Scientific Publications 2009
2009. "Defect-Enhanced Charge Transfer by Ion-Solid Interactions in SiC using Large-Scale Ab Initio Molecular Dynamics Simulations." Physical Review Letters 103(2):Article number: 027405. doi:10.1103/PhysRevLett.103.027405 Abstract Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge-transfer occurs between atoms and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge transfer effects on recoil atoms.
2009. "Formation and properties of defects and small vacancy clusters in SiC: Ab initio calculations ." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 267(18):2995-2998. doi:10.1016/j.nimb.2009.06.018 Abstract Large-scale ab initio simulation methods have been employed to investigate the configurations and properties of defects in SiC. Atomic structures, formation energies and binding energies of small vacancy clusters have also been studied as a function of cluster size, and their relative stabilities are determined. The calculated formation energies of point defects are in good agreement with previously theoretical calculations. The results show that the most stable configuration of a di-vacancy cluster consists of two C vacancies located at second nearest neighbor sites, while a di-vacancy with two Si vacancies is not stable and may dissociate at room temperature. In general, the formation energies of small vacancy clusters increase with size, but the formation energies for clusters with a Si vacancy and n C vacancies (VSi-nVC) are much smaller than those with a C vacancy and n Si vacancies (VC-nVSi). These results demonstrate that the VSi-nVC clusters are more stable than the VC-nVSi clusters in SiC, and provide possible nucleation sites for larger vacancy clusters or voids to grow. For these small vacancy clusters, the binding energy decreases with increasing cluster size, and ranges from 2.5 to 4.6 eV. These results indicate that the small vacancy clusters in SiC are stable at temperatures up to 1900 K, which is consistent with experimental observations.
2009. "Damage Evolution in GaN Under MeV Heavy Ion Implantation." Journal of Vacuum Science and Technology B--Microelectronics and Nanometer Structures 27(6):2342-2346. doi:10.1116/1.3244591 Abstract Damage evaluation processes in patterned GaN implanted by 3 MeV Au2+ ions were investigated as function of ion fluences and annealing temperatures. Surface swelling was observed by using AFM and the results showed that the swelling height depends on ion fluence and annealing temperature. A four-stage of implantatation-induced damage evolution, including point defects, defect clustering, disordering or amorphization and even decomposition, was found and was contributed to defect formation, accumulation and N bubble formation induced at different level of dpa. Crater-like holes were observed on the surface of GaN implanted at the ion fluence of 2×1016 cm-2, and it is considered as an evidence of N loss and broken bubbles formed during implantation.
2009. "Detecting Weak Interactions between Au- and Gas Molecules: A Photoelectron Spectroscopic and Ab Initio Study." Journal of the American Chemical Society 131(27):9484-9485. doi:10.1021/ja903043d Abstract In this communication, we report a joint experimental and theoretical study of the interactions between gold anion, Au-, and an NG atom (NG ) Ne, Ar, Kr, Xe) or a molecule of O2, CH4, or H2O. Except for the Au- · · ·H2O interaction, which is comparable to strong hydrogen bonding, all of these are weak charge-induced intermolecular interactions. The observation of a weakly bound Au(O2)- complex shows the inertness of Au- toward O2, in line with the previous observation of the odd-even effect in the reactions of Aun - clusters and O2. By comparing with results of high-level ab initio calculations, we demonstrate that anion PES is a good technique for probing weak charge-induced intermolecular interactions.
2009. "Bonded Interactions in Silica Polymorphs, Silicates and Siloxane Molecules ." American Mineralogist 94(8-9):1085-1102. Abstract Experimental model electron density distributions recorded for the silica polymorphs coesite and stishovite are comparable with electron density distributions calculated for a variety of silicates and siloxane molecules. The Si-O bond lengths and Si-O-Si angles calculated with first principles density functional theory methods as a function of pressure are also comparable with the bond lengths and angles observed for coesite and quartz within the experimental error. The similarity of the topological properties of the Si-O bonded interactions and the experimental and the geometry optimized structures for the silica polymorphs provides a basis for understanding the properties and crystal chemistry in terms of a molecular-based model. The agreement supports the argument that the bulk of the structural, physical and thermodynamic properties of the silica polymorphs are intrinsic properties of the molecular-like coordinated polyhedra such that the silica polymorphs can be pictured as ‘supermolecules’ of silica bound by the virtually same forces that bind the Si and O atoms in simple siloxane molecules. The topology of the electron density distribution is consistent with the assertion that the Si-O bonded interaction arises from the net electrostatic attraction exerted on the nuclei by the electron density accumulated between the Si and O atoms. The correlation between the Si-O bond length and Si-O-Si angle is ascribed to the progressive local concentration of the electron density in the nonbonded region of the O atom as the bond length increases and angle decreases rather then to bonded interactions involving the d-orbitals on Si. On the basis of the proximity of the bond critical point, rc, to the nodal surface of the Laplacian, 2(rc), and the values of (rc) and G(rc)/(rc), the Si-O bond qualifies as an intermediate bonded interaction. For bonded interactions of intermediate character, 2(rc) increases linearly as (rc) increases, the greater the shared character, the larger the value of 2(rc). In addition, a mapping of 2(r) serves to highlight those Lewis base domains that are susceptible to electrophilic attack by H like the O atom in coesite involved in bent Si-O-Si angles, the narrower the angle, the greater the affinity for H . On the basis of the net charges conferred on the Si and O atoms and the bonded radii of the two atoms, the Si-O bond of stishovite with six-coordinated Si and three-coordinated O is indicated to be more ionic in character than that in quartz with four-coordinated Si and two coordinated O. Unlike the conclusion reached for ionic and crystal radii (quantum mechanical unobservables), it is the bonded radius of the O atom that increases with the increasing coordination number of Si, not the radius of the Si atom. The modeling of the electron density distributions for quartz, coesite and beryl as a function of pressure indicates that the shared character of the bonded interactions in these minerals increases slightly with increasing pressure. The insight provided by the calculations and the modeling of the electron density distributions and the structures of the silica polymorphs bodes well for future Earth materials studies that are expected to improve and clarify our understanding of the connection between properties and structure within the framework of quantum mechanical observables, to find new and improved uses and to predict new properties for materials and to enhance our understanding of crystal chemistry and chemical reactions of materials in their natural environment at the atomic level
2009. "Role of Directed van der Waals Bonded Interactions in the Determination of the Structures of Molecular Arsenate Solids." Journal of Physical Chemistry A 113(4):736-749. Abstract Bond paths, local energy density properties, and Laplacian, L(r) = −2ρ(r), composite isosurfaces of the electron density distributions were calculated for the intramolecular and intermolecular bonded interactions for molecular solids of As2O3 and AsO2 composition, an As2O5 crystal, a number of arsenate molecules, and the arsenic metalloid, arsenolamprite. The directed intermolecular van der Waals As−O, O−O, and As−As bonded interactions are believed to serve as mainstays between the individual molecules in each of the molecular solids. As−O bond paths between the bonded atoms connect Lewis base charge concentrations and Lewis acid charge depletion domains, whereas the O−O and As−As paths connect Lewis base pair and Lewis acid pair domains, respectively, giving rise to sets of intermolecular directed bond paths. The alignment of the directed bond paths results in the periodic structures adopted by the arsenates. The arrangements of the As atoms in the claudetite polymorphs of As2O3 and the As atoms in arsenolamprite are similar. Like the As2O3 polymorphs, arsenolamprite is a molecular solid connected by relatively weak As−As intermolecular directed van der Waals bond paths between the layers of stronger As−As intramolecular bonded interactions. The bond critical point and local energy density properties of the intermolecular As−As bonded interactions in arsenolamprite are comparable with the As−As interactions in claudetite I. As such, the structure of claudetite I can be viewed as a stuffed derivative of the arsenolamprite structure with O atoms between pairs of As atoms comprising the layers of the structure. The cubic structure adopted by the arsenolite polymorph can be understood in terms of sets of directed acid−base As−O and base−base O−O pair domains and bond paths that radiate from the tetrahedral faces of its constituent molecules, serving as face-to-face key−lock mainstays in forming a periodic tetrahedral array of molecules rather than one based on some variant of close packing. The relatively dense structure and the corrugation of the layers in claudetite I can also be understood in terms of directed van der Waals As−O bonded interactions. Our study not only provides a new basis for understanding the crystal chemistry and the structures of the arsenates, but it also calls for a reappraisal of the concept of van der Waals bonded interactions, how the structures of molecular solids are viewed, and how the molecules in these solids are bonded in a periodic structure.
2009. "The Box H/ACA snoRNP Assembly Factor Shq1p is a Chaperone Protein Homologous to Hsp90 Cochaperones that Binds to the Cbf5p Enzyme." Journal of Molecular Biology 390(2):231-244. doi:10.1016/j.jmb.2009.04.076 Abstract Box H/ACA small nucleolar (sno) ribonucleoproteins (RNPs) are responsible for the formation of pseudouridine in a variety of RNAs and are essential for ribosome biogenesis, modification of spliceosomal RNAs, and telomerase stability. A mature snoRNP has been reconstituted in vitro and is composed of a single RNA and four proteins. However, snoRNP biogenesis in vivo requires multiple factors to coordinate a complex and poorly understood assembly and maturation process. Among the factors required for snoRNP biogenesis in yeast is Shq1p, an essential protein necessary for stable expression of box H/ACA snoRNAs. We have found that Shq1p consists of two independent domains that contain casein kinase 1 phosphorylation sites. We also demonstrate that Shq1p binds the pseudourydilating enzyme Cbf5p through the C-terminal domain, in synergy with the N-terminal domain. The NMR solution structure of the N-terminal domain has striking homology to the ‘Chord and Sgt1’ domain of known Hsp90 cochaperones, yet Shq1p does not interact with the yeast Hsp90 homologue in vitro. Surprisingly, Shq1p has stand-alone chaperone activity in vitro. This activity is harbored by the C-terminal domain, but it is increased by the presence of the N-terminal domain. These results provide the first evidence of a specific biochemical activity for Shq1p and a direct link to the H/ACA snoRNP.
2009. "Excitons in Potassium Bromide: A Study using Embedded Time-dependent Density Functional Theory and Equation-of-Motion Coupled Cluster Methods." Chemical Physics Letters 470(4-6):353-357. doi:10.1016/j.cplett.2009.01.073 Abstract We present a study of the electronic excitations in insulating materials using an embedded- cluster method. The excited states of the embedded cluster are studied systematically using time-dependent density functional theory (TDDFT) and high-level equation-of-motion coupled cluster (EOMCC) methods. In particular, we have used EOMCC models with singles and doubles (EOMCCSD) and two approaches which account for the e®ect of triply excited con¯gurations in non-iterative and iterative fashions. We present calculations of the lowest surface excitations of the well-studied potassium bromide (KBr) system and compare our results with experiment. The bulk-surface exciton shift is also calculated at the TDDFT level and compared with experiment.
2009. "Motions of the Substrate Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling." Journal of the American Chemical Society 131(9):3136-3137. doi:10.1021/ja808217s Abstract The Tetrahymena group I intron recognizes its oligonucleotide substrate in a two-step process. First, a substrate recognition duplex, called the P1 duplex, is formed. The P1 duplex then docks into the prefolded ribozyme core by forming tertiary contacts. P1 docking controls both the rate and the fidelity of substrate cleavage and has been extensively studied as a model for the formation of RNA tertiary structure. However, previous work has been limited to studying millisecond or slower motions. Here we investigated nanosecond P1 motions in the context of the ribozyme using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A nitroxide spin label (R5a) was covalently attached to a specific site of the substrate oligonucleotide, the labeled substrate was bound to a prefolded ribozyme to form the P1 duplex, and X-band EPR spectroscopy was used to monitor nitroxide motions in the 0.1−50 ns regime. Using substrates that favor the docked or the undocked states, it was established that R5a was capable of reporting P1 duplex motions. Using R5a-labeled substrates it was found that the J1/2 junction connecting P1 to the ribozyme core controls nanosecond P1 mobility in the undocked state. This may account for previous observations that J1/2 mutations weaken substrate binding and give rise to cryptic cleavage. This study establishes the use of SDSL to probe nanosecond dynamic behaviors of individual helices within large RNA and RNA/protein complexes. This approach may help in understanding the relationship between RNA structure, dynamics, and function.
2009. "Radionuclide Sensors and Systems for Environmental Monitoring." ECS Transactions 19(6):301-304. doi:10.1149/1.3118565 Abstract We have developed automated sensor and monitoring devices for trace radionuclides in water, using preconcentrating columns and radiometric detection. The preconcentrating minicolumn sensor concept combines selective capture and detection in a single functional unit. We have demonstrated quantification of radionuclides such as technetium-99 to levels below drinking water standards in an equilibration-based process that produces steady state signals, signal proportional to concentration, and easy re-equilibration to new concentration levels. Alternatively, monitors can be developed with separate separation and detection units that are fluidically linked. We have demonstrated detection of strontium-90 to levels below drinking water standards by this approach. We are developing autonomous systems for at-site monitoring on the Hanford Site in Washington State.
2009. "Renewable Surface Fluorescence Sandwich Immunoassay Biosensor for Rapid Sensitive Botulinum Toxin Detection in an Automated Fluidic Format." Analyst 134(5):987 - 996. doi:10.1039/B900794F Abstract A renewable surface biosensor for rapid detection of botulinum toxin is described based on fluidic automation of a fluorescence sandwich immunoassay, using a recombinant fragment of the toxin heavy chain as a structurally valid simulant. Monoclonal antibodies AR4 and RAZ1 bind to separate epitopes of both this fragment and the holotoxin. The AR4 antibody was covalently bound to Sepharose beads and used as the capture antibody. A rotating rod flow cell was used to capture these beads delivered as a suspension by the sequential injection flow system, creating a 3.6 microliter column. After perfusing the bead column with sample and washing away the matrix, the column was perfused with Alexa 647 dye-labeled RAZ1 antibody as the reporter. Optical fibers coupled to the rotating rod flow cell at a 90 degree angle to one another delivered excitation light from a HeNe laser and collected fluorescent emission light for detection. After each measurement, the used sepharose beads are released and replaced with fresh beads. In a rapid screening approach to sample analysis, the toxin simulant was detected to concentrations of 10 pM in less than 20 minutes.
2009. "Products and Kinetics of the Reactions of an Alkane Monolayer and a Terminal Alkene Monolayer with NO₃ Radicals." Journal of Geophysical Research. D. (Atmospheres) 114:D02307 (14 pp). doi:10.1029/2008JD010987 Abstract The reactions of an alkanethiol and a terminal alkenethiol self-assembled monolayer with NO₃ radicals (in the presence of NO₂ and O₂) were studied. For the alkane monolayer, infrared (IR) spectroscopy and time-of-flight secondary ion mass spectrometry (ToF-SIMS) confirmed the formation of organonitrates (RONO₂). The observation of organonitrates is in contrast to the recent X-ray photoelectron spectroscopy (XPS) data, which showed very little nitrogen-containing surface species. The identification of organonitrates may help explain why significant volatilization of the organic chain was not observed in recent studies of alkane monolayer oxidation by NO₃ radicals. The reactive uptake coefficient (g) of NO₃ on alkene monolayers determined in our study is higher than the values obtained in a recent study using liquid and solid alkene bulk films. A possible reason for this difference may be the location of the double bond at the interface. Using the g value determined in our studies, we show that under conditions where NO₃ is high the lifetime of an alkene monolayer in the atmosphere may be short (approximately 20 min). XPS, IR, and ToF-SIMS were used to identify surface functional groups after the oxidation of the alkene monolayers by NO₃. The results are consistent with the formation of C-O, aldehyde/ketone, carboxylic groups, and nitrogen containing species.
2009. "Ab initio DFT+U Study of He Atom Incorporation into UO2 Crystals." Physical Chemistry Chemical Physics. PCCP 11(33):7241-7247. doi:10.1039/b907233k Abstract We present and discuss results of the density functional theory (DFT) for perfect UO2 crystals with He atoms in octahedral interstitial positions therein. We have calculated basic bulk crystal properties and He incorporation energies into the low temperature anti-ferromagnetic UO2 phase using several exchange–correlation functionals within the spin-polarized local density (LDA) and generalized gradient (GGA) approximations. In all DFT calculations we included the on-site correlation corrections using the Hubbard model (DFT+U approach). We analysed a potential crystalline symmetry reduction from tetragonal down to orthorhombic structure and confirmed the presence of the Jahn–Teller effect in a perfect UO2. We discuss also the problem of a conducting electronic state arising when He is placed into a tetragonal antiferromagnetic phase of UO2 commonly used in defect modelling. Consequently, we found a specific monoclinic lattice distortion which allowed us to restore the semiconducting state and properly estimate He incorporation energies. Unlike the bulk properties, the He incorporation energy strongly depends on several factors, including the supercell size, the use of spin polarization, the exchange–correlation functionals and on-site correlation corrections. We compare our results for the He incorporation with the previous shell model and ab initio DFT calculations.
2009. "Influence of samaria doping on the resistance of ceria thin films and its implications to the planar oxygen sensing devices." Sensors and Actuators. B, Chemical 139(2):380-386. doi:10.1016/j.snb.2009.03.021 Abstract In order to evaluate and analyze the effect of samarium (Sm) doping on the resistance of cerium oxide, we have grown highly oriented samaria doped ceria (SDC) thin films on sapphire, Al2O3 (0001) substrates by using oxygen plasma-assisted molecular beam epitaxy (OPA-MBE). The film growth was monitored using reflection high-energy electron diffraction (RHEED) which shows two-dimensional growth throughout the deposition. Following growth, the thin films were characterized by X-ray photoelectron spectroscopy (XPS), high-resolution X-ray diffraction (HRXRD), and Rutherford backscattering spectrometry (RBS). XPS depth-profile shows Sm atoms are uniformly distributed in ceria lattice throughout the bulk of the film. The valence states of Ce and Sm in doped thin films are found to be Ce4+ and Sm3+, respectively. HRXRD shows the samaria doped ceria films on Al2O3(0001) exhibit (111) preferred orientation. Ion-channeling in RBS measurements confirms high quality of the thin films. The resistance of the samaria doped ceria films, obtained by two probe measurement capability under various oxygen pressure (1mTorr-100Torr) and temperatures (623K to 973K), is significantly lower than that of pure ceria under same conditions. The 6Sm% doped ceria film is the optimum composition for highest conductivity. This is attributed to the increased oxygen vacant sites in fluorite crystal structure of the epitaxial thin films which facilitate faster oxygen diffusion through hopping process.