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

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A molecular density functional theory approach to electron transfer reactions

Chem. Sci.2019, Advance Article 

 

Beyond the dielectric continuum description initiated by Marcus theory, the standard theoretical approach to study electron transfer (ET) reactions in solution or at interfaces is to use classical force field or ab initio molecular dynamics simulations. We present here an alternative method based on liquid-state theory, namely molecular density functional theory, which is numerically much more efficient than simulations while still retaining the molecular nature of the solvent. We begin by reformulating molecular ET theory in a density functional language and show how to compute the various observables characterizing ET reactions from an ensemble of density functional minimizations. In particular, we define within that formulation the relevant order parameter of the reaction, the so-called vertical energy gap, and determine the Marcus free energy curves of both reactant and product states along that coordinate. Important thermodynamic quantities such as the reaction free energy and the reorganization free energies follow. We assess the validity of the method by studying the model Cl0 / Cl+ and Cl0 / Cl- ET reactions in bulk water for which molecular dynamics results are available. The anionic case is found to violate the standard Marcus theory. Finally, we take advantage of the computational efficiency of the method to study the influence of a solid–solvent interface on the ET, by investigating the evolution of the reorganization free energy of the Cl0 / Cl+ reaction when the atom approaches an atomistically resolved wall.

 

Spin in a Closed-Shell Organic Molecule on a Metal Substrate Generated by a Sigmatropic Reaction

Angew. Chem. Int. Ed., 2019, 58, 821

 

Inert metal surfaces present more chances of hosting organic intact radicals than other substrates, but large amounts of delocalized electronic states favor charge transfer and thus spin quenching. Lowering the molecule–substrate interaction is a usual strategy to stabilize radicals on surfaces. In some works, thin insulating layers were introduced to provide a controllable degree of electronic decoupling. Recently, retinoid molecules adsorbed on gold have been manipulated with a scanning tunneling microscope (STM) to exhibit a localized spin, but calculations failed to find a radical derivative of the molecule on the surface. Now the formation of a neutral radical spatially localized in a tilted and lifted cyclic end of the molecule is presented. An allene moiety provokes a perpendicular tilt of the cyclic end relative to the rest of the conjugated chain, thus localizing the spin of the dehydrogenated allene in its lifted subpart. DFT calculations and STM manipulations give support to the proposed mechanism.

Chiral Crystal Packing Induces Enhancement of Vibrational Circular Dichroism

Angew. Chem. Int. Ed. 2018, 57, 13344 –13348

 

We demonstrate that molecular vibrations with originally low or zero intensity in a vibrational circular dichroism (VCD) spectrum attain chirality in molecular crystals by coordinated motion of the atoms. Ab initio molecular dynamics simulations of anharmonic solid-state VCD spectra of l-alanine crystals reveal how coherent vibrational modes exploit the space groupQs chirality, leading to nonlocal, enhanced VCD features, most significantly in the carbonyl region of the spectrum. The VCD-enhanced signal is ascribed to a helical arrangement of the oscillators in the crystal layers. No structural irregularities need to be considered to explain the amplification, but a crucial point lies in the polarization of charge, which requires an accurate description of the electronic structure. Delivering a quantitative atomic conception of supramolecular chirality induction, our ab initio scheme is applicable well beyond molecular crystals, for example, to address VCD in proteins and related compounds.

Investigation of photocurrents resulting froma living unicellular algae suspension with quinones over time

Chem. Sci.2018

Plants, algae, and some bacteria convert solar energy into chemical energy by using photosynthesis. In light of the current energy environment, many research strategies try to benefit from photosynthesis in order to generate usable photobioelectricity. Among all the strategies developed for transferring electrons from the photosynthetic chain to an outer collecting electrode, we recently implemented a method on a preparative scale (high surface electrode) based on a Chlamydomonas reinhardtii green algae suspension in the presence of exogenous quinones as redox mediators. While giving rise to an interesting performance (10–60 μA cm−2) in the course of one hour, this device appears to cause a slow decrease of the recorded photocurrent. In this paper, we wish to analyze and understand this gradual fall in performance in order to limit this issue in future applications. We thus first show that this kind of degradation could be related to over-irradiation conditions or side-effects of quinones depending on experimental conditions. We therefore built an empirical model involving a kinetic quenching induced by incubation with quinones, which is globally consistent with the experimental data provided by fluorescence measurements achieved after dark incubation of algae in the presence of quinones.

 

 

Improved chemical-genetic fluorescent markers for live cell microscopy

Biochemistry2018, 57 (39), pp 5648–5653

 

Inducible chemical-genetic fluorescent markers are promising tools for live cell imaging requiring high spatiotemporal resolution and low background fluorescence. The Fluorescence-Activating and absorption Shifting Tag (FAST) was recently developed to form fluorescent molecular complexes with a family of small, synthetic fluorogenic chromophores (so-called fluorogens). Here, we use rational design to modify the binding pocket of the protein and screen for improved fluorescence performances with four different fluorogens. The introduction of a single mutation results in improvements in both quantum yield and dissociation constant with nearly all fluorogens tested. Our improved FAST (iFAST) allowed the generation of a tandem td-iFAST that forms green and red fluorescent reporters 1.6-fold and 2-fold brighter than EGFP and mCherry, respectively, while having comparable size.