Scientific Publications 2006
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2006. "Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study." Biophysical Journal 91(3):882-891. doi:10.1529/biophysj.106.083816 Abstract The conformational deformability of nucleic acids can influence their function and recognition by proteins. A class of DNA binding proteins including the TATA box binding protein binds to the DNA minor groove, resulting in an opening of the minor groove and DNA bending toward the major groove. Explicit solvent molecular dynamics simulations in combination with the umbrella sampling approach have been performed to investigate the molecular mechanism of DNA minor groove deformations and the indirect energetic contribution to protein binding. As a reaction coordinate, the distance between backbone segments on opposite strands was used. The resulting deformed structures showed close agreement with experimental DNA structures in complex with minor groove-binding proteins. The calculated free energy of minor groove deformation was ~4–6 kcal mol-1 in the case of a central TATATA sequence. A smaller equilibrium minor groove width and more restricted minor groove mobility was found for the central AAATTT and also a significantly (~2 times) larger free energy change for opening the minor groove. The helical parameter analysis of trajectories indicates that an easier partial unstacking of a central TA versus AT basepair step is a likely reason for the larger groove flexibility of the central TATATA case.
2006. "Evaporation of Water from Particles in the Aerodynamic Lens Inlet: An Experimental Study." Analytical Chemistry 78(19):6942-6947. Abstract The extremely high particle transmission efficiency of aerodynamic lens inlets resulted in their wide use in aerosol mass spectrometers. One of the consequences of a transport of particles from high ambient pressure into the vacuum is that it is accompanied by a rapid drop in relative humidity (RH). Since many atmospheric particles exist in the form of hygroscopic water droplets, a drop in RH may result in a significant loss of water and even a change in phase. To predict how much water will be evaporated is not feasible. Because water loss can effect in addition to particle size, its transmission efficiency, ionization probability and mass spectrum it is imperative to provide definitive experimental data that can serve to guide the field to a reasonable and uniform sampling approach. In this study we present the results of a number of carefully conducted measurements that provide the first experimentally determined benchmark of water evaporation from a range of particles, during their transport through an aerodynamic lens inlet. We conclude that the only sure way to avoid ambiguities during measurements of aerodynamic diameter in instruments that utilize low pressure aerodynamic lens inlets is to dry the particles prior to sampling.
2006. "From Agglomerates of Spheres to Irregularly Shaped Particles: Determination of Dynamic Shape Factors from Measurements of Mobility and Vacuum Aerodynamic Diameters." Aerosol Science and Technology 40(3):197-217. Abstract With the advert of aerosol instrumentation it has become possible to simultaneously measure individual particle mobility and vacuum aerodynamic diameters. For spherical particles these two diameters yield individual particle density. In contrast, assigning a physical meaning to the mobility or aerodynamic diameter of aspherical particles is not straightforward. This paper presents an experimental exploration of the effect of particle shape on the relationship between mobility and vacuum aerodynamic diameters. We make measurements on systems of three types: 1) Agglomerates of spheres, for which the density and the volume are known; 2) Ammonium sulfate, sodium chloride, succinic acid and lauric acid irregularly shaped particles of known density; and 3) Internally mixed particles, containing organics and ammonium sulfate, of unknown density and shape. For agglomerates of spheres we observed alignment effects in the DMA and report the first measurements of the dynamic shape factors (DSFs) in free molecular regime. We present here the first experimental determination of the DSF of ammonium sulfate particles. We find for ammonium sulfate particles a DSF that increases from 1.03 to 1.07 as particle mobility diameter increases from 160 nm to 500 nm. Three types of NaC1 particles were generated and characterized: nearly spherical particles with DSF of ~1.02; cubic with DSF that increases from 1.065 to 1.17 as particle mobility diameter increases from 200 nm to 900 nm; and compact agglomerates with DSF 1.3-1.4. Organic particles were found very nearly spherical. The data suggest that particles composed of binary mixtures of ammonium sulfate and succinic acid have lower dynamic shape factors than pure ammonium sulfate particles. However, for internally mixed ammonium sulfate and lauric acid particles we cannot distinguish between nearly spherical particles with low density and particles with DSF of 1.17.
2006. "SpectraMiner, an Interactive Data Mining and Visualization Software for Single Particle Mass Spectroscopy: A Laboratory Test Case." International Journal of Mass Spectrometry 258(1-3):58-73. Abstract Single Particle Mass Spectrometers are sophisticated instruments designed to measure the sizes and compositions of a wide range of individual particles in-situ, in real-time. They characterize hundreds of thousands or millions of particles, generating vast amounts of rich and complex data, the proper mining of which requires dedicated state of the art tools. The analysis of individual particle mass spectra is particularly difficult because of their high dimensionality — each data point, representing a single particle, includes the 450 mass spectral peak intensities, particle size, and time of detection. The first step is to organize the data; a process typically accomplished by grouping particles of similar attributes. Since the common assumption is that the data must be reduced to become manageable, they are typically classified into a small number of clusters (~10) and represented by their average/representative spectra. Our approach is quite different. We have developed a data mining and visualization software package we call SpectraMiner that makes it possible to handle hundreds of clusters without loss of information and thus overcome the limits set by traditional statistical data analysis approaches. Data, which often include over 1 million particle spectra, are organized using K-mean clustering algorithm. The clusters are merged into nodes by sequentially combining similar clusters. The final structure is displayed in a hierarchical dynamical tree or circular dendogram. This interactive dendogram is the visual interface that allows for real-time data mining and exploration. Clicking on any of the clusters/nodes in the dendogram reveals the mass spectral and other detailed information about the particles that reside at that position. At each step the scientist is in control of the level of detail and the visualization format, rapidly switching between them while running the program on an office PC.
2006. "Probing The Electronic Properties of Dichromium Oxide Clusters Cr2On-(n=1-7) Using Photoelectron Spectroscopy." Journal of Chemical Physics 125(16):Art. No. 164315. Abstract In an effort to elucidate the variation of the electronic structure as a function of oxidation and composition, we investigated an extensive series of dichromium oxide clusters, Cr2On- (n = 1-7) using photoelectron spectroscopy (PES). Well-resolved PES spectra were obtained at several photon energies. While low photon energy spectra yielded much better spectral resolution, high photon energy data allowed both Cr 3d- and O 2p-dreived detachment features to be observed. The overall spectral evolution of Cr2On– exhibits a behavior of sequential oxidation with increasing oxygen content, where low binding energy Cr 3d-based spectral features diminish in numbers and the spectra shift towards higher binding energies as a result of charge transfer from Cr to O. Evidence was obtained for the population of low-lying isomers for Cr2O2-, Cr2O3-, and Cr2O6-. The current data are compared with previous studies and with related studies on W2On- and Mo2On-.
2006. "Gold Apes Hydrogen. The Structure and Bonding in the Planar B7Au2- and B7Au2 Clusters." Journal of Physical Chemistry A 110(5):1689-1693. Abstract We produced the B7Au2- mixed cluster and studied its electronic structure and chemical bonding using photoelectron spectroscopy and ab initio calculations. The photoelectron spectra of B7Au2- were observed to be relatively simple with vibrational resolution, in contrast to the complicated spectra observed for pure B7-, which had contributions from three isomers (Alexandrova et al., J. Phys. Chem. A, 2004, 108, 3509). Theoretical calculations show that B7Au2- possesses an extremely stable planar structure, identical to that of B7H2-, demonstrating that Au mimics H in its bonding to boron, analogous to the Au-Si bonding. The ground state structure of B7Au2- (B7H2-) can be viewed as adding two Au (H) atoms to the terminal B atoms of a higher-lying planar isomer of B7-. The bonding and stability in the planar B7Au2- (B7H2-) clusters are elucidated on the basis of the strong covalent B-Au (H) bonding and the concepts of aromaticity/antiaromaticity in these systems.
2006. "Solution structure of the complex between poxvirus-encoded CC chemokine inhibitor vCCI and human MIP-1β." Proceedings of the National Academy of Sciences of the United States of America 103(38):13985-13990. doi:10.1073/pnas.0602142103 Abstract Chemokines (chemotactic cytokines) comprise a large family of proteins that recruit and activate leukocytes, giving chemokines a major role in both the immune response and inflammation-related diseases. The poxvirus-encoded viral CC chemokine inhibitor (vCCI) binds to many CC chemokines with high affinity, acting as a potent inhibitor of chemokine action. We have used heteronuclear multidimensional NMR to determine the first structure of an orthopoxvirus vCCI in complex with a human CC chemokine MIP-1β. vCCI binds to the chemokine with 1:1 stoichiometry, using residues from its β-sheet II to interact with the a surface of MIP-1β that includes the N-terminus, the following residues in the so-called N-loop20’s region, and the 40’s loop. This structure reveals a general strategy of vCCI for selective chemokine binding, as vCCI appears to interact most stronglyinteracts most directly with residues that are conserved among a subset of CC chemokines, but are not conservednot among the other chemokine subfamilies. This structure reveals a general strategy of vCCI for selective chemokine binding. Chemokines play critical roles in the immune system, causing chemotaxis of a variety of cells to sites of infection and inflammation, as well as mediating cell homing and immune system development 1(Baggiolini 2001). To date, about 50 chemokines have been identified, and these small proteins (7-14 kDa) are believed to function by binding with endothelial or matrix glycosaminoglycans to form a concentration gradient that is then sensed by high affinity, 7-transmembrane domain G-protein coupled chemokine receptors on the surface of immune cells surface. The chemokine system is critical for host defense in healthy individuals, butand can also lead to diseases including asthma, arthritis, and atherosclerosis in the case of malfunction, often due to inappropriate inflammation and subsequent tissue damage 2(Gerard and Rollins 2001). There are four subfamilies of chemokines, CC, CXC, C, and CX3C, named for the position of conserved N-terminal cysteine residues. Members of the same subfamily often have overlapping receptor binding and cell activation ability while different subfamilies tend to functionwork on different cell subsets1{Baggiolini, 2001 #472} (REF). For example, CC chemokines mostly interact with monocytes, macrophages, T cells and eosinophils, while CXC chemokines mainly interact with neutrophils. Structures of chemokines from different subfamilies have been solved by NMR and X-ray crystallography (XXX Include Fernandez and Lolis review) 3-9{Clore, 1990 #91;Skelton, 1995 #97;Handel, 1996 #93;Crump, 1997 #92;Crump, 1998 #248;Meunier, 1997 #96;Fernandez, 2002 #496}(Clore 1990; Skelton 1995; Handel and Domaille 1996; Crump, Gong et al. 1997; Meunier 1997; Crump, Rajarathnam et al. 1998)(Clore 1990; Skelton 1995; Handel and Domaille 1996; Crump et al. 1997; Meunier 1997; Crump et al. 1998).
2006. "A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry." Proteomics 6(15):4286-4299. doi:10.1002/pmic.200500930 Abstract Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins from Desulfovibrio vulgaris grown at exponential or stationary phase on a minimal medium containing either lactate or formate as the primary carbon source, with the goal of an initial characterization of the diversity of proteins synthesized under these conditions. Across all four growth conditions, 976 gene products were identified with high confidence, which is equal to approximately 28% of all predicted proteins in the D. vulgaris genome. Among these, fifty-two out of 55 predicted ribosomal proteins (~95%) were identified with high confidence. Functional analysis showed that the proteins identified were distributed among almost all functional classes, with the energy metabolism category containing the greatest number of identified proteins. At least 154 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins, which provided verification for the authenticity of these hypothetical proteins. Proteomic analysis showed that members of the proton gradient pathway, catalyzed by alcohol dehydrogenases and heterodisulfide reductases, and [NiFe] hydrogenase (HynAB-1) of the hydrogen cycling pathway were highly expressed in all four growth conditions, suggesting they may be the primary pathways for ATP synthesis in D. vulgaris. Most of the enzymes involved in substrate-level phosphorylation were also detected in all tested conditions. However, no enzyme involved in CO cycling or formate cycling was detected, suggesting these are not the primary pathways for ATP biosynthesis under the tested conditions. This study provides the first proteomic overview of the cellular metabolism of D. vulgaris.
2006. "LC-MS/MS Based Proteomic Analysis and Functional Inference of Hypothetical Proteins in Desulfovibrio Vulgaris." Biochemical and Biophysical Research Communications 349(4):1412-1419. doi:10.1016/j.bbrc.2006.09.019 Abstract Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins extracted from Desulfovibrio vulgaris cells. While our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions (Zhang et al., 2006a, Proteomics, 6: 4286-4299), this study describes the global detection and functional inference for hypothetical D. vulgaris proteins. Across six growth conditions, 15,841 tryptic peptides were identified with high confidence. Using a criterion of peptide identification from at least two out of three independent LC-MS/MS analyses per protein, 176 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins. These proteins ranged from 6.0 to 153 kDa, and had calculated pI values ranging from 3.7 to 11.5. Based on homology search results (with E value <= 0.01 as a cutoff), 159 proteins were defined as conserved hypothetical proteins, and 17 proteins were unique to the D. vulgaris genome. Functional inference of the conserved hypothetical proteins was performed by a combination of several non-homology based methods: genomic context analysis, phylogenomic profiling, and analysis of a combination of experimental information including peptide detection in cells grown under specific culture conditions and cellular location of the proteins. Using this approach we were able to assign possible functions to 27 conserved hypothetical proteins. This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification for the authenticity of hypothetical proteins and improve annotation for the D. vulgaris genome.
2006. "Electronic Stopping Forces of Heavy Ions in Metal Oxides." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 249(1-2):18-21. doi:10.1016/j.nimb.2006.03.013 Abstract Electronic energy loss of charged particles in materials is a fundamental process accountable for the unique response of materials in applications of advanced nuclear power, radiation detectors, and advanced processing of electronic devices. For over a century, the stopping of energetic ions in matter has been a subject of great experimental and theoretical interest. In spite of a long history of studies, the electronic stopping force is not adequately described over all ranges of ions, energies and targets, particularly in the case of heavy ions in compound targets. In this study, stopping powers for ions in ceramic oxides of SiO2, ZrO2, Ta2O5 and Nb2O5 have been determined using a time-of-flight energy elastic recoil detection analysis (ToF-E ERDA) set-up. In transmission geometry, the energy loss of heavy ions in the thin foils was measured over a continuous range of energies from a few 10 keV/nucleon to over a thousand keV/nucleon using the ToF data that was tagged by a Si detector with and without the stopping foils. Comparisons are made with the SRIM-2003 (The Stopping and Range of Ions in Matter) predictions, and deviations are discussed.
2006. "Electronic Stopping Powers for Heavy Ions in Niobium and Tantalum Pentoxides." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 250(1-2):62-65. doi:10.1016/j.nimb.2006.04.148 Abstract Electronic energy loss is the fundamental mechanism accountable for the response of materials to swift heavy ions that drives many new applications. Due to experimental difficulties in preparing and handling compound targets for energy-loss measurements, stopping data in compounds are very limited. The electronic stopping power of He, Li, Be and O ions in self-supporting foils of niobium and tantalum pentoxides (Nb2O5 and Ta2O5) have been measured in transmission over a continuous range of energies. The measured stopping powers are compared with theoretical predictions based on the SRIM (stopping and range of ions in matter) code. In general, the predicted values are in reasonable agreement with the experimental data. However, significant deviations are observed in some cases, particularly around the stopping maximum.
2006. "Irradiation behavior of SrTiO3 at temperatures close to the critical temperature for amorphization." Journal of Applied Physics 100(11):113533 (8 pages). doi:10.1063/1.2399932 Abstract Damage accumulation on both the Sr and Ti sublattices in strontium titanate (SrTiO3) has been investigated under 1.0 MeV Au+ irradiation at 360 and 400 K, close to the critical temperature for amorphization (~ 370 K). Under irradiation at 360 K, the relative disorder on both sublattices follows a nonlinear dependence on ion dose. Amorphization starts from the damage peak region (at a depth of 60 nm) and grows toward the surface and into the bulk. At 400 K, evolution of point defects to extended defects occurs as ion fluence increases. The disorder initially peaks at a depth of 60 nm, saturates at disorder level of ~0.75, and then decreases with further irradiation. At an ion fluence of 6.0×1015 cm-2, an amorphous layer of ~ 10 nm thickness is formed at the sample surface. After annealing at 375 K for one hour, the microstructural features indicate that the buried amorphous layer formed during irradiation at 360 K is re-crystallized with planar defects and dislocation loops. The surface amorphous layer formed at 400 K irradiation remains amorphous and less defects are observed at the irradiated region. The irradiation-enhanced recrystallization due high flux electron energy deposition is observed.
2006. "Non-linear Damage Accumulation in Au-irradiated SrTiO3." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 251(1):127-132. doi:10.1016/j.nimb.2006.05.018 Abstract Ion-induced damage in strontium titanate (SrTiO3) has been investigated using 1.0 MeV Au ions at 150 K and room temperatures. Rutherford backscattering spectrometry using 2.0 MeV He+ beam was carried out along the <100> direction to study crystalline damage and the accumulation behavior. Damage accumulation has been determined as the relative disorder on the Sr and Ti sublattices at the damage peak as a function of local dose. A disorder accumulation model has been fit to both the Sr and Ti damage accumulation data, and contributions from the amorphous fraction and the crystalline disorder are discussed. The results indicate that defect-stimulated amorphization is the primary amorphization mechanism in SrTiO3. The sigmoidal accumulation behavior in damage accumulation leads to non-linear increase of the width of the damage profile.
2006. "Structural Studies of Vγ2Vδ2 T Cell Phosphoantigens." Chemistry & Biology 13(9):985-992. doi:10.1016/j.chembiol.2006.08.007 Abstract Human γδ T cells containing the Vγ2Vδ2 (Vγ9Vδ2) T cell receptor are stimulated by a broad variety of small, phosphorus-containing antigenic molecules called “phosphoantigens”. The structures of several species present in both Mycobacteria (TUBags1-4) and in E. coli and have been reported to contain a formyl-alkyl diphosphate core. Here, we report the synthesis of the lead member of the series, 3-formyl-1-butyl diphosphate. This compound has low activity for γδ T cell stimulation, unlike its highly active isomer (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), necessitating a revision of the structure of TUBag1. Likewise, the structure of the species identified as the pentyl analog (TUBag 2) is revised to 6-phosphogluconate. These results indicate that neither TUBag1 nor the m/e 275 species proposed for TUBag2 are 3-formyl-1-alkyl diphosphates, leading to the conclusion that none of the natural phosphoantigens (TUBags1-4) possess the structures reported previously.
2006. "Study of Hydrogen Stability in Low-k Dielectric Films by Ion Beam Techniques." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 249(1-2):335–338. doi:10.1016/j.nimb.2006.04.022 Abstract With shrinking device geometries into the 0.13 µm technology node, a transition to low-k dielectrics becomes increasingly attractive. Negative bias temperature instability, which is associated with hydrogen migration at elevated temperatures, becomes the main degradation mechanism of concern for conductivity breakdown in semiconductor devices. The possibility of hydrogen release during each of the fabrication process is, therefore, of great interest to the understanding of device reliability. In the current study, various low-k dielectric films were subjected to thermal annealing in N2 ambient at temperatures that are generally used for device fabrication. Rutherford backscattering spectrometry (RBS) and elastic recoil detection analysis (ERDA) were used to investigate composition change and hydrogen redistribution of the dielectric films. The results indicate that organosilicate glass, silicon nitride and silicon oxynitride films were stable at temperatures up to 500 °C. In phosphorus doped silicon glass and plasma-enhanced tetraethylorthosilicate films, significant hydrogen release from the surface region was evident after heat treatment in N2 purged environment at 300 °C for 30 min, further hydrogen release is observed as temperature increases.
2006. "Imaging Adsorbate O-H Bond Cleavage: Methanol on TiO2(110)." Journal of the American Chemical Society 128(13):4198-4199. doi:10.1021/ja058466a Abstract We investigated methanol adsorption and dissociation on bridge-bonded oxygen vacancies of TiO2(110) (1×1) surface using in situ scanning tunneling microscopy. We provide the first direct evidence that methanol dissociates on oxygen vacancies via O-H bond scission rather than C-O scission. For CH3OH coverages lower than the oxygen vacancy concentration, stationary methoxy-hydroxyl pairs form. At CH3OH coverages close to the oxygen vacancy concentration undissociated mobile CH3OH interacts with methoxy-hydroxyl pairs and facilitates the movement of hydroxyl away from the methoxy group
2006. "Imaging Water Dissociation on TiO2(110): Evidence for Inequivalent Geminate OH Groups." Journal of Physical Chemistry B 110(43):21840-21845. doi:10.1021/jp063619h Abstract Identical regions of partially reduced TiO2(110) surfaces with bridge-bonded oxygen vacancy (BBOV) concentrations of ~ 10 % ML (1 ML = 5.2×1014 cm-2) were imaged using scanning tunneling microscopy (STM) before and after dosing H2O at ambient temperature (~ 300 K). Provided the H2O coverage is less than the BBOV concentration, atomically resolved images confirm that the titration of individual BBOV by dissociative adsorption of H2O is strongly favored. The products are two hydroxyl species, one positioned at BBOV and denoted OHV and the other, denoted OHB, formed by protonation at either of the two nearest-neighbor bridge-bonded oxygen atoms. Proton hopping along the [001] direction is observed at ambient temperature, with a strong preference for OHB (~ 10x) proton motion. This powerful imbalance demonstrates the inequality of OHV and OHB and suggests differences in their charge and/or binding configuration.
2006. "Catalytic oxidation of HCN over a 0.5% Pt/Al2O3 catalyst." Applied Catalysis. B, Environmental 65(2006):282-290. doi:10.1016/j.apcatb.2006.02.009 Abstract The adsorption of HCN on, its catalytic oxidation with 6% O2 over 0.5% Pt/Al2O3, and the subsequent oxidation of strongly bound chemisorbed species upon heating were investigated. The observed N-containing products were N2O, NO and NO2, and some residual adsorbed N-containing species were oxidized to NO and NO2 during subsequent temperature programmed oxidation. Because N-atom balance could not be obtained after accounting for the quantities of each of these product species, we propose that N2 and was formed. Both the HCN conversion and the selectivity towards different N-containing products depend strongly on the reaction temperature and the composition of the reactant gas mixture. In particular, total HCN conversion reaches 95% above 250 C. Furthermore, the temperature of maximum HCN conversion to N2O is located between 200 and 250 C, while raising the reaction temperature increases the proportion of NOx in the products. The co-feeding of H2O and C3H6 had little, if any effect on the total HCN conversion, but C3H6 addition did increase the conversion to NO and decrease the conversion to NO2, perhaps due to the competing presence of adsorbed fragments of reductive C3H6. Evidence is also presented that introduction of NO and NO2 into the reactant gas mixture resulted in additional reaction pathways between these NOx species and HCN that provide for lean-NOx reduction coincident with HCN oxidation.
2006. "Effects of crystallinity on dilute acid hydrolysis of cellulose by cellulose ball-milling study." Energy and Fuels (20):807-811. Abstract The dilute acid (0.05 M H2SO4) hydrolysis at 175 oC of samples comprising varying fractions of crystalline (I) and amorphous cellulose was studied. The amorphous content, based on XRD and NMR, and the product (glucose) yield, based on HPLC, increased by as much as a factor of three upon ball milling. These results are interpreted in terms of a model involving mechanical disruption of crystallinity by breaking hydrogen bonds in Icellulose, opening up the structure and making more -1,4 glycosidic bonds readily accessible to the dilute acid. However, in parallel with hydrolysis to form liquid phase products, there are reactions of amorphous cellulose that form solid degradation products.
2006. "Fractional factorial study of HCN removal over a 0.5% Pt/Al₂O₃ catalyst: effects of temperature, gas flow rate, and reactant partial pressure ." Industrial and Engineering Chemistry Research 45(3):934-939. doi:10.21/ie048777e Abstract Fractional factorial design was used to determine which factors have significant effects on the HCN (hydrogen cyanide) oxidation reaction over 0.5% Pt/Al₂O₃ under lean conditions. We conclude that the reaction temperature and gas-hourly space velocity (GHSV) have significant effects on the HCN conversion, while no significant effects are caused by the presence of either NO (nitric oxide) or C₃H₆ (propene). A central composite design was used to study the effects of temperature and GHSV on HCN conversion, C₃H₆ conversion and NOx selectivity. Based on a second polynomial equation model, regression analysis was used to study the significance of each variable term and derive equations for each response. Our results show that HCN conversion was significantly affected by temperature (X3), GHSV (X4), a temperature polynomial term (X32), and a temperature and GHSV interaction term (X3X4). HCN conversion decreased with increasing values of GHSV and increased with increasing temperature, up to a transition temperature that depends on the GHSV value. The variables of temperature (X3), GHSV (X4), and the temperature polynomial term (X32) have significant effects on both C₃H₆ conversion and NOx selectivity, but in these two cases the interaction of temperature and GHSV was not significant. Contour plots of HCN conversion, C₃H₆ conversion, and NOx selectivity versus temperature and GHSV were constructed from an analysis of the measured data, and these plots can be utilized to estimate HCN conversion, C₃H₆ conversion, and NOx selectivity over the range of temperatures and GHSV investigated. Optimum catalyst operation is described by high HCN conversion and low NOx selectivity. These results show C and o that the highest HCN conversion was achieved at temperatures above 250 relatively low GHSV values, while low NOx selectivity was best achieved at a C.o temperature of 215
2006. "Interplay Between Hydrogen Bonding and Electron Solvation on Hydrated TiO2(110)." Physical Review. B, Condensed Matter 73:195309-1-195309-10. doi:10.1103/PhysRevB.73.195309 Abstract We present density functional theory calculations of partially hydrated or “wet”-electron states on H2O and H-covered TiO2(110) surfaces. Based on the investigation of different coverages and structures, we determine different patterns of hydrogen bonding for the chemisorbed H2O and H on TiO2(110). We find that a network of dangling H atoms can stabilize photoexcited electrons, in so-called wet-electron states. The energies of the wet-electron states correlate closely with the number and configuration of the dangling H atoms. The effect of the adsorbate chemisorption on the surface charge distribution is also discussed. The calculated energies of the wet-electron states are in good agreement with those measured in two-photon photoemission experiments.
2006. "Solvated Electrons on Metal Oxide Surfaces." Chemical Reviews 106:4402-4427. doi:10.1021/cr050173c Abstract An electron added to a solvent polarizes its surrounding medium to minimize the free energy. Such an electron with its polarization cloud, which we refer to as the solvated electron, is one of the most fundamental chemical reagents of significant experimental and theoretical interest. The structure and dynamics of solvated electrons in protic solvents have been explored ever since the discovery of intense blue coloration in solutions of alkali metals in ammonia.1-3 Because solvated electrons are the most fundamental chemical reagents as well as carriers of negative charge, substantial experimental and theoretical efforts have focused on elucidating their equilibrium structure and solvation dynamics in a variety of neat liquids.4,5 One of the most important but least explored environments for solvated electrons, namely, the two-dimensional liquid/solid and liquid/vacuum interfaces, is the subject of this review.
2006. "Single-Walled Carbon Nanotube Paper as a Sorbent for Organic Vapor Preconcentration." Analytical Chemistry 78(7):2442-2446. Abstract Single-walled carbon nanotubes in paper form are characterized as an adsorptive material for a thermally-desorbed preconcentrator for organic vapors. Adsorbed vapors were released by a temperature programmed desorption method and detected downstream. The tested vapors, methyl ethyl ketone, toluene, and dimethyl methylphosphonate were released from the packed column at different temperatures and simple mixtures could be partially separated by the thermal desorption process.
2006. "Fe/C Interactions During SWNT Growth with C2 Feedstock Molecules: A Quantum Chemical Molecular Dynamics Study." Journal of Nanoscience and Nanotechnology 6(5):1259-1270. Abstract An abstract for this journal article is not available at this time.
2006. "Origin of the Linear Relationship between CH2/NH/O-SWNTReaction Energies and Sidewall Curvature:Armchair Nanotubes." Journal of the American Chemical Society 128(47):15117-15126. doi:10.1021/ja061306u 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. The origin of the linear relationship between the reaction energy of the CH2/NH/O exo and endo additions to armchair (n, n) single-walled carbon nanotubes (SWNTs) and the inverse tube diameter (1/d) measuring sidewall curvature was elucidated using density functional theory and density functional tight binding methods for finite-size SWNT models with n ) 3, 4, ..., 13. A nearly perfect linear relationship between ¢E and 1/d all through exohedral (positive curvature) and endohedral (negative curvature) additions is due to cancellation between the quadratic contributions of the SWNT deformation energy and the interaction energy (INT) between the deformed SWNT and CH2/NH/O adducts. Energy decomposition analysis shows that the quadratic contributions in electrostatic, exchange, and orbital terms mostly cancel each other, making INT weakly quadratic, and that the linear 1/d dependence of INT, and therefore of ¢E, is a reflection of the 1/d dependence of the back-donative orbital interaction of b1 symmetry from the occupied CH2/NH/O pð orbital to the vacant CdC ð* LUMO of the SWNT. We also discuss the origin of the two isomers (open and three-membered ring) of the exohedral addition product and explain the behavior of their associated minima on the C-C potential energy surfaces with changing d.
2006. "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach ." Mass Spectrometry Reviews 25(3):450-482. Abstract Proteomics, and the larger field of systems biology, have recently demonstrated utility in both the understanding of cellular processes on the molecular level and the identification of potential biomarkers of various disease states. The large amount of data generated by utilizing high mass accuracy mass spectrometry for high-throughput proteomics analyses presents a challenge in data processing, analysis and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics analysis and the accompanying data processing tools that have been developed in order to interpret and display the large volumes of data produced.
2006. "Quantum Calculations on Hydrogen Bonds in CertainWater Clusters Show Cooperative Effects." Journal of Chemical Theory and Computation 3(1):103-114. doi:10.1021/ct600139d 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. Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations.
2006. "Observation of Triatomic Species with Conflicting Aromaticity: A1Si2- and A1Ge2-." Journal of Physical Chemistry B 110(20):9743-9746. doi:10.1021/jp060690e Abstract We created mixed triatomic clusters, AlCGe-, AlSi2 -, and AlGe2 -, and studied their electronic structure and chemical bonding using photoelectron spectroscopy and ab initio calculations. Excellent agreement between theoretical and experimental photoelectron spectra confirmed the predicted global minimum structures for these species. Chemical bonding analysis revealed that the AlSi2 - and AlGe2 - anions can be described as species with conflicting (ó-antiaromatic and ð-aromatic) aromaticity. The AlCGe- anion represents an interesting example of chemical species which is between classical and aromatic.
2006. "On the Structure and Chemical Bonding of Si62- and Si62- in NaSi6- Upon Na+ Coordination." Journal of Chemical Physics 124(12):Article No. 124305. doi:10.1063/1.2177254 Abstract Photoelectron spectroscopy was combined with ab initio calculations to elucidate the structure and bonding in Si62- and NaSi6-. Well-resolved electronic transitions were observed in the photoelectron spectra of Si6- and NaSi6- at three photon energies (355, 266, and 193 nm). The spectra of NaSi6- were observed to be similar to those of Si6- except that the electron binding energies of the former are lower, suggesting that the Si6 motif in NaSi6- is structurally and electronically similar to that of Si6-. The electron affinity of Si6 and NaSi6 were measured fairly accurately to be 2.23 ± 0.03 eV and 1.80 ± 0.05 eV, respectively. Global minimum structure searches for Si62- and NaSi6- were performed using Gradient Embedded Genetic Algorithm followed by B3LYP, MP2 and CCSD(T) calculations. Vertical electron detachment energies (VDEs) were calculated for the lowest Si6- and NaSi6- structures at the CCSD(T)/6-311+G(2df), ROVGF/6-311+G(2df), UOVGF/6-311+G(2d), TD B3LYP/6-311+G(2df) levels of theory. Experimental VDEs were used to verify the global minimum structure for NaSi6-. Though the octahedral Si62-, analogous to the closo-form of borane B6H62-, is the most stable form for the bare hexa-silicon dianion, it is not the kernel for the NaSi6- global minimum. The most stable isomer of NaSi6- is based on a Si62- motif, which is distorted into C2v symmetry similar to the ground state structure of Si6-. The octahedral Si62- coordinated by a Na+ is a low-lying isomer and was also observed experimentally. The chemical bonding in Si62- and NaSi6- was understood using NBO, molecular orbital, and ELF analysis.
2006. "Theoretical Probing of Deltahedral Closo-AuroBoranes BxAux2⁻(x = 5-12)." Inorganic Chemistry 45(14):5269-5271. doi:10.1021/ic060615i Abstract Since the discovery of boron hydrides (boranes) by Stock in 1912, these compounds have played a major role in advancing chemical bonding theory beyond the classical idea of two-center two-electron bonds. Longuet-Higgins and Lipscomb et al. first put forward the concept of three-center two-electron bonding to explain the structures of all known boron hydrides, in which the bridging B-H-B bond appeared to be the key structural unit. This represents a milestone in establishing the validity of the molecular orbital theory.
