Scientific Publications 2004
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
W
2004. "Precipitation of Au Nanoclusters in SrTiO₃ by Ion Implantation." Journal of Applied Physics 95(9):5060-5068. Abstract Gold nanoclusters dispersed in single crystal SrTiO₃(001) have been prepared by ion implantation at both 300 K and 975 K followed by annealing at 1275 K for 10 hours. Transmission electron microscopy (TEM), high-resolution TEM, high angle annular dark-filed (HAADF) imaging in an aberration corrected dedicated scanning TEM (STEM), and image simulations were used to study the morphology, size, and crystallographic orientation of the Au nanoclusters with respect to the SrTiO₃ matrix, as well as the interface structure between the Au nanoclusters and SrTiO₃. Implantation of gold at 300 K leads to amorphization of SrTiO₃ surface layer, which is corrugated to form bumps and valleys on the surface. Annealing at 1275 K for 10 hours leads to epitaxial re-crystallization of the amorphized layer within which Au clusters of several nanometers and a narrow size distribution were formed. Implantation at 975 K and subsequently annealing leads to Au cluster size of ~ 50 nm and a very wide size distribution. The precipitated Au clusters possess an epitaxial orientation with the SrTiO₃, such that Au[001]//SrTiO₃[001] and Au(100)//SrTiO₃(100). The critical size of the Au cluster for transition from strain-matched interface to dislocation relaxed interface has been found to be ~ 7 nm. Cavities formed by condensation of vacancies were faceted along {001} and {011} planes in the SrTiO₃ matrix. It is generally implied that implantation below a critical temperature may lead to a finer Au cluster size.
2004. "Direct Observation of Substitutional Au Atoms in SrTiO3." Physical Review. B, Condensed Matter and Materials Physics 70(17):172201-172201-4. Abstract Ion implantation and subsequent high-temperature annealing is an effective way to prepare metal nanoclusters dispersed in a dielectric for useful optical and electrical properties. However, there is very little understanding of the nucleation and growth process of these nanoclusters, their correlations with the sites of the implanted ions, and the behavior of defects (such as vacancies) generated during the ion-implantation process. Using high-angle annular dark-field imaging in aberration-corrected scanning transmission electron microscopy, we have directly observed that, at a dilute concentration, Au atoms implanted in SrTiO3 are in a substitutional lattice position for both Sr and Ti. Congregation of Au atoms by diffusion to a critical concentration leads to the nucleation of a Au lattice within the SrTiO3. The Au nanocluster and SrTiO3 were found to maintain an orientation relationship of Au[001]//SrTiO3[001] and Au(100)//SrTiO3(100), which corroborated the results of a first-principles total-energy calculation. The interface between the Au cluster and SrTiO3 was bridged by an O/Ti plane. The Au-O bond length was found to be 2.2 Å, which is the same as Au-O bond length in AuO. Furthermore, the atomic planes adjacent to the interface in both Au and SrTiO3 were found to be slightly stretched. The high concentration of vacancies generated during the Au implantation aggregated to form cavities in the SrTiO3 lattice, and were faceted mostly along the SrTiO3 {100} and (110) planes. The Au and vacancy clusters were spatially associated, indicating a strong interaction. Thus, the formation of cavities in Au-implanted materials indicates that the vacancy-clustering process prevails over the Frenkel-pair recombination.
2004. "Adsorption and Reaction of Acetaldehyde on Stoichiometric and Defective SrTiO₃ (100) Surfaces." Journal of Physical Chemistry B 108(5):1646 - 1652. Abstract The adsorption and reaction of acetaldehyde (CH₃CHO), on stoichiometric (TiO₂-terminated) and reduced SrTiO₃(100) surfaces, have been investigated using temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). Acetaldehyde adsorbs molecularly on the stoichiometric SrTiO₃(100) surface that contains predominately Ti₄⁺ cations. The Ti₄⁺ sites on the stoichiometric SrTiO₃(100) surface are not sufficiently active for surface reactions such as aldol condensation, as opposed to the Ti₄⁺ ions on the TiO₂(001) surface. However, decomposition and redox reactions of acetaldehyde occur in the presence of surface defects created by Ar⁺ sputtering. The decomposition products following reactions of acetaldehyde on the defective surface include H₂, C₂H₄, CO, C₄H₆ and C₄H₈. Reductive coupling, to produce C₂H₄ and C₄H₈, is the main reaction pathway for decomposition of acetaldehyde on the sputter reduced SrTiO₃(100) surface.
2004. "Adsorption and Reaction of Acetaldehyde on Stoichiometric and Defective SrTiO₃(100) Surfaces." Journal of Physical Chemistry B 108(5):1646-1652. Abstract The adsorption and reaction of acetaldehyde (CH₃CHO), on stoichiometric (TiO₂-terminated) and reduced SrTiO₃(100) surfaces, have been investigated using temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). Acetaldehyde adsorbs molecularly on the stoichiometric SrTiO₃(100) surface that contains predominately Ti₄⁺ cations. The Ti₄⁺ sites on the stoichiometric SrTiO₃(100) surface are not sufficiently active for surface reactions such as aldol condensation, as opposed to the Ti₄⁺ ions on the TiO₂ (001) surface. However, decomposition and redox reactions of acetaldehyde occur in the presence of surface defects created by Ar⁺ sputtering. The decomposition products following reactions of acetaldehyde on the defective surface include H₂, C2H₄, CO, C₄H6 and C₄H₈. Reductive coupling, to produce C₂H₄ and C₄H₈, is the main reaction pathway for decomposition of acetaldehyde on the sputter reduced SrTiO₃ (100) surface.
2004. "Rovibrational-State-Selected Pulsed Field Ionization-Photoelectron Study of Methyl Iodide using Two-Color Infrared-Vacuum Ultraviolet Lasers. ." Journal of Chemical Physics 121(15):7049 - 7052. Abstract The abstract for this product is not available at this time.
2004. "Interaction of H₂O and NO₂ with BaY Faujasite: Complex Contraction/Expansion Behavior of the Zeolite Unit Cell ." Journal of Physical Chemistry B 16613-16616 . Abstract In situ time-resolved X-ray diffraction in combination with the Rietveld method was used to study the contraction/expansion behavior of a BaY faujasite zeolite during dehydration and NO₂ adsorption/desorption reactions. The adsorption of water and NO₂ molecules induced a significant contraction of hte zeolite unit cell. The unexpected contraction of the unit cell was closely related to the amount of water and NOx species (NO⁺, NO₂, NO₃⁻) inside the framework. The reaction H₂O + NO₂ --> NO₃⁻ + H⁺ had a substantial effect on the structural properties of the BaY system. The NO₃⁻ groups produced a shift in the position of the Ba cations and a reduction in the zeolite unit cell.
2004. "Significant Interactions between Uranium and Noble-Gas Atoms: Coordination of the UO2+ Cation by Ne, Ar, Kr, and Xe Atoms." Angewandte Chemie International Edition 43(19):2554-2557. Abstract Laser-ablated uranium cation reacts with O2 to give UO2+, which is found to form UO2+(Ng)n (Ng = Ne, Ar, Kr, Xe) complexes on condensation with excess noble gas. Experiments with mixtures of noble gases lead to five new absorptions for the mixed UO2+(Ng)x(Ng')y complexes and show that the coordination number is five for Ng = Ar, Kr, and Xe. These results are consistent with predictions by relativistic density functional calculations and indicate significant bonding between U and noble-gas atoms.
2004. "Highly Active and Stable Rh/MgO-AI2O3 Catalysts for Methane Steam Reforming." Catalysis Today 98(4):575-581. Abstract Highly active and coke-resistant Rh catalysts were developed for methane steam reforming in microchannel chemical reactors. Rh loading was optimized on a stable MgO-Al2O3 support to improve the volumetric productivity for methane conversion. Catalyst activities were stable over a wide range of steam/carbon ratios. In particular, experimental results demonstrated that Rh/MgO-Al2O3 catalysts are extremely active for methane steam reforming and are resistant to coke formation at stoichiometric steam/carbon ratio of 1 for over 14 hours time-on-stream with no sign of deactivation. Methane steam reforming activities on this catalyst is compared in both a microchannel reactor and a conventional microtubular reactor. Significantly enhanced performances were observed in microchannel reactors owing to improved heat and mass transfer.
2004. "Cryogenic Laser Induced Fluorescence Characterization of U(VI) in Hanford Vadose Zone Pore Waters." Environmental Science and Technology 38:5591-5597. Abstract Ambient and liquid helium temperature laser-induced time-resolved uranyl fluorescence spectroscopy was applied to study the speciation of aqueous uranyl solutions containing carbonate and phosphate and two porewater samples obtained by ultra-centrifugation of U(VI)-contaminated sediments. The significantly enhanced fluorescence signal intensity and spectral resolution found at liquid helium temperature allowed, for the first time, direct fluorescence spectroscopic observation of the higher aqueous uranyl complexes with carbonate: UO2(CO3)22-, UO2(CO3)34- and (UO2)2(OH)3CO3-. The porewater samples were non-fluorescent at room temperature. However, at liquid helium temperature, both porewater samples displayed strong, well-resolved fluorescence spectra. Comparisons of the spectroscopic characteristics of the porewaters with those of the standard uranyl-carbonate complexes confirmed that U(VI) in the porewaters existed primarily as UO2(CO3)34-. A small amount of the dicalcium-urano-tricarbonate complex, Ca2UO2(CO3)3, was also observed that was consistent with thermodynamic calculation. The U(VI)-carbonate complex is apparently the mobile species responsible for the subsurface migration of U(VI), even though the majority of the in-ground U(VI) inventory at the site from which the samples were obtained exists as intragrain U(VI)-silicate precipitates.
2004. "Photoelectron Spectroscopy of the Doubly-Charged Anions [MIVO(mnt)2]2- (M=Mo, W; mnt=S2C2(CN)22-): Access to the Ground and Excited States of the [MvO(mnt)2]-Anion." Journal of the American Chemical Society 126(16):5119-5129. Abstract Photodetachment photoelectron spectroscopy was used to investigate the electronic structure of the doubly charged complexes [MIVO(mnt)2]2- (M=Mo, W;mnt=1,2 dicyanoethenedithiolato). These dianions are stable in the gas phase and are minimal models for the active sites of the dimethyl sulfoxide reductase family of molybdenum enzymes and of related tungsten enzymes. Adiabatic and vertical electron binding energies for both species were measured, providing detailed information about molecular orbital energy levels of the parent dianions as well as the ground adn excited states of the product anions [MvO(mnt)2]. Density functional theory calculations were used to assist assignment of the detachment features.
2004. "The Efficiency of Damage Production in Silicon Carbide." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 218:68-73. Abstract Molecular dynamics simulations are used to study the statistics of damage production in 3C-SiC due to C, Si and Au primary knock-on atoms (PKAs) over energies from 0.25 to 50 keV. In order to account for the different displacement energies on the Si and C sublattices and accurately assess the damage efficiency, a modified version of the SRIM (Stopping and Range of Ions in Matter) code, with the electronic stopping turned off to duplicate the molecular dynamics conditions, was used to calculate the statistics of damage production for the same PKAs over the energy range from 0.1 to 400 keV under the binary collision approximation using threshold displacement energies of 20 and 35 eV for C and Si, respectively. Using the modified SRIM predictions as a reference, the efficiencies of total damage production are determined for C, Si and Au PKAs as functions of energy. The efficiency for production of C displacements is similar for all PKAs; however, C PKAs have a much lower efficiency for producing stable Si displacements than Si and Au PKAs, which leads to a much higher ratio of C to Si displacements for C PKAs. These results are consistent with the experimental damage production behavior observed in SiC irradiated with C, Si and Au ions at 150 K.
2004. "Ion-Beam Induced Defects and Nanoscale Amorphous Clusters in Silicon Carbide." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 216:25-35. Abstract Atomic-level simulations have been employed to study the defects and nanoscale disordering induced in 3C-SiC by C, Si, and Au ions with energies up to 50 keV. Energetic C and Si ions primarily produce interstitials, vacancies, antisite defects, and small defect clusters directly during the collision cascade. The overlap of Si cascades produces nanoscale defect clusters. In the case of energetic Au ions, nanoscale amorphous domains are produced directly within the Au cascade along with point defects and smaller clusters. In about 25% of the 50 keV Au cascades, one or more of the subcascades contain nanoscale clusters that exhibit a structure that is consistent with an amorphous state. Structural image simulations of the subcascade structures produced by energetic Si and Au recoils are consistent with experimental high-resolution transmission electron microscopy images. Simulations on close-pair production and recombination in SiC indicate that the activation energies for recombination of most close pairs range from 0.24 to 0.38 eV.
2004. "Thermal Chemistry of Trimethyl Acetic Acid on TiO₂(110)." Journal of Physical Chemistry B 108(11):3592-3602. Abstract Based on temperature programmed desorption and isothermal reaction mass spectrometry, the thermal surface chemistry of trimethyl acetic acid, (CH₃)₃CCOOH, dosed onto a well characterized single crystal TiO₂(110) surface is described. Deprotonation occurs at or below 300 K to form trimethyl acetate, (CH₃)₃CCOO-, and hydroxide, OH-. (CH₃)₃CCOO- is bound to exposed Ti₄⁺ cations and OH- involves a bridging oxygen atom of the substrate. Based on temperature programmed desorption and isothermal reaction mass spectrometry, the desorbing products include (CH₃)₃CCOOH, isobutene (i-C₄H₈), carbon monoxide and water accompanied by smaller amounts of other products including methyl isopropenyl ketone (CH₂=C(CH₃)C(=O)CH₃), isobutane (i-C4H10), and di-t-butyl ketone, (CH₃)₃CC(=O)C(CH₃)₃. Much of the (CH₃)₃CCOO- is relatively stable and decomposes to release mainly carbon monoxide and isobutene above 550 K with a maximum rate at 660 K. Thermal desorption to 750 K leaves a carbon-free surface that is indistinguishable from the initially clean surface. During dosing at 550 K, a steady-state reaction condition is realized with about half the adsorption sites being occupied at any instant.
2004. "A Practical Model for Mobile, Residual, and Entrapped NAPL in Water-Wet Porous Media." Ground Water 42(5):734-746. Abstract Flow of nonvolatile nonaqueous phase liquid (NAPL) and aqueous phases that account for mobile, entrapped, and residual NAPL in variably saturated water-wet porous media is modeled and compared against results from detailed laboratory experiments. Residual saturation formation in the vadose zone is a process that is often ignored in multifluid flow simulators, which might cause an overestimation of the volume of NAPL that reaches the ground water. Mobile NAPL is defined as being continuous in the pore space and flows under a pressure gradient or gravitational body force. Entrapped NAPL is defined as being occluded by the aqueous phase, occurring as immobile ganglia surrounded by aqueous phase in the pore space and formed when NAPL is replaced by the aqueous phase. Residual NAPL is defined as immobile, nonwater entrapped NAPL that does not drain from the pore spaces and is conceptualized as being either continuous or discontinuous. Free NAPL comprises mobile and residual NAPL. The numerical model is formulated on mass conservation equations for oil and water, transported via NAPL and aqueous phases through variably saturated porous media. To account for phase transitions, a primary variable switching scheme is implemented for the oil-mass conservation equation over three phase conditions: (1) aqueous or aqueous-gas with dissolved oil, (2) aqueous or aqueous-gas with entrapped NAPL, and (3) aqueous or aqueous gas with free NAPL. Two laboratory-scale column experiments are modeled to verify the numerical model. Comparisons between the numerical simulations and experiments demonstrate the necessity to include the residual NAPL formation process in multifluid flow simulators.
2004. "Chemically Transformable Configurations of Mercaptohexadecanoic Acid Self-Assembled Monolayers Adsorbed on Au(111)." Langmuir 20(7):2746-2752. Abstract Carboxyl-terminated self-assembled monolayers (SAMs) are commonly used in a variety of applications, with the assumption that the molecules form well-ordered monolayers. In this work, near-edge X-ray absorption fine structure measurements verify that well-ordered monolayers can be formed using acetic acid in the solvent. Disordered monolayers with unbound molecules present in the film result using only ethanol. A stark reorientation occurs upon deprotonation of the end group by rinsing in a KOH solution. This reorientation of the end group is reversible with tilted-over, hydrogen-bound carboxyl groups while the carboxylate ion end groups are upright. C(1s) photoemission shows that SAMs formed and rinsed with acetic acid in ethanol have protonated end groups, while SAMs formed without acetic acid have a large fraction of carboxylate-terminated molecules.
2004. "Dissolution and Growth of (10(1) over-bar4) Calcite in Flowing Water: Estimation of Back Reaction Rates via Kinetic Monte Carlo Simulations." Journal of Crystal Growth 262(1-4):503-518. Abstract Although calcite is an important mineral for many processes, there ae been relatively few simulations of it's growth and dissolution behavior. Such simulations are complicated by the multitude of defect types and by the asymmetry of the crystal. The present work combined a kinetic Monte Carlo (KMC) technique with the Kossel crystal (100) simple cubic concept and the Blasius boundary layer model to simulate the simultaneous growth and dissoution of the (1014)calcite cleavage surface in flowing water. The objective was to determine the activation energies of the back reaction (growth) from those of the forward reaction (dissolution) by obtaining agreement with cleavage-step morphologies and step dissolution velocities previously measured using an atomic force microscope (AFM). Blasius boundary layer conditions for the flowing fluid defined a model that treated the solid, the dissolution/growth interface, and the fluid kinetics. Microscopic reversibility and the laws of large numbers gave an expression for the back reaction activation energies in terms of the forward reaction energies and the entropy of mixing, a quantity estimated from the concentration of desorbates in a very small fluid layer adjacent to the interface. The KMC simulations produced cleavage-step morphologies that were in qualitive agreement with observations from AFM. The kinetics were dominated by diffusion events on the solid/fluid interface and in the fluid, as expected. The relative magniyudes of the desorption and adsorption activation energies were consistent with experimental data, entropic arguments, and crystal roughening theories. Quantitive agrrement with measured step velocities was best when the boundary layer parameters were given physically reasonable values, indicating that the model is self consistent.
2004. "A Non-Watson-Crick Motif on B-pairing on Surfaces for Untethered Oligonucleotides." Molecular Simulation 30(2-3):121-129. Abstract Abstract unavailable for A non-Watson-Crick motif on base-pairing on surfaces for untethered oligonucleotides
2004. "Orientation of DNA on a Surface from Simulation." Biopolymers 73:570-578. Abstract DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40-ns molecular dynamics simulation to study the structure and orientation of a 12-base-pair DNA duplex tethered to a neutral, epoxide-coated silica surface. Starting with a canonical B-form tethered in an up-right position, normal to the surface, the DNA tilted to over 55° and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B-form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface.
2004. "Vibrational Spectroscopy of Trichlorethene Cation by Vacuum Ultraviolet Pulsed Field Ionization-Photoelectron Method ." Chinese Journal of Chemical Physics 17(3):292. Abstract The abstract for this prodcut is not available at this time.
2004. "Vacuum Ultraviolet (VUV) Pulsed Field Ionization-Photoelectron and VUV-IR Photo-Induced Rydberg Ionization Study of Trans-Dichloroethene." Journal of Physical Chemistry A 108(45):9637-9644. Abstract the abstract for this product is not available at this time.
2004. "Two-dimensional Pulsed EPR Studies of Vanadium-Exchanged ZSM-5 ." Journal of Physical Chemistry B 108(41):16128-16134. Abstract The pulsed electron paramagnetic resonance (EPR) technique of hyperfine sublevel correlation spectroscopy (HYSCORE) was used to obtain structural information about vanadium(VO2+) exchanged ZSM-5. HYSCORE spectra were obtained for vanadium exchanged ZSM-5 before and after dehydration and after adsorption of ammonia. For the hydrated samples, proton hyperfine coupling constants were measured and assigned to equatorial water ligands with orientations perpendicular and parallel to the equatorial plane. Nitrogen hyperfine coupling constants for adsorbed ammonia were also determined from the HYSCORE spectra. The results were compared with previous density functional theory (DFT) calculations of hyperfine coupling constants for vanadyl model complexes.
2004. "Remarkable Second-Order Optical Nonlinearity of Nano-Sized Au₂₀ Cluster: A TDDFT Study." Chemical Physics Letters 388(4-6):353-357. Abstract The dipole polarizability, static first hyperpolarizability, and UV-vis spectrum of the recently identified nano-sized tetrahedral cluster of Au₂₀ have been investigated by using time-dependent density functional response theory. We have discovered that the Au₂₀ cluster possesses remarkably large molecular second-order optical nonlinearity with the first hyperpolarizabilty ( βxyz) calculated to be 14.3 x 10⁻³⁰ electrostatic unit (esu). The analysis of the low-energy absorption band suggests that the charge transfer from the edged gold atoms to the vertex ones plays the key role in nonlinear optical (NLO) response of Au₂₀.
2004. "Proofreading activity of Pfu thermostable DNA polymerase on a 6-O-Methylguanine Containing Template Monitored by ESI-FTICR Mass Spectrometry." Chembiochem 5(7):1012-1015. Abstract Abstract DNA damage can take the form of chemical lesions that interfere with DNA polymerization and therefore, the replication of DNA within a cell. In this report we examine the effect of a particular type of base modification, a 6-O-methyl group on a guanine base. Previous reports using different DNA polymerases have identified an induced base substitution. However, this process has not been studied using polymerase chain reaction (PCR) enzyme. Electrospray ionization (ESI) mass spectrometry (MS) was used to examine the effect of this type of base on the PCR. Using Fourier transform ion cyclotron resonance (FTICR) MS, two types of amplification products were clearly resolved, one corresponding to the expected product composition, and one with a dG-dC to dA-dT base substitution. Further investigation found that the same substitution occurred when amplified with an exonuclease (exo-) form of the polymerase (lacking a proofreading function). This technique provides complementary information to other methods and is a sensitive method detecting effects of DNA damage on enzyme polymerization.
