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 |
PH-Sensitive Vibrational Probe Reveals a Cytoplasmic Protonated Cluster in Bacteriorhodopsin Article de journal V A Lorenz-Fonfria; M Saita; T Lazarova; R Schlesinger; J Heberle; J T Hynes Proceedings of the National Academy of Sciences of the United States of America, 114 (51), p. E10909-E10918, 2017, (cited By 5). @article{Lorenz-Fonfria2017E10909, title = {PH-Sensitive Vibrational Probe Reveals a Cytoplasmic Protonated Cluster in Bacteriorhodopsin}, author = {V A {Lorenz-Fonfria} and M Saita and T Lazarova and R Schlesinger and J Heberle and J T Hynes}, doi = {10.1073/pnas.1707993114}, year = {2017}, date = {2017-01-01}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {51}, pages = {E10909-E10918}, abstract = {Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 $mu$s, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1. The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.}, note = {cited By 5}, keywords = {}, pubstate = {published}, tppubtype = {article} } Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 $mu$s, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1. The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin. |
Translational versus Rotational Energy Flow in Water Solvation Dynamics Article de journal R Rey; J T Hynes Chemical Physics Letters, 683 , p. 483-487, 2017, (cited By 1). @article{Rey2017483, title = {Translational versus Rotational Energy Flow in Water Solvation Dynamics}, author = {R Rey and J T Hynes}, doi = {10.1016/j.cplett.2017.02.064}, year = {2017}, date = {2017-01-01}, journal = {Chemical Physics Letters}, volume = {683}, pages = {483-487}, abstract = {Early molecular dynamics simulations discovered an important asymmetry in the speed of water solvation dynamics for charge extinction and charge creation for an immersed solute, a feature representing a first demonstration of the breakdown of linear response theory. The molecular level mechanism of this asymmetry is examined here via a novel energy flux theoretical approach coupled to geometric probes. The results identify the effect as arising from the translational motions of the solute-hydrating water molecules rather than their rotational/librational motions, even though the latter are more rapid and dominate the energy flow. textcopyright 2017 Elsevier B.V.}, note = {cited By 1}, keywords = {}, pubstate = {published}, tppubtype = {article} } Early molecular dynamics simulations discovered an important asymmetry in the speed of water solvation dynamics for charge extinction and charge creation for an immersed solute, a feature representing a first demonstration of the breakdown of linear response theory. The molecular level mechanism of this asymmetry is examined here via a novel energy flux theoretical approach coupled to geometric probes. The results identify the effect as arising from the translational motions of the solute-hydrating water molecules rather than their rotational/librational motions, even though the latter are more rapid and dominate the energy flow. textcopyright 2017 Elsevier B.V. |
Perspective: Structure and Ultrafast Dynamics of Biomolecular Hydration Shells Article de journal D Laage; T Elsaesser; J T Hynes Structural Dynamics, 4 (4), 2017, (cited By 14). @article{Laage2017, title = {Perspective: Structure and Ultrafast Dynamics of Biomolecular Hydration Shells}, author = {D Laage and T Elsaesser and J T Hynes}, doi = {10.1063/1.4981019}, year = {2017}, date = {2017-01-01}, journal = {Structural Dynamics}, volume = {4}, number = {4}, abstract = {The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto-to picosecond time scale, with some special attention given to several issues subject to debate. textcopyright 2017 Author(s).}, note = {cited By 14}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto-to picosecond time scale, with some special attention given to several issues subject to debate. textcopyright 2017 Author(s). |
Dihydropteridine/Pteridine as a 2H+/2e- Redox Mediator for the Reduction of CO2 to Methanol: A Computational Study Article de journal C -H Lim; A M Holder; J T Hynes; C B Musgrave Journal of Physical Chemistry B, 121 (16), p. 4158-4167, 2017, (cited By 6). @article{Lim20174158, title = {Dihydropteridine/Pteridine as a 2H+/2e- Redox Mediator for the Reduction of CO2 to Methanol: A Computational Study}, author = {C -H Lim and A M Holder and J T Hynes and C B Musgrave}, doi = {10.1021/acs.jpcb.7b01224}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry B}, volume = {121}, number = {16}, pages = {4158-4167}, abstract = {Conflicting experimental results for the electrocatalytic reduction of CO2 to CH3OH on a glassy carbon electrode by the 6,7-dimethyl-4-hydroxy-2-mercaptopteridine have been recently reported [J. Am. Chem. Soc. 2014, 136, 14007-14010, J. Am. Chem. Soc. 2016, 138, 1017-1021]. In this connection, we have used computational chemistry to examine the issue of this molecule's ability to act as a hydride donor to reduce CO2. We first determined that the most thermodynamically stable tautomer of this aqueous compound is its oxothione form, termed here PTE. It is argued that this species electrochemically undergoes concerted 2H+/2e- transfers to first form the kinetic product 5,8-dihydropteridine, followed by acid-catalyzed tautomerization to the thermodynamically more stable 7,8-dihydropteridine PTEH2. While the overall conversion of CO2 to CH3OH by three successive hydride and proton transfers from this most stable tautomer is computed to be exergonic by 5.1 kcal/mol, we predict high activation free energies ($Delta$Gtextdaggerdbl HT) of 29.0 and 29.7 kcal/mol for the homogeneous reductions of CO2 and its intermediary formic acid product by PTE/PTEH2, respectively. These high barriers imply that PTE/PTEH2 is unable, by this mechanism, to homogeneously reduce CO2 on a time scale of hours at room temperature. (Chemical Equation Presented). textcopyright 2017 American Chemical Society.}, note = {cited By 6}, keywords = {}, pubstate = {published}, tppubtype = {article} } Conflicting experimental results for the electrocatalytic reduction of CO2 to CH3OH on a glassy carbon electrode by the 6,7-dimethyl-4-hydroxy-2-mercaptopteridine have been recently reported [J. Am. Chem. Soc. 2014, 136, 14007-14010, J. Am. Chem. Soc. 2016, 138, 1017-1021]. In this connection, we have used computational chemistry to examine the issue of this molecule's ability to act as a hydride donor to reduce CO2. We first determined that the most thermodynamically stable tautomer of this aqueous compound is its oxothione form, termed here PTE. It is argued that this species electrochemically undergoes concerted 2H+/2e- transfers to first form the kinetic product 5,8-dihydropteridine, followed by acid-catalyzed tautomerization to the thermodynamically more stable 7,8-dihydropteridine PTEH2. While the overall conversion of CO2 to CH3OH by three successive hydride and proton transfers from this most stable tautomer is computed to be exergonic by 5.1 kcal/mol, we predict high activation free energies ($Delta$Gtextdaggerdbl HT) of 29.0 and 29.7 kcal/mol for the homogeneous reductions of CO2 and its intermediary formic acid product by PTE/PTEH2, respectively. These high barriers imply that PTE/PTEH2 is unable, by this mechanism, to homogeneously reduce CO2 on a time scale of hours at room temperature. (Chemical Equation Presented). textcopyright 2017 American Chemical Society. |
Solvation Dynamics in Liquid Water. III. Energy Fluxes and Structural Changes Article de journal R Rey; J T Hynes Journal of Physical Chemistry B, 121 (6), p. 1377-1385, 2017, (cited By 4). @article{Rey20171377, title = {Solvation Dynamics in Liquid Water. III. Energy Fluxes and Structural Changes}, author = {R Rey and J T Hynes}, doi = {10.1021/acs.jpcb.6b11805}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry B}, volume = {121}, number = {6}, pages = {1377-1385}, abstract = {In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation - and in particular, hydration - relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent's spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible "inverse snowball" effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors' principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor. textcopyright 2017 American Chemical Society.}, note = {cited By 4}, keywords = {}, pubstate = {published}, tppubtype = {article} } In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation - and in particular, hydration - relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent's spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible "inverse snowball" effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors' principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor. textcopyright 2017 American Chemical Society. |
Chapter 3: A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications Article de journal J T Hynes; D Laage; I Tu~nón; V Moliner RSC Theoretical and Computational Chemistry Series, 2017-January (9), p. 54-88, 2017, (cited By 0). @article{Hynes201754, title = {Chapter 3: A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications}, author = {J T Hynes and D Laage and I Tu{~n}\'{o}n and V Moliner}, doi = {10.1039/9781782626831-00054}, year = {2017}, date = {2017-01-01}, journal = {RSC Theoretical and Computational Chemistry Series}, volume = {2017-January}, number = {9}, pages = {54-88}, abstract = {In this chapter we present the basic principles of transition state theory (TST) and a number of its applications to the study of enzymatic reactions. The assumptions of TST are discussed, as are the refinements to account for the failure of those assumptions, in particular that of no recrossing of the transition state surface. The selection of a reaction coordinate and the associated generation of free energy surfaces and their importance for TST receive special attention. While TST in its usual form assumes classical nuclear motion of the reaction coordinate, it can also be applied - with a special choice of classical reaction coordinate - for enzymatic reactions involving the transfer of light particles (proton, hydride and hydrogen atom transfers), where a quantum description of their motion is required. The theory and deviations from it are illustrated and discussed in detail via applications to a number of enzyme-catalysed reactions, indicating how TST and its variants can be successfully used to obtain rate constants for these reactions, to understand important aspects of their mechanism, and to identify the sources of the catalytic effect itself. textcopyright 2017 The Royal Society of Chemistry.}, note = {cited By 0}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this chapter we present the basic principles of transition state theory (TST) and a number of its applications to the study of enzymatic reactions. The assumptions of TST are discussed, as are the refinements to account for the failure of those assumptions, in particular that of no recrossing of the transition state surface. The selection of a reaction coordinate and the associated generation of free energy surfaces and their importance for TST receive special attention. While TST in its usual form assumes classical nuclear motion of the reaction coordinate, it can also be applied - with a special choice of classical reaction coordinate - for enzymatic reactions involving the transfer of light particles (proton, hydride and hydrogen atom transfers), where a quantum description of their motion is required. The theory and deviations from it are illustrated and discussed in detail via applications to a number of enzyme-catalysed reactions, indicating how TST and its variants can be successfully used to obtain rate constants for these reactions, to understand important aspects of their mechanism, and to identify the sources of the catalytic effect itself. textcopyright 2017 The Royal Society of Chemistry. |
Covalent Functionalization by Cycloaddition Reactions of Pristine Defect-Free Graphene Article de journal L Daukiya; C Mattioli; D Aubel; S Hajjar-Garreau; F Vonau; E Denys; G Reiter; J Fransson; E Perrin; M -L Bocquet; C Bena; A Gourdon; L Simon ACS Nano, 11 (1), p. 627–634, 2017. @article{Daukiya:2017, title = {Covalent Functionalization by Cycloaddition Reactions of Pristine Defect-Free Graphene}, author = {L Daukiya and C Mattioli and D Aubel and S Hajjar-Garreau and F Vonau and E Denys and G Reiter and J Fransson and E Perrin and M -L Bocquet and C Bena and A Gourdon and L Simon}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018480728&doi=10.1021%2facsnano.6b06913&partnerID=40&md5=a904965ad644c3f47104a50e432dc98d}, doi = {10.1021/acsnano.6b06913}, year = {2017}, date = {2017-01-01}, journal = {ACS Nano}, volume = {11}, number = {1}, pages = {627--634}, abstract = {Based on a low-temperature scanning tunneling microscopy study, we present a direct visualization of a cycloaddition reaction performed for some specific fluorinated maleimide molecules deposited on graphene. Up to now, it was widely admitted that such a cycloaddition reaction can not happen without pre-existing defects. However, our study shows that the cycloaddition reaction can be carried out on a defect-free basal graphene plane at room temperature. In the course of covalently grafting the molecules to graphene, the sp2 conjugation of carbon atoms was broken, and local sp3 bonds were created. The grafted molecules perturbed the graphene lattice, generating a standing-wave pattern with an anisotropy which was attributed to a (1,2) cycloaddition, as revealed by T-matrix approximation calculations. DFT calculations showed that while both (1,4) and (1,2) cycloadditions were possible on free-standing graphene, only the (1,2) cycloaddition could be obtained for graphene on SiC(0001). Globally averaging spectroscopic techniques, XPS and ARPES, were used to determine the modification in the elemental composition of the samples induced by the reaction, indicating an opening of an electronic gap in graphene. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Based on a low-temperature scanning tunneling microscopy study, we present a direct visualization of a cycloaddition reaction performed for some specific fluorinated maleimide molecules deposited on graphene. Up to now, it was widely admitted that such a cycloaddition reaction can not happen without pre-existing defects. However, our study shows that the cycloaddition reaction can be carried out on a defect-free basal graphene plane at room temperature. In the course of covalently grafting the molecules to graphene, the sp2 conjugation of carbon atoms was broken, and local sp3 bonds were created. The grafted molecules perturbed the graphene lattice, generating a standing-wave pattern with an anisotropy which was attributed to a (1,2) cycloaddition, as revealed by T-matrix approximation calculations. DFT calculations showed that while both (1,4) and (1,2) cycloadditions were possible on free-standing graphene, only the (1,2) cycloaddition could be obtained for graphene on SiC(0001). Globally averaging spectroscopic techniques, XPS and ARPES, were used to determine the modification in the elemental composition of the samples induced by the reaction, indicating an opening of an electronic gap in graphene. © 2016 American Chemical Society. |
Controlled spin switching in a metallocene molecular junction Article de journal M Ormaza; P Abufager; B Verlhac; N Bachellier; M -L Bocquet; N Lorente; L Limot Nature Communications, 8 (1), 2017. @article{Ormaza:2017, title = {Controlled spin switching in a metallocene molecular junction}, author = {M Ormaza and P Abufager and B Verlhac and N Bachellier and M -L Bocquet and N Lorente and L Limot}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038084780&doi=10.1038%2fs41467-017-02151-6&partnerID=40&md5=439be69bd0bc4564fa080a2f3de978ff}, doi = {10.1038/s41467-017-02151-6}, year = {2017}, date = {2017-01-01}, journal = {Nature Communications}, volume = {8}, number = {1}, abstract = {The active control of a molecular spin represents one of the main challenges in molecular spintronics. Up to now spin manipulation has been achieved through the modification of the molecular structure either by chemical doping or by external stimuli. However, the spin of a molecule adsorbed on a surface depends primarily on the interaction between its localized orbitals and the electronic states of the substrate. Here we change the effective spin of a single molecule by modifying the molecule/metal interface in a controlled way using a low-temperature scanning tunneling microscope. A nickelocene molecule reversibly switches from a spin 1 to 1/2 when varying the electrode-electrode distance from tunnel to contact regime. This switching is experimentally evidenced by inelastic and elastic spin-flip mechanisms observed in reproducible conductance measurements and understood using first principle calculations. Our work demonstrates the active control over the spin state of single molecule devices through interface manipulation. © 2017 The Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The active control of a molecular spin represents one of the main challenges in molecular spintronics. Up to now spin manipulation has been achieved through the modification of the molecular structure either by chemical doping or by external stimuli. However, the spin of a molecule adsorbed on a surface depends primarily on the interaction between its localized orbitals and the electronic states of the substrate. Here we change the effective spin of a single molecule by modifying the molecule/metal interface in a controlled way using a low-temperature scanning tunneling microscope. A nickelocene molecule reversibly switches from a spin 1 to 1/2 when varying the electrode-electrode distance from tunnel to contact regime. This switching is experimentally evidenced by inelastic and elastic spin-flip mechanisms observed in reproducible conductance measurements and understood using first principle calculations. Our work demonstrates the active control over the spin state of single molecule devices through interface manipulation. © 2017 The Author(s). |
Adatom Coadsorption with Three-Dimensional Cyclophanes on Ag(111) Article de journal K Scheil; N Lorente; M -L Bocquet; P C Hess; M Mayor; R Berndt Journal of Physical Chemistry C, 121 (45), p. 25303–25308, 2017. @article{Scheil:2017, title = {Adatom Coadsorption with Three-Dimensional Cyclophanes on Ag(111)}, author = {K Scheil and N Lorente and M -L Bocquet and P C Hess and M Mayor and R Berndt}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85034631252&doi=10.1021%2facs.jpcc.7b08953&partnerID=40&md5=936912ff0fe0e014a111840dca30d259}, doi = {10.1021/acs.jpcc.7b08953}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry C}, volume = {121}, number = {45}, pages = {25303--25308}, abstract = {The structure of molecular adlayers is of great interest for surface functionalization. As molecular complexity increases, the subtle interplay of the relevant interactions becomes more difficult to unravel. Here, we present a scanning tunneling microscope (STM) and atomic force microscope study along with free-energy calculations using density functional theory on two closely related NDI-cyclophane molecules. These three-dimensional double-decker molecules are designed to attach to the substrate with one subunit while the other functional moiety is exposed to the environment. The molecular arrangements obtained on Ag(111) are rationalized by the inclusion of adatoms from the substrate into the structure. The presence of adatoms is identified by a drastic change in corrugation of the STM images that takes place at moderate bias voltages. Our calculations using density functional theory of the system's free-energy yield that two adatoms favorably coadsorb with the molecules. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure of molecular adlayers is of great interest for surface functionalization. As molecular complexity increases, the subtle interplay of the relevant interactions becomes more difficult to unravel. Here, we present a scanning tunneling microscope (STM) and atomic force microscope study along with free-energy calculations using density functional theory on two closely related NDI-cyclophane molecules. These three-dimensional double-decker molecules are designed to attach to the substrate with one subunit while the other functional moiety is exposed to the environment. The molecular arrangements obtained on Ag(111) are rationalized by the inclusion of adatoms from the substrate into the structure. The presence of adatoms is identified by a drastic change in corrugation of the STM images that takes place at moderate bias voltages. Our calculations using density functional theory of the system's free-energy yield that two adatoms favorably coadsorb with the molecules. © 2017 American Chemical Society. |
Efficient Spin-Flip Excitation of a Nickelocene Molecule Article de journal M Ormaza; N Bachellier; M N Faraggi; B Verlhac; P Abufager; P Ohresser; L Joly; M Romeo; F Scheurer; M -L Bocquet; N Lorente; L Limot Nano Letters, 17 (3), p. 1877–1882, 2017. @article{Ormaza:2017a, title = {Efficient Spin-Flip Excitation of a Nickelocene Molecule}, author = {M Ormaza and N Bachellier and M N Faraggi and B Verlhac and P Abufager and P Ohresser and L Joly and M Romeo and F Scheurer and M -L Bocquet and N Lorente and L Limot}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014900265&doi=10.1021%2facs.nanolett.6b05204&partnerID=40&md5=c6499219658f645e25606f4cd7185c10}, doi = {10.1021/acs.nanolett.6b05204}, year = {2017}, date = {2017-01-01}, journal = {Nano Letters}, volume = {17}, number = {3}, pages = {1877--1882}, abstract = {Inelastic electron tunneling spectroscopy (IETS) within the junction of a scanning tunneling microscope (STM) uses current-driven spin-flip excitations for an all-electrical characterization of the spin state of a single object. Usually decoupling layers between the single object, atom or molecule, and the supporting surface are needed to observe these excitations. Here we study the surface magnetism of a sandwich nickelocene molecule (Nc) adsorbed directly on Cu(100) by means of X-ray magnetic circular dichroism (XMCD) and density functional theory (DFT) calculations and show with IETS that it exhibits an exceptionally efficient spin-flip excitation. The molecule preserves its magnetic moment and magnetic anisotropy not only on Cu(100), but also in different metallic environments including the tip apex. By taking advantage of this robusteness, we are able to functionalize the microscope tip with a Nc, which can be employed as a portable source of inelastic excitations as exemplified by a double spin-flip excitation process. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Inelastic electron tunneling spectroscopy (IETS) within the junction of a scanning tunneling microscope (STM) uses current-driven spin-flip excitations for an all-electrical characterization of the spin state of a single object. Usually decoupling layers between the single object, atom or molecule, and the supporting surface are needed to observe these excitations. Here we study the surface magnetism of a sandwich nickelocene molecule (Nc) adsorbed directly on Cu(100) by means of X-ray magnetic circular dichroism (XMCD) and density functional theory (DFT) calculations and show with IETS that it exhibits an exceptionally efficient spin-flip excitation. The molecule preserves its magnetic moment and magnetic anisotropy not only on Cu(100), but also in different metallic environments including the tip apex. By taking advantage of this robusteness, we are able to functionalize the microscope tip with a Nc, which can be employed as a portable source of inelastic excitations as exemplified by a double spin-flip excitation process. © 2017 American Chemical Society. |
Ligand-Induced Energy Shift and Localization of Kondo Resonances in Cobalt-Based Complexes on Cu(111) Article de journal T Knaak; M Gruber; C Lindström; M -L Bocquet; J Heck; R Berndt Nano Letters, 17 (11), p. 7146–7151, 2017. @article{Knaak:2017, title = {Ligand-Induced Energy Shift and Localization of Kondo Resonances in Cobalt-Based Complexes on Cu(111)}, author = {T Knaak and M Gruber and C Lindstr\"{o}m and M -L Bocquet and J Heck and R Berndt}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85033233461&doi=10.1021%2facs.nanolett.7b04181&partnerID=40&md5=df5e59413d7e50b5e2ec6c94ccfba410}, doi = {10.1021/acs.nanolett.7b04181}, year = {2017}, date = {2017-01-01}, journal = {Nano Letters}, volume = {17}, number = {11}, pages = {7146--7151}, abstract = {Magnetic sandwich complexes are of particular interest for molecular spintronics. Using scanning tunneling microscopy, we evidence the successful deposition of 1,3,5-tris(η6-borabenzene-η5-cyclopentadienylcobalt) benzene, a molecule composed of three connected magnetic sandwich units, on Cu(111). Scanning tunneling spectra reveal two distinct spatial-dependent narrow resonances close to the Fermi level for the trimer molecules as well as for molecular fragments composed of one and two magnetic units. With the help of density functional theory, these resonances are interpreted as two Kondo resonances originating from two distinct nondegenerate d-like orbitals. These Kondo resonances are found to have defined spatial extents dictated by the hybridization of the involved orbitals with that of the ligands. These results opens promising perspectives for investigating complex Kondo systems composed of several "Kondo" orbitals. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Magnetic sandwich complexes are of particular interest for molecular spintronics. Using scanning tunneling microscopy, we evidence the successful deposition of 1,3,5-tris(η6-borabenzene-η5-cyclopentadienylcobalt) benzene, a molecule composed of three connected magnetic sandwich units, on Cu(111). Scanning tunneling spectra reveal two distinct spatial-dependent narrow resonances close to the Fermi level for the trimer molecules as well as for molecular fragments composed of one and two magnetic units. With the help of density functional theory, these resonances are interpreted as two Kondo resonances originating from two distinct nondegenerate d-like orbitals. These Kondo resonances are found to have defined spatial extents dictated by the hybridization of the involved orbitals with that of the ligands. These results opens promising perspectives for investigating complex Kondo systems composed of several "Kondo" orbitals. © 2017 American Chemical Society. |
New avenues for the large-scale harvesting of blue energy Article de journal A Siria; M -L Bocquet; L Bocquet Nature Reviews Chemistry, 1 (11), 2017. @article{Siria:2017, title = {New avenues for the large-scale harvesting of blue energy}, author = {A Siria and M -L Bocquet and L Bocquet}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044247685&doi=10.1038%2fs41570-017-0091&partnerID=40&md5=6b35f62f57df15091ceb732e1fa6e1eb}, doi = {10.1038/s41570-017-0091}, year = {2017}, date = {2017-01-01}, journal = {Nature Reviews Chemistry}, volume = {1}, number = {11}, abstract = {zSalinity gradients have been identified as promising clean, renewable and non-intermittent sources of energy \textemdash so-called blue energy. However, the low efficiency of current harvesting technologies is a major limitation for large-scale viability and is mostly due to the low performances of the membrane processes currently in use. Advances in materials fabrication with dedicated chemical properties can resolve this bottleneck and lead to a new class of membranes for blue-energy conversion. In this Perspective, we briefly present current technologies for the conversion of blue energy, describe their performances and note their limitations. We then discuss new avenues for the development of a new class of membranes, combining considerations in nanoscale fluid dynamics and surface chemistry. Finally, we discuss how new functionalities originating from the exotic behaviour of fluids in the nanoscale regime can further boost energy conversion, making osmotic energy a tangible, clean alternative. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } zSalinity gradients have been identified as promising clean, renewable and non-intermittent sources of energy — so-called blue energy. However, the low efficiency of current harvesting technologies is a major limitation for large-scale viability and is mostly due to the low performances of the membrane processes currently in use. Advances in materials fabrication with dedicated chemical properties can resolve this bottleneck and lead to a new class of membranes for blue-energy conversion. In this Perspective, we briefly present current technologies for the conversion of blue energy, describe their performances and note their limitations. We then discuss new avenues for the development of a new class of membranes, combining considerations in nanoscale fluid dynamics and surface chemistry. Finally, we discuss how new functionalities originating from the exotic behaviour of fluids in the nanoscale regime can further boost energy conversion, making osmotic energy a tangible, clean alternative. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. |
Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent Article de journal E Duboué-Dijon; E Pluhařová; D Domin; K Sen; A C Fogarty; N Chéron; D Laage Journal of Physical Chemistry B, 121 (29), p. 7027–7041, 2017. @article{Duboue-Dijon:2017, title = {Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent}, author = {E Dubou\'{e}-Dijon and E Pluha\v{r}ov\'{a} and D Domin and K Sen and A C Fogarty and N Ch\'{e}ron and D Laage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85026553265&doi=10.1021%2facs.jpcb.7b03102&partnerID=40&md5=b660afe385e614dde371ae0c9cdcfd33}, doi = {10.1021/acs.jpcb.7b03102}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry B}, volume = {121}, number = {29}, pages = {7027--7041}, abstract = {Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site. © 2017 American Chemical Society. |
A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016 Article de journal T Debroise; E I Shakhnovich; N Chéron Journal of Chemical Information and Modeling, 57 (3), p. 584–593, 2017. @article{Debroise:2017, title = {A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016}, author = {T Debroise and E I Shakhnovich and N Ch\'{e}ron}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85025107228&doi=10.1021%2facs.jcim.6b00610&partnerID=40&md5=6b16dec8e3efb91720fd713ee75e44b5}, doi = {10.1021/acs.jcim.6b00610}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Information and Modeling}, volume = {57}, number = {3}, pages = {584--593}, abstract = {We present the third generation of our scoring function for the prediction of protein-ligand binding free energy. This function is now a hybrid between a knowledge-based potential and an empirical function. We constructed a diversified set of ∼1000 complexes from the PDBBinding-CN database for the training of the function, and we show that this number of complexes generates enough data to build the potential. The occurrence of 420 different types of atomic pairwise interactions is computed in up to five different ranges of distances to derive the knowledge-based part. All of the parameters were optimized, and we were able to considerably improve the accuracy of the scoring function with a Pearson correlation coefficient against experimental binding free energies of up to 0.57, which ranks our new scoring function as one of the best currently available and the second-best in terms of standard deviation (SD = 1.68 kcal/mol). The function was then further improved by inclusion of different terms taking into account repulsion and loss of entropy upon binding, and we show that it is capable of recovering native binding poses up to 80% of the time. All of the programs, tools, and protein sets are released in the Supporting Information or as open-source programs. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present the third generation of our scoring function for the prediction of protein-ligand binding free energy. This function is now a hybrid between a knowledge-based potential and an empirical function. We constructed a diversified set of ∼1000 complexes from the PDBBinding-CN database for the training of the function, and we show that this number of complexes generates enough data to build the potential. The occurrence of 420 different types of atomic pairwise interactions is computed in up to five different ranges of distances to derive the knowledge-based part. All of the parameters were optimized, and we were able to considerably improve the accuracy of the scoring function with a Pearson correlation coefficient against experimental binding free energies of up to 0.57, which ranks our new scoring function as one of the best currently available and the second-best in terms of standard deviation (SD = 1.68 kcal/mol). The function was then further improved by inclusion of different terms taking into account repulsion and loss of entropy upon binding, and we show that it is capable of recovering native binding poses up to 80% of the time. All of the programs, tools, and protein sets are released in the Supporting Information or as open-source programs. © 2017 American Chemical Society. |
Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations Article de journal N Chéron; E I Shakhnovich Journal of Computational Chemistry, 38 (22), p. 1941–1951, 2017. @article{Cheron:2017, title = {Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations}, author = {N Ch\'{e}ron and E I Shakhnovich}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020100583&doi=10.1002%2fjcc.24839&partnerID=40&md5=516fbbbbe873be6ebb343d12fe5ead0b}, doi = {10.1002/jcc.24839}, year = {2017}, date = {2017-01-01}, journal = {Journal of Computational Chemistry}, volume = {38}, number = {22}, pages = {1941--1951}, abstract = {The BACE-1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM-PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme. After showing that the most probable protonation state of the catalytic dyad is mono-protonated (on ASP32), we performed a thorough analysis of the parameters influencing the sampling of the conformational space (in total, more than 35 μs of simulations were performed). We show that ten simulations of 2 ns gives better results than one of 50 ns. We also investigated the influence of the protein force field, the water model, the periodic boundary conditions artifacts (box size), as well as the ionic strength. Amber03 with TIP3P, a minimal distance of 1.0 nm between the protein and the box edges and a ionic strength of I = 0.2 M provides the optimal correlation with experiments. Overall, when using these parameters, a Pearson correlation coefficient of R = 0.84 (R2 = 0.71) is obtained for the 46 ligands, spanning eight orders of magnitude of Kd (from 0.017 nm to 2000 μM, i.e., from −14.7 to −3.7 kcal/mol), with a ligand size from 22 to 136 atoms (from 138 to 937 g/mol). After a two-parameter fit of the binding affinities for 12 of the ligands, an error of RMSD = 1.7 kcal/mol was obtained for the remaining ligands. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The BACE-1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM-PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme. After showing that the most probable protonation state of the catalytic dyad is mono-protonated (on ASP32), we performed a thorough analysis of the parameters influencing the sampling of the conformational space (in total, more than 35 μs of simulations were performed). We show that ten simulations of 2 ns gives better results than one of 50 ns. We also investigated the influence of the protein force field, the water model, the periodic boundary conditions artifacts (box size), as well as the ionic strength. Amber03 with TIP3P, a minimal distance of 1.0 nm between the protein and the box edges and a ionic strength of I = 0.2 M provides the optimal correlation with experiments. Overall, when using these parameters, a Pearson correlation coefficient of R = 0.84 (R2 = 0.71) is obtained for the 46 ligands, spanning eight orders of magnitude of Kd (from 0.017 nm to 2000 μM, i.e., from −14.7 to −3.7 kcal/mol), with a ligand size from 22 to 136 atoms (from 138 to 937 g/mol). After a two-parameter fit of the binding affinities for 12 of the ligands, an error of RMSD = 1.7 kcal/mol was obtained for the remaining ligands. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc. |
Chapter 13: Effects of Water and Non-Aqueous Solvents on Enzyme Activity Livre E Pluhav rová; N Chéron; D Laage 2017. @book{Pluharova:2017a, title = {Chapter 13: Effects of Water and Non-Aqueous Solvents on Enzyme Activity}, author = {E Pluha{v r}ov\'{a} and N Ch\'{e}ron and D Laage}, doi = {10.1039/9781782626831-00436}, year = {2017}, date = {2017-01-01}, volume = {2017-January}, series = {RSC Theoretical and Computational Chemistry Series}, abstract = {In this chapter, we review the available experimental data and molecular models describing the effect of different solvents, including water, on the catalytic activity of enzymes. While a popular picture suggests that water acts as a lubricant of the protein conformational motions required for catalysis, we show that this dynamical picture is not supported by recent results and we discuss alternative models. textcopyright 2017 The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {book} } In this chapter, we review the available experimental data and molecular models describing the effect of different solvents, including water, on the catalytic activity of enzymes. While a popular picture suggests that water acts as a lubricant of the protein conformational motions required for catalysis, we show that this dynamical picture is not supported by recent results and we discuss alternative models. textcopyright 2017 The Royal Society of Chemistry. |
Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects Article de journal G Stirnemann; E Duboué-Dijon; D Laage Journal of Physical Chemistry B, 121 (49), p. 11189–11197, 2017. @article{Stirnemann:2017, title = {Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects}, author = {G Stirnemann and E Dubou\'{e}-Dijon and D Laage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038365173&doi=10.1021%2facs.jpcb.7b09989&partnerID=40&md5=b7eec550046aa148061de979c17e8e55}, doi = {10.1021/acs.jpcb.7b09989}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry B}, volume = {121}, number = {49}, pages = {11189--11197}, abstract = {We use ab initio molecular dynamics simulation to study the effect of hydrophobic groups on the dynamics of water molecules in aqueous solutions of trimethylamine N-oxide (TMAO). We show that hydrophobic groups induce a moderate (textless2-fold) slowdown of water reorientation and hydrogen-bond dynamics in dilute solutions, but that this slowdown rapidly increases with solute concentration. In addition, the slowdown factor is found to vary very little with temperature, thus suggesting an entropic origin. All of these results are in quantitative agreement with prior classical molecular dynamics simulations and with the previously suggested excluded-volume model. The hydrophilic TMAO headgroup is found to affect water dynamics more strongly than the hydrophobic moiety, and the magnitude of this slowdown is very sensitive to the strength of the water-solute hydrogen-bond. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We use ab initio molecular dynamics simulation to study the effect of hydrophobic groups on the dynamics of water molecules in aqueous solutions of trimethylamine N-oxide (TMAO). We show that hydrophobic groups induce a moderate (textless2-fold) slowdown of water reorientation and hydrogen-bond dynamics in dilute solutions, but that this slowdown rapidly increases with solute concentration. In addition, the slowdown factor is found to vary very little with temperature, thus suggesting an entropic origin. All of these results are in quantitative agreement with prior classical molecular dynamics simulations and with the previously suggested excluded-volume model. The hydrophilic TMAO headgroup is found to affect water dynamics more strongly than the hydrophobic moiety, and the magnitude of this slowdown is very sensitive to the strength of the water-solute hydrogen-bond. © 2017 American Chemical Society. |
Size and Origins of Long-Range Orientational Water Correlations in Dilute Aqueous Salt Solutions Article de journal E Pluhařová; D Laage; P Jungwirth Journal of Physical Chemistry Letters, 8 (9), p. 2031–2035, 2017. @article{Pluharova:2017, title = {Size and Origins of Long-Range Orientational Water Correlations in Dilute Aqueous Salt Solutions}, author = {E Pluha\v{r}ov\'{a} and D Laage and P Jungwirth}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018785153&doi=10.1021%2facs.jpclett.7b00727&partnerID=40&md5=40cc30d0945099ab568be77da9d7e1e0}, doi = {10.1021/acs.jpclett.7b00727}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {8}, number = {9}, pages = {2031--2035}, abstract = {Long-range ordering of water around solutes has been repeatedly invoked as the key to its biological function. Recently, it has been shown that in an 8 mM aqueous NaCl solution the orientational correlation between water molecules extends beyond 8 nm. This was interpreted as arising from ion-induced long-range effects on the water collective hydrogen-bond interactions. Each ion was suggested to affect textgreater10 000 water molecules, leading to a picture involving nanoscopic "ordered domains". Using molecular dynamics simulations, we show that the very small long-range tail in the correlation function is caused primarily by pairs of water molecules belonging to different ions’ hydration shells and can be made to practically disappear by rearranging the ionic positions. This means that the ion-induced water orientational ordering in millimolar salt solutions cannot be separated from ion-ion interaction effects, for which the Debye-H\"{u}ckel screening length shrinks to less than 1 nm at physiological ionic strengths. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long-range ordering of water around solutes has been repeatedly invoked as the key to its biological function. Recently, it has been shown that in an 8 mM aqueous NaCl solution the orientational correlation between water molecules extends beyond 8 nm. This was interpreted as arising from ion-induced long-range effects on the water collective hydrogen-bond interactions. Each ion was suggested to affect textgreater10 000 water molecules, leading to a picture involving nanoscopic "ordered domains". Using molecular dynamics simulations, we show that the very small long-range tail in the correlation function is caused primarily by pairs of water molecules belonging to different ions’ hydration shells and can be made to practically disappear by rearranging the ionic positions. This means that the ion-induced water orientational ordering in millimolar salt solutions cannot be separated from ion-ion interaction effects, for which the Debye-Hückel screening length shrinks to less than 1 nm at physiological ionic strengths. © 2017 American Chemical Society. |
Water Librations in the Hydration Shell of Phospholipids Article de journal G Folpini; T Siebert; M Woerner; S Abel; D Laage; T Elsaesser Journal of Physical Chemistry Letters, 8 (18), p. 4492–4497, 2017. @article{Folpini:2017, title = {Water Librations in the Hydration Shell of Phospholipids}, author = {G Folpini and T Siebert and M Woerner and S Abel and D Laage and T Elsaesser}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029752349&doi=10.1021%2facs.jpclett.7b01942&partnerID=40&md5=4ad9270337811c054c4593b4d9d0e88f}, doi = {10.1021/acs.jpclett.7b01942}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {8}, number = {18}, pages = {4492--4497}, abstract = {The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm-1 reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w0 = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm-1 is superimposed on a broad absorption band between 300 and 1000 cm-1. Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm-1 arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm-1 reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w0 = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm-1 is superimposed on a broad absorption band between 300 and 1000 cm-1. Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm-1 arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces. © 2017 American Chemical Society. |
Corrugation in the Weakly Interacting Hexagonal-BN/Cu(111) System: Structure Determination by Combining Noncontact Atomic Force Microscopy and X-ray Standing Waves Article de journal M Schwarz; A Riss; M Garnica; J Ducke; P S Deimel; D A Duncan; P K Thakur; T -L Lee; A P Seitsonen; J V Barth; F Allegretti; W Auwärter ACS Nano, 11 (9), p. 9151–9161, 2017. @article{Schwarz:2017, title = {Corrugation in the Weakly Interacting Hexagonal-BN/Cu(111) System: Structure Determination by Combining Noncontact Atomic Force Microscopy and X-ray Standing Waves}, author = {M Schwarz and A Riss and M Garnica and J Ducke and P S Deimel and D A Duncan and P K Thakur and T -L Lee and A P Seitsonen and J V Barth and F Allegretti and W Auw\"{a}rter}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029953637&doi=10.1021%2facsnano.7b04022&partnerID=40&md5=dca6ae0e2420cfd44a5ff25105bdf306}, doi = {10.1021/acsnano.7b04022}, year = {2017}, date = {2017-01-01}, journal = {ACS Nano}, volume = {11}, number = {9}, pages = {9151--9161}, abstract = {Atomically thin hexagonal boron nitride (h-BN) layers on metallic supports represent a promising platform for the selective adsorption of atoms, clusters, and molecular nanostructures. Specifically, scanning tunneling microscopy (STM) studies revealed an electronic corrugation of h-BN/Cu(111), guiding the self-assembly of molecules and their energy level alignment. A detailed characterization of the h-BN/Cu(111) interface including the spacing between the h-BN sheet and its support - elusive to STM measurements - is crucial to rationalize the interfacial interactions within these systems. To this end, we employ complementary techniques including high-resolution noncontact atomic force microscopy, STM, low-energy electron diffraction, X-ray photoelectron spectroscopy, the X-ray standing wave method, and density functional theory. Our multimethod study yields a comprehensive, quantitative structure determination including the adsorption height and the corrugation of the sp2 bonded h-BN layer on Cu(111). Based on the atomic contrast in atomic force microscopy measurements, we derive a measurable-hitherto unrecognized-geometric corrugation of the h-BN monolayer. This experimental approach allows us to spatially resolve minute height variations in low-dimensional nanostructures, thus providing a benchmark for theoretical modeling. Regarding potential applications, e.g., as a template or catalytically active support, the recognition of h-BN on Cu(111) as a weakly bonded and moderately corrugated overlayer is highly relevant. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Atomically thin hexagonal boron nitride (h-BN) layers on metallic supports represent a promising platform for the selective adsorption of atoms, clusters, and molecular nanostructures. Specifically, scanning tunneling microscopy (STM) studies revealed an electronic corrugation of h-BN/Cu(111), guiding the self-assembly of molecules and their energy level alignment. A detailed characterization of the h-BN/Cu(111) interface including the spacing between the h-BN sheet and its support - elusive to STM measurements - is crucial to rationalize the interfacial interactions within these systems. To this end, we employ complementary techniques including high-resolution noncontact atomic force microscopy, STM, low-energy electron diffraction, X-ray photoelectron spectroscopy, the X-ray standing wave method, and density functional theory. Our multimethod study yields a comprehensive, quantitative structure determination including the adsorption height and the corrugation of the sp2 bonded h-BN layer on Cu(111). Based on the atomic contrast in atomic force microscopy measurements, we derive a measurable-hitherto unrecognized-geometric corrugation of the h-BN monolayer. This experimental approach allows us to spatially resolve minute height variations in low-dimensional nanostructures, thus providing a benchmark for theoretical modeling. Regarding potential applications, e.g., as a template or catalytically active support, the recognition of h-BN on Cu(111) as a weakly bonded and moderately corrugated overlayer is highly relevant. © 2017 American Chemical Society. |
Advanced capabilities for materials modelling with Quantum ESPRESSO Article de journal P Giannozzi; O Andreussi; T Brumme; O Bunau; M Buongiorno Nardelli; M Calandra; R Car; C Cavazzoni; D Ceresoli; M Cococcioni; N Colonna; I Carnimeo; A Dal Corso; S De Gironcoli; P Delugas; R A Distasio; A Ferretti; A Floris; G Fratesi; G Fugallo; R Gebauer; U Gerstmann; F Giustino; T Gorni; J Jia; M Kawamura; H -Y Ko; A Kokalj; E Kücükbenli; M Lazzeri; M Marsili; N Marzari; F Mauri; N L Nguyen; H -V Nguyen; A Otero-De-La-Roza; L Paulatto; S Poncé; D Rocca; R Sabatini; B Santra; M Schlipf; A P Seitsonen; A Smogunov; I Timrov; T Thonhauser; P Umari; N Vast; X Wu; S Baroni Journal of Physics Condensed Matter, 29 (46), 2017. @article{Giannozzi:2017, title = {Advanced capabilities for materials modelling with Quantum ESPRESSO}, author = {P Giannozzi and O Andreussi and T Brumme and O Bunau and M Buongiorno Nardelli and M Calandra and R Car and C Cavazzoni and D Ceresoli and M Cococcioni and N Colonna and I Carnimeo and A Dal Corso and S De Gironcoli and P Delugas and R A Distasio and A Ferretti and A Floris and G Fratesi and G Fugallo and R Gebauer and U Gerstmann and F Giustino and T Gorni and J Jia and M Kawamura and H -Y Ko and A Kokalj and E K\"{u}c\"{u}kbenli and M Lazzeri and M Marsili and N Marzari and F Mauri and N L Nguyen and H -V Nguyen and A Otero-De-La-Roza and L Paulatto and S Ponc\'{e} and D Rocca and R Sabatini and B Santra and M Schlipf and A P Seitsonen and A Smogunov and I Timrov and T Thonhauser and P Umari and N Vast and X Wu and S Baroni}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85036470554&doi=10.1088%2f1361-648X%2faa8f79&partnerID=40&md5=287986808af5a316774cc3f639b71c06}, doi = {10.1088/1361-648X/aa8f79}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physics Condensed Matter}, volume = {29}, number = {46}, abstract = {Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd. |
Epitaxy-Induced Assembly and Enantiomeric Switching of an On-Surface Formed Dinuclear Organocobalt Complex Article de journal R Hellwig; T Paintner; Z Chen; M Ruben; A P Seitsonen; F Klappenberger; H Brune; J V Barth ACS Nano, 11 (2), p. 1347–1359, 2017. @article{Hellwig:2017, title = {Epitaxy-Induced Assembly and Enantiomeric Switching of an On-Surface Formed Dinuclear Organocobalt Complex}, author = {R Hellwig and T Paintner and Z Chen and M Ruben and A P Seitsonen and F Klappenberger and H Brune and J V Barth}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014296621&doi=10.1021%2facsnano.6b06114&partnerID=40&md5=c98027b857cc8e07c090b9d053df25d7}, doi = {10.1021/acsnano.6b06114}, year = {2017}, date = {2017-01-01}, journal = {ACS Nano}, volume = {11}, number = {2}, pages = {1347--1359}, abstract = {We report on the surface-guided synthesis of a dinuclear organocobalt complex, its self-assembly into a complex nanoarchitecture, and a single-molecule level investigation of its switching behavior. Initially, an organic layer is prepared by depositing hexakis((trimethylsilyl)ethynyl)-benzene under ultrahigh-vacuum conditions onto Ag(111). After Co dosage at 200 K, low-temperature scanning tunneling microscopy (STM) reveals an epitaxy-mediated organization mechanism of molecules and on-surface formed organometallic complexes. The dinuclear complexes contain two bis(η2-alkynyl) π-tweezer motifs, each stabilizing a single Co atom and express two enantiomers due to a conformation twist. The chirality is transferred to the two-dimensional architecture, whereby its Co adatoms are located at the corners of a 3.4.6.4 rhombitrihexagonal tessellation due to the systematic arrangement and anchoring of the complexes. Extensive density functional theory simulations support our interpretation of an epitaxy-guided surface tessellation and its chiral character. Additionally, STM tip-assisted manipulation experiments on isolated dinuclear complexes reveal controlled and reversible switching between the enantiomeric states via inelastic electron processes. After activation by bias pulses, structurally modified complexes display a distinctive Kondo feature attributed to metastable Co configurations. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report on the surface-guided synthesis of a dinuclear organocobalt complex, its self-assembly into a complex nanoarchitecture, and a single-molecule level investigation of its switching behavior. Initially, an organic layer is prepared by depositing hexakis((trimethylsilyl)ethynyl)-benzene under ultrahigh-vacuum conditions onto Ag(111). After Co dosage at 200 K, low-temperature scanning tunneling microscopy (STM) reveals an epitaxy-mediated organization mechanism of molecules and on-surface formed organometallic complexes. The dinuclear complexes contain two bis(η2-alkynyl) π-tweezer motifs, each stabilizing a single Co atom and express two enantiomers due to a conformation twist. The chirality is transferred to the two-dimensional architecture, whereby its Co adatoms are located at the corners of a 3.4.6.4 rhombitrihexagonal tessellation due to the systematic arrangement and anchoring of the complexes. Extensive density functional theory simulations support our interpretation of an epitaxy-guided surface tessellation and its chiral character. Additionally, STM tip-assisted manipulation experiments on isolated dinuclear complexes reveal controlled and reversible switching between the enantiomeric states via inelastic electron processes. After activation by bias pulses, structurally modified complexes display a distinctive Kondo feature attributed to metastable Co configurations. © 2017 American Chemical Society. |
N -Heterocyclic carbenes on close-packed coinage metal surfaces: Bis-carbene metal adatom bonding scheme of monolayer films on Au, Ag and Cu Article de journal L Jiang; B Zhang; G Médard; A P Seitsonen; F Haag; F Allegretti; J Reichert; B Kuster; J V Barth; A C Papageorgiou Chemical Science, 8 (12), p. 8301–8308, 2017. @article{Jiang:2017, title = {N -Heterocyclic carbenes on close-packed coinage metal surfaces: Bis-carbene metal adatom bonding scheme of monolayer films on Au, Ag and Cu}, author = {L Jiang and B Zhang and G M\'{e}dard and A P Seitsonen and F Haag and F Allegretti and J Reichert and B Kuster and J V Barth and A C Papageorgiou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85034774759&doi=10.1039%2fc7sc03777e&partnerID=40&md5=7e38258999ad67f47c16f2b5527b59d5}, doi = {10.1039/c7sc03777e}, year = {2017}, date = {2017-01-01}, journal = {Chemical Science}, volume = {8}, number = {12}, pages = {8301--8308}, abstract = {By means of scanning tunnelling microscopy (STM), complementary density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) we investigate the binding and self-assembly of a saturated molecular layer of model N-heterocyclic carbene (NHC) on Cu(111), Ag(111) and Au(111) surfaces under ultra-high vacuum (UHV) conditions. XPS reveals that at room temperature, coverages up to a monolayer exist, with the molecules engaged in metal carbene bonds. On all three surfaces, we resolve similar arrangements, which can be interpreted only in terms of mononuclear M(NHC)2 (M = Cu, Ag, Au) complexes, reminiscent of the paired bonding of thiols to surface gold adatoms. Theoretical investigations for the case of Au unravel the charge distribution of a Au(111) surface covered by Au(NHC)2 and reveal that this is the energetically preferential adsorption configuration. © 2017 The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } By means of scanning tunnelling microscopy (STM), complementary density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) we investigate the binding and self-assembly of a saturated molecular layer of model N-heterocyclic carbene (NHC) on Cu(111), Ag(111) and Au(111) surfaces under ultra-high vacuum (UHV) conditions. XPS reveals that at room temperature, coverages up to a monolayer exist, with the molecules engaged in metal carbene bonds. On all three surfaces, we resolve similar arrangements, which can be interpreted only in terms of mononuclear M(NHC)2 (M = Cu, Ag, Au) complexes, reminiscent of the paired bonding of thiols to surface gold adatoms. Theoretical investigations for the case of Au unravel the charge distribution of a Au(111) surface covered by Au(NHC)2 and reveal that this is the energetically preferential adsorption configuration. © 2017 The Royal Society of Chemistry. |
An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(III)(HPDO3A)(Ħ2O)] Article de journal S Khan; R Pollet; R Vuilleumier; J Kowalewski; M Odelius Journal of Chemical Physics, 147 (24), 2017. @article{Khan:2017, title = {An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(III)(HPDO3A)({H}2O)]}, author = {S Khan and R Pollet and R Vuilleumier and J Kowalewski and M Odelius}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040080433&doi=10.1063%2f1.5010347&partnerID=40&md5=4509ae37abb1a23cc64f76a0f4051ea8}, doi = {10.1063/1.5010347}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {147}, number = {24}, abstract = {In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field - CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field - CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates. © 2017 Author(s). |
Double differential cross sections for liquid water ionization by fast electron impact Article de journal M L de Sanctis; M -F Politis; R Vuilleumier; C R Stia; O A Fojón European Physical Journal D, 71 (5), 2017. @article{deSanctis:2017, title = {Double differential cross sections for liquid water ionization by fast electron impact}, author = {M L de Sanctis and M -F Politis and R Vuilleumier and C R Stia and O A Foj\'{o}n}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020054874&doi=10.1140%2fepjd%2fe2017-70615-y&partnerID=40&md5=de232d35d2c540570c40ce1b60a80d3f}, doi = {10.1140/epjd/e2017-70615-y}, year = {2017}, date = {2017-01-01}, journal = {European Physical Journal D}, volume = {71}, number = {5}, abstract = {Abstract: In this work we study theoretically the single ionization of liquid water by impact of energetic electrons. A realistic description of the wavefunction for an isolated water molecule in the liquid phase is made by means of a Wannier orbital formalism. We develop a first order model within the framework of an independent electron approximation in which the relaxation of the target is not taken into account. The double differential cross sections are computed and compared with experimental data and theoretical calculations for gas phase. Graphical abstract: [Figure not available: see fulltext.]. © 2017, EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract: In this work we study theoretically the single ionization of liquid water by impact of energetic electrons. A realistic description of the wavefunction for an isolated water molecule in the liquid phase is made by means of a Wannier orbital formalism. We develop a first order model within the framework of an independent electron approximation in which the relaxation of the target is not taken into account. The double differential cross sections are computed and compared with experimental data and theoretical calculations for gas phase. Graphical abstract: [Figure not available: see fulltext.]. © 2017, EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg. |
Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics Article de journal M Basire; F Mouhat; G Fraux; A Bordage; J -L Hazemann; M Louvel; R Spezia; S Bonella; R Vuilleumier Journal of Chemical Physics, 146 (13), 2017. @article{Basire:2017, title = {Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics}, author = {M Basire and F Mouhat and G Fraux and A Bordage and J -L Hazemann and M Louvel and R Spezia and S Bonella and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016765650&doi=10.1063%2f1.4979199&partnerID=40&md5=90c94c5f296db3f0df0fd4e607548cb7}, doi = {10.1063/1.4979199}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {146}, number = {13}, abstract = {Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them. © 2017 Author(s). |
Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics Article de journal F Mouhat; S Sorella; R Vuilleumier; A M Saitta; M Casula Journal of Chemical Theory and Computation, 13 (6), p. 2400–2417, 2017. @article{Mouhat:2017, title = {Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics}, author = {F Mouhat and S Sorella and R Vuilleumier and A M Saitta and M Casula}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020712757&doi=10.1021%2facs.jctc.7b00017&partnerID=40&md5=042401e811dc41f5d5e3e709943f71d8}, doi = {10.1021/acs.jctc.7b00017}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Theory and Computation}, volume = {13}, number = {6}, pages = {2400--2417}, abstract = {We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most-Advanced post-Hartree-Fock approaches, and with a favorable scaling with the system size. In order to cope with the intrinsic noise due to the stochastic nature of quantum Monte Carlo methods, we generalize the path integral molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of quantum Monte Carlo nuclear forces. The variational parameters of the quantum Monte Carlo wave function are evolved during the nuclear dynamics, such that the Born-Oppenheimer potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well-controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated, even in the presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be also very efficient in the case of noiseless (deterministic) ionic forces. The new implementation is validated on the Zundel ion (H5O2+) by direct comparison with standard path integral Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond room temperature, giving the excess proton an increased mobility by quantum tunneling. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most-Advanced post-Hartree-Fock approaches, and with a favorable scaling with the system size. In order to cope with the intrinsic noise due to the stochastic nature of quantum Monte Carlo methods, we generalize the path integral molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of quantum Monte Carlo nuclear forces. The variational parameters of the quantum Monte Carlo wave function are evolved during the nuclear dynamics, such that the Born-Oppenheimer potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well-controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated, even in the presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be also very efficient in the case of noiseless (deterministic) ionic forces. The new implementation is validated on the Zundel ion (H5O2+) by direct comparison with standard path integral Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond room temperature, giving the excess proton an increased mobility by quantum tunneling. © 2017 American Chemical Society. |
Microscopic flow around a diffusing particle Article de journal D Lesnicki; R Vuilleumier Journal of Chemical Physics, 147 (9), 2017. @article{Lesnicki:2017, title = {Microscopic flow around a diffusing particle}, author = {D Lesnicki and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029312710&doi=10.1063%2f1.4985909&partnerID=40&md5=303fd55329a5a382e531db4034965d95}, doi = {10.1063/1.4985909}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {147}, number = {9}, abstract = {We report here on the computation of the microscopic flow induced by the motion of a small tagged particle in a fluid from molecular dynamic simulations. It is found that the hydrodynamical Stokes solution with slip boundary conditions is recovered at only a few diameters away from the tagged particle. However, fluctuations of the diffusing particle itself induce a renormalization of the bath viscosity and, more strikingly, an apparent violation of the non-penetrability of the particles in the laboratory frame. The expected zero normal velocity at contact is satisfied only in the particle frame, or for heavy particles. Further evidence of this generalized boundary condition is given by the evaluation of the flow in a granular gas using data from particle tracking experiments. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report here on the computation of the microscopic flow induced by the motion of a small tagged particle in a fluid from molecular dynamic simulations. It is found that the hydrodynamical Stokes solution with slip boundary conditions is recovered at only a few diameters away from the tagged particle. However, fluctuations of the diffusing particle itself induce a renormalization of the bath viscosity and, more strikingly, an apparent violation of the non-penetrability of the particles in the laboratory frame. The expected zero normal velocity at contact is satisfied only in the particle frame, or for heavy particles. Further evidence of this generalized boundary condition is given by the evaluation of the flow in a granular gas using data from particle tracking experiments. © 2017 Author(s). |
On the mass of atoms in molecules: Beyond the born-oppenheimer approximation Article de journal A Scherrer; F Agostini; D Sebastiani; E K U Gross; R Vuilleumier Physical Review X, 7 (3), 2017. @article{Scherrer:2017, title = {On the mass of atoms in molecules: Beyond the born-oppenheimer approximation}, author = {A Scherrer and F Agostini and D Sebastiani and E K U Gross and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029807679&doi=10.1103%2fPhysRevX.7.031035&partnerID=40&md5=d047b54d649a075da40660c4eb3e1f96}, doi = {10.1103/PhysRevX.7.031035}, year = {2017}, date = {2017-01-01}, journal = {Physical Review X}, volume = {7}, number = {3}, abstract = {Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the computation of high-precision molecular spectra.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the computation of high-precision molecular spectra. |
Transient hydrodynamic finite-size effects in simulations under periodic boundary conditions Article de journal A J Asta; M Levesque; R Vuilleumier; B Rotenberg Physical Review E, 95 (6), 2017. @article{Asta:2017, title = {Transient hydrodynamic finite-size effects in simulations under periodic boundary conditions}, author = {A J Asta and M Levesque and R Vuilleumier and B Rotenberg}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021425888&doi=10.1103%2fPhysRevE.95.061301&partnerID=40&md5=214359f07ec0a14040b68cb22b376893}, doi = {10.1103/PhysRevE.95.061301}, year = {2017}, date = {2017-01-01}, journal = {Physical Review E}, volume = {95}, number = {6}, abstract = {We use lattice-Boltzmann and analytical calculations to investigate transient hydrodynamic finite-size effects induced by the use of periodic boundary conditions. These effects are inevitable in simulations at the molecular, mesoscopic, or continuum levels of description. We analyze the transient response to a local perturbation in the fluid and obtain the local velocity correlation function via linear response theory. This approach is validated by comparing the finite-size effects on the steady-state velocity with the known results for the diffusion coefficient. We next investigate the full time dependence of the local velocity autocorrelation function. We find at long times a crossover between the expected t-3/2 hydrodynamic tail and an oscillatory exponential decay, and study the scaling with the system size of the crossover time, exponential rate and amplitude, and oscillation frequency. We interpret these results from the analytic solution of the compressible Navier-Stokes equation for the slowest modes, which are set by the system size. The present work not only provides a comprehensive analysis of hydrodynamic finite-size effects in bulk fluids, which arise regardless of the level of description and simulation algorithm, but also establishes the lattice-Boltzmann method as a suitable tool to investigate such effects in general. © 2017 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We use lattice-Boltzmann and analytical calculations to investigate transient hydrodynamic finite-size effects induced by the use of periodic boundary conditions. These effects are inevitable in simulations at the molecular, mesoscopic, or continuum levels of description. We analyze the transient response to a local perturbation in the fluid and obtain the local velocity correlation function via linear response theory. This approach is validated by comparing the finite-size effects on the steady-state velocity with the known results for the diffusion coefficient. We next investigate the full time dependence of the local velocity autocorrelation function. We find at long times a crossover between the expected t-3/2 hydrodynamic tail and an oscillatory exponential decay, and study the scaling with the system size of the crossover time, exponential rate and amplitude, and oscillation frequency. We interpret these results from the analytic solution of the compressible Navier-Stokes equation for the slowest modes, which are set by the system size. The present work not only provides a comprehensive analysis of hydrodynamic finite-size effects in bulk fluids, which arise regardless of the level of description and simulation algorithm, but also establishes the lattice-Boltzmann method as a suitable tool to investigate such effects in general. © 2017 American Physical Society. |