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The desorption kinetics of methanol, ethanol, and water from graphene covered Pt(111) are investigated. The temperature programmed desorption (TPD) spectra for both methanol and ethanol have well-resolved first, second, third, and multilayer layer desorption peaks. The alignment of the leading edges is consistent with zero-order desorption kinetics from all layers. In contrast, for water, the first and second layers are not resolved. At low water coverages (<1 monolayer (ML)) the initial desorption leading edges are aligned but then fall out of alignment at higher temperatures. For thicker water layers (10-100 ML), the desorption leading edges are in alignment throughout the desorption of the film. The coverage dependence of the desorption behavoir suggests that at low water coverages the nonalignment of the desorption leading edges is due to water dewetting from the graphene substrate. Kinetic simulations reveal that the experimental results are consistent with zero-order desorption. The simulations also show that fractional order desorption kinetics would be readily apparent in the experimental TPD spectra.

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We study the diffusivity of three-methylpentane (3MP) using the permeation of inert gases (Ar, Kr, Xe) through the supercooled liquid created when initially amorphous overlayers are heated above T(g). We find that the permeation rates for all of the gases have non-Arrhenius temperature dependences that are well described by the Vogel-Fulcher-Tamman equation. Comparison with the literature viscosity shows that the Stokes-Einstein equation breaks down at temperatures approaching T(g). The fractional Stokes-Einstein equation, D ∝ (T∕η)(n), does fit the permeation data, albeit with different values of n for each gas. There is qualitative agreement with the Stokes-Einstein equation in that the permeation rate decreases with increasing radius of the rare gas probe, but the small differences in radii significantly underestimate the observed differences in the permeation rates. Instead the permeation rates are better correlated with the rare gas-3MP interaction energy than with the atomic radius.

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Temperature-programmed desorption (TPD) and reflection absorption infrared spectroscopy (RAIRS) are used to investigate the crystallization kinetics and measure the excess free energy of metastable amorphous solid water films (ASW) of H(2)O and D(2)O grown using molecular beams. The desorption rates from the amorphous and crystalline phases of ASW are distinct, and as such, crystallization manifests can be observed in the TPD spectrum. The crystallization kinetics were studied by varying the TPD heating rate from 0.001 to 3 K/s. A coupled desorption-crystallization kinetic model accurately simulates the desorption spectra and accurately predicts the observed temperature shifts in the crystallization. Isothermal crystallization studies using RAIRS are in agreement with the TPD results. Furthermore, highly sensitive measurements of the desorption rates were used to determine the excess free energy of ASW near 150 K. The excess entropy obtained from these data is consistent with there being a thermodynamic continuity between ASW and supercooled liquid water.

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We describe in detail a diffusion model used to simulate inert gas transport through supercooled liquid overlayers. In recent work, the transport of the inert gas has been shown to be an effective probe of the diffusivity of supercooled liquid methanol in the experimentally challenging regime near the glass transition temperature. The model simulations accurately and quantitatively describe the inert gas permeation desorption spectra. The simulation results are used to validate universal scaling relationships between the diffusivity, overlayer thickness, and the temperature ramp rate for isothermal and temperature programmed desorption. From these scaling relationships we derive simple equations from which the diffusivity can be obtained using the peak desorption time or temperature for an isothermal or set of TPD experiments, respectively, without numerical simulation. The results presented here demonstrate that the permeation of gases through amorphous overlayers has the potential to be a powerful technique to obtain diffusivity data in deeply supercooled liquids.

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We present an experimental technique to measure the diffusivity of supercooled liquids at temperatures near their T(g). The approach uses the permeation of inert gases through supercooled liquid overlayers as a measure of the diffusivity of the supercooled liquid itself. The desorption spectra of the probe gas are used to extract the low temperature supercooled liquid diffusivities. In the preceding companion paper, we derived equations using ideal model simulations from which the diffusivity could be extracted using the desorption peak times for isothermal or peak temperatures for temperature programmed desorption experiments. Here, we discuss the experimental conditions for which these equations are valid and demonstrate their utility using amorphous methanol with Ar, Kr, Xe, and CH(4) as probe gases. The approach offers a new method by which the diffusivities of supercooled liquids can be measured in the experimentally challenging temperature regime near the glass transition temperature.

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Molecular beam techniques, temperature-programmed desorption (TPD), and reflection absorption infrared spectroscopy (RAIRS) are used to explore the relationship between krypton permeation through and the self-diffusivity of supercooled liquid methanol at temperatures (100-115 K) near the glass transition temperature, T(g) (103 K). Layered films, consisting of CH(3)OH and CD(3)OH, are deposited on top of a monolayer of Kr on a graphene covered Pt(111) substrate at 25 K. Concurrent Kr TPD and RAIRS spectra are acquired during the heating of the composite film to temperatures above T(g). The CO vibrational stretch is sensitive to the local molecular environment and is used to determine the supercooled liquid diffusivity from the intermixing of the isotopic layers. We find that the Kr permeation and the diffusivity of the supercooled liquid are directly and quantitatively correlated. These results validate the rare-gas permeation technique as a tool for probing the diffusivity of supercooled liquids.

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The structure of water at interfaces is crucial for processes ranging from photocatalysis to protein folding. Here, we investigate the structure and lattice dynamics of two-layer crystalline ice films grown on a hydrophobic substrate, graphene on Pt(111), with low energy electron diffraction, reflection-absorption infrared spectroscopy, rare-gas adsorption/desorption, and ab initio molecular dynamics. Unlike hexagonal ice, which consists of stacks of puckered hexagonal "bilayers", this new ice polymorph consists of two flat hexagonal sheets of water molecules in which the hexagons in each sheet are stacked directly on top of each other. Such two-layer ices have been predicted for water confined between hydrophobic walls, but not previously observed experimentally. Our results show that the two-layer ice forms even at zero pressure at a single hydrophobic interface by maximizing the number of hydrogen bonds at the expense of adopting a nontetrahedral geometry with weakened hydrogen bonds.

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By means of high-resolution scanning tunneling microscopy (STM), we have revealed unprecedented details about the intermediate steps for a surface-catalyzed reaction. Specifically, we studied the oxidation of H adatoms by O(2) molecules on the rutile TiO(2)(110) surface. O(2) adsorbs and successively reacts with the H adatoms, resulting in the formation of water species. Using time-lapsed STM imaging, we have unraveled the individual reaction intermediates of HO(2), H(2)O(2), and H(3)O(2) stoichiometry and the final reaction product-pairs of water molecules, [H(2)O](2). Because of their different appearance and mobility, these four species are discernible in the time-lapsed STM images. The interpretation of the STM results is corroborated by density functional theory calculations. The presented experimental and theoretical results are discussed with respect to previous reports where other reaction mechanisms have been put forward.

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The permeation of rare-gas atoms through deeply supercooled metastable liquid methanol films is used to probe the diffusivity. The technique allows for measurement of supercooled liquid mobility at temperatures near the glass transition. The temperature dependence of the diffusivity is well described by a Vogel-Fulcher-Tamman equation. These new measurements and the temperature dependent kinetic parameters obtained from their analysis provide clear evidence that methanol is a fragile liquid near the glass transition.

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Titanium dioxide (TiO2) has a number of uses in catalysis, photochemistry, and sensing that are linked to the reducibility of the oxide. Usually, bridging oxygen (Obr) vacancies are assumed to cause the Ti3d defect state in the band gap of rutile TiO2(110). From high-resolution scanning tunneling microscopy and photoelectron spectroscopy measurements, we propose that Ti interstitials in the near-surface region may be largely responsible for the defect state in the band gap. We argue that these donor-specific sites play a key role in and may dictate the ensuing surface chemistry, such as providing the electronic charge required for O2 adsorption and dissociation. Specifically, we identified a second O2 dissociation channel that occurs within the Ti troughs in addition to the O2 dissociation channel in O(br) vacancies. Comprehensive density functional theory calculations support these experimental observations.

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LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.

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The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gene expression. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale. Here we report, using the budding yeast Saccharomyces cerevisiae as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25% of the yeast proteome. Numerous protein complexes were identified, including many new interactions in various signalling pathways and in the DNA damage response. Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies. Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks.

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