Scientific Publications 2009
2009. "Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet." Journal of the American Society for Mass Spectrometry 20(12):2265-2272. doi:10.1016/j.jasms.2009.08.018 Abstract The standard heated capillary inlet of an electrospray ionization mass spectrometry (ESI-MS) interface was compared with shorter versions of the inlet to determine the effects on transmission and ionization efficiencies for low-flow electrosprays. The primary finding of the study was a large bias towards higher mobility species in the electrospray current losses to the inside walls of the inlet. The transmission efficiency increased with decreasing capillary length due to reduced losses along the capillary. A decrease in transmission efficiency was also confirmed for electrosprays of higher conductivity solvents. A direct correlation between mass spectrometry sensitivity and the transmitted electrospray current was not observed as some analytes showed little to no increase in sensitivity while others showed as high as a 15 – fold increase. The variation was shown to at least be partially dependent on the analytes’ mobilities. Higher mobility analytes demonstrated a larger increase in sensitivity when shorter inlets were used. The results indicate that considerable biases against higher mobility species can be produced by the use of long capillary inlets in the ESI-MS interface and strategies are provided to minimize the bias against higher mobility species for efficient ion transmission through the heated capillary interface.
2009. "Structural Evolution of Doped Gold Clusters: MAux-(M = Si,Ge,Sn; X=5-8)." Journal of the American Chemical Society 131(9):3396-3404. Abstract We report a joint experimental and theoretical study on the structures of a series of gold clusters doped with a group-14 atom: MAux - (M ) Si, Ge, Sn; x ) 5-8). Well-resolved hotoelectron spectra were obtained and compared to calculations at several levels of theory to identify the low-lying structures of MAu5-8 -. We found that the structure of SiAu5 - is dominated by the tetrahedrally coordinated Si motif, which can be viewed as built from the tetrahedral SiAu4 - by an extra Au atom bonded to a terminal gold atom. However, SiAu6 - and SiAu7 - have quasi-planar structures, similar to those of GeAu6 -/SnAu6 - and GeAu7 /SnAu7 -, respectively. SiAu8 - again has a tetrahedrally coordinated Si structure, which displays a structural motif of a dangling Au-Si unit sitting on a gold cluster surface, resembling that of the larger Si-doped gold cluster SiAu16 -. For M ) Ge, Sn, our results show that the major isomers of GeAu5-8 - have structures similar to those of the corresponding SnAu5-8 - clusters, and they can be viewed as grown from the previously suggested square-pyramidal GeAu4 - and SnAu4 -, respectively. Population of minor isomers was observed for SnAu5 -, GeAu6 -, SnAu6 -, and GeAu8 -. The 3D to quasi-2D to 3D structural evolution for SiAu5 - to SiAu8 - and the structural convergence for MAux - (M ) Si, Ge, Sn) at x ) 6, 7 manifest competitions between the tendency of forming molecule-like structures around the group-14 dopant (optimizing M-Au interactions) and the strong tendency of forming planar structures for small gold anion clusters (optimizing Au-Au interactions).
2009. "Dual spatial maps of transcript and protein abundance in the mouse brain." Expert Review of Proteomics 6(3):243-249. Abstract Integrating quantitative proteomic and transcriptomic datasets promises valuable insights in unraveling the molecular mechanisms of the brain. We concentrate on recent studies using mass spectrometry and microarray data to investigate transcript and protein abundance in normal and diseased neural tissues. Highlighted are dual spatial maps of these molecules obtained using voxelation of the mouse brain. We demonstrate that the relationship between transcript and protein levels displays a specific anatomical distribution, with greatest fidelityin midline structures and the hypothalamus. Genes are also identified that have strong correlations between mRNA and protein abundance. In addition, transcriptomic and proteomic analysis of mouse models of Parkinson's disease are discussed.
2009. "Reactivity of Fe-0 Atoms, Clusters, and Nanoparticles with CC14 Multilayers on FeO(111)." Journal of Physical Chemistry C 113(5):1818-1829. Abstract The interaction of Fe0 atoms and clusters with CCl4 multilayers was investigated using a novel "atom dropping" method at 30 K over a FeO(111) thin film. Temperature programmed desorption experiments over a range of Fe0 and CCl4 coverages demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. X-ray photoelectron spectroscopy data show that the initial reactive interaction occurs spontaneously at 30 K, with the experimentally observed reaction products formed at higher temperature, in agreement with the results of theoretical calculations. The formation of OCCl2 and CO is concluded to occur through abstraction of O atoms from the generally inert FeO(111) substrate. The buffer layer assisted growth technique is used to show that the reactivity, and interestingly the reaction products, is determined by the size of Fe0 nanoparticles which interact with CCl4.
2009. "Sensing Mechanisms for Carbon Nanotube Based NH3 Gas Detection." Nano Letters 9(4):1626-1630. doi:10.1021/nl803930w Abstract There has been an argument on carbon nanotube (CNT) based gas detectors with a field-effect transistor (FET) geometry: do the response signals result from charge transfer between adsorbed gas molecules and the CNT channel and/or from the gas species induced Schottky barrier modulation at the CNT/metal contacts? To differentiate the sensing mechanisms, we employed three CNTFET structures, i.e., (1) the entire CNT channel and CNT/electrode contacts are accessible to NH3 gas; (2) the CNT/electrode contacts are passivated with a Si3N4 thin film, leaving the CNT channel open to the gas and, in contrast, (3) the CNT channel is covered with the film, while the contacts are open to the gas. We suggest that the Schottky barrier modulation at the contacts is the dominant mechanism from room temperature to 150°C. At higher temperatures, the charge transfer process contributes to the response signals. There is a clear evidence that the adsorption of NH3 on the CNT channel is facilitated by environmental oxygen.
2009. "Mineralogical transformations controlling acid mine drainage chemistry." Chemical Geology 262(3-4):169-178. Abstract The role of Fe(III) minerals in controlling acid mine drainage (AMD) chemistry was studied using samples from two AMD sites [Gum Boot (GB) and Fridays-2 (FR)] located in northern Pennsylvania. Chemical extractions, X-ray diffraction (XRD), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) were used to identify and characterize Fe(III) phases. The mineralogical analysis revealed that schwertmannite and goethite were the principal Fe(III) phases in the sediments. Schwertmannite transformation occurred at the GB site where poorly-crystallized goethite rich in surface-bound sulfate was initially formed. In contrast, no schwertmannite transformation occurred at the FR site. The goethite in GB sediments had spherical morphology due to preservation of schwertmannite structure by adsorbed sulfate. Results of chemical extractions showed that poorly-crystallized goethite was subject to further crystallization accompanied by sulfate desorption. Changes in sulfate speciation preceded its desorption, with a conversion of bidentate- to monodentate-bound sulfate surface complexes. Laboratory sediment incubation experiments were conducted to evaluate the effect of mineral transformation on water chemistry. Incubation experiments were carried out with schwertmannite-containing sediments and AMD waters with different pH and chemical composition. The pH decreased to 1.9-2.2 in all suspensions and the concentrations of dissolved Fe and S increased significantly. Regardless of differences in the initial water composition, pH, Fe and S were similar in suspensions of the same sediment. XRD measurements revealed that schwertmannite transformed into goethite in GB and FR sediments during laboratory incubation. The incubation experiment demonstrated that schwertmannite transformation controlled AMD water chemistry during “closed system” laboratory contact.
2009. "Formation of GaSb core-shell nanofibers by a thermally-induced phase decomposition process." Journal of Materials Research 24(7):2286-2292. doi:10.1557/JMR.2009.0287 Abstract Amorphous GaSb nanofiber networks can be fabricated by ion irradiation of bulk GaSb, however the nanofibers require crystallization to be useful for implementation in a variety of optoelectronic devices. We report that the thermal annealing of GaSb nanofibers at very low temperature, over 450°C below the bulk melting temperature of GaSb, results in complete chemical decomposition of the nanofibers into crystalline Sb cores surrounded by amorphous shells. Although temperature shifts in phase equilibria of nanoparticles are expected, the complete decomposition of GaSb nanofibers at low temperature gives insight into the highly sensitive interaction between material thermodynamics and size-dependant material properties.
2009. "Chemical Reactivity of Reduced TiO2(110): The dominant role of surface defects in oxygen chemisorption." Journal of Physical Chemistry C 113(28):12407-12411. doi:10.1021/jp901989x Abstract O2 chemisorption on reduced, rutile TiO2(110) with various concentrations of oxygen vacancies (Ov) and bridging hydroxyls (OHb) is investigated with scanning tunneling microscopy, temperature programmed desorption and electron-stimulated desorption. On the annealed surface, 2 oxygen molecules can be chemisorbed per Ov. The same amount of O2 chemisorbs on surfaces where each Ov is converted to two OHb’s by exposure to water (i.e. 1 O2 per OHb). Surfaces with few or no Ov’s or OHb’s can be created by exposing the hydroxylated surface to O2 at room temperature, and the amount of O2 that chemisorbs on these surfaces at low temperatures is only ~20% of the amount on the annealed (reduced) surface. In contrast, the amount of chemisorbed O2 increases by more than a factor of two when the OHb concentration is enhanced – without changing the concentration of sub-surface Ti interstitials. The results indicate that the reactivity of TiO2(110) is primarily controlled by the amount of electron-donating surface species such as Ov’s and/or OHb’s, and not Ti3+ interstitials.
2009. "Nonthermal Water Splitting on Rutile TiO2: Electron-Stimulated Production of H-2 and O-2 in Amorphous Solid Water Films on TiO2(110)." Journal of Physical Chemistry C 113(11):4451-4460. Abstract Electron-stimulated desorption (ESD) of H2, O2 and H2O from 0 - 60 ML films of amorphous solid water (ASW) adsorbed on TiO2(110) are investigated as function of film thickness and isotopic composition. For 100 eV incident electrons, both the H2 and O2 ESD yields have maxima when the ASW coverage is ~ 20 monolayer (ML), while the H2O ESD yield increases monotonically with water coverage. All the products reach a coverage-independent yield above 40 - 50 ML. Experiments using isotopically layered films of H2O and D2O demonstrate that the molecular hydrogen is produced in reactions that occur preferentially at or near both the ASW/TiO2 interface and the ASW/vacuum interface. However, electronic excitations or ionic defects created within the interior of the ASW films by the energetic electrons can subsequently migrate to the interfaces where they initiate reactions. Electron irradiation of ASW films results in the formation of bridge-bonded hydroxyls on the TiO2(110). These hydroxyls do not contribute to the H2 produced near the ASW/TiO2 interface. Instead, the results suggest that this H2 is produced from a stable precursor, trapped near the substrate. The proposed mechanism for the H2 production near the ASW/TiO2(110) interface is supported by a kinetic model that semi-quantitatively reproduces the main features of the non-thermal reactions.
2009. "A Simple Procedure for Effective Quenching of Trypsin Activity andPrevention of 18O-Labeling Back-Exchange." Journal of Proteome Research 8(5):2157-2163. doi:10.1021/pr800971w Abstract Stable isotope 16O/18O-labeling of the C-terminal carboxyl groups of peptides is among the methods used in shotgun proteomics for relative protein quantitation. However, precise quantitative measurements can be difficult when 18O is replaced with the more common isotope 16O during a trypsin-catalyzed process called “back-exchange” that occurs after labeling. Attempts to improve this method by targeting trypsin activity and/or implementing immobilized trypsin because it can be easily separated from the sample ultimately lead to sample loss. Because of this, the 18O-labeling method cannot be applied toward small-abundant samples that are commonly found in clinical studies. Here, we show that sample loss is minimized by using solution-phase trypsin rather than immobilized trypsin during the labeling process and that trypsin can be effectively quenched by boiling the sample after labeling for 10 minutes.
2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3:486-496. doi:10.1074/mcp.M900217-MCP200 Abstract Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and MS/MS fragmentation have become widely available in recent years and have allowed for sig-nificantly better discrimination between true and false MS/MS pep-tide identifications by applying relatively narrow windows for maxi-mum allowable deviations for parent ion mass measurements. To fully gain the advantage of highly accurate parent ion mass meas-urements, it is important to limit systematic mass measurement errors. The DtaRefinery software tool can correct systematic errors in parent ion masses by reading a set of fragmentation spectra, searching for MS/MS peptide identifications, then fitting a model that can estimate systematic errors, and removing them. This results in a new fragmentation spectrum file with updated parent ion masses.
2009. "Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study." Physical Chemistry Chemical Physics. PCCP 12:1369 - 1378. doi:10.1039/b919354e Abstract Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is definitely not negligible, e.g. in the case of the GC step it represents about 16% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.
2009. "Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes." Biochemistry 48(36):8540-8550. doi:10.1021/bi900860w Abstract In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to “scan” a given DNA molecule in order to interrogate its local structural and dynamic features.
2009. "Fe-Al interface intermixing and the role of Ti, V, and Zr as a stabilizing interlayer at the interface." Journal of Applied Physics 105(5):Art. No. 053504. Abstract Fe-Al bilayer interfaces with and without interface stabilizing layers (Ti, V or Zr) were fabricated using dc magnetron sputtering. Intermixing layer thickness and the effectiveness of the stabilizing layer (Ti, V, Zr) at the interface were studied using Rutherford backscattering spectrometry (RBS) and X-ray reflectometry (XRR). The result for the intermixing thickness of the AlFe layer is always larger when Fe is deposited on Al as compared to when Al is deposited on Fe. By comparing measurements with computer simulations, the thicknesses of the AlFe layers were determined to be 20.6 Å and 41.1 Å for Al/Fe and Fe/Al bilayer systems, respectively. The introduction of Ti and V stabilizing layers at the Fe-Al interface reduced the amount of intermixing between Al and Fe, consistent with the predictions of model calculations. The Zr interlayer, however, was ineffective in stabilizing the Fe-Al interface in spite of the chemical similarities between Ti and Zr. In addition, analysis suggests that the Ti interlayer is not effective in stabilizing the Fe-Al interface when the Ti interlayer is extremely thin (~3 Å) for these sputtered metallic films.