Free energy calculations of elemental sulphur crystals via molecular dynamics simulations

Free energy calculations of two crystalline phases of the molecular compound S8 were performed via molecular dynamics simulations of these crystals. The elemental sulphur S8 molecule model used in our MD calculations consists of a semi-flexible closed chain, with fixed bond lengths and intra-molecular potentials for its bending and torsional angles. The intermolecular potential is of the atom-atom Lennard-Jones type. Two free energy calculation methods were implemented: the accurate thermodynamic integration method proposed by Frenkel and Ladd and an estimation that takes into account the contribution of the zero point energy and the entropy of the crystalline vibrational modes to the free energy of the crystal. The last estimation has the enormous advantage of being easily obtained from a single MD simulation. Here we compare both free energy calculation methods and analyze the reliability of the fast estimation via the vibrational density of states obtained from constrained MD simulations. New results on alpha- and alpha'- S8 crystals are discussedComment: 18 pages, 2 figures, submitted to J. Chem. Phy

Correlated dynamics of water and amphiphilic molecules in thin Newton black films

The dynamical properties of amphiphilics in Newton black films, as well as those of the water confined between the two charged hydrophilic surfaces, have been calculated via a series of molecular dynamic calculations in several films with different water content. A charged semi-flexible amphiphilic model and the TIP5P model of water are used in our simulations [J. Chem. Phys. 129, 164901 (2008)]. We calculate the diffusion coefficients, reorientational dynamics and the atomic density profile of water molecules as a function of the number of water molecules per amphiphilic (nw). We also analyse the reorientational motion of the amphiphilics and  determine a strong correlation between the dynamics of water molecules and the translational and reorientational dynamics of the amphiphilics, as well as a correlation between the reorientational dynamics of the amphiphilics belonging to the  upper and lower halves of the studied thin films.Fil: Di Napoli, Solange Mariel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica; ArgentinaFil: Gamba, Z.. Comisión Nacional de Energía Atómica; Argentin

Macroscopic electrostatic potentials and interactions in self-assembled molecular bilayers: the case of Newton black films

We propose a very simple but 'realistic' model of amphiphilic bilayers,simple enough to be able to include a large number of molecules in the sample, but nevertheless detailed enough to include molecular charge distributions, flexible amphiphilic molecules and a reliable model of water. All these parameters are essential in a nanoscopic scale study of intermolecular and long range electrostatic interactions. We also propose a novel, simple and more accurate macroscopic electrostatic field for model bilayers. This model goes beyond the total dipole moment of the sample, which on a time average is zero for this type of symmetrical samples, i. e., it includes higher order moments of this macroscopic electric field. We show that by representing it with a superposition of gaussians it can be 'analytically' integrated, and therefore its calculation is easily implemented in a MD simulation (even in simulations of non-symmetrical bi- or multi-layers). In this paper we test our model by molecular dynamics simulations of Newton black films

Test of a simple and flexible molecule model for alpha-, beta- and gamma-S8 crystals

S8 is the most stable compound of elemental sulfur in solid and liquid phases, at ambient pressure and below 400K. Three crystalline phases of S8 have been clearly identified in this range of thermodynamic parameters, although no calculation of its phase diagram has been performed yet. alpha- and gamma-S8 are orientationally ordered crystals while beta-S8 is measured as orientationally disordered. In this paper we analyze the phase diagram of S8 crystals, as given by a simple and flexible molecule model, via a series of molecular dynamics (MD) simulations. The calculations are performed in the constant pressure- constant temperature ensemble, using an algorithm that is able to reproduce structural phase transitions.Comment: RevTex,7 pages, 5 figures,to appear in J. Chem. Phy

Toward an anisotropic atom-atom model for the crystalline phases of the molecular S8 compound

We analize two anisotropic atom-atom models used to describe the crystalline alpha,beta and gamma phases of S8 crystals, the most stable compound of elemental sulfur in solid phases, at ambient pressure and T<=400 K. The calculations are performed via a series of classical molecular dynamics (MD) simulations, with flexible molecular models and using a constant pressure-constant temperature algorithm for the numerical simulations. All intramolecular modes that mix with lattice modes, and are therefore relevant on the onset of structural phase transitions, are taken into account. Comparisons with experimental data and previous results obtained with an isotropic atom-atom molecular model are also performed.Comment: Major changes, new simulations and figures added, revtex4, to appear in J. Chem. Phy

Effective potentials and electrostatic interactions in self-assembled molecular bilayers II: the case of biological membranes

We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible amphiphilic molecules and a reliable model of water. All these parameters are essential in a nanoscopic scale study of intermolecular and long range electrostatic interactions. This model was previously used by us to simulate a Newton black film and in this paper we extend our investigation to bilayers of the biological membrane type. The electrostatic interactions are calculated using Ewald sums and, for the macroscopic long range electrostatic interactions, we use our previously proposed coarsed fit of the (perpendicular to the bilayer plane) molecular charge distributions with gaussian distributions. To study an unique biological membrane (not an stack of bilayers), we propose a simple effective external potential that takes into account the microscopic pair distribution functions of water and is used to simulate the interaction with the surrounding water. The method of effective macroscopic and external potentials is extremely simple to implement in numerical simulations, and the spatial and temporal charge inhomogeneities are then roughly taken into account. Molecular dynamics simulations of several models of a single biological membrane, of neutral or charged polar amphiphilics, with or without water (using the TIP5P intermolecular potential for water) are included