Infrared study of the bacterial autoinducer N-hexanoyl-homoserine lactone (C6-HSL) in the gas-phase, water, and octanol solutions

The N-hexanoyl-homoserine lactone (C6-HSL) molecule has been investigated by means of infrared multiphoton dissociation (IRMPD) and Fourier-transform infrared spectroscopy (FT-IR) under different conditions in an attempt to mimic biological situations encountered in communication between bacteria for quorum sensing. The protonated molecular ion was studied in the gas-phase that corresponds to a solvent-free situation somewhat analogous to that encountered in the receptor. The simulation of the IRMPD spectrum of the isolated ion was then conducted by means of quantum chemistry calculations in vacuum. In the case of the neutral species, the FT-IR spectra were recorded in D(2)O, mimicking the cytosolic and extracellular media as well as in 1-octanol that is often used for simulation of cell membranes. The interpretation was conducted by considering a C6-HSL molecule in its endo or exo conformation hydrogen-bonded to, respectively, six D(2)O and four 1-octanol molecules. A satisfying agreement with the experimental FT-IR studies conducted in solution at room temperature was obtained as long as a continuum IEFPCM model was added to the explicit solvent environment.     

Direct functionalisation of group 10 N-heterocyclic carbene complexes for diversity enhancement

The synthesis of alkyne-substituted N-heterocyclic carbene complexes of Pd(II) and Pt(II) is reported. Catalyzed 1,3-dipolar cycloaddition with azides has been applied as a modular way of functionalisation of group 10 transition metal NHC complexes to generate potentially new metallodrugs.     

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.     

Structure-property relations in crystalline L-leucine obtained from calorimetry, X-rays, neutron and Raman scattering

We have studied the amino acid L-leucine (LEU) using inelastic neutron scattering, X-rays and neutron diffraction, calorimetry and Raman scattering as a function of temperature, focusing on the relationship between the local dynamics of the NH(3), CH(3), CH(2) and CO(2) moieties and the molecular structure of LEU. Calorimetric and diffraction data evidenced two novel phase transitions at about 150 K (T(1)) and 275 K (T(2)). The dynamical susceptibility function, obtained from the inelastic neutron scattering results, shows a re-distribution of the intensity of the vibrational bands that can be directly correlated with the phase transitions observed at T(1) and T(2), as well as with the already reported phase transition at T(3) = 353 K. Through the analysis of the Raman modes, the new structural arrangement observed below T(1) was related to conformational modifications of the CH and CH(3) groups, while the behavior of the N-H stretching vibration, ν(NH(3)), gave insight into the intermolecular N-H…O interactions. The observation of changes in the translational symmetry in the crystalline lattice, as well as anharmonic dynamics, allows for localized motions in LEU.     

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.     

Comparison of Fe and Ni opacity calculations for a better understanding of pulsating stellar envelopes

Opacity is an important ingredient of the evolution of stars. The calculation of opacity coefficients is complicated by the fact that the plasma contains partially ionized heavy ions that contribute to opacity dominated by H and He. Up to now, the astrophysical community has greatly benefited from the work of the contributions of Los Alamos [1], Livermore [2], [2a] and [2b] and the Opacity Project (OP) [3]. However unexplained differences of up to 50% in the radiative forces and Rosseland mean values for Fe have been noticed for conditions corresponding to stellar envelopes. Such uncertainty has a real impact on the understanding of pulsating stellar envelopes, on the excitation of modes, and on the identification of the mode frequencies. Temperature and density conditions equivalent to those found in stars can now be produced in laboratory experiments for various atomic species. Recently the photo-absorption spectra of nickel and iron plasmas have been measured during the LULI 2010 campaign, for temperatures between 15 and 40 eV and densities of ∼3 mg/cm³. A large theoretical collaboration, the “OPAC”, has been formed to prepare these experiments. We present here the set of opacity calculations performed by eight different groups for conditions relevant to the LULI 2010 experiment and to astrophysical stellar envelope conditions.     

Geometric analysis for the metropolis algorithm on Lipschitz domains

This paper gives geometric tools: comparison, Nash and Sobolev inequalities for pieces of the relevant Markov operators, that give useful bounds on rates of convergence for the Metropolis algorithm. As an example, we treat the random placement of N hard discs in the unit square, the original application of the Metropolis algorithm.     

On the numerical solution of large-scale sparse discrete-time Riccati equations

We discuss the numerical solution of large-scale discrete-time algebraic Riccati equations (DAREs) as they arise, e.g., in fully discretized linear-quadratic optimal control problems for parabolic partial differential equations (PDEs). We employ variants of Newton??s method that allow to compute an approximate low-rank factor of the solution of the DARE. The principal computation in the Newton iteration is the numerical solution of a Stein (aka discrete Lyapunov) equation in each step. For this purpose, we present a low-rank Smith method as well as a low-rank alternating-direction-implicit (ADI) iteration to compute low-rank approximations to solutions of Stein equations arising in this context. Numerical results are given to verify the efficiency and accuracy of the proposed algorithms.