Molecular modeling is applied to a representative array of kerogens for the purpose of obtaining quantitative predictions of thermodynamic properties from quantum mechanics and volumetric properties from molecular dynamics. The kerogen model units (175−260 carbon atoms) have been built in the MedeA environment from the sole consideration of the elemental analysis and functional group analysis documented in the work of Exxon and IFP-EN scientists [Kelemen, S. R., et al., Energy Fuels, 2007, 21 (3), pp 1548−1561. The density results are in good agreement with the well-documented trends of kerogen density with thermal maturity and organic type. The heat capacity in the ideal gas state is predicted to increase as a function of temperature, as obtained from quantum mechanics at the semiempirical level (MOPAC-PM7). This result is in quantitative agreement with experimental heat capacity data on type I kerogen and on coal. This behavior appears clearly as a nonclassical feature, because of the quantization of energy levels in molecular vibrations. Also, the residual heat capacity estimated from molecular dynamics appears subordinate, compared with the ideal heat capacity evaluated from quantum mechanics. The change from negative to positive standard enthalpy of formation when changing from low-maturity kerogen to high-maturity kerogen is also predicted in agreement with correlative methods based on numerous experimental data from coals and fossil fuels. Kerogen model units are available for download free of charge in .xyz or .sci formats from www.materialsdesign. com/science/structures/kerogens_and_coals.

In this work, we use molecular simulations to determine the structural and physical properties of the organic matter present in type II shales in the middle of the oil generation window. The construction of molecular models of organic matter constrained by experimental data is discussed. Using a realistic molecular model of organic matter, we generate, by molecular dynamics simulations, structures that mimic bulk organic matter under typical reservoir conditions. Consistent results on density, diffusion, and specific adsorption are found between simulated and experimental data. These structures enable us to provide information on the fluid distribution within the organic matter, the pore size distributions, the isothermal compressibility, and the dynamic of the fluids within the kerogen matrix. This study shows that a consistent description at the molecular level combined with molecular simulations can be useful, in complement of experiments, to investigate the organic matter present in shales.

International audienceDuring the past decade, gas recovered from shale reservoirs has jumped from 2 to 40% of natural gas production in the United States. However, in response to the drop of gas prices, the oil and gas industry has set its sights on the oil-prone shale plays, potentially more lucrative. This shift from dry to condensate-rich gas has raised the need for a better understanding of the transport of hydrocarbon mixtures through organic-rich shale reservoirs. At the micrometer scale, hydrocarbons in shales are mostly located in amorphous microporous nodules of organic matter, the so-called kerogen, dispersed in an heterogeneous mineral matrix. In such multiscale materials, a wide range of physical mechanisms might affect the composition of the recovered hydrocarbon mixtures. More specifically, kerogen nodules are likely to act as selective barriers due to their amorphous microporous structure. In this work, we study the transport of hydrocarbon mixtures through kerogen by means of molecular simulations. We performed molecular dynamics simulations of hydrocarbons permeating through a molecular model representative of oil-prone type II kerogen. Our results show that the permeation mechanisms through this type of material is purely diffusive. Consequently, we have computed the Onsager's species-specific transport coefficients of a typical condensate-rich gas mixture within kerogen. Interestingly, we have observed that the transport coefficients matrix can be reasonably approximated by its diagonal terms, the so-called Onsager's autocorrelation coefficients. Inspired by the classical Rouse model of polymer dynamics and surface diffusion theory, we propose a simple scaling law to predict the transport coefficient of linear alkanes in the mixture. In good agreement with our simulations results, the Onsager's autocorrelation coefficients scale linearly with the adsorption loading and inversely with the alkane chain length. We believe our results and predictions are applicable to other materials, such as carbon-based synthetic microporous membranes, with structural properties close to that of kerogen

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Re´sume´-Mode´lisation mole´culaire de l'adsorption dans les solides microporeux -L'existence de logiciels industriels, la baisse du couˆt du calcul et la disponibilite´de champs de force e´prouve´s rendent la simulation mole´culaire de plus en plus attrayante pour les applications du domaine du ge´nie chimique. Nous pre´sentons ici plusieurs applications des techniques de simulation de Monte-Carlo, applique´es a`l'adsorption de fluides dans des solides microporeux (pores < 2 nm) comme les ze´olithes et des structures microporeuses a`base de carbone. L'adsorption a e´teḿ ode´lise´e par simulation dans l'ensemble Grand Canonique graˆce au logiciel MedeA Ò -GIBBS, en utilisant des grilles tridimensionnelles de valeurs pre´-calcule´es de l'e´nergie pour optimiser le temps calcul. MedeA Ò -GIBBS a aussi e´te´utilise´pour obtenir les potentiels chimiques ou les fugacite´s dans les phases fluides libres au moyen de l'ensemble Canonique (NVT) ou de l'ensemble isotherme-isobare (NPT). Les re´sultats de simulation ont e´te´compare´s avec des donne´es expe´rimentales d'isothermes d'adsorption de corps purs (gaz hydrocarbures, eau, aromatiques, e´thanethiol) dans plusieurs ze´olithes et a`plusieurs tempe´ratures. La coadsorption de me´langes (me´thane-e´thane, n-hexane-benze`ne) dans les ze´olithes a aussi e´te´e´tudie´e. Par exemple, l'inversion de se´lectivite´n-hexane/benze`ne entre la silicalite et les Na-faujasites est bien pre´dite avec des champs de force publie´s, et permettent de comprendre les me´canismes sousjacents. De meˆme, les isothermes d'adsorption des hydrocarbures le´gers et d'un mercaptan (e´thyl-thiol) sont bien de´crite. En ce qui concerne les adsorbants organiques (ke´roge`ne et charbons matures), des mode`les mole´culaires moyens ont e´te´construits en rendant compte des principaux traits connus de la structure chimique de ces mate´riaux. Par une simple relaxation ab ase de dynamique mole´culaire, nous avons pu obtenir des densite´s moyennes en bon accord avec les donne´es expe´rimentales disponibles, ce qui est tre`s encourageant. Nous avons aussi de´termine´les courbes isothermes d'exce`s d'adsorption en bon accord qualitatif avec celles re´cemment mesure´es sur des e´chantillons de charbon ou d'argiles en l'absence d'eau. Bien que pre´liminaires, ces re´sultats illustrent la puissance et la ge´ne´ralite´de la mode´lisation mole´culaire en vue de la compre´hension de syste`mes complexes dans des conditions ou`l'expe´rimentation est difficile.Abstract -Molecular Simulation of Adsorption in Microporous Materials -The development of industrial software, the decreasing cost of computing time, and the availability of well-tested Oil & Gas Science and Technology -Rev. IFP Energies nouvelles, Vol. 68 (2013), No. 6, pp. 977-994 Copyright Ó 2013, IFP Energies nouvelles DOI: 10.2516 forcefields make molecular simulation increasingly attractive for chemical engineers. We present here several applications of Monte-Carlo simulation techniques, applied to the adsorption of fluids in microporous solids such as...

We propose a computational framework to study the lipid-mediated clustering of integral membrane proteins. Our method employs a hierarchical approach. The potential of mean force (PMF) of two interacting proteins is computed under a coarse-grained 3-D model that successfully describes the structural properties of reconstituted lipid bilayers of dymiristoylphophatidylcholine (DMPC) molecules. Subsequently, a 2-D model is adopted, where proteins represented as self-avoiding disks interact through the previously computed PMF, which is modified to take into account three body corrections. The aggregation of the proteins is extensively studied under the condition of negative hydrophobic mismatch: the formation of clusters with increasing size agrees with previous computational and experimental findings.

We have studied the crystalline-amorphous coexistence for systems of polydisperse soft spheres that interact via a purely repulsive power law potential. Potential softness quantified by the exponent of the potential was a primary input in our simulations. Simulations were performed in the isobaric semigrand statistical ensemble, i.e., the composition of the parent distribution was not fixed in our systems. Gibbs-Duhem integration was used to trace the coexistence pressure as a function of potential softness for monodisperse systems. A second Gibbs-Duhem integration, initiated from the monodisperse coexistence curve, was employed to determine coexistence pressure versus imposed variance of the activity distribution. Amorphous-crystalline coexistence densities and volume fractions were determined to be monotonically increasing functions of the breadth of particle size dispersity. Semigrand ensemble simulations testified to the existence of a terminal diameter dispersity, i.e., a dispersity above which no amorphous-crystalline phase coexistence was observed. At the terminus size dispersity increases from 5.8% to 6.1% to 6.4% and to 6.7% and 6.5% for the crystalline phase as the steepness parameter n, takes on smaller values: from 100 to 50 to 12 to 10 and 8, respectively. In sharp contrast to the crystalline phases' enhanced, by potential softness, allowable size dispersity the amorphous phase exhibits an opposite trend, as potential interactions soften. Furthermore, amorphous phases accommodate, on average, smaller particles than those of the ordered (fcc) phase. Contrary to widely accepted intuition crystalline phases composed of size-disperse particulates exhibit a higher degree of local order than their monodisperse counterparts, admittedly at differing thermodynamic conditions.