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Fogarty A.C.,CNRS PASTEUR Laboratory | Duboue-Dijon E.,CNRS PASTEUR Laboratory | Sterpone F.,University of Paris Pantheon Sorbonne | Hynes J.T.,CNRS PASTEUR Laboratory | And 2 more authors.
Chemical Society Reviews | Year: 2013

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. © 2013 The Royal Society of Chemistry. Source

Lefevre G.,CNRS PASTEUR Laboratory | Lefevre G.,University of British Columbia | Jutand A.,CNRS PASTEUR Laboratory
Chemistry - A European Journal | Year: 2014

The mechanism of the reactions of aryl/heteroaryl halides with aryl Grignard reagents catalyzed by [FeIII(acac)3] (acac=acetylacetonate) has been investigated. It is shown that in the presence of excess PhMgBr, [FeIII(acac)3] affords two reduced complexes: [PhFeII(acac)(thf)n] (n=1 or 2) (characterized by 1H NMR and cyclic voltammetry) and [PhFeI(acac)(thf)] - (characterized by cyclic voltammetry, 1H NMR, EPR and DFT). Whereas [PhFeII(acac)(thf)n] does not react with any of the investigated aryl or heteroaryl halides, the FeI complex [PhFeI(acac)(thf)]- reacts with ArX (Ar=Ph, 4-tolyl; X=I, Br) through an inner-sphere monoelectronic reduction (promoted by halogen bonding) to afford the corresponding arene ArH together with the Grignard homocoupling product PhPh. In contrast, [PhFeI(acac)(thf)] - reacts with a heteroaryl chloride (2-chloropyridine) to afford the cross-coupling product (2-phenylpyridine) through an oxidative addition/reductive elimination sequence. The mechanism of the reaction of [PhFeI(acac)(thf)]- with the aryl and heteroaryl halides has been explored on the basis of DFT calculations. Iron(I) does the job: The reduction of [FeIII(acac)3] by PhMgBr gives [PhFe I(acac)(thf)]-, which reacts with ArX (Ar=Ph, 4-tol; X=I, Br) through an inner-sphere monoelectronic reduction promoted by halogen bonding to afford ArH and PhPh (see scheme; acac=acetylacetonate). In contrast, [PhFeI(acac)(thf)]- reacts with 2-chloropyridine to give the cross-coupling product (2-phenylpyridine) through a classical oxidative addition/reductive elimination sequence. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Ferrer Flegeau E.,CNRS PASTEUR Laboratory | Bruneau C.,CNRS Chemistry Institute of Rennes | Dixneuf P.H.,CNRS Chemistry Institute of Rennes | Jutand A.,CNRS PASTEUR Laboratory
Journal of the American Chemical Society | Year: 2011

Kinetic data for the C - H bond activation of 2-phenylpyridine by Ru II(carboxylate)2(p-cymene) I (acetate) and I′ (pivalate) are available for the first time. They reveal an irreversible autocatalytic process catalyzed by the coproduct HOAc or HOPiv (acetonitrile, 27 °C). The overall reaction is indeed accelerated by the carboxylic acid coproduct and water. It is retarded by a base, in agreement with an autocatalytic process induced by HOAc or HOPiv that favors the dissociation of one carboxylate ligand from I and I′ and consequently the ensuing complexation of 2-phenylpyridine (2-PhPy). The C - H bond activation initially delivers Ru(O2CR)(o-C6H4-Py)(p-cymene) A or A′, containing one carboxylate ligand (OAc or OPiv, respectively). The overall reaction is accelerated by added acetates. Consequently, C - H bond activation (faster for acetate I than for pivalate I′) proceeds via an intermolecular deprotonation of the C - H bond of the ligated 2-PhPy by the acetate or pivalate anion released from I or I′, respectively. The 18e complexes A and A′ easily dissociate, by displacement of the carboxylate by the solvent (also favored by the carboxylic acid), to give the same cationic complex B+ {[Ru(o-C6H4-Py)(p-cymene)(MeCN)] +}. Complex B+ is reactive toward oxidative addition of phenyl iodide, leading to the diphenylated 2-pyridylbenzene. © 2011 American Chemical Society. Source

Fogarty A.C.,CNRS PASTEUR Laboratory | Laage D.,CNRS PASTEUR Laboratory
Journal of Physical Chemistry B | Year: 2014

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. © 2014 American Chemical Society. Source

Sterpone F.,CNRS PASTEUR Laboratory | Sterpone F.,French National Center for Scientific Research | Stirnemann G.,CNRS PASTEUR Laboratory | Stirnemann G.,Columbia University | Laage D.,CNRS PASTEUR Laboratory
Journal of the American Chemical Society | Year: 2012

Hydration shell dynamics plays a critical role in protein folding and biochemical activity and has thus been actively studied through a broad range of techniques. While all observations concur with a slowdown of water dynamics relative to the bulk, the magnitude and molecular origin of this retardation remain unclear. Via numerical simulations and theoretical modeling, we establish a molecular description of protein hydration dynamics and identify the key protein features that govern it. Through detailed microscopic mapping of the water reorientation and hydrogen-bond (HB) dynamics around lysozyme, we first determine that 80% of the hydration layer waters experience a moderate slowdown factor of ∼2-3, while the slower residual population is distributed along a power-law tail, in quantitative agreement with recent NMR results. We then establish that the water reorientation mechanism at the protein interface is dominated by large angular jumps similar to the bulk situation. A theoretical extended jump model is shown to provide the first rigorous determination of the two key contributions to the observed slowdown: a topological excluded-volume factor resulting from the local protein geometry, which governs the dynamics of the fastest 80% of the waters, and a free energetic factor arising from the water-protein HB strength, which is especially important for the remaining waters in confined sites at the protein interface. These simple local factors are shown to provide a nearly quantitative description of the hydration shell dynamics. © 2012 American Chemical Society. Source

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