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Professeur des Universités, Sorbonne Université ENS – Département de chimie Email: rodolphe.vuilleumier@ens.psl.eu |
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Publications
2011 |
Molecular density functional theory of solvation: From polar solvents to water Article de journal S Zhao; R Ramirez; R Vuilleumier; D Borgis Journal of Chemical Physics, 134 (19), 2011. @article{Zhao:2011, title = {Molecular density functional theory of solvation: From polar solvents to water}, author = {S Zhao and R Ramirez and R Vuilleumier and D Borgis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79957617663&doi=10.1063%2f1.3589142&partnerID=40&md5=9c9d2e79a7c7473971eea54466ad378b}, doi = {10.1063/1.3589142}, year = {2011}, date = {2011-01-01}, journal = {Journal of Chemical Physics}, volume = {134}, number = {19}, abstract = {A classical density functional theory approach to solvation in molecular solvent is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, limited to two-body correlations, the unknown excess term of the functional approximated by the angular-dependent direct correlation function of the pure solvent. We show that this function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation using a discrete angular representation. The corresponding functional can then be minimized in the presence of an arbitrary solute on a three-dimensional cubic grid for positions and Gauss-Legendre angular grid for orientations to provide the solvation structure and free-energy. This two-step procedure is proved to be much more efficient than direct molecular dynamics simulations combined to thermodynamic integration schemes. The approach is shown to be relevant and accurate for prototype polar solvents such as the Stockmayer solvent or acetonitrile. For water, although correct for neutral or moderately charged solute, it tends to underestimate the tetrahedral solvation structure around H-bonded solutes, such as spherical ions. This can be corrected by introducing suitable three-body correlation terms that restore both an accurate hydration structure and a satisfactory energetics. © 2011 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A classical density functional theory approach to solvation in molecular solvent is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, limited to two-body correlations, the unknown excess term of the functional approximated by the angular-dependent direct correlation function of the pure solvent. We show that this function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation using a discrete angular representation. The corresponding functional can then be minimized in the presence of an arbitrary solute on a three-dimensional cubic grid for positions and Gauss-Legendre angular grid for orientations to provide the solvation structure and free-energy. This two-step procedure is proved to be much more efficient than direct molecular dynamics simulations combined to thermodynamic integration schemes. The approach is shown to be relevant and accurate for prototype polar solvents such as the Stockmayer solvent or acetonitrile. For water, although correct for neutral or moderately charged solute, it tends to underestimate the tetrahedral solvation structure around H-bonded solutes, such as spherical ions. This can be corrected by introducing suitable three-body correlation terms that restore both an accurate hydration structure and a satisfactory energetics. © 2011 American Institute of Physics. |
2010 |
An ab initio molecular dynamics study on the hydrolysis of the Po(IV) aquaion in water Article de journal R Ayala; R Spezia; R Vuilleumier; J M Martínez; R R Pappalardo; E Sánchez Marcos Journal of Physical Chemistry B, 114 (40), p. 12866–12874, 2010. @article{Ayala:2010, title = {An ab initio molecular dynamics study on the hydrolysis of the Po(IV) aquaion in water}, author = {R Ayala and R Spezia and R Vuilleumier and J M Mart\'{i}nez and R R Pappalardo and E S\'{a}nchez Marcos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77957851129&doi=10.1021%2fjp1010956&partnerID=40&md5=3aa25dd7af47d17fa1b68a9dd6d665ca}, doi = {10.1021/jp1010956}, year = {2010}, date = {2010-01-01}, journal = {Journal of Physical Chemistry B}, volume = {114}, number = {40}, pages = {12866--12874}, abstract = {Po(IV) in water has been studied by means of Car - Parrinello molecular dynamics (CPMD) simulations. A new Trouiller - Martins pseudopotential for Po(IV) has been developed. This pseudopotential was tested by comparing the structure and energetics of small [Po(H2O)n(OH) m]4-m clusters optimized quantum-mechanically. CP-MD simulations of 1 Po + 60 H2O were carried out starting from three different degrees of hydrolysis of the aquaion (m = 0, 2, and 3), in order to check the stability of the hydrolyzed forms under the simulation conditions. The three simulations converge to a description of the solution where the same hydrolyzed species are present. Dynamics of the octahydrate aquaion in water indicates that dehydration couples to hydrolysis processes, and the total coordination number decreases with the hydrolysis degree. The time evolution of the initial [Po(H2O)8]4+ aquaion in aqueous solution indicates that hydrolysis precedes to dehydration in the process from aquaion to hydroxoaquaion. Structural and dynamical properties of the ligands in the first coordination shell are analyzed. The power spectra and its contribution from fragments of the first coordination shell are also examined. © 2010 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Po(IV) in water has been studied by means of Car - Parrinello molecular dynamics (CPMD) simulations. A new Trouiller - Martins pseudopotential for Po(IV) has been developed. This pseudopotential was tested by comparing the structure and energetics of small [Po(H2O)n(OH) m]4-m clusters optimized quantum-mechanically. CP-MD simulations of 1 Po + 60 H2O were carried out starting from three different degrees of hydrolysis of the aquaion (m = 0, 2, and 3), in order to check the stability of the hydrolyzed forms under the simulation conditions. The three simulations converge to a description of the solution where the same hydrolyzed species are present. Dynamics of the octahydrate aquaion in water indicates that dehydration couples to hydrolysis processes, and the total coordination number decreases with the hydrolysis degree. The time evolution of the initial [Po(H2O)8]4+ aquaion in aqueous solution indicates that hydrolysis precedes to dehydration in the process from aquaion to hydroxoaquaion. Structural and dynamical properties of the ligands in the first coordination shell are analyzed. The power spectra and its contribution from fragments of the first coordination shell are also examined. © 2010 American Chemical Society. |
Theoretical investigation of the ultrafast dissociation of ionised biomolecules immersed in water: Direct and indirect effects Article de journal M -P Gaigeot; P Lopez-Tarifa; F Martin; M Alcami; R Vuilleumier; I Tavernelli; M -A Hervé du Penhoat; M -F Politis Mutation Research - Reviews in Mutation Research, 704 (1-3), p. 45–53, 2010. @article{Gaigeot:2010, title = {Theoretical investigation of the ultrafast dissociation of ionised biomolecules immersed in water: Direct and indirect effects}, author = {M -P Gaigeot and P Lopez-Tarifa and F Martin and M Alcami and R Vuilleumier and I Tavernelli and M -A Herv\'{e} du Penhoat and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77952092866&doi=10.1016%2fj.mrrev.2010.01.004&partnerID=40&md5=8ea4dbae6930e8b1682e1c6771fff650}, doi = {10.1016/j.mrrev.2010.01.004}, year = {2010}, date = {2010-01-01}, journal = {Mutation Research - Reviews in Mutation Research}, volume = {704}, number = {1-3}, pages = {45--53}, abstract = {Theoretical simulations are particularly well suited to investigate, at a molecular level, direct and indirect effects of ionising radiations in DNA, as in the particular case of irradiation by swift heavy ions such as those used in hadron therapy. In the past recent years, we have developed the modeling at the microscopic level of the early stages of the Coulomb explosion of DNA molecules immersed in liquid water that follows the irradiation by swift heavy ions. To that end, Time-Dependent Density Functional Theory molecular dynamics simulations (TD-DFT MD) have been developed where localised Wannier orbitals are propagated. This latter enables to separate molecular orbitals of each water molecule from the molecular orbitals of the biomolecule. Our main objective is to demonstrate that the double ionisation of one molecule of the liquid sample, either one water molecule from the solvent or the biomolecule, may be in some cases responsible for the formation of an atomic oxygen as a direct consequence of the molecule Coulomb explosion. Our hypothesis is that the molecular double ionisation arising from irradiation by swift heavy ions (about 10% of ionisation events by ions whose velocity is about the third of speed of light), as a primary event, though maybe less probable than other events resulting from the electronic cascading (for instance, electronic excitations, electron attachments), may be systematically more damageable (and more lethal), as supported by experiments that have been carried out in our group in the 1990s (in studies of damages created by K holes in DNA). The chemical reactivity of the produced atomic oxygen with other radicals present in the medium will ultimately lead to chemical products that are harmful to DNA. In the present paper, we review our theoretical methodology in an attempt that the community be familiar with our new approach. Results on the production of atomic oxygen as a result of the double ionisation of water or as a result of the double ionisation of the Uracil RNA base will be presented. © 2010 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Theoretical simulations are particularly well suited to investigate, at a molecular level, direct and indirect effects of ionising radiations in DNA, as in the particular case of irradiation by swift heavy ions such as those used in hadron therapy. In the past recent years, we have developed the modeling at the microscopic level of the early stages of the Coulomb explosion of DNA molecules immersed in liquid water that follows the irradiation by swift heavy ions. To that end, Time-Dependent Density Functional Theory molecular dynamics simulations (TD-DFT MD) have been developed where localised Wannier orbitals are propagated. This latter enables to separate molecular orbitals of each water molecule from the molecular orbitals of the biomolecule. Our main objective is to demonstrate that the double ionisation of one molecule of the liquid sample, either one water molecule from the solvent or the biomolecule, may be in some cases responsible for the formation of an atomic oxygen as a direct consequence of the molecule Coulomb explosion. Our hypothesis is that the molecular double ionisation arising from irradiation by swift heavy ions (about 10% of ionisation events by ions whose velocity is about the third of speed of light), as a primary event, though maybe less probable than other events resulting from the electronic cascading (for instance, electronic excitations, electron attachments), may be systematically more damageable (and more lethal), as supported by experiments that have been carried out in our group in the 1990s (in studies of damages created by K holes in DNA). The chemical reactivity of the produced atomic oxygen with other radicals present in the medium will ultimately lead to chemical products that are harmful to DNA. In the present paper, we review our theoretical methodology in an attempt that the community be familiar with our new approach. Results on the production of atomic oxygen as a result of the double ionisation of water or as a result of the double ionisation of the Uracil RNA base will be presented. © 2010 Elsevier B.V. All rights reserved. |
Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water Article de journal C R Stia; M -P Gaigeot; R Vuilleumier; O A Fojón; M -A Hervé Du Penhoat; M -F Politis European Physical Journal D, 60 (1), p. 77–83, 2010. @article{Stia:2010, title = {Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water}, author = {C R Stia and M -P Gaigeot and R Vuilleumier and O A Foj\'{o}n and M -A Herv\'{e} Du Penhoat and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77958482556&doi=10.1140%2fepjd%2fe2010-00013-0&partnerID=40&md5=4a5c83df72276dbc0afdef6efa0b1dd6}, doi = {10.1140/epjd/e2010-00013-0}, year = {2010}, date = {2010-01-01}, journal = {European Physical Journal D}, volume = {60}, number = {1}, pages = {77--83}, abstract = {We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s 2 pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s 1 core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule. © 2010 EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s 2 pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s 1 core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule. © 2010 EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg. |
Molecular property investigations of an ortho-Hydroxy schiff base type compound with the first-principle molecular dynamics approach Article de journal A Jezierska-Mazzarello; R Vuilleumier; J J Panek; G Ciccotti Journal of Physical Chemistry B, 114 (1), p. 242–253, 2010. @article{Jezierska-Mazzarello:2010, title = {Molecular property investigations of an ortho-Hydroxy schiff base type compound with the first-principle molecular dynamics approach}, author = {A Jezierska-Mazzarello and R Vuilleumier and J J Panek and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-75649090084&doi=10.1021%2fjp903501m&partnerID=40&md5=b35c197d0696c62fe5dbac1dba1bb1ba}, doi = {10.1021/jp903501m}, year = {2010}, date = {2010-01-01}, journal = {Journal of Physical Chemistry B}, volume = {114}, number = {1}, pages = {242--253}, abstract = {The structure, proton transfer, and vibrational dynamics under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(Af-methyl-α-miinoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized on the nitrogen side of the O ⋯ H ⋯ N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while a more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects on this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm-1 assigned to the labile proton. In mere contrast, a much more localized absorption band around 2600-2700 cm-1 is predicted in the crystal phase. Finally, effects of the quantization of the proton motion on the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (1D) potential energy surface (PES) for the proton along the O ⋯ H ⋯ N bridge in a vacuum. The 1D Schr\"{o}dinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal. © 2010 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure, proton transfer, and vibrational dynamics under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(Af-methyl-α-miinoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized on the nitrogen side of the O ⋯ H ⋯ N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while a more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects on this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm-1 assigned to the labile proton. In mere contrast, a much more localized absorption band around 2600-2700 cm-1 is predicted in the crystal phase. Finally, effects of the quantization of the proton motion on the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (1D) potential energy surface (PES) for the proton along the O ⋯ H ⋯ N bridge in a vacuum. The 1D Schrödinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal. © 2010 American Chemical Society. |
2009 |
Ionization and fragmentation of water clusters by fast highly charged ions Article de journal L Adoui; A Cassimi; B Gervais; J -P Grandin; L Guillaume; R Maisonny; S Legendre; M Tarisien; P López-Tarifa; M -F Politis; M -A H D Penhoat; R Vuilleumier; M -P Gaigeot; I Tavernelli; M Alcamí; F Martín Journal of Physics B: Atomic, Molecular and Optical Physics, 42 (7), 2009. @article{Adoui:2009, title = {Ionization and fragmentation of water clusters by fast highly charged ions}, author = {L Adoui and A Cassimi and B Gervais and J -P Grandin and L Guillaume and R Maisonny and S Legendre and M Tarisien and P L\'{o}pez-Tarifa and M -F Politis and M -A H D Penhoat and R Vuilleumier and M -P Gaigeot and I Tavernelli and M Alcam\'{i} and F Mart\'{i}n}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-63749112329&doi=10.1088%2f0953-4075%2f42%2f7%2f075101&partnerID=40&md5=8ad2e3bcc56e669de64d204eed8f2e1a}, doi = {10.1088/0953-4075/42/7/075101}, year = {2009}, date = {2009-01-01}, journal = {Journal of Physics B: Atomic, Molecular and Optical Physics}, volume = {42}, number = {7}, abstract = {We study the dissociative ionization of water clusters by impact of 12 MeV/u Ni25+ ions. Cold target recoil ion momentum spectroscopy (COLTRIMS) is used to obtain information about stability, energetics and charge mobility of the ionized water clusters. An unusual stability of the H 9O+4 ion is observed, which could be the signature of the so-called Eigen structure in gas-phase water clusters. From the analysis of coincidences between charged fragments, we conclude that charge mobility is very high and is responsible for the formation of protonated water clusters, (H2O)nH+, that dominate the mass spectrum. These results are supported by Car-Parrinello molecular dynamics and time-dependent density functional theory simulations, which also reveal the mechanisms of such mobility. © 2009 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study the dissociative ionization of water clusters by impact of 12 MeV/u Ni25+ ions. Cold target recoil ion momentum spectroscopy (COLTRIMS) is used to obtain information about stability, energetics and charge mobility of the ionized water clusters. An unusual stability of the H 9O+4 ion is observed, which could be the signature of the so-called Eigen structure in gas-phase water clusters. From the analysis of coincidences between charged fragments, we conclude that charge mobility is very high and is responsible for the formation of protonated water clusters, (H2O)nH+, that dominate the mass spectrum. These results are supported by Car-Parrinello molecular dynamics and time-dependent density functional theory simulations, which also reveal the mechanisms of such mobility. © 2009 IOP Publishing Ltd. |
Improved modeling of liquid GeSe2: Impact of the exchange-correlation functional Article de journal M Micoulaut; R Vuilleumier; C Massobrio Physical Review B - Condensed Matter and Materials Physics, 79 (21), 2009. @article{Micoulaut:2009, title = {Improved modeling of liquid GeSe2: Impact of the exchange-correlation functional}, author = {M Micoulaut and R Vuilleumier and C Massobrio}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949116670&doi=10.1103%2fPhysRevB.79.214205&partnerID=40&md5=012bfda6fe80aa3fbdf7dcca6ce1da2d}, doi = {10.1103/PhysRevB.79.214205}, year = {2009}, date = {2009-01-01}, journal = {Physical Review B - Condensed Matter and Materials Physics}, volume = {79}, number = {21}, abstract = {The structural properties of liquid GeSe2 are studied by using first-principles molecular dynamics in conjunction with the Becke, Lee, Yang, and Parr (BLYP) generalized gradient approximation for the exchange and correlation energy. The results on partial pair-correlation functions, coordination numbers, bond-angle distributions, and partial-structure factors are compared with available experimental data and with previous first-principles molecular-dynamics results obtained within the Perdew and Wang (PW) generalized gradient approximation for the exchange and correlation energy. We found that the BLYP approach substantially improves upon the PW one in the case of the short-range properties. In particular, the Ge-Ge pair-correlation function takes a more structured profile that includes a marked first peak due to homopolar bonds, a first maximum exhibiting a clear shoulder, and a deep minimum, all these features being absent in the previous PW results. Overall, the amount of tetrahedral order is significantly increased in spite of a larger number of Ge-Ge homopolar connections. Due to the smaller number of miscoordinations, diffusion coefficients obtained by the present BLYP calculation are smaller by at least one order of magnitude than in the PW case. © 2009 The American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structural properties of liquid GeSe2 are studied by using first-principles molecular dynamics in conjunction with the Becke, Lee, Yang, and Parr (BLYP) generalized gradient approximation for the exchange and correlation energy. The results on partial pair-correlation functions, coordination numbers, bond-angle distributions, and partial-structure factors are compared with available experimental data and with previous first-principles molecular-dynamics results obtained within the Perdew and Wang (PW) generalized gradient approximation for the exchange and correlation energy. We found that the BLYP approach substantially improves upon the PW one in the case of the short-range properties. In particular, the Ge-Ge pair-correlation function takes a more structured profile that includes a marked first peak due to homopolar bonds, a first maximum exhibiting a clear shoulder, and a deep minimum, all these features being absent in the previous PW results. Overall, the amount of tetrahedral order is significantly increased in spite of a larger number of Ge-Ge homopolar connections. Due to the smaller number of miscoordinations, diffusion coefficients obtained by the present BLYP calculation are smaller by at least one order of magnitude than in the PW case. © 2009 The American Physical Society. |
2008 |
Time-dependent density functional theory molecular dynamics simulations of liquid water radiolysis Article de journal I Tavernelli; M -P Gaigeot; R Vuilleumier; C Stia; M -A H Du Penhoat; M -F Politis ChemPhysChem, 9 (14), p. 2099–2103, 2008. @article{Tavernelli:2008, title = {Time-dependent density functional theory molecular dynamics simulations of liquid water radiolysis}, author = {I Tavernelli and M -P Gaigeot and R Vuilleumier and C Stia and M -A H Du Penhoat and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-54349117726&doi=10.1002%2fcphc.200800177&partnerID=40&md5=85fb1901c0364bedc383c0c756128ede}, doi = {10.1002/cphc.200800177}, year = {2008}, date = {2008-01-01}, journal = {ChemPhysChem}, volume = {9}, number = {14}, pages = {2099--2103}, abstract = {The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD-DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B1, 3A1, 1B2 and 2A1 in turn. We show that the doubly charged H2O 2+ molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD-DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B1, 3A1, 1B2 and 2A1 in turn. We show that the doubly charged H2O 2+ molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA. |
Water nanodroplets confined in zeolite pores Article de journal F -X Coudert; F Cailliez; R Vuilleumier; A H Fuchs; A Boutin Faraday Discussions, 141 , p. 377–398, 2008. @article{Coudert:2008, title = {Water nanodroplets confined in zeolite pores}, author = {F -X Coudert and F Cailliez and R Vuilleumier and A H Fuchs and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-57449088628&doi=10.1039%2fb804992k&partnerID=40&md5=8bca46f18108fb666b9ab8ad60e3868f}, doi = {10.1039/b804992k}, year = {2008}, date = {2008-01-01}, journal = {Faraday Discussions}, volume = {141}, pages = {377--398}, abstract = {We provide a comprehensive depiction of the behaviour of a nanodroplet of ≃20 water molecules confined in the pores of a series of 3D-connected isostructural zeolites with varying acidity, by means of molecular simulations. Both grand canonical Monte Carlo simulations using classical interatomic forcefields and first-principles Car-Parrinello molecular dynamics were used in order to characterise the behaviour of confined water by computing a range of properties, from thermodynamic quantities to electronic properties such as dipole moment, including structural and dynamical information. From the thermodynamic point of view, we have identified the all-silica zeolite as hydrophobic, and the cationic zeolites as hydrophilic; the condensation transition in the first case was demonstrated to be of first order. Furthermore, in-depth analysis of the dynamical and electronic properties of water showed that water in the hydrophobic zeolite behaves as a nanodroplet trying to close its hydrogen-bond network onto itself, with a few short-lived dangling OH groups, while water in hydrophilic zeolites "opens up" to form weak hydrogen bonds with the zeolite oxygen atoms. Finally, the dipole moment of confined water is studied and the contributions of water self-polarisation and the zeolite electric field are discussed. © The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We provide a comprehensive depiction of the behaviour of a nanodroplet of ≃20 water molecules confined in the pores of a series of 3D-connected isostructural zeolites with varying acidity, by means of molecular simulations. Both grand canonical Monte Carlo simulations using classical interatomic forcefields and first-principles Car-Parrinello molecular dynamics were used in order to characterise the behaviour of confined water by computing a range of properties, from thermodynamic quantities to electronic properties such as dipole moment, including structural and dynamical information. From the thermodynamic point of view, we have identified the all-silica zeolite as hydrophobic, and the cationic zeolites as hydrophilic; the condensation transition in the first case was demonstrated to be of first order. Furthermore, in-depth analysis of the dynamical and electronic properties of water showed that water in the hydrophobic zeolite behaves as a nanodroplet trying to close its hydrogen-bond network onto itself, with a few short-lived dangling OH groups, while water in hydrophilic zeolites "opens up" to form weak hydrogen bonds with the zeolite oxygen atoms. Finally, the dipole moment of confined water is studied and the contributions of water self-polarisation and the zeolite electric field are discussed. © The Royal Society of Chemistry. |
Polarizabilities of individual molecules and ions in liquids from first principles Article de journal M Salanne; R Vuilleumier; P A Madden; C Simon; P Turq; B Guillot Journal of Physics Condensed Matter, 20 (49), 2008. @article{Salanne:2008, title = {Polarizabilities of individual molecules and ions in liquids from first principles}, author = {M Salanne and R Vuilleumier and P A Madden and C Simon and P Turq and B Guillot}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-58149343848&doi=10.1088%2f0953-8984%2f20%2f49%2f494207&partnerID=40&md5=bceb4208a46ed530858d1bf09f1de0d9}, doi = {10.1088/0953-8984/20/49/494207}, year = {2008}, date = {2008-01-01}, journal = {Journal of Physics Condensed Matter}, volume = {20}, number = {49}, abstract = {Dipole polarizabilities of individual ionic or molecular species are computed in three different liquid systems: liquid water, molten salts and magmatic melts, the last two belonging to the class of ionic liquids. The method is based on a purely first-principles procedure. The liquid water polarizability tensor is found to be nearly isotropic in the molecular framework. Important environmental effects occur in the two ionic systems when the nature and concentration of the cations are changed. The results of these calculations will be useful in the building of interaction potentials which include polarization effects. © 2008 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dipole polarizabilities of individual ionic or molecular species are computed in three different liquid systems: liquid water, molten salts and magmatic melts, the last two belonging to the class of ionic liquids. The method is based on a purely first-principles procedure. The liquid water polarizability tensor is found to be nearly isotropic in the molecular framework. Important environmental effects occur in the two ionic systems when the nature and concentration of the cations are changed. The results of these calculations will be useful in the building of interaction potentials which include polarization effects. © 2008 IOP Publishing Ltd. |