Laboratoire de Chimie Physique

The theoretical description of charge distribution, and related properties, such as chemical reactivity descriptors of chemical compounds, has greatly benefited from the development of density functional theory (DFT) methods. Indeed, most concepts stemmed from DFT but, up to now, they have been used mostly within semiempirical MO methods, Hartree–Fock, or post-Hartree–Fock methods. During the last decade, however, DFT has enabled theoretical chemistry to predict accurately structures and energetics of clusters and molecules. Therefore, more attention should also now be paid to these reactivity descriptors determined directly from DFT calculations. In this work, chemical reactivity is explored in DFT through a functional Taylor expansion of energy that introduces various energy derivatives of chemical significance. This review summarizes their main features and examines the limitations of some indexes presently used for the characterization of reactivity. Also, several perspectives are given. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 129–154, 1999

Atomic force microscopy-based infrared spectroscopy (AFM-IR) is a rapidly emerging technique that provides chemical analysis and compositional mapping with spatial resolution far below conventional optical diffraction limits. AFM-IR works by using the tip of an AFM probe to locally detect thermal expansion in a sample resulting from absorption of infrared radiation. AFM-IR thus can provide the spatial resolution of AFM in combination with the chemical analysis and compositional imaging capabilities of infrared spectroscopy. This article briefly reviews the development and underlying technology of AFM-IR, including recent advances, and then surveys a wide range of applications and investigations using AFM-IR. AFM-IR applications that will be discussed include those in polymers, life sciences, photonics, solar cells, semiconductors, pharmaceuticals, and cultural heritage. In the Supporting Information , the authors provide a theoretical section that reviews the physics underlying the AFM-IR measurement and detection mechanisms.

The development of recording media based on molecular spin‐transition (ST) materials is discussed and applications demonstrated for the first time. The figure shows a compound which exhibits an ST and which is based on Fe II and 1,2,4‐triazole units. The central Fe II ion undergoes an ST at around 210 K which is accompanied by a purple‐white color change. Requirements for future progress are reviewed. magnified image

Plants, green algae, and cyanobacteria synthesize storage polysaccharides by a similar ADPglucose-based pathway. Plant starch metabolism can be distinguished from that of bacterial glycogen by the presence of multiple forms of enzyme activities for each step of the pathway. This multiplicity does not coincide with any functional redundancy, as each form has seemingly acquired a distinctive and conserved role in starch metabolism. Comparisons of phenotypes generated by debranching enzyme-defective mutants in Escherichia coli and plants suggest that enzymes previously thought to be involved in polysaccharide degradation have been recruited during evolution to serve a particular purpose in starch biosynthesis. Speculations have been made that link this recruitment to the appearance of semicrystalline starch in photosynthetic eukaryotes. Besides the common core pathway, other enzymes of malto-oligosaccharide metabolism are required for normal starch metabolism. However, according to the genetic and physiological system under study, these enzymes may have acquired distinctive roles.

We present a review of experimental, theoretical, and molecular simulation studies of confinement effects on freezing and melting. We consider both simple and more complex adsorbates that are confined in various environments (slit or cylindrical pores and also disordered porous materials). The most commonly used molecular simulation, theoretical and experimental methods are first presented. We also provide a brief description of the most widely used porous materials. The current state of knowledge on the effects of confinement on structure and freezing temperature, and the appearance of new surface-driven and confinement-driven phases are then discussed. We also address how confinement affects the glass transition.

We present a novel chemical database for gas-phase astrochemistry. Named the KInetic Database for Astrochemistry
\n(KIDA), this database consists of gas-phase reactions with rate coefficients and uncertainties that will be vetted
\nto the greatest extent possible. Submissions of measured and calculated rate coefficients are welcome, and will
\nbe studied by experts before inclusion into the database. Besides providing kinetic information for the interstellar
\nmedium, KIDA is planned to contain such data for planetary atmospheres and for circumstellar envelopes. Each
\nyear, a subset of the reactions in the database (kida.uva) will be provided as a network for the simulation of the
\nchemistry of dense interstellar clouds with temperatures between 10 K and 300 K. We also provide a code, named
\nNahoon, to study the time-dependent gas-phase chemistry of zero-dimensional and one-dimensional interstellar
\nsources.

The crystal structure of two new cubic phases in the silicon-sodium system have been solved from their x-ray diffraction patterns. Both structures are of the clathrate type found for gas hydrates, consisting of tetrahedral networks which are combinations of pentagonal dodecahedra with 14-face polyhedra in one case and with 16-face polyhedra in the other case. There is strict correspondence between the silicon positions and the oxygen positions of the hydrate structures. For one compound, Na(8)Si(46), the centers of all polyhedra are occupied by sodium atoms. For the other compound, there occurs only partial occupancy of the polyhedral cages.

The grafting of the triangular 1,3,5-benzene tricarboxylate linkers (denoted trim) on tetrahedral ε-Keggin polyoxometalates (POMs) capped by Zn(II) ions, formed in situ under hydrothermal conditions, has generated three novel POM-based metal organic frameworks (POMOFs). (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(36)(OH)(4)Zn(4)][C(6)H(3)(COO)(3)](4/3)·6H(2)O (ε(trim)(4/3)) is a 3D open-framework built of molecular Keggin units connected by trim linkers, with channels occupied by tetrabutylammonium (TBA) counterions. ε(trim)(4/3) is a novel (3,4)-connected net, named ofp for open-framework polyoxometalate, and computer simulations have been used to evaluate its relative stability in comparison with ctn- and bor-like polymorphs, showing the stability of this novel phase directly related to its greatest density. A computational study was also undertaken with the aim of locating TBA molecules, the positions of which could not be deduced from single crystal X-ray diffraction, and further rationalizes their structure directing role. In (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(37)(OH)(3)Zn(4)][C(6)H(3)(COO)(3)] (ε(2)(trim)(2)), the building unit is not the molecular Keggin but a dimerized form of this POM. Their connection via trim linkers generates a 3D framework with channels filled by TBA cations. In (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(37)(OH)(3)Zn(4)][C(6)H(3)(COO)(3)]·8H(2)O ([ε(trim)](∞)), zigzag chains are connected via the organic linkers, forming 2D grids. Modified electrodes were fabricated by direct adsorption of the POMOFs on glassy carbon or entrapment in carbon paste (CPE). A remarkable electrocatalytic hydrogen evolution reaction (HER) was detected with a yield greater than 95%, and a turnover number as high as 1.2 × 10(5) was obtained after 5 h. The reported POMOF-based electrodes are more active than platinum, with a roughly 260 mV anodic shift. Finally, the electrocatalytic activities of ε(trim)(4/3)/CPE electrodes in various XCl (X = Li, Na, K, Cs) media have been studied. This allowed us to detect a cation effect and propose an electrocatalytic mechanistic pathway for the HER.

Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The approximately 3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.

We report the suppression by electric fields of longitudinal resistivity anomalies at 145 and 59 K in the compound Nb${\mathrm{Se}}_{3}$. Sample resistance was determined by conventional four-probe dc measurement as well as with short current pulses. We attribute the observed suppression to Zener breakdown across extremely small gaps introduced by the presence of charge density waves.

Though molecular beam experiments have revealed deficiencies in the Lorentz-Berthelot combining rules, these rules are still used widely to parametrize effective pair potential models or to calculate the thermodynamic properties of mixtures. Gibbs ensemble Monte Carlo and isothermal isobaric Monte Carlo simulations were used to compute the liquid-vapour phase equilibria and the liquid properties of binary mixtures of rare gases modelled by effective pair potentials. Three sets of simple combining rules were tested in this work: the commonly used Lorentz-Berthelot rules, the Kong rules (Kong, J., 1973, J. chem. Phys., 59, 2464) and the Waldman-Hagler rules (Waldman, M., and Hagler, A. T., 1993, J. comput. Chem., 14, 1077). These three sets of rules do not require any additional parameter. It is shown that: (1) the choice of a set of combining rules has a significant effect on the thermodynamic properties, (2) using the Lorentz-Berthelot rules yields significant deviations from experiment and (3) the Kong rules provide a much better description of the mixture properties both for coexistence curves and liquid properties. We therefore recommend the use of the Kong rules instead of the Lorentz-Berthelot when parametrizing potential models.

We have obtained bulk samples of the graphite intercalation compound, CaC6, by a novel method of synthesis from highly oriented pyrolytic graphite. The crystal structure has been completely determined showing that it is the only member of the MC6, metal-graphite compounds that has rhombohedral symmetry. We have clearly shown the occurrence of superconductivity in the bulk sample at 11.5 K, using magnetization measurements.

We present a new microscopy system for imaging in turbid media that is based on the spatial coherence gate principle and generates in parallel a complete two-dimensional head-on image without scanning. This system has been implemented in a commercial microscope and preserves the lateral resolution of the optics used. With a spatially incoherent source, speckle-free images with diffraction-limited resolution are recorded at successive depths with shot-noise-limited detection. The setup comprises a photoelastic modulator for path difference modulation and a two-dimensional CCD array and uses a multiplexed lock-in detection scheme.

Nanoparticles combining enhanced cellular drug delivery with efficient fluorescence detection are important tools for the development of theranostic agents. Here, we demonstrate this concept by a simple, fast, and robust protocol of cationic polymer-mediated gold nanocluster (Au NCs) self-assembly into nanoparticles (NPs) of ca. 120 nm diameter. An extensive characterization of the monodisperse and positively charged NPs revealed pH-dependent swelling properties, strong fluorescence enhancement, and excellent colloidal and photostability in water, buffer, and culture medium. The versatility of the preparation is demonstrated by using different Au NC surface ligands and cationic polymers. Steady-state and time-resolved fluorescence measurements give insight into the aggregation-induced emission phenomenon (AIE) by tuning the Au NC interactions in the self-assembled nanoparticles using the pH-dependent swelling. In vitro studies in human monocytic cells indicate strongly enhanced uptake of the NPs compared to free Au NCs in endocytic compartments. The NPs keep their assembly structure with quite low cytotoxicity up to 500 μg Au/mL. Enhanced drug delivery is demonstrated by loading peptides or antibodies in the NPs using a one-pot synthesis. Fluorescence microscopy and flow cytometry confirmed intracellular colocalization of the biomolecules and the NP carriers with a respective 1.7-fold and 6.5-fold enhanced cellular uptake of peptides and antibodies compared to the free biomolecules.

Recently, the use of gold nanoparticles as potential tumor selective radiosensitizers has been proposed as a breakthrough in radiotherapy. Experiments in living cells and in vivo have demonstrated the efficiency of the metal nanoparticles when combined with low energy x-ray radiations (below conventional 1 MeV Linac radiation). Further studies on DNA have been performed in order to better understand the fundamental processes of sensitization and to further improve the method. In this work, we propose a new strategy based on the combination of platinum nanoparticles with irradiation by fast ions effectively used in hadron therapy. It is observed in particular that nanoparticles enhance strongly lethal damage in DNA, with an efficiency factor close to 2 for double strand breaks. In order to disentangle the effect of the nano-design architecture, a comparison with the effects of dispersed metal atoms at the same concentration has been performed. It is thus shown that the sensitization in nanoparticles is enhanced due to auto-amplified electronic cascades inside the nanoparticles, which reinforces the energy deposition in the close vicinity of the metal. Finally, the combination of fast ion radiation (hadron therapy) with platinum nanoparticles should strongly improve cancer therapy protocols.

Il existe un domaine de température dans lequel la première couche d’adsorption de gaz rares et de méthane sur graphite passe par trois états successifs au cours de sa formation. Il s’agit très vraisemblablement d’états « gazeux », « liquide » et « solide » bidimensionnels. Il y aurait donc analogie avec le cas tridimensionnel.

Reproducible and optimized complex formation between polyanionic DNA and a polycationic vector is a key aspect of nonviral gene transfer systems. To this end, several factors relevant to in vivo delivery have been tested repeatedly on several cell types. Gene transfer with a lipopolyamine (transfectam) in the presence of serum was increased over 10-fold by sequential addition of the lipid to DNA. Paradoxically, high complex concentrations (> 200 micrograms DNA/ml) led to large enhancements too, which points to the fact that formation of productive complexes is a slow process. Each parameter, more than compensates for the decreased efficiency generally observed with nonviral vectors in serum. Transfectam and PEI (polyethylenimine)-mediated transfection also improved after mild centrifugation of the complexes on to the cells. These individual factors were shown to be essentially multiplicative, leading altogether to approximately a 1000-fold transfection increase with a luciferase reporter gene. Finally, 25 cell lines and primary cells (including fibroblasts, hepatocytes and endothelial cells) were successfully transfected over a five orders-of-magnitude efficiency range, From this large set of data, a general relation between the overall transfection level (as measured by luciferase reporter gene expression) and the fraction of transfected cells (histochemically stained for beta-galactosidase) could be inferred. Finally, transfectam and PEI displayed similar trends over this large range of efficiencies, which reinforces the hypothesis of a common transfection mechanism where the key endosome-releasing stop occurs through a "proton sponge' effect.

We provide a general thermodynamic framework for the understanding of guest-induced structural transitions in hybrid organic-inorganic materials. The method is based on the analysis of experimental adsorption isotherms. It allows the determination of the free energy differences between host structures involved in guest-induced transitions, especially hard to obtain experimentally. We discuss the general case of adsorption in flexible materials and show how a few key quantities, such as pore volumes and adsorption affinities, entirely determine the phenomenology of adsorption, including the occurrence of structural transitions. On the basis of adsorption thermodynamics, we then propose a taxonomy of guest-induced structural phase transitions and the corresponding isotherms. In particular, we derive generic conditions for observing a double structural transition upon adsorption, often resulting in a two-step isotherm. Finally, we show the wide applicability and the robustness of the model through three case studies of topical hybrid organic-inorganic frameworks: the hysteretic hydrogen adsorption in Co(1,4-benzenedipyrazolate), the guest-dependent gate-opening in Cu(4,4'-bipyridine)(2,5-dihydroxybenzoate)2 and the CO2-induced "breathing" of hybrid material MIL-53.

We present a theoretical investigation of the physics involved in a recently developed spectromicroscopy technique, called photothermal induced resonance (PTIR). With this technique, one measures the local infrared absorption spectrum of a sample shined with a tunable infrared laser pulse, and detects the induced photothermal expansion with the tip of an atomic force microscope (AFM). Simple physical assumptions allow us to describe analytically the heating and expansion of the sample, the excitation of the vibration modes of the AFM cantilever, and the detected signal. We show that the signal depends on the thermal expansion velocity rather than on the absolute displacement of the tip, and we investigate the influence of the laser pulse length. Eventually, we express the PTIR signal in terms of relevant parameters, and prove its proportionality to the sample absorbance. This analytical approach complement our experimental results and validates the PTIR method as a technique of choice for infrared spectroscopy of nanoscopic samples, getting around optical artifacts like reflectance perturbation.

Pyrite, the most abundant metal sulfide at the surface of Earth, plays a key role in many processes such as acid mine drainage, redox cycling of metals at oxic-anoxic boundaries of lake bottom, and degradation of pollutants. The oxidation of pyrite was studied in batch experiments over a large range of pH (2.5−12), with trace oxygen. Surface analysis of the samples was performed using X-ray photoelectron spectroscopy (XPS). Speciation of the aqueous species was investigated by inductively coupled plasma atomic emission spectrometry (ICP-AES), ionic chromatography, and UV−vis spectrophotometry. The pyrite surface can drastically change with the pH, which was never at steady state and tended to reach an acidic value whatever the initial pH. For pH <4, Fe(II) and SO42- were released into solution; from XPS analyses, the pyrite surface presented O−H groups, an Fe-deficient composition Fe1-xS2, and iron(III) (hydr)oxide traces. Whatever the pH, the sulfur of the FeS2 surface was mainly under the (−I) state oxidation. When the pH increased, Fe(II) disappeared and the surface was covered with iron(III) (hydr)oxides. This overlayer did not passivate the sample against further oxidation, and a decrease in pH was still observed.