Showing papers by "Environmental Molecular Sciences Laboratory published in 1998"
TL;DR: A molecular memory phenomenon, in which an enzymatic turnover was not independent of its previous turnovers because of a slow fluctuated of protein conformation, was evidenced by spontaneous spectral fluctuation of FAD.
Abstract: Enzymatic turnovers of single cholesterol oxidase molecules were observed in real time by monitoring the emission from the enzyme's fluorescent active site, flavin adenine dinucleotide (FAD). Statistical analyses of single-molecule trajectories revealed a significant and slow fluctuation in the rate of cholesterol oxidation by FAD. The static disorder and dynamic disorder of reaction rates, which are essentially indistinguishable in ensemble-averaged experiments, were determined separately by the real-time single-molecule approach. A molecular memory phenomenon, in which an enzymatic turnover was not independent of its previous turnovers because of a slow fluctuation of protein conformation, was evidenced by spontaneous spectral fluctuation of FAD.
1,352 citations
TL;DR: Using photoelectron spectroscopy of size-selected clusters, the authors studied the electronic structure evolution of the Al $3s$- and $3p$-derived bands and observed that the Al bands evolve and broaden with cluster size and begin to overlap at the same time.
Abstract: Using photoelectron spectroscopy of size-selected ${\mathrm{Al}}_{x}^{\ensuremath{-}}$ $(x\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1--162)$ clusters, we studied the electronic structure evolution of ${\mathrm{Al}}_{x}$ and observed that the Al $3s$- and $3p$-derived bands evolve and broaden with cluster size and begin to overlap at ${\mathrm{Al}}_{9}$. Direct spectroscopic signatures were obtained for electron shell structures with spherical shell closings at ${\mathrm{Al}}_{11}^{\ensuremath{-}}$, ${\mathrm{Al}}_{13}^{\ensuremath{-}}$, ${\mathrm{Al}}_{19}^{\ensuremath{-}}$, ${\mathrm{Al}}_{23}^{\ensuremath{-}}$, ${\mathrm{Al}}_{35}^{\ensuremath{-}}$, ${\mathrm{Al}}_{37}^{\ensuremath{-}}$, ${\mathrm{Al}}_{46}$, ${\mathrm{Al}}_{52}$, ${\mathrm{Al}}_{55}^{\ensuremath{-}}$, ${\mathrm{Al}}_{56}$, ${\mathrm{Al}}_{66}$, and ${\mathrm{Al}}_{73}^{\ensuremath{-}}$. The electron shell effect diminishes above ${\mathrm{Al}}_{75}$ and new spectral features appearing in ${\mathrm{Al}}_{x}^{\ensuremath{-}}$ $(xg100)$ suggest a possible geometrical packing effect in large clusters.
301 citations
TL;DR: In this article, the authors proposed a method for high-resolution near-field optical imaging that relies on the highly enhanced fields at sharp metal tips under laser illumination, which are laterally confined to the tip size and can be used to locally excite the sample surface.
271 citations
TL;DR: This article showed that at low temperatures, O2 dissociates at oxygen vacancies filling each defect site with one O atom and depositing a second O adatom at a five-coordinate Ti4+ site or that O2 interacts with surface hydroxyl groups resulting in O 2 dissociation and the presence of the O atom.
267 citations
TL;DR: In this article, the reaction of water vapor with clean (0001) surfaces of single-crystal corundum and thin-film hematite (α -Fe 2 O 3 ) was studied.
246 citations
TL;DR: The present results suggest that it will be feasible to realize close to 100% ion transmission efficiency for analytically relevant ions through the electrospray ionization interface and into the mass analyzer.
Abstract: To improve upon the already impressive sensitivity achievable with electrospray ionization sources, a novel electrohydrodynamic ion funnel interface has been developed and implemented with a triple-quadrupole mass spectrometer. The ion funnel interface effectively consists of a series of ring electrodes of increasingly small internal diameters to which rf and dc electric potentials are coapplied. In the 1−10-Torr pressure range, the electric fields cause the collisionally damped ions to be more effectively focused and transmitted as a collimated ion beam. This paper describes the ion funnel design and presents an evaluation of its performance using a triple-quadrupole mass spectrometer. Ion transmission and m/z discriminating parameters (resulting in both effective low- and high-m/z cutoffs) are presented based upon both ion current measurements and mass spectra. Electrospray ionization mass spectra of selected protein solutions demonstrated well over 1 order of magnitude increase in signal relative to th...
243 citations
TL;DR: In this article, the reaction of CO 2 and H 2 O to form bicarbonate (HCO − 3 ) was examined on the nearly perfect and vacuum annealed surfaces of TiO 2 (110) with temperature programmed desorption (TPD), static secondary ion mass spectrometry (SSIMS) and high resolution electron energy loss spectrometers (HREELS).
209 citations
182 citations
TL;DR: In this paper, photoelectron spectroscopy was combined with an electrospray ion source to probe the repulsive Coulomb barriers, excess electron binding, and intramolecular electron-electron interactions in a series of dicarboxylate dianions.
Abstract: Multiply charged anions, though ubiquitous in nature, have been difficult to produce and study in the gas phase. Photoelectron spectroscopy has been combined with an electrospray ion source to probe the repulsive Coulomb barriers, excess electron binding, and intramolecular electron-electron interactions in a series of dicarboxylate dianions, ${}^{\ensuremath{-}}{\mathrm{O}}_{2}\mathrm{C}({\mathrm{CH}}_{2}{)}_{n}{\mathrm{CO}}_{2}^{\ensuremath{-}}$ $(n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}3--10)$. These experiments provide quantitative information about the repulsive Coulomb barriers and how the excess electron binding energy and the barrier height depend on the intramolecular Coulomb repulsion.
163 citations
TL;DR: A laser microfabricated device was constructed for rapid microdialysis cleanup of biological samples for analysis by electrospray ionization mass spectrometry (ESI-MS) in both off-line and on-line modes, allowing reduced sample utilization and improved sensitivity with ESI-MS.
Abstract: A laser microfabricated device was constructed for rapid microdialysis cleanup of biological samples for analysis by electrospray ionization mass spectrometry (ESI-MS) in both off-line and on-line modes. A microdialysis membrane was sandwiched between two chips having micromachined serpentine channels. The total volume of the sample serpentine channel used for the microdialysis was 1 μL. Efficient desalting was demonstrated for both DNA and protein samples using ESI with an ion trap mass spectrometer after microdialysis against a counter flow of ESI-compatible buffer. Signal-to-noise ratios were also greatly enhanced compared to direct infusion of the original nondialyzed samples. Importantly, the microfabricated device allowed use of sample flow rates 1 order of magnitude smaller than previous designs based on a microdialysis fiber, allowing reduced sample utilization and improved sensitivity with ESI-MS. The effectiveness of the cleanup was attributed to the size difference between the sample channel an...
152 citations
TL;DR: The large cross-section for O2 production suggests that electronic excitation plays an important part in the formation of O2 on Ganymede and Europa, rather than by diffusion and chemical recombination of precursor fragments as has been previously thought.
Abstract: The signature of condensed molecular oxygen has been reported in recent optical-reflectance measurements of the jovian moon Ganymede1, and a tenuous oxygen atmosphere has been observed on Europa2. The surfaces of these moons contain large amounts of water ice, and it is thought that O2 is formed by the sputtering ofice by energetic particles from the jovian magnetosphere3,4,5,6,7,8. Understanding how O2 might be formed from low-temperature ice is crucial for theoretical and experimental simulations of the surfaces and atmospheres of icy bodies in the Solar System. Here we report laboratory measurements of the threshold energy, cross-section and temperature dependence of O2 production by electronic excitation of ice in vacuum, following electron-beam irradiation. Molecular oxygen is formed by direct excitation and dissociation of a stable precursor molecule, rather than (as has been previously thought) by diffusion and chemical recombination of precursor fragments. The large cross-section for O2 production suggests that electronic excitation plays an important part in the formation of O2 on Ganymede and Europa.
TL;DR: In this paper, a single-molecule measurement of the allophycocyanin trimer (APC), a light-harvesting protein complex from cyanobacteria, is presented.
Abstract: We report a study of the allophycocyanin trimer (APC), a light-harvesting protein complex from cyanobacteria, by room-temperature single-molecule measurements of fluorescence spectra, lifetimes, intensity trajectories, and polarization modulation. Emission spectra of individual APC trimers are found to be homogeneous on the time scale of seconds. In contrast, their emission lifetimes are found to be widely distributed because of generation of long-lived exciton traps during the course of measurements. The intensity trajectories and polarization modulation experiments indicate reversible exciton trap formation within the three quasiindependent pairs of strong interacting R84 and ‚84 chromophores in APC, as well as photobleaching of individual chromophores. Comparison experiments under continuous-wave and pulsed excitation reveal a two-photon mechanism for generating exciton traps and/or photobleaching, which involves exciton-exciton annihilation. These single-molecule experiments provide new insights into the spectroscopy, exciton dynamics, and photochemistry of light-harvesting complexes.
TL;DR: By combination of fast magic-angle spinning (MAS) and detection of the free-induction decay during a rotor-synchronized quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) train of refocusing pulses, the sensitivity of Quadrupolar-echo MAS NMR spectra for the central transition of half-integer quadrupol nuclei exhibiting largequadrupolar couplings may be significantly enhanced.
TL;DR: The interaction of water with the α-Fe2O3(012) and (2×1) surfaces of the (1×1)-surface was examined with temperature programmed desorption (TPD), static secondary ion mass spectrometry (SSIMS), low energy electron diffraction (LEED) and high resolution electron energy loss spectroscopy (HREELS) in the temperature range between 100 and 950 K.
TL;DR: In this article, the photodetachment experiments of a multiply charged anion were performed and the repulsive Coulomb barrier due to the two excess charges was directly probed and estimated to be about 1.9 ε 2.5 eV.
Abstract: Photoelectron spectra of citric acid doubly charged anion were measured. The repulsive Coulomb barrier due to the two excess charges was directly probed and estimated to be about {approximately}1.9{endash} 2.5 eV . The adiabatic binding energy of the second electron was measured to be 1.0thinspthinspeV. Two detachment channels were observed, with the second channel at {approximately}0.6 eV higher in binding energy. The current study presents the first photodetachment experiments of a multiply charged anion and opens up new opportunities to study these novel molecular species. {copyright} {ital 1998} {ital The American Physical Society}
TL;DR: The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[ cs ]TAAG)·d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz as mentioned in this paper.
TL;DR: In this article, high-level ab initio molecular orbital theory has been used to predict the proton affinities of H2O and NH3 at the CCSD(T) level with correlation-consistent basis sets through augmented quintuple-ζ...
Abstract: High-level ab initio molecular orbital theory has been used to predict the proton affinities of H2O and NH3 at the CCSD(T) level with correlation-consistent basis sets through augmented quintuple-ζ...
TL;DR: In this paper, the heat of formation of CF2O has been calculated at high levels of ab initio molecular orbital theory and the best values were obtained by extrapolating CCSD(T) energies obtained from the correlation consistent basis sets, up through augmented quadruple-ζ to the complete basis set limit.
Abstract: The heat of formation of CF2O has been calculated at high levels of ab initio molecular orbital theory. The best values were obtained by extrapolating CCSD(T) energies obtained from the correlation consistent basis sets, up through augmented quadruple-ζ, to the complete basis set limit. Core/valence corrections were obtained from basis sets designed to recover such effects. Zero-point energies were taken from experiment, and missing values were calculated at the MP2/cc-pVTZ level and scaled to approximate experimental values. The calculated ΔHf° values are CF = −58.2 ± 0.5 kcal/mol, CF2 = −46.6 ± 0.7 kcal/mol, FCO = −44.1 ± 0.5 kcal/mol, and CF2O = −145.2 ± 0.8 kcal/mol.
TL;DR: Hartree−Fock and second-order perturbation theory methods were used to determine structures and binding enthalpies of complexes formed from a single alkali metal cation (Li+ through Cs+) and one or two 1,2-dimethoxyethane ligands or 12-crown-4 as discussed by the authors.
Abstract: Hartree−Fock and second-order perturbation theory methods were used to determine structures and binding enthalpies of complexes formed from a single alkali metal cation (Li+ through Cs+) and one or two 1,2-dimethoxyethane ligands or 12-crown-4. These calculations employed multiple basis sets in order to determine the sensitivity of the results to the completeness in the one-particle basis. The results are compared with recently reported collision-induced dissociation experimental findings. In general, good agreement was found between the experimental and theoretical bond dissociation enthalpies, although for the heavier cations discrepancies of as much as 14 kcal/mol or more were uncovered. Possible reasons for these anomalies are discussed.
TL;DR: In this article, a photoelectron spectroscopic study of ScOn- and YOn- was carried out at three photon energies: (1.35 eV) within the experimental accuracy (± 0.02 eV).
Abstract: A photoelectron spectroscopic study of ScOn- (n = 1−4) and YOn- (n = 1−5) was carried out at three photon energies: 532, 355, and 266 nm. Vibrationally resolved photoelectron spectra were obtained for ScO- and YO-. The electron affinities of both ScO and YO were measured to be identical (1.35 eV) within the experimental accuracy (±0.02 eV). Three low-lying excited states were observed for the monoxides, A‘2Δ, A2Π, and B2Σ+. The latter two excited states resulted from two-electron detachment, suggesting unusually strong electron correlation (configuration interaction) effects in the ground state of the anions. The excitation energies of the low-lying states were also found to be similar for the two monoxides except that YO has a smaller vibrational frequency and larger spin−orbit splitting. The A‘2Δ states of both ScO and YO show very strong photon energy-dependent detachment cross sections. Four similar photoelectron features were observed for the dioxides with those of YO2- having lower binding energies...
TL;DR: In this paper, the authors used a sequence of correlation consistent Gaussian basis sets to estimate the core/valence correlation effects of BH and BH2, BH3, and B2H6.
Abstract: The heats of formation of BH, BH2, BH3, and B2H6 have been obtained from ab initio coupled cluster calculations by using a systematic sequence of correlation consistent Gaussian basis sets. The best values were obtained by extrapolating the finite basis set results to the complete basis set limit and by incorporating an estimate of core/valence correlation effects. In general, the largest calculations in this study utilized quadruple-ζ-level basis sets that were augmented by an additional shell of diffuse functions. Even larger basis set calculations were performed on the smallest of the four systems in order to test the accuracy of the complete basis set extrapolation. Vibrational zero point energies were taken from experiment when available. Missing values were replaced by theoretical harmonic frequencies scaled to more closely approximate the experimental values. The calculated heats of formation are ΔHf 0(BH) = 106.2 ± 0.3 kcal/mol, ΔHf 0(BH2) = 78.4 ± 0.6 kcal/mol, ΔHf 0(BH3) = 25.8 ± 0.7 kcal/mol, a...
TL;DR: Dang et al. as mentioned in this paper evaluated the importance of polarization effects in the hydrogen-bonding structures of water using classical molecular dynamics techniques with a polarizable potential model, and showed that the effect of polarization on the hydrogen bonding structure of water is significant.
Abstract: The importance of polarization effects in the hydrogen-bonding structures of water is evaluated using classical molecular dynamics techniques with a polarizable potential model [Dang, L. X.; Chang,...
TL;DR: In this article, a series of linear dicarboxylate dianions (DC2-), -O2C(CH2)nCO2- (n = 3−6), solvated by one and two waters were investigated.
Abstract: Photoelectron spectroscopy has been combined with an electrospray ionization technique to study gas-phase multiply charged anions and their intramolecular Coulomb repulsion and solvation stabilization. We report an initial study on a series of linear dicarboxylate dianions (DC2-), -O2C(CH2)nCO2- (n = 3−6), solvated by one and two waters. The second electron binding energy of DC2- decreases with decreasing aliphatic chain length owing to the increasing Coulomb repulsion between the two charges; the dianion with n = 2 has a binding energy close to zero and is not stable in the gas phase. We found that this dianion can be stabilized by one water, and in general the first water stabilizes the electron binding energy of DC2- by ∼0.3 eV. The second water, however, was observed to show a much stronger stabilization effect (∼0.6 eV), suggesting that the two waters solvate the two carboxylate groups separately.
TL;DR: The structure calculations indicate that XPA-MBD contains elements of well-defined secondary structure interspaced with disordered loops organized into two non-interactive sub-domains: a zinc-binding core and a loop-rich domain.
Abstract: XPA, an essential protein in nucleotide excision repair (NER), interacts with damaged DNA and other proteins (RPA, ERCC1 and TFIIH) to remove a wide variety of chemically and structurally distinct DNA lesions from the eukaryotic genome. To understand the structural basis for the role of XPA in the repair process, the structure of the minimal DNA binding domain of human XPA [XPA-MBD (M98-F219)] was studied by NMR spectroscopy. A three-dimensional structure for XPA-MBD was generated using distance geometry and simulated annealing methods from NOE-based distance restraints, hydrogen bond and Zn-S distance restraints, and dihedral restraints. The structure calculations indicate that XPA-MBD contains elements of well-defined secondary structure interspaced with disordered loops organized into two non-interactive sub-domains: a zinc-binding core (D101-K137) and a loop-rich domain (L138-F219). The zinc-associated core contains an antiparallel beta-sheet (Y102-C105 and K110-M113) and an alpha-helix (C126-K137) separated by a poorly defined turn, reminiscent of the structure of the zinc-binding domain of the chicken erythroid transcription factor GATA-1 when bound to its cognate DNA sequence. The loop-rich domain contains a triple-strand antiparallel beta-sheet (L138-T140, L182-M178 and K163-K167), three loops (K151-L162, N169-D177 and Q208-F219) and three alpha-helices (K141-L150, K183-W194 and Q197-R207). The XPA-MBD structure is discussed in terms of known functions: binding single- and double-stranded DNA and binding RPA.
TL;DR: In this paper, the authors analyzed the effect of magic-angle spinning on half-integer (I > 1/2) quadrupolar nuclei with large quadrupole coupling constants.
Abstract: The quadrupole Carr-Purcell-Meiboom-Gill NMR experiment using magic-angle spinning (QCPMG-MAS) is analysed as a means of determining quadrupolar coupling and anisotropic chemical shielding tensors for half-integer (I > 1/2) quadrupolar nuclei with large quadrupole coupling constants (C Q). This is accomplished by numerical simulations and 87Rb NMR experiments wih Rb2SO4 and Rb2CrO4 using different magnetic fields. It is demonstrated that (i) QCPMG-MAS experiments typically provide a sensitivity gain by more than an order of magnitude relative to quadrupolar-echo MAS experiments, (ii) non-secular second-order terms do not affect the spin evolution appreciably, and (iii) the effect of finite RF pulses needs to be considered when 2ω2 Q/(ω0ωRF) > 0.1, where ωQ = 2πC Q/(4I(2I—1)), ωRF is the RF amplitude, and ω0 the Larmor frequency. Using numerical simulations and iterative fitting the magnitudes and relative orientation of 87Rb quadrupolar coupling and chemical shielding tensors for Rb2SO4 and Rb2CrO4 have b...
TL;DR: In this paper, the chemical shift tensors for acetone and 12 complexes of acetone with Bronsted and Lewis acids were calculated with the gauge including atomic orbital (GIAO) approach at the RHF and MP2 levels of theory.
Abstract: We calculated the chemical shift tensors for acetone and 12 complexes of acetone with Bronsted and Lewis acids. Each complex was optimized at the MP2/6-311+G* or B3LYP/DZVP2 level of theory. Chemical shift tensors were calculated with the gauge including atomic orbital (GIAO) approach at the RHF and MP2 levels of theory. We discovered a strong correlation between the MP2 and RHF 13C isotropic shifts of the carbonyl carbon in the complexes studied. Linear regression indicates that the MP2 isotropic shifts can be predicted by δMP2 = [1.12 (±0.04)]δRHF − 42.1 (±10.5) ppm (R2 = 0.9974). We were thus able to study two systems that are currently intractable at the GIAO-MP2 level. One is the complex of acetone with a large model of a zeolite, (H3SiO)3SiOHAl(OSiH3)3. The RHF shift of the carbonyl carbon of acetone on the zeolite model (238.4 ppm) is in poor agreement with the experimental (223 ppm) value. However, the MP2 result predicted by the linear correlation (224.0 ppm) is in much closer agreement. We were ...
TL;DR: A novel dual-microdialysis approach has been developed for fast and efficient fractionation and cleanup for ESI-MS and ESI MS/MS analyses of biological samples, and preliminary application of this technique for direct characterization of microorganism lysates is presented.
Abstract: A novel dual-microdialysis approach has been developed for fast and efficient fractionation and cleanup for ESI-MS and ESI MS/MS analyses of biological samples. A modified dynamic microdialyzer utilizing two mirror-image serpentine channels, which sandwich a regenerated cellulose membrane of selected molecular weight cutoff, serves as the first stage for the removal of high-molecular-weight components and cellular residue. The second stage employs a hollow microdialysis capillary to remove low-molecular-weight species (e.g., salts) which can degrade or preclude analysis ESI-MS. A protein mixture consisting of 30 μM bovine serum albumin (BSA), 4.0 μM cytochrome c, 2.3 μM ubiquitin, and 9.4 μM bradykinin in 0.5 M NaCl was used to evaluate the performance of this system. Essentially complete removal of both BSA and NaCl was achieved, resulting in high-quality mass spectra containing only the lower molecular weight proteins. After passing through the on-line dual-microdialysis system, a crude bacteria cell ly...
TL;DR: In this article, high and low-energy X-ray photoelectron diffraction was used to determine the structure of formate adsorbed on TiO 2 (110).
TL;DR: In this article, the voltage was measured via a Kelvin probe while the sample temperature was ramped to 50 K, due to dielectric responses occurring at much less than the expected 135 K. This was due to relaxations of the highly strained amorphous ice.
Abstract: ${\mathrm{D}}_{3}{\mathrm{O}}^{+}$ and ${\mathrm{Cs}}^{+}$ ions $(\ensuremath{\le}1\mathrm{eV})$ were soft landed on vacuum-deposited amorphous water ice at 30 K. The samples charged capacitively with an initial dielectric constant of 2. Then the voltage was measured via a Kelvin probe while the sample temperature was ramped. A sharp drop in voltage occurred near 50 K, due to dielectric responses occurring at much less than the expected 135 K. This was due to relaxations of the highly strained amorphous ice. Preannealing the ice could move the electrical relaxation up to as high as 120 K. Ion migration through the ice was not observed below 190 K.