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.
2016 |
Mechanism of water adsorption in the large pore form of the gallium-based MIL-53 metal-organic framework Article de journal G Weber; I Bezverkhyy; J -P Bellat; A Ballandras; G Ortiz; G Chaplais; J Patarin; F -X Coudert; A H Fuchs; A Boutin Microporous and Mesoporous Materials, 222 , p. 145–152, 2016. @article{Weber:2016, title = {Mechanism of water adsorption in the large pore form of the gallium-based MIL-53 metal-organic framework}, author = {G Weber and I Bezverkhyy and J -P Bellat and A Ballandras and G Ortiz and G Chaplais and J Patarin and F -X Coudert and A H Fuchs and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84945546147&doi=10.1016%2fj.micromeso.2015.10.003&partnerID=40&md5=a52eb07d01a83392f06ae166075ac9f9}, doi = {10.1016/j.micromeso.2015.10.003}, year = {2016}, date = {2016-01-01}, journal = {Microporous and Mesoporous Materials}, volume = {222}, pages = {145--152}, abstract = {Water adsorption in the large pore (lp-empty) form of Ga-MIL-53 was studied by TGA, DSC and in situ XRD and FTIR at 298 K. The large pore form can be stabilized at room temperature after activation under vacuum at 553 K. The isotherm of water adsorption in this large pore form (pore dimensions: 1.67 × 1.33 nm) is very similar to that measured on the narrow pore (np-empty) form (pore dimensions: 1.97 × 0.76 nm). Such a similarity is rather unusual given that the pore sizes of these two phases are very different. In order to understand the origin of this effect in situ XRD and FTIR measurements were particularly helpful. It was found that the adsorption of even small amount of water (0.05 mol per Ga atom at 0.2 hPa) in the large pore form of Ga-MIL-53 transforms ca. 50% of the solid into a narrow pore int phase, which is assumed to be present as a shell around the lp-empty core. Additional water molecules adsorbed at higher pressures do not interact with the parent lp-empty phase but with the narrow pore int phase. The phase transformations were confirmed by FTIR revealing significant band displacements in the corresponding pressure ranges. Such easy pore shrinking which occurs at very low water pressure (textless0.2 hPa) can have undesirable consequences in working conditions, as for example in separation adsorption processes, because the large pore structure of Ga-MIL-53 can be preserved only under anhydrous conditions. © 2015 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Water adsorption in the large pore (lp-empty) form of Ga-MIL-53 was studied by TGA, DSC and in situ XRD and FTIR at 298 K. The large pore form can be stabilized at room temperature after activation under vacuum at 553 K. The isotherm of water adsorption in this large pore form (pore dimensions: 1.67 × 1.33 nm) is very similar to that measured on the narrow pore (np-empty) form (pore dimensions: 1.97 × 0.76 nm). Such a similarity is rather unusual given that the pore sizes of these two phases are very different. In order to understand the origin of this effect in situ XRD and FTIR measurements were particularly helpful. It was found that the adsorption of even small amount of water (0.05 mol per Ga atom at 0.2 hPa) in the large pore form of Ga-MIL-53 transforms ca. 50% of the solid into a narrow pore int phase, which is assumed to be present as a shell around the lp-empty core. Additional water molecules adsorbed at higher pressures do not interact with the parent lp-empty phase but with the narrow pore int phase. The phase transformations were confirmed by FTIR revealing significant band displacements in the corresponding pressure ranges. Such easy pore shrinking which occurs at very low water pressure (textless0.2 hPa) can have undesirable consequences in working conditions, as for example in separation adsorption processes, because the large pore structure of Ga-MIL-53 can be preserved only under anhydrous conditions. © 2015 Elsevier Inc. |
2015 |
T Bryk; G Ruocco; T Scopigno; A P Seitsonen Journal of Chemical Physics, 143 (10), 2015. @article{Bryk:2015, title = {Pressure-induced emergence of unusually high-frequency transverse excitations in a liquid alkali metal: Evidence of two types of collective excitations contributing to the transverse dynamics at high pressures}, author = {T Bryk and G Ruocco and T Scopigno and A P Seitsonen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941144410&doi=10.1063%2f1.4928976&partnerID=40&md5=3ad1016788c17003e3ba6d9413ac5728}, doi = {10.1063/1.4928976}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {10}, abstract = {Unlike phonons in crystals, the collective excitations in liquids cannot be treated as propagation of harmonic displacements of atoms around stable local energy minima. The viscoelasticity of liquids, reflected in transition from the adiabatic to elastic high-frequency speed of sound and in absence of the long-wavelength transverse excitations, results in dispersions of longitudinal (L) and transverse (T) collective excitations essentially different from the typical phonon ones. Practically, nothing is known about the effect of high pressure on the dispersion of collective excitations in liquids, which causes strong changes in liquid structure. Here dispersions of L and T collective excitations in liquid Li in the range of pressures up to 186 GPa were studied by ab initio simulations. Two methodologies for dispersion calculations were used: direct estimation from the peak positions of the L/T current spectral functions and simulation-based calculations of wavenumber-dependent collective eigenmodes. It is found that at ambient pressure, the longitudinal and transverse dynamics are well separated, while at high pressures, the transverse current spectral functions, density of vibrational states, and dispersions of collective excitations yield evidence of two types of propagating modes that contribute strongly to transverse dynamics. Emergence of the unusually high-frequency transverse modes gives evidence of the breakdown of a regular viscoelastic theory of transverse dynamics, which is based on coupling of a single transverse propagating mode with shear relaxation. The explanation of the observed high-frequency shift above the viscoelastic value is given by the presence of another branch of collective excitations. With the pressure increasing, coupling between the two types of collective excitations is rationalized within a proposed extended viscoelastic model of transverse dynamics. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Unlike phonons in crystals, the collective excitations in liquids cannot be treated as propagation of harmonic displacements of atoms around stable local energy minima. The viscoelasticity of liquids, reflected in transition from the adiabatic to elastic high-frequency speed of sound and in absence of the long-wavelength transverse excitations, results in dispersions of longitudinal (L) and transverse (T) collective excitations essentially different from the typical phonon ones. Practically, nothing is known about the effect of high pressure on the dispersion of collective excitations in liquids, which causes strong changes in liquid structure. Here dispersions of L and T collective excitations in liquid Li in the range of pressures up to 186 GPa were studied by ab initio simulations. Two methodologies for dispersion calculations were used: direct estimation from the peak positions of the L/T current spectral functions and simulation-based calculations of wavenumber-dependent collective eigenmodes. It is found that at ambient pressure, the longitudinal and transverse dynamics are well separated, while at high pressures, the transverse current spectral functions, density of vibrational states, and dispersions of collective excitations yield evidence of two types of propagating modes that contribute strongly to transverse dynamics. Emergence of the unusually high-frequency transverse modes gives evidence of the breakdown of a regular viscoelastic theory of transverse dynamics, which is based on coupling of a single transverse propagating mode with shear relaxation. The explanation of the observed high-frequency shift above the viscoelastic value is given by the presence of another branch of collective excitations. With the pressure increasing, coupling between the two types of collective excitations is rationalized within a proposed extended viscoelastic model of transverse dynamics. © 2015 AIP Publishing LLC. |
C Pinilla; M Blanchard; E Balan; S K Natarajan; R Vuilleumier; F Mauri Geochimica et Cosmochimica Acta, 167 , p. 313–314, 2015. @article{Pinilla:2015, title = {Corrigendum to "Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics" [Geochim. Cosmochim. Acta 163, (2015), 126-139]}, author = {C Pinilla and M Blanchard and E Balan and S K Natarajan and R Vuilleumier and F Mauri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941259826&doi=10.1016%2fj.gca.2015.07.031&partnerID=40&md5=b41947dde52a6f26db2101956257fc16}, doi = {10.1016/j.gca.2015.07.031}, year = {2015}, date = {2015-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {167}, pages = {313--314}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
A NMR and molecular dynamics study of CO2-bearing basaltic melts and glasses Article de journal Y Morizet; R Vuilleumier; M Paris Chemical Geology, 418 , p. 89–103, 2015. @article{Morizet:2015, title = {A NMR and molecular dynamics study of CO2-bearing basaltic melts and glasses}, author = {Y Morizet and R Vuilleumier and M Paris}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84958605430&doi=10.1016%2fj.chemgeo.2015.03.021&partnerID=40&md5=d70084bc8c941a58d6d7f9a46d2d173e}, doi = {10.1016/j.chemgeo.2015.03.021}, year = {2015}, date = {2015-01-01}, journal = {Chemical Geology}, volume = {418}, pages = {89--103}, abstract = {The presence of volatile, especially carbon dioxide (CO2), in silicate liquids is considered as a key parameter to magmatic degassing and eruptive processes. Unfortunately, due to experimental difficulties, our current knowledge on the CO2 effect on silicate melt structure is weak and relies on the observation of ex-situ recovered CO2-bearing glasses.In the present work, we confront the results obtained from NMR spectroscopic observations of glass synthesised at pressure between 0.5 and 3.0 GPa and theoretical investigations from first-principles molecular dynamics (FPMD) simulations conducted at 5.0 and 8.0 GPa on high temperature melt for a simplified basaltic composition.The results obtained on the aluminosilicate framework (molar fraction of silicon species and Al average coordination number) suggest that both ex-situ and in-situ results compare adequately. The results are in agreement with our current knowledge on the change in aluminosilicate melt/glass structure with changing intensive conditions. Increasing pressure from 0.5 to 8.0 GPa induces 1) an increase in the average Al coordination number from 4.1 to almost 5.0 and 2) an increase in the degree of polymerisation with NBO/Si changing from 1.30 to 0.80.The presence of CO2 does not seem to induce a dramatic change on both the average Al coordination number and the NBO/Si. FPMD simulations performed with 0 and 20 wt.% CO2 at 8.0 GPa result in a change from 4.84 to 4.96 for the average Al coordination number and in a change from 0.87 to 0.80 for the NBO/Si value, respectively.On the contrary, there is a lack of consistency in between the CO2 speciation obtained from NMR spectroscopy and from FPMD simulations. Whereas the analysis of glasses does not reveal the presence of CO2 mol species, the FPMD simulation results suggests the existence of a small proportion of CO2 mol. Further work with in-situ experimental approach is therefore required to explain the observed lack of consistency between the CO2 speciation in glass and in high temperature melt with basaltic composition. © 2015 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The presence of volatile, especially carbon dioxide (CO2), in silicate liquids is considered as a key parameter to magmatic degassing and eruptive processes. Unfortunately, due to experimental difficulties, our current knowledge on the CO2 effect on silicate melt structure is weak and relies on the observation of ex-situ recovered CO2-bearing glasses.In the present work, we confront the results obtained from NMR spectroscopic observations of glass synthesised at pressure between 0.5 and 3.0 GPa and theoretical investigations from first-principles molecular dynamics (FPMD) simulations conducted at 5.0 and 8.0 GPa on high temperature melt for a simplified basaltic composition.The results obtained on the aluminosilicate framework (molar fraction of silicon species and Al average coordination number) suggest that both ex-situ and in-situ results compare adequately. The results are in agreement with our current knowledge on the change in aluminosilicate melt/glass structure with changing intensive conditions. Increasing pressure from 0.5 to 8.0 GPa induces 1) an increase in the average Al coordination number from 4.1 to almost 5.0 and 2) an increase in the degree of polymerisation with NBO/Si changing from 1.30 to 0.80.The presence of CO2 does not seem to induce a dramatic change on both the average Al coordination number and the NBO/Si. FPMD simulations performed with 0 and 20 wt.% CO2 at 8.0 GPa result in a change from 4.84 to 4.96 for the average Al coordination number and in a change from 0.87 to 0.80 for the NBO/Si value, respectively.On the contrary, there is a lack of consistency in between the CO2 speciation obtained from NMR spectroscopy and from FPMD simulations. Whereas the analysis of glasses does not reveal the presence of CO2 mol species, the FPMD simulation results suggests the existence of a small proportion of CO2 mol. Further work with in-situ experimental approach is therefore required to explain the observed lack of consistency between the CO2 speciation in glass and in high temperature melt with basaltic composition. © 2015 Elsevier B.V. |
Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics Article de journal C Pinilla; M Blanchard; E Balan; S K Natarajan; R Vuilleumier; F Mauri Geochimica et Cosmochimica Acta, 163 , p. 126–139, 2015. @article{Pinilla:2015a, title = {Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics}, author = {C Pinilla and M Blanchard and E Balan and S K Natarajan and R Vuilleumier and F Mauri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929333698&doi=10.1016%2fj.gca.2015.04.008&partnerID=40&md5=108fbec7d44f74103d9856891f0089fa}, doi = {10.1016/j.gca.2015.04.008}, year = {2015}, date = {2015-01-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {163}, pages = {126--139}, abstract = {The theoretical determination of the isotopic fractionation between an aqueous solution and a mineral is of utmost importance in Earth sciences. While for crystals, it is well established that equilibrium isotopic fractionation factors can be calculated using a statistical thermodynamic approach based on the vibrational properties, several theoretical methods are currently used to model ions in aqueous solution. In this work, we present a systematic study to determine the reduced partition function ratio (β-factor) of aqueous Mg2+ using several levels of theory within the simulations. In particular, using an empirical force field, we compare and discuss the performance of the exact results obtained from path integral molecular dynamics (PIMD) simulations, with respect to the more traditional methods based on vibrational properties and the cluster approximation. The results show the importance of including configurational disorder for the estimation of the equilibrium isotope fractionation factor. We also show that using the vibrational frequencies computed from snapshots taken from equilibrated classical molecular dynamics represents a good approximation for the study of aqueous ions. Based on these conclusions, the β-factor of aqueous Mg2+ have been estimated from a Car-Parrinello molecular dynamics (CPMD) simulation with an ab initio force field, and combined with the β-factors of carbonate minerals (magnesite, dolomite, calcite and aragonite). Mg β-factor of Mg-bearing aragonite, calculated here for the first time, displays a lower value than the three other carbonate minerals. This is explained by a strong distortion of the cationic site leading to a decrease of the coordination number during Ca-Mg substitution. Overall, the equilibrium magnesium isotope fractionation factors between aqueous Mg2+ and carbonate minerals that derive from this methodological study support the previous theoretical results obtained from embedded cluster models. © 2015 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The theoretical determination of the isotopic fractionation between an aqueous solution and a mineral is of utmost importance in Earth sciences. While for crystals, it is well established that equilibrium isotopic fractionation factors can be calculated using a statistical thermodynamic approach based on the vibrational properties, several theoretical methods are currently used to model ions in aqueous solution. In this work, we present a systematic study to determine the reduced partition function ratio (β-factor) of aqueous Mg2+ using several levels of theory within the simulations. In particular, using an empirical force field, we compare and discuss the performance of the exact results obtained from path integral molecular dynamics (PIMD) simulations, with respect to the more traditional methods based on vibrational properties and the cluster approximation. The results show the importance of including configurational disorder for the estimation of the equilibrium isotope fractionation factor. We also show that using the vibrational frequencies computed from snapshots taken from equilibrated classical molecular dynamics represents a good approximation for the study of aqueous ions. Based on these conclusions, the β-factor of aqueous Mg2+ have been estimated from a Car-Parrinello molecular dynamics (CPMD) simulation with an ab initio force field, and combined with the β-factors of carbonate minerals (magnesite, dolomite, calcite and aragonite). Mg β-factor of Mg-bearing aragonite, calculated here for the first time, displays a lower value than the three other carbonate minerals. This is explained by a strong distortion of the cationic site leading to a decrease of the coordination number during Ca-Mg substitution. Overall, the equilibrium magnesium isotope fractionation factors between aqueous Mg2+ and carbonate minerals that derive from this methodological study support the previous theoretical results obtained from embedded cluster models. © 2015 Elsevier Ltd. |
Gas phase infrared spectra from quasi-classical Kubo time correlation functions Article de journal J Beutier; R Vuilleumier; S Bonella; G Ciccotti Molecular Physics, 113 (17-18), p. 2894–2904, 2015. @article{Beutier:2015, title = {Gas phase infrared spectra from quasi-classical Kubo time correlation functions}, author = {J Beutier and R Vuilleumier and S Bonella and G Ciccotti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84943582680&doi=10.1080%2f00268976.2015.1064550&partnerID=40&md5=d9f397e5e12a264abe7ee76e1eb1ff6a}, doi = {10.1080/00268976.2015.1064550}, year = {2015}, date = {2015-01-01}, journal = {Molecular Physics}, volume = {113}, number = {17-18}, pages = {2894--2904}, abstract = {We generalise the recently developed phase integration method (PIM) to obtain a computable approximation of the Kubo expression for quantum time correlation functions. Our scheme combines exact sampling of the quantum thermal density with classical dynamics to provide a quasi-classical approximation for the correlation function. The method will be specialised to the evaluation of the momentum autocorrelation function, with the goal to compute infrared spectra of simple molecules in the gas phase. Application to two simple but interesting benchmark systems shows that the approach is accurate and stable over a broad range of temperatures. © 2015 © 2015 Taylor & Francis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We generalise the recently developed phase integration method (PIM) to obtain a computable approximation of the Kubo expression for quantum time correlation functions. Our scheme combines exact sampling of the quantum thermal density with classical dynamics to provide a quasi-classical approximation for the correlation function. The method will be specialised to the evaluation of the momentum autocorrelation function, with the goal to compute infrared spectra of simple molecules in the gas phase. Application to two simple but interesting benchmark systems shows that the approach is accurate and stable over a broad range of temperatures. © 2015 © 2015 Taylor & Francis. |
Investigation of the fragmentation of core-ionised deoxyribose: A study as a function of the tautomeric form Article de journal M -A Hervé Du Penhoat; K Kamol Ghose; M -P Gaigeot; R Vuilleumier; K Fujii; A Yokoya; M -F Politis Physical Chemistry Chemical Physics, 17 (48), p. 32375–32383, 2015. @article{HerveDuPenhoat:2015, title = {Investigation of the fragmentation of core-ionised deoxyribose: A study as a function of the tautomeric form}, author = {M -A Herv\'{e} Du Penhoat and K Kamol Ghose and M -P Gaigeot and R Vuilleumier and K Fujii and A Yokoya and M -F Politis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948800288&doi=10.1039%2fc5cp05196g&partnerID=40&md5=f37e8538f25dddc75ac8d9e34a927115}, doi = {10.1039/c5cp05196g}, year = {2015}, date = {2015-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {17}, number = {48}, pages = {32375--32383}, abstract = {We have investigated the gas phase fragmentation dynamics following the core ionisation of 2-deoxy-d-ribose (dR), a major component in the DNA chain. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics simulations. The ultrafast dissociation dynamics of the core-ionised biomolecule, prior Auger decay, is first modelled for 10 fs to generate initial configurations (atomic positions and velocities) for the subsequent dynamics of the doubly ionised biomolecule in the ground state. The furanose, linear and pyranose conformations of dR were investigated. We show that fragmentation is relatively independent of the atom struck or of the duration of the core vacancy, but depends rather critically on the molecular orbital removed following Auger decay. © 2015 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have investigated the gas phase fragmentation dynamics following the core ionisation of 2-deoxy-d-ribose (dR), a major component in the DNA chain. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics simulations. The ultrafast dissociation dynamics of the core-ionised biomolecule, prior Auger decay, is first modelled for 10 fs to generate initial configurations (atomic positions and velocities) for the subsequent dynamics of the doubly ionised biomolecule in the ground state. The furanose, linear and pyranose conformations of dR were investigated. We show that fragmentation is relatively independent of the atom struck or of the duration of the core vacancy, but depends rather critically on the molecular orbital removed following Auger decay. © 2015 the Owner Societies. |
Hydrothermal Breakdown of Flexible Metal-Organic Frameworks: A Study by First-Principles Molecular Dynamics Article de journal V Haigis; F -X Coudert; R Vuilleumier; A Boutin; A H Fuchs Journal of Physical Chemistry Letters, 6 (21), p. 4365–4370, 2015. @article{Haigis:2015, title = {Hydrothermal Breakdown of Flexible Metal-Organic Frameworks: A Study by First-Principles Molecular Dynamics}, author = {V Haigis and F -X Coudert and R Vuilleumier and A Boutin and A H Fuchs}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84946822800&doi=10.1021%2facs.jpclett.5b01926&partnerID=40&md5=1ca30978fa4ef2cf6cb576e3f7b9ef21}, doi = {10.1021/acs.jpclett.5b01926}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {6}, number = {21}, pages = {4365--4370}, abstract = {Flexible metal-organic frameworks, also known as soft porous crystals, have been proposed for a vast number of technological applications, because they respond by large changes in structure and properties to small external stimuli, such as adsorption of guest molecules and changes in temperature or pressure. While this behavior is highly desirable in applications such as sensing and actuation, their extreme flexibility can also be synonymous with decreased stability. In particular, their performance in industrial environments is limited by a lack of stability at elevated temperatures and in the presence of water. Here, we use first-principles molecular dynamics to study the hydrothermal breakdown of soft porous crystals. Focusing on the material MIL-53(Ga), we show that the weak point of the structure is the bond between the metal center and the organic linker and elucidate the mechanism by which water lowers the activation free energy for the breakdown. This allows us to propose strategies for the synthesis of MOFs with increased heat and water stability. © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Flexible metal-organic frameworks, also known as soft porous crystals, have been proposed for a vast number of technological applications, because they respond by large changes in structure and properties to small external stimuli, such as adsorption of guest molecules and changes in temperature or pressure. While this behavior is highly desirable in applications such as sensing and actuation, their extreme flexibility can also be synonymous with decreased stability. In particular, their performance in industrial environments is limited by a lack of stability at elevated temperatures and in the presence of water. Here, we use first-principles molecular dynamics to study the hydrothermal breakdown of soft porous crystals. Focusing on the material MIL-53(Ga), we show that the weak point of the structure is the bond between the metal center and the organic linker and elucidate the mechanism by which water lowers the activation free energy for the breakdown. This allows us to propose strategies for the synthesis of MOFs with increased heat and water stability. © 2015 American Chemical Society. |
Maximum probability domains for the analysis of the microscopic structure of liquids Article de journal F Agostini; G Ciccotti; A Savin; R Vuilleumier Journal of Chemical Physics, 142 (6), 2015. @article{Agostini:2015, title = {Maximum probability domains for the analysis of the microscopic structure of liquids}, author = {F Agostini and G Ciccotti and A Savin and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84923823374&doi=10.1063%2f1.4907406&partnerID=40&md5=c56bda95081ac55e95ed6320cf51b6bb}, doi = {10.1063/1.4907406}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {142}, number = {6}, abstract = {We introduce the concept of maximum probability domains (MPDs), developed in the context of the analysis of electronic densities, in the study of the microscopic spatial structures of liquids. The idea of locating a particle in a three dimensional region, by determining the domain where the probability of finding that, and only that, particle is maximum, gives an interesting characterization of the local structure of the liquid. The optimization procedure, required for the search of the domain of maximum probability, is carried out by the implementation of the level set method. Results for a couple of case studies are presented, to illustrate the structure of liquid water at ambient conditions and upon increasing pressure from the point of view of MPDs and to compare the information encoded in the solvation shells of sodium in water with, once again, that extracted from the MPDs. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We introduce the concept of maximum probability domains (MPDs), developed in the context of the analysis of electronic densities, in the study of the microscopic spatial structures of liquids. The idea of locating a particle in a three dimensional region, by determining the domain where the probability of finding that, and only that, particle is maximum, gives an interesting characterization of the local structure of the liquid. The optimization procedure, required for the search of the domain of maximum probability, is carried out by the implementation of the level set method. Results for a couple of case studies are presented, to illustrate the structure of liquid water at ambient conditions and upon increasing pressure from the point of view of MPDs and to compare the information encoded in the solvation shells of sodium in water with, once again, that extracted from the MPDs. © 2015 AIP Publishing LLC. |
Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function Article de journal A Scherrer; F Agostini; D Sebastiani; E K U Gross; R Vuilleumier Journal of Chemical Physics, 143 (7), 2015. @article{Scherrer:2015, title = {Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function}, author = {A Scherrer and F Agostini and D Sebastiani and E K U Gross and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939805732&doi=10.1063%2f1.4928578&partnerID=40&md5=11621b3149fe6735185b7f11d9afb3a1}, doi = {10.1063/1.4928578}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {7}, abstract = {The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similar to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similar to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach. © 2015 AIP Publishing LLC. |
Theoretical study of the ionization of liquid water from its several initial orbitals by fast electron impact Article de journal M L D Sanctis; M -F Politis; R Vuilleumier; C R Stia; O A Fojón Journal of Physics B: Atomic, Molecular and Optical Physics, 48 (15), 2015. @article{Sanctis:2015, title = {Theoretical study of the ionization of liquid water from its several initial orbitals by fast electron impact}, author = {M L D Sanctis and M -F Politis and R Vuilleumier and C R Stia and O A Foj\'{o}n}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84936760668&doi=10.1088%2f0953-4075%2f48%2f15%2f155201&partnerID=40&md5=d6920aaa90104dd081eab90d80ab9735}, doi = {10.1088/0953-4075/48/15/155201}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physics B: Atomic, Molecular and Optical Physics}, volume = {48}, number = {15}, abstract = {We theoretically study the single ionization of liquid water by energetic electrons through one active-electron first-order model. We analyze the angular ejected electron spectra corresponding to the most external orbitals 1B1, 2A1, 1B2 and 1A1 of a single water molecule. We work to create a realistic description of those orbitals corresponding to single molecules in the liquid phase. This goal is achieved by means of a Wannier orbital formalism. Multiple differential cross sections are computed and compared with previous calculations for both liquid and gas phases. In addition, our present results are integrated over all orientations and compared with experimental ones for randomly oriented vapour water molecules, as no experiments currently exist for the liquid phase. Moreover, we estimate the influence of the passive electrons on the reaction by means of a model potential. © 2015 IOP Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We theoretically study the single ionization of liquid water by energetic electrons through one active-electron first-order model. We analyze the angular ejected electron spectra corresponding to the most external orbitals 1B1, 2A1, 1B2 and 1A1 of a single water molecule. We work to create a realistic description of those orbitals corresponding to single molecules in the liquid phase. This goal is achieved by means of a Wannier orbital formalism. Multiple differential cross sections are computed and compared with previous calculations for both liquid and gas phases. In addition, our present results are integrated over all orientations and compared with experimental ones for randomly oriented vapour water molecules, as no experiments currently exist for the liquid phase. Moreover, we estimate the influence of the passive electrons on the reaction by means of a model potential. © 2015 IOP Publishing Ltd. |
Solvation free-energy pressure corrections in the three dimensional reference interaction site model Article de journal V Sergiievskyi; G Jeanmairet; M Levesque; D Borgis Journal of Chemical Physics, 143 (18), 2015. @article{Sergiievskyi:2015, title = {Solvation free-energy pressure corrections in the three dimensional reference interaction site model}, author = {V Sergiievskyi and G Jeanmairet and M Levesque and D Borgis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84947092925&doi=10.1063%2f1.4935065&partnerID=40&md5=ee2c4ce70ca6fdbcaef9b44530fd8eb7}, doi = {10.1063/1.4935065}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {18}, abstract = {Solvation free energies are efficiently predicted by molecular density functional theory if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [J. Phys. Chem. Lett. 5, 1935-1942 (2014)] recently derived the rigorous compensation of this excess of pressure (referred as "pressure correction" or PC) and proposed an empirical "ideal gas" supplementary correction (referred as "advanced pressure correction" or PC+) that further enhances the calculated solvation free energies. In a recent paper [M. Misin, M. V. Fedorov, and D. S. Palmer, J. Chem. Phys. 142, 091105 (2015)], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we derive rigorously the expression of the pressure in 3D-RISM as well as the associated PC and PC+. This provides a consistent way to correct the solvation free-energies calculated by 3D-RISM method. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Solvation free energies are efficiently predicted by molecular density functional theory if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [J. Phys. Chem. Lett. 5, 1935-1942 (2014)] recently derived the rigorous compensation of this excess of pressure (referred as "pressure correction" or PC) and proposed an empirical "ideal gas" supplementary correction (referred as "advanced pressure correction" or PC+) that further enhances the calculated solvation free energies. In a recent paper [M. Misin, M. V. Fedorov, and D. S. Palmer, J. Chem. Phys. 142, 091105 (2015)], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we derive rigorously the expression of the pressure in 3D-RISM as well as the associated PC and PC+. This provides a consistent way to correct the solvation free-energies calculated by 3D-RISM method. © 2015 AIP Publishing LLC. |
Unexpected coupling between flow and adsorption in porous media Article de journal J -M Vanson; F -X Coudert; B Rotenberg; M Levesque; C Tardivat; M Klotz; A Boutin Soft Matter, 11 (30), p. 6125–6133, 2015. @article{Vanson:2015, title = {Unexpected coupling between flow and adsorption in porous media}, author = {J -M Vanson and F -X Coudert and B Rotenberg and M Levesque and C Tardivat and M Klotz and A Boutin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84937501168&doi=10.1039%2fc5sm01348h&partnerID=40&md5=27c27798ab0f7ff6c97d12fbfeea602a}, doi = {10.1039/c5sm01348h}, year = {2015}, date = {2015-01-01}, journal = {Soft Matter}, volume = {11}, number = {30}, pages = {6125--6133}, abstract = {We study the interplay between transport and adsorption in porous systems under a fluid flow, based on a lattice Boltzmann scheme extended to account for adsorption. We performed simulations on well-controlled geometries with slit and grooved pores, investigating the influence of adsorption and flow on dispersion coefficient and adsorbed density. In particular, we present a counterintuitive effect where fluid flow induces heterogeneity in the adsorbate, displacing the adsorption equilibrium towards downstream adsorption sites in grooves. We also present an improvement of the adsorption-extended lattice Boltzmann scheme by introducing the possibility for saturating Langmuir-like adsorption, while earlier work focused on linear adsorption phenomena. We then highlight the impact of this change in situations of high concentration of adsorbate. © The Royal Society of Chemistry 2015.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study the interplay between transport and adsorption in porous systems under a fluid flow, based on a lattice Boltzmann scheme extended to account for adsorption. We performed simulations on well-controlled geometries with slit and grooved pores, investigating the influence of adsorption and flow on dispersion coefficient and adsorbed density. In particular, we present a counterintuitive effect where fluid flow induces heterogeneity in the adsorbate, displacing the adsorption equilibrium towards downstream adsorption sites in grooves. We also present an improvement of the adsorption-extended lattice Boltzmann scheme by introducing the possibility for saturating Langmuir-like adsorption, while earlier work focused on linear adsorption phenomena. We then highlight the impact of this change in situations of high concentration of adsorbate. © The Royal Society of Chemistry 2015. |
Softening upon Adsorption in Microporous Materials: A Counterintuitive Mechanical Response Article de journal F Mouhat; D Bousquet; A Boutin; L Bouëssel Du Bourg; F -X Coudert; A H Fuchs Journal of Physical Chemistry Letters, 6 (21), p. 4265–4269, 2015. @article{Mouhat:2015, title = {Softening upon Adsorption in Microporous Materials: A Counterintuitive Mechanical Response}, author = {F Mouhat and D Bousquet and A Boutin and L Bou\"{e}ssel Du Bourg and F -X Coudert and A H Fuchs}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84946593609&doi=10.1021%2facs.jpclett.5b01965&partnerID=40&md5=a6ad98701fd642025fbeb18e719ad1a3}, doi = {10.1021/acs.jpclett.5b01965}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {6}, number = {21}, pages = {4265--4269}, abstract = {We demonstrate here that microporous materials can exhibit softening upon adsorption of guest molecules, at low to intermediate pore loading, in parallel to the pore shrinking that is well-known in this regime. This novel and counterintuitive mechanical response was observed through molecular simulations of both model pore systems (such as slit pore) and real metal-organic frameworks. It is contrary to common belief that adsorption of guest molecules necessarily leads to stiffening due to increased density, a fact that we show is the high-loading limit of a more complex behavior: a nonmonotonic softening-then-stiffening. © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We demonstrate here that microporous materials can exhibit softening upon adsorption of guest molecules, at low to intermediate pore loading, in parallel to the pore shrinking that is well-known in this regime. This novel and counterintuitive mechanical response was observed through molecular simulations of both model pore systems (such as slit pore) and real metal-organic frameworks. It is contrary to common belief that adsorption of guest molecules necessarily leads to stiffening due to increased density, a fact that we show is the high-loading limit of a more complex behavior: a nonmonotonic softening-then-stiffening. © 2015 American Chemical Society. |
Reaction of Phthalocyanines with Graphene on Ir(111) Article de journal S J Altenburg; M Lattelais; B Wang; M -L Bocquet; R Berndt Journal of the American Chemical Society, 137 (29), p. 9452–9458, 2015. @article{Altenburg:2015, title = {Reaction of Phthalocyanines with Graphene on Ir(111)}, author = {S J Altenburg and M Lattelais and B Wang and M -L Bocquet and R Berndt}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84938346221&doi=10.1021%2fjacs.5b05558&partnerID=40&md5=b8f03839e289e91f43c411e58edcd556}, doi = {10.1021/jacs.5b05558}, year = {2015}, date = {2015-01-01}, journal = {Journal of the American Chemical Society}, volume = {137}, number = {29}, pages = {9452--9458}, abstract = {Iron phthalocyanine (FePc) is adsorbed to graphene on Ir(111) at cryogenic temperature. In addition to mobile FePc with four lobes, imaging and spectroscopy with a scanning tunneling microscope reveal immobile molecules that exhibit fewer lobes. A reversible transformation between four- and three-lobed molecules has been induced by current injection. The data are consistent with chemical bonding of lobes to graphene on Ir, pinning down the graphene area toward Ir. Similar observations are made from NiPc, CoPc, CuPc, and Htextlessinftextgreater2textless/inftextgreaterPc. The experimental findings can be explained by ab initio calculations, which suggest that a Diels-Alder-type reaction may be involved with an allyl unit of graphene in the top-fcc moir\'{e} registry. (Figure Presented). © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Iron phthalocyanine (FePc) is adsorbed to graphene on Ir(111) at cryogenic temperature. In addition to mobile FePc with four lobes, imaging and spectroscopy with a scanning tunneling microscope reveal immobile molecules that exhibit fewer lobes. A reversible transformation between four- and three-lobed molecules has been induced by current injection. The data are consistent with chemical bonding of lobes to graphene on Ir, pinning down the graphene area toward Ir. Similar observations are made from NiPc, CoPc, CuPc, and Htextlessinftextgreater2textless/inftextgreaterPc. The experimental findings can be explained by ab initio calculations, which suggest that a Diels-Alder-type reaction may be involved with an allyl unit of graphene in the top-fcc moiré registry. (Figure Presented). © 2015 American Chemical Society. |
Scrutinizing individual CoTPP molecule adsorbed on coinage metal surfaces from the interplay of STM experiment and theory Article de journal T Houwaart; T Le Bahers; P Sautet; W Auwärter; K Seufert; J V Barth; M -L Bocquet Surface Science, 635 , p. 108–114, 2015. @article{Houwaart:2015, title = {Scrutinizing individual CoTPP molecule adsorbed on coinage metal surfaces from the interplay of STM experiment and theory}, author = {T Houwaart and T Le Bahers and P Sautet and W Auw\"{a}rter and K Seufert and J V Barth and M -L Bocquet}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84921478611&doi=10.1016%2fj.susc.2014.12.011&partnerID=40&md5=55c994f6cec219d3c3c089f0e6df5ab3}, doi = {10.1016/j.susc.2014.12.011}, year = {2015}, date = {2015-01-01}, journal = {Surface Science}, volume = {635}, pages = {108--114}, abstract = {The cobalt tetraphenyl porphyrin (CoTPP) molecule and its adsorption on clean Cu and Ag surfaces are comparatively analyzed within the Density Functional Theory (DFT) framework. Different sets of exchange-correlation functionals - the Local Density Approximation (LDA) and the Gradient Generalized Approximation (along with the PBE functional and the semi-empirical Grimme's corrections of dispersion) - are compared. Two prominent structural adsorption properties are disclosed in all sets of calculations: an asymmetric saddle deformation of CoTPP with an enhanced tilting of the upwards bent pyrroles and a single adsorption site where the Co center occupies a bridge position and one molecular axis (along the direction of the lowered pair of opposite pyrroles) is aligned with the dense-packed 〈11¯0〉 substrate direction. The similarities between Cu(111) and Ag(111) surfaces extend to the interfacial electronic structure with similar electronic redistribution and molecular charging. However subtle differences between the two substrates are revealed with bias-dependent STM simulations, especially in the low-bias imaging range. The STM calculations underline the difficulty for the commonly used GGA + D2 DFT framework to quantitatively predict the energy positions of the frontier molecular orbitals (MOs). © 2014 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The cobalt tetraphenyl porphyrin (CoTPP) molecule and its adsorption on clean Cu and Ag surfaces are comparatively analyzed within the Density Functional Theory (DFT) framework. Different sets of exchange-correlation functionals - the Local Density Approximation (LDA) and the Gradient Generalized Approximation (along with the PBE functional and the semi-empirical Grimme's corrections of dispersion) - are compared. Two prominent structural adsorption properties are disclosed in all sets of calculations: an asymmetric saddle deformation of CoTPP with an enhanced tilting of the upwards bent pyrroles and a single adsorption site where the Co center occupies a bridge position and one molecular axis (along the direction of the lowered pair of opposite pyrroles) is aligned with the dense-packed 〈11¯0〉 substrate direction. The similarities between Cu(111) and Ag(111) surfaces extend to the interfacial electronic structure with similar electronic redistribution and molecular charging. However subtle differences between the two substrates are revealed with bias-dependent STM simulations, especially in the low-bias imaging range. The STM calculations underline the difficulty for the commonly used GGA + D2 DFT framework to quantitatively predict the energy positions of the frontier molecular orbitals (MOs). © 2014 Elsevier B.V. All rights reserved. |
Repurposing of Rutin for the Inhibition of Norovirus Replication Article de journal N Chéron; C Yu; A O Kolawole; E I Shakhnovich; C E Wobus Archives of Virology, 160 (9), p. 2353-2358, 2015. @article{Cheron:2015, title = {Repurposing of Rutin for the Inhibition of Norovirus Replication}, author = {N Ch\'{e}ron and C Yu and A O Kolawole and E I Shakhnovich and C E Wobus}, doi = {10.1007/s00705-015-2495-y}, year = {2015}, date = {2015-01-01}, journal = {Archives of Virology}, volume = {160}, number = {9}, pages = {2353-2358}, abstract = {Drug repurposing is a strategy employed to circumvent some of the bottlenecks involved in drug development, such as the cost and time needed for developing new molecular entities. Noroviruses cause recurrent epidemics and sporadic outbreaks of gastroenteritis associated with significant mortality and economic costs, but no treatment has been approved to date. Herein, a library of molecules previously used in humans was screened to find compounds with anti-noroviral activity. Antiviral testing for four selected compounds against murine norovirus infection revealed that rutin has anti-murine norovirus activity in cell-based assays. textcopyright 2015, Springer-Verlag Wien.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Drug repurposing is a strategy employed to circumvent some of the bottlenecks involved in drug development, such as the cost and time needed for developing new molecular entities. Noroviruses cause recurrent epidemics and sporadic outbreaks of gastroenteritis associated with significant mortality and economic costs, but no treatment has been approved to date. Herein, a library of molecules previously used in humans was screened to find compounds with anti-noroviral activity. Antiviral testing for four selected compounds against murine norovirus infection revealed that rutin has anti-murine norovirus activity in cell-based assays. textcopyright 2015, Springer-Verlag Wien. |
Characterization of the Local Structure in Liquid Water by Various Order Parameters Article de journal E Duboué-Dijon; D Laage Journal of Physical Chemistry B, 119 (26), p. 8406–8418, 2015. @article{Duboue-Dijon:2015, title = {Characterization of the Local Structure in Liquid Water by Various Order Parameters}, author = {E Dubou\'{e}-Dijon and D Laage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84947447573&doi=10.1021%2facs.jpcb.5b02936&partnerID=40&md5=8b8fd9fc25e519c0e64f289617f35af7}, doi = {10.1021/acs.jpcb.5b02936}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {26}, pages = {8406--8418}, abstract = {A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism. © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism. © 2015 American Chemical Society. |
Carbon dioxide in silicate melts at upper mantle conditions: Insights from atomistic simulations Article de journal R Vuilleumier; A P Seitsonen; N Sator; B Guillot Chemical Geology, 418 , p. 77–88, 2015. @article{Vuilleumier:2015, title = {Carbon dioxide in silicate melts at upper mantle conditions: Insights from atomistic simulations}, author = {R Vuilleumier and A P Seitsonen and N Sator and B Guillot}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84958665894&doi=10.1016%2fj.chemgeo.2015.02.027&partnerID=40&md5=62a518b8dcbfe60b1aa13ae37521ed88}, doi = {10.1016/j.chemgeo.2015.02.027}, year = {2015}, date = {2015-01-01}, journal = {Chemical Geology}, volume = {418}, pages = {77--88}, abstract = {The detail of the incorporation of carbon dioxide in silicate melts at upper mantle conditions is still badly known. To give some theoretical guidance, we have performed first-principle molecular dynamics simulations (FPMD) to quantify the speciation and the incorporation of carbon dioxide in two CO2-rich silicate melts (textasciitilde20 wt.% CO2 at 2073 K and 12 GPa), a basaltic and a kimberlitic composition chosen in the CaO-MgO-Al2O3-SiO2 system. In the basaltic composition, carbon dioxide is incorporated under the form of a minority population of CO2 molecules and a prevailing population of carbonate ions (CO3 2-). In contrast, the amount of CO2 molecules is found to be very small in the kimberlitic melt. Moreover, a new (transient) species has been identified, the pyrocarbonate ion C2O5 2- issued from the reaction between CO2 and CO3 2-. With regard to the structure of the CO2-bearing melts, it is shown that the carbonate ions modify the silicate network by transforming some of the oxygen atoms into bridging carbonates, non-bridging carbonates, and free carbonates, with a distribution depending on the melt composition. In the basaltic melt a majority of carbonate ions are non-bridging or free, whereas in the kimberlitic melt, most of the carbonate ions are under the form of free carbonates linked to alkaline earth cations. Surprisingly, the addition of CO2 only has a weak influence on the diffusion coefficients of the elements of the melt. The consequence is that the strong enhancement of the electrical conductivity reported recently for carbonated basalts (Sifr\'{e} et al., 2014, Nature 509, 81), can be reproduced by simulation only if one assumes that the ionic charges assigned to the elements of the melt depend, in a non-trivial way, on the CO2 content. Finally, a comparison of the FPMD calculations with classical molecular dynamics simulations using an empirical force field of the literature (Guillot and Sator, 2011, GCA 75, 1829) shows that the latter one needs some improvement. © 2015 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The detail of the incorporation of carbon dioxide in silicate melts at upper mantle conditions is still badly known. To give some theoretical guidance, we have performed first-principle molecular dynamics simulations (FPMD) to quantify the speciation and the incorporation of carbon dioxide in two CO2-rich silicate melts (textasciitilde20 wt.% CO2 at 2073 K and 12 GPa), a basaltic and a kimberlitic composition chosen in the CaO-MgO-Al2O3-SiO2 system. In the basaltic composition, carbon dioxide is incorporated under the form of a minority population of CO2 molecules and a prevailing population of carbonate ions (CO3 2-). In contrast, the amount of CO2 molecules is found to be very small in the kimberlitic melt. Moreover, a new (transient) species has been identified, the pyrocarbonate ion C2O5 2- issued from the reaction between CO2 and CO3 2-. With regard to the structure of the CO2-bearing melts, it is shown that the carbonate ions modify the silicate network by transforming some of the oxygen atoms into bridging carbonates, non-bridging carbonates, and free carbonates, with a distribution depending on the melt composition. In the basaltic melt a majority of carbonate ions are non-bridging or free, whereas in the kimberlitic melt, most of the carbonate ions are under the form of free carbonates linked to alkaline earth cations. Surprisingly, the addition of CO2 only has a weak influence on the diffusion coefficients of the elements of the melt. The consequence is that the strong enhancement of the electrical conductivity reported recently for carbonated basalts (Sifré et al., 2014, Nature 509, 81), can be reproduced by simulation only if one assumes that the ionic charges assigned to the elements of the melt depend, in a non-trivial way, on the CO2 content. Finally, a comparison of the FPMD calculations with classical molecular dynamics simulations using an empirical force field of the literature (Guillot and Sator, 2011, GCA 75, 1829) shows that the latter one needs some improvement. © 2015 Elsevier B.V. |
Dispersion effects in SiO2 polymorphs: An ab initio study Article de journal H Hay; G Ferlat; M Casula; A P Seitsonen; F Mauri Physical Review B - Condensed Matter and Materials Physics, 92 (14), 2015. @article{Hay:2015, title = {Dispersion effects in SiO2 polymorphs: An ab initio study}, author = {H Hay and G Ferlat and M Casula and A P Seitsonen and F Mauri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84946720248&doi=10.1103%2fPhysRevB.92.144111&partnerID=40&md5=62b35cf2e10cc6f722c5a936f99ec01e}, doi = {10.1103/PhysRevB.92.144111}, year = {2015}, date = {2015-01-01}, journal = {Physical Review B - Condensed Matter and Materials Physics}, volume = {92}, number = {14}, abstract = {The effect of electronic dispersion over a wide variety of SiO2 polymorphs (faujasite, ferrierite, α-cristobalite, α-quartz, coesite, and stishovite) is investigated using state-of-the-art density functional theory. Different functionals and dispersion correction schemes are compared, ranging from the local density approximation to fully nonlocal exchange-correlation functionals. It is shown that both empirical dispersion corrections and fully nonlocal functionals improve the energetics and give correct volumetric data. However, the correct volume results come from error cancellation between an overestimation of the Si-O distance and an underestimation of the Si-O-Si angle. Quantum Monte Carlo is used to compute the quartz-cristobalite energy difference within an accuracy of 0.2 kCal/mol per SiO2 unit. This demonstrates the feasability of achieving subchemical accuracy on extended systems, and confirms the validity of the Slater-Jastrow ansatz for describing SiO2 polymorphs. © 2015 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of electronic dispersion over a wide variety of SiO2 polymorphs (faujasite, ferrierite, α-cristobalite, α-quartz, coesite, and stishovite) is investigated using state-of-the-art density functional theory. Different functionals and dispersion correction schemes are compared, ranging from the local density approximation to fully nonlocal exchange-correlation functionals. It is shown that both empirical dispersion corrections and fully nonlocal functionals improve the energetics and give correct volumetric data. However, the correct volume results come from error cancellation between an overestimation of the Si-O distance and an underestimation of the Si-O-Si angle. Quantum Monte Carlo is used to compute the quartz-cristobalite energy difference within an accuracy of 0.2 kCal/mol per SiO2 unit. This demonstrates the feasability of achieving subchemical accuracy on extended systems, and confirms the validity of the Slater-Jastrow ansatz for describing SiO2 polymorphs. © 2015 American Physical Society. |
Erratum: Van der Waals effects in ab initio water at ambient and supercritical conditions (Journal of Chemical Physics (2011) 135 (154503)) Article de journal R Jonchiere; A P Seitsonen; G Ferlat; A M Saitta; R Vuilleumier Journal of Chemical Physics, 143 (20), 2015. @article{Jonchiere:2015, title = {Erratum: Van der Waals effects in ab initio water at ambient and supercritical conditions (Journal of Chemical Physics (2011) 135 (154503))}, author = {R Jonchiere and A P Seitsonen and G Ferlat and A M Saitta and R Vuilleumier}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948685389&doi=10.1063%2f1.4934928&partnerID=40&md5=c314d85d336c9b42596248a39e27a8f8}, doi = {10.1063/1.4934928}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {20}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Many-body transitions in a single molecule visualized by scanning tunnelling microscopy Article de journal F Schulz; M Ijäs; R Drost; S K Hämäläinen; A Harju; A P Seitsonen; P Liljeroth Nature Physics, 11 (3), p. 229–234, 2015. @article{Schulz:2015, title = {Many-body transitions in a single molecule visualized by scanning tunnelling microscopy}, author = {F Schulz and M Ij\"{a}s and R Drost and S K H\"{a}m\"{a}l\"{a}inen and A Harju and A P Seitsonen and P Liljeroth}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924205259&doi=10.1038%2fnphys3212&partnerID=40&md5=e802d1344564c50e37e39dcafec001e6}, doi = {10.1038/nphys3212}, year = {2015}, date = {2015-01-01}, journal = {Nature Physics}, volume = {11}, number = {3}, pages = {229--234}, abstract = {Many-body effects arise from the collective behaviour of large numbers of interacting particles, for example, electrons, and the properties of such a system cannot be understood considering only single or non-interacting particles. Despite the generality of the many-body picture, there are only a few examples of experimentally observing such effects in molecular systems. Measurements of the local density of states of single molecules by scanning tunnelling spectroscopy is usually interpreted in terms of single-particle molecular orbitals. Here, we show that the simple single-particle picture fails qualitatively to account for the resonances in the tunnelling spectra of different charge states of cobalt phthalocyanine molecules. Instead, these resonances can be understood as a series of many-body excitations of the different ground states of the molecule. Our theoretical approach opens an accessible route beyond the single-particle picture in quantifying many-body states in molecules.. © 2015 Macmillan Publishers Limited. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Many-body effects arise from the collective behaviour of large numbers of interacting particles, for example, electrons, and the properties of such a system cannot be understood considering only single or non-interacting particles. Despite the generality of the many-body picture, there are only a few examples of experimentally observing such effects in molecular systems. Measurements of the local density of states of single molecules by scanning tunnelling spectroscopy is usually interpreted in terms of single-particle molecular orbitals. Here, we show that the simple single-particle picture fails qualitatively to account for the resonances in the tunnelling spectra of different charge states of cobalt phthalocyanine molecules. Instead, these resonances can be understood as a series of many-body excitations of the different ground states of the molecule. Our theoretical approach opens an accessible route beyond the single-particle picture in quantifying many-body states in molecules.. © 2015 Macmillan Publishers Limited. All rights reserved. |
Proton disorder in cubic ice: Effect on the electronic and optical properties Article de journal V Garbuio; M Cascella; I Kupchak; O Pulci; A P Seitsonen Journal of Chemical Physics, 143 (8), 2015. @article{Garbuio:2015, title = {Proton disorder in cubic ice: Effect on the electronic and optical properties}, author = {V Garbuio and M Cascella and I Kupchak and O Pulci and A P Seitsonen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940496050&doi=10.1063%2f1.4929468&partnerID=40&md5=cab0a0ef9cd8dea5cd9324701b889fbb}, doi = {10.1063/1.4929468}, year = {2015}, date = {2015-01-01}, journal = {Journal of Chemical Physics}, volume = {143}, number = {8}, abstract = {The proton disorder in ice has a key role in several properties such as the growth mode, thermodynamical properties, and ferroelectricity. While structural phase transitions from proton disordered to proton ordered ices have been extensively studied, much less is known about their electronic and optical properties. Here, we present ab initio many body perturbation theory-based calculations of the electronic and optical properties of cubic ice at different levels of proton disorder. We compare our results with those from liquid water, that acts as an example of a fully (proton- and oxygen-)disordered system. We find that by increasing the proton disorder, a shrinking of the electronic gap occurs in ice, and it is smallest in the liquid water. Simultaneously, the excitonic binding energy decreases, so that the final optical gaps result to be almost independent on the degree of proton disorder. We explain these findings as an interplay between the local dipolar disorder and the electronic correlation. © 2015 AIP Publishing LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The proton disorder in ice has a key role in several properties such as the growth mode, thermodynamical properties, and ferroelectricity. While structural phase transitions from proton disordered to proton ordered ices have been extensively studied, much less is known about their electronic and optical properties. Here, we present ab initio many body perturbation theory-based calculations of the electronic and optical properties of cubic ice at different levels of proton disorder. We compare our results with those from liquid water, that acts as an example of a fully (proton- and oxygen-)disordered system. We find that by increasing the proton disorder, a shrinking of the electronic gap occurs in ice, and it is smallest in the liquid water. Simultaneously, the excitonic binding energy decreases, so that the final optical gaps result to be almost independent on the degree of proton disorder. We explain these findings as an interplay between the local dipolar disorder and the electronic correlation. © 2015 AIP Publishing LLC. |
Catalytic Reduction of CO2 by Renewable Organohydrides Article de journal C -H Lim; A M Holder; J T Hynes; C B Musgrave Journal of Physical Chemistry Letters, 6 (24), p. 5078-5092, 2015, (cited By 34). @article{Lim20155078, title = {Catalytic Reduction of CO2 by Renewable Organohydrides}, author = {C -H Lim and A M Holder and J T Hynes and C B Musgrave}, doi = {10.1021/acs.jpclett.5b01827}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {6}, number = {24}, pages = {5078-5092}, abstract = {Dihydropyridines are renewable organohydride reducing agents for the catalytic reduction of CO2 to MeOH. Here we discuss various aspects of this important reduction. A centerpiece, which illustrates various general principles, is our theoretical catalytic mechanism for CO2 reduction by successive hydride transfers (HTs) and proton transfers (PTs) from the dihydropyridine PyH2 obtained by 1H+/1e-/1H+/1e- reductions of pyridine. The Py/PyH2 redox couple is analogous to NADP+/NADPH in that both are driven to effect HTs by rearomatization. High-energy radical intermediates and their associated high barriers/overpotentials are avoided because HT involves a 2e- reduction. A HT-PT sequence dictates that the reduced intermediates be protonated prior to further reduction for ultimate MeOH formation; these protonations are aided by biased cathodes that significantly lower the local pH. In contrast, cathodes that efficiently reduce H+ such as Pt and Pd produce H2 and create a high interfacial pH, both obstructing dihydropyridine production and formate protonation and thus ultimately CO2 reduction by HTPTs. The role of water molecule proton relays is discussed. Finally, we suggest future CO2 reduction strategies by organic (photo)catalysts. textcopyright 2015 American Chemical Society.}, note = {cited By 34}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dihydropyridines are renewable organohydride reducing agents for the catalytic reduction of CO2 to MeOH. Here we discuss various aspects of this important reduction. A centerpiece, which illustrates various general principles, is our theoretical catalytic mechanism for CO2 reduction by successive hydride transfers (HTs) and proton transfers (PTs) from the dihydropyridine PyH2 obtained by 1H+/1e-/1H+/1e- reductions of pyridine. The Py/PyH2 redox couple is analogous to NADP+/NADPH in that both are driven to effect HTs by rearomatization. High-energy radical intermediates and their associated high barriers/overpotentials are avoided because HT involves a 2e- reduction. A HT-PT sequence dictates that the reduced intermediates be protonated prior to further reduction for ultimate MeOH formation; these protonations are aided by biased cathodes that significantly lower the local pH. In contrast, cathodes that efficiently reduce H+ such as Pt and Pd produce H2 and create a high interfacial pH, both obstructing dihydropyridine production and formate protonation and thus ultimately CO2 reduction by HTPTs. The role of water molecule proton relays is discussed. Finally, we suggest future CO2 reduction strategies by organic (photo)catalysts. textcopyright 2015 American Chemical Society. |
Are There Dynamical Effects in Enzyme Catalysis? Some Thoughts Concerning the Enzymatic Chemical Step Article de journal I Tu~nón; D Laage; J T Hynes Archives of Biochemistry and Biophysics, 582 , p. 42-55, 2015, (cited By 25). @article{Tu\~{n}\'{o}n201542, title = {Are There Dynamical Effects in Enzyme Catalysis? Some Thoughts Concerning the Enzymatic Chemical Step}, author = {I Tu{~n}\'{o}n and D Laage and J T Hynes}, doi = {10.1016/j.abb.2015.06.004}, year = {2015}, date = {2015-01-01}, journal = {Archives of Biochemistry and Biophysics}, volume = {582}, pages = {42-55}, abstract = {We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned about the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions. textcopyright 2015 The Authors.}, note = {cited By 25}, keywords = {}, pubstate = {published}, tppubtype = {article} } We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned about the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions. textcopyright 2015 The Authors. |
Effect of Solvent Dielectric Constant and Acidity on the OH Vibration Frequency in Hydrogen-Bonded Complexes of Fluorinated Ethanols Article de journal D Pines; S Keinan; P M Kiefer; J T Hynes; E Pines Journal of Physical Chemistry B, 119 (29), p. 9278-9286, 2015, (cited By 6). @article{Pines20159278, title = {Effect of Solvent Dielectric Constant and Acidity on the OH Vibration Frequency in Hydrogen-Bonded Complexes of Fluorinated Ethanols}, author = {D Pines and S Keinan and P M Kiefer and J T Hynes and E Pines}, doi = {10.1021/jp509914w}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {29}, pages = {9278-9286}, abstract = {Infrared spectroscopy measurements were used to characterize the OH stretching vibrations in a series of similarly structured fluoroethanols, RCH$<$inf$>$2$<$/inf$>$OH (R = CH$<$inf$>$3$<$/inf$>$, CH$<$inf$>$2$<$/inf$>$F, CHF$<$inf$>$2$<$/inf$>$, CF$<$inf$>$3$<$/inf$>$), a series which exhibits a systematic increase in the molecule acidity with increasing number of F atoms. This study, which expands our earlier efforts, was carried out in non-hydrogen-bonding solvents comprising molecules with and without a permanent dipole moment, with the former solvents being classified as polar solvents and the latter designated as nonpolar. The hydrogen bond interaction in donor-acceptor complexes formed in solution between the fluorinated ethanol H-donors and the H-acceptor base DMSO was investigated in relation to the solvent dielectric and to the differences $Delta$PA of the gas phase proton affinities (PAs) of the conjugate base of the fluorinated alcohols and DMSO. We have observed that $nu<$inf$>$OH$<$/inf$>$ decreases as the acidity of the alcohol increases ($Delta$PA decreases) and that $nu<$inf$>$OH$<$/inf$>$ varies inversely with $epsilon$, exhibiting different slopes for nonpolar and polar solvents. These 1/$epsilon$ slopes tend to vary linearly with $Delta$PA, increasing with increasing acidity. These experimental findings, including the $Delta$PA trends, are described with our recently published two-state Valence Bond-based theory for acid-base H-bonded complexes. Lastly, the correlation of the alcohol's conjugate base PAs with Taft $sigma_ast$ values of the fluorinated ethyl groups CH$<$inf$>$n$<$/inf$>$F$<$inf$>$3-n$<$/inf$>$CH$<$inf$>$2$<$/inf$>$- provides a connection of the inductive effects for these groups with the acidity parameter $Delta$PA associated with the H-bonded complexes. (Graph Presented). textcopyright 2014 American Chemical Society.}, note = {cited By 6}, keywords = {}, pubstate = {published}, tppubtype = {article} } Infrared spectroscopy measurements were used to characterize the OH stretching vibrations in a series of similarly structured fluoroethanols, RCH$<$inf$>$2$<$/inf$>$OH (R = CH$<$inf$>$3$<$/inf$>$, CH$<$inf$>$2$<$/inf$>$F, CHF$<$inf$>$2$<$/inf$>$, CF$<$inf$>$3$<$/inf$>$), a series which exhibits a systematic increase in the molecule acidity with increasing number of F atoms. This study, which expands our earlier efforts, was carried out in non-hydrogen-bonding solvents comprising molecules with and without a permanent dipole moment, with the former solvents being classified as polar solvents and the latter designated as nonpolar. The hydrogen bond interaction in donor-acceptor complexes formed in solution between the fluorinated ethanol H-donors and the H-acceptor base DMSO was investigated in relation to the solvent dielectric and to the differences $Delta$PA of the gas phase proton affinities (PAs) of the conjugate base of the fluorinated alcohols and DMSO. We have observed that $nu<$inf$>$OH$<$/inf$>$ decreases as the acidity of the alcohol increases ($Delta$PA decreases) and that $nu<$inf$>$OH$<$/inf$>$ varies inversely with $epsilon$, exhibiting different slopes for nonpolar and polar solvents. These 1/$epsilon$ slopes tend to vary linearly with $Delta$PA, increasing with increasing acidity. These experimental findings, including the $Delta$PA trends, are described with our recently published two-state Valence Bond-based theory for acid-base H-bonded complexes. Lastly, the correlation of the alcohol's conjugate base PAs with Taft $sigma_ast$ values of the fluorinated ethyl groups CH$<$inf$>$n$<$/inf$>$F$<$inf$>$3-n$<$/inf$>$CH$<$inf$>$2$<$/inf$>$- provides a connection of the inductive effects for these groups with the acidity parameter $Delta$PA associated with the H-bonded complexes. (Graph Presented). textcopyright 2014 American Chemical Society. |
Solvation Dynamics in Liquid Water. 1. Ultrafast Energy Fluxes Article de journal R Rey; J T Hynes Journal of Physical Chemistry B, 119 (24), p. 7558-7570, 2015, (cited By 13). @article{Rey20157558, title = {Solvation Dynamics in Liquid Water. 1. Ultrafast Energy Fluxes}, author = {R Rey and J T Hynes}, doi = {10.1021/jp5113922}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {24}, pages = {7558-7570}, abstract = {Solvation dynamics in liquid water is addressed via nonequilibrium energy-transfer pathways activated after a neutral atomic solute acquires a unit charge, either positive or negative. It is shown that the well-known nonequilibrium frequency shift relaxation function can be expressed in a novel fashion in terms of energy fluxes, providing a clear-cut and quantitative account of the processes involved. Roughly half of the initial excess energy is transferred into hindered rotations of first hydration shell water molecules, i.e., librational motions, specifically those rotations around the lowest moment of inertia principal axis. After integration over all water solvent molecules, rotations account for roughly 80% of the energy transferred, while translations have a secondary role; transfer to intramolecular water stretch and bend vibrations is negligible. This picture is similar to that for relaxation of a single vibrationally or rotationally excited water molecule in neat liquid water, although solvation relaxation is more nonlocal. In addition, we find a remarkable independence of the main relaxation channels on the newly created charges sign. Although the methodology is applied here to the simplest solute case, the approach is rather general, and it should be at least equally useful in more realistic and complex scenarios. textcopyright 2015 American Chemical Society.}, note = {cited By 13}, keywords = {}, pubstate = {published}, tppubtype = {article} } Solvation dynamics in liquid water is addressed via nonequilibrium energy-transfer pathways activated after a neutral atomic solute acquires a unit charge, either positive or negative. It is shown that the well-known nonequilibrium frequency shift relaxation function can be expressed in a novel fashion in terms of energy fluxes, providing a clear-cut and quantitative account of the processes involved. Roughly half of the initial excess energy is transferred into hindered rotations of first hydration shell water molecules, i.e., librational motions, specifically those rotations around the lowest moment of inertia principal axis. After integration over all water solvent molecules, rotations account for roughly 80% of the energy transferred, while translations have a secondary role; transfer to intramolecular water stretch and bend vibrations is negligible. This picture is similar to that for relaxation of a single vibrationally or rotationally excited water molecule in neat liquid water, although solvation relaxation is more nonlocal. In addition, we find a remarkable independence of the main relaxation channels on the newly created charges sign. Although the methodology is applied here to the simplest solute case, the approach is rather general, and it should be at least equally useful in more realistic and complex scenarios. textcopyright 2015 American Chemical Society. |
Solvent-Induced O-Ħ Vibration Red-Shifts of Oxygen-Acids in Hydrogen-Bonded O-Ħ$cdots$base Complexes Article de journal S Keinan; D Pines; P M Kiefer; J T Hynes; E Pines Journal of Physical Chemistry B, 119 (3), p. 679-692, 2015, (cited By 6). @article{Keinan2015679, title = {Solvent-Induced O-{H} Vibration Red-Shifts of Oxygen-Acids in Hydrogen-Bonded O-{H}$cdots$base Complexes}, author = {S Keinan and D Pines and P M Kiefer and J T Hynes and E Pines}, doi = {10.1021/jp502553r}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {3}, pages = {679-692}, abstract = {Infrared spectroscopy has been used to characterize the solvent effect on the OH stretching vibrations $nu$OH of phenol, 1-naphthol, 2-naphthol, 1-hydroxypyrene, and ethanol. We distinguish the dielectric (nonspecific) effect of the solvent on $deltanu$OH, the observed red-shifts in $nu$OH, from the much larger red-shift caused by direct hydrogen (H)-bonding interactions with the solvents. To isolate the solvent dielectric constant $epsilon$ effect on $nu$OH, the OH oscillator was also studied when it is already H-bonded with an invariant oxygen base, dimethyl sulfoxide. We find that $deltanu$OH depends importantly on $delta$PA, the difference between the proton affinities of the conjugate base of the proton donor and the proton acceptor. For a given H-bonded complex, $nu$OH tends to vary inversely with $epsilon$, exhibiting different slopes for polar and nonpolar solvents, i.e., solvents comprising molecules with and without a permanent dipole moment, respectively. We use a two-state valence-bond-based theory to analyze our experimental data. This demonstrates that the OH oscillator acquires a more ionic-like character in the vibrational excited state, i.e., charge transfer; this results in a stronger H-bond in a more anharmonic potential for the OH vibration. The theory distinguishes between nonpolar and polar solvents and successfully accounts for the observed 1/$epsilon$ and $delta$PA variations. textcopyright 2014 American Chemical Society.}, note = {cited By 6}, keywords = {}, pubstate = {published}, tppubtype = {article} } Infrared spectroscopy has been used to characterize the solvent effect on the OH stretching vibrations $nu$OH of phenol, 1-naphthol, 2-naphthol, 1-hydroxypyrene, and ethanol. We distinguish the dielectric (nonspecific) effect of the solvent on $deltanu$OH, the observed red-shifts in $nu$OH, from the much larger red-shift caused by direct hydrogen (H)-bonding interactions with the solvents. To isolate the solvent dielectric constant $epsilon$ effect on $nu$OH, the OH oscillator was also studied when it is already H-bonded with an invariant oxygen base, dimethyl sulfoxide. We find that $deltanu$OH depends importantly on $delta$PA, the difference between the proton affinities of the conjugate base of the proton donor and the proton acceptor. For a given H-bonded complex, $nu$OH tends to vary inversely with $epsilon$, exhibiting different slopes for polar and nonpolar solvents, i.e., solvents comprising molecules with and without a permanent dipole moment, respectively. We use a two-state valence-bond-based theory to analyze our experimental data. This demonstrates that the OH oscillator acquires a more ionic-like character in the vibrational excited state, i.e., charge transfer; this results in a stronger H-bond in a more anharmonic potential for the OH vibration. The theory distinguishes between nonpolar and polar solvents and successfully accounts for the observed 1/$epsilon$ and $delta$PA variations. textcopyright 2014 American Chemical Society. |
Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere Article de journal J T Hynes Annual Review of Physical Chemistry, 66 , p. 1-20, 2015, (cited By 12). @article{Hynes20151, title = {Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere}, author = {J T Hynes}, doi = {10.1146/annurev-physchem-040214-121833}, year = {2015}, date = {2015-01-01}, journal = {Annual Review of Physical Chemistry}, volume = {66}, pages = {1-20}, abstract = {After my acceptance of the kind invitation from Todd Mart'y'nez and Mark Johnson, Co-Editors of this journal, to write this article, I had to decide just how to actually do this, given the existence of a fairly personal and extended autobiographical account of recent vintage detailing my youth, education, and assorted experiences and activities at the University of Colorado, Boulder, and later also at Ecole Normale Sup\'{e}rieure in Paris (1). In the end, I settled on a differently styled recounting of the adventures with my students, postdocs, collaborators, and colleagues in trying to unravel, comprehend, describe, and occasionally even predict the manifestations and consequences of the myriad assortment of molecular dances that contribute to and govern the rates and mechanisms of chemical reactions in solution (and elsewhere). The result follows. textcopyright 2015 by Annual Reviews. All rights reserved.}, note = {cited By 12}, keywords = {}, pubstate = {published}, tppubtype = {article} } After my acceptance of the kind invitation from Todd Mart'y'nez and Mark Johnson, Co-Editors of this journal, to write this article, I had to decide just how to actually do this, given the existence of a fairly personal and extended autobiographical account of recent vintage detailing my youth, education, and assorted experiences and activities at the University of Colorado, Boulder, and later also at Ecole Normale Supérieure in Paris (1). In the end, I settled on a differently styled recounting of the adventures with my students, postdocs, collaborators, and colleagues in trying to unravel, comprehend, describe, and occasionally even predict the manifestations and consequences of the myriad assortment of molecular dances that contribute to and govern the rates and mechanisms of chemical reactions in solution (and elsewhere). The result follows. textcopyright 2015 by Annual Reviews. All rights reserved. |
2014 |
Origins of the Non-Exponential Reorientation Dynamics of Nanoconfined Water Article de journal Aoife C Fogarty; Elise Duboue-Dijon; D Laage; Ward H Thompson Journal of Chemical Physics, 141 (18), p. 18C523, 2014, ISSN: 0021-9606, (WOS:000344847600067). @article{Fogarty:2014, title = {Origins of the Non-Exponential Reorientation Dynamics of Nanoconfined Water}, author = {Aoife C Fogarty and Elise {Duboue-Dijon} and D Laage and Ward H Thompson}, doi = {10.1063/1.4896983}, issn = {0021-9606}, year = {2014}, date = {2014-11-01}, journal = {Journal of Chemical Physics}, volume = {141}, number = {18}, pages = {18C523}, abstract = {The dynamics of water are dramatically modified upon confinement in nanoscale hydrophilic silica pores. In particular, the OH reorientation dynamics of the interfacial water are non-exponential and dramatically slowed relative to the bulk liquid. A detailed analysis of molecular dynamics simulations is carried out to elucidate the microscopic origins of this behavior. The results are analyzed in the context of the extended jump model for water that describes the reorientation as a combination of hydrogen-bond exchanges, or jumps, and rotation of intact hydrogen bonds, with the former representing the dominant contribution. Within this model, the roles of surface and dynamical heterogeneities are considered by spatially resolving the hydrogen-bond jump dynamics into individual sites on the silica pore surface. For each site the dynamics is nearly mono-exponential, indicating that dynamical heterogeneity is at most a minor influence, while the distribution of these individual site jump times is broad. The non-exponential dynamics can also not be attributed to enthalpic contributions to the barriers to hydrogen-bond exchanges. Two entropic effects related to the surface roughness are found to explain the retarded and diverse dynamics: those associated with the approach of a new hydrogen-bond acceptor and with the breaking of the initial hydrogen-bond. (C) 2014 AIP Publishing LLC.}, note = {WOS:000344847600067}, keywords = {}, pubstate = {published}, tppubtype = {article} } The dynamics of water are dramatically modified upon confinement in nanoscale hydrophilic silica pores. In particular, the OH reorientation dynamics of the interfacial water are non-exponential and dramatically slowed relative to the bulk liquid. A detailed analysis of molecular dynamics simulations is carried out to elucidate the microscopic origins of this behavior. The results are analyzed in the context of the extended jump model for water that describes the reorientation as a combination of hydrogen-bond exchanges, or jumps, and rotation of intact hydrogen bonds, with the former representing the dominant contribution. Within this model, the roles of surface and dynamical heterogeneities are considered by spatially resolving the hydrogen-bond jump dynamics into individual sites on the silica pore surface. For each site the dynamics is nearly mono-exponential, indicating that dynamical heterogeneity is at most a minor influence, while the distribution of these individual site jump times is broad. The non-exponential dynamics can also not be attributed to enthalpic contributions to the barriers to hydrogen-bond exchanges. Two entropic effects related to the surface roughness are found to explain the retarded and diverse dynamics: those associated with the approach of a new hydrogen-bond acceptor and with the breaking of the initial hydrogen-bond. (C) 2014 AIP Publishing LLC. |