compared to the small cyclic cluster cases. We use a partitioning scheme for the kinetic energy of the << OLE Object: Microsoft Equation 3.0 >> system that distinguishes the “reactive trimer” and the surrounding medium. The analysis of the simulation indicates that the kinetic energy of the surrounding medium increases markedly right after the event of ionization. The increase in kinetic energy is consistent with a reorganization of the surrounding medium, in this case an orientation relaxation, from a configuration as a hydrogen bond donor to the “ionized” tetra-coordinated water molecule, into a configuration where the surrounding water molecule have turned their dipoles for a more favorable interaction with the “ionized” water cation. Battelle operates the Pacific Northwest National Laboratory for the US Department of Energy.
