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

International audienceAcid-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 Delta(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; Delta(acid)H = 1393, 1391, 1396, 1411; Delta(acid)G = 1363, 1362, 1367, 1382 kJ mol-1. This study also confirms that a non-negligible Delta(p)S° 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 reexamination of several IRMPD spectra

Protonation Thermochemistry of Gaseous 2,2\u27-, 4,4\u27- and 2,4\u27-Bipyridines and 1,10-phenanthroline

Quantum chemical composite methods G3MP2B3, G3B3, G4MP2 and G4 have been used to calculate enthalpies of formation and gas phase basicities of the title compounds. Comparison of the results with the available experimental heats of formation values reveals correct agreement (to within ≈ 2 kJ/mol) with G3B3 and G4 methods. Systematic errors on the heats of formation of these aromatic molecules are detected when calculated using the G3MP2B3 and G4MP2 methods. Using G3B3 and G4 atomization energies, ΔfH°298 of 2,2’-bipyridine, 1, 1,10-phenanthroline, 2, 4,4’-bipyridine, 3, and 2,4’-bipyridine, 4, equal to 269, 316, 287 and 282 kJ/mol, respectively were obtained. Homodesmotic reactions confirm these ΔfH° estimates for the three isomeric bipyridines 1, 3 and 4. G3MP2B3, G3B3, G4MP2 and G4 methods lead to comparable proton affinities (PA) values for the four molecules 1−4, in particular because of error compensation in the case of G3MP2B3 and G4MP2 results. Excellent agreement is found with experimental PA values of reference nitrogen bases (within less than 1.2 kJ/mol) allowing us to safely predict PA values of 974, 999, 933 and 958 kJ/mol for 2,2’-bipyridine, 1, 1,10-phenanthroline, 2, 4,4’-bipyridine, 3, and 2,4’-bipyridine (protonated at the most basic site N(4\u27)), 4, respectively. Estimate of the corresponding gas phase basicities is also proposed after con-sideration of the entropy of hindered rotations: GB(1) = 943, GB(2) = 966, GB(3) = 900, GB(4) = 927 kJ/mol

From the mobile proton to wandering hydride ion: mechanistic aspects of gas-phase ion chemistry.

International audienceStructural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(-) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments. Most fragmentation processes of molecular and pseudo-molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion-neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic

Heats of formation and protonation thermochemistry of gaseous benzaldehyde, tropone and quinone methides.

International audienceQuantum chemistry calculations using composite G3B3, G3MP2B3 and CBS-QB3 methods were performed for benzaldehyde, 1, tropone, 2, ortho-quinone methide, 3, para-quinone methide, 4, their protonated forms 1H(+)-4H(+) and the isomeric meta-hydroxybenzyl cation 5H(+). The G3B3 298 K heats of formation values obtained in this work are: -39, 61, 52, 39, 661, 679, 699, 680 and 733 kJ mol(-1) for 1-4, 1H(+)-5H(+), respectively. At the same level of theory, computed proton affinities are equal to 834, 916, 887 and 892 kJ mol(-1) for molecules 1-4. These results allow to correct discrepancies on the previously reported thermochemistry of molecules 2-4 and cations 2H(+)-5H(+)

Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods.

International audienceThe experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules

Evaluation of the protonation thermochemistry obtained by the extended kinetic method.

International audienceAn evaluation of the results obtained by the extended kinetic method for a series of representative bases is presented here. Analysis of the original experimental data is conducted using the orthogonal distance regression (ODR) statistical treatment. A comparison with the proton affinities and protonation entropies obtained from variable temperature equilibrium constant measurements demonstrate deviations, which may be ascribed to random and systematic errors. Considerable random errors are associated with the extended kinetic method if the number of reference bases and the range of effective temperatures are too low. It is also confirmed that large systematic errors on proton affinities and protonation entropies are obtained when large protonation entropy is associated with the considered system. It is, however, encouraging to note that the gas phase basicities obtained by the extended kinetic method are generally comparable to that obtained by other methods within a few kJ/mol. Copyright 2006 John Wiley & Sons, Ltd

Microcanonical Modeling of the thermokinetic method

International audienceA microcanonical analysis of the thermokinetic method is performed using statistical rate calculations based on orbiting transition state theory in order to model a proton transfer process: MH+ + Bi → M + BiH+. The reaction efficiency is calculated as a function of the difference in zero point energy of reactants and products. Several models of reactions were investigated in order to simulate situations where the base of interest M exhibits loss of entropy upon protonation of up to 40 J mol-1 K-1. It is shown that the standard thermokinetic method would predict correct 298 K gas phase basicities, GB298(M), even for polydentate molecules M, if experiments are conducted at this temperature. Proton affinity, PA298(M), and protonation entropy may be obtained by the thermokinetic method only in special circumstances such as, for example, experiments conducted at various temperatures

Gas-phase basicities of polyfunctional molecules. Part 4: Carbonyl groups as basic sites

International audienceThis article constitutes the fourth part of a general review of the gas‐phase protonation thermochemistry of polyfunctional molecules (Part 1: Theory and methods, Mass Spectrom Rev 2007, 26:775–835, Part 2: Saturated basic sites, Mass Spectrom Rev 2012, 31:353–390, Part 3: Amino acids, Mass Spectrom Rev 2012, 31:391–435). This fourth part is devoted to carbonyl containing polyfunctional molecules. After a short reminder of the methods of determination of gas‐phase basicity and the underlying physicochemical concepts, specific examples are examined under two major chapters. In the first one, aliphatic and unsaturated (conjugated and cyclic) ketones, diketones, ketoalcohols, and ketoethers are considered. A second chapter describes the protonation energetic of gaseous acids and derivatives including diacids, diesters, diamides, anhydrides, imides, ureas, carbamates, amino acid derivatives, and peptides. Experimental data were re‐evaluated according to the presently adopted basicity scale. Structural and energetic information given by G3 and G4 quantum chemistry computations on typical systems are presented

Pierre Longevialle remembered

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