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.     

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.     

Local Defects are Always Neutral in the Thomas–Fermi–von Weiszäcker Theory of Crystals

The aim of this article is to propose a mathematical model describing the electronic structure of crystals with local defects in the framework of the Thomas–Fermi–von Weizsäcker (TFW) theory. The approach follows the same lines as that used in Cancès et al. (Commun Math Phys 281:129–177, 2008) for the reduced Hartree–Fock model, and is based on thermodynamic limit arguments. We prove, in particular, that it is not possible to model charged defects within the TFW theory of crystals.     

Numerical modeling of guided wave interaction with non-axisymmetric cracks in elastic cylinders

A three dimensional (3D) hybrid method combining the classical finite element (FE) method with the semi-analytical finite element (SAFE) technique is developed. This hybrid method is employed to study the interaction of guided waves with non-axisymmetric damages in cylinders. The near field surrounding the damage is analysed with the 3D FE method. The solution is expanded into sums of guided modes on both inlet and outlet cross-sections. Such eigenmode expansions enable separation into ingoing and outgoing waves, i.e., incident, reflected and transmitted waves. Using the SAFE method, elastic guided modes are then computed at the aforementioned cross-sections thus reducing the analysis to two dimensions (2D). The amplitudes of the incident modes are imposed, whereas those of the scattered modes are determined by solving the global system of the 3D hybrid FE-SAFE model. In this paper, a formula is proposed for the calculation of eigenforces and modal power flows from eigendisplacements and SAFE matrices. This has the advantage of simplifying the post-process of load eigenvectors in hybrid FE-SAFE methods. Results obtained for a vertical free-end cylinder are in good agreement with those published in the literature. Moreover, first results of the interaction of the fundamental compressional, flexural and torsional Pochhammer–Chree modes with non-axisymmetric vertical cracks are obtained and discussed. Then, the interactions of the fundamental compressional mode with oblique free-ends and cracks are briefly addressed. The power balance is shown to be satisfied with a good accuracy.     

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.     

Preface to the special issue of JOGO on the occasion of the 40th anniversary of the Group for Research in Decision Analysis (GERAD).

Journal of Global Optimization -     

Infrared and Raman Spectra of Solid Guanine Derivatives. 7-METHYLGUANINE, 9-METHYLGUANINE, 9-ETHYLGUANINE, 1,7-DIMETHYLGUANINE,and 1,9-DIMETHYLGUANINE.

The infrared and Raman spectra of 7-methylguanine, 9-methylguanine, 9-ethylguanine, 1,7-dimethylguanine, and 1,9-dimethylguanine in the solid state have been reported and discussed. Hydrogen bonds in these solid guanine derivatives bring about strong perturbations which are discussed in terms of structural data given by X-ray diffraction methods. The spectra of guanine and 9-methylguanine are compared with the spectra of the monomers isolated in low-temperature matrices.