Guy Bouchoux

A relationship between the kinetics and thermochemistry of proton transfer reactions in the gas phase

Abstract For the proton transfer reaction [MH]+ + B → M + [BH]+ (I) a correlation is observed between the experimental reaction rate kexp and the standard free energy variation ΔG°. This correlation may be described by a relationship of the type k exp /k coll = 1 [1 + exp (ΔG° + G a °)/RT] where kcoll is the collision rate constant and ΔGa° an apparent energy barrier for reaction (I). It is found that ΔGa° is of the same order as RT and thus the preceding relationship allows the determination of unknown gas-phase basicities. Implications for the use of the “bracketing” and the “kinetic” methods are discussed.

Alternative Neisseria spp. type IV pilin glycosylation with a glyceramido acetamido trideoxyhexose residue.

The importance of protein glycosylation in the interaction of pathogenic bacteria with their host is becoming increasingly clear. Neisseria meningitidis, the etiological agent of cerebrospinal meningitis, crosses cellular barriers after adhering to host cells through type IV pili. Pilin glycosylation genes (pgl) are responsible for the glycosylation of PilE, the major subunit of type IV pili, with the 2,4-diacetamido-2,4,6-trideoxyhexose residue. Nearly half of the clinical isolates, however, display an insertion in the pglBCD operon, which is anticipated to lead to a different, unidentified glycosylation. Here the structure of pilin glycosylation was determined in such a strain by “top-down” MS approaches. MALDI-TOF, nanoelectrospray ionization Fourier transform ion cyclotron resonance, and nanoelectrospray ionization quadrupole TOF MS analysis of purified pili preparations originating from N. meningitidis strains, either wild type or deficient for pilin glycosylation, revealed a glycan mass inconsistent with 2,4-diacetamido-2,4,6-trideoxyhexose or any sugar in the databases. This unusual modification was determined by in-source dissociation of the sugar from the protein followed by tandem MS analysis with collision-induced fragmentation to be a hexose modified with a glyceramido and an acetamido group. We further show genetically that the nature of the sugar present on the pilin is determined by the carboxyl-terminal region of the pglB gene modified by the insertion in the pglBCD locus. We thus report a previously undiscovered monosaccharide involved in posttranslational modification of type IV pilin subunits by a MS-based approach and determine the molecular basis of its biosynthesis.

FeIII‐Hydroperoxo and Peroxo Complexes with Aminopyridyl Ligands and the Resonance Raman Spectroscopic Identification of the Fe−O and O−O Stretching Modes

Nonheme Fe(III)-hydroperoxo and Fe(III)-peroxo complexes with aminopyridyl-type ligands have been prepared and characterized by UV/Vis, EPR, mass and Resonance Raman (RR) spectroscopy. The Fe(III)(OOH) species are low-spin and exhibit a deep purple color due to the ligand-to-metal charge transfer (LMCT) hand centered at ca. 550 nm. The RR spectra of the Fe(III)(OOH) complexes display two bands at ca. 620 and 800 cm-1 that are assigned to the respective Fe-O and O-O stretching modes on the basis of the characteristic H/D and 16O/18O frequency shifts. Upon deprotonation, Fe(III)(O2) species are obtained which possess a high-spin configuration of nearly axial symmetry and a LMCT transition in the near infrared (ca. 750 nm). The frequencies of the Fe-O and O-O stretching modes at ca. 465 and 820 cm-1, as well as their respective 16O/18O shifts of -16 and -45 cm-1, indicate an ?2 coordination geometry for the Fe(III)(O2) complex.

Gas-phase basicity of glycine, alanine, proline, serine, lysine, histidine and some of their peptides by the thermokinetic method.

The thermokinetic method is applied to a set of six amino acids (glycine, alanine, proline, serine, lysine, histidine) and 30 of their di-and tri-peptides for which experimental proton transfer rate constants were available. The comparison between the presently determined gas-phase basicities, GBs, of the amino acids with values obtained from equilibrium constant determination is generally good (a mean deviation of ∼3 kJ mol−1 is observed). Derived proton affinities values are discussed. The gas-phase basicities of peptides provided by the present study correct several previously estimated values thus offering a more firm basis for structural discussion. Composite reaction efficiency curves indicate the existence, for several peptides, of at least two non-interconverting populations of protonated forms.

Biomimetic Catalysis of Catechol Cleavage by O2 in Organic Solvents − Role of Accessibility of O2 to FeIII in 2,11‐Diaza[3,3](2,6)pyridinophane‐Type Catalysts

Three new complexes, [Fe(LN4H2)Cl2]+, [Fe(LN4H2)(Cat)]+, and [Fe(LN4H2)(DBC)]+, were synthesized by using the tetradentate macrocyclic ligand LN4H2 (where LN4H2, Cat, and DBC stand for 2,11-diaza[3,3](2,6) pyridinophane, catecholate, and 3,5-di-tert-butylcatecholate, respectively). The structure of [Fe(LN4H2)Cl2]+ was determined by X-ray diffraction. It crystallizes in the monoclinic space group C2/c with a = 9.613(1), b = 11.589(1), c = 14.063(2) A, β=110.20(2)°, V = 1541.9(3) A3, and Z = 4. These complexes were found to catalyze the oxidation of catechol groups using O2. This was performed in various organic solvents at 20 °C. The reaction rates were measured for the stoichiometric complexes [Fe(LN4H2)(Cat)]+ and [Fe(LN4H2)(DBC)]+. It was found that despite the relatively high energy of the ligand-to-metal charge transfer O(DBC or Cat)FeIII, their activity was comparable to that of the fast TPA systems [TPA indicates tris(2-pyridylmethyl)amine]. The oxidation products of DBCH2 have been studied. It has then been shown that the LN4H2 systems catalyse by means of both intra- and extradiol cleavage of catechol groups. The existence of multiple reactive pathways can account for the fast reactivity observed.

Structural and energetic aspects of the protonation of phenol, catechol, resorcinol, and hydroquinone.

The various protonated forms of phenol (1), catechol (2), resorcinol (3), and hydroquinone (4) were explored by ab initio quantum chemical calculations at the MP2/6-31G(d) and B3LYP/6-31G(d) levels. Proton affinities (PA) of 1-4 were calculated by the combined G2(MP2,SVP) method, and their gas-phase basicities were estimated after calculation of the change in entropy on protonation. These theoretical data were compared with the corresponding experimental values determined in a high-pressure mass spectrometer. This comparison confirmed that phenols are essentially carbon bases and that protonation generally occurs in a position para to the hydroxyl group. Resorcinol is the most effective base (PA = 856 kJ mol-1) due to the participation of both oxygen atoms in the stabilization of the protonated form. Since protonation is accompanied by a freezing of the two internal rotations, a significant decrease in entropy is observed. The basicity of catechol (PA = 823 kJ mol-1) is due to the existence of an intramolecular hydrogen bond, which is strengthened upon protonation. The lower basicity of hydroquinone (PA = 808 kJ mol-1) is a consequence of the fact that protonation necessarily occurs in a position ortho to the hydroxyl group. When the previously published data are reconsidered and a corrected protonation entropy is used, a proton affinity value of 820 kJ mol-1 is obtained for phenol.

Keto–enol tautomerism and dissociation of ionized acetaldehyde and vinyl alcohol. A G2 Molecular Orbital Study

Part of the potential energy surface for ionized vinyl alcohol, [CH2=CHOH].+, 1.+, acetaldehyde, [CH3CHO].+, 2.+, and hydroxycarbene [CH3COH].+, 3.+, is calculated at the G2 level of theory. It is confirmed that the latter structure is a stable species (predicted 298K heat of formation = 835 kJ/mol) which serves as intermediate during dissociation of 1.+ and its isomerization to 2.+.

Protonation thermochemistry of alpha-aminoacids bearing a basic residue.

The proton affinity (PA) and protonation entropy, ΔpS°, of glycine (Gly), 1, aspartic acid (Asp), 2, asparagine (Asn), 3, histidine (His), 4, lysine (Lys), 5, glutamic acid (Glu), 6, and glutamine (Gln), 7, have been reinvestigated by the extended kinetic method, using the “isothermal point” method and the orthogonal distance regression technique. The proton affinity values of α-amino acids bearing a basic residue (PA = 926.8, 965.2, 996.0, 993.9, 981.8 and 988.1 kJ mol−1 for 2–7, respectively) show significant deviation from the tabulated values. As expected from the effect of a strong intramolecular hydrogen bond in the protonated forms of these peculiar amino acids, negative protonation entropies are detected (ΔpS° = −36, −43, −37, −29, −95 and −55 J mol−1 K−1 for 2–7, respectively).

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.

Application of the kinetic method to bifunctional bases: ESI tandem quadrupole experiments

Abstract The applicability of the kinetic method to the determination of the basicity of bidentate molecules has been assessed by considering several molecules M previously studied by equilibrium method (M=acetone (1), 1,3-propanediol (2), glycerol (3), 1,4-butanediol (4), 1,3-propanolamine (5), 1,4-butanolamine (6), 1,3-propanediamine (7) and 1,4-butanediamine (8)). Protonated adducts [MHBi]+ (where Bi is a reference base) were produced by electrospray ionisation and analysed by tandem quadrupole mass spectrometry. Application of the classical correlation of the natural logarithm of the ratio of peak intensities, ln([MH]+/[BiH]+), with either the proton affinities (PA) or the gas phase basicities (GB) of the reference bases Bi to deduce PA(M) or GB(M) has been examined. It is confirmed that only the use of several experiments at different collision energies (“extended” or “isothermal point” methods) may lead to meaningful results. Good agreement is observed between the PA(M) values tabulated or obtained from the isothermal point for molecule M = 1 and 5–8. However, the present PA values appear to be different from that obtained by equilibrium method in the case of diols 2–4. It is generally observed that the measured “apparent” protonation entropies of all the bifunctional molecules examined are significantly less than that obtained by equilibrium methods.