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Principal Component Analysis (PCA) for Powder Diffraction Data: Towards Unblinded Applications
Laboratoire Institut des Matériaux Poreux de Paris - Dmitry Chernyshov, Iurii Dovgaliuk, Vadim Dyadkin and Wouter van Beek
CRYSTALS - 10 7 - https://doi.org/10.3390/cryst10070581 - 2020
We analyze the application of Principal Component Analysis (PCA) for untangling the main contributions to changing diffracted intensities upon variation of site occupancy and lattice dimensions induced by external stimuli. The information content of the PCA output consists of certain functions of Bragg angles (loadings) and their evolution characteristics that depend on external variables like pressure or temperature (scores). The physical meaning of the PCA output is to date not well understood. Therefore, in this paper, the intensity contributions are first derived analytically, then compared with the PCA components for model data; finally PCA is applied for the real data on isothermal gas uptake by nanoporous framework γ –Mg(BH 4 ) 2 . We show that, in close agreement with previous analysis of modulation diffraction, the variation of intensity of Bragg lines and the displacements of their positions results in a series of PCA components. Every PCA extracted component may be a mixture of terms carrying information on the average structure, active sub-structure, and their cross-term. The rotational ambiguities, that are an inherently part of PCA extraction, are at the origin of the mixing. For the experimental case considered in the paper, the extraction of the physically meaningful loadings and scores can only be achieved with a rotational correction. Finally, practical recommendations for non-blind applications, i.e., what boundary conditions to apply for the the rotational correction, of PCA for diffraction data are given.
Non-Isothermal Kinetics of Kr Adsorption by Nanoporous γ-Mg(BH4)2 from in Situ Synchrotron Powder Diffraction
Laboratoire Institut des Matériaux Poreux de Paris - Iurii Dovgaliuk*, Vadim Dyadkin, Mathieu Vander Donckt, Yaroslav Filinchuk*, and Dmitry Chernyshov
ACS Publications - 12(6) 7710–7716 - https://doi.org/10.1021/acsami.9b19239 - 2020
Crystalline materials with pore dimensions comparable to the kinetic diameters of the guest molecules are attractive for their potential use in adsorption and separation applications. The nanoporous γ-Mg(BH4)2 features one-dimensional channels matching this criterion for Kr uptake, which has been probed using synchrotron powder diffraction at various pressures and temperatures. It results in two coexisting crystalline phases with the limiting composition Mg(BH4)2·0.66Kr expecting the highest Kr content (50.7 wt % in the crystalline phase) reported for porous materials. Quasi-equilibrium isobars built from Rietveld refinements of Kr site occupancies were rationalized with a noncooperative lattice gas model, yielding the values of the thermodynamic parameters. The latter were independently confirmed from Kr fluorescence. We have also parameterized the pronounced kinetic hysteresis with a modified mean-field model adopted for the Arrhenius kinetics.
Factors Determining Microporous Material Stability in Water: The Curious Case of SAPO-37
Laboratoire Institut des Matériaux Poreux de Paris - Georgios N. Kalantzopoulos, Fredrik Lundvall, Knut Thorshaug, Anna Lind, Ponniah Vajeeston, Iurii Dovgaliuk, Bjørnar Arstad, David S. Wragg, and Helmer Fjellvåg
ACS Publications - 32(4) 1495–1505 - https://doi.org/10.1021/acs.chemmater.9b04510 - 2020
Silicoaluminophosphates (SAPOs) are a special class of zeolites that, due to their acidic and shape-selective properties, play a major role in ion exchange and separation processes and in crude oil cracking. SAPO-37 has the faujasite (FAU) topology same as zeolites X and Y, which are involved in more than 40% of the total crude oil conversion worldwide. A critical parameter that promotes detrimental structural transformations in SAPOs during real-life applications is the presence of humidity. In this study, we employ a multidisciplinary approach combining in situ synchrotron radiation powder X-ray diffraction (SR-PXRD), water adsorption, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and density functional theory (DFT) calculations to describe the mechanism and reveal the reasons why SAPO-37 collapses upon contact with humidity below 345 K. SR-PXRD revealed that the sodalite (SOD) cages (subunits of the FAU structure) have the strongest affinity to water during hydration below 345 K. Furthermore, below 345 K, the faujasite framework takes up an order of magnitude more water molecules than at temperatures above 345 K. DRIFTS confirmed the presence of Si–OH and P–OH surface structural defects that act as hydration centers, accelerating the loss of a long-range order. Finally, DFT calculations showed that the enthalpy of water adsorption in the sodalite cage and the faujasite supercage is −212 and −13 kJ/mol, respectively. The results presented in this work are highly topical for understanding the effect of water on the frameworks of the SAPO microporous catalysts family. The notorious instability of SAPO-37 is the result of the accumulative contribution of topological, physical, and chemical effects, leading to an array of rapidly evolving cascading effects. Our work shows how advancements in SR-PXRD methodology and hardware give new insight into highly dynamic features previously difficult to observe. In addition, this work introduces the conceptual insight that nonhomogeneous sorption of molecular species will induce dynamic features with dramatic consequences at both molecular and atomic levels. This is a highly impactful factor opening research paths for further work within catalysis, porous material design and chemistry, and sorption reactions and processes.
Metal-organic magnets with large coercivity and ordering temperatures up to 242°C
Laboratoire Institut des Matériaux Poreux de Paris - Panagiota Perlepe, Itziar Oyarzabal, Aaron Mailman4, Morgane Yquel, Mikhail
Science - 370(6516) 587-592 - DOI: 10.1126/science.abb3861 - 2020
Permanent magnets are generally produced from solid metals or alloys. Less dense compositions involving lighter elements tend to demagnetize well below room temperature or under modest applied external fields. Perlepe et al. now report that chemical reduction of a low-density chromium-pyrazine network produces a magnet that remains stable above 200°C and resists demagnetization with 7500-oersted coercivity at room temperature. The straightforward synthetic route to the material shows promise for broad exploration of potential applications.
Kinetic Barriers and Microscopic Mechanisms of Noble Gas Adsorption by Nanoporous γ‐Mg(BH4)2 Obtained by means of Sub‐Second X‐Ray Diffraction
Laboratoire Institut des Matériaux Poreux de Paris - Iurii Dovgaliuk Irena Senkovska Xiao Li Vadim Dyadkin Yaroslav Filinchuk Dmitry Chernyshov
Angew. Chem. Int. Ed - - https://doi.org/10.1002/anie.202015019 - 2020
Gas adsorption by porous frameworks sometimes result in structure “breathing”, “pores opening/closing”, “negative gas adsorption”, and other fascinating phenomena which can be revealed and explained with the use of in situ diffraction methods. The time‐dependent diffraction is able to address both kinetics of the guest uptake and structural response of the host framework, since the time evolution of the crystal structure bears the information on the mechanisms and kinetic barriers of guest adsorption. Using such advanced sub‐second in situ powder X‐ray diffraction, three various intracrystalline diffusion scenarios have been evaluated from the isothermal kinetics of Ar, Kr, and Xe adsorption by nanoporous γ‑Mg(BH4)2. These scenarios are dictated by two possible simultaneous transport mechanisms: diffusion through the intra‐ (i) and interchannel apertures (ii) of γ‐Mg(BH4)2 crystal structure. The contribution of i and ii changes depending on the kinetic diameter of the noble gas molecule and temperature regime. The lowest single activation barrier for the smallest Ar suggests equal diffusion of the atoms trough both pathways. Contrary, for the medium sized Kr we resolve the contributions of two parallel transport mechanisms, which tentatively can be attributed to the smaller barrier of the migration paths via the channel like pores and the higher barrier for the diffusion via narrow aperture between these channels. Remarkably, the largest Xe atoms diffuse only along 1D channels and show the highest single activation barrier. This work demonstrates a potential of sub‐second diffraction to access site‐specific kinetics of guest uptake in multi‐adsorption site frameworks.

A Robust Titanium Isophthalate Metal-Organic Framework for Visible-Light Photocatalytic CO2 Methanation
Laboratoire Institut des Matériaux Poreux de Paris - Sujing Wang Maria Cabrero-Antonino SergioNavalón Chen-chenCao AntoineTissot IuriiDovgaliuk JérômeMarrot CharlotteMartineau-Corcos LiangYu HaoWang WilliamShepard HermenegildoGarcía ChristianSerre1
Science - - https://doi.org/10.1016/j.chempr.2020.10.017 - 2020
Isophthalic acid (IPA) has been considered to build metal-organic frameworks (MOFs), owing to its facile availability, unique connection angle-mode, and a wide range of functional groups attached. Constructing titanium-IPA frameworks that possess photoresponse properties is an alluring characteristic with respect to the challenge of synthesizing new titanium-based MOFs (Ti-MOFs). Here, we report the first Ti-IPA MOF (MIP-208) that efficiently combines the use of preformed Ti8 oxoclusters and in situ acetylation of the 5-NH2-IPA linker. The mixed solid-solution linkers strategy was successfully applied, resulting in a series of multivariate MIP-208 structures with tunable chemical environments and sizable porosity. MIP-208 shows the best result among the pure MOF catalysts for the photocatalytic methanation of carbon dioxide. To improve the photocatalytic performance, ruthenium oxide nanoparticles were photo-deposited on MIP-208, forming a highly active and selective composite catalyst, MIP-208@RuOx, which features a notable visible-light response coupled with excellent stability and recycling ability.
A Mesoporous Zirconium-Isophthalate Multifunctional Platform
Laboratoire Institut des Matériaux Poreux de Paris - Ilich A.Ibarra, AídaGutiérrez-Alejandre, Ji Sun Lee, Jong-SanChang, ZhengLiu JérômeMarrot, WilliamShepard, GuillaumeMaurin, QiangXu, ChristianSerre
MATTER - - https://doi.org/10.1016/j.matt.2020.10.009 - 2020
Mesoporous materials suffer from poor crystallinity and hydrolytic stability, lack of chemical diversity, insufficient pore accessibility, complex synthesis, and toxicity issues. Here the association of Zr-oxo clusters and isophthalate via a homometallic-multicluster-dot strategy results in a robust mesoporous metal-organic framework, denoted as MIP-206 (MIP stands for materials of the Institute of Porous Materials of Paris), that overcomes the aforementioned limitations. MIP-206, with a combination of Zr6 and Zr12 oxo-cluster inorganic building units into a single structure, exhibits meso-channels of ca. 2.6 nm and displays excellent chemical stability. Owing to the abundant variety of functionalized isophthalic acid linkers, the chemical environment of MIP-206 can be tuned without hampering pore accessibility. MIP-206 loaded with palladium nanoparticles acts as an efficient and durable catalyst for the dehydrogenation of formic acid, outperforming benchmark mesoporous materials. This paves the way toward the utilization of MIP-206 as a mesoporous platform for a wide range of potential applications.
Formation of a Single Crystal Aluminum Based MOF Nanowire with Graphene Oxide Nanoscrolls as Structure& Directing Agents
Laboratoire Institut des Matériaux Poreux de Paris - Dr. Mégane Muschi Anusha Lalitha Dr. Saad Sene Dr. Damien Aureau Dr. Mathieu Fregnaux Dr. Imène Esteve Dr. Lucie Rivier Dr. Naseem Ramsahye
Angew. Chem. Int. Ed - 59(26) - https://doi.org/10.1002/anie.202000795 - 2020
An innovative strategy is proposed to synthesize single‐crystal nanowires (NWs) of the Al3+ dicarboxylate MIL‐69(Al) MOF by using graphene oxide nanoscrolls as structure‐directing agents. MIL‐69(Al) NWs with an average diameter of 70±20 nm and lengths up to 2 μm were found to preferentially grow along the [001] crystallographic direction. Advanced characterization methods (electron diffraction, TEM, STEM‐HAADF, SEM, XPS) and molecular modeling revealed the mechanism of formation of MIL‐69(Al) NWs involving size‐confinement and templating effects. The formation of MIL‐69(Al) seeds and the self‐scroll of GO sheets followed by the anisotropic growth of MIL‐69(Al) crystals are mediated by specific GO sheets/MOF interactions. This study delivers an unprecedented approach to control the design of 1D MOF nanostructures and superstructures.
Tuning Cellular Biological Functions Through the Controlled Release of NO from a Porous Ti‐MOF
Laboratoire Institut des Matériaux Poreux de Paris - Rosana V. Pinto Dr. Sujing Wang Dr. Sergio R. Tavares Prof. João Pires Prof. Fernando Antunes Dr. Alexandre Vimont Prof. Guillaume Clet Prof. Marco Daturi
Angew. Chem. Int. Ed - 59(13) - https://doi.org/10.1002/anie.201913135 - 2020
Materials for the controlled release of nitric oxide (NO) are of interest for therapeutic applications. However, to date, many suffer from toxicity and stability issues, as well as poor performance. Herein, we propose a new NO adsorption/release mechanism through the formation of nitrites on the skeleton of a titanium‐based metal–organic framework (MOF) that we named MIP‐177, featuring a suitable set of properties for such an application: (i) high NO storage capacity (3 μmol mg−1solid), (ii) excellent biocompatibility at therapeutic relevant concentrations (no cytotoxicity at 90 μg mL−1 for wound healing) due to its high stability in biological media (<9 % degradation in 72 hours) and (iii) slow NO release in biological media (≈2 hours for 90 % release). The prospective application of MIP‐177 is demonstrated through NO‐driven control of mitochondrial respiration in cells and stimulation of cell migration, paving the way for the design of new NO delivery systems for wound healing therapy.
Encapsulation of Microperoxidase-8 in MIL-101(Cr)-X Nanoparticles: Influence of Metal–Organic Framework Functionalization on Enzymatic Immobilization and Catalytic Activity
Laboratoire Institut des Matériaux Poreux de Paris - Effrosyni Gkaniatsou, Rémy Ricoux*, Kalani Kariyawasam, Ingrid Stenger, Benhui Fan, Narjès Ayoub, Samanta Salas, Gilles Patriarche, Christian Serre, Jean-Pierre Mahy, Nathalie Steunou, and Clémence Sicard
ACS Publications - 3(4) 3233–3243 - https://doi.org/10.1021/acsanm.9b02464 - 2020
Microperoxidase 8 (MP8) was immobilized within MIL-101(Cr) bearing terephthalate linkers with functionalized groups (-NH2 and -SO3H). A synthesis protocol for MIL-101(Cr)-SO3H that avoids the use of toxic Cr(VI) and HF was developed. The electrostatic interactions between the MP8 molecules and the MOF matrices were found to be crucial for a successful immobilization. Raman spectroscopy revealed the dispersion of the immobilized MP8 molecules in MIL-101(Cr)-X matrices as monomers without aggregation. The presence of functional groups resulted in higher amounts of immobilized MP8 in comparison to the bare MIL-101(Cr). The catalytic activity of MP8@MIL-101(Cr)-NH2 per material mass was higher than that for MP8@MIL-101(Cr). The presence of free amino groups can thus improve the immobilization efficiency, leading to a higher amount of catalytically active species and improving the subsequent catalytic activity of the heterogeneous biocatalysts. MP8@MIL(Cr)-X also successfully catalyzed the selective oxidation of thioanisole derivatives into sulfoxides
Toward a Rational Design of Titanium Metal-Organic Frameworks
Laboratoire Institut des Matériaux Poreux de Paris - Author links open overlay panelSujingWang128HelgeReinsch3NicolasHeymans4MohammadWahiduzzaman5CharlotteMartineau-Corcos67GuyDe Weireld4GuillaumeMaurin5ChristianSerre1
MATTER - 2(2) 440-450 - https://doi.org/10.1016/j.matt.2019.11.002 - 2020
Rational design and synthesis of metal-organic frameworks (MOFs) is of particular interest in fine-tuning the crystalline structures for given targeting applications. Considerable advance of this topic has been achieved for MOFs built with a large number of metal species but not titanium. The complex and unpredictable titanium chemistry in solution not only leads to the difficulty of isolating crystalline Ti-MOFs via direct synthesis but also results in the challenge of maintaining control over ordered structures. We demonstrated a Ti-O cluster guided green scalable preparation of a Ti-MOF (MIP-207) in a controlled manner with both post-synthetic and one-pot reaction routes. The chemical environment and functionality of the MOF structural void could be easily tuned by adopting the mixed-linker strategy, which finally resulted in an adjustable performance in CO2 capture over N2. This provides a new avenue for the rational design of Ti-MOFs in energy- and environment-related applications.
Highly Porous Hybrid Metal–Organic Nanoparticles Loaded with Gemcitabine Monophosphate: a Multimodal Approach to Improve Chemo‐ and Radiotherapy
Laboratoire Institut des Matériaux Poreux de Paris - Dr. Xue Li Dr. Erika Porcel Dr. Mario Menendez‐Miranda Jingwen Qiu Xiaomin Yang Dr. Christian Serre Alexandra Pastor Dr. Didier Desmaële
ChemMedChem - 15(3) - https://doi.org/10.1002/cmdc.201900596 - 2020
Nanomedicine recently emerged as a novel strategy to improve the performance of radiotherapy. Herein we report the first application of radioenhancers made of nanoscale metal‐organic frameworks (nanoMOFs), loaded with gemcitabine monophosphate (Gem‐MP), a radiosensitizing anticancer drug. Iron trimesate nanoMOFs possess a regular porous structure with oxocentered Fe trimers separated by around 5 Å (trimesate linkers). This porosity is favorable to diffuse the electrons emitted from nanoMOFs due to activation by γ radiation, leading to water radiolysis and generation of hydroxyl radicals which create nanoscale damages in cancer cells. Moreover, nanoMOFs act as “Trojan horses”, carrying their Gem‐MP cargo inside cancer cells to interfere with DNA repair. By displaying different mechanisms of action, both nanoMOFs and incorporated Gem‐MP contribute to improve radiation efficacy. The radiation enhancement factor of Gem‐MP loaded nanoMOFs reaches 1.8, one of the highest values ever reported. These results pave the way toward the design of engineered nanoparticles in which each component plays a role in cancer treatment by radiotherapy.
Methanol and Humidity Capacitive Sensors Based on Thin Films of MOF Nanoparticles
Laboratoire Institut des Matériaux Poreux de Paris - Miguel A. Andrés, Mani Teja Vijjapu, Sandeep G. Surya, Osama Shekhah, Khaled Nabil Salama, Christian Serre, Mohamed Eddaoudi, Olivier Roubeau, and Ignacio Gascón
ACS Publications - 12(3) 4155–4162 - https://doi.org/10.1021/acsami.9b20763 - 2020
The successful development of modern gas sensing technologies requires high sensitivity and selectivity coupled to cost effectiveness, which implies the necessity to miniaturize devices while reducing the amount of sensing material. The appealing alternative of integrating nanoparticles of a porous metal–organic framework (MOF) onto capacitive sensors based on interdigitated electrode (IDE) chips is presented. We report the deposition of MIL-96(Al) MOF thin films via the Langmuir–Blodgett (LB) method on the IDE chips, which allowed the study of their gas/vapor sensing properties. First, sorption studies of several organic vapors like methanol, toluene, chloroform, etc. were conducted on bulk MOF. The sorption data revealed that MIL-96(Al) presents high affinity toward water and methanol. Later on, ordered LB monolayer films of MIL-96(Al) particles of ∼200 nm were successfully deposited onto IDE chips with homogeneous coverage of the surface in comparison to conventional thin film fabrication techniques such as drop-casting. The sensing tests showed that MOF LB films were selective for water and methanol, and short response/recovery times were achieved. Finally, chemical vapor deposition (CVD) of a porous thin film of Parylene C (thickness ∼250–300 nm) was performed on top of the MOF LB films to fabricate a thin selective layer. The sensing results showed an increase in the water selectivity and sensitivity, while those of methanol showed a huge decrease. These results prove the feasibility of the LB technique for the fabrication of ordered MOF thin films onto IDE chips using very small MOF quantities.
Hexane isomers separation on an isoreticular series of microporous Zr carboxylate metal organic frameworks
Laboratoire Institut des Matériaux Poreux de Paris - Adriano Henrique, Tanmoy Maity, Hengli Zhao, de Pedro F. Brântuas, Alírio E. Rodrigues, Farid Nouar, Aziz Ghoufi, Guillaume Maurin, José A. C. Silva and Christian Serre
journal of materials chemistry A - 8 17780-17789 - https://doi.org/10.1039/D0TA05538G - 2020
A series of isoreticular Zr carboxylate MOFs, MIL-140A, B and C, exhibiting 1D microporous triangular shaped channels and based on different aromatic dicarboxylate ligands (1,4-BDC, 2,6-NDC and 4,4′-BPDC, respectively), were investigated by chromatographic breakthrough experiments regarding their ability to separate hexane isomers (nC6/2MP/3MP/23DMB/22DMB). Both single and equimolar multicomponent experiments were performed at the temperatures 343, 373, and 423 K and a total hydrocarbon pressure up to 50.0 kPa using the MIL-140B form. The elution order is similar to that of the normal boiling point of the compounds nC6 > 2MP > 3MP > 23DMB > 22DMB. It is noteworthy that this material enables separation of the hexane isomers by class, linear > mono-branched > di-branched, with a selectivity (linear + mono-branched isomers/di-branched isomers) up to 10 at 343 K, decreasing, however, as the temperature increases. Grand canonical Monte Carlo simulations were further performed to gain insight into the adsorption/separation mechanisms, highlighting the crucial need to consider a tiny tilting of the organic linkers for capturing the experimental observations. The impact of the pore size was finally assessed through the comparison with MIL-140A and MIL-140C, respectively, based on multicomponent experiments at 343 K. We evidenced a significant decrease of the selectivity (about 2) in both cases while the loadings were decreased or increased for MIL-140A and MIL-140C, respectively. Additionally, MIL-140C was demonstrated to exhibit an uncommon shift in the elution order occurring between nC6 and 3MP, 3MP being the last compound to saturate in the column.
First Example of Protonation of Ruddlesden–Popper Sr 2 IrO 4 : A Route to Enhanced Water Oxidation Catalysts
Laboratoire Institut des Matériaux Poreux de Paris - Ronghuang Zhang, Paul E. Pearce, Vanessa Pimenta, Jordi Cabana, Heifang Li, Daniel Alves Dalla Corte, Artem M. Abakumov, Gwenaëlle Rousse, Domitille Giaume, Michael Deschamps, and Alexis Grimaud
Chemistry of Materials, American Chemical Society - 32 (8) 3499-3509 - https://doi.org/10.1021/acs.chemmater.0c00432 - 2020
Water electrolysis is considered to be a promising way to store and convert excess renewable energies into hydrogen, which is of high value for many chemical transformation processes such as the Haber-Bosch process. The main challenge to promote the deployment of the polymer electrolyte membrane water electrolysis (PEMWE) technology lies in the design of robust catalysts for the oxygen evolution reaction (OER) under acidic conditions, since most of the transition metal-based oxides undergo structural degradation under these harsh acidic conditions. To broaden the variety of candidate materials as OER catalysts, a cation-exchange synthetic route was recently explored to reach crystalline pronated iridates with unique structural properties and stability. In this work, a new protonated phase H3.6IrO4·3.7H2O, prepared via Sr2+/H+ cation exchange at room temperature starting from the parent Ruddlesden–Popper Sr2IrO4 phase, is described. This is the first discovery of crystalline protonated iridate forming from a perovskite-like phase, adopting a layered structure with apex-linked IrO6 octahedra. Furthermore, H3.6IrO4·3.7H2O is found to possess not only an enhanced specific catalytic activity, superior to that of other perovskite-based iridates, but also a mass activity comparable to that of nanosized IrOx particles, while showing an improved catalytic stability owing to its ability to reversibly exchange protons in acid.
Revealing the Impact of Electrolyte Composition for Co-Based Water Oxidation Catalysts by the Study of Reaction Kinetics Parameters
Laboratoire Institut des Matériaux Poreux de Paris - Yan Duan, Nicolas Dubouis, Jiaqiang Huang, Daniel Alves Dalla Corte, Vanessa Pimenta, Zhichuan J. Xu, and Alexis Grimaud
ACS Publications - 7 4160–4170 - https://doi.org/10.1021/acscatal.0c00490 - 2020
Recent studies have revealed the critical role played by the electrolyte composition on the oxygen evolution reaction (OER) kinetics on the surface of highly active catalysts. While numerous works were devoted to understand the effect of the electrolyte composition on the physical properties of the catalysts’ surface, very little is known yet about its exact impact on the OER kinetics parameters. In this work, we reveal that the origin for the electrolyte-dependent OER activity for Co-based catalysts originates from two different effects. Increasing the alkaline electrolyte concentration for La1–xSrxCoO3−δ perovskites with x > 0 and for amorphous CoOOH increases the pre-exponential factor, which can be explained either by an increase of the concentration of active sites or by a change in the entropy of activation. However, changing the alkali cation results in a decrease of the apparent activation enthalpy for Fe-containing amorphous films, traducing a change in intermediates’ binding energies.
Machine Learning to Improve the Sensing of Biomolecules by Conical Track-Etched Nanopore
Laboratoire Institut des Matériaux Poreux de Paris - Nathan Meyer, Jean-Marc Janot , Mathilde Lepoitevin , Michaël Smietana ,Jean-Jacques Vasseur ,Joan Torrent and Sébastien Balme
Biosensors - 10(10) 140 - https://doi.org/10.3390/bios10100140 - 2020
Single nanopore is a powerful platform to detect, discriminate and identify biomacromolecules. Among the different devices, the conical nanopores obtained by the track-etched technique on a polymer film are stable and easy to functionalize. However, these advantages are hampered by their high aspect ratio that avoids the discrimination of similar samples. Using machine learning, we demonstrate an improved resolution so that it can identify short single- and double-stranded DNA (10- and 40-mers). We have characterized each current blockade event by the relative intensity, dwell time, surface area and both the right and left slope. We show an overlap of the relative current blockade amplitudes and dwell time distributions that prevents their identification. We define the different parameters that characterize the events as features and the type of DNA sample as the target. By applying support-vector machines to discriminate each sample, we show accuracy between 50% and 72% by using two features that distinctly classify the data points. Finally, we achieved an increased accuracy (up to 82%) when five features were implemented.
Metabolic cost of rapid adaptation of single yeast cells
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Gabrielle Woronoff, Philippe Nghe, Jean Baudry, Laurent Boitard, Erez Braun, Andrew D. Griffiths, and Jérôme Bibette
PNAS - 117 (20) 10660-10666 - https://doi.org/10.1073/pnas.1913767117 - 2020
Cells can rapidly adapt to changing environments through nongenetic processes; however, the metabolic cost of such adaptation has never been considered. Here we demonstrate metabolic coupling in a remarkable, rapid adaptation process (1 in 1,000 cells adapt per hour) by simultaneously measuring metabolism and division of thousands of individual Saccharomyces cerevisiae cells using a droplet microfluidic system: droplets containing single cells are immobilized in a two-dimensional (2D) array, with osmotically induced changes in droplet volume being used to measure cell metabolism, while simultaneously imaging the cells to measure division. Following a severe challenge, most cells, while not dividing, continue to metabolize, displaying a remarkably wide diversity of metabolic trajectories from which adaptation events can be anticipated. Adaptation requires a characteristic amount of energy, indicating that it is an active process. The demonstration that metabolic trajectories predict a priori adaptation events provides evidence of tight energetic coupling between metabolism and regulatory reorganization in adaptation. This process allows S. cerevisiae to adapt on a physiological timescale, but related phenomena may also be important in other processes, such as cellular differentiation, cellular reprogramming, and the emergence of drug resistance in cancer.
High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Annabelle Gérard, Adam Woolfe, […]Colin Brenan
Nat Biotechnol. - 38 715–721 - https://doi.org/10.1038/s41587-020-0466-7 - 2020
Mining the antibody repertoire of plasma cells and plasmablasts could enable the discovery of useful antibodies for therapeutic or research purposes1. We present a method for high-throughput, single-cell screening of IgG-secreting primary cells to characterize antibody binding to soluble and membrane-bound antigens. CelliGO is a droplet microfluidics system that combines high-throughput screening for IgG activity, using fluorescence-based in-droplet single-cell bioassays2, with sequencing of paired antibody V genes, using in-droplet single-cell barcoded reverse transcription. We analyzed IgG repertoire diversity, clonal expansion and somatic hypermutation in cells from mice immunized with a vaccine target, a multifunctional enzyme or a membrane-bound cancer target. Immunization with these antigens yielded 100–1,000 IgG sequences per mouse. We generated 77 recombinant antibodies from the identified sequences and found that 93% recognized the soluble antigen and 14% the membrane antigen. The platform also allowed recovery of ~450–900 IgG sequences from ~2,200 IgG-secreting activated human memory B cells, activated ex vivo, demonstrating its versatility.
Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, Rémi Monasson
e-Life - 1 619 - DOI: 10.7554/eLife.55678 - 2020
Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis and gives insight on the mechanisms through which antigen availability controls the rate of maturation and the expansion of the antibody population. It is also capable, upon maximum-likelihood inference of the parameters, to reproduce accurately the distributions of affinities of IgG-secreting cells we measure in mice immunized against Tetanus Toxoid under largely varying conditions (antigen dosage, delay between injections). Both model and experiments show that the average population affinity depends non-monotonically on the antigen dosage. We show that combining quantitative modeling and statistical inference is a concrete way to investigate biological processes underlying affinity maturation (such as selection permissiveness), hardly accessible through measurements.

628 publications.