Scientific Publications 2006
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2006. "Theoretical Impact of the Injection of Material into the Myocardium: A Finite Element Model Simulation." Circulation 114:2627-586. doi:10.1161/CIRCULATIONAHA.106.657270 Abstract No abstract is available at this time for this journal article.
2006. "Kinetics of Triscarbonato Uranyl Reduction by Aqueous Ferrous Iron: A Theoretical Study." Journal of Physical Chemistry A 110(31):9691-9701. doi:10.1021/jp062325t Abstract Uranium is a pollutant whose mobility is tied to its oxidation state. While U(VI) in the form of the uranyl cation is capable of being reduced by a range of natural reductants, complexation by carbonate greatly reduces its reduction potential as well as imposing increased electron transfer (ET) distances. Very little is known about the elementary processes involved in uranium reduction from U(VI) to U(V) to U(IV) in general. In this study, we examine the theoretical kinetics of ET from ferrous iron to triscarbonato uranyl in aqueous solution. A combination of molecular dynamics (MD) simulations and density functional theory (DFT) electronic structure calculations are employed to compute the ET parameters that enter into Marcus’ model, including the thermodynamic driving force, reorganization energies, and electronic coupling matrix elements. MD simulations predict that two ferrous iron atoms will bind in an inner-sphere fashion to the three-membered carbonate ring of tricarbonato uranium, forming the charge-neutral Fe2UO2(CO3)3(H2O)8 complex. Through a sequential proton-coupled electron transfer mechanism, the first ET step converting U(VI) to U(V) is predicted by DFT to occur at a rate on the order of 1 s^-1. The second ET step converting U(V) to U(IV) is predicted to be significantly endergonic. Therefore, U(V) is a stabilized end-product in this ET system.
2006. "Atomic level imaging of Au nanocluster dispersed in TiO2 and SrTiO3 ." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 242(1-2):380-382. doi:10.1016/j.nimb.2005.08.144 Abstract Au nanoclusters dispersed in single crystal TiO2 and SrTiO3 have been prepared by ion implantation at 300 and 975 K and subsequent annealing at 1275 K for 10 hours. High resolution transmission electron microscopy and high-angle-annular-dark-field (HAADF) imaging in an aberration corrected scanning transmission electron microscope (STEM) have been used to characterize the microstructure of the dispersed gold nanoclusters. The results indicate that Au atoms substitute for cations in these systems. Cavities of up to several tens of nanometers are observed in TiO2 and SrTiO3. The nanometer-sized cavities and Au clusters are faceted along the same lattice plane of the matrix, indicating that the interfacial energy (defined by the Au cluster and the matrix) and the surface energy of the matrix (defined by cavity and the matrix ) follow a similar trend of change with respect to different lattice planes of the matrix.
2006. "Morphological Evolution of Ba(NO3)2 Supported on -Al2O3(0001): An In-Situ TEM Study." Journal of Physical Chemistry B 110(24):11878-11883. doi:10.1021/jp060235i Abstract One of the key questions for the BaO-based NOx catalyst system is the morphological evolution of Ba(NO3)2 to BaO upon heating for releasing of NOx or vice versa from BaO to Ba(NO3)2 upon uptaking of NOx. However, associated with the small crystallite size of high-surface area Al2O3, it can be difficult to extract structural and morphological features of Ba(NO3)2 supported on -Al2O3 by any direct imaging method including transmission electron microscopy. In this work, by choosing a model system of Ba(NO3)2 particles supported on single crystal -Al2O3, we have investigated the structural and morphological features of Ba(NO3)2 as well as the formation of BaO from Ba(NO3)2 during the release of NOx using ex-situ and in-situ TEM imaging, electron diffraction, energy dispersive spectroscopy (EDS), and Wulff shape construction. We find that Ba(NO3)2 supported on -Al2O3 possesses a platelet morphology, with the interface and facets being invariably the 8 {111} planes. Formation of the platelet structure leads to an enlarged interface area between Ba(NO3)2 and -Al2O3, indicating that the interfacial energy is lower than the Ba(NO3)2 surface free energy. In fact, Wulff shape constructions indicate that the interfacial energy is ~1/4 of the {111} surface free energy of Ba(NO3)2. The orientation relationship between Ba(NO3)2 and the -Al2O3 is: -Al2O3[0001]//Ba(NO3)2[111] and -Al2O3(1-2 10)//Ba(NO3)2(110).
2006. "Surface-Mediated Growth of Transparent, Oriented, and Well-Defined Nanocrystalline Anatase Titania Films ." Journal of the American Chemical Society 128(42):13670-13671. doi:10.1021/ja0655993 Abstract Numerous chemical and physical methods have been investigated for preparing anatase TiO2 films due to their important electronic, optical and catalytic properties. Among these, chemical methods (sol-gel synthesis1, 2 and solution deposition3) are of particular interest because of the simplicity and wide applicability. However, up to date, chemical synthesis of oriented transparent anatase films with well-defined crystallinity and morphology has not been reported. Literature results strongly suggest that in TiO2 the electrochemical4, 5 and catalytic properties,6 and the energy conversion efficiency in photovoltaics,7 depend on specific surfaces and growth orientation. Even though anatase is catalytically more active, fundamental understanding of the surface chemistry of this important material falls far behind that of the rutile phase due to the difficulty to obtain quality crystals.8 The ability to prepare oriented, well-defined nanocrystalline anatase films would provide new opportunities to study the orientation and structure dependent properties and optimize the device performance.
2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5(2):361-369. Abstract Given the growing interest in applying genomic and proteomic approaches for studying the mammalian brain using mouse models, we hereby present for the first time a comprehensive characterization of the mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 non-redundant proteins (~34% of the predicted mouse proteome). 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models.
2006. "A Simple Model for the Effect of Hydration on the Distributionof Ferrous Iron at Reduced Hematite (012) Surfaces." Geochimica et Cosmochimica Acta 70(21):5285-5292. doi:10.1016/j.gca.2006.08.022 Abstract Using a simple ionic model with polarizable oxygen ions and dissociating water molecules, we have calculated the energetics governing the distribution of Fe(II)/Fe(III) ions at the reduced (2 · 1) surface of a-Fe2O3 (hematite) (012) under dry and hydrated conditions. The results show that systems with Fe(II) ions located in the near-surface region have lower potential energy for both dry and hydrated surfaces. The distribution is governed by coupling of the ferrous iron centers to positive charge associated with missing oxygen atoms on the dry reduced (2 · 1) (021) surface. As the surface is hydroxylated, the missing oxygen rows are filled and protons from dissociated water molecules become the positive charge centers, which couple more weakly to the ferrous iron centers. At the same time, the first-layer iron centers change from fourfold or fivefold coordination to sixfold coordination lowering the potential energy of ferric iron in the first layer and favoring migration of ferrous iron from the immediate surface sites. This effect can also be understood as reflecting stronger solvation of Fe(III) by the adsorbed water molecules and by hydrolysis reactions favoring Fe(III) ions at the immediate surface. The balance between these two driving forces, which changes as a function of hydration, provides a compelling explanation for the anomalous coverage dependence of water desorption in ultra-high vacuum experiments.
2006. "Amperometric Choline Biosensor Fabricated through Electrostatic Assembly of Bienzyme/Polyelectrolyte Hybrid Layers on Carbon Nanotubes." Analyst 131(4):477-483. doi: 10.1039/b516038c Abstract We report a flow injection amperometric choline biosensors based on the electrostatic assembly of an enzyme of choline oxidase (ChO) and a bi-enzyme of ChO and horseradish peroxidase (HRP) onto multi-wall carbon nanotubes (MWCNT) modified glassy carbon (GC) electrodes. These choline biosensors were fabricated by immobilization of enzymes on the negatively charged MWCNT surface through alternatively assembling a cationic polydiallydiimethylammonium choride (PDDA) layer and an enzyme layer. Using this layer-by-layer assembling approach, bioactive nanocomposite film of a PDDA/ChO/PDDA/HRP/PDDA/CNT (ChO/HRP/CNT) and a PDDA/ChO/PDDA/ CNT (ChO/ CNT) were fabricated on GC surface, respectively. Owning to the electrocatalytic effect of carbon nanotubes, the measurement of faradic responses resulting from enzymatic reactions has been realized at low potential with acceptable sensitivity. It is found the ChO/ HRP /CNT biosensor is more sensitive than the ChO/CNT one. Experimental parameters affecting the sensitivity of biosensors, e.g. applied potential, flow rate, etc. were optimized and potential interference was examined. The response time for this choline biosensor is fast (less than a few seconds). The linear range of detection for the choiline biosensor is from 5 x10-5 to 5x10-3 M and the detection limit is determined to be about 1.0 x 10-5 M.
2006. "Catalytic Adsorptive Stripping Voltammetric Measurements of Trace Vanadium at Bismuth Film Electrodes ." Talanta 69(4):914-917. Abstract Bismuth-coated glassy-carbon electrodes have been successfully applied for catalytic adsorptive-stripping voltammetric measurements of low levels of vanadium(V) in the presence of chloranilic acid (CAA) and bromate ion. The new protocol is based on the accumulation of the vanadium-chloranilic acid complex from an acetate-buffer (pH 5.5) solution at a preplated bismuth film electrode held at -0.35 V (vs. Ag/AgCl), followed by a square-wave voltammetric scan. Factors influencing the adsorptive stripping performance, including the CAA and bromate concentrations, solution pH, and accumulation potential or time have been optimized. The response compares favorably with that observed at mercury film electrodes. A linear response is observed over the 5 - 25 ug/L concentration range (two min accumulation), along with a detection limit of 0.20 ug/L vanadium (10 min accumulation). High stability is indicated from the reproducible response of a 50 ug/L vanadium solution (n=25; RSD = 3.1%). Applicability to a groundwater sample is illustrated.
2006. "Electroactive Silica Nanoparticles for Biological Labeling." Small 2(10):1134-1138. Abstract A novel electrochemical immuno-biosensor based on poly(guanine)-functionalized silica nanoparticle labels and mediator-generated catalytic reaction was described. The functionalized silica NPs conjugates were characterized by atomic force microscopy, X-ray photoelectron spectroscopy, and electrochemistry. This immunobiosensor is very sensitive and the limit of detection was found to be down to 0.2 ng/ml (4 pM), which was attributed to signal amplification by poly[G] functionalized silica NPs and guanine catalytic oxidation. Attractive feature of this approach is feasible to develop a cheap, sensitive and portable device for multiplexed diagnoses of different proteins. This method is simple, selective and reproducible for trace protein analysis and can be extended to study protein/protein, peptide/protein, and DNA/ protein interactions.
2006. "Sensitive Immunoassay of a Biomarker TumorNecrosis Factor-[alpha] Based on Poly(guanine)-Functionalized Silica Nanoparticle Label." Analytical Chemistry 78(19):6974-6979. doi:10.1021/ac060809f Abstract A novel electrochemical immunosensor for the detection of tumor necrosis factor-alpha (TNF-a) based on poly(guanine)-functionalized silica nanoparticles (NPs) label is presented. The detection of mouse TNF-a via immunological reaction is based on a dual amplification: 1) a large amount of guanine residues is introduced on the electrode surface through the silica nanoparticle and immunoreaction, 2) mediator-induced catalytic oxidation of guanine, which results in great enhancement of anodic current. The synthesized silica NP conjugates were characterized with atomic force microscopy, X-ray photoelectron spectroscopy, and electrochemistry. These experiments confirmed that poly[G] and avidin were immobilized on the surface of silica NPs. The performance of the electrochemical immunosensor was evaluated and some experiment parameters (e.g., concentration of Ru(bpy)32+, incubation time of TNF-a, etc.) were optimized. The detection of limit for TNF-a is found to be 5.0x10-11 g mL-1 (2.0 pM), which corresponds to 60 attomoles TNF-a in 30 uL. This immunosensor based on the poly[G] functionalized silica NP label offers great promise for rapid, simple, cost-effective analysis of biological samples.
2006. "Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition ." PLoS Computational Biology 2(7):842-852. doi:10.1371/journal.pcbi.0020078 Abstract The study of associations between two biomolecules is the key to understand molecular recognition and function. Molecular function is often thought to be determined by the underlying structures. Here, combining single molecule study of protein binding with an energy landscape inspired microscopic model, we found strong evidences that bio-molecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse grained molecular dynamics performed on the residue level with the energy function biased towards the native binding structure (Go model). With our model, the underlying free energy landscape of the binding can be explored. Two distinct conformational states as free energy minimum, one with partially folding of CBD and significant binding of CBD to CDC42, and another with native folding of CBD and native binding of CBD to CDC42, are clearly seen. This shows the binding process proceeds with significant interface binding of CBD with CDC42 first without complete folding of CBD. Finally binding and folding are coupled with each other cooperatively to reach the native binding state. The single molecule experimental finding of the dynamic fluctuations between the loosely bound and closely bound conformational states can be identified with theoretically calculated free energy minimum and quantitatively explained in our model as a result of binding associated with large conformational changes. Theoretical predictions have identified certain key residues for binding which are consistent with mutational experiments. The combined study provides a test ground for fundamental mechanisms as well as insights into design and further explorations on biomolecular recognition with large conformational changes.
2006. "Experimental and Theoretical Investigations of IR Spectra and Electronic Structures of the U(OH)₂, UO₂(OH), and UO₂(OH)₂ Molecules." Inorganic Chemistry 45(10):4157-4166. Abstract Reactions of laser-ablated U atoms and H₂O₂ molecules produce UO₂, H₂UO₂, and UO₂(OH)₂ as major products and U(OH)₂ and HU(O)OH as minor products. Complementary information is obtained from similar reactions of U atoms with D₂O₂, with H₂+O₂ mixtures, and with water in excess argon. Through extensive relativistic density functional theory (DFT) calculations we have determined the geometry structures and ground states of these uranium species with a variety of oxidation states U(II), U(IV), U(V), and U(VI). The calculated vibrational frequencies, infrared (IR) intensities, and isotopic frequency ratios are in good agreement with the experimental values, thus supporting assignments of the observed matrix IR spectra. We propose that the reactions proceed by forming an energized [U(OH)₄]* intermediate from reactions of the excited U atom with two H₂O₂ molecules. Due to the special stability of the U(VI) oxidation state this intermediate decomposes to the UO₂(OH)₂ molecule, which reveals a distinctive difference between the chemistries of uranium and thorium, where the major product in analogous thorium reactions is the tetrahedral Th(OH)₄ molecule owing to the stable Th(IV) oxidation state.
2006. "Determination of the Electron Affinity of the Acetyloxyl Radical (CH3COO) by Low-Temperature Anion Photoelectron Spectroscopy and ab Initio Calculations ." Journal of Physical Chemistry A 110(15):5047-5050. doi:10.1021/jp060138p Abstract The electronic structure and electron affinity of the acetyloxyl radical (CH3COO) were investigated by low-temperature anion photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of the acetate anion (CH3COO-) were obtained at two photon energies (355 and 266 nm) and under three different temperatures (300, 70, and 20 K) using a new low temperature ion-trap photoelectron spectroscopy apparatus. In contrast to a featureless spectrum at 300 K, a well-resolved vibrational progression corresponding to the OCO bending mode was observed at low temperatures in the 355 nm spectrum, yielding an accurate electron affinity for the acetyloxyl radical as 3.250 + 0.010 eV. This experimental result is supported by ab initio calculations, which also indicate three low-lying electronic states observed in the 266 nm spectrum. The calculations suggest a 19° decrease of the OCO angle upon detaching an electron from acetate, consistent with the vibrational progression observed experimentally.
2006. "Direct Experimental Probe of the On-Site Coulomb Repulsion in the Doubly Charged Fullerene Anion C702-." Physical Review Letters 96:143002-1-4. doi:10.1103/PhysRevLett.96.143002 Abstract Vibrationally resolved photoelectron spectra were obtained for cold C70- and C702-. Accurate values for the first and second electron affinities (EA’s) of C70 were measured as 2.765 ± 0.010 and eV, respectively, establishing that C702- is an electronically stable dianion in the gas phase. The difference between the first and second EA (2.745 eV) provides a direct experimental measure for the onsite coulomb and exchange interactions between the two excess electrons in C702-. Strong electron correlation effects were also observed between the two excess electrons in C702-.
2006. "First Steps Towards Dissolution of NaSO4- by Water." Physical Chemistry Chemical Physics. PCCP 8(37):4294-4296. Abstract NaSO4-(H2O)n (n = 0–4) clusters have been generated in the gas phase as model systems to simulate the first dissolution steps of sulfate salts in water; photoelectron spectroscopy and theoretical calculations indicate that the first three water molecules strongly interact with both Na+ and SO4 2-, forming a threewater solvation ring to pry apart the Na+SO4 2- contact ion pair.
2006. "Free Tetra-and hexa-coordinated Platinum-Cyanide Dianions, PT(CN)4 2- and PT(CN)6 2-: A Combined Photodetachment Photoelectron Spectroscopic and Theoretical Study." Chemical Physics 329(1-3):230-238. Abstract Two doubly charged transition metal complexes, PTðCNÞ2_ 4 and PTðCNÞ2_ 6 commonly found in the condensed phases, are produced as isolated species from solutions to the gas phase using electrospray ionization. Their stability and electronic structures are investigated by photodetachment photoelectron spectroscopy and density functional theory (DFT) calculations. The adiabatic electron detachment energies for the dianions to monoanions are measured to be 1.69 and 3.85 eV for PTðCNÞ2_ 4 and PTðCNÞ2_ 6 , respectively. The magnitude of the repulsive Coulomb barrier is estimated to be _2.5 eV for PtðCNÞ2_ 4 , and _1.7 eV for PTðCNÞ2_ 6 . Well-resolved and distinct peaks are observed in the spectra, yielding rich electronic structure information for these complexes. DFT calculations including scalar relativistic and spin–orbit effects are carried out to determine the geometries and to interpret the observed spectral features. The calculations show that the frontier occupied molecular orbitals are largely metal-based for PTðCNÞ2_ 4 and ligand-based for PTðCNÞ2_ 6 , in contrast to the standard ligand field theory description.
2006. "Nanostructured Vanadium Oxide Electrodes for Enhanced Lithium-Ion Intercalation." Advanced Functional Materials 16(9):1133–1144. doi:10.1002/adfm.200500662 Abstract This article summarizes our most recent studies on improved Li+-intercalation properties in vanadium oxides by engineering the nanostructure and interlayer structure. The intercalation capacity and rate are enhanced by almost two orders of magnitude with appropriately fabricated nanostructures. Processing methods for single-crystal V2O5 nanorod arrays, V2O5·nH2O nanotube arrays, and Ni/V2O5·nH2O core/shell nanocable arrays are presented; the morphologies, structures, and growth mechanisms of these nanostructures are discussed. Electrochemical analysis demonstrates that the intercalation properties of all three types of nanostructure exhibit significantly enhanced storage capacity and rate performance compared to the film electrode of vanadium pentoxide. Addition of TiO2 to orthorhombic V2O5 is found to affect the crystallinity, microstructure, and possible interaction force between adjacent layers in V2O5, and subsequently leads to enhanced Li+-intercalation properties in V2O5. The amount of water intercalated in V2O5 is found to have a significant influence on the interlayer spacing and electrochemical performance of V2O5·nH2O. A systematic electrochemical study has demonstrated that the V2O5·0.3H2O film has the optimal water content and exhibits the best Li+-intercalation performance.
2006. "Synthesis and Enhanced Intercalation Properties of Nanostructured Vanadium Oxides." Journal of the American Chemical Society 18(12):2787-2804. doi:10.1021/cm052765h Abstract Nanomaterials lie at the heart of the fundamental advances in efficient energy storage/conversion and other types of nanodevices in which the surface process and transport kinetics play determining roles. This review describes some recent developments in the synthesis and characterizations of various vanadium oxide nanostructures including nanowires, nanorolls, nanobelts, and ordered arrays of nanorods, nanotubes, and nanocables for significantly enhanced intercalation properties. The major topic of this article is to highlight the lithium ion intercalation properties of nanostructured vanadium oxides for energy storage as well as other applications in sensors, actuators, and transistors.
2006. "Atomic-Level Study of Melting Behavior of GaN Nanotubes." Journal of Applied Physics 100(06):063503, 1-6. doi:10.1063/1.2345616 Abstract Molecular dynamics simulations with a Stillinger-Weber potential have been used to investigate the melting behavior of wurtzite-type single crystalline GaN nanotubes. The simulations show that the melting temperature of GaN nanotubes is much lower than that of bulk GaN, which may be associated with the large surface-to-volume ratio of the nanotubes. The melting temperature of the GaN nanotubes increases with the thickness of the nanotubes to a saturation value, which is close to the melting temperature of a GaN slab. The results reveal that the nanotubes begin to melt at the surface, and then the melting rapidly extends to the interior of the nanotubes as the temperature increases. The melting temperature of a single-crystalline GaN nanotube with [100]-oriented lateral facets is higher than that with [110]-oriented lateral facets for the same thickness.
2006. "Atomistic Simulation of Brittle to Ductile Transition in GaN Nanotubes." Applied Physics Letters 89(24):243123, 1-3. doi:10.1063/1.2405879 Abstract Molecular dynamics methods with a Stillinger-Weber potential have been used to investigate the mechanical properties of wurtzite-type single crystalline GaN nanotubes under applied tensile stresses. At lower temperatures, the nanotubes show brittle properties; whereas at higher temperatures, they behave as ductile materials. The brittle to ductile transition (BDT) is systemically investigated, and the corresponding transition temperatures have been determined in GaN. The BDT temperature generally increases with increasing thickness of nanotubes and strain rate.
2006. "Observation of Aqueous Cm(III)/Eu(III) and UO22+ Nanoparticulates at Concentrations Approaching Solubility Limit by Laser-Induced Fluorescence Spectroscopy." Journal of Alloys and Compounds 418(1-2):166-170. Abstract Eu(III), Cm(III) and the uranyl ion display intense fluorescence spectra in the visible range and the spectroscopic characteristics are dependent on the composition and structure of the individual metal complexes. In this work, we demonstrate the application of laser-induced time-resolved fluorescence spectroscopy in identification of nanoparticles of i) Eu(III) and Cm(III) in basic solutions (pH > 10) in the presence of organic chelates including EDTA, HEDTA, NTA and oxalate and ii) sodium uranyl phosphate after equilibration with synthetic sodium uranyl phosphate suspensions. Fluorescence spectral and SEM results indicate that Eu(III) and Cm(III) can exist as colloidal nanoparticles in filtered 0.1 M NaOH solutions. Such nanoparticles, which display largely red-shifted fluorescence spectra as compared with the aqueous complexes and unusually short fluorescence lifetimes, contribute to the measured concentrations of Eu(III)/Cm(III) in the aqueous solutions. Similarly, uranyl spectroscopic signatures indicate that the determination of the solubility of uranium phosphate minerals is prone to the presence of uranyl phosphate nanoparticles. Due to the presence of such nanoparticles, the common solubility measurements may only indicate an upper limit of the “true” solubility.
2006. "Photoelectron Spectroscopy of Free Multiply Charged Keggin Anions α-[PM12O40]3- (M = Mo, W) in the Gas Phase." Journal of Physical Chemistry A 110(37):10737-10741. doi:10.1021/jp063594m Abstract Two polyoxometalate Keggin-type anions, a-PM12O403- (M = Mo, W), were transferred to the gas phase by electrospray; their electronic structure and stability were probed by photoelectron spectroscopy. These triply charged anions were found to be highly stable in the gas phase with large adiabatic electron detachment energies of 1.7 and 2.1 eV for M = Mo and W, respectively. The magnitude of the repulsive Coulomb barrier was measured as ~3.4 eV for both anions, providing an experimental estimate for the intramolecular Coulomb repulsion present in these highly charged anions. Density functional theory calculations were carried out and compared with the experimental data, providing insight into the electronic structure and valence molecular orbitals of the two Keggin anions. The calculations indicated that the highest occupied molecular orbital and other frontier orbitals for PM12O403- are localized primarily on the u2-oxo bridging ligands of the polyoxometalate framework, consistent with the reactivity on the u2-oxo sites observed in solution. It was shown that the HOMO of PW12O403- is stabilized relative to that of PMo12O403- by ~0.35 eV. The experimental adiabatic electron detachment energies of PM12O403- (i.e., the electron affinities of PM12O402-) are combined with recent calculations on the proton affinity of PM12O403- to yield O-H bond dissociation energies in PM12O39(OH)2- as ~5.1 eV
2006. "Photoelectron Spectroscopy of the Bis(dithiolene) Anions [M(mnt)2]n- (M = Fe − Zn; n = 1, 2): Changes in Electronic Structure with Variation of Metal Center and with Oxidation." Inorganic Chemistry 45(15):5841-5851. doi:10.1021/ic060255z Abstract A detailed understanding of the electronic structures of transition metal bis(dithiolene) centers is important in the context of their interesting redox, magnetic and optical properties. The electronic structures of the series [M(mnt)2]n- (M = Fe - Zn; mnt = 1,2-S2C2(CN)2; n = 1, 2) were examined by a combination of photodetachment photoelectron spectroscopy and density functional theory calculations, providing insights into changes in electronic structure with variation of the metal center and with oxidation. Significant changes were observed for the dianions [M(mnt)2]2- due to stabilization of the metal 3d levels from Fe to Zn and the transition from square-planar to tetrahedral coordination about the metal center (Fe-Ni, D2h →Cu D2 →Zn, D2d). Changes with oxidation from [M(mnt)2]2- to [M(mnt)2]1- were largely dependent on the nature of the redox-active orbital in the couple [M(mnt)2]2-/1-. In particular, the first detachment feature for [Fe(mnt)2]2- originated from a metal-based orbital (FeII →FeIII) while that for [Fe(mnt)2]1- originated from a ligand-based orbital, a consequence of stabilization of Fe 3d levels in the latter. In contrast, the first detachment feature for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- originated from the same ligand-based orbital in both cases, a result of occupied Ni 3d levels being stabilized relative those of Fe 3d and occurring below the highest energy occupied ligand-based orbital for both of [Ni(mnt)2]2- and [Ni(mnt)2]1-. The combined data illustrate the subtle interplay between metal- and ligand-based redox chemistry in these species, and demonstrate changes in their electronic structures with variation of metal center, with oxidation, and with coordination geometry.
2006. "Probing the Intrinsic Electronic Structure of the Bis(dithiolene) Anions [M(mnt)2]2- and [M(mnt)2]1- (M=Ni, Pd, Pt; mnt=1,2-S2C2(CN)2) in the Gas Phase By Photoelectron Spectroscopy." Journal of the American Chemical Society 128(13):4282-4291. doi:10.1021/ja056342s Abstract A detailed understanding of the electronic structure of transition metal bis(dithiolene) complexes is important because of their interesting redox, magnetic, optical, and conducting properties and their relevance to enzymes containing molybdenum and tungsten bis(dithiolene) centers. The electronic structures of the bis(dithiolene) anions [M(mnt)2] n- (M ) Ni, Pd, Pt; mnt ) 1,2-S2C2(CN)2; n) 0-2) were examined by a combination of photodetachment photoelectron spectroscopy (PES) and density functional theory calculations. The combined experimental and theoretical data provide insight into the molecular orbital energy levels of [M(mnt)2]2- and the ground and excited states of [M(mnt)2]1- and [M(mnt)2]. Detachment features from ligand-based orbitals of [M(mnt)2]2- occur at similar energies for each species, independent of the metal center, while those arising from metal-based orbitals occur at higher energies for the heavier congeners. Electronic excitation energies inferred for [M(mnt)2]1- from the PES experiments agree well with those obtained in optical absorption experiments in solution, with the PES experiments providing additional insight into the changes in energy of these transitions as a function of metal. The singly charged anions [M(mnt)2]1- were also prepared and studied independently. Electron detachment from the ground states of these doublet anions accessed the lowest singlet and triplet states of neutral [M(mnt)2], thereby providing a direct experimental measure of their singlet-triplet splitting.
2006. "Anaerobic Redox Cycling of Iron by Freshwater Sediment Microorganisms." Environmental Microbiology 8(1):100-113. Abstract The potential for microbially-mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. MPN enumerations revealed the presence of significant populations of Fe(III)-reducing (ca. 108 cells mL-1) and Fe(II)-oxidizing, nitrate-reducing organisms (ca. 105 cells mL-1) in the sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (ca. 1 mM) medium with a small quantity (1% vol/vol) of wetland sediment, and resulted in the transient accumulation of NO2- and production of a mixture of end-products including NH4+. Fe(III) oxide (high surface area goethite) reduction took place - after NO3- was depleted and continued until all the acetate was utilized. Addition of NO3 after Fe(III) reduction ceased resulted in the immediate oxidation of Fe(II) coupled to reduction of + NO3-to NH4 . No significant NO2- accumulation was observed during nitrate-dependent Fe(II) oxidation. No Fe(II) oxidation occurred in pasteurized controls. Microbial community structure in the enrichment was monitored by DGGE analysis of PCR amplified 16s rDNA and RT-PCR amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different time points during the experiment. Strong similarities in dominant members of the microbial community were observed in the Fe(III) reduction and nitrate-dependent Fe(II) oxidation phases of the experiment, specifically the common presence of organisms closely related (= 95% sequence similarity) to the genera Geobacter and Dechloromonas. These results indicate that the wetland sediments contained organisms such as Geobacter sp. which are capable of both + dissimilatory Fe(III) reduction and oxidation of Fe(II) with reduction of NO3-reduction to NH4 . Our findings suggest that microbially-catalyzed nitrate-dependent Fe(II) oxidation has the potential to contribute to a dynamic anaerobic Fe redox cycle in freshwater sediments.
2006. "Synthesis of organically templated nanoporous tin (II/IV) phosphate for radionuclide and metal sequestration." Inorganic Chemistry 45(6):2382-2384. doi:10.1021/ic051949v Abstract Nanoporous tin (II/IV) phosphate materials, with spherical morphology, have been synthesized using cetyltrimethylammonium chloride (CH3(CH2)15N(CH3)3Cl) as the surfactant. The structure of the material is stable at 500°C; however, partial oxidation of the material occurs with redox conversion of Sn2+ to Sn4+, resulting in a mixed Sn(II)/ Sn(IV) material. Preliminary batch contact studies were conducted to assess the effectiveness of nanoporous tin phosphate, NP-SnPO, in sequestering redox sensitive metals and radionuclides, technetium(VII), neptunium(V), thorium(IV), and a toxic metal, chromium(VI), from aqueous matrices. Results indicate tin (II) phosphate removed > 95% of all contaminants investigated from solution.
2006. "Formation of cobalt silicide from filter metal vacuum arc deposited films." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 247(2):271-278. doi:10.1016/j.nimb.2006.02.016 Abstract The thermal reaction of Co film deposited on Si (111) surfaces by a high current filter metal vacuum arc (FMEVAD) system has been studied. After deposition the films were annealed over the 400-900 ◦C temperature range for 30 min. Rutherford Backscattering Spectrometry (RBS) was used to charactrise the elemental depth distributions in the films subjected to different annealing temperatures. Ordered chemical phases were determined by glancing-incidence X-ray diffraction (GIXRD) and the morphology was determined by cross section transmission electron microscopy (TEM). The results show that the phases formed are Co2Si at 400 ◦C, CoSi + CoO at 500 ◦C, CoSi + CoSi2 at 600 ◦C, and CoSi2 at (700-800 ◦C). At 900 ◦C, CoSi2 was formed with a mixture of cubic cobalt and probably an amorphous cobalt oxide surface layer. The interface morphology was a rough cusp-like crenellation at 600 ◦C which became less pronounced after annealing at 800 ◦C.
2006. "Systems Biology." The Scientist Vol. 20 No. 6(June 2006 ):52-57. Abstract The biology revolution over the last 50 years has been driven by the ascendancy of molecular biology. This was enthusiastically embraced by most biologists because it took us into increasingly familiar territory. It took mysterious processes, such as the replication of genetic material and assigned them parts that could be readily understood by the human mind. When we think of "molecular machines" as being the underlying basis of life, we are using a paradigm derived from everyday experience. However, the price that we paid was a relentless drive towards reductionism and the attendant balkanization of biology. Now along comes “systems biology” that promises us a solution to the problem of “knowing more and more about less and less”. Unlike molecular biology, systems biology appears to be taking us into unfamiliar intellectual territory, such as statistics, mathematics and computer modeling. Not surprisingly, systems biology has met with widespread skepticism and resistance. Why do we need systems biology anyway and how does this new area of research promise to change the face of biology in the next couple of decades?
2006. "In vivo and ex vivo high-resolution ¹H NMR in biological systems using low-speed magic angle spinning." Progress in Nuclear Magnetic Resonance Spectroscopy 49(3-4):207-259. Abstract Metabolism refers to the network of interacting chemical processes that constitute (and define) cell life and provide the chemical energy and materials required for all work at the cellular and whole-organism levels. These processes take the form of metabolic pathways, an interdependent network of chemical reactions that is regulated by catalytic enzymes. Metabolites are chemical compounds that participate as reactants (substrates), intermediate compounds, or byproducts in a cellular metabolic pathway, and include carbon compounds with a molecular weight typically in the range 100-1000, which are usually present as solutes in the cytoplasm. Four broad classes of such metabolites can be distinguished [Alberts et al 1989]: sugars, the food molecules of the cell; fatty acids, present as droplets of triglyceride molecules in the cells and serving as energy resources, and as phospholipids present in the cell membranes; amino acids, the subunits of proteins; and nucleotides, the subunits of RNA and DNA, that can also act as carriers of chemical energy (adenosine triphosphate, i.e. ATP). Metabolomics involves characterizing the metabolic composition of a single cell type measured under defined physiological conditions and can be considered as analogous to genomics or proteomics [Lindon et al 2003]. Metabonomics involves quantitative studies of the changes in the metabolic profiles of living systems in response to patho-physiological stimuli or genetic modification [Nicholson et al 1999, Lindon 2003]. Metabolic changes are the earliest cellular response to environmental or physiological changes such as toxin exposure or disease state, so a snapshot of the various metabolite concentrations within cells, tissues, or biofluids, and how these concentrations change under different physiological, pharmacological and toxicological conditions provides valuable information that is complementary to gene expression and proteomic studies. Hence metabol(n)omics may be capable of, e.g., detecting and diagnosing a disease or evaluating the efficacy of therapy in an early stage, and provide powerful new tools for gaining insight into functional biology.
2006. "Localized in Vivo Isotropic-Anisotropic Correlation 1H NMR Spectroscopy Using Ultraslow Magic Angle Spinning." Magnetic Resonance in Medicine 55(1):41-49. Abstract Previous work has shown that it is possible to separate the susceptibility broadening in the 1H NMR metabolite spectrum obtained in a live mouse from the isotropic information, thus significantly increasing the spectral resolution. This was achieved using ultra-slow magic angle spinning of the animal combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. However, PHORMAT cannot be used for spatially selective spectroscopy. In this article a modified sequence called LOCMAT (localized magic angle turning) is introduced that makes this possible. Proton LOCMAT spectra are shown for the liver and heart of a live mouse, while spinning the animal at a speed of 4 Hz in a 2 Tesla field. It was found that even in this relatively low field LOCMAT provided isotropic line widths that are a factor 4-10 times smaller than the ones obtained in a stationary animal, and that the susceptibility broadening of the heart metabolites shows unusual features not observed for a dead animal. Finally, the limitations of LOCMAT and possible ways to improve the technique are discussed. It is concluded that in vivo LOCMAT can significantly enhance the utility of NMR spectroscopy for biomedical research.
2006. "Modeling Carbon Nanostructures with the Self-Consistent Charge Density-Functional Tight-Binding Method: Vibrational Spectra and Electronic Structure of C₂₈, C₆₀, and C₇₀." Journal of Chemical Physics 125(21):Art. No. 214706. Abstract The self-consistent charge density-functional tight-binding (SCC-DFTB) method is employed for studying various molecular properties of small fullerenes: C₂₈, C₆₀, and C₇₀. The computed optimized bond distances, vibrational infrared and Raman spectra, vibrational densities of states, and electronic densities of states are compared with experiment (where available) and density functional theory (DFT) calculations using various basis sets. The presented DFT benchmark calculations using the correlation-consistent polarized valence triple zeta (cc-pVTZ) basis set of Dunning are at present the most extensive calculations on harmonic frequencies of these species. Possible limitations of the SCC-DFTB method for the prediction of molecular vibrational and optical properties are discussed. The presented results suggest that SCC-DFTB is a computationally feasible and reliable method for predicting vibrational and electronic properties of such carbon nanostructures comparable in accuracy with small to medium size basis set DFT calculations at the computational cost of standard semiempirical methods.
2006. "Low-Temperature Photoelectron Spectroscopy of Aliphatic Dicarboxylate Monoanions, HO2C(CH2)nCO2-(n=1-10): Hydrogen Bond Induced Cyclization and Strain Energies." Journal of Physical Chemistry A 110(25):7801-7805. doi:10.1021/jp0616009 Abstract Photoelectron spectra of singly-charged dicarboxylate anions HO2C(CH2)nCO2 - (n = 1 – 10) are obtained at two different temperatures (300 and 70 K) at 193 nm. The electron binding energies of these species are observed to be much higher than the singly-charged monocarboxylate anions, suggesting the singly-charged dicarboxylate anions are cyclic due to strong intramolecular hydrogen bonding between the terminal –CO2H and –CO2 - groups. The measured electron binding energies are observed to depend on the chain length, reflecting the different –CO2H…-O2C– hydrogen bonding strength as a result of strain in the cyclic conformation. A minimum binding energy is found at n = 5, indicating that its intramolecular hydrogen bond is the weakest. At 70 K, all spectra are blue-shifted relative to the room temperature spectra with the maximum binding energy shift occurring at n = 5. These observations suggest that the cyclic conformation of HO2C(CH2)5CO2 - (a ten-membered ring) is the most strained among the ten anions. The present study shows that the –CO2H…-O2C– hydrogen bonding strength is different among the ten anions and it is very sensitive to the strain in the cyclic conformations.
2006. "Observation of Cysteine Thiolate and -S...H-O Intermolecular Hydrogen Bond." Journal of Physical Chemistry A 110(46):12603-12606. Abstract The cysteine anion was produced in the gas phase by electrospray ionization and investigated by photoelectron spectroscopy at low-temperature (70K). The cysteine anion was found to exhibit the thiolate form [-SCH2CH(NH2)CO2H], rather than the expected carboxylate form [HSCH2CH(NH2)CO2 -]. This observation was confirmed by two control experiments i.e. methyl cysteine [CH3SCH2CH(NH2)CO2-] and cysteine methyl ester [-SCH2CH(NH2)CO2CH3]. The electron binding energy of [-CH2CH(NH2)CO2H] was measured to be about 0.7 eV blue-shifted relative to [-SCH2CH(NH2)CO2CH3] due to the formation of an intramolecular –S-…HO2C– hydrogen bond in the cysteine hiolate. Theoretical calculations at the CCSD(T)/6-311++G(2df,p) and B3LYP/6-311++G(2df,p) levels were carried out to estimate the strength of this intramolecular –S-…HO2C– hydrogen bond. Combining experimental measurements and theoretical calculations yielded an estimated value of 16.4 ± 2.0 kcal/mol for the –S-…HO2C– intramolecular hydrogen bond strength.
2006. "Dynamical Structure, Bonding, and Thermodynamics of the Superionic Sublattice in ∝-AgI." Physical Review Letters 97(166401):1-4. doi:10.1103/PhysRevLett.97.166401 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. We characterize the superionic phase transition and the lattice and electronic structures of the archetypal type-I superionic conductor ∝-AgI using extensive first-principles molecular dynamics calculations. We find that superionicity is signaled by a phase transition of the silver ions alone. In the superionic phase, the first silver shell surrounding an iodine displays a distinct dynamical structure that would escape a time-averaged characterization, and we capture this structure in a set of ordering rules. The electronic structure demonstrates a unique chemical signature of the weakest-bound silver in the first shell, which in turn is most likely to diffuse. Silver diffusion decreases upon melting, pointing to an unusual entropic contribution to the stability of the superionic phase.
