Molecular Simulation of the Impact of Defects on Electrolyte Intrusion in Zeolites.

We have investigated through molecular simulation the intrusion of electrolytes in two representative pure-silica zeolites, silicalite-1 and chabazite, in which point defects were introduced in varying amounts. We distinguish between two types of defects, considering either "weak" or "strong" silanol nest defects, resulting in different hydration behaviors. In the presence of weak defects, the hydration process occurs through a homogeneous nucleation process, while with strong defects, we observe an initial adsorption followed by a filling of the nanoporous volume at a higher pressure. However, we show that electrolytes do not penetrate the zeolites, and these defects appear to have only marginal influence on the thermodynamics of electrolyte intrusion. While replacing pure water by the electrolyte solution shifts the intrusion pressure toward higher values because of the drop of water saturation vapor pressure, an increase in hydrophilicity of the framework due to point defects has the opposite effect, showing that controlling the amount of defects in zeolites is crucial for storage energy applications.

[Rosai-Dorfman-Destombes disease with a misleading laryngeal presentation]. / Une maladie de Rosai­Dorfman­Destombes de présentation laryngée trompeuse.

Rosai-Dorfman-Destombes disease is a rare non-Langerhansian cell histiocytosis characterized by the accumulation of large activated histiocytes in the affected tissues with images of emperipolesis. The diagnosis is not really problematic in the classical forms, with a lymph node presentation, whose histology is very suggestive. However, it can be much more difficult in the extra-nodal forms, which are misleading in both their clinical and histological presentation. We report here a case illustrating this diagnostic difficulty. Firstly, clinically, the disease was revealed by an unusual laryngeal location, responsible for acute obstructive respiratory distress and requiring urgent surgical management. Secondly, histologically, the diagnosis was not evoked in the first instance by analysis of the laryngeal lesion. Indeed, there was a not specific appearing polymorphic infiltrate, associating small lymphocytes, plasma cells and numerous histiocytes, without evidence for a lymphoma after immunohistochemistry and lymphocyte clonality analysis. However, after re-examination of the slides, the histiocytes sometimes appeared large or xanthomised and have a PS100+, CD1a-, langerhine- phenotype, with rare images of emperipolesis. These aspects finally suggested the diagnosis of Rosai-Dorfman-Destombes disease, then confirmed by a cervical lymph node biopsy showing characteristic histological features. Simultaneously, NGS analysis of the laryngeal lesion showed a mutation in the MAP2K1 gene, in accordance with the diagnosis. The patient was treated with revlimid and dexamethasone for 6 months, with complete remission, and is currently undergoing maintenance treatment with revlimid.

Structure and Dynamics of Water Confined in Imogolite Nanotubes.

We have studied the properties of water adsorbed inside nanotubes of hydrophilic imogolite, an aluminum silicate clay mineral, by means of molecular simulations. We used a classical force field to describe the water and the flexible imogolite nanotube and validated it against the data obtained from first-principles molecular dynamics. With it, we observe a strong structuration of the water confined in the nanotube, with specific adsorption sites and a distribution of hydrogen bond patterns. The combination of number of adsorption sites, their geometry, and the preferential tetrahedral hydrogen bonding pattern of water leads to frustration and disorder. We further characterize the dynamics of the water, as well as the hydrogen bonds formed between water molecules and the nanotube, which is found to be more than 1 order of magnitude longer than water-water hydrogen bonds.

Forced intrusion of water and aqueous solutions in microporous materials: from fundamental thermodynamics to energy storage devices.

We review the high pressure forced intrusion studies of water in hydrophobic microporous materials such as zeolites and MOFs, a field of research that has emerged some 15 years ago and is now very active. Many of these studies are aimed at investigating the possibility of using these systems as energy storage devices. A series of all-silica zeolites (zeosil) frameworks were found suitable for reversible energy storage because of their stability with respect to hydrolysis after several water intrusion-extrusion cycles. Several microporous hydrophobic zeolite imidazolate frameworks (ZIFs) also happen to be quite stable and resistant towards hydrolysis and thus seem very promising for energy storage applications. Replacing pure water by electrolyte aqueous solutions enables to increase the stored energy by a factor close to 3, on account of the high pressure shift of the intrusion transition. In addition to the fact that aqueous solutions and microporous silica materials are environmental friendly, these systems are thus becoming increasingly interesting for the design of new energy storage devices. This review also addresses the theoretical approaches and molecular simulations performed in order to better understand the experimental behavior of nano-confined water. Molecular simulation studies showed that water condensation takes place through a genuine first-order phase transition, provided that the interconnected pores structure is 3-dimensional and sufficiently open. In an extreme confinement situations such as in ferrierite zeosil, condensation seem to take place through a continuous supercritical crossing from a diluted to a dense fluid, on account of the fact that the first-order transition line is shifted to higher pressure, and the confined water critical point is correlatively shifted to lower temperature. These molecular simulation studies suggest that the most important features of the intrusion/extrusion process can be understood in terms of equilibrium thermodynamics considerations.

Kinetic Accessibility of Porous Material Adsorption Sites Studied through the Lattice Boltzmann Method.

We present here a computational model based on the lattice Boltzmann scheme to investigate the accessibility of active adsorption sites in hierarchical porous materials to adsorbates in a flowing liquid. By studying the transport and adsorption of tracers after they enter the pore space of the virtual sample, we characterize their kinetics as they pass through the pore space and adsorb on the solid-liquid interface. The model is validated on simple geometries with a known analytical solution. We then use it to investigate the influence of regular grooves or disordered roughness on the walls of a slit pore geometry, looking at the impact on adsorption and transport. In particular, we highlight the importance of adsorption site accessibility, which depends on the shape and connectivity of the pore space as well as the fluid flow profile and velocity.

Transport and adsorption under liquid flow: the role of pore geometry.

We study here the interplay between transport and adsorption in porous systems with complex geometries under fluid flow. Using a lattice Boltzmann scheme extended to take into account the adsorption at solid/fluid interfaces, we investigate the influence of pore geometry and internal surface roughness on the efficiency of fluid flow and the adsorption of molecular species inside the pore space. We show how the occurrence of roughness on pore walls acts effectively as a modification of the solid/fluid boundary conditions, introducing slippage at the interface. We then compare three common pore geometries, namely honeycomb pores, inverse opal, and materials produced by spinodal decomposition. Finally, we quantify the influence of those three geometries on fluid transport and tracer adsorption. This opens perspectives for the optimization of materials' geometries for applications in dynamic adsorption under fluid flow.

Mutation in Brachypodium caffeic acid O-methyltransferase 6 alters stem and grain lignins and improves straw saccharification without deteriorating grain quality.

Cereal crop by-products are a promising source of renewable raw material for the production of biofuel from lignocellulose. However, their enzymatic conversion to fermentable sugars is detrimentally affected by lignins. Here the characterization of the Brachypodium Bd5139 mutant provided with a single nucleotide mutation in the caffeic acid O-methyltransferase BdCOMT6 gene is reported. This BdCOMT6-deficient mutant displayed a moderately altered lignification in mature stems. The lignin-related BdCOMT6 gene was also found to be expressed in grains, and the alterations of Bd5139 grain lignins were found to mirror nicely those evidenced in stem lignins. The Bd5139 grains displayed similar size and composition to the control. Complementation experiments carried out by introducing the mutated gene into the AtCOMT1-deficient Arabidopsis mutant demonstrated that the mutated BdCOMT6 protein was still functional. Such a moderate down-regulation of lignin-related COMT enzyme reduced the straw recalcitrance to saccharification, without compromising the vegetative or reproductive development of the plant.

Endomembrane proteomics reveals putative enzymes involved in cell wall metabolism in wheat grain outer layers.

Cereal grain outer layers fulfil essential functions for the developing seed such as supplying energy and providing protection. In the food industry, the grain outer layers called 'the bran' is valuable since it is rich in dietary fibre and other beneficial nutriments. The outer layers comprise several tissues with a high content in cell wall material. The cell wall composition of the grain peripheral tissues was investigated with specific probes at a stage of active cell wall synthesis. Considerable wall diversity between cell types was revealed. To identify the cellular machinery involved in cell wall synthesis, a subcellular proteomic approach was used targeting the Golgi apparatus where most cell wall polysaccharides are synthesized. The tissues were dissected into outer pericarp and intermediate layers where 822 and 1304 proteins were identified respectively. Many carbohydrate-active enzymes were revealed: some in the two peripheral grain fractions, others only in one tissue. Several protein families specific to one fraction and with characterized homologs in other species might be related to the specific detection of a polysaccharide in a particular cell layer. This report provides new information on grain cell walls and its biosynthesis in the valuable outer tissues, which are poorly studied so far. A better understanding of the mechanisms controlling cell wall composition could help to improve several quality traits of cereal products (e.g. dietary fibre content, biomass conversion to biofuel).

Unexpected coupling between flow and adsorption in porous media.

We study the interplay between transport and adsorption in porous systems under a fluid flow, based on a lattice Boltzmann scheme extended to account for adsorption. We performed simulations on well-controlled geometries with slit and grooved pores, investigating the influence of adsorption and flow on dispersion coefficient and adsorbed density. In particular, we present a counterintuitive effect where fluid flow induces heterogeneity in the adsorbate, displacing the adsorption equilibrium towards downstream adsorption sites in grooves. We also present an improvement of the adsorption-extended lattice Boltzmann scheme by introducing the possibility for saturating Langmuir-like adsorption, while earlier work focused on linear adsorption phenomena. We then highlight the impact of this change in situations of high concentration of adsorbate.

The E domains of pentatricopeptide repeat proteins from different organelles are not functionally equivalent for RNA editing.

RNA editing in plants is an essential post-transcriptional process that modifies the genetic information encoded in organelle genomes. Forward and reverse genetics approaches have revealed the prevalent role of pentatricopeptide repeat (PPR) proteins in editing in both plastids and mitochondria, confirming the shared origin of this process in both organelles. The E domain at or near the C terminus of these proteins has been shown to be essential for editing, and is presumed to recruit the enzyme that deaminates the target cytidine residue. Here, we describe two mutants, otp71 and otp72, disrupted in genes encoding mitochondrial E-type PPR proteins with single editing defects in ccmFN 2 and rpl16 transcripts, respectively. Comparisons between the E domains of these proteins and previously reported editing factors from chloroplasts suggested that there are characteristic differences in the proteins between the two organelles. To test this, we swapped E domains between two mitochondrial and two chloroplast editing factors. In all cases investigated, E domains from the same organelle (chloroplast or mitochondria) were found to be exchangeable; however, swapping the E domain between organelles led to non-functional editing factors. We conclude that the E domains of mitochondrial and plastid PPR proteins are not functionally equivalent, and therefore that an important component of the putative editing complexes in the two organelles may be different.

Remarkable pressure responses of metal-organic frameworks: proton transfer and linker coiling in zinc alkyl gates.

Metal-organic frameworks demonstrate a wide variety of behavior in their response to pressure, which can be classified in a rather limited list of categories, including anomalous elastic behavior (e.g., negative linear compressibility, NLC), transitions between crystalline phases, and amorphization. Very few of these mechanisms involve bond rearrangement. Here, we report two novel piezo-mechanical responses of metal-organic frameworks, observed under moderate pressure in two materials of the zinc alkyl gate (ZAG) family. Both materials exhibit NLC at high pressure, due to a structural transition involving a reversible proton transfer between an included water molecule and the linker's phosphonate group. In addition, the 6-carbon alkyl chain of ZAG-6 exhibits a coiling transition under pressure. These phenomena are revealed by combining high-pressure single-crystal X-ray crystallography and quantum mechanical calculations. They represent novel pressure responses for metal-organic frameworks, and pressure-induced proton transfer is a very rare phenomenon in materials in general.

Reorientational dynamics of water confined in zeolites.

We present a detailed molecular-dynamics study of water reorientation and hydrogen-bond dynamics in a strong confinement situation, within the narrow pores of an all-silica Linde type A (LTA) zeolite. Two water loadings of the zeolite are compared with the bulk case. Water dynamics are retarded in this extreme hydrophobic confinement and the slowdown is more pronounced at higher water loading. We show that water reorientation proceeds mainly by large-amplitude angular jumps, whose mechanism is similar to that determined in the bulk. The slowdown upon hydrophobic confinement arises predominantly from an excluded-volume effect on the large fraction of water molecules lying at the interface with the zeolite matrix, with an additional minor contribution coming from a structuring effect induced by the confinement.

What makes zeolitic imidazolate frameworks hydrophobic or hydrophilic? The impact of geometry and functionalization on water adsorption.

We demonstrate, by means of Grand Canonical Monte Carlo simulation on different members of the ZIF family, how topology, geometry, and linker functionalization drastically affect the water adsorption properties of these materials, tweaking the ZIF materials from hydrophobic to hydrophilic. We show that adequate functionalization of the linkers allows one to tune the host-guest interactions, even featuring dual amphiphilic materials whose pore space features both hydrophobic and hydrophilic regions. Starting from an initially hydrophobic material (ZIF-8), various degrees of hydrophilicity could be obtained, with a gradual evolution from a type V adsorption isotherm in the liquid phase to a type I isotherm in the gas phase. This behavior is similar to what was described earlier in families of hydrophobic all-silica zeolites, with hydrophilic "defects" of various strength, such as silanol nests or the presence of extra-framework cations.

Challenges in first-principles NPT molecular dynamics of soft porous crystals: a case study on MIL-53(Ga).

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material.

Investigation of structure and dynamics of the hydrated metal-organic framework MIL-53(Cr) using first-principles molecular dynamics.

The hydration behavior of metal-organic frameworks (MOFs) is of interest both from a practical and from a fundamental point of view: it is linked, on the one hand, to the hydrothermal stability (or instability) of the nanoporous material, which might limit its use in technological applications. On the other hand, it sheds light on the behavior of water in a strongly confined environment. Here, we use first-principles molecular dynamics (MD) to investigate two hydrated phases of the flexible MOF MIL-53(Cr), which adopts a narrow- or a large-pore form, depending on the water loading. Structure and dynamics of the two phases are thoroughly analyzed and compared, with a focus on the hydroxyl group of MIL-53(Cr) and the water molecules in the nanopores. Furthermore, the behavior of the confined water is compared to that of bulk water. Whereas in the narrow-pore form, water is adsorbed at specific crystalline sites, it shows a more disordered, bulk-like structure in the large-pore form. However, reorientation dynamics of water molecules in the latter is considerably slowed down with respect to bulk water, which highlights the confinement effect of the nanoporous framework.

Adsorption induced transitions in soft porous crystals: an osmotic potential approach to multistability and intermediate structures.

Soft porous crystals are flexible metal-organic frameworks that respond to physical stimuli (temperature, pressure, and gas adsorption) by large changes in their structure and unit cell volume. We propose here a thermodynamic treatment, based on the osmotic ensemble, of the interplay between guest adsorption and host deformation, where the bare host material can undergo elastic deformation, as well as structural transitions between metastable phases in the case of a multistable material. We show that in addition to structural transitions between metastable phases of bistable or multistable host frameworks, a new guest-stabilized host phase can be created when the size of the adsorbate is larger than the empty material's pore size. We then confront the findings of our approach with experimental data for systems exhibiting phenomena such as gate opening and breathing.

Alchemical Osmostat for Monte Carlo Simulation: Sampling Aqueous Electrolyte Solution in Open Systems.

Molecular simulations involving electrolytes are usually performed at a fixed amount of salt ions in the simulation box, reproducing macroscopic concentration. Although this statement is valid in the bulk, the concentration of an electrolyte confined in nanoporous materials such as MOFs or zeolites is greatly affected and remains a priori unknown. The nanoporous material in equilibrium with the bulk electrolyte exchange water and ions at a given chemical potential Δµ in the semi-grand-canonical ensemble, that must be calibrated in order to determine the concentration in the nanoporous material. In this work, we propose an algorithm based on nonequilibrium candidate Monte Carlo (NCMC) moves to ultimately perform MC simulations in contact with a saline reservoir. First, we adapt the Widom insertion technique to calibrate the chemical potential by alchemically transmuting water molecules into ions by using NCMC moves. The chemical potential defines a Monte Carlo osmostat in the semi-grand-constant volume and temperature ensemble (Δµ, N, V, T) to be added in a Monte Carlo simulation where the number of ions fluctuates. In order to validate the method, we adapted the NCMC move to determine the free energy of water solvation and subsequently explore thermodynamics of electrolyte solvation at infinite dilution in water. Finally, we implemented the osmostat in MC simulations initialized with bulk water that are driven toward electrolyte solutions of similar concentration as the saline reservoir. Our results demonstrate that alchemical osmostat for MC simulation is a promising tool for use to sample electrolyte insertion in nanoporous materials.

New Growth-Related Features of Wheat Grain Pericarp Revealed by Synchrotron-Based X-ray Micro-Tomography and 3D Reconstruction.

Wheat (Triticum aestivum L.) is one of the most important crops as it provides 20% of calories and proteins to the human population. To overcome the increasing demand in wheat grain production, there is a need for a higher grain yield, and this can be achieved in particular through an increase in the grain weight. Moreover, grain shape is an important trait regarding the milling performance. Both the final grain weight and shape would benefit from a comprehensive knowledge of the morphological and anatomical determinism of wheat grain growth. Synchrotron-based phase-contrast X-ray microtomography (X-ray µCT) was used to study the 3D anatomy of the growing wheat grain during the first developmental stages. Coupled with 3D reconstruction, this method revealed changes in the grain shape and new cellular features. The study focused on a particular tissue, the pericarp, which has been hypothesized to be involved in the control of grain development. We showed considerable spatio-temporal diversity in cell shape and orientations, and in tissue porosity associated with stomata detection. These results highlight the growth-related features rarely studied in cereal grains, which may contribute significantly to the final grain weight and shape.

OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1.

Over 20 proteins of the pentatricopeptide repeat (PPR) family have been demonstrated to be involved in RNA editing in plant mitochondria and chloroplasts. All of these editing factors contain a so-called 'E' domain that has been shown to be essential for editing to occur. The presumption has been that this domain recruits the (unknown) editing enzyme to the RNA. In this report, we show that not all putative E-class PPR proteins are directly involved in RNA editing. Disruption of the OTP70 gene leads to a strong defect in splicing of the plastid transcript rpoC1, leading to a virescent phenotype. The mutant has a chloroplast transcript pattern characteristic of a reduction in plastid-encoded RNA polymerase activity. The E domain of OTP70 is not required for splicing, and can be deleted or replaced by the E domain from the known editing factor CRR4 without loss of rpoC1 splicing. Furthermore, the E domain of OTP70 is incapable of inducing RNA editing when fused to the RNA binding domain of CRR4. We conclude that the truncated E domain of OTP70 is no longer functional in RNA editing, and that the protein has acquired a new function in promoting RNA splicing.