Journal of chemical physics

Vol. 150, num. 12, p. 124506-1-124506-14

DOI: 10.1063/1.5084217

Date of publication: 2019-03-28

Abstract:

We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each phase.]]>

Journal of chemical physics

Vol. 149, num. 16, p. 164906-1-164906-10

DOI: 10.1063/1.5029430

Date of publication: 2018-10-25

Abstract:

The characterization of the microscopical forces between the essential a-amino-acid tryptophan, precursor of the neurotransmitter serotonin and of the hormone melatonin, and the basic components of cell membranes and their environments (phospholipids, cholesterol, ionic species, and water) is of central importance to elucidate their local structure and dynamics as well as the mechanisms responsible for the access of tryptophan to the interior of the cell. We have performed nanosecond molecular dynamics simulations of tryptophan embedded in model zwitterionic bilayer membranes made by di-palmitoyl-phosphatidyl-choline and cholesterol inside aqueous sodium-chloride solution in order to systematically examine tryptophan-lipid, tryptophan-cholesterol, and tryptophan-water interactions under liquid-crystalline phase conditions. Microscopic properties such as the area per lipid, lipid thickness, radial distribution functions, hydrogen-bonding lengths, atomic spectral densities, and self-diffusion coefficients have been evaluated. Our results show that the presence of tryptophan significantly affects the structure and dynamics of the membrane. Tryptophan spends long periods of time at the water-membrane interface, and it plays a central role by bridging a few lipids and cholesterol chains by means of hydrogen-bonds. The computed spectral densities, in excellent agreement with experimental infrared and Raman data, revealed the participation of each atomic site of tryptophan to the complete spectrum of the molecule. Tryptophan self-diffusion coefficients have been found to be in between 10^(-7) and 10^(-6) cm^2/s and strongly depending of the concentration of cholesterol in the system.]]>

Journal of chemical physics

Vol. 148, num. 8, p. 1-12

DOI: 10.1063/1.5008991

Date of publication: 2018-02-27

Abstract:

Thermodynamic properties for a system composed of dipolar molecules are computed. Free energy is evaluated by means of the thermodynamic integration technique, and it is also estimated by using a perturbation theory approach, in which every molecule is modeled as a hard sphere within a square well, with an electric dipole at its center. The hard sphere diameter, the range and depth of the well, and the dipole moment have been calculated from properties easily obtained in molecular dynamics simulations. Connection between entropy and dynamical properties is explored in the liquid and supercooled states by using instantaneous normal mode calculations. A model is proposed in order to analyze translation and rotation contributions to entropy separately. Both contributions decrease upon cooling, and a logarithmic correlation between excess entropy associated with translation and the corresponding proportion of imaginary frequency modes is encountered. Rosenfeld scaling law between reduced diffusion and excess entropy is tested, and the origin of its failure at low temperatures is investigated.]]>

Journal of chemical physics

Vol. 147, num. 18, p. 1-9

DOI: 10.1063/1.5004671

Date of publication: 2017-11-14

Abstract:

The family of compounds CBrnCl4-n has been proven helpful in unraveling microscopic mechanisms responsible for glassy behavior. Some of the family members show translational ordered phases with minimal disorder which appears to reveal glassy features, thus deserving special attention in the search for universal glass anomalies. In this work, we studied CBrCl3 dynamics by performing extensive molecular dynamics simulations. Molecules of this compound perform reorientational discrete jumps, where the atoms exchange equivalent positions among each other revealing a cage-orientational jump motion fully comparable to the cage-rototranslational jump motion in supercooled liquids. Correlation times were calculated from rotational autocorrelation functions showing good agreement with previous reported dielectric results. From mean waiting and persistence times calculated directly from trajectory results, we are able to explain which microscopic mechanisms lead to characteristic times associated with a- and ß-relaxation times measured experimentally. We found that two nonequivalent groups of molecules have a longer characteristic time than the other two nonequivalent groups, both of them belonging to the asymmetric unit of the monoclinic (C2/c) lattice.]]>

Journal of chemical physics

Vol. 146, num. 1, p. 1-19

DOI: 10.1063/1.4973381

Date of publication: 2017-01-07

Abstract:

Weakly bound triatomic molecules consisting of two helium atoms and one alkali metal atom are studied by means of the diffusion Monte Carlo method. We determined the stability of 4He2A, 4He3HeA, and 3He2A, where A is one of the alkali atoms Li, Na, K, Rb, or Cs. Some of the trimers with 3He are predicted to be self-bound for the first time, but this is observed to be dependent on the He–A interaction potential model. In addition to the ground-state energy of the trimers, we determined their density, radial, and angular distributions. Many of them are spatially very extended, which qualifies them as quantum halo states]]>

Journal of chemical physics

Vol. 145, num. 17, p. 1-33

DOI: 10.1063/1.4966262

Date of publication: 2016-11-07

Abstract:

Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and ß-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.]]>

Journal of chemical physics

Vol. 145, num. 9

DOI: 10.1063/1.4962181

Date of publication: 2016-09-07

Abstract:

The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å-1 related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.]]>

Journal of chemical physics

Vol. 144, p. 164505-

DOI: 10.1063/1.4947477

Date of publication: 2016

Abstract:

We employ dielectricspectroscopy and molecular dynamic simulations to investigate the dipolar dynamics in the orientationally disordered solid phase of (1,1,2,2)tetrachloroethane. Three distinct orientational dynamics are observed as separate dielectric loss features, all characterized by a simply activated temperature dependence. The slower process, associated to a glassytransition at 156 ± 1 K, corresponds to a cooperative motion by which each molecule rotates by 180° around the molecular symmetry axis through an intermediate state in which the symmetry axis is oriented roughly orthogonally to the initial and final states. Of the other two dipolar relaxations, the intermediate one is the Johari-Goldstein precursor relaxation of the cooperative dynamics, while the fastest process corresponds to an orientational fluctuation of single molecules into a higher-energy orientation. The Kirkwood correlation factor of the cooperative relaxation is of the order of one tenth, indicating that the molecular dipoles maintain on average a strong antiparallel alignment during their collective motion. These findings show that the combination of dielectricspectroscopy and molecular simulations allows studying in great detail the orientational dynamics in molecular solids.]]>

Journal of chemical physics

Vol. 143, num. 13, p. 134502-1-134502-8

DOI: 10.1063/1.4931824

Date of publication: 2015-10-07

Abstract:

A thorough characterization of the gamma, beta, and glass phases of deuterated 1,1,2,2 tetrachloroethane (C2D2Cl4) via nuclear quadrupole resonance and Molecular Dynamic Simulations (MDSs) is reported. The presence of molecular reorientations was experimentally observed in the glass phase and in the beta phase. In the beta phase, and from MDS, these reorientations are attributed to two possible movements, i.e., a 180 degrees reorientation around the C-2 molecular symmetry axis and a reorientation of the molecule between two non-equivalent positions. In the glass phase, the spin-lattice relaxation time T-1 is of the order of 16 times lower than in the crystalline phase and varies as T-1 below 100 K in good agreement with the strong quadrupolar relaxation observed in amorphous materials and in the glassy state of molecular organic systems. The activation energy of molecular reorientations in the glass phase (19 kJ/mol) is comparable to that observed in the glassy crystal of a "molecular cousin" compound, Freon 112 (C2F2Cl4), for the secondary beta-relaxation. Moreover, the on-site orientational motion of tetrachloroethane molecules offers a new indirect evidence of the prominent role of such orientational disorder in glassy dynamics. (C) 2015 AIP Publishing LLC.

A thorough characterization of the gamma, beta, and glass phases of deuterated 1,1,2,2 tetrachloroethane (C2D2Cl4) via nuclear quadrupole resonance and Molecular Dynamic Simulations (MDSs) is reported. The presence of molecular reorientations was experimentally observed in the glass phase and in the beta phase. In the beta phase, and from MDS, these reorientations are attributed to two possible movements, i.e., a 180 degrees reorientation around the C-2 molecular symmetry axis and a reorientation of the molecule between two non-equivalent positions. In the glass phase, the spin-lattice relaxation time T-1 is of the order of 16 times lower than in the crystalline phase and varies as T-1 below 100 K in good agreement with the strong quadrupolar relaxation observed in amorphous materials and in the glassy state of molecular organic systems. The activation energy of molecular reorientations in the glass phase (19 kJ/mol) is comparable to that observed in the glassy crystal of a]]>

Journal of chemical physics

Vol. 143, num. 8, p. 084510-1-084510-10

DOI: 10.1063/1.4929530

Date of publication: 2015-08-28

Abstract:

The thermal conductivity, specific heat, and specific volume of the orientational glass former 1,1,2-trichloro-1,2,2-trifluoroethane (CCl2F-CClF2, F-113) have been measured under equilibrium pressure within the low-temperature range, showing thermodynamic anomalies at ca. 120, 72, and 20 K. The results are discussed together with those pertaining to the structurally related 1,1,2,2-tetrachloro-1,2-difluoroethane (CCl2F-CCl2F, F-112), which also shows anomalies at 130, 90, and 60 K. The rich phase behavior of these compounds can be accounted for by the interplay between several of their degrees of freedom. The arrest of the degrees of freedom corresponding to the internal molecular rotation, responsible for the existence of two energetically distinct isomers, and the overall molecular orientation, source of the characteristic orientational disorder of plastic phases, can explain the anomalies at higher and intermediate temperatures, respectively. The soft-potential model has been used as the framework to describe the thermal properties at low temperatures. We show that the low-temperature anomaly of the compounds corresponds to a secondary relaxation, which can be associated with the appearance of Umklapp processes, i.e., anharmonic phononphonon scattering, that dominate thermal transport in that temperature range. (C) 2015 AIP Publishing LLC.]]>

Journal of chemical physics

Vol. 142, num. 11, p. 1-12

DOI: 10.1063/1.4914995

Date of publication: 2015-03-21

Abstract:

We present a method based on the path integral Monte Carlo formalism for the calculation of ground-state time correlation functions in quantum systems. The key point of the method is the consideration of time as a complex variable whose phase d acts as an adjustable parameter. By using high-order approximations for the quantum propagator, it is possible to obtain Monte Carlo data all the way from purely imaginary time to d values near the limit of real time. As a consequence, it is possible to infer accurately the spectral functions using simple inversion algorithms. We test this approach in the calculation of the dynamic structure function S(q, omega) of two one-dimensional model systems, harmonic and quartic oscillators, for which S(q, omega) can be exactly calculated. We notice a clear improvement in the calculation of the dynamic response with respect to the common approach based on the inverse Laplace transform of the imaginary-time correlation function. (C) 2015 AIP Publishing LLC.]]>

Journal of chemical physics

Vol. 142, num. 4, p. 044102-1-044102-6

DOI: 10.1063/1.4906425

Date of publication: 2015-01-28

Abstract:

Nonlinear dimensionality reduction (NLDR) techniques are increasingly used to visualize molecular trajectories and to create data-driven collective variables for enhanced sampling simulations. The success of these methods relies on their ability to identify the essential degrees of freedom characterizing conformational changes. Here, we show that NLDR methods face serious obstacles when the underlying collective variables present periodicities, e.g., arising from proper dihedral angles. As a result, NLDR methods collapse very distant configurations, thus leading to misinterpretations and inefficiencies in enhanced sampling. Here, we identify this largely overlooked problem and discuss possible approaches to overcome it. We also characterize the geometry and topology of conformational changes of alanine dipeptide, a benchmark system for testing new methods to identify collective variables. (C) 2015 AIP Publishing LLC.

Nonlinear dimensionality reduction (NLDR) techniques are increasingly used to visualize molecular trajectories and to create data-driven collective variables for enhanced sampling simulations. The success of these methods relies on their ability to identify the essential degrees of freedom characterizing conformational changes. Here, we show that NLDR methods face serious obstacles when the underlying collective variables present periodicities, e.g., arising from proper dihedral angles. As a result, NLDR methods collapse very distant configurations, thus leading to misinterpretations and inefficiencies in enhanced sampling. Here, we identify this largely overlooked problem and discuss possible approaches to overcome it. We also characterize the geometry and topology of conformational changes of alanine dipeptide, a benchmark system for testing new methods to identify collective variables.]]>

Journal of chemical physics

Vol. 141, num. 24, p. 1

DOI: 10.1063/1.4904821

Date of publication: 2014-12-28

Abstract:

We present a study on the single ion dynamics in the molten alkali halide NaBr. Quasielastic neutron scattering was employed to extract the self-diffusion coefficient of the sodium ions at three temperatures. Molecular dynamics simulations using rigid and polarizable ion models have been performed in parallel to extract the sodium and bromide single dynamics and ionic conductivities. Two methods have been employed to derive the ion diffusion, calculating the mean squared displacements and the velocity autocorrelation functions, as well as analysing the increase of the line widths of the self-dynamic structure factors. The sodium diffusion coefficients show a remarkable good agreement between experiment and simulation utilising the polarisable potential. (C) 2014 AIP Publishing LLC.]]>

Journal of chemical physics

Vol. 140, num. 10, p. 104901-1-104901-13

DOI: 10.1063/1.4867385

Date of publication: 2014-03-10

Abstract:

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10-5 cm2/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10-8 cm2/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a “wagging of the tails” frequency around 30 cm-1, which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.]]>

Journal of chemical physics

Vol. 139, num. 22, p. 224708-1-224708-7

DOI: 10.1063/1.4843375

Date of publication: 2013-12-14

Abstract:

The experimental realization of a thin layer of spin-polarized hydrogen H double down arrow adsorbed on top of the surface of superfluid He-4 provides one of the best examples of a stable, nearly two-dimensional(2D) quantum Bose gas. We report a theoretical study of this system using quantum Monte Carlo methods in the limit of zero temperature. Using the full Hamiltonian of the system, composed of a superfluid He-4 slab and the adsorbed H double down arrow layer, we calculate the main properties of its ground state using accurate models for the pair interatomic potentials. Comparing the results for the layer with the ones obtained for a strictly 2D setup, we analyze the departure from the 2D character when the density increases. Only when the coverage is rather small the use of a purely 2D model is justified. The condensate fraction of the layer is significantly larger than in 2D at the same surface density, being as large as 60% at the largest coverage studied. (c) 2013 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4843375]]]>

Journal of chemical physics

Vol. 139, num. 18, p. 184111-1-184111-5

DOI: 10.1063/1.4829444

Date of publication: 2013-11-14

Abstract:

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r-6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r −6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.]]>

Journal of chemical physics

Vol. 138, num. 23, p. 1-14

DOI: 10.1063/1.4809593

Date of publication: 2013-06-21

Abstract:

In the preceding paper of this series (Part I [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234101 (2013)]10.1063/1.4809592) we have unveiled some ubiquitous features encoded in the systems of polynomial differential equations normally applied in the description of homogeneous and isothermal chemical kinetics (mass-action law). Here we proceed by investigating a deeply related feature: the appearance of so-called slow manifolds (SMs) which are low-dimensional hyper-surfaces in the neighborhood of which the slow evolution of the reacting system occurs after an initial fast transient. Indeed a geometrical definition of SM, devoid of subjectivity, “naturally” follows in terms of a specific sub-dimensional domain embedded in the peculiar region of the concentrations phase-space that in Part I we termed as “attractiveness region.” Numerical inspections on simple low-dimensional model cases are presented, including the benchmark case of Davis and Skodje [J. Chem. Phys. 111, 859 (1999)]10.1063/1.479372 and the preliminary analysis of a simplified model mechanism of hydrogen combustion.

In the preceding paper of this series (Part I, P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234101(2013)) we have unveiled some ubiquitous features encoded in the systems of polynomial differential equations normally applied in the description of homogeneous and isothermal chemical kinetics (mass-action law). Here we proceed by investigating a deeply related feature: the appearance of so-called slow manifolds (SMs) which are low-dimensional hyper-surfaces in the neighborhood of which the slow evolution of the reacting system occurs after an initial fast transient. Indeed a geometrical definition of SM, devoid of subjectivity, “naturally” follows in terms of a specific subdimensional domain embedded in the peculiar region of the concentrations phase-space that in Part I we termed as “attractiveness region.” Numerical inspections on simple low-dimensional model cases are presented, including the benchmark case of Davis and Skodje [J. Chem. Phys. 111, 859 (1999)] and the preliminary analysis of a simplified model mechanism of hydrogen combustion.]]>

Journal of chemical physics

num. 138, p. 234101-1-234101-16

DOI: 10.1063/1.4809592

Date of publication: 2013-06-17

Abstract:

Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as sensitivity analysis, lumping approaches, and exploitation of time scales separation. In addition, there are methods based on the existence of the so-called slow manifolds, which are hyper-surfaces of lower dimension than the one of the whole phase-space and in whose neighborhood the slow evolution occurs after an initial fast transient. On the other hand, all tools contain to some extent a degree of subjectivity which seems to be irremovable. With reference to macroscopic and spatially homogeneous reacting systems under isothermal conditions, in this work we shall adopt a phenomenological approach to let self-emerge the dimensional reduction from the mathematical structure of the evolution law. By transforming the original system of polynomial differential equations, which describes the chemical evolution, into a universal quadratic format, and making a direct inspection of the high-order time-derivatives of the new dynamic variables, we then formulate a conjecture which leads to the concept of an “attractiveness” region in the phase-space where a well-defined state-dependent rate function ¿ has the simple evolution math = -¿2 along any trajectory up to the stationary state. This constitutes, by itself, a drastic dimensional reduction from a system of N-dimensional equations (being N the number of chemical species) to a one-dimensional and universal evolution law for such a characteristic rate. Step-by-step numerical inspections on model kinetic schemes are presented. In the companion paper (10.1063/1.4809593) this outcome will be naturally related to the appearance (and hence, to the definition) of the slow manifolds.

Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as sensitivity analysis, lumping approaches, and exploitation of time scales separation. In addition, there are methods based on the existence of the so-called slow manifolds, which are hyper-surfaces of lower dimension than the one of the whole phase-space and in whose neighborhood the slow evolution occurs after an initial fast transient. On the other hand, all tools contain to some extent a degree of subjectivity which seems to be irremovable. With reference to macroscopic and spatially homogeneous reacting systems under isothermal conditions, in this work we shall adopt a phenomenological approach to let self-emerge the dimensional reduction from the mathematical structure of the evolution law. By transforming the original system of polynomial differential equations, which describes the chemical evolution, into a universal quadratic format, and making a direct inspection of the high-order time-derivatives of the new dynamic variables, we then formulate a conjecture which leads to the concept of an “attractiveness” region in the phase-space where a well-defined state-dependent rate function ω has the simple evolution math = −ω2 along any trajectory up to the stationary state. This constitutes, by itself, a drastic dimensional reduction from a system of N-dimensional equations (being N the number of chemical species) to a one-dimensional and universal evolution law for such a characteristic rate. Step-by-step numerical inspections on model kinetic schemes are presented. In the companion paper [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234102 (2013)]10.1063/1.4809593 this outcome will be naturally related to the appearance (and hence, to the definition) of the slow manifolds.]]>

Journal of chemical physics

Vol. 138, num. 21, p. 214702-1-214702-8

DOI: 10.1063/1.4807092

Date of publication: 2013-06-03

Abstract:

Molecular dynamics simulations of liquid water at ambient conditions, adsorbed at the external walls of (n,n) single-walled armchair carbon nanotubes have been performed for n = 5, 9, 12. The comparison with the case of water adsorbed on graphene has also been included. The analysis of Helmholtz free energies reveals qualitatively different ranges of thermodynamical stability, eventually starting at a given threshold surface density. We observed that, in the framework of the force field considered here, water does not wet graphene nor (12,12) tubes, but it can coat thinner tubes such as (9,9) and (5,5), which indicates that the width of the carbon nanotube plays a role on wetting. On the other hand, density profiles, orientational distributions of water, and hydrogen-bond populations indicate significant changes of structure of water for the different surfaces. Further, we computed self-diffusion of water and spectral densities of water and carbon molecules, which again revealed different qualitative behavior of interfacial water depending on the size of the nanotube. The crossover size corresponds to tube diameters of around 1 nm.]]>

Journal of chemical physics

Vol. 138, num. 14, p. 1-9

DOI: 10.1063/1.4799875

Date of publication: 2013-04-11

Abstract:

We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system param- eters (diffusion coefficients, reaction rate, and obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate, ~t-1/2 to very close to the perfect mixing rate, ~t1/2~t-1]]>

Journal of chemical physics

Vol. 138, num. 10, p. 104906-1-104906-6

DOI: 10.1063/1.4794312

Date of publication: 2013-03-14

Abstract:

We propose a phenomenological model to describe the tricritical behavior of the nematic to smectic-A (N-SmA) phase transition in liquid crystal mixture. To describe the mesophase transitions in binary mixture, nematic and smectic order parameters have been coupled with the concentration. We show that a tricritical point on the N-SmA phase transition line can be achieved under certain conditions. The predictive capability of the present model for determining the tricritical point of a binary mixture displaying the N-SmA transition has been demonstrated by testing with reported phase diagrams sharing both phases

We propose a phenomenological model to describe the tricritical behavior of the nematic to smectic- A (N-SmA) phase transition in liquid crystal mixture. To describe the mesophase transitions in binary mixture, nematic and smectic order parameters have been coupled with the concentration. We show that a tricritical point on the N-SmA phase transition line can be achieved under certain conditions. The predictive capability of the present model for determining the tricritical point of a binary mixture displaying the N-SmA transition has been demonstrated by testing with reported phase diagrams sharing both phases]]>

Journal of chemical physics

Vol. 139, p. 214101-214101-12

DOI: 10.1063/1.4830403

Date of publication: 2013

Abstract:

Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.]]>

Journal of chemical physics

Vol. 137, num. 19, p. 1-8

DOI: 10.1063/1.4766201

Date of publication: 2012-11-19

Abstract:

We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ~ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain.

We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ∼ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain.]]>

Journal of chemical physics

Vol. 137, num. 11, p. 1-6

DOI: 10.1063/1.4752426

Date of publication: 2012-09-17

Abstract:

We study the rotational dynamics of a supercooled molecular liquid by means of molecular dynamics simulations. The system under investigation is composed of rigid diatomic molecules with an associate dipole moment. At room temperature, orientational correlations decrease rapidly with increasing distances. Upon cooling, angles between dipole moments of molecules within the first coordination shell decrease. As for the dynamical properties, rotational diffusion coefficients decrease with temperature at a smaller rate than translational diffusion coefficients do, and the critical temperature associated with the former is lower than the one corresponding to their translational counterparts. Translation and rotation about an inertial axis are uncorrelated, whereas some coupling between translation and dipole reorientation is obtained.]]>

Journal of chemical physics

Vol. 137, num. 5, p. 1-9

DOI: 10.1063/1.4739531

Date of publication: 2012-08-07

Journal of chemical physics

Vol. 137, p. 1-10

DOI: 10.1063/1.4733561

Date of publication: 2012-07-17

Journal of chemical physics

Vol. 134, num. 12, p. 124514-1-124541-7

DOI: 10.1063/1.3697849

Date of publication: 2012-03-28

Journal of chemical physics

Vol. 136, num. 5, p. 054103-1-054103-10

DOI: 10.1063/1.3679402

Date of publication: 2012-02-02

Abstract:

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules.]]>

Journal of chemical physics

Vol. 135, num. 10, p. 1-4

DOI: 10.1063/1.3640002

Date of publication: 2011-09-14

Journal of chemical physics

Vol. 135, num. 10, p. 104503-1-104503-6

DOI: 10.1063/1.3632050

Date of publication: 2011-09-09

Abstract:

Molecular dynamics simulations have been carried out to investigate structural and dynamical characteristics of NaCl aqueous solutions confined within silica nanopores in contact with a “bulk-like” reservoir. Two types of pores, with diameters intermediate between 20 Å and 37.5 Å, were investigated: The first one corresponded to hydrophobic cavities, in which the prevailing wall-solution interactions were of the Lennard-Jones type. In addition, we also examined the behavior of solutions trapped within hydrophilic cavities, in which a set of unsaturated O-sites at the wall were transformed in polar silanol Si–OH groups. In all cases, the overall concentrations of the trapped electrolytes exhibited important reductions that, in the case of the narrowest pores, attained 50% of the bulk value. Local concentrations within the pores also showed important fluctuations. In hydrophobic cavities, the close vicinity of the pore wall was coated exclusively by the solvent, whereas in hydrophilic pores, selective adsorption of Na+ ions was also observed. Mass and charge transport were also investigated. Individual diffusion coefficients did not present large codifications from what is perceived in the bulk; contrasting, the electrical conductivity exhibited important reductions. The qualitative differences are rationalized in terms of simple geometrical considerations.]]>

Journal of chemical physics

Vol. 134, num. 14, p. 144505-144505-4

DOI: 10.1063/1.3576152

Date of publication: 2011-04-13

Abstract:

Recently, Nielsen et al. [J. Chem. Phys. 130, 154508 (2009); Philos. Mag. 88, 4101 (2008)] demonstrated a universal pattern for the high frequency wing of the loss curve for primary relaxation time on approaching the glass transition for organic liquids. In this contribution it is presented that a similar universality occurs for glass-forming liquid crystals and orientationally disordered crystals (plastic crystals). Empirical correlations of the found behavior are also briefly discussed]]>

Journal of chemical physics

Vol. 134, num. 5, p. 054509-1-054509-8

DOI: 10.1063/1.3530837

Date of publication: 2011-02-07

Abstract:

We report results for the ground-state energy and structural properties of small 4He–T↓ clusters consisting of up to four T↓ and eight 4He atoms. These results have been obtained using very well-known 4He–4He and T↓– T↓ interaction potentials and several models for the 4He– T↓ interatomic potential. All the calculations have been performed with variational and diffusion Monte Carlo methods. It takes at least three atoms to form a mixed bound state. In particular, for small clusters the binding energies are significantly affected by the precise form of the 4He– T↓ interatomic potential but the stability limits remain unchanged. The only exception is the 4He2T↓ trimer whose stability in the case of the weakest 4He– T↓ interaction potential is uncertain while it seems stable for other potentials. The mixed trimer 4He(T↓)2, a candidate for the Borromean state, is not bound. All other studied clusters are stable. Some of the weakest bound clusters can be classified as quantum halo as a consequence of having high probability of being in a classically forbidden region.]]>

Journal of chemical physics

Vol. 134, num. 4, p. 044501-1-044501-6

DOI: 10.1063/1.3525461

Date of publication: 2011-01-24

Abstract:

The results are reported of the molecular dynamics simulations of the coherent static structure factor of molten CuI at 938 K using a polarizable ion model. This model is based on a rigid ion potential to which the many body interactions due to the anions induced polarization are added. The calculated structure factor reproduces the clear sharp prepeak observed in neutron diffraction data. The corresponding partial structure factors and the related radial distribution functions calculated by molecular dynamics are compared with those found in the literature derived from a combination of neutron and x-ray diffraction data with the aid of the reverse Monte Carlo simulation technique, as well as those calculated by ab initio MD simulations.]]>

Journal of chemical physics

Vol. 134, num. 2, p. 024512-1-024512-7

DOI: 10.1063/1.3514589

Date of publication: 2011-01-14

Journal of chemical physics

Vol. 134, p. 014505-014505-9

DOI: 10.1063/1.3506867

Date of publication: 2011-01-05

Journal of chemical physics

Vol. 133, num. 23, p. 1-14

DOI: 10.1063/1.3511713

Date of publication: 2010-12-21

Journal of chemical physics

Vol. 133, num. 4, p. 044501-044508

DOI: 10.1063/1.3466749

Date of publication: 2010-07-28

Abstract:

Dynamical properties of low weight alcohols have been analyzed both in the liquid and the supercooled states. Realistic interatomic potential models for methanol and ethanol have been used. The influence of temperature on the hydrogen-bonded structure has been undertaken. Remarkable similarities have been obtained in both systems. Velocity autocorrelation functions have been evaluated for molecules participating in zero, one, and two hydrogen bonds at a wide range of temperatures. A backscattering area preceded by a shoulder has been identified as a signature of this function when evaluated for the subset of molecules that participate in two hydrogen bonds. Memory functions have also been evaluated. Their initial decay depends only slightly upon temperature. A more marked temperature dependence is observed for the nonassociated molecules. For them, reasonable agreement with the mode-coupling approach predictions has been encountered.]]>

Journal of chemical physics

Vol. 132, num. 21, p. 214505-1-214505-11

DOI: 10.1063/1.3429253

Date of publication: 2010-06-03

Abstract:

The study of NaCl solutions in water at finite concentration, explicitly including polarization in water molecules and ions, has been carried out by molecular dynamics simulations. A comparison of the RPOL polarizable model with the rigid SPC/E potential for water has been included. Structure obtained with the two models does not show significant differences, although some deviations in the NaNa radial distribution functions at all concentrations are observed. Dielectric properties such as total and molecular dipole moment correlation functions revealed decay times of the order of 10 ps, roughly independent of concentration. The analysis of electric conductivity by means of current-current correlation functions also included the calculation of cross terms corresponding to dipole moment-current correlations, which proved to be non-neglectable at short times and especially relevant at high concentrations (m = 4 mol kg−1). Frequency dependent dielectric constants and conductivities have been computed and the role of cross correlations has been analyzed. In all cases both concentration and cross correlations have significant influence in the results]]>

Journal of chemical physics

Vol. 132, num. 16, p. 164516/1-164516/10

DOI: 10.1063/1.3397997

Date of publication: 2010-04-29

Abstract:

The α-relaxation dynamics of 1-cyano-adamantane (CNA) and its mixtures with 1-chloro-adamantane (ClA) has been studied by means of broadband dielectric spectroscopy. The existence of orientationally disordered (OD) face centered cubic mixed crystals (ClA1−XCNAX) for 0.5 ≤ X ≤ 1 has been put in evidence by thermodynamics and structural analyses. In addition to the OD phase of CNA, mixed crystals with compositions higher than the equimolar one exhibit a freezing of the orientational degrees of freedom into a glassy state, which involves also a strong increase of the antiferroelectric order at temperatures higher than the dielectric glass transition temperature. This experimental evidence is revealed by a stairlike effect in the variation of the Kirkwood factor with the temperature as a consequence of a twin effect in the dielectric strength without any anomaly in the temperature-density curves. The characteristic relaxation times are analyzed as a function of temperature and mole fraction. By setting a common temporal origin ("isochronal origin") at τ(Tg) = 100 s for each mole fraction, it emerges that the substitution of ClA molecules by those of CNA (diminution of X) gives rise to a slow down in the dynamics, despite that the molecular volume of ClA molecules are smaller than those of CNA. This fact goes along and is accompanied by a diminution of the lattice packing with the decrease of composition. It is also shown that the heterogeneities produced by the concentration fluctuations due to the chemical disorder are the main contribution to the non-exponential character of the α-relaxation peaks.]]>

Journal of chemical physics

Vol. 132, num. 054503, p. 1-10

DOI: 10.1063/1.3298863

Date of publication: 2010-02-07

Journal of chemical physics

Vol. 132, num. 7, p. 1-10

DOI: 10.1063/1.3305326

Date of publication: 2010-02

Abstract:

Molecular dynamics simulations have been performed in a wide range of densities along a near critical isotherm of supercritical water in order to reveal the interconnection between the local hydrogen bonding (HB) network and several related dynamic properties. The results obtained have revealed a significant slowing down of reorientational dynamics of the water molecules as the value of the number of hydrogen bond per molecule increases and this is reflected on the increase in the reorientational correlation times. The calculated reorientational times exhibit also an increasing trend by increasing the bulk density, and this effect is more pronounced in the case of the first-order Legendre reorientational correlation functions. A clear nonlinear dependence of the librational mode frequencies of the water molecules on the augmented local density around them has also been revealed. This result could be regarded as an additional support of experimental observations suggesting the use of a nonlinear relation when analyzing the density dependence of spectroscopic peak frequencies in order to extract information about local density augmentation in supercritical fluids. The HB dynamics have been also investigated, revealing a plateau in the calculated HB lifetimes at intermediate and higher liquidlike densities and a small increase at low, gaslike densities.]]>

Journal of chemical physics

Vol. 131, num. 18, p. 184504-1-184504-6

DOI: 10.1063/1.3254207

Date of publication: 2009-11-14

Abstract:

The evolution of the primary relaxation time of orientationally disordered (OD) mixed crystals [(CH3)2C(CH2OH)2]1-X[(CH3)C(CH2OH)3]X[(CH3)2C(CH2OH)2]1-X[(CH3)C(CH2OH)3]X, with 0

The evolution of the primary relaxation time of orientationally disordered (OD) mixed crystals [(CH3)2C(CH2OH)2]1−X[(CH3)C(CH2OH)3]X, with 0

Journal of chemical physics

Vol. 131, num. 6, p. 4502

DOI: 10.1063/1.3204467

Date of publication: 2009-08

Journal of chemical physics

Vol. 131, num. 1, p. 5104-5113

Date of publication: 2009-07

Journal of chemical physics

Vol. 130, p. 234504-1-234504-10

DOI: 10.1063/1.3152241

Date of publication: 2009-06

Journal of chemical physics

Vol. 130, num. 204109, p. 1-10

DOI: 10.1063/1.3143522

Date of publication: 2009-05

Journal of chemical physics

Vol. 131, num. 24, p. 1-6

DOI: 10.1063/1.3275520

Date of publication: 2009

Abstract:

This work expands recent investigations in the field of spin-polarized tritium T↓ clusters. We report the results for the ground-state energy and structural properties of large T↓ clusters consisting of up to 320 atoms. All calculations have been performed with variational and diffusion Monte Carlo methods, using an accurate ab initio interatomic potential. Our results for N 40 are in good agreement with results obtained by other groups. Using a liquid-drop expression for the energy per particle, we estimate the liquid equilibrium density, which is in good agreement with our recently obtained results for bulk T↓. In addition, the calculations of the energy for large clusters have allowed for an estimation of the surface tension. From the mean-square radius of the drop, determined using unbiased estimators, we determine the dependence of the radii on the size of the cluster and extract the unit radius of the T↓ liquid.]]>

Journal of chemical physics

Vol. 129, num. 224509, p. 1

DOI: 10.1063/1.3039514

Date of publication: 2008-12

Journal of chemical physics

Vol. 129, num. 6, p. 45051-45059

DOI: 10.1063/1.2965878

Date of publication: 2008-08

Abstract:

Spatial heterogeneities have been investigated in a supercooled system composed of diatomic molecules with an associated dipole moment by using the molecular dynamics simulation technique. Pair distribution functions of molecules with different mobilities have been evaluated, and it has been found that molecules belonging to the same dynamic domain are spatially correlated. Molecules with extremely large mobilities form larger clusters than those resulting from random statistics. These clusters are stringlike shaped. The mean cluster size displays a maximum at times between the ballistic and the diffusive regime, approximately at the end of the ß-relaxation zone. The value of this maximum increases upon cooling the system. An analogous profile has been observed for the characteristic cluster length when plotted against time. Agreement with Adam–Gibbs predictions has been encountered when considering these clusters as the basic dynamic units of the theory. For the extremely slow molecules, a cluster distribution has also been encountered. These clusters are smaller than the ones composed by fast molecules; they do not have a quasilinear geometry and no maximum is observed for their mean cluster size.]]>

Journal of chemical physics

Vol. 128, p. 154114-1-154114-8

DOI: 10.1063/1.2907242

Date of publication: 2008-04-18

Abstract:

We propose a general method for simplifying master equations by eliminating from the description rapidly evolving states. The physical recipe we impose is the suppression of these states and a renormalization of the rates of all the surviving states. In some cases, this decimation procedure can be analytically carried out and is consistent with other analytical approaches, such as in the problem of the random walk in a double well potential. We discuss the application of our method to nontrivial examples: diffusion in a lattice with defects and a model of an enzymatic reaction outside the steady state regime.]]>