SIMCON - Grup de Recerca de Simulació per Ordinador en Matèria Condensada
http://hdl.handle.net/2117/394
Sat, 03 Dec 2016 08:49:33 GMT2016-12-03T08:49:33ZPotentials of mean force in acidic proton transfer reactions in constrained geometries
http://hdl.handle.net/2117/97725
Potentials of mean force in acidic proton transfer reactions in constrained geometries
Martí Rabassa, Jordi
Free energy barriers associated with the transfer of an excess proton in water and related to the potentials of mean force in proton transfer episodes have been computed in a wide range of thermodynamic states, from low-density amorphous ices to high-temperature liquids under the critical point for unconstrained and constrained systems. The latter were represented by set-ups placed inside hydrophobic graphene slabs at the nanometric scale allocating a few water layers, namely one or two in the narrowest case. Water–proton and carbon–proton forces were modelled with a Multi-State Empirical Valence Bond method. As a general trend, a competition between the effects of confinement and temperature is observed on the local hydrogen-bonded structures around the lone proton and, consequently, on the mean force exerted by its environment on the water molecule carrying the proton. Free energy barriers estimated from the computed potentials of mean force tend to rise with the combined effect of increasing temperatures and the packing effect due to a larger extent of hydrophobic confinement. The main reason observed for such enhancement of the free energy barriers was the breaking of the second coordination shell around the lone proton.
Fri, 02 Dec 2016 17:12:43 GMThttp://hdl.handle.net/2117/977252016-12-02T17:12:43ZMartí Rabassa, JordiFree energy barriers associated with the transfer of an excess proton in water and related to the potentials of mean force in proton transfer episodes have been computed in a wide range of thermodynamic states, from low-density amorphous ices to high-temperature liquids under the critical point for unconstrained and constrained systems. The latter were represented by set-ups placed inside hydrophobic graphene slabs at the nanometric scale allocating a few water layers, namely one or two in the narrowest case. Water–proton and carbon–proton forces were modelled with a Multi-State Empirical Valence Bond method. As a general trend, a competition between the effects of confinement and temperature is observed on the local hydrogen-bonded structures around the lone proton and, consequently, on the mean force exerted by its environment on the water molecule carrying the proton. Free energy barriers estimated from the computed potentials of mean force tend to rise with the combined effect of increasing temperatures and the packing effect due to a larger extent of hydrophobic confinement. The main reason observed for such enhancement of the free energy barriers was the breaking of the second coordination shell around the lone proton.A comparative molecular dynamics study of sulfuric and methanesulfonic acids
http://hdl.handle.net/2117/97448
A comparative molecular dynamics study of sulfuric and methanesulfonic acids
Canales Gabriel, Manel; Guàrdia Manuel, Elvira
The molecular dynamics computer simulation method has been used to study sulfuric and methanesulfonic acids. Calculations have been carried out between 200 K and 400 K using reliable force fields. Thermodynamic properties, such as the density, the heat of vaporization and the melting temperature, have been computed. Moreover, structural and dynamical quantities, such as the radial distribution functions, the shear viscosity and the diffusion coefficients, have also been calculated. The results display a noticeable good agreement with the available experimental data. A hydrogen bond analysis has also been performed, which shows, on one hand, that sulfuric acid has a hydrogen bond network which resembles the one of water; and, on the other hand, that methanesulfonic acid has a hydrogen bond structure which, in some details, recalls the one of methanol, but with a more important presence of single bonds and, to a lesser extent, of branching. Finally, the dynamics of the formation and rupture of hydrogen bonds has also been analyzed. To this end, the interrupted or slow hydrogen bonding lifetimes have been calculated using two different procedures. Our findings suggest that the sulfuric acid hydrogen bond network is more labile than the methanesulfonic acid one.
Tue, 29 Nov 2016 15:36:51 GMThttp://hdl.handle.net/2117/974482016-11-29T15:36:51ZCanales Gabriel, ManelGuàrdia Manuel, ElviraThe molecular dynamics computer simulation method has been used to study sulfuric and methanesulfonic acids. Calculations have been carried out between 200 K and 400 K using reliable force fields. Thermodynamic properties, such as the density, the heat of vaporization and the melting temperature, have been computed. Moreover, structural and dynamical quantities, such as the radial distribution functions, the shear viscosity and the diffusion coefficients, have also been calculated. The results display a noticeable good agreement with the available experimental data. A hydrogen bond analysis has also been performed, which shows, on one hand, that sulfuric acid has a hydrogen bond network which resembles the one of water; and, on the other hand, that methanesulfonic acid has a hydrogen bond structure which, in some details, recalls the one of methanol, but with a more important presence of single bonds and, to a lesser extent, of branching. Finally, the dynamics of the formation and rupture of hydrogen bonds has also been analyzed. To this end, the interrupted or slow hydrogen bonding lifetimes have been calculated using two different procedures. Our findings suggest that the sulfuric acid hydrogen bond network is more labile than the methanesulfonic acid one.Influence of hydrogen bonds and temperature on dielectric properties
http://hdl.handle.net/2117/97367
Influence of hydrogen bonds and temperature on dielectric properties
Ortiz de Urbina Viade, Jordi; Sesé Castel, Gemma
Dielectric properties are evaluated by means of molecular dynamics simulations on two model systems made up of dipolar molecules. One of them mimics methanol, whereas the other differs from the former only in the ability to form hydrogen bonds. Static dielectric properties such as the permittivity and the Kirkwood factor are evaluated, and results are analyzed by considering the distribution of relative orientations between molecular dipoles. Dipole moment–time correlation functions are also evaluated. The relevance of contributions associated with autocorrelations of molecular dipoles and with cross-correlations between dipoles belonging to different molecules has been investigated. For methanol, the Debye approximation for the overall dipole moment correlation function is not valid at room temperature. The model applies when hydrogen bonds are suppressed, but it fails upon cooling the nonassociated liquid. Important differences between relaxation times associated with dipole auto- versus cross-correlations as well as their relative relevance are at the root of the Debye model breakdown.
Mon, 28 Nov 2016 19:36:18 GMThttp://hdl.handle.net/2117/973672016-11-28T19:36:18ZOrtiz de Urbina Viade, JordiSesé Castel, GemmaDielectric properties are evaluated by means of molecular dynamics simulations on two model systems made up of dipolar molecules. One of them mimics methanol, whereas the other differs from the former only in the ability to form hydrogen bonds. Static dielectric properties such as the permittivity and the Kirkwood factor are evaluated, and results are analyzed by considering the distribution of relative orientations between molecular dipoles. Dipole moment–time correlation functions are also evaluated. The relevance of contributions associated with autocorrelations of molecular dipoles and with cross-correlations between dipoles belonging to different molecules has been investigated. For methanol, the Debye approximation for the overall dipole moment correlation function is not valid at room temperature. The model applies when hydrogen bonds are suppressed, but it fails upon cooling the nonassociated liquid. Important differences between relaxation times associated with dipole auto- versus cross-correlations as well as their relative relevance are at the root of the Debye model breakdown.Ultradilute low-dimensional liquids
http://hdl.handle.net/2117/97363
Ultradilute low-dimensional liquids
Petrov, D. S.; Astrakharchik, Grigori
We calculate the energy of one- and two-dimensional weakly interacting Bose-Bose mixtures analytically in the Bogoliubov approximation and by using the diffusion Monte Carlo technique. We show that in the case of attractive inter- and repulsive intraspecies interactions the energy per particle has a minimum at a finite density corresponding to a liquid state. We derive the Gross-Pitaevskii equation to describe droplets of such liquids and solve it analytically in the one-dimensional case.
Mon, 28 Nov 2016 18:51:51 GMThttp://hdl.handle.net/2117/973632016-11-28T18:51:51ZPetrov, D. S.Astrakharchik, GrigoriWe calculate the energy of one- and two-dimensional weakly interacting Bose-Bose mixtures analytically in the Bogoliubov approximation and by using the diffusion Monte Carlo technique. We show that in the case of attractive inter- and repulsive intraspecies interactions the energy per particle has a minimum at a finite density corresponding to a liquid state. We derive the Gross-Pitaevskii equation to describe droplets of such liquids and solve it analytically in the one-dimensional case.Continuous pressure-induced structural transition in the noble-metal halide melts
http://hdl.handle.net/2117/90953
Continuous pressure-induced structural transition in the noble-metal halide melts
Silbert, Moises; Giró Roca, Antoni; Trullàs Simó, Joaquim
The reduction of the charge of the species in molten salts, including the complete removal of the Coulomb interaction, appears to have the same effect as an increase in the pressure on these systems. This observation leads to the prediction that a continuous pressure-induced structural change is to be found in the noble-metal halide melts at much lower pressures than those used to induce a similar transition in the alkali halide melts.
Fri, 21 Oct 2016 15:07:08 GMThttp://hdl.handle.net/2117/909532016-10-21T15:07:08ZSilbert, MoisesGiró Roca, AntoniTrullàs Simó, JoaquimThe reduction of the charge of the species in molten salts, including the complete removal of the Coulomb interaction, appears to have the same effect as an increase in the pressure on these systems. This observation leads to the prediction that a continuous pressure-induced structural change is to be found in the noble-metal halide melts at much lower pressures than those used to induce a similar transition in the alkali halide melts.Elusive structure of helium trimers
http://hdl.handle.net/2117/90935
Elusive structure of helium trimers
Stipanovic, P.; Vranješ Markic, Leandra; Boronat Medico, Jordi
Over the years many He–He interaction potentials have been developed, some very sophisticated, including various corrections beyond the Born–Oppenheimer approximation. Most of them were used to predict properties of helium dimers and trimers, examples of exotic quantum states, whose experimental study proved to be very challenging. Recently, detailed structural properties of helium trimers were measured for the first time, allowing a comparison with theoretical predictions and possibly enabling the evaluation of different interaction potentials. The comparisons already made included adjusting the maxima of both theoretical and experimental correlation functions to one, so the overall agreement between theory and experiment appeared satisfactory. However, no attempt was made to evaluate the quality of the interaction potentials used in the calculations. In this work, we calculate the experimentally measured correlation functions using both new and old potentials, compare them with experimental data and rank the potentials. We use diffusion Monte Carlo simulations at T = 0, which give within statistical noise exact results of the ground state properties. All models predict both trimers 4He3 and 4He${}_{2}{}^{3}$He to be in a quantum halo state.
Thu, 20 Oct 2016 15:55:03 GMThttp://hdl.handle.net/2117/909352016-10-20T15:55:03ZStipanovic, P.Vranješ Markic, LeandraBoronat Medico, JordiOver the years many He–He interaction potentials have been developed, some very sophisticated, including various corrections beyond the Born–Oppenheimer approximation. Most of them were used to predict properties of helium dimers and trimers, examples of exotic quantum states, whose experimental study proved to be very challenging. Recently, detailed structural properties of helium trimers were measured for the first time, allowing a comparison with theoretical predictions and possibly enabling the evaluation of different interaction potentials. The comparisons already made included adjusting the maxima of both theoretical and experimental correlation functions to one, so the overall agreement between theory and experiment appeared satisfactory. However, no attempt was made to evaluate the quality of the interaction potentials used in the calculations. In this work, we calculate the experimentally measured correlation functions using both new and old potentials, compare them with experimental data and rank the potentials. We use diffusion Monte Carlo simulations at T = 0, which give within statistical noise exact results of the ground state properties. All models predict both trimers 4He3 and 4He${}_{2}{}^{3}$He to be in a quantum halo state.The structure of liquid water beyond the first hydration shell
http://hdl.handle.net/2117/90080
The structure of liquid water beyond the first hydration shell
Henao Aristizábal, Andrés; Busch, Sebastian; Guàrdia Manuel, Elvira; Tamarit Mur, José Luis; Pardo Soto, Luis Carlos
To date there is a general consensus on the structure of the first coordination shells of liquid water, namely tetrahedral short range order of molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about similar to 6 angstrom: from a predominantly orientational order at shorter distances to a regime at larger distances of up to similar to 9 angstrom where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.
Tue, 20 Sep 2016 14:24:47 GMThttp://hdl.handle.net/2117/900802016-09-20T14:24:47ZHenao Aristizábal, AndrésBusch, SebastianGuàrdia Manuel, ElviraTamarit Mur, José LuisPardo Soto, Luis CarlosTo date there is a general consensus on the structure of the first coordination shells of liquid water, namely tetrahedral short range order of molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about similar to 6 angstrom: from a predominantly orientational order at shorter distances to a regime at larger distances of up to similar to 9 angstrom where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.Br diffusion in molten NaBr explored by coherent quasielastic neutron scattering
http://hdl.handle.net/2117/88971
Br diffusion in molten NaBr explored by coherent quasielastic neutron scattering
Demmel, F; Alcaraz Sendra, Olga; Trullàs Simó, Joaquim
Molten sodium bromide has been investigated by quasielastic neutron scattering focusing on the wave vector range around the first structure factor peak. The linewidth of the scattering function shows a narrowing around the wave number of the structure factor peak, known as deGennes narrowing. In a monatomic system, this narrowing or in the time domain slowing down, has been related to a self-diffusion process of the caged particle. Here we show that this methodology can be applied to the molten alkali halide NaBr. The incoherent scattering from the sodium ions at small wave vectors provides the self-diffusion coefficient of sodium and the dynamics of bromine ions can be studied at wave numbers around the structure factor peak. With input from molecular dynamics simulations on the partial structure factors, diffusion coefficients of the bromine ions can be obtained. These experimentally derived diffusion coefficients are in good agreement with molecular dynamics simulation results. This methodology to extract self-diffusion coefficients from coherent quasielastic neutron scattering is applicable to binary fluids in general when one particle dominates the scattering response at the structure factor maximum.
Wed, 20 Jul 2016 12:05:25 GMThttp://hdl.handle.net/2117/889712016-07-20T12:05:25ZDemmel, FAlcaraz Sendra, OlgaTrullàs Simó, JoaquimMolten sodium bromide has been investigated by quasielastic neutron scattering focusing on the wave vector range around the first structure factor peak. The linewidth of the scattering function shows a narrowing around the wave number of the structure factor peak, known as deGennes narrowing. In a monatomic system, this narrowing or in the time domain slowing down, has been related to a self-diffusion process of the caged particle. Here we show that this methodology can be applied to the molten alkali halide NaBr. The incoherent scattering from the sodium ions at small wave vectors provides the self-diffusion coefficient of sodium and the dynamics of bromine ions can be studied at wave numbers around the structure factor peak. With input from molecular dynamics simulations on the partial structure factors, diffusion coefficients of the bromine ions can be obtained. These experimentally derived diffusion coefficients are in good agreement with molecular dynamics simulation results. This methodology to extract self-diffusion coefficients from coherent quasielastic neutron scattering is applicable to binary fluids in general when one particle dominates the scattering response at the structure factor maximum.One dimensional H-1, H-2 and H-3
http://hdl.handle.net/2117/88635
One dimensional H-1, H-2 and H-3
Vidal, A.J.; Astrakharchik, Grigori; Vranješ Markic, Leandra; Boronat, J.
The ground-state properties of one-dimensional electron-spin-polarized hydrogen H-1, deuterium H-2, and tritium 3 Hare obtained by means of quantum Monte Carlo methods. The equations of state of the three isotopes are calculated for a wide range of linear densities. The pair correlation function and the static structure factor are obtained and interpreted within the framework of the Luttinger liquid theory. We report the density dependence of the Luttinger parameter and use it to identify different physical regimes: Bogoliubov Bose gas, super-Tonks-Girardeau gas, and quasi-crystal regimes for bosons; repulsive, attractive Fermi gas, and quasi-crystal regimes for fermions. We find that the tritium isotope is the one with the richest behavior. Our results show unambiguously the relevant role of the isotope mass in the properties of this quantum system.
Fri, 08 Jul 2016 16:41:50 GMThttp://hdl.handle.net/2117/886352016-07-08T16:41:50ZVidal, A.J.Astrakharchik, GrigoriVranješ Markic, LeandraBoronat, J.The ground-state properties of one-dimensional electron-spin-polarized hydrogen H-1, deuterium H-2, and tritium 3 Hare obtained by means of quantum Monte Carlo methods. The equations of state of the three isotopes are calculated for a wide range of linear densities. The pair correlation function and the static structure factor are obtained and interpreted within the framework of the Luttinger liquid theory. We report the density dependence of the Luttinger parameter and use it to identify different physical regimes: Bogoliubov Bose gas, super-Tonks-Girardeau gas, and quasi-crystal regimes for bosons; repulsive, attractive Fermi gas, and quasi-crystal regimes for fermions. We find that the tritium isotope is the one with the richest behavior. Our results show unambiguously the relevant role of the isotope mass in the properties of this quantum system.Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels
http://hdl.handle.net/2117/88634
Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels
Tahat, Amani; Martí Rabassa, Jordi
Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 1/Å^3 have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent.
Fri, 08 Jul 2016 15:50:09 GMThttp://hdl.handle.net/2117/886342016-07-08T15:50:09ZTahat, AmaniMartí Rabassa, JordiMicroscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 1/Å^3 have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent.