Effect of metal Ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms

Methods of quantum chemistry have been applied to double-charged complexes involving the transition metals Ni2+, Cu2+ and Zn2+ with the aromatic amino acids (AAA) phenylalanine, tyrosine and tryptophan. The effect of hydration on the relative stability and geometry of the individual species studied has been evaluated within the supermolecule approach. The interaction enthalpies, entropies and Gibbs energies of nine complexes Phe•M, Tyr•M, Trp•M, (M = Ni2+, Cu2+ and Zn2+) were determined at the Becke3LYP density functional level of theory. Of the transition metals studied the bivalent copper cation forms the strongest complexes with AAAs. For Ni2+and Cu2+ the most stable species are the NO coordinated cations in the AAA metal complexes, Zn2+cation prefers a binding to the aromatic part of the AAA (complex II). Some complexes energetically unfavored in the gas-phase are stabilized upon microsolvation

Absolute affinities of alpha-amino acids for Cu+ in the gas phase. A theoretical study

International audienceAb initio calculations have been carried out on the [glycine-Cu](+), [serine-Cu](+), and [cysteine-Cu](+) complexes. Investigation of several types of structures for each complex shows that the preferred binding site of Cu+ involves chelation between the carbonyl oxygen and the amino nitrogen. With glycine, this leads to a complexation energy (best estimate of D-0) of 64.3 kcal/mol. Additional chelation with the alcohol group of serine or the thiol group of cysteine leads to larger binding energies, with cysteine binding more strongly than serine, in good agreement with a recent experimental scale of relative Cu+ affinities of all alpha-amino acids present in natural peptides. Combining this scale to the accurate determination of the Cu+ affinity of glycine from the present work leads to absolute values of Cu+ affinities of all amino acids. Calculations were also carried out on the complexes of Cu+ with water, ammonia, formaldehyde, and hydrogen sulfide. The geometrical and electronic structures of these complexes are used to analyze the binding of Cu+ to amino acids

Interaction of alkali metal cations (Li+-Cs+) with glycine in the gas phase: A theoretical study

International audienceThe complexes formed by alkali metal cations (Cat(+)) and glycine (Gly) were studied by means of ab initio quantum chemical methods. Seven types of Gly-Cat(+) interaction were considered in each case. It was found that in the most stable forms of Gly-Li+ and Gly-Na+ the metal ion is chelated between the carbonyl oxygen and nitrogen ends of glycine. For Gly-K+ an isomer involving complexation with both oxygens of the carboxylic function is found to be degenerate with the above chelate, and becomes slightly more stable for Gly-Rb+ and Gly-Cs+. In all cases, interaction of the ion with the carboxylate group of zwitterionic glycine is also low in energy. Computed binding energies (Delta H-298, kcal mol(-1)) are 54.5 (Gly-Li+), 36.3 (Gly-Na+), 26.5 (Gly-K+), 24.1 (Gly-Rb+) and 21.4 (Gly-Cs+). The values for Gly-Na+ and Gly-K+ are in good agreement with recent experimental determinations. For Gly-Li+, a revised experimental value of 54.0 kcal mol(-1) is obtained, based on the computed complexation enthalpy and entropy of Li+ with N,N-dimethylformamide (51.7 kcal mol(-1) and 23.8 cal mol(-1) K-1, respectively). Three isomers among the most stable of the lithiated dimer Gly-Li+-Gly have been determined and found to involve local Gly-Li+ interactions analogous to those in the monomer However, the relative energies of the various isomers show nonnegligible differences between the monomer and the dimer, implying that the kinetic method must be used with care for the determination of cation affinities of larger molecules. Finally, the fluxionality of the Gly-Na+ complex has been considered by locating the transition states for interconversion of the lowest energy isomers. In particular it is found that the lowest isomer can be transformed into the one involving zwitterionic Gly with a rate-determining barrier of 20.4 kcal mol(-1)

A quantitative basis for a scale of Na+ affinities of organic and small biological molecules in the gas phase.

International audienceHigh Pressure Mass Spectrometric experiments and ab initio calculations have been carried out in order to establish a series of accurate gas phase sodium ion affinities of organic molecules with a wide variety of functional groups. Ab initio calculations have also been performed on the sodium complexes of three amino acids, serine, cysteine and proline. A systematic critical evaluation of experimental and computational literature results shows that a significant number require revision. Based on comparisons with accurate experimental measurements, the ab initio procedure used is shown to yield sodium ion affinities with an accuracy of ca. 1 kcal.mol-1. This enables the construction of the first reliable table of gas phase Na+ affinities for organic and small biological molecules

Na+ binding to cyclic and linear dipeptides. Bond energies, entropies of Na+ complexation, and attachment sites from the dissociation of Na+-bound heterodimers and ab initio calculations

International audienceThe Na+ affinities of simple cyclic and linear dipeptides and of selected derivatives are determined in the gas-phase based on the dissociations of Na+-bound heterodimers [peptide + Bi]Na+, in which Bi represents a reference base of known Na+ affinity (kinetic method). The decompositions of [peptide + Bi]Na+ are assessed at three different internal energies; this approach permits the deconvolution of entropic contributions from experimentally measured free energies to thus obtain affinity (i.e. enthalpy or bond energy) values. The Na+affinities of the peptides studied increase in the order (kJ mol-1) cyclo-glycylglycine (143) < cyclo-alanylglycine (149) < cyclo-alanylalanine (151) < N-acetyl glycine (172) < glycylglycine (177) < alanylglycine (178) < glycylalanine (179) < alanylalanine (180) < glycylglycine ethyl ester (181) < glycylglycine amide (183). The method used provides quantitative information about the difference in bond entropies between the peptide-Na+ and Bi-Na+ bonds, which is most significant when Na+ complexation alters rotational degrees of freedom either in the peptide or in Bi. From the relative bond entropies, it is possible to appraise absolute entropies of Na+ attachment, which are 104 and 116 J mol-1 K-1 for the cyclic and linear molecules, respectively. The combined affinity and entropy data point out that the cyclic dipeptides bind Na+ in a monodentate fashion through one of their amide carbonyl oxygens, while the linear molecules coordinate Na+ in a multidentate arrangement involving the two carbonyl oxygens and, possibly, the N-terminal amino group. High-level ab initio calculations reveal that the most stable [glycylglycine]Na+ structure arises upon bidentate chelation of Na+ by the two carbonyls and concomitant formation of a hydrogen bond between the amino group and the amide nitrogen. Such a structure agrees very well with the experimental enthalpy and entropy trends observed for the linear molecules. According to theory, zwitterionic forms of [glycylglycine]Na+ are the least stable isomers, as also suggested by the experimental results