How natural materials remove heavy metals from water: mechanistic insights from molecular dynamics simulations

Water pollution by heavy metals is of increasing concern due to its devastating effects on the environment and on human health. For the removal of heavy metals from water sources, natural materials, such as spent-coffee-grains or orange/banana/chestnut peels, appear to offer a potential cheap alternative to more sophisticated and costly technologies currently in use. However, in order to employ them effectively, it is necessary to gain a deeper understanding - at the molecular level - of the heavy metals-bioorganic-water system and exploit the power of computer simulations. As a step in this direction, we investigate via atomistic simulations the capture of lead ions from water by hemicellulose - the latter being representative of the polysaccharides that are common components of vegetables and fruit peels - as well as the reverse process. A series of independent molecular dynamics simulations, both classical and ab initio, reveals a coherent scenario which is consistent with what one would expect of an efficient capture, i.e. that it be fast and irreversible: (i) binding of the metal ions via adsorption is found to happen spontaneously on both carboxylate and hydroxide functional groups; (ii) in contrast, metal ion desorption, leading to solvation in water, involves sizable free-energy barriers.

Release kinetics of volatiles from smectite clay minerals

Pascal Clausen

The focus of this thesis was on the mechanisms of release of volatile molecules from smectite clay minerals. The weight loss was monitored by thermogravimetry, differential calorimetry, and mass spectrometry under isothermal conditions and under ramp temperature conditions. Modeling of the clay-volatile release systems was performed with the help of finite element method calculations at the macroscopic level and ab initio calculations at the molecular level. A first comparison between finite element method simulations and experimental data for the evaporation of bulk volatile liquids under a convective gas flow showed the calculations to be in good agreement with experiments. Results of the simulations were used to develop a semi-analytical model explaining the dependence of the evaporation on the total pressure, the carrier gas flow, the temperature, and material constants. In particular, its temperature dependence could be approximated to good accuracy by an Arrhenius-type equation derived from the semi-analytical model. Differential calorimetry measurements of the heats of vaporization showed equilibrium conditions at the surface of the liquids to be satisfied. The same approach was extended to the release of model volatiles (water, ethanol, ethyl acetate and toluene) from smectite clays. At high coverage, the release was found to be close to that for the bulk liquids. Its decrease with time followed the behaviour observed in the respective curves of the gas/condensed phase partition coefficients, the equilibrium desorption isotherms. Equilibrium condition at the surface of the sample was evidenced by a comparison between the measured heats of vaporization and the equilibrium desorption isotherms. The differences observed in the measured equilibrium desorption isotherms of the volatile on the smectite clays could be rationalized by the use of ab initio calculations of the binding of the volatiles on the surface of a sodium smectite clay. At low coverage, the differences could be attributed to their differences in binding energies with the clay counter ions, which could be explained in terms of the chemical nature of the interacting species. At high coverage, the differences could be related to the properties of the bulk liquids, because high coverage corresponds to high activities of the volatiles on the clay samples. The differences observed in the measured rates of release of the volatiles from the smectite clays could be rationalized by the use of finite element calculations and the semi-analytical model developed for the bulk liquids, taking as input parameters the measured equilibrium desorption isotherms, that determines the volatile gas phase concentration at the surface of the sample. The slower rates of release of ethanol and ethyl acetate from the smectite clay, compared to water, could be explained from their differences in their equilibrium desorption isotherms from the clay, though diffusion effects also played a minor role. However, the slower rate of release of toluene, compared to water, could only be explained by its slow diffusion in the smectite clay. Diffusion effects were found to be enhanced with an increase in the size of the aggregate, such that, in addition to the binding strength of the counter ions, the swelling capacity of the clay, allowing the clay to clump, was also found to be an important factor for the controlled release of volatiles from the clay. Ion-exchange of the clay with lithium cations was found to be optimal in terms of ionic strength of the cation and swelling capacity, as compared to other metallic cations and small organic cations. This clay modification was tested on the release of malodorous compounds determined in cat urine by mass spectrometry and sniffing experiments. The smectite clay modified by ion-exchange with lithium cations showed improved controlled release of volatile organic compounds found in cat urine, compared to the sodium smectite, and improved clumping capacity compared to the calcium smectite. The calcium smectite clay used by Nestlé Purina could be modified by column exchange with lithium cations in high quantities. However the potential toxicity of the lithium is unknown. Additional information was obtained by ab initio calculations on the interaction of water with the smectite. The calculations of the binding of one to six water molecules on the surface of a sodium clay showed the water molecules bind to the cation and form hydrogen bonds between each other and with the clay oxygens, leading to the formation of different configurations for the same number of water molecules on the clay surface. With an increase in the number of water molecules on the surface of the clay, intermolecular interaction between the water molecules became gradually more important than sodium-water interactions. The binding energy was also found to be dependent on the location of the charge substitution in the clay (tetrahedral or octahedral) and to the formation of hydrogen bonds between the water molecule and a basal oxygen linked to a tetrahedral replacement. With an increase in the number of water molecules bound to one counter ion, the sodium counter ion was found to move away from the clay surface. The dynamic calculations of water molecules in the clay interlayer showed both the water molecules and the cations to be mobile. The average diffusion coefficient of the water molecules was reduced compared to that of bulk water, due to restrictions imposed by both the clay platelets and the counter ions. The structure of the water molecules showed to be similar to that of bulk water with a preferential orientation of their hydroxyl group almost perpendicular to the clay surface. The difference in the state of order of the water molecules around the sodium cation was interpreted as a symptom of hysteresis as observed in the measured equilibrium sorption isotherm.

EPFL2009

Analysis of nano-sized irradiation-induced defects in Fe-base materials by means of small angle neutron scattering and molecular dynamics simulations

Gang Yu

Thermonuclear fusion of light atoms is considered since decades as an unlimited, safe and reliable source of energy that could eventually replace classical sources based on fossile fuel or nuclear fuel. Fusion reactor technology and materials studies are important parts of the fusion energy development program. For the time being, the most promising materials for structural applications in the future fusion power reactors are the Reduced Activation Ferritic/Martensitic (RAFM) steels for which the greatest technology maturity has been achieved, i.e., qualified fabrication routes, welding technology and a general industrial experience are almost available. The most important issues concerning the future use of RAFM steels in fusion power reactors are derived from their irradiation by 14 MeV neutrons that are the product, together with 3.5 MeV helium ions, of the envisaged fusion reactions between deuterium and tritium nuclei. Indeed, exposure of metallic materials to intense fluxes of 14 MeV neutrons will result in the formation of severe displacement damage (about 20-30 dpa per year) and high amounts of helium, which are at the origin of significant changes in the physical and mechanical of materials, such as hardening and embrittlement effects, for instance. This PhD Thesis work was aimed at investigating how far the Small Angle Neutron Scattering (SANS) technique could be used for detecting and characterizing nano-sized irradiation-induced defects in RAFM steels. Indeed, the resolution limit of Transmission Electron Microscopy (TEM) is about 1 nm in weak beam TEM imaging, and it is usually thought that a large number of irradiation-induced effects have a size below 1 nm in RAFM steels and that these very small defects actually contribute to the irradiation-induced hardening and embrittlement of RAFM steels occurring at irradiation temperatures below about 400°C. The aim of this work was achieved by combing SANS experiments on unirradiated and irradiated specimens of RAFM steels with Molecular Dynamics (MD) simulations of main expected nano-sized defects in irradiated pure Fe and Fe-He alloys, as model materials for RAFM steels, and simulations of their corresponding TEM images and SANS signals. In particular, the SANS signal of various types of defects was simulated for the first time. The methodology used in this work was the following: SANS experiments were performed by applying a strong saturating magnetic field to unirradiated and irradiated specimens of three types of RAFM steels, namely the European EUROFER 97, the Japanese F82H and the Swiss OPTIMAX A steels. The available irradiated specimens included specimens which had been irradiated with 590 MeV protons in the Proton IRradiation EXperiment (PIREX) facility at the Paul Scherrer Institute (PSI) at temperatures in the range of 50-350°C to doses in the range of 0.3-2.0 dpa. SANS spectra as well as values of the so-called A ratio, which represents the ratio of the total scattered intensity to the nuclear scattered intensity, were obtained for the various irradiation doses and temperatures investigated. MD simulations of atomic displacement cascades in pure Fe and in Fe-He alloys were performed using Embedded Atom Method (EAM) many-body interatomic potentials. The main nano-sized defects that should be produced in RAFM steels under irradiation were created by means of MD in pure Fe. These included dislocation loops of various types, voids, helium bubbles with various He concentration and Cr precipitates. TEM images of cascade damage and all the defects created by MD were simulated in the dark field/weak beam imaging modes by using the Electron Microscopy Software (EMS) developed by P.A. Stadelmann (EPFL) and analyzed in terms of variations of contrast intensities versus depth inside the specimen. The SANS signal provided by cascade damage and all the defects created by MD was simulated by using a slightly modified version of EMS, accounting for neutrons instead of electrons. The SANS technique has been proven in this work to be a very powerful tool for detecting nano-sized irradiation-induced defects and a tool well complementary to TEM for characterizing such very small irradiation-induced defects. Indeed, TEM appears most adapted to investigate structural defects, such as dislocation loops and helium bubbles with high helium concentration, which yield significant lattice deformation of the surrounding matrix, while SANS is most adapted to investigate phase defects, such as voids, helium bubbles with low helium concentration and Cr precipitates. By combining the results of SANS experiments with those of MD simulations, TEM image simulations and SANS signal simulations, the nano-sized irradiation-induced defects were tentatively identified as small helium bubbles. While the radiation hardening measured for RAFM steels cannot be explained by accounting only for the defects observed in TEM, it could be successfully modeled by accounting also for a reasonable number density of the nano-sized defects evidenced using the SANS technique.

EPFL2008

Modeling non-covalent interactions in condensed phase

Veronika Juraskova

The modeling of non-covalent interactions, solvation effects, and chemical reactions in complex molecular environment is a challenging task. Current state-of-the-art approaches often rely on static computations using implicit solvent models and harmonic approximations. Owing to the rich interaction network characteristic of molecular species in the condensed phase, the neglect of the dynamic fluctuations and of the mutual competition with the solvent molecules often leads to an incomplete picture.While ab initio molecular dynamics can, in principle, capture all these effects, the associated computational cost requires compromising the accuracy of the electronic structure method and the statistical convergence of the simulation.The main objective of this thesis is to develop a robust simulation workflow based on neural network potentials and enhanced sampling techniques to describe molecules and reactions in complex environment. The validity and usefulness of the proposed workflow is illustrated on three applications: (a) the solvation environment and protonation state of a mixture of phenol, hydrogen peroxide and methanesulfonic acid relevant to catalyzed industrial phenol hydroxylation, (b) the extension of the above to model the hydroxylation reaction, and (c) the description of a chalcogen-bonded complex in tetrahydrofuran featuring multiple and heavy chemical elements as a potential route for anion transport and catalysis. The developed workflow is illustrated in detail through the first example, for which the solvation environment and protonation states are dominated by strongly competing hydrogen bonds. We demonstrate the relevance of relying upon surrogate neural network potentials, enhanced sampling techniques, and nuclear quantum effects to achieve an accurate description of the complex mixture. The second example extends the simulation pipeline, combining the neural network potentials with metadynamics to enable the modeling of the catalyzed phenol hydroxylation reaction with a special emphasis on its regioselectivity. Finally, the third example broadens the application of neural network potentials to the description of molecular systems containing up to seven chemical elements, which participate in very subtle and specific types of non-covalent interactions.Overall, this work highlights the potential of using neural network-based potentials to model complex reactive systems in condensed phase and to accurately describe competing non-covalent interactions. The developed workflow extends the range of applicability of ab initio molecular dynamics toolbox to real-life chemical systems.

EPFL2022