Scientific Publications 2004
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2004. "Analysis of Some Combination-Overtone Infrared Bands of (SO3)-S-32-O-16." Journal of Molecular Spectroscopy 225(2):109-122. Abstract Several new bands for 32S16O3 have been measured and analyzed. The principal bands observed were v1+v2 (at 1561 cm-1), v1+v4 (at 1594 cm -1) v3+ v4 (at 1918 cm-1), and 3v3 (at 4136 cm-1). Except for 3v3, these bands are very complicated because of (a) the Coriolis coupling between v2 and v4 (b) the Fermi resonance between v1 and 2v4, (c) the Fermi resonance between v1 and 2v2, (d) ordinary l-type resonance that couples levels that differ by 2 in both the k and l quantum numbers, and (e) the vibrational l-type resonance between the A1 and A2 levels of v3+v4. The unraveling of the complex pattern of these bands was facilitated by a systematic approach to the understanding of the various interactions. Fortunately, previous work on the fundamentals permitted good estimates of many constants necessary to begin the assignments and the fit of the measurements. In addition, the use of hot band transitions accompanying the v3 band was an essential aid in fitting the v3+v4 transitions since these could be directly observed for only one of four interacting states. From the hot band analysis we find that the A1 vibrational level is 3.50cm-1 above the A2 level, i.e., r34=1.75236(7) cm-1.
2004. "Colloid Formation in Hanford Sediments Reacted with Simulated Tank Waste." Environmental Science and Technology 38(21):5750-5756. Abstract Solutions of high pH, ionic strength, and aluminum concentration have leaked into the subsurface from underground waste storage tanks at the Hanford Reservation in Washington State. Here, we test the hypothesis that these waste solutions alter and dissolve the native minerals present in the sediments and that colloidal (diameter < 2 m) feldspathoids form. We reacted Hanford sediments with simulated solutions representative of Hanford waste tanks. The solutions consisted of 1.4 or 2.8 mol/kg NaOH, 0.125 or 0.25 mol/kg NaAlO4, and 3.7 mol/kg NaNO3 and were contacted with the sediments for a period of 25 or 40 days at 50 C. The colloidal size fraction was separated from the sediments and characterized in terms of mineralogy, morphology, chemical composition, and electrophoretic mobility. Upon reaction with tank waste solutions, native minerals released Si and other elements into the solution phase. This Si precipitated with the Al present in the waste solutions to form secondary minerals, identified as the feldspathoids cancrinite and sodalite. The solution phase was modeled with the chemical equilibrium model GMIN for solution speciation and saturation indices with respect to sodalite and cancrinite. The amount of colloidal material in the sediments increased upon reaction with waste solutions. At the natural pH found in Hanford sediments (pH 8) the newly formed minerals are negatively charged, similar to the unreacted colloidal material present in the sediments. The formation of colloidal material in Hanford sediments upon reaction with tank waste solutions is an important aspect to consider in the characterization of Hanford tank leaks and may affect the fate of hazardous radionuclides present in the tank waste.
2004. "Analysis of High-Resolution Infrared and CARS Spectra of ³⁴S¹⁸O₃." Journal of Molecular Spectroscopy 223(2004):84-95. Abstract Three fundamental modes and several hot bands of 34S18O3 have been investigated using both infrared spectroscopy and coherent anti-Stokes Raman scattering spectroscopy (CARS). Coriolis coupling effects are particularly noticeable in 34S18O3 due to the close proximity of the v2 and v4 fundamental vibrations, whose wavenumber values are 477.508 64(5) and 502.055 65(4) cm-1. The uncertainties in the last digits are shown in parentheses and are two standard deviations. Hot band transitions from v2, v4 levels give access to infrared inactive v2, v4 combination/overtone levels which interact strongly with levels of the Raman-active v1 symmetric stretching mode due to indirect Coriolis couplings, l-resonances, and Fermi resonances. The result is a complex v1 CARS Q- branch spectrum that is the most perturbed of the four SO3 isotopomers we have studied. The relative importance of these interaction terms on the v1 CARS spectrum is examined in some detail and accurate rovibrational constants are determined for all of the mixed states, leading to deperturbed values of 1004.662(24), 0.000 350 3(9), and 0.000 706 6(12) cm-1 for v1, α1B, and α1C, respectively. The B e value is found to be 0.310 817(12) cm-1, which gives an equilibrium bond length re of 141.7339(3) pm, in excellent agreement with values of 141.7340(1) and 141.7347(7) pm reported earlier for 32S16O3 and 34S16O3.
2004. "Analysis of High-Resolution Infrared and CARS Spectra of ³⁴S¹⁸O₃." Journal of Molecular Spectroscopy 227(1):50-59. Abstract As part of a series of investigations of isotopic forms of sulfur trioxide, high-resolution infrared and coherent anti-Stokes Raman spectroscopies were used to study the fundamental modes and several hot bands of 32S18O3. Hot bands originating from the v2 and v4 bending mode levels have been found to couple strongly to the IR-inactive v1 symmetric stretching mode through indirect Coriolis interactions and Fermi resonances. Coriolis coupling effects are particularly noticeable in 32S18O3 due to the close proximity of the v2 and v4 fundamental vibrations, whose deperturbed wavenumber values are 486.488 13(4) and 504.284 77(4) cm-1. The uncertainties in the last digits are shown in parentheses and are two standard deviations. From the infrared transitions, accurate rovibrational constants are deduced for all of the mixed states, leading to deperturbed values for v1, and of 1004.68(2), 0.000 713(2), and 0.000 348(2) cm-1, respectively. The Be value is found to be 0.310 820(2) cm-1, yielding an equilibrium bond length re of 141.7333(4) pm that is, within experimental error, identical to the value of 141.7339(3) pm reported previously for 34S18O3. With this work, precise and accurate spectroscopic constants have now been determined in a systematic and consistent manner for all the fundamental vibrational modes of the sulfur trioxide D3h isotopomeric forms 32S16O3, 34S16O3, 32S18O3, and 34S18O3.
2004. "Compensating Bends in a 16 base-pair DNA Oligomer Containing a T3A3 Segment: A NMR Study of Global DNA Curvature." Biopolymers 75(6):497-511. Abstract DNA curvature but no single model has been able to explain all the experimental data. An intriguing observation is that AnTn segments ligated in phase exhibit retarded migration in polyacrylamide gel electrophoresis (PAGE) but TnAn segments do not. We have determined a high-resolution structure of a 16 base-pair DNA oligomer [d(CGAGGTTTAAACCTCG)2] containing a T3A3 tract. The refinement included residual dipolar coupling (RDC) restraints. A radius of curvature, Rc, analysis was used to measure the overall bending in the molecule. A plot of the helical axis reference points showed a sigmoidal shape indicating a discontinuity at the central TpA step in the overall curvature. Because of the length of the 16mer it was possible to accurately measure Rc for the two halves of the molecule centered about the TpA step. The Rc for the overall molecule (Rc=128 nm) is large, i.e. a low overall magnitude of global bending, whereas the Rc for the two halves of the molecule (Rc=72 nm) is small indicating a much larger magnitude of localized bending. However the direction of bending in the two halves is in partial opposition leading to cancellation of the overall bending. This indicates that TnAn-containing DNA sequences are strongly and multiply bent locally, but are nearly straight globally which is consistent with PAGE results. The RDC refined structure lacked anomalous features present in NOE-only structures indicating the RDC and NOE measurements have a different sensitivity to conformational dynamics at the central TpA step. Because of its increased length and refinement using RDC restraints, the structure of the 16mer reported here provides new insight into the structural origins of the enigmatic PAGE behavior of AnTn and TnAn tracts and the large amplitude, slow base dynamics observed at TpA steps.
2004. "Microscale Distribution of Cesium Sorbed to Biotite and Muscovite." Environmental Science and Technology 38(4):1017-1023. Abstract Individual 1 – 3 mm biotite and muscovite clasts from Hanford sediment were contacted with 0.001 – 0.08 M CsNO--3, then either left whole or sectioned perpendicular to their basal planes for examination by electron or X-ray microprobe. Cs+ was observed to preferentially sorb to mica edges, steps on mica surfaces, or to fractured regions. The observed localization conformed to hypothesized strong binding to frayed edge sites in preference to sites on basal planes. In section, Cs+ was found to penetrate the mica interior, forming discrete zones of concentration, particularly in muscovite. In biotite, Cs was more abundant, permeating the clasts at low abundance and forming also discrete zones of higher concentration. Concentrated Cs on both clast edges and within clast interiors corresponded to microscopic but relatively extensive zones where K was depleted. The localization of sorbed Cs in areas where K was depleted suggested that weathering reactions caused the formation of frayed edges sites within the micas. Cs+ accessed crystal interiors by diffusion along channels following crystal defects, cracks, or partings where pore fluids had previously migrated to form the interior alteration zones. At nm scale, areas with localized Cs were disordered, confirming that FES were developed in clast interiors. Cs+ that was adsorbed in this manner could be very resistant to desorption, as has been often observed.
2004. "Correlated Atomic Force Microscopy and Flourescence Lifetime Imaging of Live Bacterial Cells." Colloids and Surfaces. B, Biointerfaces 34:205-212. Abstract We report on the imaging of living bacterial cells by using a new correlated tapping-mode atomic force microscopy (AFM) and confocal al fluorescence lifetime imaging microscopy (FLIM). Different methods of preparing the bacterial sample were explored for optimal imaging of Gram-negative Shewanella oneidensis MR-1 cells on poly-1-lysine coated surfaces and agarose gel coated surfaces. We have found that the agarose gel containing 99% buffer can provide a local aqueous environment for single bacterial cells. Furthermore, the cell surface topography can be characterized by tapping-mode in-air AFM imaging for the single bacterial cells that are partially embedded. Using in-air rather than under-water AFM imaging of the living cells significantly enhanced the contrast and single-to-noise ration of the AFM images. Near-field AFM-tip enhanced fluorescence lifetime imaging (AFM-FLIM) holds great promise for obtaining fluorescence images beyond the optical diffraction limited spatial resolution. We have previously demonstrated near-field AFM-FLIM imaging of polymer beads beyond the diffraction limited spatial resolution. Here, as the first step of applying AFM-FLIM on imaging living bacterial cells, we demonstrate a correlated and consecutive AFM topographic imaging, fluorescence intensity imaging, and FLIM imaging to characterize cell polarity.
2004. "Finite Element Method Simulations of the Near-Field Enhancement at the Vicinity of Fractal Rough Metallic Surfaces." Journal of Physical Chemistry B 108(9):2939-2947. Abstract Near-field optical enhancement at metal surfaces and methods such as surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS), fluorescent quenching and enhancement, and various near-field scanning microscopies (NSOM) all depend on a metal’s surface properties, mainly on its morphology and SPR resonant frequency. We report on simulations of the influence of different surface morphologies on electromagnetic field enhancements at the rough surfaces of noble metals and also evaluate the optimal conditions for the generation of a surface-enhanced Raman signal of absorbed species on a metallic substrate. All simulations were performed with a classical electrodynamics approach using the full set of Maxwell’s equations, which were solved with the three-dimensional finite element method (FEM). Two different classes of surfaces where modeled using fractals, representing diffusion limited aggregation growth dendritic structures, such as on eon the surface of electrodes, and second one representing the sponge-like structure used to model surfaces of particles with high porosity, such as metal coated catalyst supports. The simulations depict the high inhomogeneity of an enhanced electromagnetic field as both a field enhancement and field attenuation near the surface. While the diffusion limited aggregation dendritical fractals enhanced the near-field electromagnetic field, the sponge fractals significantly reduced the local electromagnetic field intensity. Moreover, the fractal orders of the fractal objects did not significantly alter the total enhancement, and the distribution of a near-field enhancement was essentially invariant to the changes in the angle of an incoming laser beam.
2004. "Diversity of Contaminant Reduction Reactions by Zero-Valent Iron: Role of the Reductate." Environmental Science and Technology 38(1):139-147 . Abstract Abstract The reactions of 8 model contaminants with 9 types of granular Fe(0) were studied in batch experiments using consistent experimental conditions. The model contaminants (herein referred to as “reductates†because they were reduced by the iron metal) included cations (Cu2+), anions (CrO42-; NO3-; and 5,5’,7,7’-indigotetrasulfonate), and neutral species (2-chloroacetophenone; 2,4,6-trinitrotoluene; carbon tetrachloride; and trichloroethene). The diversity of this range of reductates offers a uniquely broad perspective on the reactivity of Fe(0). Rate constants for disappearance of the reductates vary over as much as 4 orders of magnitude for particular reductates (due to differences in the 9 types of iron) but differences among the reductates were even larger, ranging over almost 7 orders of magnitude. Various ways of summarizing the data all suggest that relative reactivities with Fe(0) varies in the order: Cu2, I4S > 2CAP, TNT > CT, Cr6 > TCE > NO3. Although the reductate has the largest effect on disappearance kinetics, more subtle differences in reactivity due to the type of Fe(0) suggests that removal of Cr6 and NO3 (the inorganic anions) involves adsorption to oxides on the Fe(0), whereas the disappearance kinetics of all other types of reductants is favored by reduction on comparatively oxide-free metal. Correlation analysis of the disappearance rate constants using descriptors of the reductates calculated by molecular modeling (energies of the lowest unoccupied molecular orbitals, LUMO, highest occupied molecular orbitals, HOMO, and HOMO-LUMO gaps) showed that reactivities generally increase with decreasing ELUMO and increasing EGAP (and, therefore, increasing chemical hardness h).
2004. "Bulk Versus Interfacial Aqueous Solvation of Dicarboxylate Dianions." Journal of the American Chemical Society 126(37):11691-11698. Abstract The propensity of certain atomic and small molecular ions for the water/vapor interface has important implications for heterogeneous chemistry at aqueous surfaces. In particular, important tropsopheric reactions involving polluting gases such as ozone or OH and leading to the production of reactive halogen compounds take place at the surface of aqueous sea salt aerosols in the lower marine troposphere(1,2) or salt solution films sprayed over the polar snowpack(3). There is mounting computational and experimental evidence that heavier halides (iodine, bromide, and, to lesser extent, chloride) penetate the aqueous surface, where they can react with atmospheric gases. Among small molecular ions, nitrate and azide were also shown to exhibit a similar surface behavior, Note that the propensity for the water/vapor interface of these ions cannot be attributed to hydrophobicity since they lack any hydrophobic center. Results of molecular dynamics (MD) simulations indicate that in these caseds the main force that drives the above anions to the aqueous surface is their large polarizability (softness).
2004. "An Improved MUSIC Model for Gibbsite Surfaces." Geochimica et Cosmochimica Acta 68(11):A123, (Supplement S). Abstract Here we use gibbsite as a model system with which to test a recently published, bond-valence method for predicting intrinsic pKa values for surface functional groups on oxides. At issue is whether the method is adequate when valence parameters for the functional groups are derived from ab initio structure optimization of surfaces terminated by vacuum. If not, ab initio molecular dynamics (AIMD) simulations of solvated surfaces (which are much more computationally expensive) will have to be used. To do this, we had to evaluate extant gibbsite potentiometric titration data that where some estimate of edge and basal surface area was available. Applying BET and recently developed atomic force microscopy methods, we found that most of these data sets were flawed, in that their surface area estimates were probably wrong. Similarly, there may have been problems with many of the titration procedures. However, one data set was adequate on both counts, and we applied our method of surface pKa int prediction to fitting a MUSIC model to this data with considerable success—several features of the titration data were predicted well. However, the model fit was certainly not perfect, and we experienced some difficulties optimizing highly charged, vacuum-terminated surfaces. Therefore, we conclude that we probably need to do AIMD simulations of solvated surfaces to adequately predict intrinsic pKa values for surface functional groups.
2004. "Computational Modeling of Di-Transition-Metal-Substituted -Keggin Polyoxometalate Anions. Structural Refinement of the Protonated Divacant Computational Modeling of Di-Transition-Metal-Substituted γ-Keggin Polyoxometalate Anions. Structural Refinement of the Protonated Divacant Lacunary Silicodecatungstate ." Inorganic Chemistry 43(24):7702 -7708. doi:10.1021/ic0490674 S0020-1669(04)09067-6 Abstract the abstract for this product is not available at this time.
