Fernando Pflüger

Kinetics of oxidative addition of zerovalent palladium to aromatic iodides

Abstract The kinetics of oxidative addition of zerovalent palladium to aromatic iodides in tetrahydrofuran in the presence of the ligand triphenylphosphine have been studied by amperometry on the oxidation wave of palladium. The reaction is first order in aromatic iodide and first order in palladium and the rate constant is inversely proportional to the free ligand concentration. The reactive palladium intermediate is assumed to be Pd{P(C 6 H 5 ) 3 } 2 . This assumpion is compatible with the observed activation parameters Δ H ‡  +77 kJ mol −1 ; Δ S ‡  13 J mol −1 K −1 . With substituted aromatic iodides, the rate constants give a linear Hammett relationship with ϱ  +2. The suggested mechanism can be regarded as related to an aromatic nucleophilic substitution with some assitance from halogen—palladium interaction.

Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VIII. Amino Acids with Aromatic Side Chains: L-Phenylalanine, L-Tyrosine, and L-Tryptophan

Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly hydrated amino acids.

Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. IV. Amino Acids with Hydrophobic Side Chains: L-Alanine, L-Valine, and L-Isoleucine

In the framework of our investigations on the analysis of vibrational spectra of amino acids (AAs) in hydrated media, Raman scattering and Fourier transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of three alpha-amino acids with hydrophobic hydrocarbon side chains, i.e., alanine, valine, and isoleucine, were measured in H2O and D2O solutions. The present data complete those recently published by our group on glycine and leucine. This series of observed vibrational data gave us the opportunity to analyze the vibrational features of these amino acids in hydrated media by means of the density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing five water molecules interacting with H-donor and H-acceptor sites of amino acids are performed and allowed the observed main Raman and infrared bands to be assigned. Additional calculations on a cluster formed by leucine (L) and five water (W) molecules and the comparison of the obtained data with those recently published by our group on L+12W, allowed us to justify the number of hydration considered in the present report.

Vibrational analysis of amino acids and short peptides in hydrated media. VII. Energy landscapes, energetic and geometrical features of L-histidine with protonated and neutral side chains.

In manuscript VI of the same series (J. Phys. Chem. B 2010, 114, 1077-1088), we reported the geometrical and vibrational features of lysine and arginine, that is, two alpha-amino acids (alpha-AAs) with positively charged side chains, at physiological conditions. Here, we report our results on histidine, one of the most biologically important alpha-AAs, whose side chain can be neutral or positively charged through a protonation-deprotonation process of the nitrogens involved in its cyclic side chain at pH values in the physiological range. We have recorded at room temperature Raman scattering and Fourier-transform infrared (FT-IR) absorption spectra from the aqueous solutions of the AA at pH values 4, 6.8, and 8. It has been shown that a Raman spectrum recorded at the intermediate pH (6.8) can be perfectly reconstituted by a linear combination of those observed at two extreme pH values (4 and 8), allowing determination of the populations of histidine with protonated and neutral side chains in solution. The above-mentioned experimental data were completed by the vibrational spectra recorded in D(2)O. On the other hand, quantum mechanical calculations at the DFT/B3LYP/6-31++G* allowed us to analyze the energetic, geometrical, and vibrational features of histidine. Through a discussion on the basis of experimental and theoretical results, we comment on (i) the potential energy surfaces of histidine placed in a polarizable dielectric continuum, providing molecular energy landscapes as a function of its side chain orientations around C(alpha)-C(beta) and C(beta)-C(gamma) bonds; (ii) the full geometry optimization of the low energy conformers placed in a solvent continuum or in the presence of n explicit water molecules (n = 3, 7); (iii) the energy value separating the two histidine forms with neutral side chains; (iv) the determination of the side chain pK(a) by means of Raman spectra; and (v) the assignment of the observed vibrational modes by means of the lowest-energy conformers of hydrated histidine.

Vibrational analysis of amino acids and short peptides in hydrated media. VI. Amino acids with positively charged side chains: L-lysine and L-arginine.

In two recent reports of the same series (J. Phys. Chem. B 2007, 111, 1470-1477 and J. Phys. Chem. B 2009, 113, 3169-3178), we have described the geometrical and vibrational analysis of glycine and amino acids (AAs) with hydrophobic side chains through the joint use of optical spectroscopy and quantum mechanical calculations. Here, we report Raman scattering and Fourier-Transform Infrared (FT-IR) Attenuated Total Reflectance (ATR) spectra measured from the aqueous solutions (H(2)O and D(2)O) of L-lysine and L-arginine, i.e. two alpha-AAs with positively charged hydrophilic side chains. The discussion on the vibrational features of both AAs could be carried out thanks to the theoretical calculations performed by means of the Density Functional Theory (DFT) approach at the B3LYP/6-31++G* level. We have analyzed the influence of implicit (with a polarizable dielectric continuum) and explicit (by means of an H(2)O cluster interacting with H-donor and H-acceptor sites of AAs) hydration models. In addition, through the calculated geometrical parameters and vibrational wavenumbers, a discussion was performed on the effect of the Cl(-) anion interacting with the positively charged side chains of explicitly hydrated AAs.

Energy maps, side chain conformational flexibility, and vibrational features of polar amino acids L-serine and L-threonine in aqueous environment.

A comprehensive description of the energetic, conformational, and vibrational features of the two amino acids (AAs) with polar side chains, i.e., serine and threonine, in aqueous environment, is provided. To adequately analyze the side chain conformational flexibility of these amino acids, we resorted to quantum mechanical calculations with the use of density functional theory, which allowed the determination of the energetic features of these AAs through 236 clusters. Each cluster contains a zwitterionic AA surrounded by seven explicit water molecules. The obtained data could evidence the effect of the side chain conformational angle (χ(1) and χ(2)) as well as the location of water molecules on the energy landscapes of both AAs. Four of the lowest energy clusters of each AA, which give rise to distinct side chain conformations, were selected in order to reproduce the FT-IR and Raman spectra recorded in aqueous solutions and to assign the vibrational modes responsible of the main observed bands.

Protonation-deprotonation and structural dynamics of antidiabetic drug metformin.

Since the late 1950s, metformin is the worldwide first-line pharmacologic treatment for type 2 diabetes. Beyond the fact that the mode of action of this drug has always been very difficult to elucidate, little is known about its physicochemical properties in aqueous solution. Herein, we focus on the protonation-deprotonation features of metformin by using jointly Raman scattering and theoretical calculations. Vibrational markers evidence the fact that within a wide pH interval extended at either side of the physiological one, i.e. ∼7 ± 4, metformin is mainly monoprotonated. Although the biprotonated form appears as major population at very low pH values (<1.5), Raman markers of neutral species do not dominate even at very high pH values (>13), presumably because of the extreme basicity of metformin as described by recent NMR measurements. Density functional theory calculations using both explicit and implicit hydration models, have led to presume a possible coexistence of two possible monoprotonated forms in aqueous environment. In conclusion, the biophysical features of this molecule and the amount used in clinical practice might certainly explain the pleiotropic actions toward several targets where metformin could be a permanent cationic partner, a proton donor/acceptor, as well as a good candidate for stabilizing the so-called π→π interactions.

Heparin-like functionalized polymer surfaces: discrimination between catalytic and adsorption processes during the course of thrombin inhibition.

Thrombus formation on blood-contacting artificial surfaces is a major problem. Antithrombogenic polymer surfaces have been obtained either by heparin binding, or by grafting sulphonate and/or amino acid sulphonamide groups on insoluble polystyrene. In addition to their capacity to adsorb thrombin, such surfaces were shown to be able to catalyse its inhibition by antithrombin III (AT), i.e. they are endowed with heparin-like activity. The results were mainly obtained by using clotting assays. In many cases, delineating adsorption and catalytic processes by such assays is not possible when evaluating anticoagulant polymer surfaces. To overcome this problem, the kinetics of thrombin adsorption and inhibitions by AT and heparin cofactor II (HC) in the presence of such surfaces have been measured by using an assay performed with a thrombin-specific chromogenic substrate. A simple kinetic model of thrombin consumption is proposed. The relevant calculations, carried out with the help of a computer program, lead to determination of relative second order rate constants of thrombin adsorption and inhibitions by AT and HC in the presence of the polymers. In addition to thrombin adsorption, polystyrene surfaces bearing only sulphonate groups catalyse inhibition by AT, whereas polystyrene surfaces bearing either aspartate, glycinate or isophthalate sulphonamide groups catalyse both inhibitions by AT and HC.

Side chain flexibility and protonation states of sulfur atom containing amino acids

We present a set of new data allowing elucidation of the energetic, conformational and vibrational features of cysteine (Cys) and methionine (Met), i.e. two natural amino acids (AAs) containing a sulfur atom in their side chains. Special attention has been paid to cysteine, for which vibrational features were analysed in a wide pH range (6-to-12), where its backbone can switch from a zwitterionic to an anionic form, and its side chain SH group can be deprotonated. Through a detailed discussion on the relative acidity of the three protonation sites of this AA, as well as on the vibrational markers arising from zwitterionic and anionic backbones, we could assign the spectra recorded at pH 6, 9.2 and 12 to three species, referred to as Cys(0), Cys(1-)(a) and Cys(2-), where the superscripts designate their global net charges. To bring clarification to the structural and vibrational features, quantum mechanical calculations based on the Density Functional Theory (DFT) were carried out, allowing (i) a quasi exhaustive energetic and side chain conformational analysis through 804 clusters of explicitly hydrated AAs; (ii) simulation of the observed aqueous solution vibrational spectra of Cys(0), Cys(-2) and Met by means of the theoretical data obtained from their conformationally distinct lowest energy clusters.

Raman scattering-based multiconformational analysis for probing the structural differences between acetylcholine and acetylthiocholine

&NA; Acetylcholine is the first discovered neurotransmitter that has received a great attention regarding its capability of binding to several cellular targets. The chemical composition of acetylcholine, including a positively charged trimethylammonium and a carbonyl group, as well as its conformational flexibility was pointed out as the key factors in the stabilization of its interactions. Here, the possibilities offered by a Raman scattering‐based multiconformatioal analysis to access the most stable conformers of acetylcholine, is discussed. To control the validity of this protocol, acetylcholine and one of its closely structured analogues, acetylthiocholine, were simultaneously analyzed. Solution Raman spectra revealed distinct and well resolved strong markers for each molecule. Density functional theory calculations were consistent with the fact that the energy order of the low energy conformers is considerably affected by the acyloxy oxygen → sulfur atom substitution. Raman spectra were calculated on the basis of the thermal average of the spectra arising from the low energy conformers. It has been evidenced that the carbonyl and trimethylammonium groups are the most favorable hydration sites in aqueous environment. Taking into account the large gap between the carbonyl bond‐stretch and aliphatic bending bands, Raman spectra also allowed separation of the HOH bending vibrations arising from the bound and bulk water molecules. Graphical abstract Figure. No caption available. HighlightsAcetylcholine and acetylthiocholine provide strong Raman markers in aqueous solution.Low energy conformers are considerably affected by the O → S atom substitution.A multiconformational approach permitted assignment of observed markers.Raman spectra allowed the contributions of bulk and bound water, to be separated.