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Chiavarino B.,University of Rome La Sapienza | Crestoni M.E.,University of Rome La Sapienza | Fornarini S.,University of Rome La Sapienza | Scuderi D.,University Paris - Sud | Salpin J.-Y.,CNRS Laboratory for Analysis and Modelling for Biology and Environment
Journal of the American Chemical Society | Year: 2013

Infrared multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(G)Cl]+ and cis-[Pt(NH 3)2(A)Cl]+ ions (where A is adenine and G is guanine) has been performed in two spectral regions, 950-1900 and 2900-3700 cm-1. Quantum chemical calculations at the B3LYP/LACV3P/6-311G* level yield the optimized geometries and IR spectra for the conceivable isomers of cis-[Pt(NH3)2(G)Cl]+ and cis-[Pt(NH 3)2(A)Cl]+, whereby the cisplatin residue is attached to the N7, N3, or carbonyl oxygen atom, (O6), of guanine and to the N7, N3, or N1 position of adenine, respectively. In addition to the conventional binding sites of native adenine, complexes with N7-H tautomers have also been considered. In agreement with computational results, the IR characterization of cis-[Pt(NH3)2(G)Cl]+ points to a covalent structure where Pt is bound to the N7 atom of guanine. The characterized conformer has a hydrogen-bonding interaction between a hydrogen atom of one NH3 ligand and the carbonyl group of guanine. The experimental C-O stretching feature of cis-[Pt(NH3)2(G)Cl]+ at 1718 cm-1, remarkably red-shifted with respect to an unperturbed C-O stretching mode, is indicative of a lengthened CO bond in guanine, a signature that this group is involved in hydrogen bonding. The IRMPD spectra of cis-[Pt(NH3)2(A)Cl]+ are consistent with the presence of two major isomers, PtAN3 and PtAN1, where Pt is bound to the N3 and N1 positions of native adenine, respectively. © 2012 American Chemical Society.

Oukhaled A.G.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Biance A.-L.,University Claude Bernard Lyon 1 | Pelta J.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Auvray L.,University Paris Diderot | Bacri L.,CNRS Laboratory for Analysis and Modelling for Biology and Environment
Physical Review Letters | Year: 2012

We investigate the entrance of single poly(ethylene glycol) chains into an I-hemolysin channel. We detect the frequency and duration of the current blockades induced by large neutral polymers, where chain radius is larger than pore diameter. In the semidilute regime, these chains pass only if the monomer concentration is larger than a well-defined threshold. Experiments are performed in a very large domain of concentration and molecular mass, up to 35% and 200kDa, respectively, which was previously unexplored. The variation of the dwell time as a function of molecular mass shows that the chains are extracted from the semidilute solution in contact with the pore by a reptation mechanism. © 2012 American Physical Society.

Oukhaled A.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Bacri L.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Pastoriza-Gallego M.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Betton J.-M.,French National Center for Scientific Research | Pelta J.,CNRS Laboratory for Analysis and Modelling for Biology and Environment
ACS Chemical Biology | Year: 2012

Proteins subjected to an electric field and forced to pass through a nanopore induce blockades of ionic current that depend on the protein and nanopore characteristics and interactions between them. Recent advances in the analysis of these blockades have highlighted a variety of phenomena that can be used to study protein translocation and protein folding, to probe single-molecule catalytic reactions in order to obtain kinetic and thermodynamic information, and to detect protein-antibody complexes, proteins with DNA and RNA aptamers, and protein-pore interactions. Nanopore design is now well controlled, allowing the development of future biotechnologies and medicine applications. © 2012 American Chemical Society.

Bouchoux G.,Ecole Polytechnique - Palaiseau | Bouchoux G.,French National Center for Scientific Research | Salpin J.-Y.,University of Évry Val d'Essonne | Salpin J.-Y.,CNRS Laboratory for Analysis and Modelling for Biology and Environment
Mass Spectrometry Reviews | Year: 2012

The present article is the second part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules. The first part of the review (Mass Spectrom. Rev., 2007, 26:775-835) was devoted to the description of the physico-chemical concepts and of the methods of determination, both experimental and theoretical, of gas-phase basicity. Several clues concerning the structural and energetic aspects of the protonation of isolated species have been emphasized. In the present article, specific examples are examined. The field of investigation is limited to molecules containing a "saturated" basic site, that is, nitrogen or oxygen atoms engaged in simple Ï bonds with their neighboring. Aliphatic, cyclic and aromatic poly-amines, aminoalcohols, alcohols, ethers, and hydroxyl-ethers, are successively presented. © 2011 Wiley Periodicals, Inc.

Jaeqx S.,Radboud University Nijmegen | Oomens J.,Radboud University Nijmegen | Cimas A.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Gaigeot M.-P.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Rijs A.M.,Radboud University Nijmegen
Angewandte Chemie - International Edition | Year: 2014

Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides.1 Although the far-IR region (<500 cm-1) may contain a wealth of structural information, as recognized in condensed phase studies,2 DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two γ-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide A features. The use of low-frequency modes (towards 100 cm-1) for structural assignment of peptides is explored. This far-IR region possibly contains detailed information on the secondary structure. The use of Born-Oppenheimer molecular dynamics simulations is discussed to calculate the far-IR signature of peptides. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Motta A.,University of Catania | Gaigeot M.-P.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Gaigeot M.-P.,Institut Universitaire de France | Costa D.,Chimie Paristech
Journal of Physical Chemistry C | Year: 2012

The investigation of metal oxide/water interfaces at the molecular level represents a fundamental issue for the understanding of chemical, physical, and biological processes involved in several fields such as erosion, heterogeneous catalysis, prebiotic chemistry, corrosion, hygiene, or biocompatibility. In this context we have studied the mineral (101) γ-AlOOH (boehmite) surface/water interface by means of density functional theory based molecular dynamics (DFT-MD). Boehmite (101) is a stepped surface, covered with monocoordinated (μ 1) OH groups placed at the step edge and dicoordinated (μ 2) OH groups placed along the terraces. At the surface, the respective concentrations of different OH species are found as 0.48 μ 2-OH + 0.26 μ 1-OH 2 + 0.24 μ 1-OH + 0.02 μ 2-OH 2. We show that the interfacial water molecules are somehow frozen in specific orientations, with 60% having one proton pointing to the surface (water is a H-bond donor to the surface) and 40% with one proton directed away from the surface (water is a H-bond acceptor with the surface). The effect of the surface on the water organization is lost at 6 Å from the surface, where liquid bulk is fully recovered. Proton transfers are observed at the interface between μ 1 and μ 2 species involving a Grotthus mechanism between distant μ 1/μ 2 groups. A bridge of interfacial water molecules has been found to assist this proton transfer. A pK value of 1.4 is calculated for this acid-base reaction, where μ 2-HOH is found to be a stronger acid than μ 1-HOH. These results represent a first step toward the understanding of the increased reactivity of defective surfaces in the presence of explicit solvent, using a first-principle representation of the full interface. © 2012 American Chemical Society.

Borgis D.,CNRS PASTEUR Laboratory | Gendre L.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Ramirez R.,CNRS Laboratory for Analysis and Modelling for Biology and Environment
Journal of Physical Chemistry B | Year: 2012

A molecular density functional theory of solvation is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position- and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, the unknown excess term of the functional can be approximated by the angular-dependent direct correlation function of the pure solvent. This function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation. The corresponding functional can then be minimized on a three-dimensional cubic grid for positions and a Gauss-Legendre angular grid for orientations to provide the solvation free energy of embedded molecules at the same time as the solvent three-dimensional microscopic structure. This functional minimization procedure is much more efficient than direct molecular dynamics simulations combined with thermodynamic integration schemes. The approach is shown to be also pertinent to the molecular-level determination of electron-transfer properties such as reaction free energy and reorganization energy. It is illustrated for molecular solvation and photochemical electron-transfer reactions in acetonitrile, a prototypical polar aprotic solvent. © 2012 American Chemical Society.

Przybylski C.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Bonnet V.,University of Picardie Jules Verne
Rapid Communications in Mass Spectrometry | Year: 2013

RATIONALE: Carbohydrates have essential functions in living organisms and cells, but, due to the presence of numerous linkage combinations, substituent sites and possible conformations, they are the class of biomolecules which exhibits the huge structural diversity found in nature. Thereby, due to such diversity and poor ionization, their structural deciphering by mass spectrometry is still a very challenging task. METHODS: Here, we studied a series of linear and cyclic neutral oligosaccharides using electrospray with collisioninduced dissociation (CID), pulsedQdissociation (PQD) and the higherenergy Ctrap dissociation (HCD) feature of a linear ion trap Orbitrap hybrid mass spectrometer (LTQOrbitrap). The collision energy necessary to obtain 50% fragmentation (CE50 values) in CID, PQD and HCD was used to correlate both size and structures. RESULTS: The default settings for activation time and/or activation Q are the most appropriate, except for HCD, where 100 ms instead of 30 ms gave more intense fragment ions. PQD exhibits a 2-8-fold lower sensitivity than CID. HCD provides signals closer or slightly superior by 1.5-fold than PQD, and offers a more balanced ion distribution through the spectrum. Furthermore, HCD offers the possibility to make fine adjustments of the energy via the eV scale to further increase the yield of lowmass fragments. CONCLUSIONS: The complementarity of CID, PQD and HCD was clearly demonstrated by obtaining structural information on hexa, hepta and octasaccharides. Together, these results clearly indicate the usefulness of the CID/HCD pair for further structural deciphering, and analysis of more complex structures such as multiantennary carbohydrates or glycoconjuguates alone or in mixture. Copyright © 2012 John Wiley & Sons, Ltd.

Pflieger D.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Bigeard J.,University of Évry Val d'Essonne | Hirt H.,University of Évry Val d'Essonne
Proteomics | Year: 2011

The components that enable cells and organisms to fulfill a plethora of chemical and physical reactions, including their ability to metabolize, replicate, repair and communicate with their environment are mostly based on the functioning of highly complex cellular machines which are to a large extent composed of proteins. With the development of MS techniques compatible with the analysis of minute amounts of biological material, it has become more and more feasible to dissect the composition and modification of these protein machineries. Indeed, new purification methods of protein complexes followed by MS analysis together with the genomic sequencing of various organisms - and in particular of crop species - now provide unforeseen insight to understand biological processes at a molecular level. We here review the current state of the art of in vivo protein complex isolation and their MS-based analytical characterization, emphasizing on the tandem affinity purification approach. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Jeanvoine Y.,CNRS Laboratory for Analysis and Modelling for Biology and Environment | Spezia R.,CNRS Laboratory for Analysis and Modelling for Biology and Environment
Journal of Molecular Structure: THEOCHEM | Year: 2010

In this work, we have investigated the binding of Cu2+ with the simplest chalcogen-chalcogen bridge models, i.e. H2O2, H2S2 and H2Se2. Different functionals were used to calculate binding energies and electronic properties: the simple local spin density (SVWN), some GGA (BLYP and PBE), some meta-GGA (TPSS and VSXC), different hybrid-GGA, moduling also the percentage of Hartree-Fock on the exchange contribution (B3LYP, PBE0, B98, MPW1PW91, BHandH, BHandHLYP) and two new hybrid-meta-GGA (M05 and M05-2X) functionals. Results are compared with CCSD(T) calculations and, when available, with experimental data. DFT seems to provide very different results as a function of the chosen functional and the only almost uniform message is that results can be improved by modifying the contribution of Hartree-Fock exchange. In particular, changing progressively the weight of nonlocal Hartree-Fock exchange, we found that using a value of 45% we can minimize differences with respect to CCSD(T) calculations. Finally, we noticed that adding another ligand, and thus saturating the metal coordination sphere, energies for ligand exchange reactions are less dependent to the choice of the functional. © 2010 Elsevier B.V.

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