UMR 8640 : Physico-Chimie Théorique

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(January 2017)

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.

Direct quantitative identification of the “surface trans-effect”

Chemical Science, 2016

 

The strong parallels between coordination chemistry and adsorption on metal surfaces, with molecules and ligands forming local bonds to individual atoms within a metal surface, have been established over many years of study. The recently proposed “surface trans-effect” (STE) appears to be a further manifestation of this analogous behaviour, but so far the true nature of the modified molecule-metal surface bonding has been unclear. The STE could play an important role in determining the reactivities of surface-supported metal-organic complexes, influencing the design of systems for future applications. However, the current understanding of this effect is incomplete and lacks reliable structural parameters with which to benchmark theoretical calculations. Using X-ray standing waves, we demonstrate that ligation of ammonia and water to iron phthalocyanine (FePc) on Ag(111) increases the adsorption height of the central Fe atom; dispersion corrected density functional theory calculations accurately model this structural effect. The calculated charge redistribution in the FePc/H2O electronic structure induced by adsorption shows an accumulation of charge along the σ- bonding direction between the surface, the Fe atom and the water molecule, similar to the redistribution caused by ammonia. This apparent σ-donor nature of the observed STE on Ag(111) is shown to involve bonding to the delocalised metal surface electrons rather than local bonding to one or more surface atoms, thus indicating that this is a true surface trans-effect. 

Molecular Hydrodynamics from Memory Kernels

PRL 116, 147804 (2016)

 

The memory kernel for a tagged particle in a fluid, computed from molecular dynamics simulations, decays algebraically as t-3/2. We show how the hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail and generalize the concept of hydrodynamic added mass. This mass term is negative in the present case of a molecular solute, which is at odds with incompressible hydrodynamics predictions. Lastly, we discuss the various contributions to the friction, the associated time scales, and the crossover between the molecular and hydrodynamic regimes upon increasing the solute radius.