Jean-Marc Leyssale

An image-guided atomistic reconstruction of pyrolytic carbons

A method for the generation of atomistic models of dense nanotextured carbons is presented. This method is based on the statistical analysis of high resolution transmission electron microscopy images and their three-dimensional (3D) extension through image synthesis under constraint. The resulting 3D images then serve as an external potential bringing the atoms to settle preferentially on the black areas during a conventional simulated annealing simulation. Application of this method to the case of two laminar pyrocarbons, differing in their degree of disorder, highlights the promising nature of this approach.

Atomistic simulation of the homogeneous nucleation and of the growth of N2 crystallites

We report on a computer simulation study of the early stages of the crystallization of molecular nitrogen. First, we study how homogeneous nucleation takes place in supercooled liquid N(2) for a moderate degree of supercooling. Using the umbrella sampling technique, we determine the free energy barrier of formation for a critical nucleus of N(2). We show that, in accord with Ostwalds rule of stages, the structure of the critical nucleus is predominantly that of a metastable polymorph (alpha-N(2) for the state point investigated). We then monitor the evolution of several critical nuclei through a series of unbiased molecular dynamics trajectories. The growth of N(2) crystallites is accompanied by a structural evolution toward the stable polymorph beta-N(2). The microscopic mechanism underlying this evolution qualitatively differs from that reported previously. We do not observe any dissolution or reorganization of the alpha-like core of the nucleus. On the contrary, we show that alpha-like and beta-like blocks coexist in postcritical nuclei. We relate the structural evolution to a greater adsorption rate of beta-like molecules on the surface and show that this transition actually starts well within the precritical regime. We also carefully investigate the effect of the system size on the height of the free energy barrier of nucleation and on the structure and size of the critical nucleus.

Molecular simulation of the homogeneous crystal nucleation of carbon dioxide

We report on a molecular simulation study of the homogeneous nucleation of CO2 in the supercooled liquid at low pressure (P = 5 MPa) and for degrees of supercooling ranging from 32% to 60%. In all cases, regardless of the degree of supercooling, the structure of the crystal nuclei is that of the Pa3 phase, the thermodynamically stable phase. For the more moderate degree of supercooling of 32%, the nucleation is an activated process and requires a method to sample states of high free energy. In this work, we apply a series of bias potentials, which promote the ordering of the centers of mass of the molecules and allow us to gradually grow crystal nuclei. The reliability of the results so obtained is assessed by studying the evolution of the nuclei in the absence of any bias potential, and by determining their probability of growth. We estimate that the size of the critical nucleus, for which the probability of growth is 0.5, is approximately 240 molecules. Throughout the nucleation process, the crystal nuclei clearly exhibit a Pa3 structure, in apparent contradiction with Ostwalds rule of stages. The other polymorphs have a much larger free energy. This makes their formation highly unlikely and accounts for the fact that the nucleation of CO2 proceeds directly in the stable Pa3 structure.

A molecular dynamics study of homogeneous crystal nucleation in liquid nitrogen

Abstract The crystal nucleation of nitrogen is studied by molecular dynamics. Using the umbrella sampling technique, we are able to determine the free energy barrier of nucleation and the structure of the critical nucleus formed under typical experimental supercoolings. In agreement with Ostwald’s ‘step rule’, nucleation is shown to proceed into an orientationally disordered cubic phase instead of the thermodynamically stable hexagonal β phase. We also give an account of the system size dependence of the free energy profiles so obtained.

Hit and miss of classical nucleation theory as revealed by a molecular simulation study of crystal nucleation in supercooled sulfur hexafluoride

Classical nucleation theory pictures the homogeneous nucleation of a crystal as the formation of a spherical crystalline embryo, possessing the properties of the macroscopic crystal, inside a parent supercooled liquid. In this work we study crystal nucleation in moderately supercooled sulfur hexafluoride by umbrella sampling simulations. The nucleation free energy evolves from 5.2kBT at T=170 K to 39.1kBT at T=195 K. The corresponding critical nucleus size ranges from 40 molecules at T=170 K to 266 molecules at T=195 K. Both nucleation free energy and critical nucleus size are shown to evolve with temperature according to the equations derived from the classical nucleation theory. Inspecting the obtained nuclei we show, however, that they present quite anisotropic shapes in opposition to the spherical assumption of the theory. Moreover, even though the critical nuclei possess the structure of the stable bcc plastic phase, the only mechanically stable crystal phase for SF6 in the temperature range investigated, they are shown to be less ordered than the corresponding macroscopic crystal. Their crystalline order is nevertheless shown to increase regularly with their size. This is confirmed by a study of a nucleus growth from a critical size to a size of the order of 10(4) molecules. Similarly to the fact that it does not affect the temperature dependence of the nucleation free energy and of the critical nucleus size, the ordering of the nucleus with size does not affect the growth rate of the nucleus.

Molecular Dynamics of Carbon Dioxide, Methane and Their Mixtures in a Zeolite Possessing Two Independent Pore Networks as Revealed by Computer Simulations†

The molecular motion of methane (CH(4)) and carbon dioxide (CO(2)) sorbed in the two independent pore networks, being termed hereafter as large cavity (LC) and sinusoidal channel (SC) regions of the siliceous MWW-framework-type zeolite ITQ-1, is studied by means of atomistic computer simulation. Equilibrium molecular dynamics predicts different loading dependences for the two gases, for both the self and the collective (Maxwell-Stefan) diffusion coefficients; in particular, the transport coefficients of CH(4) go through a maximum as its loading in the zeolite increases, whereas CO(2) dynamics exhibits the decreasing trend with loading usually observed in nanoporous materials. The different loading dependence of the self-diffusivity for the two sorbates is attributed to their different probability density distribution within the supercages in the LC system of the ITQ-1 unit cell. The composition and occupancy dependence of the self-diffusivity of each component in their binary mixtures can be explained in terms of the selectivity for CO(2) sorption thermodynamics in the zeolite. The collective diffusivity loading dependence of the single and binary sorbate system is explainable on the basis of the strength of intermolecular interactions along the diffusion direction connecting the supercages by invoking the quasichemical mean field theory.

Hindered rotor models with variable kinetic functions for accurate thermodynamic and kinetic predictions

We present an extension of some popular hindered rotor (HR) models, namely, the one-dimensional HR (1DHR) and the degenerated two-dimensional HR (d2DHR) models, allowing for a simple and accurate treatment of internal rotations. This extension, based on the use of a variable kinetic function in the Hamiltonian instead of a constant reduced moment of inertia, is extremely suitable in the case of rocking/wagging motions involved in dissociation or atom transfer reactions. The variable kinetic function is first introduced in the framework of a classical 1DHR model. Then, an effective temperature and potential dependent constant is proposed in the cases of quantum 1DHR and classical d2DHR models. These methods are finally applied to the atom transfer reaction SiCl(3)+BCl(3)→SiCl(4)+BCl(2). We show, for this particular case, that a proper accounting of internal rotations greatly improves the accuracy of thermodynamic and kinetic predictions. Moreover, our results confirm (i) that using a suitably defined kinetic function appears to be very adapted to such problems; (ii) that the separability assumption of independent rotations seems justified; and (iii) that a quantum mechanical treatment is not a substantial improvement with respect to a classical one.

Rippled nanocarbons from periodic arrangements of reordered bivacancies in graphene or nanotubes

We report on various nanocarbons formed from a unique structural pattern containing two pentagons, three hexagons, and two heptagons, resulting from local rearrangements around a divacancy in pristine graphene, or nanotubes. This defect can be inserted in sheets or tubes either individually or as extended defect lines. Sheets or tubes containing only this defect as a pattern can also be obtained. These fully defective sheets, and most of the tubes, present a very pronounced rippled (wavy) structure and their energies are lower than other structures based on pentagons and heptagons published so far. Another particularity of these rippled carbon sheets is their ability to fold themselves into a two-dimensional porous network of interconnected tubes upon heat treatment as shown by hybrid Monte Carlo simulations. Finally, contrary to the common belief that pentagon/heptagon based structures are metallic, this work shows that this defect pattern should give rise to semimetallic conduction.

Temperature induced transition from hexagonal to circular pits in graphite oxidation by O2

We report on an in-situ monitoring of graphite oxidation using a high temperature environmental scanning electron microscope. A morphological transition is clearly identified around 1040 K between hexagonal pits at low temperatures and circular pits at high temperatures, with apparently no change in the kinetic law. A kinetic Monte Carlo model allows rationalizing these findings in terms of the competitive oxidation of armchair and zig-zag edge sites and provides an estimate of the rate laws associated to these two events. Extended to three dimensions, the model also explains the “in-depth” transition between the stepwise hexagons and the hemispheres observed by atomic force microscopy.

The self-referential method combined with thermodynamic integration

The self-referential method [M. B. Sweatman, Phys. Rev. E 72, 016711 (2005)] for calculating the free energy of crystalline solids via molecular simulation is combined with thermodynamic integration to produce a technique that is convenient and efficient. Results are presented for the chemical potential of hard sphere and Lennard-Jones face centered cubic crystals that agree well with this previous work. For the small system sizes studied, this technique is about 100 times more efficient than the parameter hopping technique used previously.