Scientific Publications 2009
2009. "Decon2LS: An Open-Source Software Package for Automated Processing and Visualization of High Resolution Mass Spectrometry Data." BMC Bioinformatics 10:87. doi:10.1186/1471-2105-10-87 Abstract Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting these data uses the mass spectra to infer masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as raw data readers, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls.
2009. "Correlating Acid Properties and Catalytic Function: A First-Principles Analysis of Alcohol Dehydration Pathways on Polyoxometalates." Journal of Physical Chemistry C 113(5):1872-1885. doi:10.1021/jp8078748 Abstract Density functional theory calculations and reactivity data were used to examine the mechanism of alcohol dehydration on Keggin-type polyoxometalate (POM) catalysts and the influence of the POM composition and the degree of substitution of the alcohol on kinetically relevant elimination steps. Dehydration was found to proceed through E1 pathways in which the alcohol CsO bond is cleaved heterolytically via a carbeniumion transition state. Dehydration rates were found to depend on the elimination rate constant and the equilibrium constant for the formation of unreactive alcohol dimers. E2-type elimination transition states, involving concerted CsH and CsO bond cleavage, were not found. The extent of substitution at the R-carbon on the alcohol was found to lead to marked effects on elimination barriers, because substitution increases the proton affinity of the alcohol and the stability of the carbenium-ion transition state. Changes in the central and addenda atoms of the POM cluster and the presence of n-donors, a support, vicinal POM clusters, or charge-compensating cations were found to lead to changes in the deprotonation energy (DPE) of the POM cluster, activation barriers to dehydration, and the stability of the unreactive dimer. These effects are all captured in a general linear relation between activation barriers and deprotonation energy, a rigorous measure of acid strength. The explicit dependence of the E1 activation barrier on the acid deprotonation energy is much weaker than that on reactant proton affinity. This results from the more effective compensation between the acid deprotonation energy and the interaction energy between the cationic hydrocarbon fragment and the anionic POM cluster at the transition state. The direct interactions between the POM protons and the support, other POM clusters, n-donors, base probe molecules, and charge-compensating cations increased the negative charge of the oxide shell of the W12O40 conjugate base, which increased the DPE and decreased the POM acid strength. This decrease in acidity is not fully compensated by the concomitant increase in the interaction energy, leading to elimination barriers that generally increase with increasing DPE.
2009. "αB-Crystallin: A Hybrid Solid-State/Solution-State NMR Investigation Reveals Structural Aspects of the Heterogeneous Oligomer." Journal of Molecular Biology 385(5):1482-1497. doi:10.1016/j.jmb.2008.10.097 Abstract Atomic-level structural information on αB-Crystallin (αB), a prominent member of the small heat-shock protein family, has been a challenge to obtain due its polydisperse oligomeric nature. We show that magic-angle spinning solid-state NMR can be used to obtain high-resolution information on an ∼580-kDa human αB assembled from 175-residue 20-kDa subunits. An ∼100-residue α-crystallin domain is common to all small heat-shock proteins, and solution-state NMR was performed on two different α- crystallin domain constructs isolated from αB. In vitro, the chaperone-like activities of full-length αB and the isolated α-crystallin domain are identical. Chemical shifts of the backbone and Cβ resonances have been obtained for residues 64–162 (α-crystallin domain plus part of the C-terminus) in αB and the isolated α-crystallin domain by solid-state and solution-state NMR, respectively. Both sets of data strongly predict six β-strands in the α-crystallin domain. A majority of residues in the α-crystallin domain have similar chemical shifts in both solid-state and solution-state, indicating similar structures for the domain in its isolated and oligomeric forms. Sites of intersubunit interaction are identified from chemical shift differences that cluster to specific regions of the α-crystallin domain. Multiple signals are observed for the resonances of M68 in the oligomer, identifying the region containing this residue as existing in heterogeneous environments within αB. Evidence for a novel dimerization motif in the human α-crystallin domain is obtained by a comparison of (i) solid-state and solution-state chemical shift data and (ii) 1H–15N heteronuclear single quantum coherence spectra as a function of pH. The isolated α-crystallin domain undergoes a dimer–monomer transition over the pH range 7.5–6.8. This steep pHdependent switch may be important for αB to function optimally (e.g., to preserve the filament integrity of cardiac muscle proteins such as actin and desmin during cardiac ischemia, which is accompanied by acidosis).
2009. "Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory." Journal of Physical Chemistry A 113(36):9761-9765. Abstract In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.
2009. "Reply to Comment on 'Excited states of DNA base pairs using long-range corrected time-dependent density functional theory." Journal of Physical Chemistry A 113(41):11095. doi:10.1021/jp908490z Abstract In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.
2009. "Anisotropy of disorder accumulation and recovery in 6H-SiC irradiated with Au2+ ions at 140 K." Journal of Nuclear Materials 389(2):332-335. doi:10.1016/j.jnucmat.2009.02.023 Abstract Single crystal <0001>-oriented 6H-SiC was irradiated with Au2+ ions to fluences of 0.032, 0.058 and 0.105 ions/nm2 at 140 K and was subsequently annealed at various temperatures up to 500 K. The relative disorder on both the Si and C sublattices has been determined simultaneously using in-situ D+ ion channeling along the <0001> and <2-201> axes. A higher level of disorder on both the Si and C sublattices is observed along the <2-201>. There is a preferential C disordering and more C interstitials are aligned with <0001>. Room-temperature recovery along <2-201> occurs, which is associated with the <0001>-aligned interstitials that annihilate due to close-pair recombination. Disorder recovery between 400 and 500 K is primarily attributed to annihilation of interstitials that are misaligned with <0001>. Effects of stacking order in SiC on disorder accumulation are insignificant; however, noticeable differences of low-temperature recovery in Au2+-irradiated 6H-SiC and 4H-SiC are observed.
2009. "Disorder accumulation and recovery in gold-ion irradiated 3C-SiC." Journal of Applied Physics 105(1):Art. No. 013529. doi:10.1063/1.3055797 Abstract A single-crystal 3C-SiC film on the Si/SiO2/Si (SIMOX) substrate was irradiated in different areas at 156 K with Au2+ ions to low fluences. The disorder profiles as a function of dose on both the Si and C sublattices have been determined in situ using a combination of 0.94 MeV D+ Rutherford backscattering spectrometry and nuclear reaction analysis in channeling geometry along the <100>, <110> and <111> axes. The results indicate that for the same damage state, the level of disorder on the Si sublattice in 3C-SiC follows a decreasing order along the <111>, <100> and <110> axes, while that on the C sublattice shows comparable values. Similar levels of Si and C disorder are observed along the <111> axis over the applied dose range. However, the level of C disorder is higher than that of Si disorder along either <100> or <110>. The amount of disorder recovery during thermal annealing processes depends on the sublattice (Si or C) and crystallographic orientation. Room-temperature recovery occurs for both sublattices in 3C-SiC irradiated to a dose of 0.047 dpa or lower. Significant recovery is observed along all directions during thermal annealing at 600 K. The results will be discussed and compared to those for 6H- and 4H-SiC under similar irradiation conditions.
2009. "Response of Nanocrystalline 3C Silicon Carbide to Heavy-Ion Irradiation." Physical Review. B, Condensed Matter 80(16):Art. No.161301(R). doi:10.1103/PhysRevB.80.161301 Abstract Nanostructured materials are generally believed to be more radiation resistant. This study reports on Au ion induced amorphization in nanocrystalline 3C-SiC, characterized using x-ray diffraction, transmission electron microscopy and Raman spectroscopy. Full amorphization at room temperature occurs at a comparable dose to that for bulk SiC single crystals. The behavior is attributed to a high ion flux and sluggish migration of point defects produced during irradiation. The results may have a significant implication of using nanophased SiC in extremely high radiation environments.
2009. "Synthesis and Characterization of Bulk Vitreous Cadmium Germanium Arsenide." Journal of the American Ceramic Society 92(6):1236-1243. doi:10.1111/j.1551-2916.2009.03001.x Abstract Abstract Cadmium-germanium-diarsenide (“CGA”) glasses were synthesized in bulk form (~2.4 cm3) using the procedures adapted from the literature. Several issues involved in the fabrication and quenching of amorphous CdGexAs2 (x = 0.45, 0.65, 0.85, 1.00) are described. An innovative processing route is presented to enable quenching of vitreous, crack-free ingots with sizes up to 10 mm diameter, and 30 – 40 mm long. Specimens from selected ingots were characterized using thermal analysis, optical microscopy, scanning electron microscopy, energy dispersive spectroscopy, particle-induced X-ray emission, Rutherford backscattering, secondary ion mass spectrometry, X-ray diffraction, density, and optical spectroscopy. Variations in properties as a function of processing conditions and composition are described. Results show that the density of defect states in the middle of the band gap and near the band edges can be decreased three ways: through suitable control of the processing conditions, by doping the material with hydrogen, and by increasing the concentration of Ge in the glass.
2009. "Absolute integrated intensities of vapor-phase hydrogen peroxide (H202) in the mid-infrared at atmospheric pressure." Analytical and Bioanalytical Chemistry 395(2):377-386. doi:10.1007/s00216-009-2805-x Abstract We report quantitative broadband infrared spectra of vapor-phase hydrogen peroxide (H2O2) with all spectra pressure broadened to atmospheric pressure. The spectra were generated by flowing a concentrated solution (83 weight%) of H2O2 into a gently heated disseminator and diluting with a flow of pure nitrogen carrier gas. The water vapor lines were subtracted from the resulting spectra to yield the spectrum of pure H2O2. Comparison with previous results for the ν6 band strength (including hot bands) compares favorably with the results of Klee et al. [(1999) J. Mol. Spectr. 195, 154] as well as HITRAN. The present results are 433 and 467 cm-2 atm-1 (±8% and ±3% at 298 and 323 K, respectively) for the band strength, matching well the Klee value (S = 467 cm-2 atm-1 at 296 K) for the integrated band. Other bands in the 520-7500 cm-1 interval and their potential for atmospheric monitoring are discussed.