Scientific Publications 2007
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2007. "Effect of an Electric Field on the Adsorption of Metal Clusters on Boron-Doped CarbonSurfaces." Journal of Physical Chemistry C 111(40):14804-14812. doi:10.1021/jp073643a Abstract Fuel cell catalysts can lose their activity over a period of time due to the sintering of the nanometer-sized catalyst particles. However, the sintering of metal clusters on carbon supports may be reduced by increasing the interaction between the metal and the support. To manipulate this metal-support interaction, carbonsubstituted boron defects were introduced in a graphite lattice, and the adsorption energies of metal clusters (Pt, PtRu, and Au) on the pristine and on the boron-doped carbon were calculated using first-principles density functional theory. The metal-support interaction was also calculated in the presence of an external electric field. Although the metal-support interaction is slightly weakened in the electric field, the boron-doped carbons are still predicted to maintain a significant stabilizing effect.
2007. "Platinum Monolayer Fuel Cell Electrocatalysts." Topics in Catalysis 46(3-4):249-262. doi:10.1007/s11244-007-9003-x Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We describe a new class of electrocatalysts for the O2 reduction, and H2 and methanol oxidation reactions, consisting of a monolayer of Pt deposited on a metal or alloy carbon-supported nanoparticles. These electrocatalysts show up to a 20-fold increase in Pt mass activity compared with conventional all-Pt electrocatalysts. The origin of their increased activity was identified through a combination of experimental methods, employing electrochemical and surface science techniques, X-ray absorption spectroscopy, and density functional theory calculations. The long-term tests in fuel cells demonstrated excellent stability of the anode and good stability of the cathode electrocatalysts. We also describe the stabilization of Pt electrocatalysts against dissolution under potential cycling regimes effected by a submonolayer of Au clusters deposited on Pt surfaces. These new electrocatalysts promise to alleviate some of the major problems of existing fuel cell technology.
2007. "Informatics Strategies for Large-Scale Novel Cross-linking Analysis." Journal of Proteome Research 6(9):3412-3421. doi:10.1021/pr070035z Abstract The analysis of protein interactions in biological systems represents a significant challenge for today's technology. Chemical cross-linking provides the potential to impart new chemical bonds in a complex system that result in mass changes in the analysis of a set of tryptic peptides. However, system complexity and cross-linking product heterogeneity have precluded widespread chemical cross-linking use for large-scale identification of protein-protein interactions.The development of mass spectrometry identifiable cross-linkers called Protein Interaction Reporters (PIRs) has enabled on-cell chemical cross-linking experiments with product type differentiation. However, the complex datasets resultant from PIR experiments demand new informatics capabilities to allow interpretation. This manuscript details our efforts to develop such capabilities and describes the program X-links which allows PIR product type differentiation. Furthermore, we also present the results from Monte Carlo simulation of PIRtype experiments to provide false positive identification rate estimates for the PIR product type identification through observed precursor and released peptide masses. Our simulations also provide peptide identification calculations based on accurate masses and database complexity that can provide an estimation of false positive rates for peptide identification. Overall, the calculations show a low rate of false positive identification of PIR product types due to random mass matching of approximately 12% with 10 ppm mass measurement accuracy. In addition, consideration of a reduced database resulting from stage 1 analysis of Shewanella oneidensis MR-1 containing 367 proteins resulted in a significant reduction of expected identification false positive identification rate estimation compared to that from the entire Shewanella oneidensis MR-1 proteome.
2007. "Informatics Strategies for Large-Scale Novel Cross-linking Analysis ." Journal of Proteome Research 6(9):3412-3421. doi:10.1021/pr070035z Abstract The analysis of protein interactions in biological systems represents a significant challenge for today's technology. Chemical cross-linking provides the potential to impart new chemical bonds in a complex system that result in mass changes in the analysis of a set of tryptic peptides. However, system complexity and cross-linking product heterogeneity have precluded widespread chemical cross-linking use for large-scale identification of protein-protein interactions. The development of mass spectrometry identifiable cross-linkers called Protein Interaction Reporters (PIRs) has enabled on-cell chemical cross-linking experiments with product type differentiation. However, the complex datasets resultant from PIR experiments demand new informatics capabilities to allow interpretation. This manuscript details our efforts to develop such capabilities and describes the program X-links which allows PIR product type differentiation. Furthermore, we also present the results from Monte Carlo simulation of PIRtype experiments to provide false positive identification rate estimates for the PIR product type identification through observed precursor and released peptide masses. Our simulations also provide peptide identification calculations based on accurate masses and database complexity that can provide an estimation of false positive rates for peptide identification. Overall, the calculations show a low rate of false positive identification of PIR product types due to random mass matching of approximately 12% with 10 ppm mass measurement accuracy. In addition, consideration of a reduced database resulting from stage 1 analysis of Shewanella oneidensis MR-1 containing 367 proteins resulted in a significant reduction of expected identification false positive identification rate estimation compared to that from the entire Shewanella oneidensis MR-1 proteome.
2007. "Ferromagnetic Semiconductor Nanoclusters: Co-doped Cu2O." Applied Physics Letters 90(1):art. no. 013106 (3 pages). doi:10.1063/1.2429018 Abstract 5% Co-doped cuprous oxide dilute magnetic semiconductor (DMS) cluster film composed of crystalline nanoclusters in the range of ~ 4.2 nm average crystallite size, prepared using sputtering-aggregation technique is found to be ferromagnetic at 400 K with a coercivity of 29 Oe. With the increase in average crystallite size from 4.2 nm to 8 nm, the coercivity increased, whereas the saturation magnetization was achieved at 3 KOe field in both cases. Cu2O phase is observed from the cluster film deposited on the Si wafer when analyzed using XRD. Co in Cu2O host reveals a +2 oxidation state via XPS measurements. Positive magneto resistance (MR) data from the sample exhibits a temperature dependent decrease.
2007. "The solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family." Proteins. Structure, Function, and Bioinformatics 68:789-795. doi:10.1002/prot.21450 Abstract We report the solution NMR structure of the 113-residue protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP_ECOLI), target ER111 of the Northeast Structural Genomics Consortium (www.nesg.org). The structure is characterized by a mixed a/b-fold consisting of two helices and eight beta strands. The structure features a large cavity formed by five antiparallel beta strands and the two helices capped by another two strands, as well as an unusual “crossover” of two long beta stranded segments. Comparisons with recent crystal structures of homologues from Pyrococcus horikoshii and Mus musculus reveal that the fold is highly unique to the functionally uncharacterized UPF0131 pfamA protein domain family. The structure expands the modeling leverage coverage of the UPF0131 domain family.
2007. "Direct Observation of sp-d Exchange Interactions in Colloidal Mn2+- and Co2+-Doped CdSe Quantum Dots." Nano Letters 7(4):1037-1043. doi:10.1021/nl0702362 Abstract The defining attribute of a diluted magnetic semiconductor (DMS) is the existence of dopant-carrier magnetic exchange interactions. In this letter, we report the first direct observation of such exchange interactions in colloidal doped CdSe nanocrystals. Doped CdSe quantum dots were synthesized by thermal decomposition of (Me4N)2[Cd4(SePh)10] in the presence of TMCl2 (TM2+ ) Mn2+ or Co2+) in hexadecylamine and were characterized by several analytical and spectroscopic techniques. Using magnetic circular dichroism spectroscopy, successful doping and the existence of giant excitonic Zeeman splittings in both Mn2+- and Co2+-doped wurtzite CdSe quantum dots are demonstrated unambiguously.
2007. "Planar Nitrogen-Doped Aluminum Clusters AIxN- (x=3-5)." Journal of Chemical Physics 125(12):124305. doi:10.1063/1.2335449 Abstract The electronic and geometrical structures of three nitrogen-doped aluminum clusters, AlxN−(x=3–5), are investigated using photoelectron spectroscopy and ab initio calculations. Well-resolved photoelectron spectra have been obtained for the nitrogen-doped aluminum clusters at four photon energies (532, 355, 266, and 193 nm). Global minimum structure searches for AlxN−(x=3–5) and their corresponding neutrals are performed using several theoretical methods. Vertical electron detachment energies are calculated using three different methods for the lowest energy structures and low-lying isomers are compared with the experimental observations. Planar structures have been established for all the three AlxN− (x=3–5) anions from the joint experimental and theoretical studies. For Al5N−, a low-lying nonplanar isomer is also found to contribute to the experimental spectra, signifying the onset of two-dimensional to three-dimensional transition in nitrogen-doped aluminum clusters. The chemical bonding in all the planar clusters has been elucidated on the basis of molecular orbital and natural bond analyses.
2007. "Probing the Structure and Bonding in Al6N- and Al6N by Photoelectron Spectroscopy and Ab Initio Calculations." Journal of Physical Chemistry A 111(1):34-41. doi:10.1021/jp066747e Abstract The electronic and geometrical structure of a nitrogen-doped Al6 - cluster (Al6N-) is investigated using photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of Al6N- have been obtained at three photon energies with seven resolved spectral features. The electron affinity of Al6N has been determined to be 2.58 (0.04 eV. Global minimum structure searches for A6N- and its corresponding neutral form are performed using several theoretical methods. Vertical electron detachment energies, calculated using three different methods for the lowest energy structure and a low-lying isomer, are compared with the experimental data. The ground-state structure of Al6N- is established from the joint experimental and theoretical study to consist of an Al2 dimer bonded to the top of a quasi-planar tetracoordinated N unit, Al4N-, or it can be viewed as a distorted trigonal prism structure with the N atom bonded in one of the prism faces. For neutral Al6N, three low-lying isomers are found to compete for the global minimum, two of which are built from the tetracoordinated Al4N unit. The chemical bonding in Al6N- is discussed on the basis of molecular orbital and natural bond analyses.
