Scientific Publications 2008
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2008. "Probing the Electronic and Structural Properties of Doped Aluminium Clusters: MAI12-(M=Li,Cu, and Au)." Journal of Chemical Physics 128(2):Art. No. 024305. doi:10.1063/1.2805386 Abstract Photoelectron spectroscopy (PES) is combined with theoretical calculations to investigate the electronic and atomic structures of three doped aluminum clusters, MAl12 (M = Li, Cu, and Au). Well-resolved PES spectra have been obtained at two detachment photon energies, 266 nm (4.661 eV) and 193 nm (6.424 eV). Basin-hopping global optimization method in combination with density-functional theory calculations has been used for the structural searches. Good agreement between the measured PES spectra and theoretical simulations helps to identify the global minimum structures. It is found that LiAl12‾ (C5v) can be viewed as replacing a surface Al atom by Li on an icosahedral Al13‾, whereas Cu prefers the central site to form the encapsulated D3d-Cu@Al12‾. For AuAl12‾ (C1), Au also prefers the central site, but severely distorts the Al12 cage due to its large size.
2008. "Low-Lying Isomers of the B9- Boron Cluster: The Planar Molecular Wheel Versus Three-Dimensional Structures." Journal of Chemical Physics 129(2):187-193. Article number: 024302. doi:10.1063/1.2948405 Abstract The B9- cluster was found previously to be an unprecedented molecular wheel containing an octacoordinate planar boron with D8h symmetry in a combined photoelectron spectroscopy (PES) and theoretical study [H. J. Zhai et al., Angew. Chem. Int. Ed. 42, 6004 (2003)]. However, the PES spectra of B9- exhibit minor features that cannot be explained by the global minimum D8h structure, suggesting possible contributions from low-lying isomers at finite temperatures. Here we present Car-Parrinello molecular dynamics with simulated annealing simulations to fully explore the potential energy surface of B9- and search for low-lying isomers that may account for the minor PES features. We performed density functional theory (DFT) calculations with different exchange-correlation functionals and ab initio calculations at various levels of theory with different basis sets. Two three-dimensional low-lying isomers were found, both of Cs symmetry, 6.29 (Cs-2) and 10.23 (Cs-1) kcal/mol higher in energy than the D8h structure at the highest CCSD(T) level of theory. Calculated detachment transitions from the Cs-2 isomer are in excellent agreement with the minor features observed in the PES spectra of B9-. The B9- cluster proves to be a challenge for most DFT methods and the calculated relative energies strongly depend on the exchange-correlation functionals, providing an excellent example for evaluating the accuracies of various DFT methods.
2008. "Accelerated Analyte Uptake on Single Beads in Microliter-scale Batch Separations using Acoustic Streaming: Plutonium Uptake by Anion Exchange for Analysis by Mass Spectrometry ." Analytical Chemistry 80(11):4070-4077. doi:10.1021/ac800160n Abstract The use of acoustic streaming as a non-contact mixing platform to accelerate mass transport-limited diffusion processes in small volume heterogeneous reactions has been investigated. Single bead anion exchange of plutonium at nanomolar and sub-picomolar concentrations in 20 microliter liquid volumes was used to demonstrate the effect of acoustic mixing. Pu uptake rates on individual ~760 micrometer diameter AG 1x4 anion exchange resin beads were determined using acoustic mixing and compared with Pu uptake rates achieved by static diffusion alone. An 82 MHz surface acoustic wave (SAW) device was placed in contact with the underside of a 384-well microplate containing flat-bottomed semiconical wells. Acoustic energy was coupled into the solution in the well, inducing acoustic streaming. Pu uptake rates were determined by the plutonium remaining in solution after specific elapsed time intervals, using liquid scintillation counting (LSC) for nanomolar concentrations and thermal ionization mass spectrometry (TIMS) analysis for the sub-picomolar concentration experiments. It was found that this small batch uptake reaction could be accelerated by a factor of about five-fold or more, depending on the acoustic power applied.
2008. "Reduction of Tc(VII) by Fe(II) Sorbed on Al (hydr)oxides." Environmental Science & Technology 42(15):5499-5506. doi:10.1021/es8003156 Abstract Technetium speciation, solubility and sorption behavior is strongly dependent on its valence state. Under oxic conditions, Tc exists as the soluble, weakly-sorbing pertechnetate [TcO4-] anion. The reduced form of technetium, Tc(IV), is stable in anoxic environments and is sparingly soluble as TcO2·xH2O(s). Here we investigate the heterogeneous reduction of Tc(VII) by Fe(II) sorbed on Al (hydr)oxides [diaspore (α-AlOOH) and corundum (α-Al2O3)]. Experiments were performed to study the kinetics of Tc(VII) reduction, examine changes in Fe surface speciation during Tc(VII) reduction (Mössbauer spectroscopy), and identify the nature of Tc(IV)-containing reaction products (X-ray absorption spectroscopy). We found that Tc(VII) was completely reduced by adsorbed Fe(II) within 11d (diaspore suspension) and 4d (corundum suspension). Mössbauer measurements revealed that the Fe(II) signal became less intense with Tc(VII) reduction, and was accompanied by increase in Fe(III) doublet and magnetically-ordered Fe(III) sextet signals, with latter parameters close to those for hematite. Formation of magnetically ordered Fe(III) did not depend on the oxidant nature, as both Tc(VII) or O2 lead to the formation of a virtually identical hematite-like phase. The Fe(II) doublet displayed no differences in Mössbauer parameters before and after Tc(VII) reduction, likely due to Fe(II) adsorption to similar sites and no Fe(II) sorption to or precipitation within solid phases formed. Tc-EXAFS spectroscopy revealed that the final heterogeneous redox product on corundum was similar to Tc(IV) oxyhydroxide, TcO2·xH2O. The formation of precursor polymeric TcnOy (4n-2y)+ chains prior to TcO2⋅xH2O precipitation might explain the formation of the separate TcO2-like phase on corundum without coprecipitated Fe.
2008. "Aluminoborosilicate Waste Glass Dissolution under Alkaline Conditions at 40°C: Implications for a Chemical Affinity-Based Rate Equation." Environmental Chemistry 5(1):73-85. doi:10.1071/EN07058 Abstract Single-pass flow-through (SPFT) experiments were conducted with aluminoborosilicate waste glasses to evaluate how changes in solution composition affect the dissolution rate (r) at 40°C and pH(23°C) = 9.0. The three prototypic low-activity waste (LAW) glasses; LAWE-1A, -95A, and -290A, used in these experiments span a wide range covering the expected processing composition of candidate immobilized low-activity waste (ILAW) glasses. Results suggest incongruent release of Al, B, Na, and Si at low flow-rate (q) to sample surface area (S) [log10 (q/S) < -8.9 (m s-1)] whereas congruent release was observed at high q/S [log10 (q/S) > -7.9 (m s-1)]. Dissolution rates increase from log10 (q/S) ≈ -9.3 to -8.0 (m s-1) and then become constant at log10 (q/S) > -7.9 (m s-1). Forward (maximum) dissolution rates, based on B release, are the same irrespective of glass composition, evident by the dissolution rates being within the experimental error of one another (r1A = 0.0301 ±0.0153 g m-2 d-1, r95A = 0.0248 ±0.0125 g m-2 d-1, and r290A = 0.0389 ±0.0197 g m-2 d-1). Finally these results support the use of a chemical affinity based rate law to describe glass dissolution as a function of solution composition.
2008. "An Experimental Study of the Dissolution Rates of Simulated Aluminoborosilicate Waste Glasses as a Function of pH and Temperature under Dilute Conditions." Applied Geochemistry 23(9):2559-2573. doi:10.1016/j.apgeochem.2008.05.006 Abstract Single-pass flow-through tests were conducted to determine the pH (7 - 12) and temperature (23- 90°C) dependence of kinetic rate-law parameters; ko, η, and Ea, for the dissolution of glass in aqueous solution. Experiments were performed with three prototypic nuclear waste glasses that span a wide compositional range, which covers, with high probability, the expected processing composition range for candidate immobilized low-activity waste (ILAW) glasses. Comparison of the B to Na release rates for one glass was incongruent at 23 and 40°C, and pH(23°C) = 7.0 and 8.0, suggesting two distinct mechanisms are responsible for the Na+ release, namely Na+-H+ ion exchange and matrix dissolution. Matrix dissolution became the dominant dissolution mechanism for all glasses at pH values greater than 9.0 as evident by the congruent release of Al, B, Na, and Si to solution. By combining the results collected for each ILAW glass at pH values greater than 9.0, pH and temperature dependent rate law parameters were determined for Al, B, Na, and Si release. A comparison of the pH power-law coefficient for Al, B, Na, and Si at each temperature suggest that η does not depend on temperature within experimental error and suggests the release of these elements into solution is controlled by the same dissolution mechanism at the forward rate of reaction. The activation energy (Ea), based on B release, range from 52 ±4 to 56 ±6 kJ/mol which suggest that dissolution is a surface-controlled reaction mechanism. The data presented in this manuscript suggest that for these three ILAW glasses the chemical durability for each glass is relatively the same under these test conditions. A lack of compositional dependence on the dissolution rate is observed even though there is as much as a 39 kJ/mol difference in the free energy of hydration (ΔGhyd) among the borosilicate waste glasses tested. This similarity in dissolution rate despite the large ΔGhyd difference is almost certainly the result of the structural similarities between these glasses, which suggests that ILAW glasses have similar, if not identical, polymerization states. This is evident from their almost identical 29Si chemical shifts and molar ratio of the alkali elements, Σ(Na+ K + Li), to the network former elements, Σ(AlIV + BIV + Fe + Si), contained in each glass. The polymerization state is an indication of the number of framework SiO4 linkages contained in the glass network. In general, the greater the number of framework SiO4 linkages the more durable the glass. Finally, in agreement with previous work, these results suggest breakage of the Si-O bond is the rate-determining dissolution mechanism under alkaline conditions [pH(23°C) > 9.0] far from saturation with respect to a alteration phase or phases.
2008. "Highly Accurate CCSD(T) and DFT–SAPT Stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer." Chemphyschem 9(11):1636-1644. doi:10.1002/cphc.200800286 Abstract The CCSD(T) interaction energies for the H-bonded and stacked structures of the uracil dimer are determined at the aug-cc-pVDZ and aug-cc-pVTZ levels. On the basis of these calculations we can construct the CCSD(T) interaction energies at the complete basis set (CBS) limit. The most accurate energies, based either on direct extrapolation of the CCSD(T) correlation energies obtained with the aug-cc-pVDZ and aug-cc-pVTZ basis sets or on the sum of extrapolated MP2 interaction energies (from aug-cc-pVTZ and aug-cc-pVQZ basis sets) and extrapolated ΔCCSD(T) correction terms [difference between CCSD(T) and MP2 interaction energies] differ only slightly, which demonstrates the reliability and robustness of both techniques. The latter values, which represent new standards for the H-bonding and stacking structures of the uracil dimer, differ from the previously published data for the S22 set by a small amount. This suggests that interaction energies of the S22 set are generated with chemical accuracy. The most accurate CCSD(T)/CBS interaction energies are compared with interaction energies obtained from various computational procedures, namely the SCS–MP2 (SCS: spin-component-scaled), SCS(MI)–MP2 (MI: molecular interaction), MP3, dispersion-augmented DFT (DFT–D), M06–2X, and DFT–SAPT (SAPT: symmetry-adapted perturbation theory) methods. Among these techniques, the best results are obtained with the SCS(MI)–MP2 method. Remarkably good binding energies are also obtained with the DFT–SAPT method. Both DFT techniques tested yield similarly good interaction energies. The large magnitude of the stacking energy for the uracil dimer, compared to that of the benzene dimer, is explained by attractive electrostatic interactions present in the stacked uracil dimer. These interactions force both subsystems to approach each other and the dispersion energy benefits from a shorter intersystem separation.
2008. "Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data." Chemphyschem 10(1):282-289. doi:10.1002/cphc.200800718 Abstract Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled thirdorder energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS–MP2, SCSN–MP2 and SCS(MI)–MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.
2008. "Correlation between self-diffusion in Si and the migration mechanisms of vacancies and self-interstitials: An atomistic study." Physical Review. B, Condensed Matter 78:035208. doi:10.1103/PhysRevB.78.035208 Abstract The migration of point defects in silicon and the corresponding atomic mobility are investigated by classical molecular dynamics simulations using the Stillinger-Weber potential and the Tersoff potential. In contrast to most of the previous studies both the point defect diffusivity and the self-diffusion coefficient per defect are calculated separately so that the diffusion-correlation factor can be determined. Simulations with both the Stillinger-Weber and the Tersoff potential show that vacancy migration is characterized by the transformation of the tetrahedral vacancy to the split vacancy and vice versa and the diffusion-correlation factor is about 0.5. This value was also derived by the statistical diffusion theory under the assumption of the same migration mechanism. The mechanisms of self-interstitial migration are more complex. The detailed study, including a visual analysis and investigations with the nudged elastic band method, reveals a variety of transformations between different self-interstitial configurations. Molecular dynamics simulations using the Stillinger-Weber potential show, that the self-interstitial migration is dominated by a dumbbell mechanism, whereas the interstitialcy mechanism prevails with the Tersoff potental. The corresponding values of the correlation factor are different, namely 0.59 and 0.69 for the dumbbell and the interstitialcy mechanism, respectively. The latter value is nearly equal to that obtained by the statistical theory which assumes the interstitialcy mechanism. Recent analysis of experimental results demonstrated, that in the framework of state-of-the-art diffusion and reaction models the best interpretation of point defect data can be given by assuming . The comparison with the present atomistic study leads to the conclusion that a dumbbell mechanism governs the self-interstitial migration in Si. Simulations using the Stillinger-Weber potential reveal two dominating migration paths which are characterized by transformation between the extended <110> dumbbell and the <110> dumbbell and vice versa. This process occurs either in a single {110} plane or includes a change into an equivalent {110} plane.
2008. "Interface mixing of Al/Fe and Fe/Al bilayer systems and the role of Ti as a stabilizing interlayer using Rutherford backscattering spectrometry and x-ray reflectometry." Journal of Applied Physics 103(1):Art. No. 014508. doi:10.1063/1.2829803 Abstract Al/Fe and Fe/Al bilayer films with and without a Ti stabilizing interlayer at the interface have been grown on Si wafers using dc magnetron sputtering. X-ray reflectometry and Rutherford backscattering spectrometry were used to probe individual layer thicknesses and intermixing lengths. It is observed that the intermixing length is always higher when the Fe layer is on top of the Al layer. The samples with the Ti stabilizing layer, particularly when the Al layer is on top of the Fe, show that the Ti layer promotes the formation of abrupt interfaces.
2008. "Isolation and characterization of an NAD+-degrading bacterium PTX1 and its role in chromium biogeochemical cycle." Biodegradation 19(3):417-424. doi:10.1007/s10532-007-9147-1 Abstract Microorganisms can reduce toxic chromate to less toxic trivalent chromium [Cr(III)]. Besides Cr(OH)3 precipitates, some soluble organo-Cr(III) complexes are readily formed upon microbial, enzymatic, and chemical reduction of chromate. However, the biotransformation of the organo-Cr(III) complexes has not been characterized. We have previously reported the formation of a nicotinamide adenine dinucleotide (NAD+)-Cr(III) complex after enzymatic reduction of chromate. Although the NAD+-Cr(III) complex was stable under sterile conditions, microbial cells were identified as precipitates in a non-sterile NAD+-Cr(III) solution after extended incubation. The most dominant bacterium PTX1 was isolated and assigned to Leifsonia genus by phylogenetic analysis of 16S rRNA gene sequence. PTX1 grew slowly on NAD+ with a doubling time of 17 h, and even more slowly on the NAD+-Cr(III) complex with an estimated doubling time of 35 days. The slow growth suggests that PTX1 passively grew on trace NAD+ dissociated from the NAD+-Cr(III) complex, facilitating further dissociation of the complex and formation of Cr(III) precipitates. Thus, organo-Cr(III) complexes might be an intrinsic link of the chromium biogeochemical cycle; they can be produced during chromate reduction and then further mineralized by microorganisms.
