Scientific Publications 2004
2004. "Response to Comments on "Reactions at Interfaces as a Source of Sulfate Formation in Sea-Salt Particles"." Science 303(5658):1. Abstract Our paper (1) demonstrated that the oxidation of chloride at the interface will be a new source of alkalinity that can modulate the acidification of particles during the day when gaseous OH is present. We proposed that this modulation of the acidity of sea-salt particles could potentially affect the rate of uptake and oxidation of SO2 [S(IV)], which is very sensitive to pH.
2004. "Energetics and Dynamics of Peptide Fragmentation from Multiple-Collision Activation and Surface-Induced Dissociation Studies." European Journal of Mass Spectrometry 10(2):259-267. Abstract This account summarizes the energetics and dynamics of peptide fragmentation obtained using a new approach recently developed in our laboratory. The approach involves RRKM modeling of time- and energy-resolved MS/MS data obtained using collisional activation. We demonstrate that surface-induced dissociation (SID) on a long timescale of Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) is perfectly suited for studying the energetics and dynamics of peptide fragmentation. The advantages provided by SID include very fast ion activation, which eliminates possible discrimination against higher-energy dissociation pathways, and efficient â€œamplificationâ€ of small changes in dissociation parameters. We present a summary of results obtained for small alanine-containing peptides as well as larger peptides including angiotensin analogs and a series of peptides containing the LDIFSDF motif.
2004. "Energetics and Dynamics of Peptide Fragmentation from Multiple-Collision Activation and Surface-Induced Dissociation Studies." European Journal of Mass Spectrometry 10(2):259-267. doi:10.1255/ejms.641 Abstract This account summarizes the energetics and dynamics of peptide fragmentation obtained using a new approach recently developed in our laboratory. The approach involves RRKM modeling of time- and energy-resolved MS/MS data obtained using collisional activation. We demonstrate that surface-induced dissociation (SID) on a long timescale of Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) is perfectly suited for studying the energetics and dynamics of peptide fragmentation.
2004. "Fragmentation Energetics for Angiotensin II and its Analogs from Time-and Energy-Resolved Surface-Induced Dissociation Studies." International Journal of Mass Spectrometry 234(1-3):89-99. Abstract Surface-induced dissociation (SID) of four model peptides: DRVYIHPF, RVYIHPF, RVYIHAF, and RVYIHDF was studied using a novel Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for SID experiments.
2004. "Surface-Induced Dissociation of Ions Produced by Matrix-Assisted Laser Desorption Ionization in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer." Analytical Chemistry 76(2):351-356. Abstract Intermediate pressure matrix assisted laser ionizaton (MALDI) source was constructed and interfaced with a 6T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for surface-induced dissociation (SID) studies.
2004. "Fourier Transform Spectroscopy of CH3OH: Rotation-Torsion-Vibration Structure for the CH3-Rocking and OH-Bending Modes." Journal of Molecular Spectroscopy 228(2):528-543. Abstract High-resolution Fourier Transform Spectra of CH3OH have been investigated in the infrared region from 930 -1450 cm-1 in order to map the torsion-rotation energy manifolds associated with the v7 in-plane CH3 rock, the v11 out-of-plane CH3 rock, and the v6 OH bend. Upper-state term values have been determined from the assigned spectral subbands, and have been fitted to power-series expansions to obtain substate origins and effective B-values for the three modes. The substate origins have been grouped into related families according to systemic trends observed in the torsion-vibration energy map, but there are substantial differences from the traditional torsional patterns. There appears to be significant torsion-mediated spectral fractionation, and a variety of subbands of mixed torsion-vibration parentage have been observed. For example, coupling of the v6=1 OH bend to nearby torsionally excited (v1, vt) = (1,1) CH3-rock and (v8, vt) = (1,1) CO-stretch states introduces (v6, vt) = (1,0) ← (0,1) "forbidden" subbands into the spectrum and makes the v7+v12-v12 torsional hot band stronger than the v7 fundamental. The results suggest a picture of strong coupling the OH-bending, CH3-rocking and CO-stretching modes that modifies the traditional energy structure and raises interesting and provocative questions about the torsion-vibration identity of a number of the observed states.
2004. "NMR Properties of Platinum --Thallium Bonded Complexes: Analysis of Relativistic Density Functional Theory Results." Magnetic Resonance in Chemistry 42(S1):S99-S116. doi:10.1002/mrc.1450 Abstract A portion of the following research was conducted at EMSL. The metal NMR parameters of the complexes [(NC)5Pt–Tl(CN)n]n− (n = 0–3, I–IV) and [(NC)5Pt–Tl–Pt(CN)5]3− (V), as well as [fPt(NO3)(NH3/2L2gTl(NO3/2(MeOH)] (VI) and [fPt(NO3)(NH3/2L2g2Tl]+ (VII) with L =NHCOtBu,were computationally investigated by relativistic density functional theory. Complexes I–V were previously studied by us. We briefly review the main findings here. Their spin–spin coupling constants are analyzed in terms ofmolecular orbital and fragment orbital contributions which demonstrate the various influences of the solvent and of the ligands on the extraordinarily large metal–metal coupling constants. Complexes VI and VII and various model systems were investigated in more detail. It is shown that the same computational model which performs best for I–V yields too large metal–metal coupling constants for VI and VII. The analysis shows that this is likely to be attributable to a strong sensitivity of the coupling constants to the rather small Pt 6s contributions in the occupied metal–metal s-bonding orbitals. Bulk solvent effects on the metal–metal couplings are sizeable and should be considered in the computational model. Both calculated and experimental Pt–Tl coupling constants for VI and VII are substantially larger than those for I–V, thereby representing the largest heteronuclear coupling constants known so far experimentally. Metal chemical shifts for VI and VII were also investigated. The computational results indicate that the choice of the Pt reference is rather problematic. Tl chemical shifts agree much better with experimental data.
2004. "A constitutive model for air-NAPL-water flow in the vadose zone accounting for immobile, non-occluded (residual) NAPL in strongly water-wet porous media." Journal of Contaminant Hydrology 71(1-4):261-282. Abstract A hysteretic constitutive model describing relations among relative permeabilities, saturations, and pressures in fluid systems consisting of air, nonaqueous-phase liquid (NAPL), and water is modified to account for NAPL that is postulated to be immobile in small pores and pore wedges and as films or lenses on water surfaces. A direct outcome of the model is prediction of the NAPL saturation that remains in the vadose zone after long drainage periods (residual NAPL). Using the modified model, water and NAPL (free, trapped by water, and residual) saturations can be predicted from the capillary pressures and the water and total-liquid saturation-path histories. Relations between relative permeabilities and saturations are modified to account for the residual NAPL by adjusting the limits of integration in the integral expression used for predicting the NAPL relative permeability. When all of the NAPL is either residual or trapped (i.e., no free NAPL), then the NAPL relative permeability will be zero. We model residual NAPL using concepts similar to those used to model residual water. As an initial test of the constitutive model, we compare predictions to published measurements of residual NAPL. Furthermore, we present results using the modified constitutive theory for a scenario involving NAPL imbibition and drainage.
2004. "A constitutive model for air-NAPL-water flow in the vadose zone accounting for immobile, non-occluded (residual) NAPL in strongly water-wet porous media." Journal of Contaminant Hydrology 73(1-4):283-304. Abstract A hysteretic constitutive model describing relations among relative permeabilities, saturations, and pressures in fluid systems consisting of air, nonaqueous-phase liquid (NAPL), and water is modified to account for NAPL that is postulated to be immobile in small pores and pore wedges and as films or lenses on water surfaces. A direct outcome of the model is prediction of the NAPL saturation that remains in the vadose zone after long drainage periods (residual NAPL). Using the modified model, water and NAPL (free, entrapped by water, and residual) saturations can be predicted from the capillary pressures and the water and total-liquid saturation-path histories. Relations between relative permeabilities and saturations are modified to account for the residual NAPL by adjusting the limits of integration in the integral expression used for predicting the NAPL relative permeability. When all of the NAPL is either residual or entrapped (i.e., no free NAPL), then the NAPL relative permeability will be zero. We model residual NAPL using concepts similar to those used to model residual water. As an initial test of the constitutive model, we compare predictions to published measurements of residual NAPL. Furthermore, we present results using the modified constitutive theory for a scenario involving NAPL imbibition and drainage.
2004. "On The Electronic Structure of Molecular UO2 in the Presence of Ar Atoms: Evidence for Direct U-Ar Bonding." Journal of the American Chemical Society 126(11):3424-3425. Abstract Calculations via scalar-relativistic density functional theory (DFT) and ab initio CCSD(T) methodologies are used to explore the possibility of direct interactions between molecular UO2 and Ar atoms. The 3Hg electronic state of UO2, which is an excited state of the isolated molecule, exhibits significant bonding to Ar in the model complexes UO2(Ar) and UO2(Ar)5. The calculated vibrational frequencies of ground-state 3Φu UO2 and UO2(Ar)5 with an (fφ)1(fδ)1 electron configuration agree well with the observed frequencies of UO2 in solid neon and solid argon, respectively. The results strongly suggest that the ground electron configuration of UO2 changes from 5f17s1 to 5f2 when the matrix host is changed from neon to argon.
2004. "Method for Determining Performance of Sulfur Oxide Adsorbents for Diesel Emission Control Using Online Measurement of SO2 and SO3 in the Effluent ." Industrial and Engineering Chemistry Research 43(15):4452-4456. Abstract Upcoming regulations regarding diesel engine emissions require substantial reduction in particulate matter and nitrogen oxides through aftertreatment methods. Since sulfur oxides in the exhaust greatly reduce the performance of the aftertreatment system, a dedicated trap for removal of sulfur oxides has been considered. Most adsorbents are more effective in removing SO3 than SO2; hence oxidation catalysts have been employed to maximize the concentration of SO3 in the effluent. Although SO2 concentrations are easily measured, SO3 is less easily quantified. As a result, the only figure of merit for the SOx trap performance has been total capacity, provided by post-characterization. In this paper we describe a chromatographic method for measurement of SO2 and SO3 adsorption in real time, which provides adsorbent performance data on breakthrough capacities and sulfur slip, especially important when operating at high space velocities. We also provide experimental measurements of breakthrough capacities for SO2 and SO3 adsorption for some common metal oxide adsorbents using this analytical system.
2004. "Effects of Template and Precursor Chemistry on Structure and Properties of Mesoporous TiO2 Thin Films ." Langmuir 20(21):9095-9102. Abstract Mesoporous TiO2 thin films were synthesized by sol-gel processing using an aqueous-based, inexpensive and environmentally friendly precursor and cationic surfactants as templates. The films were prepared by spin-coating on glass substrates followed by calcination to remove the surfactant. N2 sorption, x-ray diffraction and TEM were used to characterize the porosity, pore size and pore structure before and after calcination. Films were found to have wormlike pore structures after calcination. These results show that the mesostructure and porosity of the thin films can be controlled by the surfactant template chemistry such as surfactant/Ti ratio, pH, and the speed of solvent removal.
2004. "On the Noble-Gas Induced Intersystem Crossing for the CUO Molecule: Experimental and Theoretical investigations of CUO(Ng)n (Ng = Ar, Kr, Xe; n = 1, 2, 3, 4) Complexes in Solid Neon." Inorganic Chemistry 43(3):882-894. Abstract Uranium atoms excited by laser ablation react with CO in excess neon to produce the novel CUO molecule, which forms distinct Ng complexes (Ng = Ar, Kr, Xe) when the heavier noble gases are added. The CUO(Ng) complexes are identified through CO isotopic and Ng substitution on the neon matrix infrared spectra and by comparison to DFT frequency calculations. The U-C and U-O stretching frequencies of CUO(Ng) complexes are slightly red shifted from frequencies for the 1S+ CUO ground state, which identifies singlet ground state CUO(Ng) complexes. In solid neon the CUO molecule is also a complex CUO(Ne)n, and the CUO(Ne)n-1(Ng) complexes are likewise specified. The next singlet CUO(Ne)x(Ng)2 complexes in excess neon follow in like manner. However, the higher CUO(Ne)x(Ng)n complex (n = 3, 4) stretching modes approach pure argon matrix CUO(Ar)n values and isotopic behavior, which are characterized as triplet ground state complexes by DFT frequency calculations. This work suggests that the singlet-triplet crossing occurs with 3 Ar, 3 Kr or 4 Xe and a balance of Ne atoms coordinated to CUO in the neon matrix host.
2004. "Disposable Carbon Nanotube Modified Screen-Printed Biosensor for Amperometric Detection of Organophosphorus Pesticides and Nerve Agents." Electroanalysis 16(1-2):145-149. Abstract A disposable biosensor based on carbon nanotube was develped for detection of pesticides and nerve agents.
2004. "Glucose Biosensors Based on Carbon Nanotube Nanoelectrode Ensembles." Nano Letters 4(2):191-195. Abstract This paper describes the development of glucose biosensors based on carbon nanotube (CNT) nanoelectrode ensembles (NEEs) for the selective detection of glucose. Glucose oxidase was covalently immobilized on CNT NEEs via carbodiimide chemistry by forming amide linkages between their amine residues and carboxylic acid groups on the CNT tips. The catalytic reduction of hydrogen peroxide liberated from the enzymatic reaction of glucose oxidase upon the glucose and oxygen on CNT NEEs leads to the selective detection of glucose. The biosensor effectively performs selective electrochemical analysis of glucose in the presence of common interferents (e.g. acetaminophen, uric and ascorbic acids), avoiding the generation of an overlapping signal from such interferents. Such an operation eliminates the need for permselective membrane barriers or artificial electron mediators, thus greatly simplifying the sensor design and fabrication.
2004. "Low Temperature Solid-State NMR Experiments of Half-Integer Quadrupolar Nuclides: Caveats and Data Analysis." Journal of Magnetic Resonance 168:66-74. Abstract Solid-state NMR spectroscopy of half-integer quadrupolar metals has received a lot of interest recently with the advent of new methodologies and higher magnetic fields. We present here the extension of our previous low temperature method to an 18.8 T system. This new probe entailed a total redesign including a cross coil and variable capacitors that are operational at cryogenic temperatures. The limitations to sensitivity are also discussed; including a new diode network, the utilization of a cryogenic band pass filter, and the consequences of the RF profiles of the coil. Further, details of the spectroscopy of a spin 5/2 metal in a protein are discussed, such as the observation of the outer transitions and how to distinguish them from the desired ±1/2 transition
2004. "A Cation Exchange Model to Describe Cs+ Sorption at High Ionic Strength in Subsurface Sediments at Hanford Site, USA." Journal of Contaminant Hydrology 68(3-4):217-238. Abstract A Cation Exchange Model to Describe Cs Sorption at High Ionic Strength in Subsurface Sediments at Hanford Site, USA
2004. "Dissolution of Uranyl Microprecipitates from Subsurface Sediments at Hanford Site, USA." Geochimica et Cosmochimica Acta 68(22):4519-4537. Abstract This paper describes a study of thermodynamics and Kinetics of uranyl microprecipitates from subsurface sediments at Hanford Site, USA.
2004. "Adsorption and Reaction of SO₂ on Model Ce₁-xZrxO₂(111) Catalysts." Journal of Physical Chemistry B 108(9):2931-2938. Abstract The interaction of SO₂ with ceria-zirconia model catalysts was studied using high-resolution synchrotron-based X-ray photoelectron spectroscopy (XPS). Epitaxial Ce₁ xZrxO₂(111) (x = 0.1 and 0.3) thin films (500-700 Å in thickness) were grown by oxygen-plasma-assisted molecular beam epitaxy on single crystal yttria-stabilized ZrO₂(111). Slightly defective surfaces were achieved by vacuum annealing at 900 K and highly defective surfaces with O vacancies were obtained by 1.5 keV Ne⁺ sputtering. On the slightly defective Ce₀․₉Zr₀․₁O₁․₉₅ (111) and Ce₀․₇Zr₀․₃O₁.₉₅ (111) surfaces, the only product upon SO₂ adsorption at 300 K is sulfate, in the form of Ce(SO₄) ₂, which gradually desorbs from the surface between 300 and 900 K. SO₂ adsorption on the heavily reduced surfaces results in a different behavior. A complex set of compounds is observed during adsorption and thermal conversion processes. The Ce₃⁺ states play a dominant role in the adsorption of SO₂ and cleavage of S-O bonds. The relative amount of sulfur-derived adsorbates depends on the defect concentration: the higher the Ce₃⁺ concentration, the larger the amount of chemisorbed species. On Ce₀․₉Zr₀․₁O₁.₅₀ (111) and Ce₀․₇Zr₀․₃O₁.₅₀ (111) surfaces, SO₄ (in the form of Ce₂(SO₄)₃), SO₃, and atomic sulfur species coexist at 300 K. Thermal annealing (for Ce₀․₉Zr₀․₁O₁.₅₀ (111), > 400 K; for Ce₀․₇Zr₀․₃O₁.₅₀ (111), > 700 K) leads to the formation of an oxy-sulfide (Ce₂O₂S), which is converted from either SO₄ or SO₃.
2004. "Interaction of CH4, CH3Cl, CH2CI2, and CCl4 with O-terminated FeO(111)." Journal of Physical Chemistry B 108(11):3644-3650. Abstract Well-ordered FeO(111) thin films are epitaxially grown on a Pt(111) substrate. A series of molecules including CH4, CH3Cl, CH2Cl2, CHCl3, and CCl4 are used as probes to test the chemical reactivity of the FeO(111) surface. The temperature programmed desorption spectra show no evidence of dissociative adsorption or chemical reaction between the substrate and the adsorbates. The desorption kinetics studies reveal that all the molecules are physisorbed and have desorption kinetics with an order between 0 and 1. Kinetic analysis is conducted, assuming both zero and first order desorption, and shows that an uncertainty in the desorption order introduces an error in determination of the terrace site desorption energies ( = 0.5 ML) of only ~ 2%. The desorption energies for the series of molecules increase with the number of chlorine atoms in the molecule. The increase of desorption energies is not linear with the molecular polarizability and the deviations from linearity are attributed to the permanent dipole in some of the molecules. We conclude that the oxygen terminated FeO(111) surface is in general unreactive toward both C-H and C-Cl bonds.
2004. "High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Analytical Chemistry 76(18):5345-5353. Abstract A new quantitative cysteinyl-peptide enrichment technology (QCET) was developed to achieve higher efficiency, greater dynamic range, and higher throughput in quantitative proteomics that use stable-isotope labeling techniques combined with high resolution liquid chromatography (LC)-mass spectrometry (MS). This approach involves 18O labeling of tryptic peptides, high efficiency enrichment of cysteine-containing peptides, and confident protein identification and quantification using the accurate mass and time tag strategy. Proteome profiling of naïve and in vitro-differentiated human mammary epithelial cells using QCET resulted in the identification and quantification of 603 proteins in a single LC-Fourier transform ion cyclotron resonance MS analysis. Advantages of this technology include: (1) a simple, highly efficient method for enriching cysteinyl-peptides; (2) a high throughput strategy suitable for extensive proteome analysis; and (3) improved labeling efficiency for better quantitative measurements. This technology enhances both the functional analysis of biological systems and the detection of potential clinical biomarkers.
2004. "Single-Molecule Spectroscopy Studies of Conformational Change Dynamics in Enzymatic Reactions." Current Pharmaceutical Biotechnology 5(3):261-269. Abstract Enzymatic reaction dynamics have usually been studied using ensemble-averaged experimental approaches and often in solution phase.
2004. "A NEW EXTRACTION CHROMATOGRAPHY RESIN CONTAINING KLÄUI LIGANDS FOR APPLICATION IN ACTINIDE SEPARATIONS." Solvent Extraction and Ion Exchange 22(6):947-960. doi:10.1081/SEI-200037442 Abstract An extraction chromatography resin containing the anionic ligand (η5-pentamethylcyclopentadienyl)tris-(diethylphosphito-P)cobalt(III), (L) has been prepared. The resin consists of 1 wt% L on Amberlite® XAD-7. This resin strongly sorbs Am(III) and Pu(IV). The sorption of these ions decreases with increasing nitric acid concentration, but this effect is more pronounced for Am(III). This allows for convenient separation of Am(III) from Pu(IV) by simple adjustments in the nitric acid concentration. The tripodal geometry of L disfavors the complexation of uranyl ion, so sorption of U(VI) by the L-containing resin is weak.
2004. "Spectroscopic Characterizations of Molecularly-Linked Gold Nanoparticle Assemblies Upon Thermal Treatment." Langmuir 20(10):4254-4260. Abstract Nanostructured gold catalysts have attracted increasing interest since the pioneer work of Haruta which demonstrated unusually high catalytic activities for CO oxidation when the nanoparticles were made less than ~10 nm diameter in size and supported on oxides. It is possible to use core-shell gold nanoparticles to construct the catalyst and activate the catalytic activity by applying a thermal-treatment process. The understanding of how the core-shell surface components reconstitute in such a catalytic activation process will have important implications in expanding this approach to the design and fabrication of nanostructured catalysts. We report herein the results of a study of decanethiolate-capped gold nanoparticles of 2-nm and 5-nm core sizes assembled on planar substrates using 1,9-nonanedithiol (NDT) and 11-mercaptoundecanoic acid (MUA) as molecular linkers were studied as a model system. XPS and IR are employed to detect the identity of surface species and to analyze the elemental composition or oxidation states of the nanomaterials, from which we derive structural information about the surface reconstitution of the core-shell nanostructured catalysts. Electrochemical methods are used to characterize the electrocatalytic activities.
2004. "Initial Stages of Oxide Nanodot Heteroepitaxial Growth: Cu2O on SrTiO3(100)." Applied Physics Letters 85(19):4481-4483. Abstract The growth mechanism in a heteroepitaxy of oxide nanodots is investigated by combination of the x-ray photoelectron spectroscopy (XPS), atomic force microscopy and theoretical modeling. In contrast to the majority of semiconductor systems, in the studied metal oxide system of Cu2O – SrTiO3(100) the growth process starts without wetting layer formation with appearance of small ( ~ 10 nm) square-based planar Cu2O nanodots. Continued deposition leads mainly to increase of the nanodot density, practically, without change of their size. Only after reaching some critical density (~ 1013 cm-2 for 760 K growth temperature), growth of scattered, significantly larger islands starts through the coalescence of small nanodots. XPS analysis suggests that the interface between small nanodots and substrate is abrupt with only weak Cu – O(SrTiO3) interaction.