Electrochemical meso-functionalization of magnesium(II) porphine

Regioselective meso-functionalization of the totally unsubstituted magnesium(II) porphine was performed by controlled potential electrolysis with pyridine and triphenylphosphine as nucleophiles leading to the original pyridinium and phosphonium substituted derivatives, respectively. The crystallographic structure of the latter is described as the only meso-phosphonium porphyrin reported to date.     

Experimental and Theoretical Investigation of Vibrational Spectra of Coordination Polymers Based on TCE‐TTF

The room‐temperature infrared and Raman spectra of a series of four isostructural polymeric salts of 2,3,6,7‐tetrakis(2‐cyanoethylthio)‐tetrathiafulvalene (TCE‐TTF) with paramagnetic (Co^II, Mn^II) and diamagnetic (Zn^II, Cd^II) ions, together with BF₄^? or ClO₄^? anions are reported. Infrared and Raman‐active modes are identified and assigned based on theoretical calculations for neutral and ionized TCE‐TTF using density functional theory (DFT) methods. It is confirmed that the TCE‐TTF molecules in all the materials investigated are fully ionized and interact in the crystal structure through cyanoethylthio groups. The vibrational modes related to the C?C stretching vibrations of TCE‐TTF are analyzed assuming the occurrence of electron–molecular vibration coupling (EMV). The presence of the antisymmetric C?C dimeric mode provides evidence that charge transfer takes place between TCE‐TTF molecules belonging to neighboring polymeric networks.     

Structural features and protonation site of epibatidine in the gas phase: an investigation through infrared multiphoton dissociation spectroscopy and computational chemistry

The gas phase structures of epibatidine, one of the most potent agonists of nicotinic acetylcholine receptors (nAChRs), are determined by means of infrared multiphoton dissociation (IRMPD) spectroscopy and quantum chemistry calculations. Comparison of the experimental and theoretical spectra provides evidence that about 15% of epibatidine is protonated on the Nsp(2) nitrogen in the gas phase. In contrast, the computational study of deschloroepibatidine shows that in the gas phase, the molecule is present only protonated on the Nsp(2) nitrogen. The main minima of the Nsp(2) protonated forms of the two molecules are strongly stabilized by intramolecular CH···Nsp(3) hydrogen bonds. The fundamental insights obtained in the present study on these two important nAChRs agonists show how subtle chemical modifications can have a deep impact on important physicochemical properties.     

Acid-base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met)

Acid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Δ(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol(-1). From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Δ(acid)H = 1393, 1391, 1396, 1411; Δ(acid)G = 1363, 1362, 1367, 1382 kJ mol(-1). This study also confirms that a non-negligible ΔpS° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a re-examination of several IRMPD spectra.     

A novel ruthenium(II) complex for two-photon absorption-based optical power limiting in the near-IR range

In this article, the synthesis of a novel high-conjugated ligand and its corresponding Ru(II) complex PTFTF:Ru is reported, along with the linear and nonlinear optical characterizations. Two-photon absorption based optical power limiting properties (OPL), especially in the near infrared, are described and compared to those of the analogous complexes previously published. Combined with a preliminary theoretical approach, this allows us to highlight several key parameters for OPL optimization in such molecular systems and more particularly the spectral overlap between TPA and excited-state absorption.     

Isolation of C-glycosyl xanthones from Coffea pseudozanguebariae and their location

The biochemical composition of leaves from Coffea pseudozanguebariae, a wild caffeine-free coffee species, was determined. Two phenolic compounds were extracted from leaves, separated and characterized. Their structures were elucidated by mass spectrometry, and 1D and 2D NMR spectroscopy and were shown to be mangiferin (1) and isomangiferin (2), which were the main polyphenol products. Multiphoton fluorescence imaging was performed to visualize polyphenol distribution in leaf cross sections. Consistent biochemical analysis cell imaging techniques on leaves revealed yellow fluorescence in the epidermis and parenchyma cells corresponding to xanthone compounds.     

Long-Time Convergence of an Adaptive Biasing Force Method: The Bi-Channel Case

We present convergence results for an adaptive algorithm to compute free energies, namely the adaptive biasing force (ABF) method (Darve and Pohorille in J Chem Phys 115(20):9169–9183, 2001; Hénin and Chipot in J Chem Phys 121:2904, 2004). The free energy is the effective potential associated to a so-called reaction coordinate ξ(q), where q = (q ₁, … , q _3N ) is the position vector of an N-particle system. Computing free energy differences remains an important challenge in molecular dynamics due to the presence of metastable regions in the potential energy surface. The ABF method uses an on-the-fly estimate of the free energy to bias dynamics and overcome metastability. Using entropy arguments and logarithmic Sobolev inequalities, previous results have shown that the rate of convergence of the ABF method is limited by the metastable features of the canonical measures conditioned to being at fixed values of ξ (Lelièvre et al. in Nonlinearity 21(6):1155–1181, 2008). In this paper, we present an improvement on the existing results in the presence of such metastabilities, which is a generic case encountered in practice. More precisely, we study the so-called bi-channel case, where two channels along the reaction coordinate direction exist between an initial and final state, the channels being separated from each other by a region of very low probability. With hypotheses made on ‘channel-dependent’ conditional measures, we show on a bi-channel model, which we introduce, that the convergence of the ABF method is, in fact, not limited by metastabilities in directions orthogonal to ξ under two crucial assumptions: (i) exchange between the two channels is possible for some values of ξ and (ii) the free energy is a good bias in each channel. This theoretical result supports recent numerical experiments (Minoukadeh et al. in J Chem Theory Comput 6:1008–1017, 2010), where the efficiency of the ABF approach is demonstrated for such a multiple-channel situation.