Professeur des Universités, Sorbonne Université ENS – Département de chimie Email: rodolphe.vuilleumier@ens.psl.eu |
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Publications
2014 |
Structure, equation of state and transport properties of molten calcium carbonate (CaCO3) by atomistic simulations Article de journal R Vuilleumier; A P Seitsonen; N Sator; B Guillot Geochimica et Cosmochimica Acta, 141 , p. 547–566, 2014. @article{Vuilleumier:2014a, title = {Structure, equation of state and transport properties of molten calcium carbonate (CaCO3) by atomistic simulations}, author = {R Vuilleumier and A P Seitsonen and N Sator and B Guillot}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907303498&doi=10.1016%2fj.gca.2014.06.037&partnerID=40&md5=5879c45d615d720a6bf6e1fec39b9c28}, doi = {10.1016/j.gca.2014.06.037}, year = {2014}, date = {2014-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {141}, pages = {547--566}, abstract = {First-principle molecular dynamics (FPMD) calculations have been performed to evaluate the physical properties of liquid calcium carbonate (CaCO3), which are up to now poorly known. The liquid structure, the density, the atomic vibration motions, the diffusion coefficients of calcium and carbonate ions and the electrical conductivity have been evaluated. As compared with silicate melts, molten CaCO3 is characterized by a low density (textasciitilde2.25g/cm3 at 1623K and 0.5GPa), a viscosity almost as low as that of water (textasciitilde5mPas), and a high conductivity (textasciitilde200S/m). In using the FPMD calculations for benchmark, an empirical force field has been developed for predicting the properties of molten CaCO3 at any state point in the liquid stability field. This force field is implemented into a classical molecular dynamics (MD) code, much cheaper in computer time, and the equation of state and the phase diagram of the liquid phase have been obtained. The evolutions of the self diffusion coefficients, viscosity, and the electrical conductivity with pressure and temperature have been investigated and the results fitted with analytical forms. It is shown that the Stokes-Einstein equation, expressing the viscosity as a function of diffusion motion, is well followed, and that the Nernst-Einstein equation relating the electrical conductivity to the diffusion coefficients of charge carriers leads to an accurate prediction of the conductivity, provided that a constant correcting factor is applied. Consequently, viscosity and electrical conductivity of the liquid are found to be anticorrelated with each other and can be described by a simple law; λ=A/η0.9 (where A=1.905, λ is in S/m, and η in Pas). © 2014 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } First-principle molecular dynamics (FPMD) calculations have been performed to evaluate the physical properties of liquid calcium carbonate (CaCO3), which are up to now poorly known. The liquid structure, the density, the atomic vibration motions, the diffusion coefficients of calcium and carbonate ions and the electrical conductivity have been evaluated. As compared with silicate melts, molten CaCO3 is characterized by a low density (textasciitilde2.25g/cm3 at 1623K and 0.5GPa), a viscosity almost as low as that of water (textasciitilde5mPas), and a high conductivity (textasciitilde200S/m). In using the FPMD calculations for benchmark, an empirical force field has been developed for predicting the properties of molten CaCO3 at any state point in the liquid stability field. This force field is implemented into a classical molecular dynamics (MD) code, much cheaper in computer time, and the equation of state and the phase diagram of the liquid phase have been obtained. The evolutions of the self diffusion coefficients, viscosity, and the electrical conductivity with pressure and temperature have been investigated and the results fitted with analytical forms. It is shown that the Stokes-Einstein equation, expressing the viscosity as a function of diffusion motion, is well followed, and that the Nernst-Einstein equation relating the electrical conductivity to the diffusion coefficients of charge carriers leads to an accurate prediction of the conductivity, provided that a constant correcting factor is applied. Consequently, viscosity and electrical conductivity of the liquid are found to be anticorrelated with each other and can be described by a simple law; λ=A/η0.9 (where A=1.905, λ is in S/m, and η in Pas). © 2014 Elsevier Ltd. |
Hydration properties of lanthanoid(iii) carbonate complexes in liquid water determined by polarizable molecular dynamics simulations Article de journal F Martelli; Y Jeanvoine; T Vercouter; C Beuchat; R Vuilleumier; R Spezia Physical Chemistry Chemical Physics, 16 (8), p. 3693–3705, 2014. @article{Martelli:2014, title = {Hydration properties of lanthanoid(iii) carbonate complexes in liquid water determined by polarizable molecular dynamics simulations}, author = {F Martelli and Y Jeanvoine and T Vercouter and C Beuchat and R Vuilleumier and R Spezia}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893482714&doi=10.1039%2fc3cp54001d&partnerID=40&md5=b287fafcfeb0e7a75eaec6fd0b0955ea}, doi = {10.1039/c3cp54001d}, year = {2014}, date = {2014-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, number = {8}, pages = {3693--3705}, abstract = {In this work we have studied the structure and dynamics of complexes formed by three and four carbonates and a central lanthanoid(iii) ion in liquid water by means of polarizable molecular dynamics simulations. With this aim we have developed a force field employing an extrapolation procedure that was previously developed for lanthanoid(iii) aqua ions and then we have validated it against DFT-based data. In this way we were able to shed light on properties of the whole series, finding some similarities and differences across the series, and to help in interpreting experiments on those systems. We found that the bi-dentate tri-carbonate complexes are the most stable for all the atoms, but a variation of the number of water molecules in the first ion shell, and the associated exchange dynamics, is observed from lighter to heavier elements. On the other hand, for four-carbonate systems only one water molecule is observed in the first shell, with 10-20% probability, for La(iii) and Ce(iii), while for the rest of the series it seems impossible for a water molecule to enter the first ion shell in the presence of such an excess of carbonate ligands. Finally, the good performance of our extrapolation procedure, based on ionic radii, makes us confident in extending such approaches to study the structure and dynamics of other systems in solution containing Ln(iii) and An(iii) ions. This parametrization method results particularly useful since it does not need expensive quantum chemistry calculations for all the atoms in the series. © 2014 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work we have studied the structure and dynamics of complexes formed by three and four carbonates and a central lanthanoid(iii) ion in liquid water by means of polarizable molecular dynamics simulations. With this aim we have developed a force field employing an extrapolation procedure that was previously developed for lanthanoid(iii) aqua ions and then we have validated it against DFT-based data. In this way we were able to shed light on properties of the whole series, finding some similarities and differences across the series, and to help in interpreting experiments on those systems. We found that the bi-dentate tri-carbonate complexes are the most stable for all the atoms, but a variation of the number of water molecules in the first ion shell, and the associated exchange dynamics, is observed from lighter to heavier elements. On the other hand, for four-carbonate systems only one water molecule is observed in the first shell, with 10-20% probability, for La(iii) and Ce(iii), while for the rest of the series it seems impossible for a water molecule to enter the first ion shell in the presence of such an excess of carbonate ligands. Finally, the good performance of our extrapolation procedure, based on ionic radii, makes us confident in extending such approaches to study the structure and dynamics of other systems in solution containing Ln(iii) and An(iii) ions. This parametrization method results particularly useful since it does not need expensive quantum chemistry calculations for all the atoms in the series. © 2014 the Owner Societies. |
Computing thermal Wigner densities with the phase integration method Article de journal J Beutier; D Borgis; R Vuilleumier; S Bonella Journal of Chemical Physics, 141 (8), 2014. @article{Beutier:2014, title = {Computing thermal Wigner densities with the phase integration method}, author = {J Beutier and D Borgis and R Vuilleumier and S Bonella}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84906861065&doi=10.1063%2f1.4892597&partnerID=40&md5=bf34df35be093ca2ad2ab651f76c5e5b}, doi = {10.1063/1.4892597}, year = {2014}, date = {2014-01-01}, journal = {Journal of Chemical Physics}, volume = {141}, number = {8}, abstract = {We discuss how the Phase Integration Method (PIM), recently developed to compute symmetrized time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)], can be adapted to sampling/generating the thermal Wigner density, a key ingredient, for example, in many approximate schemes for simulating quantum time dependent properties. PIM combines a path integral representation of the density with a cumulant expansion to represent the Wigner function in a form calculable via existing Monte Carlo algorithms for sampling noisy probability densities. The method is able to capture highly non-classical effects such as correlation among the momenta and coordinates parts of the density, or correlations among the momenta themselves. By using alternatives to cumulants, it can also indicate the presence of negative parts of the Wigner density. Both properties are demonstrated by comparing PIM results to those of reference quantum calculations on a set of model problems. © 2014 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We discuss how the Phase Integration Method (PIM), recently developed to compute symmetrized time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)], can be adapted to sampling/generating the thermal Wigner density, a key ingredient, for example, in many approximate schemes for simulating quantum time dependent properties. PIM combines a path integral representation of the density with a cumulant expansion to represent the Wigner function in a form calculable via existing Monte Carlo algorithms for sampling noisy probability densities. The method is able to capture highly non-classical effects such as correlation among the momenta and coordinates parts of the density, or correlations among the momenta themselves. By using alternatives to cumulants, it can also indicate the presence of negative parts of the Wigner density. Both properties are demonstrated by comparing PIM results to those of reference quantum calculations on a set of model problems. © 2014 AIP Publishing LLC. |
Atomic partial charges in condensed phase from an exact sum rule for infrared absorption Article de journal R Vuilleumier Molecular Physics, 112 (9-10), p. 1457–1462, 2014. @article{Vuilleumier:2014, title = {Atomic partial charges in condensed phase from an exact sum rule for infrared absorption}, author = {R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901036308&doi=10.1080%2f00268976.2014.906671&partnerID=40&md5=10c371f6882d97a8a4d857bc712bf16b}, doi = {10.1080/00268976.2014.906671}, year = {2014}, date = {2014-01-01}, journal = {Molecular Physics}, volume = {112}, number = {9-10}, pages = {1457--1462}, abstract = {A general sum rule for infrared intensities provides a definition of effective partial charges which can be experimentally obtained using isotopic substitutions and is valid in both gas and condensed phases. Of particular interest is the case of molecular liquids. We have, therefore, determined the hydrogen partial charges in liquid methanol and liquid water from the available literature. The resulting charges are 0.63 e and 0.14 e for hydrogen atoms bounded to the methanol oxygen and carbon atoms, respectively, and 0.55 e for hydrogen atoms in liquid water. The effective partial charges in liquid water were also computed from density functional based ab initio molecular dynamics simulations and found in good agreement with experiment. © 2014 Taylor & Francis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A general sum rule for infrared intensities provides a definition of effective partial charges which can be experimentally obtained using isotopic substitutions and is valid in both gas and condensed phases. Of particular interest is the case of molecular liquids. We have, therefore, determined the hydrogen partial charges in liquid methanol and liquid water from the available literature. The resulting charges are 0.63 e and 0.14 e for hydrogen atoms bounded to the methanol oxygen and carbon atoms, respectively, and 0.55 e for hydrogen atoms in liquid water. The effective partial charges in liquid water were also computed from density functional based ab initio molecular dynamics simulations and found in good agreement with experiment. © 2014 Taylor & Francis. |
Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga) Article de journal V Haigis; Y Belkhodja; F -X Coudert; R Vuilleumier; A Boutin Journal of Chemical Physics, 141 (6), 2014. @article{Haigis:2014, title = {Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)}, author = {V Haigis and Y Belkhodja and F -X Coudert and R Vuilleumier and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84906216632&doi=10.1063%2f1.4891578&partnerID=40&md5=ec0fa9a19fe3fa728216508d915c19a2}, doi = {10.1063/1.4891578}, year = {2014}, date = {2014-01-01}, journal = {Journal of Chemical Physics}, volume = {141}, number = {6}, abstract = {Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material. © 2014 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material. © 2014 AIP Publishing LLC. |
Hydration properties of Cm(iii) and Th(iv) combining coordination free energy profiles with electronic structure analysis Article de journal R Spezia; Y Jeanvoine; C Beuchat; L Gagliardi; R Vuilleumier Physical Chemistry Chemical Physics, 16 (12), p. 5824–5832, 2014. @article{Spezia:2014, title = {Hydration properties of Cm(iii) and Th(iv) combining coordination free energy profiles with electronic structure analysis}, author = {R Spezia and Y Jeanvoine and C Beuchat and L Gagliardi and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84894814187&doi=10.1039%2fc3cp54958e&partnerID=40&md5=9f931dfe95b26380ffc6eececde7b6e9}, doi = {10.1039/c3cp54958e}, year = {2014}, date = {2014-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, number = {12}, pages = {5824--5832}, abstract = {The hydration structure of two actinoid ions of different charge, Cm(iii) and Th(iv), was investigated. Density Functional Theory, DFT-based molecular dynamics and the single sweep method were used to obtain free energy landscapes of ion-water coordination. Free energy curves as a function of the ion-water coordination number were obtained for both ions. The number of water molecules in the first coordination shell of Cm(iii) varies between 8 and 10. For Th(iv), on the other hand, the 9-fold structure is stable and only the 10-fold structure seems to be accessible with a small but non-negligible free energy barrier. Finally, by combining molecular dynamics simulations with electronic structure calculations, we showed that the differences between Cm(iii) and Th(iv) are mainly due to electrostatic effects. Cm(iii) is less charged and it has fewer water molecules in its first shell, while Th(iv) has more water molecules because of a stronger electrostatic interaction. © 2014 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hydration structure of two actinoid ions of different charge, Cm(iii) and Th(iv), was investigated. Density Functional Theory, DFT-based molecular dynamics and the single sweep method were used to obtain free energy landscapes of ion-water coordination. Free energy curves as a function of the ion-water coordination number were obtained for both ions. The number of water molecules in the first coordination shell of Cm(iii) varies between 8 and 10. For Th(iv), on the other hand, the 9-fold structure is stable and only the 10-fold structure seems to be accessible with a small but non-negligible free energy barrier. Finally, by combining molecular dynamics simulations with electronic structure calculations, we showed that the differences between Cm(iii) and Th(iv) are mainly due to electrostatic effects. Cm(iii) is less charged and it has fewer water molecules in its first shell, while Th(iv) has more water molecules because of a stronger electrostatic interaction. © 2014 the Owner Societies. |
Equilibrium fractionation of Ħ and O isotopes in water from path integral molecular dynamics Article de journal C Pinilla; M Blanchard; E Balan; G Ferlat; R Vuilleumier; F Mauri Geochimica et Cosmochimica Acta, 135 , p. 203–216, 2014. @article{Pinilla:2014, title = {Equilibrium fractionation of {H} and O isotopes in water from path integral molecular dynamics}, author = {C Pinilla and M Blanchard and E Balan and G Ferlat and R Vuilleumier and F Mauri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899125383&doi=10.1016%2fj.gca.2014.03.027&partnerID=40&md5=5b7714eaa316b308f726da24136c6a87}, doi = {10.1016/j.gca.2014.03.027}, year = {2014}, date = {2014-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {135}, pages = {203--216}, abstract = {The equilibrium fractionation factor between two phases is of importance for the understanding of many planetary and environmental processes. Although thermodynamic equilibrium can be achieved between minerals at high temperature, many natural processes involve reactions between liquids or aqueous solutions and solids. For crystals, the fractionation factor α can be theoretically determined using a statistical thermodynamic approach based on the vibrational properties of the phases. These calculations are mostly performed in the harmonic approximation, using empirical or ab-initio force fields. In the case of aperiodic and dynamic systems such as liquids or solutions, similar calculations can be done using finite-size molecular clusters or snapshots obtained from molecular dynamics (MD) runs. It is however difficult to assess the effect of these approximate models on the isotopic fractionation properties. In this work we present a systematic study of the calculation of the D/H and 18O/16O equilibrium fractionation factors in water for the liquid/vapour and ice/vapour phases using several levels of theory within the simulations. Namely, we use a thermodynamic integration approach based on Path Integral MD calculations (PIMD) and an empirical potential model of water. Compared with standard MD, PIMD takes into account quantum effects in the thermodynamic modeling of systems and the exact fractionation factor for a given potential can be obtained. We compare these exact results with those of modeling strategies usually used, which involve the mapping of the quantum system on its harmonic counterpart. The results show the importance of including configurational disorder for the estimation of isotope fractionation in liquid phases. In addition, the convergence of the fractionation factor as a function of parameters such as the size of the simulated system and multiple isotope substitution is analyzed, showing that isotope fractionation is essentially a local effect in the investigated system. © 2014 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The equilibrium fractionation factor between two phases is of importance for the understanding of many planetary and environmental processes. Although thermodynamic equilibrium can be achieved between minerals at high temperature, many natural processes involve reactions between liquids or aqueous solutions and solids. For crystals, the fractionation factor α can be theoretically determined using a statistical thermodynamic approach based on the vibrational properties of the phases. These calculations are mostly performed in the harmonic approximation, using empirical or ab-initio force fields. In the case of aperiodic and dynamic systems such as liquids or solutions, similar calculations can be done using finite-size molecular clusters or snapshots obtained from molecular dynamics (MD) runs. It is however difficult to assess the effect of these approximate models on the isotopic fractionation properties. In this work we present a systematic study of the calculation of the D/H and 18O/16O equilibrium fractionation factors in water for the liquid/vapour and ice/vapour phases using several levels of theory within the simulations. Namely, we use a thermodynamic integration approach based on Path Integral MD calculations (PIMD) and an empirical potential model of water. Compared with standard MD, PIMD takes into account quantum effects in the thermodynamic modeling of systems and the exact fractionation factor for a given potential can be obtained. We compare these exact results with those of modeling strategies usually used, which involve the mapping of the quantum system on its harmonic counterpart. The results show the importance of including configurational disorder for the estimation of isotope fractionation in liquid phases. In addition, the convergence of the fractionation factor as a function of parameters such as the size of the simulated system and multiple isotope substitution is analyzed, showing that isotope fractionation is essentially a local effect in the investigated system. © 2014 Elsevier Ltd. |
Fermi resonance as a tool for probing peridinin environment Article de journal E Kish; M M Mendes Pinto; D Bovi; M Basire; L Guidoni; R Vuilleumier; B Robert; R Spezia; A Mezzetti Journal of Physical Chemistry B, 118 (22), p. 5873–5881, 2014. @article{Kish:2014, title = {Fermi resonance as a tool for probing peridinin environment}, author = {E Kish and M M Mendes Pinto and D Bovi and M Basire and L Guidoni and R Vuilleumier and B Robert and R Spezia and A Mezzetti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84902007714&doi=10.1021%2fjp501667t&partnerID=40&md5=f6835e96d679936ace1c6bd8be622fa7}, doi = {10.1021/jp501667t}, year = {2014}, date = {2014-01-01}, journal = {Journal of Physical Chemistry B}, volume = {118}, number = {22}, pages = {5873--5881}, abstract = {In the present paper, we provide an extended study of the vibrational signature of a butenolide carotenoid, peridinin, in various solvents by combining resonance Raman spectroscopy (RRS) with theoretical calculations. The presence of a Fermi resonance due to coupling between the lactonic C-O stretching and the overtone of the wagging of the C-H in the lactonic ring provides a spectroscopic way of differentiating between peridinins lying in different environments. This is a significant achievement, given that simultaneous presence of several peridinins (each with a peculiar photophysical role) in different environments occurs in the most important peridinin containing proteins, the peridinin-chlorophyll proteins (PCPs) and the Chl a-c2-peridinin binding proteins. In RRS, small modifications of solvent polarity can give rise to large differences in the intensity and splitting between the two bands, resulting from the Fermi resonance. By changing the polarity, we can tune the frequency of stretching of the C-O and, while the C-H wagging frequency is almost always constant in different solvents, move the system from a perfect resonance condition to off-resonance ones. We have corroborated our spectroscopic findings with a quasi-classical dynamical model of two coupled oscillators, and DFT calculations on peridinin in different solvents; we have also used calculations to complete the peridinin vibrational mode assignments in the 800-1600 cm-1 region of RRS spectra, corresponding to polyene chain motion. Finally, the presence of Fermi resonance has been used to reinterpret previous vibrational spectroscopic experiments in PCPs. © 2014 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In the present paper, we provide an extended study of the vibrational signature of a butenolide carotenoid, peridinin, in various solvents by combining resonance Raman spectroscopy (RRS) with theoretical calculations. The presence of a Fermi resonance due to coupling between the lactonic C-O stretching and the overtone of the wagging of the C-H in the lactonic ring provides a spectroscopic way of differentiating between peridinins lying in different environments. This is a significant achievement, given that simultaneous presence of several peridinins (each with a peculiar photophysical role) in different environments occurs in the most important peridinin containing proteins, the peridinin-chlorophyll proteins (PCPs) and the Chl a-c2-peridinin binding proteins. In RRS, small modifications of solvent polarity can give rise to large differences in the intensity and splitting between the two bands, resulting from the Fermi resonance. By changing the polarity, we can tune the frequency of stretching of the C-O and, while the C-H wagging frequency is almost always constant in different solvents, move the system from a perfect resonance condition to off-resonance ones. We have corroborated our spectroscopic findings with a quasi-classical dynamical model of two coupled oscillators, and DFT calculations on peridinin in different solvents; we have also used calculations to complete the peridinin vibrational mode assignments in the 800-1600 cm-1 region of RRS spectra, corresponding to polyene chain motion. Finally, the presence of Fermi resonance has been used to reinterpret previous vibrational spectroscopic experiments in PCPs. © 2014 American Chemical Society. |
Gas phase infrared spectra via the phase integration quasi-classical method Article de journal J Beutier; M Monteferrante; S Bonella; R Vuilleumier; G Ciccotti Molecular Simulation, 40 (1-3), p. 196–207, 2014. @article{Beutier:2014a, title = {Gas phase infrared spectra via the phase integration quasi-classical method}, author = {J Beutier and M Monteferrante and S Bonella and R Vuilleumier and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896776836&doi=10.1080%2f08927022.2013.843776&partnerID=40&md5=ca73d39f6f6c0fa93f7ff85167b8db16}, doi = {10.1080/08927022.2013.843776}, year = {2014}, date = {2014-01-01}, journal = {Molecular Simulation}, volume = {40}, number = {1-3}, pages = {196--207}, abstract = {We apply the recently developed phase integration method (PIM) (Monteferrante et al. Mol Phys. 2011;109:3015-3027) to the calculation of infrared spectra of gas phase molecules. The PIM combines a generalised Monte Carlo sampling of the exact thermal density of the system with classical molecular dynamics to obtain approximate time quantum correlation functions. To describe the molecules, we adopt very simple analytical potentials that have, however, proved interesting, and surprisingly challenging, benchmarks for approximate quantum dynamical schemes. We show that, in contrast with two other commonly applied methods, our spectra do not exhibit spurious features or unphysical shifts depending on the temperature. Identifying the positions of the peaks requires only a few tens of trajectories, while an accurate evaluation of the relative intensities of the peaks is computationally more demanding. © 2014 © 2013 Taylor & Francis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We apply the recently developed phase integration method (PIM) (Monteferrante et al. Mol Phys. 2011;109:3015-3027) to the calculation of infrared spectra of gas phase molecules. The PIM combines a generalised Monte Carlo sampling of the exact thermal density of the system with classical molecular dynamics to obtain approximate time quantum correlation functions. To describe the molecules, we adopt very simple analytical potentials that have, however, proved interesting, and surprisingly challenging, benchmarks for approximate quantum dynamical schemes. We show that, in contrast with two other commonly applied methods, our spectra do not exhibit spurious features or unphysical shifts depending on the temperature. Identifying the positions of the peaks requires only a few tens of trajectories, while an accurate evaluation of the relative intensities of the peaks is computationally more demanding. © 2014 © 2013 Taylor & Francis. |
2013 |
Ultrafast damage following radiation-induced oxidation of uracil in aqueous solution Article de journal P López-Tarifa; M -P Gaigeot; R Vuilleumier; I Tavernelli; M Alcamí; F Martín; M -A Hervé Du Penhoat; M -F Politis Angewandte Chemie - International Edition, 52 (11), p. 3160–3163, 2013. @article{Lopez-Tarifa:2013, title = {Ultrafast damage following radiation-induced oxidation of uracil in aqueous solution}, author = {P L\'{o}pez-Tarifa and M -P Gaigeot and R Vuilleumier and I Tavernelli and M Alcam\'{i} and F Mart\'{i}n and M -A Herv\'{e} Du Penhoat and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84874859008&doi=10.1002%2fanie.201208038&partnerID=40&md5=bedfc7e60e8054d2da8d6fb0849b4458}, doi = {10.1002/anie.201208038}, year = {2013}, date = {2013-01-01}, journal = {Angewandte Chemie - International Edition}, volume = {52}, number = {11}, pages = {3160--3163}, abstract = {Coulombic explosion of uracil: Ionizing radiation is used in cancer therapy to induce molecular damage in cells. Ab initio molecular dynamics were used to probe the early dissociation processes and ensuing chemical reactions following selective ionization of either uracil or the surrounding water molecules (see scheme; C gray, N blue, O red, H white). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Coulombic explosion of uracil: Ionizing radiation is used in cancer therapy to induce molecular damage in cells. Ab initio molecular dynamics were used to probe the early dissociation processes and ensuing chemical reactions following selective ionization of either uracil or the surrounding water molecules (see scheme; C gray, N blue, O red, H white). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Investigation of structure and dynamics of the hydrated metal-organic framework MIL-53(Cr) using first-principles molecular dynamics Article de journal V Haigis; F -X Coudert; R Vuilleumier; A Boutin Physical Chemistry Chemical Physics, 15 (43), p. 19049–19056, 2013. @article{Haigis:2013, title = {Investigation of structure and dynamics of the hydrated metal-organic framework MIL-53(Cr) using first-principles molecular dynamics}, author = {V Haigis and F -X Coudert and R Vuilleumier and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84886894083&doi=10.1039%2fc3cp53126k&partnerID=40&md5=71f35bfbf47a044dc1b725bc8d6d6493}, doi = {10.1039/c3cp53126k}, year = {2013}, date = {2013-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {15}, number = {43}, pages = {19049--19056}, abstract = {The hydration behavior of metal-organic frameworks (MOFs) is of interest both from a practical and from a fundamental point of view: it is linked, on the one hand, to the hydrothermal stability (or instability) of the nanoporous material, which might limit its use in technological applications. On the other hand, it sheds light on the behavior of water in a strongly confined environment. Here, we use first-principles molecular dynamics (MD) to investigate two hydrated phases of the flexible MOF MIL-53(Cr), which adopts a narrow- or a large-pore form, depending on the water loading. Structure and dynamics of the two phases are thoroughly analyzed and compared, with a focus on the hydroxyl group of MIL-53(Cr) and the water molecules in the nanopores. Furthermore, the behavior of the confined water is compared to that of bulk water. Whereas in the narrow-pore form, water is adsorbed at specific crystalline sites, it shows a more disordered, bulk-like structure in the large-pore form. However, reorientation dynamics of water molecules in the latter is considerably slowed down with respect to bulk water, which highlights the confinement effect of the nanoporous framework. © 2013 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hydration behavior of metal-organic frameworks (MOFs) is of interest both from a practical and from a fundamental point of view: it is linked, on the one hand, to the hydrothermal stability (or instability) of the nanoporous material, which might limit its use in technological applications. On the other hand, it sheds light on the behavior of water in a strongly confined environment. Here, we use first-principles molecular dynamics (MD) to investigate two hydrated phases of the flexible MOF MIL-53(Cr), which adopts a narrow- or a large-pore form, depending on the water loading. Structure and dynamics of the two phases are thoroughly analyzed and compared, with a focus on the hydroxyl group of MIL-53(Cr) and the water molecules in the nanopores. Furthermore, the behavior of the confined water is compared to that of bulk water. Whereas in the narrow-pore form, water is adsorbed at specific crystalline sites, it shows a more disordered, bulk-like structure in the large-pore form. However, reorientation dynamics of water molecules in the latter is considerably slowed down with respect to bulk water, which highlights the confinement effect of the nanoporous framework. © 2013 the Owner Societies. |
Unexpected remote effect in red fluorescent sensors based on extended APTRA Article de journal M Collot; A Lasoroski; A I Zamaleeva; A Feltz; R Vuilleumier; J -M Mallet Tetrahedron, 69 (48), p. 10482–10487, 2013. @article{Collot:2013, title = {Unexpected remote effect in red fluorescent sensors based on extended APTRA}, author = {M Collot and A Lasoroski and A I Zamaleeva and A Feltz and R Vuilleumier and J -M Mallet}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84887051380&doi=10.1016%2fj.tet.2013.09.073&partnerID=40&md5=35d1266782ecad0b5d18db7baa238dc6}, doi = {10.1016/j.tet.2013.09.073}, year = {2013}, date = {2013-01-01}, journal = {Tetrahedron}, volume = {69}, number = {48}, pages = {10482--10487}, abstract = {Herein is described the synthesis and spectroscopic characterizations of three new OFF-ON red-emitting and water-soluble sensors, CAXR (Clicked APTRA X-Rhodamine). These dyes are based on an extended APTRA (aminophenol triacetic acid) motif. Three different side chains were added by click chemistry in order to complete the coordination sphere with a chelate moiety composed of a triazolyl and an iminol. The fluorescent response (F/F0) of these probes follows the order: Cd2+>Zn2+>Pb 2+>Hg2+. An important and unexpected effect of the side chain structure on the Kd was observed (up to one order of magnitude, Cadmium Kd from 252 to 21 μM). This remote effect of the side chains was studied by DFT calculations and was attributed to a twisted conformation of the CAXR-Py:Cd2+ complex. © 2013 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Herein is described the synthesis and spectroscopic characterizations of three new OFF-ON red-emitting and water-soluble sensors, CAXR (Clicked APTRA X-Rhodamine). These dyes are based on an extended APTRA (aminophenol triacetic acid) motif. Three different side chains were added by click chemistry in order to complete the coordination sphere with a chelate moiety composed of a triazolyl and an iminol. The fluorescent response (F/F0) of these probes follows the order: Cd2+>Zn2+>Pb 2+>Hg2+. An important and unexpected effect of the side chain structure on the Kd was observed (up to one order of magnitude, Cadmium Kd from 252 to 21 μM). This remote effect of the side chains was studied by DFT calculations and was attributed to a twisted conformation of the CAXR-Py:Cd2+ complex. © 2013 Elsevier Ltd. All rights reserved. |
Lanthanoids(III) and actinoids(III) in water: Diffusion coefficients and hydration enthalpies from polarizable molecular dynamics simulations Article de journal F Martelli; S Abadie; J -P Simonin; R Vuilleumier; R Spezia Pure and Applied Chemistry, 85 (1), p. 237–246, 2013. @article{Martelli:2013, title = {Lanthanoids(III) and actinoids(III) in water: Diffusion coefficients and hydration enthalpies from polarizable molecular dynamics simulations}, author = {F Martelli and S Abadie and J -P Simonin and R Vuilleumier and R Spezia}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868338776&doi=10.1351%2fPAC-CON-12-02-08&partnerID=40&md5=154c470024922d4aea57b876dfc920a2}, doi = {10.1351/PAC-CON-12-02-08}, year = {2013}, date = {2013-01-01}, journal = {Pure and Applied Chemistry}, volume = {85}, number = {1}, pages = {237--246}, abstract = {By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion-water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes' diffusive regime. © 2012 IUPAC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion-water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes' diffusive regime. © 2012 IUPAC. |
Hyperfine interactions in a gadolinium-based MRI contrast agent: High-frequency modulations from ab initio simulations Article de journal A Lasoroski; R Vuilleumier; R Pollet Journal of Chemical Physics, 139 (10), 2013. @article{Lasoroski:2013, title = {Hyperfine interactions in a gadolinium-based MRI contrast agent: High-frequency modulations from ab initio simulations}, author = {A Lasoroski and R Vuilleumier and R Pollet}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884858818&doi=10.1063%2f1.4820791&partnerID=40&md5=0a31ef86ddbea75be46daec14c58c2c7}, doi = {10.1063/1.4820791}, year = {2013}, date = {2013-01-01}, journal = {Journal of Chemical Physics}, volume = {139}, number = {10}, abstract = {Hyperfine coupling tensors of the water molecule coordinated to the Prohance contrast agent in liquid water were calculated within and beyond the point dipole approximation along an ab initio molecular dynamics trajectory. We observe the non-equivalence at short time scales on structural as well as magnetodynamical properties of inner sphere water protons due to hydrogen bonds formation with the solvent. In addition, the influence of ultrafast internal motions on the anisotropic, dipolar, contribution to hyperfine couplings was probed thanks to a decomposition of its fluctuations in terms of a small set of meaningful collective variables. © 2013 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperfine coupling tensors of the water molecule coordinated to the Prohance contrast agent in liquid water were calculated within and beyond the point dipole approximation along an ab initio molecular dynamics trajectory. We observe the non-equivalence at short time scales on structural as well as magnetodynamical properties of inner sphere water protons due to hydrogen bonds formation with the solvent. In addition, the influence of ultrafast internal motions on the anisotropic, dipolar, contribution to hyperfine couplings was probed thanks to a decomposition of its fluctuations in terms of a small set of meaningful collective variables. © 2013 AIP Publishing LLC. |
Silver in geological fluids from in situ X-ray absorption spectroscopy and first-principles molecular dynamics Article de journal G S Pokrovski; J Roux; G Ferlat; R Jonchiere; A P Seitsonen; R Vuilleumier; J -L Hazemann Geochimica et Cosmochimica Acta, 106 , p. 501–523, 2013. @article{Pokrovski:2013, title = {Silver in geological fluids from in situ X-ray absorption spectroscopy and first-principles molecular dynamics}, author = {G S Pokrovski and J Roux and G Ferlat and R Jonchiere and A P Seitsonen and R Vuilleumier and J -L Hazemann}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84874387159&doi=10.1016%2fj.gca.2012.12.012&partnerID=40&md5=1f9f2a803226461263fbdf022ce7e89e}, doi = {10.1016/j.gca.2012.12.012}, year = {2013}, date = {2013-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {106}, pages = {501--523}, abstract = {The molecular structure and stability of species formed by silver in aqueous saline solutions typical of hydrothermal settings were quantified using in situ X-ray absorption spectroscopy (XAS) measurements, quantum-chemical modeling of near-edge absorption spectra (XANES) and extended fine structure spectra (EXAFS), and first-principles molecular dynamics (FPMD). Results show that in nitrate-bearing acidic solutions to at least 200°C, silver speciation is dominated by the hydrated Ag+ cation surrounded by 4-6 water molecules in its nearest coordination shell with mean Ag-O distances of 2.32±0.02r{a}. In NaCl-bearing acidic aqueous solutions of total Cl concentration from 0.7 to 5.9mol/kg H2O (m) at temperatures from 200 to 450°C and pressures to 750bar, the dominant species are the di-chloride complex AgCl2 - with Ag-Cl distances of 2.40±0.02r{a} and Cl-Ag-Cl angle of 160±10°, and the tri-chloride complex AgCl3 2- of a triangular structure and mean Ag-Cl distances of 2.60±0.05r{a}. With increasing temperature, the contribution of the tri-chloride species decreases from ∼50% of total dissolved Ag in the most concentrated solution (5.9m Cl) at 200°C to less than 10-20% at supercritical temperatures for all investigated solutions, so that AgCl2 - becomes by far the dominant Ag-bearing species at conditions typical of hydrothermal-magmatic fluids. Both di- and tri-chloride species exhibit outer-sphere interactions with the solvent as shown by the detection, using FPMD modeling, of H2O, Cl-, and Na+ at distances of 3-4r{a} from the silver atom. The species fractions derived from XAS and FPMD analyses, and total AgCl(s) solubilities, measured in situ in this work from the absorption edge height of XAS spectra, are in accord with thermodynamic predictions using the stability constants of AgCl2 - and AgCl3 2- from Akinfiev and Zotov (2001) and Zotov et al. (1995), respectively, which are based on extensive previous AgCl(s) solubility measurements. These data are thus recommended for chemical equilibrium calculations in mineral-fluid systems above 200°C. In contrast, our data disagree with SUPCRT-based datasets for Ag-Cl species, which predict large fractions of high-order chloride species, AgCl3 2- and AgCl4 3- in high-temperature saline fluids. Comparisons of the structural and stability data of Ag-Cl species derived in this study with those of their Au and Cu analogs suggest that molecular-level differences amongst the chloride complexes such as geometry, dipole moment, distances, and resulting outer-sphere interactions with the solvent may account, at least partly, for the observed partitioning of Au, Ag and Cu in vapor-brine and fluid-melt systems. In hydrothermal environments dominated by fluid-rock interactions, the contrasting affinity of these metals for sulfur ligands and the differences both in chemistry and stability of their main solid phases (Ag sulfides, Cu-Fe sulfides, and native Au) largely control the concentration and distribution of these metals in their economic deposits. © 2012 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The molecular structure and stability of species formed by silver in aqueous saline solutions typical of hydrothermal settings were quantified using in situ X-ray absorption spectroscopy (XAS) measurements, quantum-chemical modeling of near-edge absorption spectra (XANES) and extended fine structure spectra (EXAFS), and first-principles molecular dynamics (FPMD). Results show that in nitrate-bearing acidic solutions to at least 200°C, silver speciation is dominated by the hydrated Ag+ cation surrounded by 4-6 water molecules in its nearest coordination shell with mean Ag-O distances of 2.32±0.02å. In NaCl-bearing acidic aqueous solutions of total Cl concentration from 0.7 to 5.9mol/kg H2O (m) at temperatures from 200 to 450°C and pressures to 750bar, the dominant species are the di-chloride complex AgCl2 - with Ag-Cl distances of 2.40±0.02å and Cl-Ag-Cl angle of 160±10°, and the tri-chloride complex AgCl3 2- of a triangular structure and mean Ag-Cl distances of 2.60±0.05å. With increasing temperature, the contribution of the tri-chloride species decreases from ∼50% of total dissolved Ag in the most concentrated solution (5.9m Cl) at 200°C to less than 10-20% at supercritical temperatures for all investigated solutions, so that AgCl2 - becomes by far the dominant Ag-bearing species at conditions typical of hydrothermal-magmatic fluids. Both di- and tri-chloride species exhibit outer-sphere interactions with the solvent as shown by the detection, using FPMD modeling, of H2O, Cl-, and Na+ at distances of 3-4å from the silver atom. The species fractions derived from XAS and FPMD analyses, and total AgCl(s) solubilities, measured in situ in this work from the absorption edge height of XAS spectra, are in accord with thermodynamic predictions using the stability constants of AgCl2 - and AgCl3 2- from Akinfiev and Zotov (2001) and Zotov et al. (1995), respectively, which are based on extensive previous AgCl(s) solubility measurements. These data are thus recommended for chemical equilibrium calculations in mineral-fluid systems above 200°C. In contrast, our data disagree with SUPCRT-based datasets for Ag-Cl species, which predict large fractions of high-order chloride species, AgCl3 2- and AgCl4 3- in high-temperature saline fluids. Comparisons of the structural and stability data of Ag-Cl species derived in this study with those of their Au and Cu analogs suggest that molecular-level differences amongst the chloride complexes such as geometry, dipole moment, distances, and resulting outer-sphere interactions with the solvent may account, at least partly, for the observed partitioning of Au, Ag and Cu in vapor-brine and fluid-melt systems. In hydrothermal environments dominated by fluid-rock interactions, the contrasting affinity of these metals for sulfur ligands and the differences both in chemistry and stability of their main solid phases (Ag sulfides, Cu-Fe sulfides, and native Au) largely control the concentration and distribution of these metals in their economic deposits. © 2012 Elsevier Ltd. All rights reserved. |
2012 |
A transferable ab initio based force field for aqueous ions Article de journal S Tazi; J J Molina; B Rotenberg; P Turq; R Vuilleumier; M Salanne Journal of Chemical Physics, 136 (11), 2012. @article{Tazi:2012, title = {A transferable ab initio based force field for aqueous ions}, author = {S Tazi and J J Molina and B Rotenberg and P Turq and R Vuilleumier and M Salanne}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859229699&doi=10.1063%2f1.3692965&partnerID=40&md5=78759145150d71d642fedd2eec6f1109}, doi = {10.1063/1.3692965}, year = {2012}, date = {2012-01-01}, journal = {Journal of Chemical Physics}, volume = {136}, number = {11}, abstract = {We present a new polarizable force field for aqueous ions (Li +, Na +, K +, Rb +, Cs +, Mg 2+, Ca 2+, Sr 2+, and Cl -) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions. © 2012 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present a new polarizable force field for aqueous ions (Li +, Na +, K +, Rb +, Cs +, Mg 2+, Ca 2+, Sr 2+, and Cl -) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions. © 2012 American Institute of Physics. |
Varying the charge of small cations in liquid water: Structural, transport, and thermodynamical properties Article de journal F Martelli; R Vuilleumier; J -P Simonin; R Spezia Journal of Chemical Physics, 137 (16), 2012. @article{Martelli:2012, title = {Varying the charge of small cations in liquid water: Structural, transport, and thermodynamical properties}, author = {F Martelli and R Vuilleumier and J -P Simonin and R Spezia}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868352721&doi=10.1063%2f1.4758452&partnerID=40&md5=fdaa90e6cde2296804f4404a3d74c10b}, doi = {10.1063/1.4758452}, year = {2012}, date = {2012-01-01}, journal = {Journal of Chemical Physics}, volume = {137}, number = {16}, abstract = {In this work, we show how increasing the charge of small cations affects the structural, thermodynamical, and dynamical properties of these ions in liquid water. We have studied the case of lanthanoid and actinoid ions, for which we have recently developed accurate polarizable force fields, and the ionic radius is in the 0.995-1.250 r{A} range, and explored the valency range from 0 to 4. We found that the ion charge strongly structures the neighboring water molecules and that, in this range of charges, the hydration enthalpies exhibit a quadratic dependence with respect to the charge, in line with the Born model. The diffusion process follows two main regimes: a hydrodynamical regime for neutral or low charges, and a dielectric friction regime for high charges in which the contraction of the ionic radius along the series of elements causes a decrease of the diffusion coefficient. This latter behavior can be qualitatively described by theoretical models, such as the Zwanzig and the solvated ion models. However, these models need be modified in order to obtain agreement with the observed behavior in the full charge range. We have thus modified the solvated ion model by introducing a dependence of the bare ion radius as a function of the ionic charge. Besides agreement between theory and simulation this modification allows one to obtain an empirical unified model. Thus, by analyzing the contributions to the drag coefficient from the viscous and the dielectric terms, we are able to explain the transition from a regime in which the effect of viscosity dominates to one in which dielectric friction governs the motion of ions with radii of ca. 1 r{A}. © 2012 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, we show how increasing the charge of small cations affects the structural, thermodynamical, and dynamical properties of these ions in liquid water. We have studied the case of lanthanoid and actinoid ions, for which we have recently developed accurate polarizable force fields, and the ionic radius is in the 0.995-1.250 Å range, and explored the valency range from 0 to 4. We found that the ion charge strongly structures the neighboring water molecules and that, in this range of charges, the hydration enthalpies exhibit a quadratic dependence with respect to the charge, in line with the Born model. The diffusion process follows two main regimes: a hydrodynamical regime for neutral or low charges, and a dielectric friction regime for high charges in which the contraction of the ionic radius along the series of elements causes a decrease of the diffusion coefficient. This latter behavior can be qualitatively described by theoretical models, such as the Zwanzig and the solvated ion models. However, these models need be modified in order to obtain agreement with the observed behavior in the full charge range. We have thus modified the solvated ion model by introducing a dependence of the bare ion radius as a function of the ionic charge. Besides agreement between theory and simulation this modification allows one to obtain an empirical unified model. Thus, by analyzing the contributions to the drag coefficient from the viscous and the dielectric terms, we are able to explain the transition from a regime in which the effect of viscosity dominates to one in which dielectric friction governs the motion of ions with radii of ca. 1 Å. © 2012 American Institute of Physics. |
Solvation of complex surfaces via molecular density functional theory Article de journal M Levesque; V Marry; B Rotenberg; G Jeanmairet; R Vuilleumier; D Borgis Journal of Chemical Physics, 137 (22), 2012. @article{Levesque:2012b, title = {Solvation of complex surfaces via molecular density functional theory}, author = {M Levesque and V Marry and B Rotenberg and G Jeanmairet and R Vuilleumier and D Borgis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84871237464&doi=10.1063%2f1.4769729&partnerID=40&md5=41e0fb3772e70490453246c792a62611}, doi = {10.1063/1.4769729}, year = {2012}, date = {2012-01-01}, journal = {Journal of Chemical Physics}, volume = {137}, number = {22}, abstract = {We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development. © 2012 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development. © 2012 American Institute of Physics. |
Scalar fundamental measure theory for hard spheres in three dimensions: Application to hydrophobic solvation Article de journal M Levesque; R Vuilleumier; D Borgis Journal of Chemical Physics, 137 (3), 2012. @article{Levesque:2012a, title = {Scalar fundamental measure theory for hard spheres in three dimensions: Application to hydrophobic solvation}, author = {M Levesque and R Vuilleumier and D Borgis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864238670&doi=10.1063%2f1.4734009&partnerID=40&md5=006610a0b4ebed33d3b422d407d53e0d}, doi = {10.1063/1.4734009}, year = {2012}, date = {2012-01-01}, journal = {Journal of Chemical Physics}, volume = {137}, number = {3}, abstract = {Hard-sphere mixtures provide one a solvable reference system that can be used to improve the density functional theory of realistic molecular fluids. We show how the Kierlik-Rosinbergs scalar version of the fundamental measure density functional theory of hard spheres [E. Kierlik and M. L. Rosinberg, Phys. Rev. A 42, 3382 (1990)10.1103/PhysRevA.42.3382], which presents computational advantages with respect to the original Rosenfelds vectorial formulation or its extensions, can be implemented and minimized in three dimensions to describe fluid mixtures in complex environments. This implementation is used as a basis for defining a molecular density functional theory of water around molecular hydrophobic solutes of arbitrary shape. © 2012 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hard-sphere mixtures provide one a solvable reference system that can be used to improve the density functional theory of realistic molecular fluids. We show how the Kierlik-Rosinbergs scalar version of the fundamental measure density functional theory of hard spheres [E. Kierlik and M. L. Rosinberg, Phys. Rev. A 42, 3382 (1990)10.1103/PhysRevA.42.3382], which presents computational advantages with respect to the original Rosenfelds vectorial formulation or its extensions, can be implemented and minimized in three dimensions to describe fluid mixtures in complex environments. This implementation is used as a basis for defining a molecular density functional theory of water around molecular hydrophobic solutes of arbitrary shape. © 2012 American Institute of Physics. |
Unravelling the hydration structure of ThX4 (X = Br, Cl) water solutions by molecular dynamics simulations and X-ray absorption spectroscopy Article de journal R Spezia; C Beuchat; R Vuilleumier; P D'Angelo; L Gagliardi Journal of Physical Chemistry B, 116 (22), p. 6465–6475, 2012. @article{Spezia:2012, title = {Unravelling the hydration structure of ThX4 (X = Br, Cl) water solutions by molecular dynamics simulations and X-ray absorption spectroscopy}, author = {R Spezia and C Beuchat and R Vuilleumier and P D'Angelo and L Gagliardi}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84861849952&doi=10.1021%2fjp210350b&partnerID=40&md5=b1fd27ee5bda0e5ebf7bb68c138acb85}, doi = {10.1021/jp210350b}, year = {2012}, date = {2012-01-01}, journal = {Journal of Physical Chemistry B}, volume = {116}, number = {22}, pages = {6465--6475}, abstract = {The hydration of Th(IV) in ThCl4 and ThBr4 water solutions at different salt concentrations was studied in order to understand the structure of Th(IV) in liquid water and the effect of Br- and Cl- anions on its hydration structure. Several theoretical methods were employed: density functional theory and classical molecular dynamics based on both semiempirical polarizable potentials and ab initio derived polarizable potentials. The results of the computations were combined with extended X-ray absorption fine structure (EXAFS) experimental data. The results of this study show that in pure water the Th-O distance of 2.45 r{A} corresponds to a first shell coordination number between 9 and 10. In the salt solutions, while Br- does not affect directly the hydration of Th(IV) also at relatively high concentrations, Cl-, on the other hand, is more structured around Th(IV), in agreement with recent high-energy X-ray scattering experiments. Counterions, even at relatively high concentrations (0.8 m), do not enter in the first solvation shell of Th(IV), but they induce an increase of water molecules in the first and second hydration shells of Th(IV). © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hydration of Th(IV) in ThCl4 and ThBr4 water solutions at different salt concentrations was studied in order to understand the structure of Th(IV) in liquid water and the effect of Br- and Cl- anions on its hydration structure. Several theoretical methods were employed: density functional theory and classical molecular dynamics based on both semiempirical polarizable potentials and ab initio derived polarizable potentials. The results of the computations were combined with extended X-ray absorption fine structure (EXAFS) experimental data. The results of this study show that in pure water the Th-O distance of 2.45 Å corresponds to a first shell coordination number between 9 and 10. In the salt solutions, while Br- does not affect directly the hydration of Th(IV) also at relatively high concentrations, Cl-, on the other hand, is more structured around Th(IV), in agreement with recent high-energy X-ray scattering experiments. Counterions, even at relatively high concentrations (0.8 m), do not enter in the first solvation shell of Th(IV), but they induce an increase of water molecules in the first and second hydration shells of Th(IV). © 2012 American Chemical Society. |
Extension of Marcus picture for electron transfer reactions with large solvation changes Article de journal R Vuilleumier; K A Tay; G Jeanmairet; D Borgis; A Boutin Journal of the American Chemical Society, 134 (4), p. 2067–2074, 2012. @article{Vuilleumier:2012, title = {Extension of Marcus picture for electron transfer reactions with large solvation changes}, author = {R Vuilleumier and K A Tay and G Jeanmairet and D Borgis and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856424997&doi=10.1021%2fja2069104&partnerID=40&md5=dad87e02b14fa27cc4d1c79a79892e4b}, doi = {10.1021/ja2069104}, year = {2012}, date = {2012-01-01}, journal = {Journal of the American Chemical Society}, volume = {134}, number = {4}, pages = {2067--2074}, abstract = {The standard Marcus theory of charge transfer reaction in solution, relying on a Gaussian solvation picture, or, equivalently, on a linear response approximation, and involving two parameters, the reorganization energy and the reaction free-energy parameter, may fail when the solvation has a different character in the reactant and product state. We propose two complementary theoretical extensions of Marcus theory applying to those cases, based either on a two-Gaussian-states solvation picture, or on a non-Gaussian solvation picture. As illustration, we show that such situations arise even for simple half oxido-reduction reactions involving the Cu +/Cu 2+ or Ag 0/Ag + couples, for which electron transfer free-energy surfaces have been generated using first-principle molecular dynamics simulations. The two theoretical extensions are shown to exhibit the correct nonlinear response behavior and to reproduce the simulation results quantitatively, whereas a simple one-Gaussian-state Marcus description breaks down. © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The standard Marcus theory of charge transfer reaction in solution, relying on a Gaussian solvation picture, or, equivalently, on a linear response approximation, and involving two parameters, the reorganization energy and the reaction free-energy parameter, may fail when the solvation has a different character in the reactant and product state. We propose two complementary theoretical extensions of Marcus theory applying to those cases, based either on a two-Gaussian-states solvation picture, or on a non-Gaussian solvation picture. As illustration, we show that such situations arise even for simple half oxido-reduction reactions involving the Cu +/Cu 2+ or Ag 0/Ag + couples, for which electron transfer free-energy surfaces have been generated using first-principle molecular dynamics simulations. The two theoretical extensions are shown to exhibit the correct nonlinear response behavior and to reproduce the simulation results quantitatively, whereas a simple one-Gaussian-state Marcus description breaks down. © 2011 American Chemical Society. |
Liquid water ionization by fast electron impact: A multiple differential study for the 1B 1 orbital Article de journal M L De Sanctis; M -F Politis; R Vuilleumier; C R Stia; O A Fojón Journal of Physics B: Atomic, Molecular and Optical Physics, 45 (4), 2012. @article{DeSanctis:2012, title = {Liquid water ionization by fast electron impact: A multiple differential study for the 1B 1 orbital}, author = {M L De Sanctis and M -F Politis and R Vuilleumier and C R Stia and O A Foj\'{o}n}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857090146&doi=10.1088%2f0953-4075%2f45%2f4%2f045206&partnerID=40&md5=95356ee4d040a60a2927739ea17a974f}, doi = {10.1088/0953-4075/45/4/045206}, year = {2012}, date = {2012-01-01}, journal = {Journal of Physics B: Atomic, Molecular and Optical Physics}, volume = {45}, number = {4}, abstract = {We study theoretically the single ionization of water molecules in a liquid phase by impact of fast electrons in a coplanar geometry. For the first time, the wavefunction for a single water molecule in the liquid phase is described in a realistic way by means of a Wannier orbital formalism. Multiple differential cross sections for the most external 1B 1 orbital are obtained through a first-order model within the framework of an independent electron approximation. Moreover, the relaxation of the target is not taken into account. We compare our results with previous theoretical and experimental ones for water in a gas phase. The main physical features of the reaction observed in measurements for vapour (such as binary and recoil peaks) are also observed in our theoretical predictions. © 2012 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study theoretically the single ionization of water molecules in a liquid phase by impact of fast electrons in a coplanar geometry. For the first time, the wavefunction for a single water molecule in the liquid phase is described in a realistic way by means of a Wannier orbital formalism. Multiple differential cross sections for the most external 1B 1 orbital are obtained through a first-order model within the framework of an independent electron approximation. Moreover, the relaxation of the target is not taken into account. We compare our results with previous theoretical and experimental ones for water in a gas phase. The main physical features of the reaction observed in measurements for vapour (such as binary and recoil peaks) are also observed in our theoretical predictions. © 2012 IOP Publishing Ltd. |
2011 |
Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases-A comparative molecular dynamics study Article de journal A Jezierska-Mazzarello; J J Panek; R Vuilleumier; A Koll; G Ciccotti Journal of Chemical Physics, 134 (3), 2011. @article{Jezierska-Mazzarello:2011, title = {Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases-A comparative molecular dynamics study}, author = {A Jezierska-Mazzarello and J J Panek and R Vuilleumier and A Koll and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79551639762&doi=10.1063%2f1.3528721&partnerID=40&md5=9876460650485456c7af752094cd578e}, doi = {10.1063/1.3528721}, year = {2011}, date = {2011-01-01}, journal = {Journal of Chemical Physics}, volume = {134}, number = {3}, abstract = {We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r(ON) 2.6 ), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects. © 2011 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r(ON) 2.6 ), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects. © 2011 American Institute of Physics. |
Ultrafast nonadiabatic fragmentation dynamics of doubly charged uracil in a gas phase Article de journal P López-Tarifa; M -A Hervé Du Penhoat; R Vuilleumier; M -P Gaigeot; I Tavernelli; A Le Padellec; J -P Champeaux; M Alcamí; P Moretto-Capelle; F Martín; M -F Politis Physical Review Letters, 107 (2), 2011. @article{Lopez-Tarifa:2011, title = {Ultrafast nonadiabatic fragmentation dynamics of doubly charged uracil in a gas phase}, author = {P L\'{o}pez-Tarifa and M -A Herv\'{e} Du Penhoat and R Vuilleumier and M -P Gaigeot and I Tavernelli and A Le Padellec and J -P Champeaux and M Alcam\'{i} and P Moretto-Capelle and F Mart\'{i}n and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79961050767&doi=10.1103%2fPhysRevLett.107.023202&partnerID=40&md5=f93284a19cfd9e9f60d393292c4a292a}, doi = {10.1103/PhysRevLett.107.023202}, year = {2011}, date = {2011-01-01}, journal = {Physical Review Letters}, volume = {107}, number = {2}, abstract = {A combination of time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods is used to investigate fragmentation of doubly charged gas-phase uracil in collisions with 100keV protons. The results are in good agreement with ion-ion coincidence measurements. Orbitals of similar energy and/or localized in similar bonds lead to very different fragmentation patterns, thus showing the importance of intramolecular chemical environment. In general, the observed fragments do not correspond to the energetically most favorable dissociation path, which is due to dynamical effects occurring in the first few femtoseconds after electron removal. © 2011 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A combination of time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods is used to investigate fragmentation of doubly charged gas-phase uracil in collisions with 100keV protons. The results are in good agreement with ion-ion coincidence measurements. Orbitals of similar energy and/or localized in similar bonds lead to very different fragmentation patterns, thus showing the importance of intramolecular chemical environment. In general, the observed fragments do not correspond to the energetically most favorable dissociation path, which is due to dynamical effects occurring in the first few femtoseconds after electron removal. © 2011 American Physical Society. |
Visualizing chemical reactions with x-rays Article de journal S Bratos; M Wulff; J -C Leicknam; R Vuilleumier; X Rozanska Ukrainian Journal of Physics, 56 (8), p. 763–768, 2011. @article{Bratos:2011, title = {Visualizing chemical reactions with x-rays}, author = {S Bratos and M Wulff and J -C Leicknam and R Vuilleumier and X Rozanska}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052402222&partnerID=40&md5=a65875e5e4c924fbd4cdecad370cd5b1}, year = {2011}, date = {2011-01-01}, journal = {Ukrainian Journal of Physics}, volume = {56}, number = {8}, pages = {763--768}, abstract = {The recombination of laser-dissociated iodine molecules dissolved in CCl4 is explored by time-resolved x-ray diffraction. The x-ray pulses employed in our experiments were generated by the ESRF synchrotron in Grenoble. The solvent contribution to the measured signals was eliminated using appropriate experimental procedures. Motions of iodine atoms were then studied from 200 ps to 10 ps. Different relaxation processes are shown to operate in this time domain. It is proved that the iodine recombination follows two reaction paths, taking place in the electronic states X and A/A′ of I2, respectively. In spite of widely different experimental approaches, laser optical and x-ray studies provide a similar picture of this prototype reaction. © 2011.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The recombination of laser-dissociated iodine molecules dissolved in CCl4 is explored by time-resolved x-ray diffraction. The x-ray pulses employed in our experiments were generated by the ESRF synchrotron in Grenoble. The solvent contribution to the measured signals was eliminated using appropriate experimental procedures. Motions of iodine atoms were then studied from 200 ps to 10 ps. Different relaxation processes are shown to operate in this time domain. It is proved that the iodine recombination follows two reaction paths, taking place in the electronic states X and A/A′ of I2, respectively. In spite of widely different experimental approaches, laser optical and x-ray studies provide a similar picture of this prototype reaction. © 2011. |
Van der Waals effects in ab initio water at ambient and supercritical conditions Article de journal R Jonchiere; A P Seitsonen; G Ferlat; A M Saitta; R Vuilleumier Journal of Chemical Physics, 135 (15), 2011. @article{Jonchiere:2011, title = {Van der Waals effects in ab initio water at ambient and supercritical conditions}, author = {R Jonchiere and A P Seitsonen and G Ferlat and A M Saitta and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80155147748&doi=10.1063%2f1.3651474&partnerID=40&md5=3e21456298da6da9cf1f4e7f04fabf17}, doi = {10.1063/1.3651474}, year = {2011}, date = {2011-01-01}, journal = {Journal of Chemical Physics}, volume = {135}, number = {15}, abstract = {Density functional theory (DFT) within the generalized gradient approximation (GGA) is known to poorly reproduce the experimental properties of liquid water. The poor description of the dispersion forces in the exchange correlation functionals is one of the possible causes. Recent studies have demonstrated an improvement in the simulated properties when they are taken into account. We present here a study of the effects on liquid water of the recently proposed semi-empirical correction of Grimme [J. Chem. Phys. 132, 154104 (2010)]. The difference between standard and corrected DFT-GGA simulations is rationalized with a detailed analysis upon modifying an accurate parameterised potential. This allows an estimate of the typical range of dispersion forces in water. We also show that the structure and diffusivity of ambient-like liquid water are sensitive to the fifth neighbor position, thus highlighting the key role played by this neighbor. Our study is extended to water at supercritical conditions, where experimental and theoretical results are much more scarce. We show that the semi-empirical correction by Grimme improves significantly, although somewhat counter-intuitively, both the structural and the dynamical description of supercritical water. © 2011 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Density functional theory (DFT) within the generalized gradient approximation (GGA) is known to poorly reproduce the experimental properties of liquid water. The poor description of the dispersion forces in the exchange correlation functionals is one of the possible causes. Recent studies have demonstrated an improvement in the simulated properties when they are taken into account. We present here a study of the effects on liquid water of the recently proposed semi-empirical correction of Grimme [J. Chem. Phys. 132, 154104 (2010)]. The difference between standard and corrected DFT-GGA simulations is rationalized with a detailed analysis upon modifying an accurate parameterised potential. This allows an estimate of the typical range of dispersion forces in water. We also show that the structure and diffusivity of ambient-like liquid water are sensitive to the fifth neighbor position, thus highlighting the key role played by this neighbor. Our study is extended to water at supercritical conditions, where experimental and theoretical results are much more scarce. We show that the semi-empirical correction by Grimme improves significantly, although somewhat counter-intuitively, both the structural and the dynamical description of supercritical water. © 2011 American Institute of Physics. |
Environmental effects on vibrational properties of carotenoids: Experiments and calculations on peridinin Article de journal D Bovi; A Mezzetti; R Vuilleumier; M -P Gaigeot; B Chazallon; R Spezia; L Guidoni Physical Chemistry Chemical Physics, 13 (47), p. 20954–20964, 2011. @article{Bovi:2011, title = {Environmental effects on vibrational properties of carotenoids: Experiments and calculations on peridinin}, author = {D Bovi and A Mezzetti and R Vuilleumier and M -P Gaigeot and B Chazallon and R Spezia and L Guidoni}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-82355175592&doi=10.1039%2fc1cp21985e&partnerID=40&md5=f86c5920f1cd1c0d0f259a77ccf4dd4d}, doi = {10.1039/c1cp21985e}, year = {2011}, date = {2011-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {13}, number = {47}, pages = {20954--20964}, abstract = {Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm -1 region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm -1 region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates. © 2011 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm -1 region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm -1 region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates. © 2011 the Owner Societies. |
Stability and instability of the isoelectronic UO22+ and PaO2+ actinyl oxo-cations in aqueous solution from density functional theory based molecular dynamics Article de journal R Spezia; B Siboulet; S Abadie; R Vuilleumier; P Vitorge Journal of Physical Chemistry B, 115 (13), p. 3560–3570, 2011. @article{Spezia:2011, title = {Stability and instability of the isoelectronic UO22+ and PaO2+ actinyl oxo-cations in aqueous solution from density functional theory based molecular dynamics}, author = {R Spezia and B Siboulet and S Abadie and R Vuilleumier and P Vitorge}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953268231&doi=10.1021%2fjp111726b&partnerID=40&md5=6ef96953249f08f68851397f82848a58}, doi = {10.1021/jp111726b}, year = {2011}, date = {2011-01-01}, journal = {Journal of Physical Chemistry B}, volume = {115}, number = {13}, pages = {3560--3570}, abstract = {In this work, Pa(V) monocations have been studied in liquid water by means of density functinal theory (DFT) based molecular dynamic simulations (CPMD) and compared with their U(VI) isoelectronic counterparts to understand the peculiar chemical behavior of Pa(V) in aqueous solution. Four different Pa(V) monocationic isomers appear to be stable in liquid water from our simulations: [PaO2(H2O)5]+(aq), [Pa(OH) 4(H2O)2]+(aq), [PaO(OH) 2(H2O)4]+(aq), and [Pa(OH) 4(H2O)3]+(aq). On the other hand, in the case of U(VI) only the uranyl, [UO2(H2O) 5]2+(aq), is stable. The other species containing hydroxyl groups replacing one or two oxo bonds are readily converted to uranyl. The Pa - OH bond is stable, while it is suddenly broken in U - OH. This makes possible the formation of a broad variety of Pa(V) species in water and participates to its unique chemical behavior in aqueous solution. Further, the two actinyl oxocations in water are different in the ability of the oxygen atoms to form stable and extended H-bond networks for Pa(V) contrary to U(VI). In particular, protactinyl is found to have between 2 and 3 hydrogen bonds per oxygen atom while uranyl has between zero and one. © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, Pa(V) monocations have been studied in liquid water by means of density functinal theory (DFT) based molecular dynamic simulations (CPMD) and compared with their U(VI) isoelectronic counterparts to understand the peculiar chemical behavior of Pa(V) in aqueous solution. Four different Pa(V) monocationic isomers appear to be stable in liquid water from our simulations: [PaO2(H2O)5]+(aq), [Pa(OH) 4(H2O)2]+(aq), [PaO(OH) 2(H2O)4]+(aq), and [Pa(OH) 4(H2O)3]+(aq). On the other hand, in the case of U(VI) only the uranyl, [UO2(H2O) 5]2+(aq), is stable. The other species containing hydroxyl groups replacing one or two oxo bonds are readily converted to uranyl. The Pa - OH bond is stable, while it is suddenly broken in U - OH. This makes possible the formation of a broad variety of Pa(V) species in water and participates to its unique chemical behavior in aqueous solution. Further, the two actinyl oxocations in water are different in the ability of the oxygen atoms to form stable and extended H-bond networks for Pa(V) contrary to U(VI). In particular, protactinyl is found to have between 2 and 3 hydrogen bonds per oxygen atom while uranyl has between zero and one. © 2011 American Chemical Society. |
Infrared spectroscopy of small protonated water clusters at room temperature: An effective modes analysis Article de journal F Agostini; R Vuilleumier; G Ciccotti Journal of Chemical Physics, 134 (8), 2011. @article{Agostini:2011, title = {Infrared spectroscopy of small protonated water clusters at room temperature: An effective modes analysis}, author = {F Agostini and R Vuilleumier and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952086261&doi=10.1063%2f1.3533229&partnerID=40&md5=1481337f36e995aa1a9b3e0444e33ef2}, doi = {10.1063/1.3533229}, year = {2011}, date = {2011-01-01}, journal = {Journal of Chemical Physics}, volume = {134}, number = {8}, abstract = {We perform infrared vibrational analysis on small protonated water clusters H+(H2O)n, with n = 2, , 6, at room temperature. The absorption spectra are calculated based on classical trajectories obtained by the multistate empirical valence bond method. The analysis is carried out based on the effective modes analysis, which has been recently developed [Martinez, J. Chem. Phys. 125, 144106 (2006)] as generalization of the normal modes analysis. This technique enables us to decompose the full spectrum in maximally localized bands which are obtained by accounting for temperature and anharmonic effects. These effects are especially considered in the determination of the modes coupling. The spectra of the small clusters are interpreted by identifying the behavior of the excess charge, by understanding the role of hydrogen bonds, and by considering the effect of (micro-)solvation. Our results are presented by showing comparisons with other numerical methods and experimental measurements which are available in the literature. © 2011 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We perform infrared vibrational analysis on small protonated water clusters H+(H2O)n, with n = 2, , 6, at room temperature. The absorption spectra are calculated based on classical trajectories obtained by the multistate empirical valence bond method. The analysis is carried out based on the effective modes analysis, which has been recently developed [Martinez, J. Chem. Phys. 125, 144106 (2006)] as generalization of the normal modes analysis. This technique enables us to decompose the full spectrum in maximally localized bands which are obtained by accounting for temperature and anharmonic effects. These effects are especially considered in the determination of the modes coupling. The spectra of the small clusters are interpreted by identifying the behavior of the excess charge, by understanding the role of hydrogen bonds, and by considering the effect of (micro-)solvation. Our results are presented by showing comparisons with other numerical methods and experimental measurements which are available in the literature. © 2011 American Institute of Physics. |
Infrared spectroscopy and effective modes analysis of the protonated water dimer Ħ+(Ħ2O)2 at room temperature under Ħ/Đ substitution Article de journal F Agostini; R Vuilleumier; G Ciccotti Journal of Chemical Physics, 134 (8), 2011. @article{Agostini:2011a, title = {Infrared spectroscopy and effective modes analysis of the protonated water dimer {H}+({H}2O)2 at room temperature under {H}/{D} substitution}, author = {F Agostini and R Vuilleumier and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952074245&doi=10.1063%2f1.3521273&partnerID=40&md5=1b78cfecb6dd8bf7425c646f8b51a77b}, doi = {10.1063/1.3521273}, year = {2011}, date = {2011-01-01}, journal = {Journal of Chemical Physics}, volume = {134}, number = {8}, abstract = {We study the vibrational properties of the protonated water dimer and its deuterated forms at room temperature. Molecular dynamics simulations within the empirical valence bond (EVB) model are used to generate the vibrational spectra that are interpreted using the effective modes analysis (EMA). Quantum effects are taken into account through an effective parametrization of the EVB model. EMA allows for the assignment of the bands in the 1000 - 2000 cm-1 region of the protonated water dimer from the molecular dynamics trajectory. It is then found that although this system is very anharmonic the two main bands in this spectral region arise from a linear coupling between the asymmetric OH+O stretch and asymmetric bend of the two water molecules. This mixing explains the simulated band shifts upon isotopic substitution of the central proton or of the hydrogens of the two water molecules. © 2011 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study the vibrational properties of the protonated water dimer and its deuterated forms at room temperature. Molecular dynamics simulations within the empirical valence bond (EVB) model are used to generate the vibrational spectra that are interpreted using the effective modes analysis (EMA). Quantum effects are taken into account through an effective parametrization of the EVB model. EMA allows for the assignment of the bands in the 1000 - 2000 cm-1 region of the protonated water dimer from the molecular dynamics trajectory. It is then found that although this system is very anharmonic the two main bands in this spectral region arise from a linear coupling between the asymmetric OH+O stretch and asymmetric bend of the two water molecules. This mixing explains the simulated band shifts upon isotopic substitution of the central proton or of the hydrogens of the two water molecules. © 2011 American Institute of Physics. |