Selective Detection of Choline in Pseudophysiological Medium with a Fluorescent Cage Receptor.

A fluorescent cage receptor for the detection of choline in pseudophysiological medium is described. Not only does this capsule complex choline with an association constant greater than 9.9 × 104 M-1 in buffered medium but it is also selective toward acetylcholine.

Development of a novel ReaxFF reactive potential for organochloride molecules.

This article presents a new reactive potential in the ReaxFF formalism. It aims to include the chlorine element and opens up the fields of use of ReaxFF to the whole class of organochloride compounds including conjugated or aromatic groups. Numerous compounds in this family raise global awareness due to their environmental impact, and such a reactive potential will help investigate their degradation pathways. The new force field, named CHONCl-2022_weak, belongs to the aqueous branch. The force field parameters were fitted against high-level quantum chemistry calculations, including complete active space self-consistent field/NEVPT2 calculations and density functional theory calculations, and their accuracy was evaluated using a validation set. The root means square deviation against quantum mechanics energies is 0.38 eV (8.91 kcal mol-1). From a structural point of view, the root means square deviation is about 0.06 Å for the bond lengths, 11.86° for the angles, and 4.12° for the dihedral angles. With CHONCl-2022_weak new force field, we successfully investigated the regioselectivity for nucleophilic or electrophilic attacks on polychlorinated biphenyls, which are toxic and permanent pollutants. The rotation barriers along the bond linking the two benzene rings, which is crucial in the toxicity of these compounds, are well reproduced by CHONCl-2022_weak. Then, our new reactive potential is used to investigate the chlorobenzene reactivity in the presence of hydroxyl radicals in atmospheric condition or in aqueous solution. The reaction pathways computed with ReaxFF agree with the quantum mechanics results. We showed that, in the presence of dioxygen molecules, in atmospheric condition, the oxidation of chlorobenzene likely leads to the formation of highly oxygenated compounds after the abstraction of hydrogen radicals. In water, the addition of a hydroxyl radical leads to the formation of chlorophenol or phenol molecules, as already predicted from plasma-induced degradation experiments.

Reactivity at the Electrode-Electrolyte Interfaces in Li-Ion and Gel Electrolyte Lithium Batteries for LiNi0.6Mn0.2Co0.2O2 with Different Particle Sizes.

The layered oxide LiNi0.6Mn0.2Co0.2O2 is a very attractive positive electrode material, as shown by the good reversible capacity, chemical stability, and cyclability upon long-range cycling in Li-ion batteries and, hopefully, in the near future, in all-solid-state batteries. Three samples with variable primary particle sizes of 240 nm, 810 nm, and 2.1 µm on average and very similar structures close to the ideal 2D layered structure (less than 2% Ni2+ ions in Li+ sites) were obtained by coprecipitation followed by a solid-state reaction at high temperatures. The electrochemical performances of the materials were evaluated in a conventional organic liquid electrolyte in Li-ion batteries and in a gel electrolyte in all-solid-state batteries. The positive electrode/electrolyte interface was analyzed by X-ray photoelectron spectroscopy to determine its composition and the extent of degradation of the lithium salt and the carbonate solvents after cycling, taking into account the changes in particle size of the positive electrode material and the nature of the electrolyte.

Volatile fingerprint of food products with untargeted SIFT-MS data coupled with mixOmics methods for profile discrimination: Application case on cheese.

Volatile organic compounds (VOCs) emitted by food products are decisive for the perception of aroma and taste. The analysis of gaseous matrices is traditionally done by detection and quantification of few dozens of characteristic markers. Emerging direct injection mass spectrometry technologies offer rapid analysis based on a soft ionisation of VOCs without previous separation. The recent increase of selectivity offered by the use of several precursor ions coupled with untargeted analysis increases the potential power of these instruments. However, the analysis of complex gaseous matrix results in a large number of ion conflicts, making the quantification of markers difficult, and in a large volume of data. In this work, we present the exploitation of untargeted SIFT-MS volatile fingerprints of ewe PDO cheeses in a real farm model, using mixOmics methods allowing us to illustrate the typicality, the manufacturing processes reproducibility and the impact of the animals' diet on the final product.

Tissue localization of selenium of parental or dietary origin in rainbow trout (Oncorhynchus mykiss) fry using LA-ICP MS bioimaging.

In relation to the decrease of selenium (Se) content in aquafeeds, the impact of level and form of parental and dietary Se supplementation was investigated in rainbow trout fry using laser ablation-inductively coupled plasma mass spectrometry (LA-ICP MS) bioimaging. The offspring of rainbow trout broodstock, fed either a control diet without any Se supplementation (0.3 mg Se/kg diet) or a diet supplemented with Se (0.6 mg Se/kg diet) either as sodium selenite or hydroxy-selenomethionine, were sampled at swim-up fry stage or after 11 weeks of cross-feeding. Total body Se levels were influenced by parental Se nutrition in swim-up fry and by direct Se feeding in 11-week fry with higher levels in the Se-supplemented groups compared with the control and the highest levels in the hydroxy-selenomethionine treatment. The Se retention was lower for dietary sodium selenite. Selenomethionine levels increased when Se was provided as hydroxy-selenomethionine. LA-ICP MS maps revealed yolk in swim-up fry and intestine, liver, and kidney in 11-week fed fry as tissues with high Se abundance. In swim-up fry, muscle Se was the highest abundant when parents were fed hydroxy-selenomethionine. In 11-week fed fry, muscle Se abundance was higher in the head part of fry fed both Se-supplemented diets, but only in the tail part of fry fed hydroxy-selenomethionine. Liver Se abundance was higher in fry fed sodium selenite compared with the control diet supporting the hypothesis that tissue Se distribution can be influenced by parental and dietary Se forms and levels.

Relating the molecular topology and local geometry: Haddon's pyramidalization angle and the Gaussian curvature.

The pyramidalization angle and spherical curvature are well-known quantities used to characterize the local geometry of a molecule and to provide a measure of regio-chemical activity of molecules. In this paper, we give a self-contained presentation of these two concepts and discuss their limitations. These limitations can bypass, thanks to the introduction of the notions of angular defect and discrete Gauss curvature coming from discrete differential geometry. In particular, these quantities can be easily computed for arbitrary molecules, trivalent or not, with bond of equal lengths or not. All these quantities have been implemented. We then compute all these quantities over the Tománek database covering an almost exhaustive list of fullerene molecules. In particular, we discuss the interdependence of the pyramidalization angle with the spherical curvature, angular defect, and hybridization numbers. We also explore the dependence of the pyramidalization angle with respect to some characteristics of the molecule, such as the number of atoms, the group of symmetry, and the geometrical optimization process.

Morphology and Surface Reactivity Relationship in the Li1+xMn2-xO4 Spinel with x = 0.05 and 0.10: A Combined First-Principle and Experimental Study.

This article focuses on the surface reactivity of two spinel samples with different stoichiometries and crystal morphologies, namely Li1+xMn2-xO4 with x = 0.05 and 0.10. LiMn2O4 compounds are good candidates as positive electrode of high-power lithium-ion batteries for portable devices. The samples were investigated using both experimental and theoretical approaches. On the experimental point of view, they were characterized in depth from X-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy (XPS) analyses. Then, the reactivity was investigated through the adsorption of (SO2) gaseous probes, in controlled conditions, followed by XPS characterization. First-principle calculations were conducted simultaneously to investigate the electronic properties and the reactivity of relevant surfaces of an ideal LiMn2O4 material. The results allow us to conclude that the reactivity of the samples is dominated by an acido-basic reactivity and the formation of sulfite species. Nonetheless, on the x = 0.05 sample, both sulfite and sulfate species are obtained, the later, in lesser extent, corresponding to a redox reactivity. Combining experimental and theoretical results, this redox reactivity could be associated with the presence of a larger quantity of Mn4+ cations on the last surface layers of the material linked to a specific surface orientation.

Surface Reactivity of Li2MnO3: First-Principles and Experimental Study.

This article deals with the surface reactivity of (001)-oriented Li2MnO3 crystals investigated from a multitechnique approach combining material synthesis, X-ray photoemission spectroscopy (XPS), scanning electron microscopy, Auger electron spectroscopy, and first-principles calculations. Li2MnO3 is considered as a model compound suitable to go further in the understanding of the role of tetravalent manganese atoms in the surface reactivity of layered lithium oxides. The knowledge of the surface properties of such materials is essential to understand the mechanisms involved in parasitic phenomena responsible for early aging or poor storage performances of lithium-ion batteries. The surface reactivity was probed through the adsorption of SO2 gas molecules on large Li2MnO3 crystals to be able to focus the XPS beam on the top of the (001) surface. A chemical mapping and XPS characterization of the material before and after SO2 adsorption show in particular that the adsorption is homogeneous at the micro- and nanoscale and involves Mn reduction, whereas first-principles calculations on a slab model of the surface allow us to conclude that the most energetically favorable species formed is a sulfate with charge transfer implying reduction of Mn.

First-principle calculation of core level binding energies of LixPOyNz solid electrolyte.

We present first-principle calculations of core-level binding energies for the study of insulating, bulk phase, compounds, based on the Slater-Janak transition state model. Those calculations were performed in order to find a reliable model of the amorphous LixPOyNz solid electrolyte which is able to reproduce its electronic properties gathered from X-ray photoemission spectroscopy (XPS) experiments. As a starting point, Li2PO2N models were investigated. These models, proposed by Du et al. on the basis of thermodynamics and vibrational properties, were the first structural models of LixPOyNz. Thanks to chemical and structural modifications applied to Li2PO2N structures, which allow to demonstrate the relevance of our computational approach, we raise an issue concerning the possibility of encountering a non-bridging kind of nitrogen atoms (=N(-)) in LixPOyNz compounds.

Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale.

We have introduced a new algorithm in the parallel processing PMEMD module of the AMBER suite that allows MD simulations with a potential involving two coupled torsions. We have used this modified module to study the green fluorescent protein. A coupled torsional potential was adjusted on high accuracy quantum chemical calculations of the anionic chromophore in the first excited state, and several 15-ns-long MD simulations were performed. We have obtained an estimate of the fluorescence lifetime (2.2 ns) to be compared to the experimental value (3 ns), which is, to the best of our knowledge, the first theoretical estimate of that lifetime.

Relation between pH, structure, and absorption spectrum of Cerulean: a study by molecular dynamics and TD DFT calculations.

Molecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865-9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocyclic ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/H148D. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Complex fluorescence of the cyan fluorescent protein: comparisons with the H148D variant and consequences for quantitative cell imaging.

We have studied the fluorescence decays of the purified enhanced cyan fluorescent protein (ECFP, with chromophore sequence Thr-Trp-Gly) and of its variant carrying the single H148D mutation characteristic of the brighter form Cerulean. Both proteins exhibit highly complex fluorescence decays showing strong temperature and pH dependences. At neutral pH, the H148D mutation leads (i) to a general increase in all fluorescence lifetimes and (ii) to the disappearance of a subpopulation, estimated to be more than 25% of the total ECFP molecules, characterized by a quenched and red-shifted fluorescence. The fluorescence lifetime distributions of ECFP and its H148D mutant remain otherwise very similar, indicating a high degree of structural and dynamic similarity of the two proteins in their major form. From thermodynamic analysis, we conclude that the multiexponential decay of ECFP cannot be simply ascribed, as is generally admitted, to the slow conformational exchange characterized by NMR and X-ray crystallographic studies [Seifert, M. H., et al. (2002) J. Am. Chem. Soc. 124, 7932-7942; Bae, J. H., et al. (2003) J. Mol. Biol. 328, 1071-1081]. Parallel measurements in living cells show that these fluorescence properties in neutral solution are very similar to those of cytosolic ECFP.

Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum.

The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the beta barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.