Coarse-Grained Models of Aqueous Solutions of Polyelectrolytes: Significance of Explicit Charges.

The structure of polyelectrolytes is highly sensitive to small changes in interactions between their monomers. In particular, interactions mediated by counterions play a significant role and are affected by both specific molecular effects and generic concentration effects. The ability of coarse-grained models to reproduce the structural properties of an atomic model is thus a challenging task. Our present study compares the ability of different kinds of coarse-grained models: (i) to reproduce the structure of an atomistic model of a polyelectrolyte (the sodium polyacrylate) and (ii) to reproduce the variations of this structure with the number of monomers and with the concentration of different species. We show that adequate scalings of the gyration radius of the polymer Rg with the number of monomers N and with the box size Lbox are only obtained, first, if the monomer charges and the counterions are explicitly described and, second, if an attractive Lennard-Jones contribution is added to the interaction between distant monomers. Also, we show that implicit ion models are relevant only to the high electrostatic screening regime.

How do Nucleotides Adsorb Onto Clays?

Adsorption of prebiotic building blocks is proposed to have played a role in the emergence of life on Earth. The experimental and theoretical study of this phenomenon should be guided by our knowledge of the geochemistry of the habitable early Earth environments, which could have spanned a large range of settings. Adsorption being an interfacial phenomenon, experiments can be built around the minerals that probably exhibited the largest specific surface areas and were the most abundant, i.e., phyllosilicates. Our current work aims at understanding how nucleotides, the building blocks of RNA and DNA, might have interacted with phyllosilicates under various physico-chemical conditions. We carried out and refined batch adsorption studies to explore parameters such as temperature, pH, salinity, etc. We built a comprehensive, generalized model of the adsorption mechanisms of nucleotides onto phyllosilicate particles, mainly governed by phosphate reactivity. More recently, we used surface chemistry and geochemistry techniques, such as vibrational spectroscopy, low pressure gas adsorption, X-ray microscopy, and theoretical simulations, in order to acquire direct data on the adsorption configurations and localization of nucleotides on mineral surfaces. Although some of these techniques proved to be challenging, questioning our ability to easily detect biosignatures, they confirmed and complemented our pre-established model.

Computation of the Hydrodynamic Radius of Charged Nanoparticles from Nonequilibrium Molecular Dynamics.

We have used nonequilibrium molecular dynamics to simulate the flow of water molecules around a charged nanoparticle described at the atomic scale. These nonequilibrium simulations allowed us to compute the friction coefficient of the nanoparticle and then to deduce its hydrodynamic radius. We have compared two different strategies to thermostat the simulation box, since the low symmetry of the flow field renders the control of temperature non trivial. We show that both lead to an adequate control of the temperature of the system. To deduce the hydrodynamic radius of the nanoparticle we have employed a partial thermostat, which exploits the cylindrical symmetry of the flow field. Thereby, only a part of the simulation box far from the nanoparticle is thermostated. We have taken into account the finite concentration of the nanoparticle when calculating the friction force acting on it. We have focused on the case of polyoxometalate ions, which are inorganic charged nanoparticles. It appears that, for a given structure of the nanoparticle at the atomic level, the hydrodynamic radius significantly increases with the nanoparticles charge, a phenomenon that had not been quantified so far using molecular dynamics. The presence of an added salt only slightly modifies the hydrodynamic radius.

Soft X-ray Heterogeneous Radiolysis of Pyridine in the Presence of Hydrated Strontium-Hydroxyhectorite and its Monitoring by Near-Ambient Pressure Photoelectron Spectroscopy.

The heterogeneous radiolysis of organic molecules in clays is a matter of considerable interest in astrochemistry and environmental sciences. However, little is known about the effects of highly ionizing soft X-rays. By combining monochromatized synchrotron source irradiation with in situ Near Ambient Pressure X-ray Photoelectron Spectroscopy (in the mbar range), and using the synoptic view encompassing both the gas and condensed phases, we found the water and pyridine pressure conditions under which pyridine is decomposed in the presence of synthetic Sr2+-hydroxyhectorite. The formation of a pyridine/water/Sr2+ complex, detected from the Sr 3d and N 1s core-level binding energies, likely presents a favorable situation for the radiolytic breaking of the O-H bond of water molecules adsorbed in the clay and the subsequent decomposition of the molecule. However, decomposition stops when the pyridine pressure exceeds a critical value. This observation can be related to a change in the nature of the active radical species with the pyridine loading. This highlights the fact that the destruction of the molecule is not entirely determined by the properties of the host material, but also by the inserted organic species. The physical and chemical causes of the present observations are discussed.

Diffusion under Confinement: Hydrodynamic Finite-Size Effects in Simulation.

We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that the use of periodic boundary conditions in the directions along the surfaces results in dramatic finite-size effects, in addition to that of the physically relevant confining length. As in the simulation of bulk fluids, these effects arise from spurious hydrodynamic interactions between periodic images and from the constraint of total momentum conservation. We derive analytical expressions for the correction to the diffusion coefficient in the limits of both elongated and flat systems, which are in excellent agreement with the molecular simulation results except for the narrowest pores, where the discreteness of the fluid particles starts to play a role. The present work implies that the diffusion coefficients for wide nanopores computed using elongated boxes suffer from finite-size artifacts which had not been previously appreciated. In addition, our analytical expression provides the correction to be applied to the simulation results for finite (possibly small) systems. It applies not only to molecular but also to all mesoscopic hydrodynamic simulations, including Lattice-Boltzmann, Multiparticle Collision Dynamics or Dissipative Particle Dynamics, which are often used to investigate confined soft matter involving colloidal particles and polymers.

Solvation of complex surfaces via molecular density functional theory.

We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development.

Diffusion coefficient and shear viscosity of rigid water models.

We report the diffusion coefficient and viscosity of popular rigid water models: two non-polarizable ones (SPC/E with three sites, and TIP4P/2005 with four sites) and a polarizable one (Dang-Chang, four sites). We exploit the dependence of the diffusion coefficient on the system size (Yeh and Hummer 2004 J. Phys. Chem. B 108 15873) to obtain the size-independent value. This also provides an estimate of the viscosity of all water models, which we compare to the Green-Kubo result. In all cases, a good agreement is found. The TIP4P/2005 model is in better agreement with the experimental data for both diffusion and viscosity. The SPC/E and Dang-Chang models overestimate the diffusion coefficient and underestimate the viscosity.

Water dynamics in hectorite clays: influence of temperature studied by coupling neutron spin echo and molecular dynamics.

Within the wider context of water behavior in soils, and with a particular emphasis on clays surrounding underground radioactive waste packages, we present here the translational dynamics of water in clays in low hydrated states as studied by coupling molecular dynamics (MD) simulations and quasielastic neutron scattering experiments by neutron spin echo (NSE). A natural montmorillonite clay of interest is modeled by a synthetic clay which allows us to understand the determining parameters from MD simulations by comparison with the experimental values. We focus on temperatures between 300 and 350 K, i.e., the range relevant to the highlighted application. The activation energy Ea experimentally determined is 6.6 kJ/mol higher than that for bulk water. Simulations are in good agreement with experiments for the relevant set of conditions, and they give more insight into the origin of the observed dynamics.

Bridging molecular and continuous descriptions: the case of dynamics in clays.

The theory of transport in porous media such as clays depends on the level of description. On the macroscopic scale,hydrodynamics equations are used. These continuous descriptions are convenient to model the fluid motion in a confined system. Nevertheless, they are valid only if the pores of the material are much larger than the molecular size of the components of the system. Another approach consists in using molecular descriptions. These two methods which correspond to different levels of description are complementary. The link between them can be clarified by using a coarse-graining procedure where the microscopic laws are averaged over fast variables to get the long time macroscopic laws. We present such an approach in the case of clays. Firstly, we detail the various levels of description and the relations among them, by emphasizing the validity domain of the hydrodynamic equations. Secondly, we focus on the case of dehydrated clays where hydrodynamics is not relevant. We show that it is possible to derive a simple model for the motion of the cesium ion based on the difference on time scale between the solvent and the solute particles.

Bridging molecular and continuous descriptions: the case of dynamics in clays

The theory of transport in porous media such as clays depends on the level of description. On the macroscopic scale,hydrodynamics equations are used. These continuous descriptions are convenient to model the fluid motion in a confined system. Nevertheless, they are valid only if the pores of the material are much larger than the molecular size of the components of the system. Another approach consists in using molecular descriptions. These two methods which correspond to different levels of description are complementary. The link between them can be clarified by using a coarse-graining procedure where the microscopic laws are averaged over fast variables to get the long time macroscopic laws. We present such an approach in the case of clays. Firstly, we detail the various levels of description and the relations among them, by emphasizing the validity domain of the hydrodynamic equations. Secondly, we focus on the case of dehydrated clays where hydrodynamics is not relevant. We show that it is possible to derive a simple model for the motion of the cesium ion based on the difference on time scale between the solvent and the solute particles.

A teoria de transporte em meios porosos tais como argilasdepende do nível de descrição. Na escala macroscópica, equações da hidrodinâmica são utilizadas. Tais descrições a níveldo contínuo são convenientes para tratar o movimento do fluido em sistemas confinados. No entanto, tais equações são válidas se os poros do material são muito maiores do que as moléculas das componentes do sistema. Uma outra abordagem consiste em usar descrições moleculares. Esses dois métodos que correspondem a diferentes níveis de descriçãosão complementares. A ligação entre eles pode ser elucidada usando um procedimento de mudança de escala onde são tomadas médias das leis microscópicas sobre as variáveis rápidas para se obter as leis macroscópicas para tempos longos. Apresentamos esta abordagem no caso de argilas. Primeiramente apresentamos em detalhes os vários níveis de descrição bem como as relações entre eles, enfatizando o domínio de validade das equações hidrodinâmicas. Em seguida, focamos no caso de argilas desidratadas onde a hidrodinâmica não é relevante. Mostramos que é possível derivar um modelo simples para o movimento dos íons césio baseado na diferença entre as escalas de tempo do solvente e das partículas do soluto.

Salt exclusion in charged porous media: a coarse-graining strategy in the case of montmorillonite clays.

We study the exclusion of salt from charged porous media (Donnan effect), by using a coarse-grained approach. The porous medium is a lamellar system, namely a Montmorillonite clay, in contact with a reservoir, which contains an electrolyte solution. We develop a specific coarse-graining strategy to investigate the structural properties of this system. Molecular simulations are used to calibrate a mesoscopic model of the clay micropore in equilibrium with a reservoir. Brownian Dynamics simulations are then used to predict the structure of ions in the pore and the amount of NaCl salt entering the pore as a function of the pore size (the distance L between clay surfaces) and of the electrolyte concentration in the reservoir. These results are also compared to the predictions of a Density Functional Theory, which takes into account the excluded volumes of ions. We show that the calibration of the mesoscopic model is a key point and has a strong influence on the result. We observe that the salt exclusion increases when kappaL decreases (where kappa is the inverse of the Debye length) and that this effect is modulated by the correlations between ions. Two different regimes are revealed. At low concentrations in the reservoir, we observe a regime controlled by electrostatics: the Coulomb attraction between ions increases the amount of salt in the interlayer space. On the opposite, at high concentrations in the reservoir, the excluded volume effect dominates.

Structure and dynamics of water at a clay surface from molecular dynamics simulation.

We report a molecular dynamics study of the structure and dynamics of water at a clay surface. The negative charge of the surface and the presence of surface oxygen atoms perturbs water over two to three molecular layers, while the nature of the counterions (Na(+)or Cs(+)) has only a small effect. In the first molecular layer, approximately half of the water molecules are H-bonded to the surface. We also analyze the H-bond network between surface water molecules. The diffusion of water molecules along the surface is slowed down compared to the bulk case. As far as the orientational order and dynamics of the water dipole are concerned, only the component normal to the clay surface is perturbed. We investigate the surface H-bond formation and dissociation dynamics and their coupling to the release of molecules from the first molecular layer. We introduce a simple kinetic model in the spirit of Luzar and Chandler [Nature, 1996, 379, 55] to allow for a comparison with bulk water dynamics. This model semi-quantitatively reproduces the molecular simulation results and suggests that H-bond formation is faster with the surface than in the bulk, while H-bond dissociation is slower.

A multiscale approach to ion diffusion in clays: building a two-state diffusion-reaction scheme from microscopic dynamics.

The mobility of particles is generally lowered by the presence of a confining medium, both because of geometrical effects, and because of the interactions with the confining surfaces, especially when the latter are charged. The water/mineral interface plays a central role in the dynamics of ions. The ionic mobility in clays is often understood as an interplay between the diffusion of mobile ions and their possible trapping at the mineral surfaces. We describe how to build a two-state diffusion-reaction scheme from the microscopic dynamics of ions, controlled by their interaction with a mineral surface. The starting point is an atomic description of the clay interlayer using molecular simulations. These provide a complete description of the ionic dynamics on short time and length scales. Using the results of these simulations, we then build a robust mesoscopic (Fokker-Planck) description. In turn, this mesoscopic description is used to determine the mobility of the ions in the interlayer. These results can then be cast into a diffusion-reaction scheme, introducing in particular the fraction of mobile ions, or equivalently the distribution coefficient Kd. This coefficient is of great importance in characterizing electrokinetic phenomena in porous materials.