UMR 8640 : Theoretical physico-chemistry

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L'eau, une histoire trouble - Podcast France Culture

L’eau est un des éléments qui nous est le plus familier, mais recèle encore bien des mystères. Comment se sont construites les théories physiques et chimiques sur l’eau ? Quelles sont nos connaissances actuelles sur cette substance ?

Covalent Functionalization by Cycloaddition Reactions of Pristine Defect-Free Graphene

ACS Nano, Decembre 2016

 

 

Based on a low temperature scanning tunneling microscopy study, we present a direct visualization of a cycloaddition reaction performed for some specific fluorinated maleimide molecules deposited on graphene. Up to now it was widely admitted that such cycloaddition reaction can not happen without pre-existing defects. However, our study shows that the cycloaddition reaction can be carried out on a defect-free basal graphene plane at room temperature. In the course of covalently grafting the molecules to graphene, the sp2 conjugation of carbon atoms was broken and local sp3 bonds were created. The grafted molecules perturbed the graphene lattice, generating a standing-wave pattern with an anisotropy which was attributed to a (1,2) cycloaddition, as revealed by T-matrix approximation calculations. DFT calculations showed that while both (1,4) and (1,2) cycloaddition were possible on free standing graphene, only the (1,2) cycloaddition could be obtained for graphene on SiC(0001). Globally averaging spectroscopic techniques, XPS and ARPES, were used to determine the modification in the elemental composition of the samples induced by the reaction, indicating an opening of an electronic gap in graphene.

Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride

J. Phys. Chem. Lett. 2016, 7, 4695−4700

 

Recent nanofluidic experiments revealed strongly diff erent surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013 , 494 , 455− 458; Phys. Rev. Lett. 2016 , 116 , 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pKa around  6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario.

FAST : la start-up de chimie théorique – un nouveau paradigme pour le « drug design » !

FAST est une start-up localisée au sein du Département de Chimie de l’ENS proposant une solution logicielle pour calculer et visualiser en 3D les interactions entre l’eau et n’importe quelle molécule, médicament ou protéine et donc réduire les coûts de conception et accélérer la sélection de molécules thérapeutiques en drug design.

Dynamical Disorder in the DNA Hydration Shell

J. Am. Chem. Soc.2016

 

The reorientation and hydrogen-bond dynamics of water molecules within the hydration shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are investigated via molecular dynamics simulations and an analytic jump model, which provide valuable new molecular level insights into these dynamics. Different sources of heterogeneity in the hydration shell dynamics are determined. First, a pronounced spatial heterogeneity is found at the DNA interface and explained via the jump model by the diversity in local DNA interfacial topographies and DNA− water H-bond interactions. While most of the hydration shell is moderately retarded with respect to the bulk, some water molecules confined in the narrow minor groove exhibit very slow dynamics. An additional source of heterogeneity is found to be caused by the DNA conformational fluctuations, which modulate the water dynamics. The groove widening aids the approach of, and the jump to, a new water H-bond partner. This temporal heterogeneity is especially strong in the minor groove, where groove width fluctuations occur on the same time scale as the water H-bond rearrangements, leading to a strong dynamical disorder. The usual simplifying assumption that hydration shell dynamics is much faster than DNA dynamics is thus not valid; our results show that biomolecular conformational fluctuations are essential to facilitate the water motions and accelerate the hydration dynamics in confined groove sites.