Showing papers by "Environmental Molecular Sciences Laboratory published in 2002"

On the Enthalpy of Formation of Hydroxyl Radical and Gas-Phase Bond Dissociation Energies of Water and Hydroxyl

Abstract: In a recent letter (J. Phys. Chem. A, 2001, 105,1), we argued that, although all major thermochemical tables recommend a value of (OH) based on a spectroscopic approach, the correct value is 0.5 kcal/mol lower as determined from an ion cycle. In this paper, we expand upon and augment both the experimental and theoretical arguments presented in the letter. In particular, three separate experiments (mass-selected photoionization measurements, pulsed-field-ionization photoelectron spectroscopy measurements, and photoelectron-photoion coincidence measurements) utilizing the positive ion cycle to derive the O−H bond energy are shown to converge to a consensus value of the appearance energy AE0(OH+/H2O) = 146117 ± 24 cm-1 (18.1162 ± 0.0030 eV). With the most accurate currently available zero kinetic energy photoionization value for the ionization energy IE(OH) = 104989 ± 2 cm-1, corroborated by a number of photoelectron measurements, this leads to D0(H−OH) = 41128 ± 24 cm-1 = 117.59 ± 0.07 kcal/mol. This corres...

An accurate mass tag strategy for quantitative and high-throughput proteome measurements.

Abstract: We describe and demonstrate a global strategy that extends the sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements based upon the use of polypeptide''accurate mass tags'' (AMTs) produced by a global protein enzymatic digestion. The two stage strategy exploits Fourier transform ion cyclotron resonance mass spectrometry (FTICR) to first validate polypeptide AMTs for a specific organism, tissue or cell type from''potential mass tags'' identified using conventional tandem mass spectrometry (MS/MS) methods, providing the basis for subsequent measurements without the need for MS/MS. A single high resolution capillary liquid chromatography separation combined with high sensitivity, high resolution and accurate FTICR measurements is shown to be capable of characterizing polypeptide mixtures of significantly more than 105 components with mass accuracies of < 1 ppm, sufficient for broad protein identification using AMTs. Attractions of the approach include the capability for automated high confidence protein identification, broad and unbiased proteome coverage, the capability for exploiting stable-isotope labeling methods to realize high precision for relative protein abundance measurements, and the potential for study of mammalian proteomes when combined with additional sample fractionation. The strategy is demonstrated by selected examples using Saccharomyces cerevisiae, Deinococcus radiodurans, and mouse melanoma cells.

Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.

Abstract: Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.

Experimental observation and confirmation of icosahedral W@Au12 and Mo@Au12 molecules.

Abstract: The recently predicted W@Au12 cluster has been observed and probed experimentally using anion photoelectron spectroscopy. It is shown that this unique molecule and its Mo congener indeed possess an icosahedral structure and a large HOMO-LUMO gap. Relativistic density functional theory is used to calculate their geometries, energetics, and energy spectra. The simulated density-of-states spectra are in good agreement with the photoelectron spectra, confirming the icosahedral structure of these complexes.

High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics.

Abstract: We describe high-efficiency (peak capacities of ∼103) nanoscale (using column inner diameters down to 15 μm) liquid chromatography (nanoLC)/low flow rate electrospray (nanoESI) mass spectrometry (MS) for the sensitive analysis of complex global cellular protein enzymatic digests (i.e., proteomics). Using a liquid slurry packing method with carefully selected packing solvents, 87-cm-length capillaries having inner diameters of 14.9−74.5 μm were successfully packed with 3-μm C18-bonded porous (300-A pores) silica particles at a pressure of 18 000 psi. With a mobile-phase delivery pressure of 10 000 psi, these packed capillaries provided mobile-phase flow rates as low as ∼20 nL/min at LC linear velocities of ∼0.2 cm/s, which is near optimal for separation efficiency. To maintain chromatographic efficiency, unions with internal channel diameters as small as 10 μm were specially produced for connecting packed capillaries to replaceable nanoESI emitters having orifice diameters of 2−10 μm (depending on the pack...

Molecular Mechanism of Ion Binding to the Liquid/Vapor Interface of Water

Abstract: We have carried out extensive molecular dynamics simulations to study the electrostatic surface potentials and molecular mechanism of iodide binding to the liquid/vapor interface of water using both nonpolarizable and polarizable potential models. Both simulated electrostatic surface potentials are negative with a value of about −0.50 ± 0.01 V. The simulated results are compared to the experimental estimates of the surface potentials ranging from −1.1 V to 0.4 V. This paper contributes to a better understanding of the molecular mechanisms of ion binding to the liquid/vapor interface of water. A free energy minimum was observed near the Gibbs dividing surface for simulations that employed polarizable models. In contrast, simulations that used nonpolarizable models provided no surface state as the iodide crossed the liquid/vapor interface of water. Corroborating observations were recently reported by Finlayson-Pitts and co-workers (Knipping, E. M.; Lakin, M. J.; Foster, K. L.; Jungwirth, P.; Tobias, D. J.; ...

Helical Crystalline SiC/SiO2 Core−Shell Nanowires

Abstract: Helical crystalline silicon carbide nanowires covered with a silicon oxide sheath (SiC/SiO2) have been synthesized by a chemical vapor deposition technique. The SiC core typically has diameters of 10-40 nm with a helical periodicity of 40-80 nm and is covered by a uniform layer of 30-60 nm thick amorphous SiO2. A screw-dislocation-driven growth process is proposed for the formation of this novel structure based on detailed structural characterizations. The helical nanostructures may find applications as building blocks in nanomechanical or nanoelectronic devices. The screw-dislocation-induced growth mechanism suggests that similar helical nanostructures of a wide range of materials may be synthesized.

Computational Study of Ion Binding to the Liquid Interface of Water

Abstract: We have performed extensive classical molecular dynamics simulations to examine the molecular transport mechanisms of the I-, Br-, Cl- and Na+ ions across the liquid/vapor interface of water. The potentials of mean force were calculated using the constrained mean force approach and polarizable potential models were used to describe the interactions among the species. The simulated potentials of mean force were found to be different, depending on the type of anion. The larger I- and Br- anions bind more strongly to the liquid/vapor interface of water than did the smaller Cl-ion. It is important to note here that most of the gas phase and solution phase properties of the Br- anion are quite similar to that of the Cl- ion. At the interface, however, the interactions of the Br- and Cl- anions with the water interface appeared to be significantly different. We found that the anions approach the interface more closely do than cations. We have also studied the transport mechanism of an I- across the water/dichloromethane interface. The computed potential of mean force showed no well-defined minimum as in the liquid/vapor case, but a stabilization free energy of about?1 kcal/mol near the interface with respect to the bulk liquidmore » was observed. The I- anion carried a water molecule with it as it crossed the interface. This result is in agreement with a recent experimental study on a similar system. Our work differs from earlier contributions in that our potential models have taken many-body effects into account, and in some cases, these effects cannot be neglected. To the best of our knowledge, this work significantly advances our understanding of molecular processes at the liquid interfaces.« less

Noble gas-actinide compounds: complexation of the CUO molecule by Ar, Kr, and Xe atoms in noble gas matrices.

Abstract: The CUO molecule, formed from the reaction of laser-ablated U atoms with CO in a noble gas, exhibits very different stretching frequencies in a solid argon matrix [804.3 and 852.5 wave numbers (cm−1)] than in a solid neon matrix (872.2 and 1047.3 cm−1). Related experiments in a matrix consisting of 1% argon in neon suggest that the argon atoms are interacting directly with the CUO molecule. Relativistic density functional calculations predict that CUO can bind directly to one argon atom (U-Ar = 3.16 angstroms; binding energy = 3.2 kilocalories per mole), accompanied by a change in the ground state from a singlet to a triplet. Our experimental and theoretical results also suggest that multiple argon atoms can bind to a single CUO molecule.

An NMR approach to structural proteomics.

Abstract: The influx of genomic sequence information has led to the concept of structural proteomics, the determination of protein structures on a genome-wide scale. Here we describe an approach to structural proteomics of small proteins using NMR spectroscopy. Over 500 small proteins from several organisms were cloned, expressed, purified, and evaluated by NMR. Although there was variability among proteomes, overall 20% of these proteins were found to be readily amenable to NMR structure determination. NMR sample preparation was centralized in one facility, and a distributive approach was used for NMR data collection and analysis. Twelve structures are reported here as part of this approach, which allowed us to infer putative functions for several conserved hypothetical proteins.

Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR

Abstract: Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry coupled with capillary reverse-phase liquid chromatography was used to characterize intact proteins from the large subunit of the yeast ribosome. High mass measurement accuracy, achieved by “mass locking” with an internal standard from a dual electrospray ionization source, allowed identification of ribosomal proteins. Analyses of the intact proteins revealed information on cotranslational and posttranslational modifications of the ribosomal proteins that included loss of the initiating methionine, acetylation, methylation, and proteolytic maturation. High-resolution separations permitted differentiation of protein isoforms having high structural similarity as well as proteins from their modified forms, facilitating unequivocal assignments. The study identified 42 of the 43 core large ribosomal subunit proteins and 58 (of 64 possible) core large subunit protein isoforms having unique masses in a single analysis. These results demonstrate the basis for the high-throughput analyses of complex mixtures of intact proteins, which we believe will be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations.

Proteomics based on high-efficiency capillary separations

Abstract: Identifying and quantifying in a high throughput manner the proteins expressed by cells, tissues or an organism provides the basis for understanding the functions of its constituents at a "systems" level. As a result, proteome analysis has increasingly become the focus of significant interest and research over the past decade. This is especially true following the recent stunning achievements in genomics analyses. However, unlike the static genome, the complexities and dynamism of the proteome present significant analytical challenges and demand highly efficient separations and detection technologies. A number of recent technological advancements have been in direct response to these challenges. Currently, strategically mated combinations of sophisticated separations techniques and advanced mass spectrometric detection represent the best approach to addressing the intricacies of the proteome. Liquid-phase separations, often within capillaries, are increasingly recognized as the best separations technique for this approach. In combination on-line with mass spectrometry, liquid-phase separations provide the improved analytical sensitivity, sample throughput, and quantitation capabilities necessitated by the multifaceted problems within proteomics analyses. This review focuses primarily on current high-efficiency capillary separations techniques, including both capillary liquid chromatography and capillary electrophoresis, applied to the analysis of complex proteomic samples. We emphasize developments at our laboratory and illustrate technical advances that attempt to review the role of separations within the broader context of a state-of-the-art integrated proteomics effort.

Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels

Abstract: Conformations of an important model system, the alanine dipeptide, have been calculated by using high-level, ab initio electronic structure theory. A Ramachandran plot, with the angle φ in the range −180° to 90° and the angle ψ in the range −60° to 180°, was generated by using density functional theory with the generalized-gradient BLYP functional and a polarized triple-ζ basis set (TZVP+). Six conformers, C7eq, C5, C7ax, β2, αL, and α‘, have been identified in this region of the Ramachandran plot. A second derivative (frequency) analysis showed that all conformers are stable at this level of theory. These structures were used as starting points for geometry optimizations at the MP2/aug-cc-pVDZ level. Single-point energies were calculated at the MP2/aug-cc-pVTZ and MP2/aug-cc-pVQZ levels at the final MP2/aug-cc-pVDZ structures and together with the MP2/aug-cc-pVDZ results were used in extrapolations to the complete basis set limit. The N−H···O, N−H···N, and C−H···O hydrogen bond interactions that are key ...

A hierarchical family of global analytic Born-Oppenheimer potential energy surfaces for the H+H2 reaction ranging in quality from double-zeta to the complete basis set limit

Abstract: A hierarchical family of analytical Born–Oppenheimer potential energy surfaces has been developed for the H+H2 system. Ab initio calculations of near full configuration interaction (FCI) quality (converged to within ≈1 μEh) were performed for a set of 4067 configurations with the aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets. The complete basis set (CBS) limit energies were obtained using a highly accurate many-body basis set extrapolation scheme. Surfaces were fitted for the estimated CBS limit, as well as for the aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets using a robust new functional form. The mean unsigned fitting error for the CBS surface is a mere 0.0023 kcal/mol, and deviations for data not included in the fitting process are of similarly small magnitudes. Highly accurate calculations of the saddle point and van der Waals minimum configurations were performed using basis sets as large as aug-mcc-pV7Z, and these data show excellent agreement with the results of the extrapolated pote...

Al62- − Fusion of Two Aromatic Al3- Units. A Combined Photoelectron Spectroscopy and ab Initio Study of M+[Al62-] (M = Li, Na, K, Cu, and Au)

Abstract: Photoelectron spectroscopy is combined with ab initio calculations to elucidate the structure and chemical bonding of a series of MAl6- (M = Li, Na, K, Cu, and Au) bimetallic clusters. Well-resolved photoelectron spectra were obtained for MAl6- (M = Li, Na, Cu, and Au) at several photon energies. The ab initio calculations showed that all of the MAl6- clusters can be viewed as an M+ cation interacting with an Al62- dianion. Al62- was found to possess an Oh ground-state structure, and all of the MAl6- clusters possess a C3v ground-state structure derived from the Oh Al62-. Careful comparison between the photoelectron spectral features and the ab initio one-electron detachment energies allows us to establish firmly the C3v ground-state structures for the MAl6- clusters. A detailed molecular orbital (MO) analysis is conducted for Al62- and compared with Al3-. It was shown that Al62- can be considered as the fusion of two Al3- units. We further found that the preferred occupation of those MOs derived from the...

Syntheses, Crystal Structures, and Density Functional Theory Calculations of the closo-[1-M(CO)(3)(eta(4)-E-9)](4-) (E= Sn, Pb; M= Mo, W) Cluster Anions and Solution NMR Spectroscopic Characterization of[1-M(CO)(3)(eta(4)-Sn-9)](4-) (M= Cr, Mo, W)

Abstract: The closo-[1-M(CO)3(η4-E9)]4- (E = Sn, Pb; M = Mo, W) anions have been obtained by extracting the binary alloys KSn2.05 and KPb2.26 in ethylenediamine (en) in the presence of 2,2,2-crypt or in liquid NH3 followed by reaction with M(CO)3·mes (M = Mo, W) or Cr(CO)3·tol in en or liquid NH3 solution. Crystallization of the molybdenum and tungsten salts was induced by vapor diffusion of tetrahydrofuran into the en solutions. The salts [2,2,2-crypt-K]4[1-M(CO)3(η4-Sn9)]·en (M = Mo, W) crystallize in the triclinic system, space group P1, Z = 4, a = 16.187(3) A, b = 25.832(4) A, c = 29.855(5) A, α = 111.46(1)°, β = 102.84(2)°, γ = 92.87(2)° at −95 °C (M = Mo) and a = 17.018(3) A, b = 27.057(5) A, c = 28.298(6) A, α = 66.42(3)°, β = 76.72(3)°, γ = 87.27(3)° at 20 °C (M = W). The salts (CO)3M(en)2[2,2,2-crypt-K]4[1-M(CO)3(η4-Pb9)]·2.5en (M = Mo, W) crystallize in the triclinic system, space group P1, Z = 2, a = 16.319(3) A, b = 17.078(3) A, c = 24.827(5) A, α = 71.82(3)°, β = 83.01(3)°, γ = 81.73(3)° at −133 °C (...

First-Principles Determination of the Absolute Hydration Free Energy of the Hydroxide Ion†

Abstract: The absolute hydration free energy of the hydroxide ion, Δ (HO-), a fundamental quantity in solution chemistry, has “experimental” values ranging from −90.6 to −110.0 kcal/mol. We report a first-principles determination of Δ (HO-) by using a reliable computational protocol of high-level first-principles supermolecule-continuum calculations, the same approach recently used to determine the absolute hydration free energy of the proton. In the supermolecule-continuum approach, part of the solvent surrounding the solute is treated quantum mechanically, and the remaining bulk solvent is approximated by a dielectric continuum medium accounted for by a recently developed self-consistent reaction field model known as surface and volume polarization for electrostatic interaction (SVPE) or the fully polarizable continuum model (FPCM). With this approach, the calculated results can systematically be improved by increasing the number of quantum mechanically treated solvent molecules, and Δ (HO-) is accurately predict...

Surface-Induced Dissociation in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: Instrument Design and Evaluation

Abstract: A new Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) has been constructed in our laboratory. The instrument employs surface-induced dissociation (SID) as an activation method for obtaining structural information on biomolecules in the gas phase. Tandem SID mass spectra can be acquired using either a continuous or a pulsed mode of operation. Collision energy of precursor ion is controlled by a dc offset of the ICR cell. This approach eliminates defocusing of the ion beam by the ion-transfer optics as a function of ion kinetic energy and constitutes a significant improvement over our previous experimental setup. Furthermore, it can be easily implemented on any FTICR mass spectrometer. Very high signal-to-noise ratios of 200-500 were obtained in single-scan SID mass spectra of model peptides with acquisition time less than 1.1 s. Reasonable SID signal was detected in single-scan spectra with total acquisition time of only 0.3 s. The high signal-to-noise ratio and the fast acquisition time point on a potential application of SID for high-throughput studies in FTICR MS.

Experimental search and characterization of icosahedral clusters: Al 12 X − ( X = C , G e , S n , Pb )

Abstract: Photoelectron spectra of ${\mathrm{Al}}_{12}{X}^{\ensuremath{-}}$ $(X=\mathrm{C},$ Ge, Sn, Pb) were measured to probe the electronic structure of ${\mathrm{Al}}_{12}X.$ These clusters, all possessing 40 valence electrons, were expected to be magic numbers with ${I}_{h}\ensuremath{-}X@{\mathrm{Al}}_{12}$ structures, closed electron shells, and large energy gaps. We showed that for $X=\mathrm{Ge},$ Sn, and Pb that was indeed the case, although non-${I}_{h}$ isomers were also observed. The energy gaps of the three ${I}_{h}\ensuremath{-}X@{\mathrm{Al}}_{12}$ species range from 1.1 to 1.3 eV. The spectra of ${\mathrm{Al}}_{12}{\mathrm{C}}^{\ensuremath{-}}$ were distinctly different from the other species, confirming that it does not possess an icosahedral structure.

Quantitative Time-Resolved Monitoring of Nitrate Formation in Sea Salt Particles Using a CCSEM/EDX Single Particle Analysis

Abstract: Progress of the nitrate formation in individual sea salt particles was detected as a function of time using aerosol samples collected during the TexAQS 2080 experiment We demonstrate that the time-resolved collection approach coupled with the automated EDX single particle analysis made it possible to follow in detail the time evolution of sea salt particles within a diverse aerosol mixture. Using a custom built Time-Resolved Aerosol Collector (TRAC), particulate samples were taken sequentially on grid-supported 50 nm carbon films with a time resolution of 10 min between two consecutive samples. The samples were analyzed in the laboratory using Computer Controlled Scanning Electron Microscopy with Energy-Dispersed analysis of X-rays (CCSEM/EDX). Between midnight of 08/16/00 and the early morning of 08/17/00, a steady, particularly sea salt rich aerosol was observed at the measurement site, which later showed the effects of atmospheric processing. During the night of 08/17/00 the sea salt particles were almost unprocessed, having elemental composition close to that of seawater. By 12 noon, the evolving atmosphere was able to completely convert them, predominantly to sodium nitrate particles. During the next night this process had nearly stopped and fairly virgin sea salt particles appeared again.

Nitric Acid−Water Complexes: Theoretical Calculations and Comparison to Experiment†

Abstract: The formation of HNO3·(H2O)n complexes is studied both theoretically and experimentally. First principles electronic structure calculations were used to produce minimum structures and harmonic vibrational frequencies of HNO3·(H2O)n and DNO3·(H2O)n complexes (n = 0−4). They also provide insight into the ionization of HNO3 in water, predicting that ionization in isolated clusters occurs for n = 4 or larger. Vibrational absorption spectra of matrix isolated nitric acid/water complexes were obtained using an FTIR spectrometer-based instrument. By incrementally increasing the amount of H2O in the matrix, we have been able to study nitric acid/water complexes and the ionization of HNO3. New spectral assignments, the first ones for the n = 2 and 3 complexes, are suggested on the basis of the results of the electronic structure calculations.

Structural and Chemical Characterization of Aligned Crystalline Nanoporous MgO Films Grown via Reactive Ballistic Deposition

Abstract: Highly porous (∼ 90%), high-surface area (∼1000 m2/g), thermally stable (1200 K) crystalline films of MgO are synthesized using a novel reactive ballistic deposition technique. The film consists of a tilted array of porous nanoscale crystalline filaments. Surprisingly, the individual filaments exhibit a high degree of crystallographic order with respect to each other. These films have chemical binding sites analogous to those on MgO(100). However, the fraction of chemically active, high energy binding sites is greatly enhanced on the nanoporous film. This unique collection of properties makes these materials attractive candidates for chemical applications such as sensors and heterogeneous catalysts.

Brines exposed to Europa surface conditions

Abstract: [1] Evidence for an ocean beneath the icy crust of Europa includes reflectance spectra of disrupted surface regions indicating hydrated materials such as salts. We simulated exposure of salty brine on the cold surface of Europa by flash-freezing sulfate and carbonate solutions. This produces materials that have near-infrared reflectance spectra distinct from those for crystalline minerals and more similar to those for Europa's non-ice regions. These new spectroscopic data, along with geophysical evidence, geochemical models, and meteorite studies, strongly suggest that the non-ice materials in the disrupted regions on Europa's surface contain large amounts of disordered and heavily hydrated MgSO4 and perhaps Na2SO4 that are endogenic in origin.

HostDesigner: a program for the de novo structure-based design of molecular receptors with binding sites that complement metal ion guests.

Abstract: This paper describes a novel approach to the discovery of host structures with binding sites that complement targeted metal ion guests. This approach uses a de novo structure-based design strategy that couples molecular building algorithms with scoring functions to prioritize candidate structures. The algorithms described herein have been implemented in a program called HostDesigner, the first structure-based design software specifically created for the discovery of metal ion receptors. HostDesigner generates and evaluates millions of candidate structures within minutes, rapidly identifying three-dimensional architectures that position binding sites to provide an optimal interaction with the metal ion.

Formic Acid Adsorption on Anatase TiO2(001)−(1 × 4) Thin Films Studied by NC-AFM and STM†

Abstract: Atomic resolution scanning tunneling microscopy (STM), noncontact atomic force microscopy (NC-AFM), X-ray photoemission spectroscopy (XPS), low-energy electron diffraction (LEED), and formic acid adsorption experiments were used to characterize the (001) surface of anatase TiO2. A combination of NC-AFM and STM imaging was used to distinguish features due to geometrical and electronic effects. The contrast in images of the bare (1 × 4) surface and the formate-covered surface is dominated by the surface topography in both NC-AFM and STM, although electronic effects in the troughs contribute features to the STM images that are absent from NC-AFM images. High-resolution imaging by STM and NC-AFM revealed that the highest point of the ridge of the (1 × 4) structure consists of a single row of atoms. Formate adsorbs at under-coordinated Ti sites in the added rows with a minimum separation of 2a0 and never adsorbs in the trenches even though the trenches also likely expose under-coordinated Ti atoms. The stickin...

Barrier-free intermolecular proton transfer in the uracil-glycine complex induced by excess electron attachment

Abstract: The photoelectron spectra (PES) of anions of uracil-glycine and uracil-phenylalanine complexes reveal broad features with maxima at 1.8 and 2.0 eV. The results of ab initio density functional B3LYP and second order Moller-Plesset theory calculations indicate that the excess electron occupies a π* orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of glycine to the O8 atom of uracil. As a result, the four most stable structures of the anion of uracil-glycine complex can be characterized as the neutral radical of hydrogenated uracil solvated by the anion of deprotonated glycine. The similarity between the PES spectra for the uracil complexes with glycine and phenylalanine suggests that the BFPT is also operative in the case of the latter anionic species. The BFPT to the O8 atom of uracil may be related to the damage of nucleic acid bases by low energy electrons because the O8 atom is involved in a hydrogen bond with adenine in the standard Watson-Crick pairing scheme.

Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation.

Abstract: On-line combination of capillary isoelectric focusing (CIEF) with capillary reversed-phase liquid chromatography (CRPLC) is developed using a microinjector as the interface for performing two-dimensional (2-D) protein/peptide separations of complex protein mixtures. The focusing effect of CIEF not only contributes to a high-resolution protein/peptide separation, but also may permit the analysis of low-abundance proteins with a typical concentration factor of 50-100 times. The preparative capabilities of CIEF are much larger than most of capillary-based electrokinetic separation techniques since the entire capillary is initially filled with a solution containing proteins/peptides and carrier ampholytes for the creation of a pH gradient inside the capillary. The focused peptides which have a similar pI are coinjected into the second separation dimension and further resolved by their differences in hydrophobicity. The resolving power of combined CIEF-CRPLC system is demonstrated using the soluble fraction of Drosophila salivary glands taken from a period beginning before steroid-triggered programmed cell death and extending to its completion. The separation mechanisms of CIEF and CRPLC are completely orthogonal and the overall peak capacity is estimated to be around approximately 1800 over a run time of less than 8 h. Significant enhancement in the separation peak capacity can be realized by further increasing the number of CIEF fractions and/or slowing the solvent gradient in CRPLC, however, at the expense of overall analysis time. The results of our preliminary studies display significant differences in the separation profiles of peptide samples obtained from salivary glands of animals staged at the 6 and 12 h following puparium formation.