You can find below the publication list of all members of the theoretical chemistry group at ENS. For the list of each individual member, please consult their personal webpage from the Members page.
2017 |
Efficient molecular density functional theory using generalized spherical harmonics expansions Article de journal L Ding; M Levesque; D Borgis; L Belloni Journal of Chemical Physics, 147 (9), 2017. @article{Ding:2017, title = {Efficient molecular density functional theory using generalized spherical harmonics expansions}, author = {L Ding and M Levesque and D Borgis and L Belloni}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029323955&doi=10.1063%2f1.4994281&partnerID=40&md5=ed5f347a509ac617f483d0d8425de9ec}, doi = {10.1063/1.4994281}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {147}, number = {9}, abstract = {We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r ≡ (x,y,z) and of the three Euler angles Ω ≡ (θ,φ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r ≡ (x,y,z) and of the three Euler angles Ω ≡ (θ,φ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water. © 2017 Author(s). |
Classical Polarizable Force Field to Study Dry Charged Clays and Zeolites Article de journal S Tesson; W Louisfrema; M Salanne; A Boutin; B Rotenberg; V Marry Journal of Physical Chemistry C, 121 (18), p. 9833–9846, 2017. @article{Tesson:2017, title = {Classical Polarizable Force Field to Study Dry Charged Clays and Zeolites}, author = {S Tesson and W Louisfrema and M Salanne and A Boutin and B Rotenberg and V Marry}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020438967&doi=10.1021%2facs.jpcc.7b00270&partnerID=40&md5=b2f537a43ee14cace7b5baa0d4ca6bbd}, doi = {10.1021/acs.jpcc.7b00270}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry C}, volume = {121}, number = {18}, pages = {9833--9846}, abstract = {We extend the classical Polarizable Ion Model (PIM) to charged clays. We focus on Na-, Ca-, Sr-, and Cs-montmorillonite with two types of structures for the octahedral sheet: trans- and cis-vacant. The full set of parameters of the force field is determined by density functional theory calculations, using maximally localized Wannier functions with a force- and dipole-optimization procedure. Simulation results for our polarizable force field are compared with the state-of-the-art nonpolarizable flexible force field named Clay Force Field (ClayFF) to assess the importance of taking polarization effects into account for the prediction of structural properties. This force field is validated by comparison with experimental data. We also demonstrate the transferability of this force field to other aluminosilicates by considering faujasite-type zeolites and comparing the cation distribution for anhydrous Na, Ca, and Sr Y (and X) faujasites predicted by the PIM model and with experimental data. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We extend the classical Polarizable Ion Model (PIM) to charged clays. We focus on Na-, Ca-, Sr-, and Cs-montmorillonite with two types of structures for the octahedral sheet: trans- and cis-vacant. The full set of parameters of the force field is determined by density functional theory calculations, using maximally localized Wannier functions with a force- and dipole-optimization procedure. Simulation results for our polarizable force field are compared with the state-of-the-art nonpolarizable flexible force field named Clay Force Field (ClayFF) to assess the importance of taking polarization effects into account for the prediction of structural properties. This force field is validated by comparison with experimental data. We also demonstrate the transferability of this force field to other aluminosilicates by considering faujasite-type zeolites and comparing the cation distribution for anhydrous Na, Ca, and Sr Y (and X) faujasites predicted by the PIM model and with experimental data. © 2017 American Chemical Society. |
Kinetic Accessibility of Porous Material Adsorption Sites Studied through the Lattice Boltzmann Method Article de journal J -M Vanson; F -X Coudert; M Klotz; A Boutin Langmuir, 33 (6), p. 1405–1411, 2017. @article{Vanson:2017, title = {Kinetic Accessibility of Porous Material Adsorption Sites Studied through the Lattice Boltzmann Method}, author = {J -M Vanson and F -X Coudert and M Klotz and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85012885074&doi=10.1021%2facs.langmuir.6b04472&partnerID=40&md5=94b707833c0990403af7aa1b2264b31d}, doi = {10.1021/acs.langmuir.6b04472}, year = {2017}, date = {2017-01-01}, journal = {Langmuir}, volume = {33}, number = {6}, pages = {1405--1411}, abstract = {We present here a computational model based on the lattice Boltzmann scheme to investigate the accessibility of active adsorption sites in hierarchical porous materials to adsorbates in a flowing liquid. By studying the transport and adsorption of tracers after they enter the pore space of the virtual sample, we characterize their kinetics as they pass through the pore space and adsorb on the solid-liquid interface. The model is validated on simple geometries with a known analytical solution. We then use it to investigate the influence of regular grooves or disordered roughness on the walls of a slit pore geometry, looking at the impact on adsorption and transport. In particular, we highlight the importance of adsorption site accessibility, which depends on the shape and connectivity of the pore space as well as the fluid flow profile and velocity. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present here a computational model based on the lattice Boltzmann scheme to investigate the accessibility of active adsorption sites in hierarchical porous materials to adsorbates in a flowing liquid. By studying the transport and adsorption of tracers after they enter the pore space of the virtual sample, we characterize their kinetics as they pass through the pore space and adsorb on the solid-liquid interface. The model is validated on simple geometries with a known analytical solution. We then use it to investigate the influence of regular grooves or disordered roughness on the walls of a slit pore geometry, looking at the impact on adsorption and transport. In particular, we highlight the importance of adsorption site accessibility, which depends on the shape and connectivity of the pore space as well as the fluid flow profile and velocity. © 2017 American Chemical Society. |
New Molecular Simulation Method to Determine Both Aluminum and Cation Location in Cationic Zeolites Article de journal M Jeffroy; C Nieto-Draghi; A Boutin Chemistry of Materials, 29 (2), p. 513–523, 2017. @article{Jeffroy:2017, title = {New Molecular Simulation Method to Determine Both Aluminum and Cation Location in Cationic Zeolites}, author = {M Jeffroy and C Nieto-Draghi and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018467127&doi=10.1021%2facs.chemmater.6b03011&partnerID=40&md5=0af6ed3299d7a76f0f476eb3d12a61ea}, doi = {10.1021/acs.chemmater.6b03011}, year = {2017}, date = {2017-01-01}, journal = {Chemistry of Materials}, volume = {29}, number = {2}, pages = {513--523}, abstract = {The knowledge of aluminum distribution in zeolites is a difficult task due to limitations in experimental measurements. In the present paper, we propose a new methodology to simultaneously determined aluminum atoms distribution as well as the extraframework cation location in a given experimental structure of the framework and thus allows comparison of different synthesis routes. Aluminum mean distribution is obtained over a great number of configurations that are generated during the course of the simulations at finite temperature. The obtained aluminum atom repartition is in agreement with the experimental and model data available. The consequences of aluminum distribution on solid properties such as extraframework Na+ cation location have been analyzed and successfully compared with the available information for different zeolite topologies. The proposed methodology can be used as a powerful complementary tool for aluminum location on X-Ray or neutron experimental structure determinations. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The knowledge of aluminum distribution in zeolites is a difficult task due to limitations in experimental measurements. In the present paper, we propose a new methodology to simultaneously determined aluminum atoms distribution as well as the extraframework cation location in a given experimental structure of the framework and thus allows comparison of different synthesis routes. Aluminum mean distribution is obtained over a great number of configurations that are generated during the course of the simulations at finite temperature. The obtained aluminum atom repartition is in agreement with the experimental and model data available. The consequences of aluminum distribution on solid properties such as extraframework Na+ cation location have been analyzed and successfully compared with the available information for different zeolite topologies. The proposed methodology can be used as a powerful complementary tool for aluminum location on X-Ray or neutron experimental structure determinations. © 2016 American Chemical Society. |
Transport and adsorption under liquid flow: the role of pore geometry Article de journal J -M Vanson; A Boutin; M Klotz; F -X Coudert Soft Matter, 13 (4), p. 875–885, 2017. @article{Vanson:2017a, title = {Transport and adsorption under liquid flow: the role of pore geometry}, author = {J -M Vanson and A Boutin and M Klotz and F -X Coudert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010756176&doi=10.1039%2fc6sm02414a&partnerID=40&md5=64e7bbfdf37a29044f640d6638941543}, doi = {10.1039/c6sm02414a}, year = {2017}, date = {2017-01-01}, journal = {Soft Matter}, volume = {13}, number = {4}, pages = {875--885}, abstract = {We study here the interplay between transport and adsorption in porous systems with complex geometries under fluid flow. Using a lattice Boltzmann scheme extended to take into account the adsorption at solid/fluid interfaces, we investigate the influence of pore geometry and internal surface roughness on the efficiency of fluid flow and the adsorption of molecular species inside the pore space. We show how the occurrence of roughness on pore walls acts effectively as a modification of the solid/fluid boundary conditions, introducing slippage at the interface. We then compare three common pore geometries, namely honeycomb pores, inverse opal, and materials produced by spinodal decomposition. Finally, we quantify the influence of those three geometries on fluid transport and tracer adsorption. This opens perspectives for the optimization of materials’ geometries for applications in dynamic adsorption under fluid flow. © The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study here the interplay between transport and adsorption in porous systems with complex geometries under fluid flow. Using a lattice Boltzmann scheme extended to take into account the adsorption at solid/fluid interfaces, we investigate the influence of pore geometry and internal surface roughness on the efficiency of fluid flow and the adsorption of molecular species inside the pore space. We show how the occurrence of roughness on pore walls acts effectively as a modification of the solid/fluid boundary conditions, introducing slippage at the interface. We then compare three common pore geometries, namely honeycomb pores, inverse opal, and materials produced by spinodal decomposition. Finally, we quantify the influence of those three geometries on fluid transport and tracer adsorption. This opens perspectives for the optimization of materials’ geometries for applications in dynamic adsorption under fluid flow. © The Royal Society of Chemistry. |
2016 |
Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics Article de journal Oluwaseun O Mesele; Anthony A Vartia; D Laage; Ward H Thompson Journal of Physical Chemistry B, 120 (8), p. 1546-1559, 2016, ISSN: 1520-6106, (WOS:000371562700018). @article{Mesele:2016, title = {Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics}, author = {Oluwaseun O Mesele and Anthony A Vartia and D Laage and Ward H Thompson}, doi = {10.1021/acs.jpcb.5b07692}, issn = {1520-6106}, year = {2016}, date = {2016-03-01}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {8}, pages = {1546-1559}, abstract = {Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.}, note = {WOS:000371562700018}, keywords = {}, pubstate = {published}, tppubtype = {article} } Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects. |
Melting temperature of water: DFT-based molecular dynamics simulations with Đ3 dispersion correction Article de journal A P Seitsonen; T Bryk Physical Review B, 94 (18), 2016. @article{Seitsonen:2016a, title = {Melting temperature of water: DFT-based molecular dynamics simulations with {D}3 dispersion correction}, author = {A P Seitsonen and T Bryk}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85000366376&doi=10.1103%2fPhysRevB.94.184111&partnerID=40&md5=887c317dfc765387038886c8492ec853}, doi = {10.1103/PhysRevB.94.184111}, year = {2016}, date = {2016-01-01}, journal = {Physical Review B}, volume = {94}, number = {18}, abstract = {Extensive ab initio simulations of ice-water basal interface at seven temperatures in the range 250-400 K were performed in NVT and NPT ensembles with a collection of 389 water molecules in order to estimate the melting point of ice from direct liquid-solid two-phase coexistence. Density functional theory with the BLYP (Becke-Lee-Yang-Parr) exchange-correlation functional and the D3 dispersion correction were used in the expression of total energy. Analysis of density profiles and the evolution of the total potential, or Kohn-Sham plus D3, energy in the simulations at different temperatures resulted in an estimate for melting temperature of ice of 325 K. © 2016 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Extensive ab initio simulations of ice-water basal interface at seven temperatures in the range 250-400 K were performed in NVT and NPT ensembles with a collection of 389 water molecules in order to estimate the melting point of ice from direct liquid-solid two-phase coexistence. Density functional theory with the BLYP (Becke-Lee-Yang-Parr) exchange-correlation functional and the D3 dispersion correction were used in the expression of total energy. Analysis of density profiles and the evolution of the total potential, or Kohn-Sham plus D3, energy in the simulations at different temperatures resulted in an estimate for melting temperature of ice of 325 K. © 2016 American Physical Society. |
Isomerism of trimeric aluminum complexes in aqueous environments: Exploration via DFT-based metadynamics simulation Article de journal G Lanzani; A P Seitsonen; M Iannuzzi; K Laasonen; S O Pehkonen Journal of Physical Chemistry B, 120 (45), p. 11800–11809, 2016. @article{Lanzani:2016, title = {Isomerism of trimeric aluminum complexes in aqueous environments: Exploration via DFT-based metadynamics simulation}, author = {G Lanzani and A P Seitsonen and M Iannuzzi and K Laasonen and S O Pehkonen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85046685520&doi=10.1021%2facs.jpcb.6b08112&partnerID=40&md5=cd36cbdfc603835d8f1900e46b0532ff}, doi = {10.1021/acs.jpcb.6b08112}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {45}, pages = {11800--11809}, abstract = {The chemistry of aluminum or oxo-aluminum in water is still relatively unknown, although it is the basis for many chemical and industrial processes, including flocculation in water treatment plants. Trimeric species have a predominant role in the formation of the Keggin cations, which are the basic building blocks of aluminum-based chemicals. Despite this, details of the structural evolution of these small solvated clusters and how this is related to the processes leading to the formation of larger aggregates are still an open issue. To address these questions, here, we have applied the metadynamics (MTD) simulation technique [Barducci, A.; Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2010, 1, © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The chemistry of aluminum or oxo-aluminum in water is still relatively unknown, although it is the basis for many chemical and industrial processes, including flocculation in water treatment plants. Trimeric species have a predominant role in the formation of the Keggin cations, which are the basic building blocks of aluminum-based chemicals. Despite this, details of the structural evolution of these small solvated clusters and how this is related to the processes leading to the formation of larger aggregates are still an open issue. To address these questions, here, we have applied the metadynamics (MTD) simulation technique [Barducci, A.; Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2010, 1, © 2016 American Chemical Society. |
Electronic structure of reconstructed Au(111) studied with density functional theory Article de journal A P Seitsonen Surface Science, 643 , p. 150–155, 2016. @article{Seitsonen:2016, title = {Electronic structure of reconstructed Au(111) studied with density functional theory}, author = {A P Seitsonen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948699985&doi=10.1016%2fj.susc.2015.08.033&partnerID=40&md5=1debbcdfb82df224b219df529cd2cf18}, doi = {10.1016/j.susc.2015.08.033}, year = {2016}, date = {2016-01-01}, journal = {Surface Science}, volume = {643}, pages = {150--155}, abstract = {The interplay between the electronic structure and reconstruction of the geometry on a surface is an intriguing and exciting investigation. One classic example that has been one of the first systems to be identified using the angularly resolved photo-emission spectroscopy and scanning tunnelling microscopy is the Herringbone reconstruction on the Au(111) surface. Here, we report on the results derived from electronic structure calculations employing the density functional theory to investigate both the atomistic geometry and the electronic states near the Fermi energy, in particular the Shockley surface state. We find that despite the reconstruction of the electronic structure at the surface, it is actually relatively little modified from its unreconstructed counterpart. We further discuss the consequences in systems of weakly adsorbed species on this surface. © 2015 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The interplay between the electronic structure and reconstruction of the geometry on a surface is an intriguing and exciting investigation. One classic example that has been one of the first systems to be identified using the angularly resolved photo-emission spectroscopy and scanning tunnelling microscopy is the Herringbone reconstruction on the Au(111) surface. Here, we report on the results derived from electronic structure calculations employing the density functional theory to investigate both the atomistic geometry and the electronic states near the Fermi energy, in particular the Shockley surface state. We find that despite the reconstruction of the electronic structure at the surface, it is actually relatively little modified from its unreconstructed counterpart. We further discuss the consequences in systems of weakly adsorbed species on this surface. © 2015 Elsevier B.V. All rights reserved. |
Ab initio molecular dynamics study of collective excitations in liquid Ħ2O and Đ2O: Effect of dispersion corrections Article de journal T Bryk; A P Seitsonen Condensed Matter Physics, 19 (2), 2016. @article{Bryk:2016, title = {Ab initio molecular dynamics study of collective excitations in liquid {H}2O and {D}2O: Effect of dispersion corrections}, author = {T Bryk and A P Seitsonen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84960942151&doi=10.5488%2fCMP.19.23604&partnerID=40&md5=6411220ce7939170906f001878a88784}, doi = {10.5488/CMP.19.23604}, year = {2016}, date = {2016-01-01}, journal = {Condensed Matter Physics}, volume = {19}, number = {2}, abstract = {The collective dynamics in liquid water is an active research topic experimentally, theoretically and via simula- tions. Here, ab initio molecular dynamics simulations are reported in heavy and ordinary water at temperature 323.15 K, or 50°C. The simulations in heavy water were performed both with and without dispersion correc- tions. We found that the dispersion correction (DFT-D3) changes the relaxation of density-density time corre- lation functions from a slow, typical of a supercooled state, to exponential decay behaviour of regular liquids. This implies an essential reduction of the melting point of ice in simulations with DFT-D3. Analysis of longitudi- nal (L) and transverse (T) current spectral functions allowed us to estimate the dispersions of acoustic and optic collective excitations and to observe the L-T mixing effect. The dispersion correction shifts the L and T optic (0) modes to lower frequencies and provides by almost thirty per cent smaller gap between the longest-wavelength LO and TO excitations, which can be a consequence of a larger effective high-frequency dielectric permittivity in simulations with dispersion corrections. Simulation in ordinary water with the dispersion correction results in frequencies of optic excitations higher than in D2O, and in a long-wavelength LO-TO gap of 24 ps-l (127 cm-1). © T. Bryk, A.P. Seitsonen, 2016.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The collective dynamics in liquid water is an active research topic experimentally, theoretically and via simula- tions. Here, ab initio molecular dynamics simulations are reported in heavy and ordinary water at temperature 323.15 K, or 50°C. The simulations in heavy water were performed both with and without dispersion correc- tions. We found that the dispersion correction (DFT-D3) changes the relaxation of density-density time corre- lation functions from a slow, typical of a supercooled state, to exponential decay behaviour of regular liquids. This implies an essential reduction of the melting point of ice in simulations with DFT-D3. Analysis of longitudi- nal (L) and transverse (T) current spectral functions allowed us to estimate the dispersions of acoustic and optic collective excitations and to observe the L-T mixing effect. The dispersion correction shifts the L and T optic (0) modes to lower frequencies and provides by almost thirty per cent smaller gap between the longest-wavelength LO and TO excitations, which can be a consequence of a larger effective high-frequency dielectric permittivity in simulations with dispersion corrections. Simulation in ordinary water with the dispersion correction results in frequencies of optic excitations higher than in D2O, and in a long-wavelength LO-TO gap of 24 ps-l (127 cm-1). © T. Bryk, A.P. Seitsonen, 2016. |
Vibrational Quantum Decoherence in Liquid Water Article de journal T Joutsuka; W H Thompson; D Laage Journal of Physical Chemistry Letters, 7 (4), p. 616–621, 2016. @article{Joutsuka:2016, title = {Vibrational Quantum Decoherence in Liquid Water}, author = {T Joutsuka and W H Thompson and D Laage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959016898&doi=10.1021%2facs.jpclett.5b02637&partnerID=40&md5=a5756d755414536733c5ecbdc14b0bb6}, doi = {10.1021/acs.jpclett.5b02637}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {7}, number = {4}, pages = {616--621}, abstract = {Traditional descriptions of vibrational energy transfer consider a quantum oscillator interacting with a classical environment. However, a major limitation of this simplified description is the neglect of quantum decoherence induced by the different interactions between two distinct quantum states and their environment, which can strongly affect the predicted energy-transfer rate and vibrational spectra. Here, we use quantum-classical molecular dynamics simulations to determine the vibrational quantum decoherence time for an OH stretch vibration in liquid heavy water. We show that coherence is lost on a sub-100 fs time scale due to the different responses of the first shell neighbors to the ground and excited OH vibrational states. This ultrafast decoherence induces a strong homogeneous contribution to the linear infrared spectrum and suggests that resonant vibrational energy transfer in H2O may be more incoherent than previously thought. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Traditional descriptions of vibrational energy transfer consider a quantum oscillator interacting with a classical environment. However, a major limitation of this simplified description is the neglect of quantum decoherence induced by the different interactions between two distinct quantum states and their environment, which can strongly affect the predicted energy-transfer rate and vibrational spectra. Here, we use quantum-classical molecular dynamics simulations to determine the vibrational quantum decoherence time for an OH stretch vibration in liquid heavy water. We show that coherence is lost on a sub-100 fs time scale due to the different responses of the first shell neighbors to the ground and excited OH vibrational states. This ultrafast decoherence induces a strong homogeneous contribution to the linear infrared spectrum and suggests that resonant vibrational energy transfer in H2O may be more incoherent than previously thought. © 2016 American Chemical Society. |
Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores Article de journal P C Burris; D Laage; W H Thompson Journal of Chemical Physics, 144 (19), 2016. @article{Burris:2016, title = {Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores}, author = {P C Burris and D Laage and W H Thompson}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971280304&doi=10.1063%2f1.4949766&partnerID=40&md5=37f7bb693ca5c44b2827d6345cf67125}, doi = {10.1063/1.4949766}, year = {2016}, date = {2016-01-01}, journal = {Journal of Chemical Physics}, volume = {144}, number = {19}, abstract = {Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra. © 2016 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra. © 2016 Author(s). |
On the Structural and Dynamical Properties of DOPC Reverse Micelles Article de journal S Abel; N Galamba; E Karakas; M Marchi; W H Thompson; D Laage Langmuir, 32 (41), p. 10610–10620, 2016. @article{Abel:2016, title = {On the Structural and Dynamical Properties of DOPC Reverse Micelles}, author = {S Abel and N Galamba and E Karakas and M Marchi and W H Thompson and D Laage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991786943&doi=10.1021%2facs.langmuir.6b02566&partnerID=40&md5=8ede1264f6cd7bdca0d2fc42f54e20bf}, doi = {10.1021/acs.langmuir.6b02566}, year = {2016}, date = {2016-01-01}, journal = {Langmuir}, volume = {32}, number = {41}, pages = {10610--10620}, abstract = {The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We report all-atom unconstrained simulations of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) reverse micelles in benzene of increasing sizes, with water-to-surfactant number ratios ranging from W0 = 1 to 16. The aggregation number, i.e., the number of DOPC molecules per reverse micelle, is determined to fit experimental light-scattering measurements of the reverse micelle diameter. The simulated reverse micelles are found to be approximately spherical. Larger reverse micelles (W0 > 4) exhibit a layered structure with a water core and the hydration structure of DOPC phosphate head groups is similar to that found in phospholipid membranes. In contrast, the structure of smaller reverse micelles (W0 ≤ 4) cannot be described as a series of concentric layers successively containing water, surfactant head groups, and surfactant tails, and the head groups are only partly hydrated and frequently present in the core. The dynamics of water molecules within the phospholipid reverse micelles slow down as the reverse micelle size decreases, in agreement with prior studies on AOT and Igepal reverse micelles. However, the average water reorientation dynamics in DOPC reverse micelles is found to be much slower than in AOT and Igepal reverse micelles with the same W0 ratio. This is explained by the smaller water pool and by the stronger interactions between water and the charged head groups, as confirmed by the red-shift of the computed infrared line shape with decreasing W0. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We report all-atom unconstrained simulations of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) reverse micelles in benzene of increasing sizes, with water-to-surfactant number ratios ranging from W0 = 1 to 16. The aggregation number, i.e., the number of DOPC molecules per reverse micelle, is determined to fit experimental light-scattering measurements of the reverse micelle diameter. The simulated reverse micelles are found to be approximately spherical. Larger reverse micelles (W0 > 4) exhibit a layered structure with a water core and the hydration structure of DOPC phosphate head groups is similar to that found in phospholipid membranes. In contrast, the structure of smaller reverse micelles (W0 ≤ 4) cannot be described as a series of concentric layers successively containing water, surfactant head groups, and surfactant tails, and the head groups are only partly hydrated and frequently present in the core. The dynamics of water molecules within the phospholipid reverse micelles slow down as the reverse micelle size decreases, in agreement with prior studies on AOT and Igepal reverse micelles. However, the average water reorientation dynamics in DOPC reverse micelles is found to be much slower than in AOT and Igepal reverse micelles with the same W0 ratio. This is explained by the smaller water pool and by the stronger interactions between water and the charged head groups, as confirmed by the red-shift of the computed infrared line shape with decreasing W0. © 2016 American Chemical Society. |
Orientational dynamics of water at an extended hydrophobic interface Article de journal S Xiao; F Figge; G Stirnemann; D Laage; J A McGuire Journal of the American Chemical Society, 138 (17), p. 5551–5560, 2016. @article{Xiao:2016, title = {Orientational dynamics of water at an extended hydrophobic interface}, author = {S Xiao and F Figge and G Stirnemann and D Laage and J A McGuire}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84968902061&doi=10.1021%2fjacs.6b01820&partnerID=40&md5=8008b1cea9705b6eac7d1100561cd39b}, doi = {10.1021/jacs.6b01820}, year = {2016}, date = {2016-01-01}, journal = {Journal of the American Chemical Society}, volume = {138}, number = {17}, pages = {5551--5560}, abstract = {We report on the orientational dynamics of water at an extended hydrophobic interface with an octadecylsilane self-assembled monolayer on fused silica. The interfacial dangling OH stretch mode is excited with a resonant pump, and its evolution followed in time by a surfacespecific, vibrationally resonant, infrared-visible sum-frequency probe. High sensitivity pump-probe anisotropy measurements and isotopic dilution clearly reveal that the decay of the dangling OH stretch excitation is almost entirely due to a jump to a hydrogen-bonded configuration that occurs in 1.61 ± 0.10 ps. This is more than twice as fast as the jump time from one hydrogen-bonded configuration to another in bulk H2O but about 50% slower than the reported out-of-plane reorientation at the air/water interface. In contrast, the intrinsic population lifetime of the dangling OH stretch in the absence of such jumps is found to be >10 ps. Molecular dynamics simulations of air/water and hexane/water interfaces reproduce the fast jump dynamics of interfacial dangling OH with calculated jump times of 1.4 and 1.7 ps for the air and hydrophobic interfaces, respectively. The simulations highlight that while the air/water and hydrophobic/water surfaces exhibit great structural similarities, a small stabilization of the OH groups by the hydrophobic interface produces the pronounced difference in the dynamics of dangling bonds. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report on the orientational dynamics of water at an extended hydrophobic interface with an octadecylsilane self-assembled monolayer on fused silica. The interfacial dangling OH stretch mode is excited with a resonant pump, and its evolution followed in time by a surfacespecific, vibrationally resonant, infrared-visible sum-frequency probe. High sensitivity pump-probe anisotropy measurements and isotopic dilution clearly reveal that the decay of the dangling OH stretch excitation is almost entirely due to a jump to a hydrogen-bonded configuration that occurs in 1.61 ± 0.10 ps. This is more than twice as fast as the jump time from one hydrogen-bonded configuration to another in bulk H2O but about 50% slower than the reported out-of-plane reorientation at the air/water interface. In contrast, the intrinsic population lifetime of the dangling OH stretch in the absence of such jumps is found to be >10 ps. Molecular dynamics simulations of air/water and hexane/water interfaces reproduce the fast jump dynamics of interfacial dangling OH with calculated jump times of 1.4 and 1.7 ps for the air and hydrophobic interfaces, respectively. The simulations highlight that while the air/water and hydrophobic/water surfaces exhibit great structural similarities, a small stabilization of the OH groups by the hydrophobic interface produces the pronounced difference in the dynamics of dangling bonds. © 2016 American Chemical Society. |
OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands Article de journal N Chéron; N Jasty; E I Shakhnovich Journal of Medicinal Chemistry, 59 (9), p. 4171-4188, 2016. @article{Cheron:2016a, title = {OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands}, author = {N Ch\'{e}ron and N Jasty and E I Shakhnovich}, doi = {10.1021/acs.jmedchem.5b00886}, year = {2016}, date = {2016-01-01}, journal = {Journal of Medicinal Chemistry}, volume = {59}, number = {9}, pages = {4171-4188}, abstract = {We present a new open-source software, called OpenGrowth, which aims to create de novo ligands by connecting small organic fragments in the active site of proteins. Molecule growth is biased to produce structures that statistically resemble drugs in an input training database. Consequently, the produced molecules have superior synthetic accessibility and pharmacokinetic properties compared with randomly grown molecules. The growth process can take into account the flexibility of the target protein and can be started from a seed to mimic R-group strategy or fragment-based drug discovery. Primary applications of the software on the HIV-1 protease allowed us to quickly identify new inhibitors with a predicted Kd as low as 18 nM. We also present a graphical user interface that allows a user to select easily the fragments to include in the growth process. OpenGrowth is released under the GNU GPL license and is available free of charge on the authors website and at http://opengrowth.sourceforge.net/. textcopyright 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present a new open-source software, called OpenGrowth, which aims to create de novo ligands by connecting small organic fragments in the active site of proteins. Molecule growth is biased to produce structures that statistically resemble drugs in an input training database. Consequently, the produced molecules have superior synthetic accessibility and pharmacokinetic properties compared with randomly grown molecules. The growth process can take into account the flexibility of the target protein and can be started from a seed to mimic R-group strategy or fragment-based drug discovery. Primary applications of the software on the HIV-1 protease allowed us to quickly identify new inhibitors with a predicted Kd as low as 18 nM. We also present a graphical user interface that allows a user to select easily the fragments to include in the growth process. OpenGrowth is released under the GNU GPL license and is available free of charge on the authors website and at http://opengrowth.sourceforge.net/. textcopyright 2015 American Chemical Society. |
Evolutionary Dynamics of Viral Escape under Antibodies Stress: A Biophysical Model Article de journal N Chéron; A W R Serohijos; J -M Choi; E I Shakhnovich Protein Science, p. 1332-1340, 2016. @article{Cheron:2016, title = {Evolutionary Dynamics of Viral Escape under Antibodies Stress: A Biophysical Model}, author = {N Ch\'{e}ron and A W R Serohijos and J -M Choi and E I Shakhnovich}, doi = {10.1002/pro.2915}, year = {2016}, date = {2016-01-01}, journal = {Protein Science}, pages = {1332-1340}, abstract = {Viruses constantly face the selection pressure of antibodies, either from innate immune response of the host or from administered antibodies for treatment. We explore the interplay between the biophysical properties of viral proteins and the population and demographic variables in the viral escape. The demographic and population genetics aspect of the viral escape have been explored before; however one important assumption was the a priori distribution of fitness effects (DFE). Here, we relax this assumption by instead considering a realistic biophysics-based genotype-phenotype relationship for RNA viruses escaping antibodies stress. In this model the DFE is itself an evolvable property that depends on the genetic background (epistasis) and the distribution of biophysical effects of mutations, which is informed by biochemical experiments and theoretical calculations in protein engineering. We quantitatively explore in silico the viability of viral populations under antibodies pressure and derive the phase diagram that defines the fate of the virus population (extinction or escape from stress) in a range of viral mutation rates and antibodies concentrations. We find that viruses are most resistant to stress at an optimal mutation rate (OMR) determined by the competition between supply of beneficial mutation to facilitate escape from stressors and lethal mutagenesis caused by excess of destabilizing mutations. We then show the quantitative dependence of the OMR on genome length and viral burst size. We also recapitulate the experimental observation that viruses with longer genomes have smaller mutation rate per nucleotide. textcopyright 2016 The Protein Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } Viruses constantly face the selection pressure of antibodies, either from innate immune response of the host or from administered antibodies for treatment. We explore the interplay between the biophysical properties of viral proteins and the population and demographic variables in the viral escape. The demographic and population genetics aspect of the viral escape have been explored before; however one important assumption was the a priori distribution of fitness effects (DFE). Here, we relax this assumption by instead considering a realistic biophysics-based genotype-phenotype relationship for RNA viruses escaping antibodies stress. In this model the DFE is itself an evolvable property that depends on the genetic background (epistasis) and the distribution of biophysical effects of mutations, which is informed by biochemical experiments and theoretical calculations in protein engineering. We quantitatively explore in silico the viability of viral populations under antibodies pressure and derive the phase diagram that defines the fate of the virus population (extinction or escape from stress) in a range of viral mutation rates and antibodies concentrations. We find that viruses are most resistant to stress at an optimal mutation rate (OMR) determined by the competition between supply of beneficial mutation to facilitate escape from stressors and lethal mutagenesis caused by excess of destabilizing mutations. We then show the quantitative dependence of the OMR on genome length and viral burst size. We also recapitulate the experimental observation that viruses with longer genomes have smaller mutation rate per nucleotide. textcopyright 2016 The Protein Society |
Surface-Guided Formation of an Organocobalt Complex Article de journal P B Weber; R Hellwig; T Paintner; M Lattelais; M Paszkiewicz; P Casado Aguilar; P S Deimel; Y Guo; Y -Q Zhang; F Allegretti; A C Papageorgiou; J Reichert; S Klyatskaya; M Ruben; J V Barth; M -L Bocquet; F Klappenberger Angewandte Chemie - International Edition, 55 (19), p. 5754–5759, 2016. @article{Weber:2016a, title = {Surface-Guided Formation of an Organocobalt Complex}, author = {P B Weber and R Hellwig and T Paintner and M Lattelais and M Paszkiewicz and P Casado Aguilar and P S Deimel and Y Guo and Y -Q Zhang and F Allegretti and A C Papageorgiou and J Reichert and S Klyatskaya and M Ruben and J V Barth and M -L Bocquet and F Klappenberger}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84979487355&doi=10.1002%2fanie.201600567&partnerID=40&md5=6fdacc6d82566f8f37029e26117f82e4}, doi = {10.1002/anie.201600567}, year = {2016}, date = {2016-01-01}, journal = {Angewandte Chemie - International Edition}, volume = {55}, number = {19}, pages = {5754--5759}, abstract = {Organocobalt complexes represent a versatile tool in organic synthesis as they are important intermediates in Pauson-Khand, Friedel-Crafts, and Nicholas reactions. Herein, a single-molecule-level investigation addressing the formation of an organocobalt complex at a solid-vacuum interface is reported. Deposition of 4,4′-(ethyne-1,2-diyl)dibenzonitrile and Co atoms on the Ag(111) surface followed by annealing resulted in genuine complexes in which single Co atoms laterally coordinated to two carbonitrile groups undergo organometallic bonding with the internal alkyne moiety of adjacent molecules. Alternative complexation scenarios involving fragmentation of the precursor were ruled out by complementary X-ray photoelectron spectroscopy. According to density functional theory analysis, the complexation with the alkyne moiety follows the Dewar-Chatt-Duncanson model for a two-electron-donor ligand where an alkyne-to-Co donation occurs together with a strong metal-to-alkyne back-donation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Organocobalt complexes represent a versatile tool in organic synthesis as they are important intermediates in Pauson-Khand, Friedel-Crafts, and Nicholas reactions. Herein, a single-molecule-level investigation addressing the formation of an organocobalt complex at a solid-vacuum interface is reported. Deposition of 4,4′-(ethyne-1,2-diyl)dibenzonitrile and Co atoms on the Ag(111) surface followed by annealing resulted in genuine complexes in which single Co atoms laterally coordinated to two carbonitrile groups undergo organometallic bonding with the internal alkyne moiety of adjacent molecules. Alternative complexation scenarios involving fragmentation of the precursor were ruled out by complementary X-ray photoelectron spectroscopy. According to density functional theory analysis, the complexation with the alkyne moiety follows the Dewar-Chatt-Duncanson model for a two-electron-donor ligand where an alkyne-to-Co donation occurs together with a strong metal-to-alkyne back-donation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Unveiling nickelocene bonding to a noble metal surface Article de journal N Bachellier; M Ormaza; M Faraggi; B Verlhac; M Vérot; T Le Bahers; M -L Bocquet; L Limot Physical Review B, 93 (19), 2016. @article{Bachellier:2016, title = {Unveiling nickelocene bonding to a noble metal surface}, author = {N Bachellier and M Ormaza and M Faraggi and B Verlhac and M V\'{e}rot and T Le Bahers and M -L Bocquet and L Limot}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84966393700&doi=10.1103%2fPhysRevB.93.195403&partnerID=40&md5=0d106e1b25a806a9951287b97708234a}, doi = {10.1103/PhysRevB.93.195403}, year = {2016}, date = {2016-01-01}, journal = {Physical Review B}, volume = {93}, number = {19}, abstract = {The manipulation of a molecular spin state in low-dimensional materials is central to molecular spintronics. The designs of hybrid devices incorporating magnetic metallocenes are very promising in this regard, but are hampered by the lack of data regarding their interaction with a metal. Here, we combine low-temperature scanning tunneling microscopy and density functional theory calculations to investigate a magnetic metallocene at the single-molecule level - nickelocene. We demonstrate that the chemical and electronic structures of nickelocene are preserved upon adsorption on a copper surface. Several bonding configurations to the surface are identified, ranging from the isolated molecule to molecular layers governed by van der Waals interactions. © 2016 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The manipulation of a molecular spin state in low-dimensional materials is central to molecular spintronics. The designs of hybrid devices incorporating magnetic metallocenes are very promising in this regard, but are hampered by the lack of data regarding their interaction with a metal. Here, we combine low-temperature scanning tunneling microscopy and density functional theory calculations to investigate a magnetic metallocene at the single-molecule level - nickelocene. We demonstrate that the chemical and electronic structures of nickelocene are preserved upon adsorption on a copper surface. Several bonding configurations to the surface are identified, ranging from the isolated molecule to molecular layers governed by van der Waals interactions. © 2016 American Physical Society. |
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. |
Dynamical Disorder in the DNA Hydration Shell Article de journal E Duboué-Dijon; A C Fogarty; J T Hynes; D Laage Journal of the American Chemical Society, 138 (24), p. 7610–7620, 2016. @article{Duboue-Dijon:2016, title = {Dynamical Disorder in the DNA Hydration Shell}, author = {E Dubou\'{e}-Dijon and A C Fogarty and J T Hynes and D Laage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976416660&doi=10.1021%2fjacs.6b02715&partnerID=40&md5=4adecb027f0596a74012aa13c1de675d}, doi = {10.1021/jacs.6b02715}, year = {2016}, date = {2016-01-01}, journal = {Journal of the American Chemical Society}, volume = {138}, number = {24}, pages = {7610--7620}, abstract = {The reorientation and hydrogen-bond dynamics of water molecules within the hydration shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are investigated via molecular dynamics simulations and an analytic jump model, which provide valuable new molecular level insights into these dynamics. Different sources of heterogeneity in the hydration shell dynamics are determined. First, a pronounced spatial heterogeneity is found at the DNA interface and explained via the jump model by the diversity in local DNA interfacial topographies and DNA-water H-bond interactions. While most of the hydration shell is moderately retarded with respect to the bulk, some water molecules confined in the narrow minor groove exhibit very slow dynamics. An additional source of heterogeneity is found to be caused by the DNA conformational fluctuations, which modulate the water dynamics. The groove widening aids the approach of, and the jump to, a new water H-bond partner. This temporal heterogeneity is especially strong in the minor groove, where groove width fluctuations occur on the same time scale as the water H-bond rearrangements, leading to a strong dynamical disorder. The usual simplifying assumption that hydration shell dynamics is much faster than DNA dynamics is thus not valid; our results show that biomolecular conformational fluctuations are essential to facilitate the water motions and accelerate the hydration dynamics in confined groove sites. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The reorientation and hydrogen-bond dynamics of water molecules within the hydration shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are investigated via molecular dynamics simulations and an analytic jump model, which provide valuable new molecular level insights into these dynamics. Different sources of heterogeneity in the hydration shell dynamics are determined. First, a pronounced spatial heterogeneity is found at the DNA interface and explained via the jump model by the diversity in local DNA interfacial topographies and DNA-water H-bond interactions. While most of the hydration shell is moderately retarded with respect to the bulk, some water molecules confined in the narrow minor groove exhibit very slow dynamics. An additional source of heterogeneity is found to be caused by the DNA conformational fluctuations, which modulate the water dynamics. The groove widening aids the approach of, and the jump to, a new water H-bond partner. This temporal heterogeneity is especially strong in the minor groove, where groove width fluctuations occur on the same time scale as the water H-bond rearrangements, leading to a strong dynamical disorder. The usual simplifying assumption that hydration shell dynamics is much faster than DNA dynamics is thus not valid; our results show that biomolecular conformational fluctuations are essential to facilitate the water motions and accelerate the hydration dynamics in confined groove sites. © 2016 American Chemical Society. |
Non-Adiabatic Transition Probability Dependence on Conical Intersection Topography Article de journal J P Malhado; J T Hynes Journal of Chemical Physics, 145 (19), 2016, (cited By 6). @article{Malhado2016, title = {Non-Adiabatic Transition Probability Dependence on Conical Intersection Topography}, author = {J P Malhado and J T Hynes}, doi = {10.1063/1.4967259}, year = {2016}, date = {2016-01-01}, journal = {Journal of Chemical Physics}, volume = {145}, number = {19}, abstract = {We derive a closed form analytical expression for the non-adiabatic transition probability for a distribution of trajectories passing through a generic conical intersection (CI), based on the Landau-Zener equation for the non-adiabatic transition probability for a single straight-line trajectory in the CI's vicinity. We investigate the non-adiabatic transition probability's variation with topographical features and find, for the same crossing velocity, no intrinsic difference in efficiency at promoting non-adiabatic decay between peaked and sloped CIs, a result in contrast to the commonly held view. Any increased efficiency of peaked over sloped CIs is thus due to dynamical effects rather than to any increased transition probability of topographical origin. It is also shown that the transition probability depends in general on the direction of approach to the CI, and that the coordinates' reduced mass can affect the transition probability via its influence on the CI topography in mass-scaled coordinates. The resulting predictions compare well with surface hopping simulation results. textcopyright 2016 Author(s).}, note = {cited By 6}, keywords = {}, pubstate = {published}, tppubtype = {article} } We derive a closed form analytical expression for the non-adiabatic transition probability for a distribution of trajectories passing through a generic conical intersection (CI), based on the Landau-Zener equation for the non-adiabatic transition probability for a single straight-line trajectory in the CI's vicinity. We investigate the non-adiabatic transition probability's variation with topographical features and find, for the same crossing velocity, no intrinsic difference in efficiency at promoting non-adiabatic decay between peaked and sloped CIs, a result in contrast to the commonly held view. Any increased efficiency of peaked over sloped CIs is thus due to dynamical effects rather than to any increased transition probability of topographical origin. It is also shown that the transition probability depends in general on the direction of approach to the CI, and that the coordinates' reduced mass can affect the transition probability via its influence on the CI topography in mass-scaled coordinates. The resulting predictions compare well with surface hopping simulation results. textcopyright 2016 Author(s). |
Solvation Dynamics in Water: 2. Energy Fluxes on Excited-and Ground-State Surfaces Article de journal R Rey; J T Hynes Journal of Physical Chemistry B, 120 (43), p. 11287-11297, 2016, (cited By 4). @article{Rey201611287, title = {Solvation Dynamics in Water: 2. Energy Fluxes on Excited-and Ground-State Surfaces}, author = {R Rey and J T Hynes}, doi = {10.1021/acs.jpcb.6b08965}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {43}, pages = {11287-11297}, abstract = {This series' first installment introduced an approach to solvation dynamics focused on expressing the emission frequency shift (following electronic excitation of, and resulting charge change or redistribution in, a solute) in terms of energy fluxes, a work and power perspective. This approach, which had been previously exploited for rotational and vibrational excitation-induced energy flow, has the novel advantage of providing a quantitative view and understanding of the molecular-level mechanisms involved in the solvation dynamics via tracing of the energy flow induced by the electronic excitation's charge change or redistribution in the solute. This new methodology, which was illustrated for the case in which only the excited electronic state surface contributes to the frequency shift (ionization of a monatomic solute in water), is here extended to the general case in which both the excited and ground electronic states may contribute. Simple monatomic solute model variations allow a discussion of the (sometimes surprising) issues involved in assessing each surface's contribution. The calculation of properly defined energy fluxes/work allows a more complete understanding of the solvation dynamics even when the real work for one of the surfaces does not directly contribute to the frequency shift, an aspect further emphasizing the utility of an energy flux approach. textcopyright 2016 American Chemical Society.}, note = {cited By 4}, keywords = {}, pubstate = {published}, tppubtype = {article} } This series' first installment introduced an approach to solvation dynamics focused on expressing the emission frequency shift (following electronic excitation of, and resulting charge change or redistribution in, a solute) in terms of energy fluxes, a work and power perspective. This approach, which had been previously exploited for rotational and vibrational excitation-induced energy flow, has the novel advantage of providing a quantitative view and understanding of the molecular-level mechanisms involved in the solvation dynamics via tracing of the energy flow induced by the electronic excitation's charge change or redistribution in the solute. This new methodology, which was illustrated for the case in which only the excited electronic state surface contributes to the frequency shift (ionization of a monatomic solute in water), is here extended to the general case in which both the excited and ground electronic states may contribute. Simple monatomic solute model variations allow a discussion of the (sometimes surprising) issues involved in assessing each surface's contribution. The calculation of properly defined energy fluxes/work allows a more complete understanding of the solvation dynamics even when the real work for one of the surfaces does not directly contribute to the frequency shift, an aspect further emphasizing the utility of an energy flux approach. textcopyright 2016 American Chemical Society. |
How Acidic Is Carbonic Acid? Article de journal D Pines; J Ditkovich; T Mukra; Y Miller; P M Kiefer; S Daschakraborty; J T Hynes; E Pines Journal of Physical Chemistry B, 120 (9), p. 2440-2451, 2016, (cited By 14). @article{Pines20162440, title = {How Acidic Is Carbonic Acid?}, author = {D Pines and J Ditkovich and T Mukra and Y Miller and P M Kiefer and S Daschakraborty and J T Hynes and E Pines}, doi = {10.1021/acs.jpcb.5b12428}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {9}, pages = {2440-2451}, abstract = {Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pKa of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pKa of carbonic acid was found to be 3.49 $pm$ 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pKa units stronger and about 1 pKa unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions. textcopyright 2016 American Chemical Society.}, note = {cited By 14}, keywords = {}, pubstate = {published}, tppubtype = {article} } Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pKa of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pKa of carbonic acid was found to be 3.49 $pm$ 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pKa units stronger and about 1 pKa unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions. textcopyright 2016 American Chemical Society. |
Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path Article de journal S Daschakraborty; P M Kiefer; Y Miller; Y Motro; D Pines; E Pines; J T Hynes Journal of Physical Chemistry B, 120 (9), p. 2281-2290, 2016, (cited By 6). @article{Daschakraborty20162281, title = {Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path}, author = {S Daschakraborty and P M Kiefer and Y Miller and Y Motro and D Pines and E Pines and J T Hynes}, doi = {10.1021/acs.jpcb.5b12744}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {9}, pages = {2281-2290}, abstract = {The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an $sim$100 fs time scale, with the proton transfer (PT) event itself being very sudden (<10 fs). This transfer is preceded by the acid-base H-bond's compression, while the water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base $Delta$pKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale $sim$120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3 +. textcopyright 2016 American Chemical Society.}, note = {cited By 6}, keywords = {}, pubstate = {published}, tppubtype = {article} } The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an $sim$100 fs time scale, with the proton transfer (PT) event itself being very sudden (<10 fs). This transfer is preceded by the acid-base H-bond's compression, while the water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base $Delta$pKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale $sim$120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3 +. textcopyright 2016 American Chemical Society. |
Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics Article de journal S Daschakraborty; P M Kiefer; Y Miller; Y Motro; D Pines; E Pines; J T Hynes Journal of Physical Chemistry B, 120 (9), p. 2271-2280, 2016, (cited By 13). @article{Daschakraborty20162271, title = {Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics}, author = {S Daschakraborty and P M Kiefer and Y Miller and Y Motro and D Pines and E Pines and J T Hynes}, doi = {10.1021/acs.jpcb.5b12742}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {9}, pages = {2271-2280}, abstract = {Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton. textcopyright 2016 American Chemical Society.}, note = {cited By 13}, keywords = {}, pubstate = {published}, tppubtype = {article} } Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton. textcopyright 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. |
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). |
Molecular density functional theory of water including density-polarization coupling Article de journal G Jeanmairet; N Levy; M Levesque; D Borgis Journal of Physics Condensed Matter, 28 (24), 2016. @article{Jeanmairet:2016, title = {Molecular density functional theory of water including density-polarization coupling}, author = {G Jeanmairet and N Levy and M Levesque and D Borgis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84969849506&doi=10.1088%2f0953-8984%2f28%2f24%2f244005&partnerID=40&md5=c3fef4367f3359f26a666329655c7468}, doi = {10.1088/0953-8984/28/24/244005}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physics Condensed Matter}, volume = {28}, number = {24}, abstract = {We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities. © 2016 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities. © 2016 IOP Publishing Ltd. |
Cation Migration and Structural Deformations upon Dehydration of Nickel-Exchanged NaY Zeolite: A Combined Neutron Diffraction and Monte Carlo Study Article de journal W Louisfrema; J -L Paillaud; F Porcher; E Perrin; T Onfroy; P Massiani; A Boutin; B Rotenberg Journal of Physical Chemistry C, 120 (32), p. 18115–18125, 2016. @article{Louisfrema:2016, title = {Cation Migration and Structural Deformations upon Dehydration of Nickel-Exchanged NaY Zeolite: A Combined Neutron Diffraction and Monte Carlo Study}, author = {W Louisfrema and J -L Paillaud and F Porcher and E Perrin and T Onfroy and P Massiani and A Boutin and B Rotenberg}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84983517960&doi=10.1021%2facs.jpcc.6b05657&partnerID=40&md5=d5dc0aa053088e7ec12d147a59adf760}, doi = {10.1021/acs.jpcc.6b05657}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry C}, volume = {120}, number = {32}, pages = {18115--18125}, abstract = {Combining neutron diffraction and classical molecular simulations, we describe the cation migration and associated structural changes taking place in a Ni-exchanged NaY faujasite zeolite upon stepwise dehydration from room temperature up to 400 °C. The cation redistribution between sites and the related framework deformations taking place upon water removal are identified and quantified. Neutron diffraction allows monitoring the zeolite structure, the average cation location and the water content, whereas molecular modeling provides insights into the correlations between the positions of cations and water molecules. Importantly, we demonstrate that the migration of Ni2+ toward highly confined sites upon dehydration is the driving force behind deformation of the hexagonal prisms. The present work illustrates the relevance of combining these two experimental and theoretical approaches to clarify the complex interplay between cation hydration, cation location, and framework deformation. It also underlines the importance to capture the flexibility of the framework in molecular simulation of hydrated zeolite in particular when multivalent ions are involved. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Combining neutron diffraction and classical molecular simulations, we describe the cation migration and associated structural changes taking place in a Ni-exchanged NaY faujasite zeolite upon stepwise dehydration from room temperature up to 400 °C. The cation redistribution between sites and the related framework deformations taking place upon water removal are identified and quantified. Neutron diffraction allows monitoring the zeolite structure, the average cation location and the water content, whereas molecular modeling provides insights into the correlations between the positions of cations and water molecules. Importantly, we demonstrate that the migration of Ni2+ toward highly confined sites upon dehydration is the driving force behind deformation of the hexagonal prisms. The present work illustrates the relevance of combining these two experimental and theoretical approaches to clarify the complex interplay between cation hydration, cation location, and framework deformation. It also underlines the importance to capture the flexibility of the framework in molecular simulation of hydrated zeolite in particular when multivalent ions are involved. © 2016 American Chemical Society. |
Heterometallic metal-organic frameworks of MOF-5 and UiO-66 families: Insight from computational chemistry Article de journal F Trousselet; A Archereau; A Boutin; F -X Coudert Journal of Physical Chemistry C, 120 (43), p. 24885–24894, 2016. @article{Trousselet:2016, title = {Heterometallic metal-organic frameworks of MOF-5 and UiO-66 families: Insight from computational chemistry}, author = {F Trousselet and A Archereau and A Boutin and F -X Coudert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021680227&doi=10.1021%2facs.jpcc.6b08594&partnerID=40&md5=1d59350c3f3c291198fe5d4379de8dd5}, doi = {10.1021/acs.jpcc.6b08594}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry C}, volume = {120}, number = {43}, pages = {24885--24894}, abstract = {We study the energetic stability and structural features of bimetallic metal-organic frameworks. Such heterometallic MOFs, which can result from partial substitutions between two types of cations, can have specific physical or chemical properties used for example in catalysis or gas adsorption. We work here to provide through computational chemistry a microscopic understanding of bimetallic MOFs and the distribution of cations within their structure. We develop a methodology based on a systematic study of possible cation distributions at all cation ratios by means of quantum chemistry calculations at the density functional theory level. We analyze the energies of the resulting bimetallic frameworks and correlate them with various disorder descriptors (functions of the bimetallic framework topology, regardless of exact atomic positions). We apply our methodology to two families of MOFs known for heterometallicity: MOF-5 (with divalent metal ions) and UiO-66 (with tetravalent metal ions). We observe that bimetallicity is overall more favorable for pairs of cations with sizes very close to each other, owing to a charge transfer mechanism inside secondary building units. For cation pairs with significant mutual size difference, metal mixing is globally less favorable, and the energy signifantly correlates with the coordination environment of linkers, determining their ability to adapt the mixing-induced strains. This effect is particularly strong in the UiO-66 family because of high cluster coordination number. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study the energetic stability and structural features of bimetallic metal-organic frameworks. Such heterometallic MOFs, which can result from partial substitutions between two types of cations, can have specific physical or chemical properties used for example in catalysis or gas adsorption. We work here to provide through computational chemistry a microscopic understanding of bimetallic MOFs and the distribution of cations within their structure. We develop a methodology based on a systematic study of possible cation distributions at all cation ratios by means of quantum chemistry calculations at the density functional theory level. We analyze the energies of the resulting bimetallic frameworks and correlate them with various disorder descriptors (functions of the bimetallic framework topology, regardless of exact atomic positions). We apply our methodology to two families of MOFs known for heterometallicity: MOF-5 (with divalent metal ions) and UiO-66 (with tetravalent metal ions). We observe that bimetallicity is overall more favorable for pairs of cations with sizes very close to each other, owing to a charge transfer mechanism inside secondary building units. For cation pairs with significant mutual size difference, metal mixing is globally less favorable, and the energy signifantly correlates with the coordination environment of linkers, determining their ability to adapt the mixing-induced strains. This effect is particularly strong in the UiO-66 family because of high cluster coordination number. © 2016 American Chemical Society. |