17,125 research outputs found

    Vibrational signature of a single water molecule adsorbed on Pt(111): toward a reliable anharmonic description

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    In this study, we present a thorough benchmarking of our direct anharmonic vibrational variation-perturbation approach for adsorbed molecules on surfaces. We then use our method to describe the vibrational structure of a water molecule adsorbed on a Pt(111) surface and compare our results with the available experimental data. By using an explicitly correlated hybrid method to describe the molecule-surface interaction, we improve on the initial periodic PBE/DZP potential energy landscape and obtain vibrational frequencies that are of near-experimental accuracy. We introduce an implementation of anharmonic z-polarized IR intensity calculation and explain the absence of antisymmetric O-H stretch in the experimental data for the adsorbed water molecule, while the symmetric O-H stretch is predicted to be visible

    Fast vibrational calculation of anharmonic OH-stretch frequencies for two low-energy noradrenaline conformers

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    We introduce a new reduced-coupling technique to accelerate direct calculations of a selected number of vibrational frequencies in large molecular systems. Our method combines the advantages of the single-to-all correlation-corrected vibrational self-consistent field (STA-CC-VSCF) approach [D. M. Benoit, J. Chem. Phys. 125, 244110 (2006)] with those of the fast-CC-VSCF technique [D. M. Benoit, J. Chem. Phys. 120, 562 (2004)] and allows the ab initio calculation of only the relevant parts of the required potential energy surface (PES). We demonstrate, using a set of five aliphatic alcohol molecules, that the new fast-STA-CC-VSCF method is accurate and leads to very substantial time gains for the computations of the PES. We then use the fast-STA-CC-VSCF method to accelerate the computation of the OH-stretch and NH-stretch frequencies of the two lowest-energy conformers of noradrenaline, namely, AG1a and GG1a. Our new approach enables us to run the calculation 89 times faster than the standard CC-VSCF technique and makes it possible to use a high-level MP2/TZP description of the PES. We demonstrate that the influence of the strong mode-mode couplings is crucial for a realistic description of the particular OH-stretch vibrational signature of each conformer. Finally, of the two possible low-energy conformers, we identify AG1a as the one most likely to have been observed in the experiments of Snoek [Mol. Phys. 101, 1239 (2003)]

    Measuring cell adhesion forces with the atomic force microscope at the molecular level

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    In the past 25 years many techniques have been developed to characterize cell adhesion and to quantify adhesion forces. Atomic force microscopy (AFM) has been used to measure forces in the pico-newton range, an experimental technique known as force spectroscopy. We modified such an AFM to measure adhesion forces between live cells or between cells and surfaces. This strategy required functionalizing the surface of the sensors for immobilizing the cell. We used Dictyostelium discoideum cells which respond to starvation by surface expression of the adhesion molecule csA and consequent aggregation to measure the adhesion force of a single csA-csA bond. Relevant experimental parameters include the duration of contact between the interacting surfaces, the force against which this contact is maintained, the number and specificity of interacting adhesion molecules and the constituents of the medium in which the interaction occurs. This technology also permits the measurement of the viscoelastic properties of single cells or cell layers. Copyright (C) 2002 S, Karger AG, Basel

    Vibrational anharmonicity of small gold and silver clusters using the VSCF method

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    We study the vibrational spectra of small neutral gold (Au2–Au10) and silver (Ag2–Au5) clusters using the vibrational self-consistent field method (VSCF) in order to account for anharmonicity. We report harmonic, VSCF, and correlation-corrected VSCF calculations obtained using a vibrational configuration interaction approach (VSCF/VCI). Our implementation of the method is based on an efficient calculation of the potential energy surfaces (PES), using periodic density functional theory (DFT) with a plane-wave pseudopotential basis. In some cases, we use an efficient technique (fast-VSCF) assisted by the Voter–Chen potential in order to get an efficient reduction of the number of pair-couplings between modes. This allows us to efficiently reduce the computing time of 2D-PES without degrading the accuracy. We found that anharmonicity of the gold clusters is very small with maximum rms deviations of about 1 cm−1, although for some particular modes anharmonicity reaches values slightly larger than 2 cm−1. Silver clusters show slightly larger anharmonicity. In both cases, large differences between calculated and experimental vibrational frequencies (when available) stem more likely from the quality of the electronic structure method used than from vibrational anharmonicity. We show that noble gas embedding often affects the vibrational properties of these clusters more than anharmonicity, and discuss our results in the context of experimental studies

    The nature and role of the gold-krypton interactions in small neutral gold clusters

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    © 2015 American Chemical Society. We investigate the nature and role of krypton embedding in small neutral gold clusters. For some of these clusters, we observe a particular site-dependent character of the Kr binding that does not completely follow the criterion of binding at low-coordinated sites, widely accepted for interaction of a noble gas with closed-shell metal systems such as metal surfaces. We aim at understanding the effect of low dimensionality and open-shell electronic structure of the odd-numbered clusters on the noble gas-metal cluster interaction. First, we investigate the role of attractive and repulsive forces, and the frontier molecular orbitals. Second, we investigate the Au-Kr interaction in terms of reactivity and bonding character. We use a reactivity index derived from Fukui formalism, and criteria provided by the electron localization function (ELF), in order to classify the type of bonding. We carry out this study on the minimum energy structures of neutral gold clusters, as obtained using pseudo potential plane-wave density functional theory (DFT). A model is proposed that includes the effect of attractive electrostatic, van der Waals and repulsive forces, together with effects originating from orbital overlap. This satisfactorily explains minimum configurations of the noble gas-gold cluster systems, the site preference of the noble gas atoms, and changes in electronic properties
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