Scientific Publications 2007
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2007. "Coupled-Cluster and Explicitly Correlated Perturbation-Theory Calculations of the Uracil Anion ." Chinese Journal of Chemical Physics 126(8):Art No. 085101. Abstract Abstract is currently not available for viewing at this time.
2007. "Electron-beam induced recrystallization in amorphous apatite." Applied Physics Letters 90(2):021912, 1-3. doi:10.1063/1.2430779 Abstract Electron-beam-induced recrystallization of irradiation-induced amorphous Sr2Nd8(SiO4)6O2 is investigated in situ using transmission electron microscopy with 200 keV electrons at room temperature. Epitaxial recrystallization is observed from both the amorphous/crystalline interface and the surface, and the recrystallization is more pronounced with increasing electron-beam flux. Since the temperature increase induced by electron-beam irradiation is estimated to be less than 7 K and maximum energies transferred to target atoms are below the displacement energies, ionization-induced processes are considered to be the primary mechanisms for the solid-phase epitaxial recrystallization observed in the present study.
2007. "Improving Surface Analysis Methods for Characterization of Advanced Materials by development of standards, reference data, and interlaboratory comparisons." Surface and Interface Analysis 39(4):283-293. doi:10.1002/sia.2508 Abstract This paper summarizes the results of two surveys examining current needs for improved analyses of surfaces. Surfaces and interfaces are increasingly important to science and to technologies associated with nanoparticles, nano-structured materials and other complex materials including those associated with information systems and medical or biological applications. Adequate characterization of advanced materials frequently requires application of more than one analysis method along with the need to analyze data in increasingly sophisticated and sometimes interrelated ways. It is useful for both new and experienced analysts to have ready access to best practices for obtaining accurate and useful information from a variety of different analysis tools. The International Organization for Standardization (ISO) Committee TC 201 on Surface Chemical Analysis and ASTM Committee E-42 on Surface Analysis are working to address these needs by assembling guides and standards reflecting the collective experience and wisdom of experts in this community.
2007. "Modeling the Preferred Shape, Orientation and Aspect Ratio of Gold Nanorods." Journal of Materials Chemistry 17:3315-3323. doi:10.1039/b704798c 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 has been widely shown that gold nanorods produced via a variety of methods may have average aspects between y2–40, depending on the synthetic conditions, and other thermodynamic considerations. This is significant, since the optical properties are highly dependant on the aspect of the nanorods. Furthermore, the number of different shapes and axial orientations produced depend partially on the aspect ratio, which clearly indicates that the relationship between shape, orientating and aspect is also significant. Presented here are the results of a systematic study of this relationship, using 30 candidate nanorod structures and an analytical shape-dependent thermodynamic model with input from relativistic first-principles calculations. The results show that gold nanorods with principle axes in the ¡[011] orientation are energetically preferred over alternative ¡[001] and ¡[111] orientations (under ambient conditions), but that the stability of the ¡[111] orientation increases significantly with both aspect and temperature, in agreement with other experimental and computational studies on selected types of structures reported in the literature.
2007. "Hydronium Ion Motion in Nanometer 3-Methyl-pentane Films." Journal of Chemical Physics 127(2):Paper # 024704. doi:10.1063/1.2748756 Abstract An ion soft-landing approach was applied to study the motion of hydronium (D3O+) and cesium (Cs+) ions from 84 to 104 K in glassy 3-methylpentane (3MP) films vapor-deposited on Pt(111). Both ions were found to have very similar mobilities in 3MP. The span of ion mobilities probed is from ~10-18 to ~10-13 m2 V-1 s-1. Ion transport in these films was studied as a function of film thickness and electric field strength. The drift velocity was found to be linear with applied field below about 2 x10(8) V/m, and deviates from linearity above this. To a large extent, D3O+ and Cs+ motion in 3MP was well predicted by a simple continuum-based ion mobility model in films from 25 to 20,000 monolayers thick, (including pronounced perturbations 7 monolayers from both the vacuum and Pt interfaces). The mobility varies with temperature more slowly than predicted by Stokes’ law, which may be due to extended inhomogeneous structures in the 3MP near the 77 K glass transition.
2007. "Multiplexed Ion Mobility Spectrometry - Orthogonal Time-Of-Flight Mass Spectrometry ." Analytical Chemistry 79(6):2451-2462. doi:10.1021/ac0617316 Abstract Ion mobility spectrometry (IMS) coupled to orthogonal time-of-flight mass spectrometry (TOF) has shown significant promise for the characterization of complex biological mixtures. The enormous complexity of biological samples (e.g. from proteomics) and the need for both biological and technical analysis replicates imposes major challenges for multidimensional separation platforms in regard to both sensitivity and sample throughput. A major potential attraction of the IMS-TOF MS platform is separation speeds exceeding that of conventional condensed-phase separations by orders of magnitude. Known limitations of the IMS-TOF MS platforms that presently mitigate this attraction include the need for extensive signal averaging due to factors that include significant ion losses in the IMS-TOF interface and an ion utilization efficiency of less than ~1% with continuous ion sources (e.g. ESI). We have developed a new multiplexed ESI-IMS-TOF mass spectrometer that enables lossless ion transmission through the IMS-TOF as well as a utilization efficiency of >50% for ions from the ESI source. Initial results with a mixture of peptides show a ~10-fold increase in signal-to-noise ratio with the multiplexed approach compared to a signal averaging approach, with no reduction in either IMS or TOF MS resolution.
2007. "Structural Criteria for the Design of Anion Receptors: The Interaction of Halides with Electron-Deficient Arenes." Journal of the American Chemical Society 129(1):48-58. Abstract This paper refines the nature of the interactions between electron-deficient arenes and halide anions. Conclusions are based on (i) new crystal structures containing alkali halide salts with 1,2,4,5-tetracyanobenzene (TCB) and 18-crown-6, (ii) evaluation of crystal structures found in the Cambridge Structural Database, and (iii) MP2/aug-cc-pVDZ calculations of F–, Cl–, and Br– complexes with TCB, 1,3,5-tricyanobenzene, triazine, and hexafluorobenzene. When the halide lies above the plane of the π system, the results establish that three distinctly different types of complexes are possible: strongly covalent σ complexes, weakly covalent donor π-acceptor complexes, and electrostatic anion-π complexes. When aryl C–H groups are present, a fourth type of interaction leads to C–H•••X– hydrogen bonding. Characterization of the different geometries encountered with the four possible binding motifs provides criteria needed to design host architectures containing electron-deficient arenes. This research was performed in part using 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 located at the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2007. "Combined Spectroscopic and Topographic Characterization of Nanoscale Domains and Their Distributions of a Redox Protein on Bacterial Cell Surfaces ." Langmuir 23(3):1333-1338. doi:10.1021/la061343z Abstract Redox protein nanoscale domains on the cell surface of a bacterium, Shewanella oneidensis MR1, grown in the absence and presence of electron acceptors, is topographically characterizedusing combined atomic force microscopy (AFM) and surface enhanced Raman scattering (SERS) spectroscopy. The protruding nanoscale domains on the outer membrane of S. oneidensis were observed, as was their disappearance upon exposure to electron acceptors such as oxygen, nitrate, fumarate, and iron nitrilotriacetate (FeNTA). Using SERS spectroscopy, a redox heme protein was identified as a major component of the cell surface domains. This conclusion was further confirmed by the disappearance of Raman vibrational frequencies, characteristic of heme proteins, upon exposure of the cells to electron acceptors. Based on experimental results from our AFM imaging and SERS spectroscopy, consistent with the literature, we suggest the protruding nanoscale surface domains as heme-containing secretions. Our results on the distributions of redox proteins on microbial cell surfaces will be helpful for a mechanistic understanding of the behaviors of surface proteins and their interactions with redox environments.
2007. "Charge Localization in Cation-Sulfate Complexes: Implications for Thermodynamic Surface Complexation Models of the Mineral/Water Interface." Journal of Physical Chemistry C 111(3):1299-1306. doi:10.1021/jp0647784 Abstract The applicability of separating charges of oxyanions across inner- and outer-Helmholtz planes according to the Charge Distribution model was tested by investigating the theoretical charge distribution in a range of metal-sulphate complexes using the methods of Atoms In Molecules and of the Electron Localisation Function. Density Functional Theory gas-phase geometry optimisation calculations revealed that unbound oxygens of the sulphate molecules contracted to relatively constant S-O bond lengths of 1.432 ± 0.019 (3 ) Å irrespective of the bond strength with the metal ions. The populations of the valence basins of the unbound oxygens also remained relatively constant, showing that even the strongest complexation induces very little charge distribution across the sulphate molecule. Maps of the Laplacian of the electron density and of the Electron Localisation Function revealed that although charge is relatively localised at oxygen centers there is not necessarily a clear charge separation between the inner- and outer-Helmholtz planes. The Proximity and Smit models are presented as alternative surface complexation schemes to provide a molecularly and electronically consistent depiction of the mineral/solution interface. These models are also presented in their capability in accounting for results from large-scale molecular models. It should nonetheless be emphasized that the Charge Distribution model remains a valuable approach and should have the best applicability at low surface loadings and with molecules with sizes similar to those of the compact layer.
2007. "Effects of surface coordination on the temperature-programmed desorption of oxalate from goethite." Journal of Physical Chemistry C 111(45):17072-17081. doi:10.1021/jp075576q Abstract The temperature-programmed desorption (TPD) of weakly-bound, hydrogen-bonded and metal-bonded oxalate complexes at the goethite surface was investigated in the 300-900 K range with concerted Fourier Transform Infrared (FTIR) measurements (TPD-FTIR). These reactions took place with the concomitant dehydroxylation reaction of goethite to hematite and decarbonation of bulk-occluded carbonate. The measurements revealed three important stages of desorption. Stage I (300-440 K) corresponds to the desorption of weakly-and/or un-bound oxalate molecules in the goethite powder with a thermal decomposition reaction pathway characteristic of oxalic acid. Stage II (440-520 K) corresponds to a thermally-driven dehydration of hydrogen-bonded surface complexes, leading to a partial desorption via oxalic acid thermal decomposition pathways and to a partial conversion to metal-bonded surface complexes. This latter mechanism led to the increase in FTIR bands characteristic of these complexes. Finally, Stage III (520-660 K) corresponds to the thermal decomposition of the metal-bonded oxalate complex, proceeding through a 2 electron reduction pathway.
2007. "Preparation of TiO2(110)-(1x1) Surface via UHV Cleavage: An scanning tunneling microscopy study." Review of Scientific Instruments 78(11):Art. No. 113907. doi:10.1063/1.2814160 Abstract TiO2(110) surface was successfully prepared in-situ by UHV cleaving of a commercial TiO2 crystal.. STM imaging revealed atomically flat more than 1 m wide terraces with (110) orientation separated by steps running in [001] direction, with very low kink density. Atomically resolved STM images show periodicity in the [001] and [ ] directions with the unit cell parameters measured to ~3 Å and 6.5 Å respectively which are closed to the expected values of bulk terminated (1x1) surface.
2007. "Surface Chemistry of 2-Propanol on TiO2(110): Low and High Temperature Dehydration, Isotope Effects, and Influence of Local Surface Structure." Journal of Physical Chemistry C 111(29):1105-11067. doi:10.1021/jp072298m Abstract Dosed on rutile TiO2(110) at 100 K, the thermal chemistry of 2-propanol in three forms—C3H7OH, C3D7OD and C3H7OD—was characterized using temperature programmed desorption. Only 2-propanol, propene and water desorb with no evidence for acetone. The propene forms and desorbs by two paths, a heretofore unreported low temperature path extending from 300 to 450 K and, concerning with prior work, a high temperature path peaking between 565 and 575 K. Both paths exhibit isotope effects. The high temperature path is interpreted in terms of decomposition of 2-propoxy species located on bridging oxygen atom rows. The low temperature path is attributed to 2-propanol dehydration on under-coordinated Ti4+ ions of the Ti4+ rows. The low temperature path characteristics vary with the long range order and bridge-bonded oxygen atom vacancy concentration.
2007. "Phonon Anharmonicities in Graphite and Graphene." Physical Review Letters 99(176802):1-4. doi:10.1103/PhysRevLett.99.176802 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. We determine from first principles the finite-temperature properties—linewidths, line shifts, and lifetimes—of the key vibrational modes that dominate inelastic losses in graphitic materials. In graphite, the phonon linewidth of the Raman-active E2g mode is found to decrease with temperature; such anomalous behavior is driven entirely by electron-phonon interactions, and does not appear in the nearly degenerate infrared-active E1u mode. In graphene, the phonon anharmonic lifetimes and decay channels of the A01 mode at K dominate over E2g at T and couple strongly with acoustic phonons, highlighting how ballistic transport in carbon-based interconnects requires careful engineering of phonon decays and thermalization.
2007. "Phosphate Imposed Limitations on Biological Reduction and Alteration of Ferrihydrite Mineralization." Environmental Science & Technology 41(1):166-172. Abstract Biogeochemical transformation (inclusive of dissolution) of iron (hydr)oxides resulting from dissimilatory reduction has a pronounced impact on the fate and transport of nutrients and contaminants in subsurface environments. Despite the reactivity noted for pristine (unreacted) minerals, iron (hydr)oxides within native environments will likely have a different reactivity owing in part to changes in surface composition. Accordingly, here we explore the impact of surface modifications induced by phosphate adsorption on ferrihydrite reduction by Shewanella putrefaciens under static and advective flow conditions. Alterations in surface reactivity induced by phosphate adsorption change the extent, nearly linearly, and pathway of iron biomineralization. Magnetite is the most appreciable mineralization product while minor amounts of vivianite and green rust-like phases are formed in systems having high aqueous concentrations of phosphate, ferrous iron, and biogenic bicarbonate. Goethite and lepidocrocite, characteristic biomineralization products at low ferrous-iron concentrations, are inhibited in the presence of adsorbed phosphate. Considering deviations in reactivity of iron (hydr)oxides with changes in surface composition is important for deciphering mineralization pathways under native conditions and predicting reactive characteristics.
2007. "High-field ⁷⁵As NMR Study of Arsenic Oxysalts." Journal of Magnetic Resonance 188(2):311-321. doi:10.1016/j.jmr.2007.07.005 Abstract Arsenic (bio)geochemistry is of intense current interest because the speciation, mobility, and natural chemical processes involving arsenic compounds are intimately related to its bioavailability and a myriad of negative health effects related to arsenic exposure. Arsenic contamination in the environment is wide-spread due to the historical use of arsenic-bearing chemicals in agriculture and industry as well as the occurrence of natural and anthropogenic arsenic-rich waters in such regions as Bangladesh, South America, and the western United States [1–5].
2007. "NMR Studies of Heat-Induced Transitions in Structure and Cation Binding Environments of a Strontium-Saturated Swelling Mica." Applied Magnetic Resonance 32(4):595-612. doi:10.1007/s00723-007-0042-z Abstract In this work we combined Al, Si, F, and Na magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to characterize the structure and interlayer cation environments in a strontium-saturated member of the swelling mica family before and after a heat induced collapse of the interlayer space.
2007. "Dynamic Phase Shifts in Nanoscale Distance Measurements by Double Electron Electron Resonance (DEER)† ." Journal of Magnetic Resonance 185(2):270-282. doi:10.1016/j.jmr.2006.12.011 Abstract The off-resonant pump pulse used in double electron electron resonance (DEER) measurements produces dynamic phase shifts that are explained here by simple analytic and vector descriptions of the full range of signal behaviors observed during DEER measurements, including: large phase shifts in the signal; changes in the position and shape of the detected echo; and changes in the signal intensity. The dynamic phase shifts depend on the width, amplitude and offset frequency of the pump pulse. Isolated radicals as well as pairs or clusters of dipolar-coupled radicals have the same dynamic phase shift that is independent of pump pulse delay in a typical measurement. A method of calibrating both the pump pulse offset frequency and the pump pulse field strength is outlined. A vector model is presented that explains the dynamic phase shifts in terms of precessing magnetization that is either spin locked or precessing about the effective pump field during the pump pulse. Implications of the dynamic phase shifts are discussed as they relate to setting up, calibrating and interpreting the results of DEER measurements.
2007. "Methanation of carbon dioxide by hydrogen reduction using the Sabatier process in microchannel reactors." Chemical Engineering Science 62(4):1161-1170. doi:10.1016/j.ces.2006.11.020 Abstract This paper describes the development of a microchannel-based Sabatier reactor for applications such as propellant production on Mars or space habitat air revitalization. Microchannel designs offer advantages for a compact reactor with excellent thermal control. This paper discusses the development of a Ru-TiO2 based catalyst using powdered form and its application and testing in a microchannel reactor. The resultant catalyst and microchannel reactor demonstrates good conversion, selectivity, and longevity in a compact device. A chemically reacting flow model is used to assist experimental interpretation and to suggest microchannel design approaches. A kinetic rate expression for the global Sabatier reaction is developed and validated using computational models to interpret packed-bed experiments with catalysts in powder form. The resulting global reaction is then incorporated into a reactive plug-flow model that considers flow within a microchannel reactor.
2007. "NMR resonance assignments of the human high mobility group protein HMGA1." Journal of Biomolecular NMR 38(2):185. doi:10.1007/s10858-006-9116-8 Abstract Human HMGA1 is a 107-residue, non-histone chromatin nuclear factor with a wide sphere of influence including embryogenesis, apoptosis, differentiation, cell proliferation, and cancer development (Reeves, 2001). Because of the repetitive nature of the three DNA-binding domains, strings of glutamic acid residues at the C-terminus, and its unstructured nature in the absence of A-T rich regions of DNA and/or other proteins, backbone assignment for HMGA1 was challenging. Especially useful was the HNN experiment (Planchal et al., 2001), a set of truncated HMGA1 constructs, and some high resolution data collected at a ¹H resonance frequency of 900 MHz. Except for absolute assignment of R60 and R86, all 82 amide were assigned to cross peaks in the ¹H-¹⁵N HSQC spectrum and many of the side chain ¹³C and ¹H resonances were assigned (BMRB code xxxx). The intensity of the amide cross peaks for residues E3 – S9 and S64 – K67 were much weaker than the other amide cross peaks in the ¹H-¹⁵N HSQC spectrum suggesting that even in this unstructured protein there are regions experiencing motion different from the molecule as a whole.
2007. "Structural Transitions from Pyramidal to Fused Planar to Tubular to Core/Shell Compact in Gold Clusters: Au-n (n=21-25)." Journal of Physical Chemistry C 111(11):4190-4198. doi:10.1021/jp068897v Abstract We report a joint theoretical and experimental study of low-lying structures and structural transitions of gold cluster anions Aun- in the size range of n ) 21-25. Well-resolved photoelectron spectra are used to compare with density functional theory calculations and to identify the low-lying structures of the gold cluster anions. Due to the high stability of the tetrahedral Au20, the pyramid-based structures are found to be competitive for n ) 21-23. In addition to the pyramid-based structures, global-minimum searches also reveal two other generic structural types of low-lying clusters in the size range of n ) 21-24, namely, the fused-planar and the hollow-tubular structures. At n ) 24, the pyramid-based structures are no longer competitive and the hollow-tubular structures dominate the low-lying population. At n ) 25, a structural transition from hollowtubular to core/shell compact structure is observed.
2007. "Potential protonation sites in the Al2SiO5 polymorphs based on polarized FTIR spectroscopy and properties of the electron density distribution ." Physics and Chemistry of Minerals 34(5):295-306. Abstract Potential protonation sites within the three aluminosilicate polymorphs, kyanite, sillimanite, and andalusite, have been examined through analysis of (3,-3) bond critical point information in comparison with polarized FTIR spectroscopy of single crystals of kyanite and sillimanite from previous studies and examination with the polarized infrared spectrum of andalusite from this study. Seven peaks were observed, four strong peaks at 3440 cm-1, 3460 cm-1, 3530 cm-1, and 3600 cm-1 and three weak peaks at 3480 cm-1, 3520 cm-1, and 3650 cm-1, when the electric vector is parallel with a, six peaks, three strong at 3440 cm-1, 3460 cm-1, and 3530 cm-1 and three weak peaks at 3480 cm-1, 3520 cm-1, and 3560 cm-1, when the electric vector is parallel with b, and no peaks when the electric vector is parallel with c. The results indicate that hydrogen is located in the (001) plane of andalusite and sillimanite and the (11-1) plane in kyanite as determined from the polarized FTIR spectrum of the three minerals. The concentration of water in the samples of andalusite examined varied between 10 and 15 ppm H20 by weight. Examination of the (3,-3) critical points in comparison with the polarized FTIR indicates that hydrogen will prefer bonding to the O1 and O2 oxygen atoms in andalusite and the O2 and O4 oxygens in sillimanite, which correspond to the oxygen with the highest Laplacian value and the underbonded oxygen in the two structures. In kyanite, comparison of the FTIR spectrum and the bond critical points indicate that hydrogen will bond to the two four-coordinated oxygens, O4 and O6.
2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10):Art.no.104505. Abstract First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300oC. The predicted six waters in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen-bonds to 12 second shell waters in agreement with the putative structure used to analyze the X-ray data, but in disagreement with results reported from conventional molecular dynamics using two- and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shell and the average radii of these shells also agreed very well with the results of the X-ray analysis. Water transfers into and out of the 2nd solvation shell were observed to occur on a picosecond (ps) time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating waters (20 ps). Limited simulations with 128 waters (5 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen-bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum was found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region,
