Laboratoire P.A.S.T.E.U.R

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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.

Unveiling nickelocene bonding to a noble metal surface

Physical Review B 93, 195403 (2016)

 

The manipulation of a molecular spin state in low-dimensional materials is central to molecular spintronics. The designs of hybrid devices incorporating magnetic metallocenes are very promising in this regard, but are hampered by the lack of data regarding their interactionwith ametal. Here, we combine low-temperature scanning tunneling microscopy and density functional theory calculations to investigate a magnetic metallocene at the single-molecule level—nickelocene. We demonstrate that the chemical and electronic structures of nickelocene are preserved upon adsorption on a copper surface. Several bonding configurations to the surface are identified, ranging from the isolated molecule to molecular layers governed by van der Waals interactions

 

Depopulation of Single-Phthalocyanine Molecular Orbitals upon Pyrrolic-Hydrogen Abstraction on Graphene

ACS Nano 2016, 10, 2010−2016

 

Single-molecule chemistry with a scanning tunneling microscope has preponderantly been performed on metal surfaces. The molecule− metal hybridization, however, is often detrimental to genuine molecular properties and obscures their changes upon chemical reactions. We used graphene on Ir(111) to reduce the coupling between Ir(111) and adsorbed phthalocyanine molecules. By local electron injection from the tip of a scanning tunneling microscope the two pyrrolic H atoms were removed from single phthalocyanines. The detachment of the H atom pair induced a strong modification of the molecular electronic structure, albeit with no change in the adsorption geometry. Spectra and maps of the diff erential conductance combined with density functional calculations unveiled the entire depopulation of the highest occupied molecular orbital upon H abstraction. Occupied π  states of intact molecules are proposed to be emptied via  intramolecular electron transfer to dangling σ states of H-free N atoms.