Scientific Publications 2008
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2008. "High-Resolution Mass Spectrometric Analysis of Secondary Organic Aerosol Produced by Ozonation of Limonene." Physical Chemistry Chemical Physics. PCCP 10(7):1009-1022. doi:10.1039/b712620d Abstract Secondary organic aerosol (SOA) particles formed from the ozone-initiated oxidation of limonene are characterized by high-resolution electrospray ionization mass spectrometry in both the positive and negative ion modes. The mass spectra reveal a large number of both monomeric (m/z < 300) and oligomeric (m/z > 300) products of oxidation. A combination of high resolving power (m/Δm ~60,000) and Kendrick mass defect analysis makes it possible to unambiguously determine the composition for hundreds of individual compounds in SOA samples. Van Krevelen analysis shows that the SOA compounds are heavily oxidized, with average O:C ratios of 0.43 and 0.50 determined from the positive and negative ion mode spectra, respectively. An extended reaction mechanism for the formation of the first generation SOA molecular components is proposed. The mechanism includes known isomerization and addition reactions of the carbonyl oxide intermediates generated during the ozonation of limonene, and numerous isomerization pathways for alkoxy radicals resulting from the decomposition of unstable carbonyl oxides. The isomerization reactions yield numerous products with a progressively increasing number of alcohol and carbonyl groups, whereas C-C bond scission reactions in alkoxy radicals shorten the carbon chain. Together these reactions yield a large number of isomeric products with broadly distributed masses. A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer range.
2008. "Effect of Saline Waste Solution Infiltration Rates on Uranium Retention and Spatial Distribution in Hanford Sediments." Environmental Science & Technology 42(6):1973-1978. doi:10.1021/es070684b Abstract The accidental overfilling of waste liquid from tank BX-102 at the Hanford Site 11 in 1951 put 10 metric tons of U(VI) in the vadose zone. In order to understand the dominant 12 geochemical reactions and transport processes occurred during the initial infiltration, and to 13 predict U current status and future mobility, we simulated the waste liquid spilling event in 14 laboratory sediment columns using synthesized metal waste solution. We found that, as the 15 plume propagating through sediments, dramatic pH reduction (up to 4 units) occurred at moving 16 plume fronts. Massive amounts of colloids, including U-colloids, formed at plume fronts. The 17 infiltration flow rates strongly affect U fate and transport. Slower flow rate resulted in higher 18 sediment-associated U concentrations, and higher flow rate permitted practically unretarded U 19 transport, and extensive colloid precipitation and accumulations at the plume fronts. Accelerated 20 U transport by size exclusion of U-colloids was revealed. U exceeded the source concentration of 21 U by up to 5 fold, and exceeded the source concentrations of sodium, carbonate, phosphate and 22 sulfate by much more. This first report of colloid induced accelerated U transport could be a 23 mechanism responsible for highly heterogeneous U distributions in the sediment and deep 24 migration to the groundwater.
2008. "Structural and Dielectric Properties of Quartz-Water Interfaces." Journal of Physical Chemistry C 112(50):19986–19994. doi:10.1021/jp803642c Abstract The structure, orientation, and dielectric of water at the quartz|water interface has been examined under different hydration levels using classical molecular dynamics. The properties of 1H₂O/10 Ų, 2H₂O/10 Ų, 4H₂O/10 Ų, and bulk water on quartz have been benchmarked against experimental data. Structurally, the simulations match existing sum-frequency spectroscopy data, which indicate the existence and orientation of both frozen and loosely bound water on the quartz surface. Good agreement has also been found with existing experimental dielectric data for the 1H₂O/10 Ų level of hydration, and a clear difference has been found in the values of εs = 48, ε| = 48, and ε⊥ = 40 for the first slice of a bulk-water-solid interface and εs= 30, ε| = 30, and ε⊥ = 10 for that of 1H₂O/10 Ų water coverage. Overall there is a fundamental difference in shielding between a single interface and the 1H₂O/10 Å2 level of hydration.
2008. "Microstructures of ZnO films deposited on (0001) and r-cut α-Al2O3 using metal organic chemical vapor deposition." Thin Solid Films 516(23):8337-8342. doi:10.1016/j.tsf.2008.04.001 Abstract Zinc oxide films were deposited on (0001) and r-cut α-Al2O3 under identical conditions using metal organic chemical vapor deposition. Microstructures of the ZnO films were studied in detail using conventional and high-resolution transmission electron microscopy (HRTEM), electron diffraction, and HRTEM image simulations. The films deposited on these two substrates show distinctive structural differences. The film grown on r-cut α-Al2O3 shows a high quality single crystal with an orientation relationship of α-Al2O3[-101-1]//ZnO[0001] and α-Al2O3(10-1-2)//ZnO(2-1-10). The interface between the film and the substrate was abrupt and decorated with high density of misfit dislocations. Film grown on α-Al2O3 (0001) shows several orientation domains. Typically, one domain correspond to the classic growth model such that α-Al2O3 (0001)//ZnO(0001) and α-Al2O3 [11-20]//ZnO[10-10]. Another domain corresponds to the growth mode such that α-Al2O3 [11-20]//ZnO[10-10] but the (0001) plane of ZnO is tilted relative to the (0001) plane of α-Al2O3 such that ZnO(0001) is almost parallel to the α-Al2O3 (-1104) plane. This orientation reduces the extent of lattice mismatch as compared with the classic growth mode. The interface between ZnO and α-Al2O3 is abrupt and possesses periodic dislocations.
2008. "Tilted domain growth of metalorganic chemical vapor (MOCVD)-grown ZnO(0001)on a-Al2O3(0001)." Journal of Materials Research 23(1):13-17. Abstract ZnO grown on -Al2O3 (0001) generally possesses an orientation such that -Al2O3 (0001)//ZnO(0001) and two in-plane domains nucleate such that: -Al2O3 [11-20]//ZnO[11-20] and/or -Al2O3 [11-20]//ZnO[10-10]. In this paper, we report a new growth mode for ZnO grown on -Al2O3 (0001) using MOCVD. We find that -Al2O3 [11-20]//ZnO[10-10] but the (0001) plane of ZnO is tilted relative to the (0001) plane of -Al2O3 such that ZnO(0001) is almost parallel to the -Al2O3 (-1104) plane. This orientation reduces the extent of lattice mismatch. The interface between ZnO and -Al2O3 is abrupt and possesses periodic dislocations.
2008. "Low-Temperature Synthesis of Tunable Mesoporous Crystalline Transition Metal Oxides and Applications as Au Catalyst Supports." Journal of Physical Chemistry C 112(35):13499-13509. doi:10.1021/jp804250f Abstract Mesoporous transition metal oxides are of great potential as catalyst supports, shape-selective catalysts, photocatalysts, and sensor materials. Previously stable crystalline mesoporous oxides were mostly obtained by thermally induced crystallization or by segregating the nanocrystals with an amorphous phase. Here we report a novel direct approach to crystalline mesoporous frameworks via the spontaneous growth and assembly of transition metal oxide nanocrystals (i.e., rutile TiO2, fluorite CeO2, cassiterite SnO2, and anatase SnxTi1-xO2) by oxidative hydrolysis and condensation in the presence of anionic surfactants. The influences of synthesis time, surfactants with different chain lengths, concentrations of the oxidant (i.e., hydrogen peroxide), and synthesis temperatures on the composition and morphologies of the resulting materials were investigated by X-ray diffraction (XRD), N2-sorption, transmission electron microscopy (TEM), selected area electron diffraction (SAED), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS). A mechanism for the templated synthesis of crystalline mesoporous metal oxides was tentatively proposed. To demonstrate the catalytic applications of these materials, gold nanoparticles were loaded on mesoporous rutile TiO2 and fluorite CeO2 supports, and their catalytic performance in CO oxidation and water-gas shift was surveyed. Au nanoparticles supported on the mesoporous crystalline metal oxides exhibit higher reactivity and excellent on-stream stability towards CO oxidation and water-gas shift reaction compared with commercial TiO2 and CeO2.
2008. "Magnetic Electrochemical Immunoassays with Quantum Dot Labels for Detection of Phosphorylated Acetylcholinesterase in Plasma." Analytical Chemistry 80(22):8477-8484. doi:10.1021/ac801211s Abstract A new magnetic electrochemical immunoassay has been developed as a tool for biomonitoring exposures to organophosphate (OP) compounds, e.g., insecticides and chemical nerve agents, by directly detecting organophosphorylated acetylcholinesterase (OP−AChE). This immunoassay uniquely incorporates highly efficient magnetic separation with ultrasensitive square wave voltammetry (SWV) analysis with quantum dots (QDs) as labels. A pair of antibodies was used to achieve the specific recognition of OP−AChE that was prepared with paraoxon as an OP model agent. Antiphosphoserine polyclonal antibodies were anchored on amorphous magnetic particles preferably chosen to capture OP−AChE from the sample matrixes by binding their phosphoserine moieties that were exposed through unfolding the protein adducts. This was validated by electrochemical examinations and enzyme-linked immunosorbent assays. Furthermore, antihuman AChE monoclonal antibodies were labeled with cadmium-source QDs to selectively recognize the captured OP−AChE, as characterized by transmission electron microscopy. The subsequent electrochemical SWV analysis of the cadmium component released by acid from the coupled QDs was conducted on disposable screen-printed electrodes. Experimental results indicated that the SWV-based immunoassays could yield a linear response over a broad concentration range of 0.3−300 ng/mL OP−AChE in human plasma with a detection limit of 0.15 ng/mL. Such a novel electrochemical immunoassay holds great promise as a simple, selective, sensitive, and field-deployable tool for the effective biomonitoring and diagnosis of potential exposures to nerve agents and pesticides.
2008. "Pyroelectricity of Water Ice." Journal of Physical Chemistry B 112(20):6379-6389. doi:10.1021/jp073870c Abstract Water ice usually is though to have zero pyroelectricity by symmetry. But biasing it with ions breaks the symmetry because of the induced partially dipole-aligned. This unmasks a large pyroelectricity. Ions were soft-landed upon 1 micron films of water ice at ≥ 160K. When cooled below 140 to 150 K this locks-in the dipole-alignment. Workfunction measurements of these films then show high and reversible pyroelectric activity from 30 to 150K. For an initial ~10V induced by the deposited ions, the at 160K, the observed bias below 150K varies approximately as 10V*(T/150K)2 This implies water has pyroelectric coefficients as large as that of many commercial pyroelectrics such as lead zirconate titanate (“PZT”). The pyroelectricity of water ice, not previously reported, is in reasonable agreement with that predicted via a monte carlo simulation of TIP4P ice. This is observed in crystalline and compact amorphous ice, deuterated or not. This implies that for water ice between 0 and 150K (such as astrophysical ices), temperature changes can induce strong electric fields (~10,000,000 V/m) that can influence their chemistry and trajectories or binding.
2008. "Carbon Nanotube-Based Electrochemical Sensor for Assay of Salivary Cholinesterase Enzyme Activity: An Exposure Biomarker of Organophosphate Pesticides and Nerve Agents." Environmental Science & Technology 42(7):2688-2693. doi:10.1021/es702335y Abstract Certain saliva enzymes may be useful biomarkers for detecting exposures to organophosphate pesticides and chemical nerve agents. In this regard, saliva biomonitoring offers a simple and noninvasive approach for rapidly evaluating those exposures in real time. An electrochemical sensor coupled with a micro-flow injection system was developed for a simple, rapid, and sensitive characterization of cholinesterase (ChE) enzyme activities in rat saliva. The electrochemical sensor is based on a carbon nanotube (CNT)-modified screen-printed carbon electrode (SPE), which is integrated into a flow cell. Because of the excellent electrocatalytic activity of the CNTs, the sensor can detect electroactive species that are produced from enzymatic reactions with extremely high sensitivity and at low potentials. The electrochemical properties of acetylcholinesterase (AChE) enzymatic products were studied using a CNT-modified SPE, and the operation parameters such as the applied potential and substrate concentration were optimized to achieve the best performance. The AChE enzyme activity was further investigated using the CNT-based electrochemical sensor with commercially available purified AChE and saliva obtained from naïve rats. It was found that the calibration curve is linear over a wide range of AChE concentrations from 5 pM to 0.5 nM, and the sensor is very sensitive with the detection limit down to 2 pM. The dynamics of the enzyme activity in saliva with organophosphate pesticides was further studied using this sensor. The results show that the senor can be used to characterize salivary enzyme activity and to detect the exposure to organophosphate compounds. This new CNT-based electrochemical sensor thus provides a sensitive and quantitative tool for noninvasive biomonitoring of the exposure to organophosphate pesticides and nerve agents.
2008. "Functionalized carbon nanotubes and nanofibers for biosensing applications." Trends in Analytical Chemistry. TrAC 27(7):619-626. doi:10.1016/j.trac.2008.05.009 Abstract This review summarizes the recent advances of carbon nanotube (CNT) and carbon nanofiber (CNF)-based electrochemical biosensors with an emphasis on the applications of CNTs. Carbon nanotubes and carbon nanofibers have unique electric, electrocatalytic, and mechanical properties which make them efficient materials for the use in electrochemical biosensor development. In this article, the functionalization of CNTs for biosensors is simply discussed. The electrochemical biosensors based on CNT and their various applications, e.g., measurement of small biological molecules and environmental pollutants, detection of DNA, and immunosensing of disease biomarkers, are reviewed. Moreover, the development of carbon nanofiber-based electrochemical biosensors and their applications are outlined. Finally, some challenges are discussed in the conclusion.
2008. "Quantum-Dot-Based Electrochemical Immunoassay for High-Throughput Screening of the Prostate-Specific Antigen." Small 4(1):82-86. doi:10.1002/smll.200700459 Abstract In this paper, we demonstrate an electrochemical high-throughput sensing platform for simple, sensitive detection of PSA based on QD labels. This sensing platform uses a microplate for immunoreactions and disposable screen-printed electrodes (SPE) for electrochemical stripping analysis of metal ions released from QD labels. With the 96-well microplate, capturing antibodies are conveniently immobilized to the well surface, and the process of immunoreaction is easily controlled. The formed sandwich complexes on the well surface are also easily isolated from reaction solutions. In particular, a microplate-based electrochemical assay can make it feasible to conduct a parallel analysis of several samples or multiple protein markers. This assay offers a number of advantages including (1) simplicity, cost-effectiveness, (2) high sensitivity, (3) capability to sense multiple samples or targets in parallel, and (4) a potentially portable device with an SPE array implanted in the microplate. This PSA assay is sensitive because it uses two amplification processes: (1) QDs as a label for enhancing electrical signal since secondary antibodies are linked to QDs that contain a large number of metal atoms and (2) there is inherent signal amplification for electrochemical stripping analysis—preconcentration of metal ion onto the electrode surface for amplifying electrical signals. Therefore, the high sensitivity of this method, stemming from dual signal amplification via QD labels and pre-concentration, allows low concentration levels to be detected while using small sample volumes. Thus, this QD-based electrochemical detection approach offers a simple, rapid, cost-effective, and high throughput assay of PSA.
2008. "Sensitive electrochemical immunoassay for 2,4,6-trinitrotoluene based on functionalized silica nanoparticle labels." Analytica Chimica Acta 610(1):112-118. doi:10.1016/j.aca.2008.01.024 Abstract We present a poly(guanine)-functionalized silica nanoparticle (NP) label-based electrochemical immunoassay for sensitively detecting 2,4,6-trinitrotoluene (TNT). This immunoassay takes advantage of magnetic bead–based platform for competitive displacement immunoreactions and separation, and use electroactive nanoparticles as labels for signal amplification. For this assay, anti-TNT-coated magnetic beads interacted with TNT analog-conjugated poly(guanine)-silica NPs and formed analog-anti-TNT immunocomplexes on magnetic beads. The immunocomplexes coated magnetic beads were exposed to TNT samples, which resulted in displacing the analog conjugated poly(guanine) silica NPs into solution by TNT. In contrast, there are no guanine residues releasing into the solution in the absence of TNT. The reaction solution was then separated from the magnetic beads and transferred to the electrode surface for electrochemical measurements of guanine oxidation with Ru(bpy)32+ as mediator. The sensitivity of this TNT assay was greatly enhanced through dual signal amplifications: 1) a large amount of guanine residues on silica nanoparticles is introduced into the test solution by displacement immunoreactions and 2) a Ru(bpy)32+-induced guanine catalytic oxidation further enhances the electrochemical signal. Some experimental parameters for the nanoparticle label-based electrochemical immunoassay were studied and the performance of this assay was evaluated. The method is found to be very sensitive and the detection limit of this assay is ~ 0.1 ng mL-1 TNT. The electrochemical immunoassay based on the poly[guanine]-functionalized silica NP label offers a new approach for sensitive detection of explosives.
2008. "Effects of aerosol organics on cloud condensation nucleus (CCN) concentration and first indirect aerosol effect." Atmospheric Chemistry and Physics 8(21):6325-6339. Abstract Abstract. Aerosol microphysics, chemical composition, and CCN properties were measured on the Department of Energy Gulfstream-1 aircraft during the Marine Stratus/ Stratocumulus Experiment (MASE) conducted over the coastal waters between Point Reyes National Seashore and Monterey Bay, California, in July 2005. Aerosols measured during MASE included free tropospheric aerosols, marine boundary layer aerosols, and aerosols with high organic concentration within a thin layer above the cloud. Closure analysis was carried out for all three types of aerosols by comparing the measured CCN concentrations at 0.2% supersaturation to those predicted based on size distribution and chemical composition using K¨ohler theory. The effect of aerosol organic species on predicted CCN concentration was examined using a single hygroscopicity parameterization.
2008. "Helical Peptide Arrays on Self-Assembled Monolayer Surfaces Through Soft and Reactive Landing of Mass-Selected Ions." Angewandte Chemie International Edition 47:6678-6680. doi:10.1002/anie.200801366 Abstract The α-helix – the common building block of the protein secondary structure - plays an important role in determining protein structure and function. The biological function of the α-helix is mainly attributed to its large macrodipole originating from the alignment of individual dipole moments of peptide bonds. Preparation of directionally aligned α-helical peptide layers on substrates has attracted significant attention because the resulting strong net dipole is useful for a variety of applications in photonics, , molecular electronics, and catalysis. - In addition, conformationally-selected α-helical peptide arrays can be used for detailed characterization of molecular recognition steps critical for protein folding, enzyme function and DNA binding by proteins. Existing technologies for the production of α-helical peptide surfaces are based on a variety of solution phase synthetic strategies - that usually require relatively large quantities of purified materials.
2008. "Reactive Landing of Peptide Ions on Self-Assembled Monolayer Surfaces: A Alternative Approach for Covalent Immobilization of Peptides on Surfaces." Physical Chemistry Chemical Physics. PCCP 10(11):1512-1522. doi:10.1039/b717617a Abstract Soft landing of mass-selected peptide ions onto reactive self-assembled monolayer surfaces (SAMs) was performed using a newly constructed ion deposition apparatus. SAM surfaces before and after soft-landing were characterized ex situ using time of flight-secondary ion mass spectrometry (TOF-SIMS) and infrared reflection absorption spectroscopy (IRRAS). We demonstrate that reactive landing (RL) results in efficient covalent linking of lysine-containing peptides onto the SAM of N-hydroxysuccinimidyl ester terminated alkylthiol on gold (NHS-SAM). Systematic studies of the factors that affect the efficiency of RL revealed that the reaction takes place upon collision and is promoted by the kinetic energy of the ion. The efficiency of RL maximizes at ca. 40 eV collision energy. At high collision energies the RL efficiency decreases because of the competition with scattering of ions off the surface. The reaction yield is independent of the charge state of the projectile ions suggesting that peptide ions undergo efficient neutralization upon collision. Chemical and physical properties of the SAM surface are also important factors that affect the outcome of RL. The presence of chemically reactive functional groups on the SAM surface significantly improves the reaction efficiency. RL of mass- and energy-selected peptide ions on surfaces provides a highly specific approach for covalent immobilization of biological molecules onto SAM surfaces.
2008. "Electrochemical Immunoassay of Carcinoembryonic Antigen Based on A Lead Sulfide Nanoparticle Label." Nanotechnology 19(43):Art. No. 435501. doi:10.1088/0957-4484/19/43/435501 Abstract We describe a Lead sulfide nanoparticle (PbS NP) based electrochemical immunoassay to detect a tumor biomarker, carcinoembryonic antigen (CEA). Cubic PbS NPs were prepared and functionalized with thioglycolic acid (TGA), which stabilized the formed NPs and offered carboxyl groups to conjugate with CEA antibodies. PbS NP conjugated with monoclonal CEA antibody was used as a label in an immnorecognition event. After a complete sandwich immunoreaction among the primary CEA antibody (immobilized on the carboxyl-modified magnetic beads), CEA, and the PbS-labeled secondary antibody (PbS-anti-CEA), PbS labels were captured to the magnetic-bead (MB) surface through the antibody-antigen immunocomplex. Electrochemical stripping analysis of the captured PbS was used to quantify the concentration of CEA after an acid-dissolution step. The MBs and the magnetic separation platform were used to integrate a facile antibody immobilization with immunoreactions and the isolation of immunocomplexes from reaction solutions in the immunoassay. The performance of this nanoparticle based electrochemical immunoassay was successfully evaluated with human serum spiked with CEA, indicating that this convenient and sensitive technique offers great promise for rapid, simple, and cost-effective analysis of tumor biomarkers in biological fluids.
2008. "Development of a Low-Temperature Photoelectron Spectroscopy Instrument Using an Electrospray Ion Source and a Cryogenically Controlled Ion Trap." Review of Scientific Instruments 79(7):Art. No. 073108. doi:10.1063/1.2957610 Abstract The ability to control ion temperatures is critical for gas phase spectroscopy and has been a challenge in chemical physics. A low-temperature photoelectron spectroscopy instrument has been developed for the investigation of complex anions in the gas phase, including multiply charged anions, solvated species, and biological molecules. The new apparatus consists of an electrospray ionization source, a 3D Paul trap for ion accumulation and cooling, a time-of-flight mass spectrometer, and a magnetic-bottle photoelectron analyzer. A key feature of the new instrument is the capability to cool and tune ion temperatures from 10 to 350 K in the 3D Paul trap, which is attached to the cold head of a closed-cycle helium refrigerator. Ion cooling is accomplished in the Paul trap via collisions with a background gas and has been demonstrated by observation of complete elimination of vibrational hot bands in photoelectron spectra of various anions ranging from small molecules to complex species. Further evidence of ion cooling is shown by the observation of H2 physisorbed anions at low temperatures. Cold anions result in better resolved photoelectron spectra due to the elimination of vibrational hot bands and yield more accurate energetic and spectroscopic information. Temperature-dependent studies are made possible for weakly-bonded molecular and solvated clusters, allowing thermodynamic information to be obtained.
2008. "High Resolution and Low-Temperature Photoelectron Spectroscopy of an Oxygen-Linked Fullerene Dimer Dianion: C120O2-." Journal of Chemical Physics 128(11):Art. No. 114307. Abstract C120O comprises two C60 cages linked by a furan ring and is formed by reactions of C60O and C60. We have produced doubly-charged anions of this fullerene dimer (C120O2–) and studied its electronic structure and stability using photoelectron spectroscopy and theoretical calculations. High resolution and vibrationally resolved photoelectron spectra were obtained at 70 K and at several photon energies. The second electron affinity of C120O was measured to be 1.02 ± 0.03 eV and the intramolecular Coulomb repulsion was estimated to be about 0.8 eV in C120O2– on the basis of the observed repulsive Coulomb barrier. A low-lying excited state (2B1) was also observed for C120O– at 0.09 eV above the ground state (2A1). The C120O2– dianion can be viewed as a single electron on each C60 ball very weakly coupled. Theoretical calculations showed that the singlet and triplet states of C120O2– are nearly degenerate and can both be present in the experiment. The computed electron binding energies and excitation energies, as well as Franck-Condon factors, are used to help interpret the photoelectron spectra. A C-C bond-cleaved isomer, C60-O-C602–, was also observed with a higher electron binding energy of 1.54 eV.
2008. "Observation of Entropic Effect on Conformation Changes of Complex Systems Under Well-Controlled Temperature Condition." Journal of Physical Chemistry A 112(2):172-175. doi:10.1021/jp711205z Abstract We report direct observation of entropic effect in determining the folding of a linear dicarboxylate dianion with a flexible aliphatic chain [–O2C-(CH2)6-CO2–] by photoelectron spectroscopy as a function of temperature (18 – 300 K) and degree of solvation from 1 to 18 water molecules. A folding transition is observed to occur at 16 solvent water molecules at room temperature, but at 14 solvent molecules below 120 K due to the entropic effect. The –O2C-(CH2)6-CO2–(H2O)14 hydrated cluster exhibits interesting temperature-dependent behaviors and its ratio of folded over linear conformations can be precisely controlled as a function of temperature, yielding the enthalpy and entropy differences between the two conformations. A folding barrier is observed at very low temperatures, resulting in kinetic trapping of the linear conformation. The current work provides a simple model system to study the dynamics and entropic effect in complex systems and may be important for understanding the hydration and conformation changes of biological molecules.
2008. "Observation of H-2 Aggregation onto a Doubly Charged Anion in a Temperature-Controlled Ion Trap." Journal of Physical Chemistry A 112(51):13271-13274. Abstract Hydrogen is the second most difficult gas to be condensed due to its weak intermolecular interactions. Here we report observation of H2 aggregation onto a doubly charged anion, –O2C(CH2)12CO2– (DC2–). Weakly-bound DC2–(H2)n clusters were formed in a temperature-controlled ion trap and studied using photoelectron spectroscopy. The onset of clustering was observed at 30 K, whereas extensive condensation was observed at 12 K with n up to 12. Photoelectron spectra were obtained for DC2–(H2)n (n = 0–6) at 193 and 266 nm. The spectra of DC2–(H2)n were observed to be identical to that of the bare DC2– dianion except a slight blue shift, indicating the weak interactions between H2 and the parent dianion. The blue shift on average amounts to ~34 meV (3.3 kJ/mol) per H2, which represents the lower limit of the H2 binding energy to DC2–.
2008. "On The Electronic Structure and Chemical Bonding in the Tantalum Trimer Cluster." Journal of Physical Chemistry A 112(43):10962-10967. doi:10.1021/jp806166h Abstract The electronic structure and chemical bonding in the Ta3− cluster are investigated using photoelectron spectroscopy and density functional theory calculations. Photoelectron spectra are obtained for Ta3− at four photon energies: 532, 355, 266 and 193 nm. While congested spectra are observed at high electron binding energies, several low-lying electronic transitions are well resolved and compared with the theoretical calculations. The electron affinity of Ta3 is determined to be 1.35±0.03 eV. Extensive density functional calculations are performed at the B3LYP/Stuttgart +2f1g level to locate the ground state and low-lying isomers for Ta3 and Ta3 −. The ground state for the Ta3 − anion is shown to be a quintet (5A1′) with D3h symmetry, whereas two nearly isoenergetic states, C2v (4A1) and D3h (6A1′), are found to compete for the ground state for neutral Ta3. A detailed molecular orbital analysis is performed to elucidate the chemical boding in Ta3−, which is found to possess multiple d-orbital aromaticity, commensurate with its highly symmetric D3h structure.
2008. "A cryogenic fluorescence spectroscopic study of uranyl carbonate, phosphate, and oxyhydroxide minerals." Radiochimica Acta 96(9-11):591-598. doi:10.1524/ract.2008.1541 Abstract In this work we have applied liquid-helium temperature (LHeT) time-resolved laser-induced fluorescence spectroscopy (TRLIF) to characterize a series of natural and synthetic minerals of uranium carbonate, phosphate and oxyhydroxides including rutherfordine, zellerite, liebigite, phosphuranylite, meta-autunite, meta-torbernite, uranyl phosphate, sodium-uranyl-phosphate, bequerelite, clarkeite, curite, schoepite and compregnacite, and compared their spectral characteristics among these minerals as well as our previously published data on uranyl silicates. For the carbonate minerals, the fluorescence spectra depend on the stoichiometry of the mineral. For the phosphate minerals the fluorescence spectra closely resemble each other despite the differences in their composition and structure. For all uranium oxyhydroxides, the fluorescence spectra are largely red-shifted as compared with those of the uranium carbonates and phosphates and their vibronic bands are broadened and less resolved. The much enhanced spectra resolution at LHeT allows more accurate calculation of the O=U=O symmetrical stretch frequency, ν1, corresponding to the average spacing of the vibronic peaks of the fluorescence spectra and the spectral origin as reflected by the position of the first vibronic band. It was found that both the average ν1 and λ1 values correlate well with the average basicity of the inorganic anion.
2008. "A Spectroscopic Study of the effect of Ligand Complexation on the Reduction of Uranium(VI) by Anthraquinone-2,6-disulfonate (AH2DS)." Radiochimica Acta 96(9-11):599-605. doi:10.1524/ract.2008.1542 Abstract In this project, the reduction rate of uranyl complexes with hydroxide, carbonate, EDTA, and Desferriferrioxamine B (DFB) by anthraquinone-2,6-disulfonate (AH2DS), a potential electron shuttle for microbial reduction of metal ions (Newman and Kolter 2000), is studied by stopped-flow kinetics techniques under anoxic atmosphere. The apparent reaction rates varied with ligand type, solution pH, and U(VI) concentration. For each ligand, a single largest kobs within the studied pH range was observed, suggesting the influence of pH-dependent speciation on the U(VI) reduction rate. The maximum reaction rate found in each case followed the order of OH- > CO32- > EDTA > DFB, consistent with the same trend of the thermodynamic stability of the uranyl complexes and ionic sizes of the ligands. Increasing the stability of uranyl complexes and ligand size decreased the maximum reduction rate. The pH-dependent rates were modeled using a second-order rate expression that was assumed to be dependent on a single U(VI) complex and AH2DS species. By quantitatively comparing the calculated and measured apparent rate constants as a function of pH, species AHDS3- was suggested as the primary reductant in all cases examined. Species UO2CO3(aq) , UO2HEDTA-, and (UO2)2(OH)22+ were suggested as the principal electron acceptors among the U(VI) species mixture in carbonate, EDTA, and hydroxyl systems, respectively.
2008. "Amorphous layer coating induced brittle to ductile transition in single crystalline SiC nanowires: an atomistic simulation." Journal of Physics D. Applied Physics 41(15):155419. doi:10.1088/0022-3727/41/15/155419 Abstract Molecular dynamics simulations with Tersoff potentials were used to study the response of SiC nanowires with and without amorphous coating to a tensile strain along the axial direction. The uncoated nanowires show brittle properties and fail through bond breaking. Although the amorphous coating leads to the decrease of Young’s modulus of nanowires, yet it also leads the appearance of plastic deformation under axial strain. These results provide an effective way to modify the brittle properties of some other semiconductor nanowires.
2008. "Analysis of the Relationship between Reaction Energies of Electrophilic SWNT Additionsand Sidewall Curvature: Chiral Nanotubes." Journal of Physical Chemistry C 112(33):12697-12705. doi:10.1021/jp802964c 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 relationship of reaction energies for CH2/NH/O exo- and endo-[2 + 1] cycloadditions to chiral singlewalled carbon nanotube (SWNT) sidewalls with the inverse tube diameter (1/d) was investigated using density functional theory (DFT) and density functional tight binding (DFTB) methods. We considered additions to the three nonequivalent C-C bond types t (bond most parallel to tube axis), d (“diagonal” bond, slightly skewed), and p (bond most perpendicular to tube axis), using hydrogen-terminated (2n,n) SWNT model systems with n ) 2-8. Exoadditions are classified into two types, one where the original C-C bond is broken (exo(l)), and one where it remains intact (exo(s)) in the addition complex. Endoadditions are found to always belong to the latter (endo(s)) type. It is found that (a) exoadditions are more exothermic than endo additions, and (b) that exoadditions are more exothermic with larger bond-tube axis angle (p > d > t). A nearly perfect linear relationship between the total reaction energy ΔE and 1/d holds only for individual endo, exo(s) and exo(l) addition series to specific t/d/p bonds, while ΔE, as well as the SWNT deformation energy (DEF) and the interaction energy (INT) between deformed SWNT and deformed addends, are quadratically dependent on 1/d, when both negative (endo) and positive (exo(s)) bond curvatures are considered in linear regression analysis. Energy decomposition analysis shows that for endo- and exo(s)- series the curvature dependence of ΔE is dominated by INT, while for exo(l) series, this quantity is dominated by DEF.
2008. "Kinetics of Reduction of Fe(III) Complexes by Outer Membrane Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 74(21):6746-6755. doi:10.1128/AEM.01454-08 Abstract Shewanella Oneidensis MR-1 possesses up to 42 c-type cytochromes with heme content varying between 1 to as many as 37. Among them, the outer-membrane cytochromes, particularly MtrC and OmcA, are suspected to function as terminal reductases and are responsible for its enzymatic catalysis capability. So far, the mechanisms of metal reduction by these outer-membrane cytochromes are unknown. In this work, we report the study of reduction kinetics of a series of Fe(III) complexes with citrate, NTA and EDTA by abiotically reduced MtrC and OmcA using a stopped-flow technique in combination with theoretical computation methods within the framework of the electron transfer theory of Marcus and speciation calculations based on the current thermodynamic database. Stopped-flow kinetic data showed that the reaction was very fast and appeared to proceed in two stages, a fast stage that completes in much less than a second and a slower stage afterwards. For a given complex, the reaction is faster by reduction with MtrC than OmcA, while for a given protein, the reaction completes in the decreasing order of Fe-EDTA > Fe-NTA > Fe-citrate. All the stopped-flow kinetic curves could be modeled by two parallel second-order bimolecular redox reactions with second-order rate constants ranging from 0.872 µM-1s-1 for the fast reaction between MtrC with Fe-EDTA complex to 0.012 µM-1s-1 for the slow reaction between OmcA and Fe-citrate complex. Speciation calculations indicated that at both metal:ligand ratios, 1:1.5 and 1:10, a single dominant ferric complex was responsible for the observed reaction for each ligand and, therefore, the observed dual-reaction pathways was attributed to the differences in the reduction behavior among various heme groups within each protein. The results of redox potential calculations with known thermodynamic data show only small differences on the scale of a few millivolts among the three complexes, suggested that the observed differences in reaction rate cannot be explained by the overall redox reaction free energy. In contrast, reorganization energies () calculated based on DFT-COSMO model are substantially different between the complexes, with a larger reorganization energy and therefore a larger activation energy associated with the citrate complex, and progressively smaller ones for the NTA and EDTA complexes. In combination with approximate electronic coupling terms, the theoretical results show good agreement with the observed trend and implicate the reorganization energy as the key factor in the kinetic reaction.
2008. "Nanomechanical Behavior of Single Crystalline SiC Nanotubes Revealed by Molecular Dynamics Simulations." Journal of Applied Physics 104(9):093506. doi:10.1063/1.3005979 Abstract Molecular dynamics simulations with Tersoff potentials were used to study the response of single crystalline SiC nanotubes under tensile, compressive, torsional, combined tension-torsional and combined compression-torsional strains. The simulation results reveal that the nanotubes deform through bond-stretching and breaking and exhibit brittle properties under uniaxial tensile strain, except for the thinnest nanotube at high temperatures, which fails in a ductile manner. Under uniaxial compressive strain, the SiC nanotubes buckle with two modes, i.e. shell buckling and column buckling, depending on the length of the nanotubes. Under torsional strain, the nanotubes buckle either collapse in the middle region into a dumbbell-like structure for thinner wall thicknesses or fail by bond breakage for the largest wall thickness. Both the tensile failure stress and buckling stress decrease under combined tension-torsional and combined compression-torsional strain, and they decrease with increasing torsional rate under combined loading.
2008. "Orientation and temperature dependence of the tensile behavior of GaN nanowires: an atomistic study." Journal of Materials Science. Materials in Electronics 19(8-9):863-867. doi:10.1007/s10854-007-9526-8 Abstract Gallium nitride (GaN) is a high-temperature semiconductor material of considerable interest. It emits brilliant light and has been considered as a key material for the next generation of high frequency and high power transistors that are capable of operating at high temperatures. Due to its anisotropic and polar nature, GaN exhibits direction-dependent properties. Growth directions along [001], [1-10] and [110] directions have all been synthesized experimentally. In this work, molecular dynamics simulations are carried out to characterize the mechanical properties of GaN nanowires with different orientations at different temperatures. The simulation results reveal that the nanowires with different growth orientations exhibit distinct deformation behavior under tensile loading. The nanowires exhibit ductility at high deformation temperatures and brittleness at lower temperature. The brittle to ductile transition (BDT) was observed in the nanowires grown along the [001] direction. The nanowires grown along the [110] direction slip in the {010} planes, whereas the nanowires grown along the [1-10] direction fracture in a cleavage manner under tensile loading.
2008. "High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex." Journal of Biological Chemistry 283(41):27829-27837. doi:10.1074/jbc.M803918200 Abstract Photosystem II (PSII) is a large membrane protein complex that performs the water oxidation reactions of the photosynthetic electron transport chain in plants, algae, and cyanobacteria. Utilizing a high-throughput proteomic analysis of isolated PSII complexes from the cyanobacterium Synechocystis sp. PCC 6803, we have identified four PSII associated proteins that are encoded by the cofactor integration operon (cio). This operon contains genes with putative binding domains for chlorophyll, iron-sulfur centers, and bilins. Protein levels of this operon are more abundant in several PSII lumenal mutants, suggesting an accumulation of cio products in partially assembled PSII complexes. This provides a rare example of a bacterial operon whose protein products are translationally coordinated and associated with a single protein complex. Genetic deletion of cio results in decreased oxygen evolution by PSII, suggesting that cio products may function as regulators of PSII complex assembly or degradation, maybe facilitating an uncharacterized step in PSII assembly.
2008. "The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle." Proceedings of the National Academy of Sciences of the United States of America 105(39):15094-15099. doi:10.1073/pnas.0805418105 Abstract Cyanobacteria are oxygenic photosynthetic bacteria that have significant roles in global biological carbon sequestration and oxygen production. They occupy a diverse range of habitats, from open ocean, to hot springs, deserts, and arctic waters. Cyanobacteria are known as the progenitors of the chloroplasts of plants and algae, and are the simplest known organisms to exhibit circadian behavior4. Cyanothece sp. ATCC 51142 is a unicellular marine cyanobacterium capable of N2-fixation, a process that is biochemically incompatible with oxygenic photosynthesis. To resolve this problem, Cyanothece performs photosynthesis during the day and nitrogen fixation at night, thus temporally separating these processes in the same cell. The genome of Cyanothece 51142 was completely sequenced and found to contain a unique arrangement of one large circular chromosome, four small plasmids, and one linear chromosome, the first report of such a linear element in a photosynthetic bacterium. Annotation of the Cyanothece genome was aided by the use of highthroughput proteomics data, enabling the reclassification of 25% of the proteins with no informative sequence homology. Phylogenetic analysis suggests that nitrogen fixation is an ancient process that arose early in evolution and has subsequently been lost in many cyanobacterial strains. In cyanobacterial cells, the circadian clock influences numerous processes, including carbohydrate synthesis, nitrogen fixation, photosynthesis, respiration, and the cell division cycle. During a diurnal period, Cyanothece cells actively accumulate and degrade different storage inclusion bodies for the products of photosynthesis and N2-fixation. This ability to utilize metabolic compartmentalization and energy storage makes Cyanothece an ideal system for bioenergy research, as well as studies of how a unicellular organism balances multiple, often incompatible, processes in the same cell.
2008. "Colloidal Nanocrystals of Wurtzite Zn 1-xCox0 (0 ≤ x ≥ 1) Models of Spinodal Decomposition in an Oxide Diluted MagneticSemiconductor." Chemistry of Materials 20(22):7107-7116. doi:10.1021/cm802280g Abstract Magnetic-ion-rich nanoscale inclusions formed by spinodal decomposition have been observed in many diluted magnetic semiconductors and have recently been implicated in the ferromagnetic ordering observed in some of these materials. In this study, colloidal nanocrystals of the ternary alloy wurtzite Zn1-xCoxO, with x ranging from 0.0 (w-ZnO) to 1.0 (w-CoO), have been synthesized as model systems for the proposed spinodal decomposition nanostrucures of ferromagnetic Zn1-xCoxO thin films and powders. As freestanding nanocrystals, these phases do not show any signs of ferromagnetism or superparamagnetism at any value of x. Changes in the electronic absorption and magnetic circular dichroism (MCD) spectra with x are described that should allow optical identification of spinodal decomposition in other Zn1-xCoxO samples. Optical and magneto-optical spectroscopic results are presented for the end member of this series (w-CoO), apparently for the first time, and show this binary oxide to be an indirect gap chargetransfer insulator with Eg ≈ 2.3 eV.
2008. "Colloidal Nanocrystals of Wurtzite Zn1-xCoxO (0 ≤ x ≤ 1): Models of Spinodal Decomposition in an Oxide Diluted Magnetic Semiconductor." Chemistry of Materials 20(22):7107-7116. doi:10.1021/cm802280g Abstract Magnetic-ion-rich nanoscale inclusions formed by spinodal decomposition have been observed in many diluted magnetic semiconductors and have recently been implicated in the ferromagnetic ordering observed in some of these materials. In this study, colloidal nanocrystals of the ternary alloy wurtzite Zn1-xCoxO, with x ranging from 0.0 (w-ZnO) to 1.0 (w-CoO), have been synthesized as model systems for the proposed spinodal decomposition nanostrucures of ferromagnetic Zn1-xCoxO thin films and powders. As freestanding nanocrystals, these phases do not show any signs of ferromagnetism or superparamagnetism at any value of x. Changes in the electronic absorption and magnetic circular dichroism (MCD) spectra with x are described that should allow optical identification of spinodal decomposition in other Zn1-xCoxO samples. Optical and magneto-optical spectroscopic results are presented for the end member of this series (w-CoO), apparently for the first time, and show this binary oxide to be an indirect gap chargetransfer insulator with Eg ≈ 2.3 eV.
2008. "Scalable Modeling of Carbon Tetrachloride Migration at the Hanford Site Using the STOMP Simulator." Vadose Zone Journal 7(2):654-666. doi:10.2136/vzj2007.0070 Abstract Numerical simulation has been applied in support of the U.S. Department of Energy’s (DOE’s) efforts to characterize the nature and distribution of carbon tetrachloride in the deep vadose zone at the Hanford site, near Richland, Washington. Three-dimensional computational domains were used, with layered and heterogeneous distributions of soil properties, in this numerical investigation into the vertical and lateral distribution of carbon tetrachloride beneath it release point (216-Z-9 trench) and the effects of soil vapor extraction process. The complexity of the modeled physical processes, namely, the nonlinearities associated with multifluid subsurface flow, including phase transitions and hysteresis in the relative permeability-saturation-capillary pressure functions, limits the grid resolution when executed using single processor computers. To achieve higher grid resolutions and acceptable detail in the subsurface distribution and remediation of carbon tetrachloride, execution on multiple processors was required. This paper describes and demonstrates a scalable implementation of a multifluid subsurface flow and transport with capabilities for volatile organic compounds, residual nonaqueous phase liquid formation in the vadose zone, and soil vapor extraction, using multiple wells. Developing scientific software for execution on parallel computers has unique challenges. The guiding objectives for developing this scalable code were to keep the source coding readable and modifiable by subsurface scientists, allow for both sequential and scalable processing, depend on domain scientists for code parallelization and scalable linear system solvers.
2008. "Evaluation of the Effects of Porous Media Structure on Mixing-Controlled Reactions Using Pore-Scale Modeling and Micromodel Experiments." Environmental Science & Technology 42(9):3185–3193. doi:10.1021/es7022835 Abstract The objectives of this work were to determine if a porescale model could accurately capture the physical and chemical processes that control transverse mixing and reaction in microfluidic pore structures (i.e., micromodels), and to directly evaluate the effects of porous media geometry on a transverse mixing-limited chemical reaction. We directly compare porescale numerical simulations using a lattice-Boltzmann finite volume model (LB-FVM) with micromodel experiments using identical pore structures and flow rates, and we examine the effects of grain size, grain orientation, and intraparticle porosity upon the extent of a fast bimolecular reaction. For both the micromodel experiments and LB-FVM simulations, two reactive substrates are introduced into a network of pores via two separate and parallel fluid streams. The substrates mix within the porous media transverse to flow and undergo instantaneous reaction. Results indicate that (i) the LB-FVM simulations accurately captured the physical and chemical process in the micromodel experiments, (ii) grain size alone is not sufficient to quantify mixing at the pore scale, (iii) interfacial contact area between reactive species plumes is a controlling factor for mixing and extent of chemical reaction, (iv) at steady state, mixing and chemical reaction can occur within aggregates due to interconnected intra-aggregate porosity, (v) grain orientation significantly affects mixing and extent of reaction, and (vi) flow focusing enhances transverse mixing by bringing stream lines which were initially distal into close proximity thereby enhancing transverse concentration gradients. This study suggests that subcontinuum effects can play an important role in the overall extent of mixing and reaction in groundwater, and hence may need to be considered when evaluating reactive transport.
2008. "High performance computations using dynamical nucleation theory." Journal of Physics: Conference Series 125:012017. doi:10.1088/1742-6596/125/1/012017 Abstract Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical challenges in science. In this paper, the Dynamical Nucleation Theory Monte Carlo (DNTMC) model - a model for determining molecular scale nucleation rate constants - and its parallel capabilities are described. The potential for bottlenecks and the challenges to running on future petascale or larger resources are delineated. A "master-slave" solution is proposed to scale to the petascale and will be developed in the NWChem software. In addition, mathematical and data analysis challenges are also described. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE.
2008. "Enhanced Surface Photochemistry in Chloride-Nitrate Ion Mixtures." Physical Chemistry Chemical Physics. PCCP 10(37):5668–5677. doi:10.1039/b806613b Abstract Heterogeneous reactions of sea salt aerosol with various oxides of nitrogen lead to replacement of chloride ion by nitrate ion. Studies of the photochemistry of a model system were carried out using deliquesced mixtures of NaCl and NaNO₃ on a Teflon® substrate. Varying molar ratios of NaCl to NaNO₃ (1 : 9 Cl¯:NO₃¯, 1:1 Cl¯:NO₃¯, 3:1 Cl¯:NO₃¯, 9:1 Cl¯:NO₃¯) and NaNO₃ at the same total concentration were irradiated in air at 299 ∓ 3 K and at a relative humidity of 75 ∓ 8% using broadband UVB light (270–380 nm). Gaseous NO₂ production was measured as a function of time using a chemiluminescence NOy detector. Surprisingly, an enhanced yield of NO₂ was observed as the chloride to nitrate ratio increased. Molecular dynamics (MD) simulations show that as the Cl¯:NO₃¯ ratio increases, the nitrate ions are drawn closer to the interface due to the existence of a double layer of interfacial Cl¯ and subsurface Na+. This leads to a decreased solvent cage effect when the nitrate ion photodissociates to NO₂+O∙¯, increasing the effective quantum yield and hence the production of gaseous NO₂. The implications of enhanced NO₂ and likely OH production as sea salt aerosols become processed in the atmosphere are discussed.
2008. "The Effects of Aging on the Luminescence of PEG-Coated Water-Soluble ZnO Nanoparticles Solutions." Journal of Physical Chemistry C 112(37):14292-14296. doi:10.1021/jp803649k Abstract Water-soluble ZnOnanoparticles coated with polyethylene glycol biscarboxymethyl (PEG(COOH)2)were prepared in ethanol/water solutions. The ZnOnanoparticles have a hexagonal structure with an average size of 10 nm. Three different luminescence bands are observed from the nanoparticle solutions: green emission at 530 nm from surface states or defects, UV emission at 380 nm from the ZnOexcitons, and an emission band at around 338 nm from the PEG(COOH)2. The fresh as-prepared samples have very strong green emission at 530 nm from surface states or defects but very weak excitonic emission at 380 nm. After dilution with ethanol, the green emission decreases in intensity and the excitonic emission increases. In the diluted samples, the excitonic luminescence intensity increases with storage time. This intensity increase is attributed to surface passivation by CH3COO-ligands resulting from precursor reactions in the ethanol solvent.
2008. "Solution Structure of Ribosomal Protein L40E, a Unique C4 Zinc Finger Protein Encoded by Archaeon Sulfolobus Solfataricus." Protein Science 17:589-596. doi:10.1110/ps.073273008 Abstract The ribosomal protein L40E from archaeon Sulfolobus solfataricus is a component of the 50S ribosomal subunit. L40E is a 56-residue, highly basic protein that contains a C4 zinc finger motif, CRKC_X10_CRRC. Homologs are found in both archaea and eukaryotes but are not present in bacteria. Eukaryotic genomes encode L40E as a ubiquitin-fusion protein. L40E was absent from the crystal structure of euryarchaeota 50S ribosomal subunit. Here we report the three-dimensional solution structure of L40E by NMR spectroscopy. The structure of L40E is a three-stranded b-sheet with a simple b2b1b3 topology. There are two unique characteristics revealed by the structure. First, a large and ordered b2–b3 loop twists to pack across the one side of the protein. L40E contains a buried polar cluster comprising Lys19, Lys20, Cys22, Asn29, and Cys36. Second, the surface of L40E is almost entirely positively charged. Ten conserved basic residues are positioned on the two sides of the surface. It is likely that binding of zinc is essential in stabilizing the tertiary structure of L40E to act as a scaffold to create a broad positively charged surface for RNA and/or protein recognition. A portion of this work was performed in the Environmental Molecular Sciences Facility, a DOE national scientific user facility.
2008. "The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain." Protein Science 17(3):583-588. Abstract The ribosomal protein S17E from the archaeon Methanobacterium thermoautotrophicum is a component of the 30S ribosomal subunit. S17E is a 62-residue protein conserved in archaea and eukaryotes and has no counterparts in bacteria. Mammalian S17E is a phosphoprotein component of eukaryotic ribosomes. Archaeal S17E proteins range from 59 to 79 amino acids, and are about half the length of the eukaryotic homologs which have an additional C-terminal region. Here we report the three-dimensional solution structure of S17E. S17E folds into a small three-helix bundle strikingly similar to the FF domain of human HYPA/FBP11, a novel phosphopeptide-binding fold. S17E bears a conserved positively charged surface acting as a robust scaffold for molecular recognition. The structure of M. thermoautotrophicum S17E provides a template for homology modeling of eukaryotic S17E proteins in the family.
2008. "Apoferritin-Templated Yttrium Phosphate Nanoparticle Conjugates for Radioimmunotherapy of Cancers." Journal of Nanoscience and Nanotechnology 8(5):2316-2322. doi:10.1166/jnn.2008.177 Abstract We report a templated-synthetic approach based on apoferritin to prepare radionuclide nanoparticle (NP) conjugates. Non-radioactive yttrium (89Y) was used as model target and surrogate for radioyttrium (90Y) to prepare the nanoparticle conjugate. The center cavity and multiple channel structure of apoferritin offer a fast and facile method to precipitate yttrium phosphate by diffusing yttrium and phosphate ions into the cavity of apofrritin, resulting a core-shell nanocomposite. The yttrium phosphate/apoferritin nanoparticle was functionalized with biotin for further application. The synthesized nanoparticle was characterized by transmission electron microscopy (TEM) and x-ray photoelectron spectroscopy (XPS). We found that the resulting nanoparticles were uniform in size, with a diameter of around 8 nm. We tested the pre-targeting capability of the biotin-modified yttrium phosphate/apoferritin nanoparticle (yttrium phosphate/apoferritin nanoparticle) conjugate with streptavidin-modified magnetic beads and with aid of biotin-modified fluorecein isothiocyanate (FITC) tracer. This work shows that an yttrium phosphate NP conjugate provides a fast, simple and efficient method to prepare radioactive yttrium conjugate for applications in radioimmunotherapy of cancer.
2008. "Dye-Doped Silica Nanoparticle Labels/Protein Microarray for Detection of Protein Biomarkers." The Analyst 133:1550 - 1555. doi:10.1039/b719810h Abstract Biomarkers serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Interleukin-6 (IL-6), a biomarker with its important biological and pathological functions, has been studied for decades. Conventional fluorescence immunoassay has been widely used for analysis of biomakers like IL-6. However, single fluorophore labeling shows its limitations of low intensity and poor stability. We report a dye-encapsulated silica nanoparticle as a label, with the advantages of high fluorescence intensity, photostability, and biocompatibility, in conjunction with microarray technology for sensitive immunoassay of IL-6 on a microarray format. The tris (2,2’-bipyridyl)ruthenium (II)chloride hexahydrate (Rubpy) dye incorporated into silica nanoparticles using a simple one-step microemulsion synthesis step. The nanoparticles are uniform in size with a diameter of 50 nm. The microarray fluorescent immunoassay approach based on dye-doped silica nanoparticle labels has high sensitivity for practical applications with a limit of detection for IL-6 down to 0.1 ng mL-1. The calibration curve is linear over the range from 0.1 ng mL-1 to 10 ng mL-1. Furthermore, results illustrated that the assay is highly specific for IL-6 in the presence of range of cytokines or proteins. The RuDS dye-labeled nanoparticles in connection with protein microarrays show the promise for clinical diagnosis of biomarkers.
2008. "Synthesis of Lutetium Phosphate/Apoferritin Core-Shell Nanoparticles for Potential Applications in Radioimmunoimaging and Radioimmunotherapy of Cancers." Journal of Materials Chemistry 18(15):1779-1783. Abstract We report a novel approach for synthesizing LuPO4/apoferritin core-shell nanoparticles based on an apoferritin template, conjugated to the protein biotin. To prepare the nanoparticle conjugates, we used non-radioactive lutetium as a model target or surrogate for radiolutetium (177Lu). The central cavity, multi-channel structure, and chemical properties of apoferritin are well-suited for sequentially diffusing lutetium and phosphate ions into the cavity--resulting in a stable core-shell composite. We characterized the synthesized LuPO4/apoferritin nanoparticle using transmission electron microscopy (TEM) and x-ray photoelectron spectroscopy (XPS). We tested the pre-targeting capability of biotin-modified lutetium/apoferritin nanoparticle using streptavidin-modified magnetic beads and streptavidin-modified fluorescein isothiocyanate (FITC) tracer. This paper presents a simple, fast, and efficient method for synthesizing LuPO4/apoferritin nanoparticle conjugates with biotin for potential applications in radioimmunotherapy and radioimmunoimaging of cancer.
