UMR 8640 : Physico-Chimie Théorique

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(January 2017)

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.

Carbon dioxide transport in molten calcium carbonate occurs through an oxo-Grotthuss mechanism via a pyrocarbonate anion

Nature Chemistry2016, Feb.


The reactivity, speciation and solvation structure of CO2 in carbonate melts are relevant both for the fate of carbon in deep geological formations and for its electroreduction to CO, to be used as fuel, by means of solvation in a molten carbonate electrolyte. In particular, the high solubility of CO2 in carbonate melts has been tentatively attributed to the formation of a new carbon species, the pyrocarbonate anion, C2O52-. In this work we study, by _rst principles molecular dynamics simulations, the behaviour of CO2 in molten calcium carbonate. We _nd that pyrocarbonate forms spontaneously and the identity of the CO2 molecule is quickly lost through O2- exchange.

The transport of CO2 in this molten carbonate thus occurs in a fashion similar to the Grotthuss mechanism in water, and is three times faster than molecular diffusion. This shows that Grotthuss- like transport is more general than thought so far.

Sulfur radical species form gold deposits on Earth

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13484-9.


Gold deposits are formed through the mobilization and transport of the metal by hydrothermal fluids circulating in the Earth crust. Precipitation occurs in localized regions leading to gold concentrations 1,000 to 1,000,000 times higher than the average gold concentration in the crust. Solvation of the metal in the hydrothermal fluid arises from the formation of stable complexes with salts present in the fluids.


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.



Biomolecular hydration dynamics: a jump model perspective

The dynamics of water molecules within the hydration shell surrounding a biomolecule can have a crucial influence on its biochemical function. Characterizing their properties and the extent to which they differ from those of bulk water have thus been long-standing questions. Following a tutorial approach, we review the recent advances in this field and the different approaches which have probed the dynamical perturbation experienced by water in the vicinity of proteins or DNA. We discuss the molecular factors causing this perturbation, and describe how they change with temperature. We finally present more biologically relevant cases beyond the dilute aqueous situation. A special focus is on the jump model for water reorientation and hydrogen bond rearrangement.