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Professeur des Universités, Sorbonne Université ENS – Département de chimie Email: rodolphe.vuilleumier@ens.psl.eu |
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Publications
2018 |
XXIXth IUPAP Conference on Computational Physics (CCP2017) Article de journal R Spezia; A M Saitta; R Vuilleumier 1136 (1), 2018. @article{Spezia:2018, title = {XXIXth IUPAP Conference on Computational Physics (CCP2017)}, author = {R Spezia and A M Saitta and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059360437&doi=10.1088%2f1742-6596%2f1136%2f1%2f011001&partnerID=40&md5=82975b1c03fbf48b7394d70a495b8b47}, doi = {10.1088/1742-6596/1136/1/011001}, year = {2018}, date = {2018-01-01}, volume = {1136}, number = {1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Roles of Hydration for Inducing Decomposition of 2-Deoxy-d-ribose by Ionization of Oxygen K-Shell Electrons Article de journal K Fujii; Y Izumi; A Narita; K K Ghose; P López-Tarifa; A Touati; R Spezia; R Vuilleumier; M -P Gaigeot; M -F Politis; M -A H Du Penhoat; A Yokoya Radiation Research, 189 (3), p. 264–272, 2018. @article{Fujii:2018, title = {Roles of Hydration for Inducing Decomposition of 2-Deoxy-d-ribose by Ionization of Oxygen K-Shell Electrons}, author = {K Fujii and Y Izumi and A Narita and K K Ghose and P L\'{o}pez-Tarifa and A Touati and R Spezia and R Vuilleumier and M -P Gaigeot and M -F Politis and M -A H Du Penhoat and A Yokoya}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042916011&doi=10.1667%2fRR14225.1&partnerID=40&md5=d10f35f67ddcf004a95dfc3665db57e1}, doi = {10.1667/RR14225.1}, year = {2018}, date = {2018-01-01}, journal = {Radiation Research}, volume = {189}, number = {3}, pages = {264--272}, abstract = {To experimentally investigate the role of hydration in the initial process of the decomposition of 2-deoxy-d-ribose (dR), which is a major component of the DNA backbone, we used mass spectrometry to monitor the ions desorbing from hydrated dR films exposed to monochromatic soft X rays (560 eV). The X-ray photons preferentially ionize the K-shell electrons of the oxygen atoms in DNA. Hydrated dR samples were prepared under vacuum by exposing a cooled (textasciitilde150 K) dR film deposited on a Si substrate to water vapor. Using a quadrupole mass spectrometer, we observed the desorption of ions such as H+, CHx +, C2Hx +, CHxO+, C3Hx + and C2HxO+ (x = 1, 2, 3 and 4). In addition, the desorption of H2O+ or H3O+ was observed in the mass spectra of hydrated dR films. Except for H+, the yields of these ions decreased when one layer of water molecules was deposited onto the film. These ions are produced by C-C or C-O bond scission. This result suggests that the water molecules act as a quencher, suppressing Coulomb repulsion and thus the extensive molecular decomposition of dR. Ab initio molecular dynamics simulations were performed to rationalize the fragments observed in the experiments. The results of the dynamical process of a hydrated dR molecule after oxygen K-ionization revealed elongation of a C-O bond of dR and the O-H bonds of both dR and water molecules prior to the Auger process, resulting in the ejection of H+ ions. These results strongly suggest that the very early process contributes to reducing the dR fragmentation, producing the H3O+ and H+ detected from the hydrated dR films. These desorbed ions may be involved in the induction of other types of damage, such as oxidatively generated base lesions, concomitantly produced with a strand break when produced in DNA. © 2018 by Radiation Research Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To experimentally investigate the role of hydration in the initial process of the decomposition of 2-deoxy-d-ribose (dR), which is a major component of the DNA backbone, we used mass spectrometry to monitor the ions desorbing from hydrated dR films exposed to monochromatic soft X rays (560 eV). The X-ray photons preferentially ionize the K-shell electrons of the oxygen atoms in DNA. Hydrated dR samples were prepared under vacuum by exposing a cooled (textasciitilde150 K) dR film deposited on a Si substrate to water vapor. Using a quadrupole mass spectrometer, we observed the desorption of ions such as H+, CHx +, C2Hx +, CHxO+, C3Hx + and C2HxO+ (x = 1, 2, 3 and 4). In addition, the desorption of H2O+ or H3O+ was observed in the mass spectra of hydrated dR films. Except for H+, the yields of these ions decreased when one layer of water molecules was deposited onto the film. These ions are produced by C-C or C-O bond scission. This result suggests that the water molecules act as a quencher, suppressing Coulomb repulsion and thus the extensive molecular decomposition of dR. Ab initio molecular dynamics simulations were performed to rationalize the fragments observed in the experiments. The results of the dynamical process of a hydrated dR molecule after oxygen K-ionization revealed elongation of a C-O bond of dR and the O-H bonds of both dR and water molecules prior to the Auger process, resulting in the ejection of H+ ions. These results strongly suggest that the very early process contributes to reducing the dR fragmentation, producing the H3O+ and H+ detected from the hydrated dR films. These desorbed ions may be involved in the induction of other types of damage, such as oxidatively generated base lesions, concomitantly produced with a strand break when produced in DNA. © 2018 by Radiation Research Society. |
Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation Article de journal M -A Hervé Du Penhoat; N R Moraga; M -P Gaigeot; R Vuilleumier; I Tavernelli; M -F Politis Journal of Physical Chemistry A, 122 (24), p. 5311–5320, 2018. @article{HerveDuPenhoat:2018, title = {Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation}, author = {M -A Herv\'{e} Du Penhoat and N R Moraga and M -P Gaigeot and R Vuilleumier and I Tavernelli and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048026702&doi=10.1021%2facs.jpca.8b04787&partnerID=40&md5=8f237ed86c71a0b5043c76457bf360aa}, doi = {10.1021/acs.jpca.8b04787}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physical Chemistry A}, volume = {122}, number = {24}, pages = {5311--5320}, abstract = {In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions. In particular, we observe proton collisions with the solute molecule DR, which leads to a complete ring opening. In DNA, damage to the DR moiety may lead to DNA strand breaking. This mechanism can be understood as one of the possible steps in the radiation-induced fragmentation of DNA chains. Copyright © 2018 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions. In particular, we observe proton collisions with the solute molecule DR, which leads to a complete ring opening. In DNA, damage to the DR moiety may lead to DNA strand breaking. This mechanism can be understood as one of the possible steps in the radiation-induced fragmentation of DNA chains. Copyright © 2018 American Chemical Society. |
Effect of puckering motion and hydrogen bond formation on the vibrational circular dichroism spectrum of a flexible molecule: The case of (: S)-1-indanol Article de journal K Le Barbu-Debus; A Scherrer; A Bouchet; D Sebastiani; R Vuilleumier; A Zehnacker Physical Chemistry Chemical Physics, 20 (21), p. 14635–14646, 2018. @article{LeBarbu-Debus:2018, title = {Effect of puckering motion and hydrogen bond formation on the vibrational circular dichroism spectrum of a flexible molecule: The case of (: S)-1-indanol}, author = {K Le Barbu-Debus and A Scherrer and A Bouchet and D Sebastiani and R Vuilleumier and A Zehnacker}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048438873&doi=10.1039%2fc8cp01695j&partnerID=40&md5=37c577390251d7b760ddadd0174f6e11}, doi = {10.1039/c8cp01695j}, year = {2018}, date = {2018-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {20}, number = {21}, pages = {14635--14646}, abstract = {The influence of flexibility and hydrogen bond formation on the IR absorption and vibrational circular dichroism (VCD) spectrum of a floppy protic molecule, namely, (S)-1-indanol, is studied in both non-polar CCl4 and polar DMSO solvents. The experimental IR absorption and VCD spectra obtained by Fourier transform spectroscopy are interpreted using both static density functional theory (DFT) calculations and first principles molecular dynamics (FPMD) within DFT, using the nuclear velocity perturbation theory (NVPT). Simulation of the spectra based on static optimised geometries is not sufficient in CCl4 and going beyond static calculations is mandatory for satisfactorily reproducing the VCD spectra. The FPMD results obtained in DMSO indicate that (S)-1-indanol is hydrogen-bonded to one DMSO molecule. As a result, static "cluster-in-the-bulk" DFT calculations in which the solute-solvent interaction is modeled as the most stable (S)-1-indanol:DMSO complexes in a DMSO continuum yield satisfactory agreement with the experiment. Correspondence between experimental and simulated spectra is slightly improved when the VCD spectrum is calculated as the summed contributions of snapshots extracted from FPMD trajectories, due to better sampling of the potential-energy surface. Finally, NVPT calculations further improve the description of experimental spectra by taking into account higher-energy structures, which are not necessary local minima. © the Owner Societies 2018.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The influence of flexibility and hydrogen bond formation on the IR absorption and vibrational circular dichroism (VCD) spectrum of a floppy protic molecule, namely, (S)-1-indanol, is studied in both non-polar CCl4 and polar DMSO solvents. The experimental IR absorption and VCD spectra obtained by Fourier transform spectroscopy are interpreted using both static density functional theory (DFT) calculations and first principles molecular dynamics (FPMD) within DFT, using the nuclear velocity perturbation theory (NVPT). Simulation of the spectra based on static optimised geometries is not sufficient in CCl4 and going beyond static calculations is mandatory for satisfactorily reproducing the VCD spectra. The FPMD results obtained in DMSO indicate that (S)-1-indanol is hydrogen-bonded to one DMSO molecule. As a result, static "cluster-in-the-bulk" DFT calculations in which the solute-solvent interaction is modeled as the most stable (S)-1-indanol:DMSO complexes in a DMSO continuum yield satisfactory agreement with the experiment. Correspondence between experimental and simulated spectra is slightly improved when the VCD spectrum is calculated as the summed contributions of snapshots extracted from FPMD trajectories, due to better sampling of the potential-energy surface. Finally, NVPT calculations further improve the description of experimental spectra by taking into account higher-energy structures, which are not necessary local minima. © the Owner Societies 2018. |
Chiral Crystal Packing Induces Enhancement of Vibrational Circular Dichroism Article de journal S Jähnigen; A Scherrer; R Vuilleumier; D Sebastiani Angewandte Chemie - International Edition, 57 (40), p. 13344–13348, 2018. @article{Jahnigen:2018, title = {Chiral Crystal Packing Induces Enhancement of Vibrational Circular Dichroism}, author = {S J\"{a}hnigen and A Scherrer and R Vuilleumier and D Sebastiani}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053736179&doi=10.1002%2fanie.201805671&partnerID=40&md5=70aebeca5f30f9ef94548575f45a28d7}, doi = {10.1002/anie.201805671}, year = {2018}, date = {2018-01-01}, journal = {Angewandte Chemie - International Edition}, volume = {57}, number = {40}, pages = {13344--13348}, abstract = {We demonstrate that molecular vibrations with originally low or zero intensity in a vibrational circular dichroism (VCD) spectrum attain chirality in molecular crystals by coordinated motion of the atoms. Ab initio molecular dynamics simulations of anharmonic solid-state VCD spectra of l-alanine crystals reveal how coherent vibrational modes exploit the space group's chirality, leading to non-local, enhanced VCD features, most significantly in the carbonyl region of the spectrum. The VCD-enhanced signal is ascribed to a helical arrangement of the oscillators in the crystal layers. No structural irregularities need to be considered to explain the amplification, but a crucial point lies in the polarization of charge, which requires an accurate description of the electronic structure. Delivering a quantitative atomic conception of supramolecular chirality induction, our ab initio scheme is applicable well beyond molecular crystals, for example, to address VCD in proteins and related compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } We demonstrate that molecular vibrations with originally low or zero intensity in a vibrational circular dichroism (VCD) spectrum attain chirality in molecular crystals by coordinated motion of the atoms. Ab initio molecular dynamics simulations of anharmonic solid-state VCD spectra of l-alanine crystals reveal how coherent vibrational modes exploit the space group's chirality, leading to non-local, enhanced VCD features, most significantly in the carbonyl region of the spectrum. The VCD-enhanced signal is ascribed to a helical arrangement of the oscillators in the crystal layers. No structural irregularities need to be considered to explain the amplification, but a crucial point lies in the polarization of charge, which requires an accurate description of the electronic structure. Delivering a quantitative atomic conception of supramolecular chirality induction, our ab initio scheme is applicable well beyond molecular crystals, for example, to address VCD in proteins and related compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim |
2017 |
An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(III)(HPDO3A)(Ħ2O)] Article de journal S Khan; R Pollet; R Vuilleumier; J Kowalewski; M Odelius Journal of Chemical Physics, 147 (24), 2017. @article{Khan:2017, title = {An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(III)(HPDO3A)({H}2O)]}, author = {S Khan and R Pollet and R Vuilleumier and J Kowalewski and M Odelius}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040080433&doi=10.1063%2f1.5010347&partnerID=40&md5=4509ae37abb1a23cc64f76a0f4051ea8}, doi = {10.1063/1.5010347}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {147}, number = {24}, abstract = {In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field - CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field - CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates. © 2017 Author(s). |
Double differential cross sections for liquid water ionization by fast electron impact Article de journal M L de Sanctis; M -F Politis; R Vuilleumier; C R Stia; O A Fojón European Physical Journal D, 71 (5), 2017. @article{deSanctis:2017, title = {Double differential cross sections for liquid water ionization by fast electron impact}, 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-s2.0-85020054874&doi=10.1140%2fepjd%2fe2017-70615-y&partnerID=40&md5=de232d35d2c540570c40ce1b60a80d3f}, doi = {10.1140/epjd/e2017-70615-y}, year = {2017}, date = {2017-01-01}, journal = {European Physical Journal D}, volume = {71}, number = {5}, abstract = {Abstract: In this work we study theoretically the single ionization of liquid water by impact of energetic electrons. A realistic description of the wavefunction for an isolated water molecule in the liquid phase is made by means of a Wannier orbital formalism. We develop a first order model within the framework of an independent electron approximation in which the relaxation of the target is not taken into account. The double differential cross sections are computed and compared with experimental data and theoretical calculations for gas phase. Graphical abstract: [Figure not available: see fulltext.]. © 2017, EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract: In this work we study theoretically the single ionization of liquid water by impact of energetic electrons. A realistic description of the wavefunction for an isolated water molecule in the liquid phase is made by means of a Wannier orbital formalism. We develop a first order model within the framework of an independent electron approximation in which the relaxation of the target is not taken into account. The double differential cross sections are computed and compared with experimental data and theoretical calculations for gas phase. Graphical abstract: [Figure not available: see fulltext.]. © 2017, EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg. |
Transient hydrodynamic finite-size effects in simulations under periodic boundary conditions Article de journal A J Asta; M Levesque; R Vuilleumier; B Rotenberg Physical Review E, 95 (6), 2017. @article{Asta:2017, title = {Transient hydrodynamic finite-size effects in simulations under periodic boundary conditions}, author = {A J Asta and M Levesque and R Vuilleumier and B Rotenberg}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021425888&doi=10.1103%2fPhysRevE.95.061301&partnerID=40&md5=214359f07ec0a14040b68cb22b376893}, doi = {10.1103/PhysRevE.95.061301}, year = {2017}, date = {2017-01-01}, journal = {Physical Review E}, volume = {95}, number = {6}, abstract = {We use lattice-Boltzmann and analytical calculations to investigate transient hydrodynamic finite-size effects induced by the use of periodic boundary conditions. These effects are inevitable in simulations at the molecular, mesoscopic, or continuum levels of description. We analyze the transient response to a local perturbation in the fluid and obtain the local velocity correlation function via linear response theory. This approach is validated by comparing the finite-size effects on the steady-state velocity with the known results for the diffusion coefficient. We next investigate the full time dependence of the local velocity autocorrelation function. We find at long times a crossover between the expected t-3/2 hydrodynamic tail and an oscillatory exponential decay, and study the scaling with the system size of the crossover time, exponential rate and amplitude, and oscillation frequency. We interpret these results from the analytic solution of the compressible Navier-Stokes equation for the slowest modes, which are set by the system size. The present work not only provides a comprehensive analysis of hydrodynamic finite-size effects in bulk fluids, which arise regardless of the level of description and simulation algorithm, but also establishes the lattice-Boltzmann method as a suitable tool to investigate such effects in general. © 2017 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We use lattice-Boltzmann and analytical calculations to investigate transient hydrodynamic finite-size effects induced by the use of periodic boundary conditions. These effects are inevitable in simulations at the molecular, mesoscopic, or continuum levels of description. We analyze the transient response to a local perturbation in the fluid and obtain the local velocity correlation function via linear response theory. This approach is validated by comparing the finite-size effects on the steady-state velocity with the known results for the diffusion coefficient. We next investigate the full time dependence of the local velocity autocorrelation function. We find at long times a crossover between the expected t-3/2 hydrodynamic tail and an oscillatory exponential decay, and study the scaling with the system size of the crossover time, exponential rate and amplitude, and oscillation frequency. We interpret these results from the analytic solution of the compressible Navier-Stokes equation for the slowest modes, which are set by the system size. The present work not only provides a comprehensive analysis of hydrodynamic finite-size effects in bulk fluids, which arise regardless of the level of description and simulation algorithm, but also establishes the lattice-Boltzmann method as a suitable tool to investigate such effects in general. © 2017 American Physical Society. |
Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics Article de journal M Basire; F Mouhat; G Fraux; A Bordage; J -L Hazemann; M Louvel; R Spezia; S Bonella; R Vuilleumier Journal of Chemical Physics, 146 (13), 2017. @article{Basire:2017, title = {Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics}, author = {M Basire and F Mouhat and G Fraux and A Bordage and J -L Hazemann and M Louvel and R Spezia and S Bonella and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016765650&doi=10.1063%2f1.4979199&partnerID=40&md5=90c94c5f296db3f0df0fd4e607548cb7}, doi = {10.1063/1.4979199}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {146}, number = {13}, abstract = {Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them. © 2017 Author(s). |
Microscopic flow around a diffusing particle Article de journal D Lesnicki; R Vuilleumier Journal of Chemical Physics, 147 (9), 2017. @article{Lesnicki:2017, title = {Microscopic flow around a diffusing particle}, author = {D Lesnicki and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029312710&doi=10.1063%2f1.4985909&partnerID=40&md5=303fd55329a5a382e531db4034965d95}, doi = {10.1063/1.4985909}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {147}, number = {9}, abstract = {We report here on the computation of the microscopic flow induced by the motion of a small tagged particle in a fluid from molecular dynamic simulations. It is found that the hydrodynamical Stokes solution with slip boundary conditions is recovered at only a few diameters away from the tagged particle. However, fluctuations of the diffusing particle itself induce a renormalization of the bath viscosity and, more strikingly, an apparent violation of the non-penetrability of the particles in the laboratory frame. The expected zero normal velocity at contact is satisfied only in the particle frame, or for heavy particles. Further evidence of this generalized boundary condition is given by the evaluation of the flow in a granular gas using data from particle tracking experiments. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report here on the computation of the microscopic flow induced by the motion of a small tagged particle in a fluid from molecular dynamic simulations. It is found that the hydrodynamical Stokes solution with slip boundary conditions is recovered at only a few diameters away from the tagged particle. However, fluctuations of the diffusing particle itself induce a renormalization of the bath viscosity and, more strikingly, an apparent violation of the non-penetrability of the particles in the laboratory frame. The expected zero normal velocity at contact is satisfied only in the particle frame, or for heavy particles. Further evidence of this generalized boundary condition is given by the evaluation of the flow in a granular gas using data from particle tracking experiments. © 2017 Author(s). |
On the mass of atoms in molecules: Beyond the born-oppenheimer approximation Article de journal A Scherrer; F Agostini; D Sebastiani; E K U Gross; R Vuilleumier Physical Review X, 7 (3), 2017. @article{Scherrer:2017, title = {On the mass of atoms in molecules: Beyond the born-oppenheimer approximation}, author = {A Scherrer and F Agostini and D Sebastiani and E K U Gross and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029807679&doi=10.1103%2fPhysRevX.7.031035&partnerID=40&md5=d047b54d649a075da40660c4eb3e1f96}, doi = {10.1103/PhysRevX.7.031035}, year = {2017}, date = {2017-01-01}, journal = {Physical Review X}, volume = {7}, number = {3}, abstract = {Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the computation of high-precision molecular spectra.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the computation of high-precision molecular spectra. |
Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics Article de journal F Mouhat; S Sorella; R Vuilleumier; A M Saitta; M Casula Journal of Chemical Theory and Computation, 13 (6), p. 2400–2417, 2017. @article{Mouhat:2017, title = {Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics}, author = {F Mouhat and S Sorella and R Vuilleumier and A M Saitta and M Casula}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020712757&doi=10.1021%2facs.jctc.7b00017&partnerID=40&md5=042401e811dc41f5d5e3e709943f71d8}, doi = {10.1021/acs.jctc.7b00017}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Theory and Computation}, volume = {13}, number = {6}, pages = {2400--2417}, abstract = {We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most-Advanced post-Hartree-Fock approaches, and with a favorable scaling with the system size. In order to cope with the intrinsic noise due to the stochastic nature of quantum Monte Carlo methods, we generalize the path integral molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of quantum Monte Carlo nuclear forces. The variational parameters of the quantum Monte Carlo wave function are evolved during the nuclear dynamics, such that the Born-Oppenheimer potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well-controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated, even in the presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be also very efficient in the case of noiseless (deterministic) ionic forces. The new implementation is validated on the Zundel ion (H5O2+) by direct comparison with standard path integral Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond room temperature, giving the excess proton an increased mobility by quantum tunneling. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most-Advanced post-Hartree-Fock approaches, and with a favorable scaling with the system size. In order to cope with the intrinsic noise due to the stochastic nature of quantum Monte Carlo methods, we generalize the path integral molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of quantum Monte Carlo nuclear forces. The variational parameters of the quantum Monte Carlo wave function are evolved during the nuclear dynamics, such that the Born-Oppenheimer potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well-controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated, even in the presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be also very efficient in the case of noiseless (deterministic) ionic forces. The new implementation is validated on the Zundel ion (H5O2+) by direct comparison with standard path integral Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond room temperature, giving the excess proton an increased mobility by quantum tunneling. © 2017 American Chemical Society. |
2016 |
Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase Article de journal A Scherrer; R Vuilleumier; D Sebastiani Journal of Chemical Physics, 145 (8), 2016. @article{Scherrer:2016, title = {Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase}, author = {A Scherrer and R Vuilleumier and D Sebastiani}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84983542252&doi=10.1063%2f1.4960653&partnerID=40&md5=d840d41e0a49ac412b1b9f57f5edb0cb}, doi = {10.1063/1.4960653}, year = {2016}, date = {2016-01-01}, journal = {Journal of Chemical Physics}, volume = {145}, number = {8}, abstract = {We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent. © 2016 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent. © 2016 Author(s). |
Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride Article de journal B Grosjean; C Pean; A Siria; L Bocquet; R Vuilleumier; M -L Bocquet Journal of Physical Chemistry Letters, 7 (22), p. 4695–4700, 2016. @article{Grosjean:2016, title = {Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride}, author = {B Grosjean and C Pean and A Siria and L Bocquet and R Vuilleumier and M -L Bocquet}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84996563991&doi=10.1021%2facs.jpclett.6b02248&partnerID=40&md5=c996527c2b197c80bcb105d4176e42c9}, doi = {10.1021/acs.jpclett.6b02248}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {7}, number = {22}, pages = {4695--4700}, abstract = {Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials - chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials - chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario. © 2016 American Chemical Society. |
Molecular Hydrodynamics from Memory Kernels Article de journal D Lesnicki; R Vuilleumier; A Carof; B Rotenberg Physical Review Letters, 116 (14), 2016. @article{Lesnicki:2016, title = {Molecular Hydrodynamics from Memory Kernels}, author = {D Lesnicki and R Vuilleumier and A Carof and B Rotenberg}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963674105&doi=10.1103%2fPhysRevLett.116.147804&partnerID=40&md5=0c14b9ad8295e2c9cfb8baa98ac84396}, doi = {10.1103/PhysRevLett.116.147804}, year = {2016}, date = {2016-01-01}, journal = {Physical Review Letters}, volume = {116}, number = {14}, abstract = {The memory kernel for a tagged particle in a fluid, computed from molecular dynamics simulations, decays algebraically as t-3/2. We show how the hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail and generalize the concept of hydrodynamic added mass. This mass term is negative in the present case of a molecular solute, which is at odds with incompressible hydrodynamics predictions. Lastly, we discuss the various contributions to the friction, the associated time scales, and the crossover between the molecular and hydrodynamic regimes upon increasing the solute radius. © 2016 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The memory kernel for a tagged particle in a fluid, computed from molecular dynamics simulations, decays algebraically as t-3/2. We show how the hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail and generalize the concept of hydrodynamic added mass. This mass term is negative in the present case of a molecular solute, which is at odds with incompressible hydrodynamics predictions. Lastly, we discuss the various contributions to the friction, the associated time scales, and the crossover between the molecular and hydrodynamic regimes upon increasing the solute radius. © 2016 American Physical Society. |
2015 |
Erratum: Van der Waals effects in ab initio water at ambient and supercritical conditions (Journal of Chemical Physics (2011) 135 (154503)) Article de journal R Jonchiere; A P Seitsonen; G Ferlat; A M Saitta; R Vuilleumier Journal of Chemical Physics, 143 (20), 2015. @article{Jonchiere:2015, title = {Erratum: Van der Waals effects in ab initio water at ambient and supercritical conditions (Journal of Chemical Physics (2011) 135 (154503))}, 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-s2.0-84948685389&doi=10.1063%2f1.4934928&partnerID=40&md5=c314d85d336c9b42596248a39e27a8f8}, doi = {10.1063/1.4934928}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {20}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Carbon dioxide in silicate melts at upper mantle conditions: Insights from atomistic simulations Article de journal R Vuilleumier; A P Seitsonen; N Sator; B Guillot Chemical Geology, 418 , p. 77–88, 2015. @article{Vuilleumier:2015, title = {Carbon dioxide in silicate melts at upper mantle conditions: Insights from 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-s2.0-84958665894&doi=10.1016%2fj.chemgeo.2015.02.027&partnerID=40&md5=62a518b8dcbfe60b1aa13ae37521ed88}, doi = {10.1016/j.chemgeo.2015.02.027}, year = {2015}, date = {2015-01-01}, journal = {Chemical Geology}, volume = {418}, pages = {77--88}, abstract = {The detail of the incorporation of carbon dioxide in silicate melts at upper mantle conditions is still badly known. To give some theoretical guidance, we have performed first-principle molecular dynamics simulations (FPMD) to quantify the speciation and the incorporation of carbon dioxide in two CO2-rich silicate melts (textasciitilde20 wt.% CO2 at 2073 K and 12 GPa), a basaltic and a kimberlitic composition chosen in the CaO-MgO-Al2O3-SiO2 system. In the basaltic composition, carbon dioxide is incorporated under the form of a minority population of CO2 molecules and a prevailing population of carbonate ions (CO3 2-). In contrast, the amount of CO2 molecules is found to be very small in the kimberlitic melt. Moreover, a new (transient) species has been identified, the pyrocarbonate ion C2O5 2- issued from the reaction between CO2 and CO3 2-. With regard to the structure of the CO2-bearing melts, it is shown that the carbonate ions modify the silicate network by transforming some of the oxygen atoms into bridging carbonates, non-bridging carbonates, and free carbonates, with a distribution depending on the melt composition. In the basaltic melt a majority of carbonate ions are non-bridging or free, whereas in the kimberlitic melt, most of the carbonate ions are under the form of free carbonates linked to alkaline earth cations. Surprisingly, the addition of CO2 only has a weak influence on the diffusion coefficients of the elements of the melt. The consequence is that the strong enhancement of the electrical conductivity reported recently for carbonated basalts (Sifr\'{e} et al., 2014, Nature 509, 81), can be reproduced by simulation only if one assumes that the ionic charges assigned to the elements of the melt depend, in a non-trivial way, on the CO2 content. Finally, a comparison of the FPMD calculations with classical molecular dynamics simulations using an empirical force field of the literature (Guillot and Sator, 2011, GCA 75, 1829) shows that the latter one needs some improvement. © 2015 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The detail of the incorporation of carbon dioxide in silicate melts at upper mantle conditions is still badly known. To give some theoretical guidance, we have performed first-principle molecular dynamics simulations (FPMD) to quantify the speciation and the incorporation of carbon dioxide in two CO2-rich silicate melts (textasciitilde20 wt.% CO2 at 2073 K and 12 GPa), a basaltic and a kimberlitic composition chosen in the CaO-MgO-Al2O3-SiO2 system. In the basaltic composition, carbon dioxide is incorporated under the form of a minority population of CO2 molecules and a prevailing population of carbonate ions (CO3 2-). In contrast, the amount of CO2 molecules is found to be very small in the kimberlitic melt. Moreover, a new (transient) species has been identified, the pyrocarbonate ion C2O5 2- issued from the reaction between CO2 and CO3 2-. With regard to the structure of the CO2-bearing melts, it is shown that the carbonate ions modify the silicate network by transforming some of the oxygen atoms into bridging carbonates, non-bridging carbonates, and free carbonates, with a distribution depending on the melt composition. In the basaltic melt a majority of carbonate ions are non-bridging or free, whereas in the kimberlitic melt, most of the carbonate ions are under the form of free carbonates linked to alkaline earth cations. Surprisingly, the addition of CO2 only has a weak influence on the diffusion coefficients of the elements of the melt. The consequence is that the strong enhancement of the electrical conductivity reported recently for carbonated basalts (Sifré et al., 2014, Nature 509, 81), can be reproduced by simulation only if one assumes that the ionic charges assigned to the elements of the melt depend, in a non-trivial way, on the CO2 content. Finally, a comparison of the FPMD calculations with classical molecular dynamics simulations using an empirical force field of the literature (Guillot and Sator, 2011, GCA 75, 1829) shows that the latter one needs some improvement. © 2015 Elsevier B.V. |
A NMR and molecular dynamics study of CO2-bearing basaltic melts and glasses Article de journal Y Morizet; R Vuilleumier; M Paris Chemical Geology, 418 , p. 89–103, 2015. @article{Morizet:2015, title = {A NMR and molecular dynamics study of CO2-bearing basaltic melts and glasses}, author = {Y Morizet and R Vuilleumier and M Paris}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84958605430&doi=10.1016%2fj.chemgeo.2015.03.021&partnerID=40&md5=d70084bc8c941a58d6d7f9a46d2d173e}, doi = {10.1016/j.chemgeo.2015.03.021}, year = {2015}, date = {2015-01-01}, journal = {Chemical Geology}, volume = {418}, pages = {89--103}, abstract = {The presence of volatile, especially carbon dioxide (CO2), in silicate liquids is considered as a key parameter to magmatic degassing and eruptive processes. Unfortunately, due to experimental difficulties, our current knowledge on the CO2 effect on silicate melt structure is weak and relies on the observation of ex-situ recovered CO2-bearing glasses.In the present work, we confront the results obtained from NMR spectroscopic observations of glass synthesised at pressure between 0.5 and 3.0 GPa and theoretical investigations from first-principles molecular dynamics (FPMD) simulations conducted at 5.0 and 8.0 GPa on high temperature melt for a simplified basaltic composition.The results obtained on the aluminosilicate framework (molar fraction of silicon species and Al average coordination number) suggest that both ex-situ and in-situ results compare adequately. The results are in agreement with our current knowledge on the change in aluminosilicate melt/glass structure with changing intensive conditions. Increasing pressure from 0.5 to 8.0 GPa induces 1) an increase in the average Al coordination number from 4.1 to almost 5.0 and 2) an increase in the degree of polymerisation with NBO/Si changing from 1.30 to 0.80.The presence of CO2 does not seem to induce a dramatic change on both the average Al coordination number and the NBO/Si. FPMD simulations performed with 0 and 20 wt.% CO2 at 8.0 GPa result in a change from 4.84 to 4.96 for the average Al coordination number and in a change from 0.87 to 0.80 for the NBO/Si value, respectively.On the contrary, there is a lack of consistency in between the CO2 speciation obtained from NMR spectroscopy and from FPMD simulations. Whereas the analysis of glasses does not reveal the presence of CO2 mol species, the FPMD simulation results suggests the existence of a small proportion of CO2 mol. Further work with in-situ experimental approach is therefore required to explain the observed lack of consistency between the CO2 speciation in glass and in high temperature melt with basaltic composition. © 2015 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The presence of volatile, especially carbon dioxide (CO2), in silicate liquids is considered as a key parameter to magmatic degassing and eruptive processes. Unfortunately, due to experimental difficulties, our current knowledge on the CO2 effect on silicate melt structure is weak and relies on the observation of ex-situ recovered CO2-bearing glasses.In the present work, we confront the results obtained from NMR spectroscopic observations of glass synthesised at pressure between 0.5 and 3.0 GPa and theoretical investigations from first-principles molecular dynamics (FPMD) simulations conducted at 5.0 and 8.0 GPa on high temperature melt for a simplified basaltic composition.The results obtained on the aluminosilicate framework (molar fraction of silicon species and Al average coordination number) suggest that both ex-situ and in-situ results compare adequately. The results are in agreement with our current knowledge on the change in aluminosilicate melt/glass structure with changing intensive conditions. Increasing pressure from 0.5 to 8.0 GPa induces 1) an increase in the average Al coordination number from 4.1 to almost 5.0 and 2) an increase in the degree of polymerisation with NBO/Si changing from 1.30 to 0.80.The presence of CO2 does not seem to induce a dramatic change on both the average Al coordination number and the NBO/Si. FPMD simulations performed with 0 and 20 wt.% CO2 at 8.0 GPa result in a change from 4.84 to 4.96 for the average Al coordination number and in a change from 0.87 to 0.80 for the NBO/Si value, respectively.On the contrary, there is a lack of consistency in between the CO2 speciation obtained from NMR spectroscopy and from FPMD simulations. Whereas the analysis of glasses does not reveal the presence of CO2 mol species, the FPMD simulation results suggests the existence of a small proportion of CO2 mol. Further work with in-situ experimental approach is therefore required to explain the observed lack of consistency between the CO2 speciation in glass and in high temperature melt with basaltic composition. © 2015 Elsevier B.V. |
Hydrothermal Breakdown of Flexible Metal-Organic Frameworks: A Study by First-Principles Molecular Dynamics Article de journal V Haigis; F -X Coudert; R Vuilleumier; A Boutin; A H Fuchs Journal of Physical Chemistry Letters, 6 (21), p. 4365–4370, 2015. @article{Haigis:2015, title = {Hydrothermal Breakdown of Flexible Metal-Organic Frameworks: A Study by First-Principles Molecular Dynamics}, author = {V Haigis and F -X Coudert and R Vuilleumier and A Boutin and A H Fuchs}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84946822800&doi=10.1021%2facs.jpclett.5b01926&partnerID=40&md5=1ca30978fa4ef2cf6cb576e3f7b9ef21}, doi = {10.1021/acs.jpclett.5b01926}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {6}, number = {21}, pages = {4365--4370}, abstract = {Flexible metal-organic frameworks, also known as soft porous crystals, have been proposed for a vast number of technological applications, because they respond by large changes in structure and properties to small external stimuli, such as adsorption of guest molecules and changes in temperature or pressure. While this behavior is highly desirable in applications such as sensing and actuation, their extreme flexibility can also be synonymous with decreased stability. In particular, their performance in industrial environments is limited by a lack of stability at elevated temperatures and in the presence of water. Here, we use first-principles molecular dynamics to study the hydrothermal breakdown of soft porous crystals. Focusing on the material MIL-53(Ga), we show that the weak point of the structure is the bond between the metal center and the organic linker and elucidate the mechanism by which water lowers the activation free energy for the breakdown. This allows us to propose strategies for the synthesis of MOFs with increased heat and water stability. © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Flexible metal-organic frameworks, also known as soft porous crystals, have been proposed for a vast number of technological applications, because they respond by large changes in structure and properties to small external stimuli, such as adsorption of guest molecules and changes in temperature or pressure. While this behavior is highly desirable in applications such as sensing and actuation, their extreme flexibility can also be synonymous with decreased stability. In particular, their performance in industrial environments is limited by a lack of stability at elevated temperatures and in the presence of water. Here, we use first-principles molecular dynamics to study the hydrothermal breakdown of soft porous crystals. Focusing on the material MIL-53(Ga), we show that the weak point of the structure is the bond between the metal center and the organic linker and elucidate the mechanism by which water lowers the activation free energy for the breakdown. This allows us to propose strategies for the synthesis of MOFs with increased heat and water stability. © 2015 American Chemical Society. |
Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics Article de journal C Pinilla; M Blanchard; E Balan; S K Natarajan; R Vuilleumier; F Mauri Geochimica et Cosmochimica Acta, 163 , p. 126–139, 2015. @article{Pinilla:2015a, title = {Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics}, author = {C Pinilla and M Blanchard and E Balan and S K Natarajan and R Vuilleumier and F Mauri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929333698&doi=10.1016%2fj.gca.2015.04.008&partnerID=40&md5=108fbec7d44f74103d9856891f0089fa}, doi = {10.1016/j.gca.2015.04.008}, year = {2015}, date = {2015-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {163}, pages = {126--139}, abstract = {The theoretical determination of the isotopic fractionation between an aqueous solution and a mineral is of utmost importance in Earth sciences. While for crystals, it is well established that equilibrium isotopic fractionation factors can be calculated using a statistical thermodynamic approach based on the vibrational properties, several theoretical methods are currently used to model ions in aqueous solution. In this work, we present a systematic study to determine the reduced partition function ratio (β-factor) of aqueous Mg2+ using several levels of theory within the simulations. In particular, using an empirical force field, we compare and discuss the performance of the exact results obtained from path integral molecular dynamics (PIMD) simulations, with respect to the more traditional methods based on vibrational properties and the cluster approximation. The results show the importance of including configurational disorder for the estimation of the equilibrium isotope fractionation factor. We also show that using the vibrational frequencies computed from snapshots taken from equilibrated classical molecular dynamics represents a good approximation for the study of aqueous ions. Based on these conclusions, the β-factor of aqueous Mg2+ have been estimated from a Car-Parrinello molecular dynamics (CPMD) simulation with an ab initio force field, and combined with the β-factors of carbonate minerals (magnesite, dolomite, calcite and aragonite). Mg β-factor of Mg-bearing aragonite, calculated here for the first time, displays a lower value than the three other carbonate minerals. This is explained by a strong distortion of the cationic site leading to a decrease of the coordination number during Ca-Mg substitution. Overall, the equilibrium magnesium isotope fractionation factors between aqueous Mg2+ and carbonate minerals that derive from this methodological study support the previous theoretical results obtained from embedded cluster models. © 2015 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The theoretical determination of the isotopic fractionation between an aqueous solution and a mineral is of utmost importance in Earth sciences. While for crystals, it is well established that equilibrium isotopic fractionation factors can be calculated using a statistical thermodynamic approach based on the vibrational properties, several theoretical methods are currently used to model ions in aqueous solution. In this work, we present a systematic study to determine the reduced partition function ratio (β-factor) of aqueous Mg2+ using several levels of theory within the simulations. In particular, using an empirical force field, we compare and discuss the performance of the exact results obtained from path integral molecular dynamics (PIMD) simulations, with respect to the more traditional methods based on vibrational properties and the cluster approximation. The results show the importance of including configurational disorder for the estimation of the equilibrium isotope fractionation factor. We also show that using the vibrational frequencies computed from snapshots taken from equilibrated classical molecular dynamics represents a good approximation for the study of aqueous ions. Based on these conclusions, the β-factor of aqueous Mg2+ have been estimated from a Car-Parrinello molecular dynamics (CPMD) simulation with an ab initio force field, and combined with the β-factors of carbonate minerals (magnesite, dolomite, calcite and aragonite). Mg β-factor of Mg-bearing aragonite, calculated here for the first time, displays a lower value than the three other carbonate minerals. This is explained by a strong distortion of the cationic site leading to a decrease of the coordination number during Ca-Mg substitution. Overall, the equilibrium magnesium isotope fractionation factors between aqueous Mg2+ and carbonate minerals that derive from this methodological study support the previous theoretical results obtained from embedded cluster models. © 2015 Elsevier Ltd. |
Theoretical study of the ionization of liquid water from its several initial orbitals by fast electron impact Article de journal M L D Sanctis; M -F Politis; R Vuilleumier; C R Stia; O A Fojón Journal of Physics B: Atomic, Molecular and Optical Physics, 48 (15), 2015. @article{Sanctis:2015, title = {Theoretical study of the ionization of liquid water from its several initial orbitals by fast electron impact}, author = {M L D 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-s2.0-84936760668&doi=10.1088%2f0953-4075%2f48%2f15%2f155201&partnerID=40&md5=d6920aaa90104dd081eab90d80ab9735}, doi = {10.1088/0953-4075/48/15/155201}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physics B: Atomic, Molecular and Optical Physics}, volume = {48}, number = {15}, abstract = {We theoretically study the single ionization of liquid water by energetic electrons through one active-electron first-order model. We analyze the angular ejected electron spectra corresponding to the most external orbitals 1B1, 2A1, 1B2 and 1A1 of a single water molecule. We work to create a realistic description of those orbitals corresponding to single molecules in the liquid phase. This goal is achieved by means of a Wannier orbital formalism. Multiple differential cross sections are computed and compared with previous calculations for both liquid and gas phases. In addition, our present results are integrated over all orientations and compared with experimental ones for randomly oriented vapour water molecules, as no experiments currently exist for the liquid phase. Moreover, we estimate the influence of the passive electrons on the reaction by means of a model potential. © 2015 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We theoretically study the single ionization of liquid water by energetic electrons through one active-electron first-order model. We analyze the angular ejected electron spectra corresponding to the most external orbitals 1B1, 2A1, 1B2 and 1A1 of a single water molecule. We work to create a realistic description of those orbitals corresponding to single molecules in the liquid phase. This goal is achieved by means of a Wannier orbital formalism. Multiple differential cross sections are computed and compared with previous calculations for both liquid and gas phases. In addition, our present results are integrated over all orientations and compared with experimental ones for randomly oriented vapour water molecules, as no experiments currently exist for the liquid phase. Moreover, we estimate the influence of the passive electrons on the reaction by means of a model potential. © 2015 IOP Publishing Ltd. |
Gas phase infrared spectra from quasi-classical Kubo time correlation functions Article de journal J Beutier; R Vuilleumier; S Bonella; G Ciccotti Molecular Physics, 113 (17-18), p. 2894–2904, 2015. @article{Beutier:2015, title = {Gas phase infrared spectra from quasi-classical Kubo time correlation functions}, author = {J Beutier and R Vuilleumier and S Bonella and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84943582680&doi=10.1080%2f00268976.2015.1064550&partnerID=40&md5=d9f397e5e12a264abe7ee76e1eb1ff6a}, doi = {10.1080/00268976.2015.1064550}, year = {2015}, date = {2015-01-01}, journal = {Molecular Physics}, volume = {113}, number = {17-18}, pages = {2894--2904}, abstract = {We generalise the recently developed phase integration method (PIM) to obtain a computable approximation of the Kubo expression for quantum time correlation functions. Our scheme combines exact sampling of the quantum thermal density with classical dynamics to provide a quasi-classical approximation for the correlation function. The method will be specialised to the evaluation of the momentum autocorrelation function, with the goal to compute infrared spectra of simple molecules in the gas phase. Application to two simple but interesting benchmark systems shows that the approach is accurate and stable over a broad range of temperatures. © 2015 © 2015 Taylor & Francis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We generalise the recently developed phase integration method (PIM) to obtain a computable approximation of the Kubo expression for quantum time correlation functions. Our scheme combines exact sampling of the quantum thermal density with classical dynamics to provide a quasi-classical approximation for the correlation function. The method will be specialised to the evaluation of the momentum autocorrelation function, with the goal to compute infrared spectra of simple molecules in the gas phase. Application to two simple but interesting benchmark systems shows that the approach is accurate and stable over a broad range of temperatures. © 2015 © 2015 Taylor & Francis. |
Investigation of the fragmentation of core-ionised deoxyribose: A study as a function of the tautomeric form Article de journal M -A Hervé Du Penhoat; K Kamol Ghose; M -P Gaigeot; R Vuilleumier; K Fujii; A Yokoya; M -F Politis Physical Chemistry Chemical Physics, 17 (48), p. 32375–32383, 2015. @article{HerveDuPenhoat:2015, title = {Investigation of the fragmentation of core-ionised deoxyribose: A study as a function of the tautomeric form}, author = {M -A Herv\'{e} Du Penhoat and K Kamol Ghose and M -P Gaigeot and R Vuilleumier and K Fujii and A Yokoya and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948800288&doi=10.1039%2fc5cp05196g&partnerID=40&md5=f37e8538f25dddc75ac8d9e34a927115}, doi = {10.1039/c5cp05196g}, year = {2015}, date = {2015-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {17}, number = {48}, pages = {32375--32383}, abstract = {We have investigated the gas phase fragmentation dynamics following the core ionisation of 2-deoxy-d-ribose (dR), a major component in the DNA chain. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics simulations. The ultrafast dissociation dynamics of the core-ionised biomolecule, prior Auger decay, is first modelled for 10 fs to generate initial configurations (atomic positions and velocities) for the subsequent dynamics of the doubly ionised biomolecule in the ground state. The furanose, linear and pyranose conformations of dR were investigated. We show that fragmentation is relatively independent of the atom struck or of the duration of the core vacancy, but depends rather critically on the molecular orbital removed following Auger decay. © 2015 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have investigated the gas phase fragmentation dynamics following the core ionisation of 2-deoxy-d-ribose (dR), a major component in the DNA chain. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics simulations. The ultrafast dissociation dynamics of the core-ionised biomolecule, prior Auger decay, is first modelled for 10 fs to generate initial configurations (atomic positions and velocities) for the subsequent dynamics of the doubly ionised biomolecule in the ground state. The furanose, linear and pyranose conformations of dR were investigated. We show that fragmentation is relatively independent of the atom struck or of the duration of the core vacancy, but depends rather critically on the molecular orbital removed following Auger decay. © 2015 the Owner Societies. |
Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function Article de journal A Scherrer; F Agostini; D Sebastiani; E K U Gross; R Vuilleumier Journal of Chemical Physics, 143 (7), 2015. @article{Scherrer:2015, title = {Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function}, author = {A Scherrer and F Agostini and D Sebastiani and E K U Gross and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939805732&doi=10.1063%2f1.4928578&partnerID=40&md5=11621b3149fe6735185b7f11d9afb3a1}, doi = {10.1063/1.4928578}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {7}, abstract = {The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similar to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similar to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach. © 2015 AIP Publishing LLC. |
Maximum probability domains for the analysis of the microscopic structure of liquids Article de journal F Agostini; G Ciccotti; A Savin; R Vuilleumier Journal of Chemical Physics, 142 (6), 2015. @article{Agostini:2015, title = {Maximum probability domains for the analysis of the microscopic structure of liquids}, author = {F Agostini and G Ciccotti and A Savin and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84923823374&doi=10.1063%2f1.4907406&partnerID=40&md5=c56bda95081ac55e95ed6320cf51b6bb}, doi = {10.1063/1.4907406}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {142}, number = {6}, abstract = {We introduce the concept of maximum probability domains (MPDs), developed in the context of the analysis of electronic densities, in the study of the microscopic spatial structures of liquids. The idea of locating a particle in a three dimensional region, by determining the domain where the probability of finding that, and only that, particle is maximum, gives an interesting characterization of the local structure of the liquid. The optimization procedure, required for the search of the domain of maximum probability, is carried out by the implementation of the level set method. Results for a couple of case studies are presented, to illustrate the structure of liquid water at ambient conditions and upon increasing pressure from the point of view of MPDs and to compare the information encoded in the solvation shells of sodium in water with, once again, that extracted from the MPDs. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We introduce the concept of maximum probability domains (MPDs), developed in the context of the analysis of electronic densities, in the study of the microscopic spatial structures of liquids. The idea of locating a particle in a three dimensional region, by determining the domain where the probability of finding that, and only that, particle is maximum, gives an interesting characterization of the local structure of the liquid. The optimization procedure, required for the search of the domain of maximum probability, is carried out by the implementation of the level set method. Results for a couple of case studies are presented, to illustrate the structure of liquid water at ambient conditions and upon increasing pressure from the point of view of MPDs and to compare the information encoded in the solvation shells of sodium in water with, once again, that extracted from the MPDs. © 2015 AIP Publishing LLC. |
C Pinilla; M Blanchard; E Balan; S K Natarajan; R Vuilleumier; F Mauri Geochimica et Cosmochimica Acta, 167 , p. 313–314, 2015. @article{Pinilla:2015, title = {Corrigendum to "Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics" [Geochim. Cosmochim. Acta 163, (2015), 126-139]}, author = {C Pinilla and M Blanchard and E Balan and S K Natarajan and R Vuilleumier and F Mauri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941259826&doi=10.1016%2fj.gca.2015.07.031&partnerID=40&md5=b41947dde52a6f26db2101956257fc16}, doi = {10.1016/j.gca.2015.07.031}, year = {2015}, date = {2015-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {167}, pages = {313--314}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase Article de journal P López-Tarifa; M -A Hervé du Penhoat; R Vuilleumier; M -P Gaigeot; U Rothlisberger; I Tavernelli; A Le Padellec; J -P Champeaux; M Alcamí; P Moretto-Capelle; F Martín; M -F Politis Central European Journal of Physics, 12 (2), p. 97–102, 2014. @article{Lopez-Tarifa:2014, title = {Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase}, author = {P L\'{o}pez-Tarifa and M -A Herv\'{e} du Penhoat and R Vuilleumier and M -P Gaigeot and U Rothlisberger 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-s2.0-84893924269&doi=10.2478%2fs11534-014-0428-0&partnerID=40&md5=35d93d17c384c60945c24d881913fa5a}, doi = {10.2478/s11534-014-0428-0}, year = {2014}, date = {2014-01-01}, journal = {Central European Journal of Physics}, volume = {12}, number = {2}, pages = {97--102}, abstract = {We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons. © 2014 Versita Warsaw and Springer-Verlag Wien.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons. © 2014 Versita Warsaw and Springer-Verlag Wien. |
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. |