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Allouche A.-R.,University Claude Bernard Lyon 1 | Allouche A.-R.,CNRS Laboratory of Ionic and Molecular Spectrometry
Journal of Computational Chemistry | Year: 2011

Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV-visible, infrared, and Raman-computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color-coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at. © 2010 Wiley Periodicals, Inc. Source


Calvo F.,CNRS Laboratory of Ionic and Molecular Spectrometry
Physica D: Nonlinear Phenomena | Year: 2011

The ring-polymer molecular dynamics (RPMD) method was recently shown to provide a powerful framework to address the time evolution of many-particle semiclassical systems. Its underlying Hamiltonian formulation is exploited here to define and compute some measures of deterministic chaos, namely the Lyapunov characteristic exponent. Applications are presented for weakly bound neon clusters, with the aim of assessing the influence of nuclear delocalization on the nonlinear dynamics. It is found that the balance between the additional degrees of freedom in the RPMD description and the harmonic nature of the additional interactions leads to more regular dynamics at high temperature, but more chaotic dynamics at low temperature. Intrinsic features of quantum effects on the isomerization dynamics also have a signature on the Lyapunov exponent. © 2011 Elsevier B.V. All rights reserved. Source


Linguerri R.,University Paris Est Creteil | Hochlaf M.,University Paris Est Creteil | Bacchus-Montabonel M.-C.,CNRS Laboratory of Ionic and Molecular Spectrometry | Desouter-Lecomte M.,CNRS Laboratory of Chemical Physics
Physical Chemistry Chemical Physics | Year: 2013

Franzreb and Williams at Arizona State University detected recently the MgO2+ molecular species in the gas phase. Here we report a very detailed theoretical investigation of the low-lying electronic states of this dication including their potentials, spin-orbit, rotational and radial couplings. Our results show that the potential energy curves of the dicationic electronic states have deep potential wells. This confirms that this dication does exist in the gas phase; it is a thermodynamically stable molecule in its ground state, and it has several excited long-lived metastable states. The potential energy curves are used then to predict a set of spectroscopic parameters for the bound states of MgO2+. We have also incorporated these potentials, rotational and radial couplings in dynamical calculations to derive the cross sections for the charge transfer Mg2+ + O → Mg+ + O+ reaction in the 1-103 eV collision energy domain via formation-decomposition of the MgO2+ dication. Our work shows the role of MgO2+ in the Earth ionosphere and more generally in atmospheric processes in solar planets, where this reaction efficiently participates in the predominance of Mg+ cations in these media compared to Mg and Mg2+. © 2013 the Owner Societies. Source


Calvo F.,CNRS Laboratory of Ionic and Molecular Spectrometry | Parneix P.,University Paris - Sud
ChemPhysChem | Year: 2012

The influence of one or several infrared laser pulses on the stability of bare and argon-tagged sodium chloride clusters is investigated theoretically by a combination of computational methods involving explicit molecular dynamics and properly calibrated unimolecular rate theories. The fragmentation spectra obtained by varying the laser frequency in the far-IR range is compared to the linear absorption spectrum resulting from the dipole moment autocorrelation function. Under appropriate laser field parameters, the action spectra are found to resemble the absorption spectra quite accurately in terms of positions, line widths, and even relative intensities. However, the action spectra exhibit residual and systematic redshifts of a few percent, which are partly due to the finite spectral bandwidth but are amplified by the progressive heating by the laser. A quantitative analysis suggests that these anharmonicity effects should generally arise upon multiple photon absorption. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Calvo F.,CNRS Laboratory of Ionic and Molecular Spectrometry | Douady J.,University of Caen Lower Normandy
Physical Chemistry Chemical Physics | Year: 2010

The structure and finite-temperature properties of hydrated nucleotide anion adenosine 5′-monophosphate (AMP) have been theoretically investigated with a variety of methods. Using a polarizable version of the Amber force field and replica-exchange molecular dynamics simulations, putative lowest-energy structures have been located for the AMP-(H 2O)n cluster anions with n = 0-20. The hydration energies obtained with the molecular mechanics potential slightly overestimate experimental measurements. However, closer values are found after reoptimizing the structures locally at more sophisticated levels, namely semi-empirical (PM6) and density-functional theory (B3LYP/6-31+G*). Upon heating the complexes, various indicators such as the heat capacity, number of hydrogen bonds or surface area provide evidence that the water cluster melts below 200 K but remains bonded to the AMP anion. The sequential loss of water molecules after sudden heating has been studied using a statistical approach in which unimolecular evaporation is described using the orbiting transition state version of phase space theory, together with anharmonic densities of vibrational states. The evaporation rates are calibrated based on the results of molecular dynamics trajectories at high internal energy. Our results indicate that between 4 and 10 water molecules are lost from AMP-(H2O) 20 after one second depending on the initial heating in the 250-350 K range, with a concomitant cooling of the remaining cluster by 75-150 K. © the Owner Societies. Source

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