No abstract

Although a two-center three-electron (2c-3e) bond between homonuclear atoms is well characterized, this is not the case for the S∴O bond, especially in neutral radicals resulting from the addition of a hydroxyl group on various sulfur substrates. A structural, energetical, and topological study is presented for prototypical radicals, ionic and neutral, RSOH -, RR′SOH 2 + , and RR′SOH, with R, R′ ) H, CH 3 . Three calculation methods have been applied, BH&HLYP, MP2, and CCSD(T), with different basis sets to determine the domains of accuracy of the more approximate ones to use them for larger systems. Qualitative and quantitative criteria, defined from the topological analysis of the electron localization function, are proposed to characterize such a 2c-3e bond. They specify the number and type of basins and their hierarchy of bifurcation, the global charge transfer between the fragments, the localization of the integrated spin density, and the electron delocalization between the lone pairs of the interacting atoms. Surprisingly, the neutral radicals show an intermediate behavior between the pure 2c-3e S∴O bond in anions and the electrostatic interaction in cations, despite the low energy of bond formation. As in the radical anions, the substitution favors the formation of a 2c-3e bond.

ABSTRACT:The topological analysis of the electron localization function (ELF) provides a convenient mathematical framework enabling an unambiguous characterization of bonds and more particularly in terms of bond types. In this contribution, we present an overview of the applications of this approach to biological and biomimetic systems.

In this paper, a review is presented of the abundant literature on the two-center three-electron (2c-3e) bonding, which plays a crucial role in elec-ously defined by Fuster and Silvi (Theor Chem Acc 2000,104,13)

One electron oxidation of methionine in peptides is highly dependent on the local structure. The sulfur-centered radical cation can complex with oxygen, nitrogen, or other sulfur atoms from a neighboring residue or from the peptidic bond, forming an intramolecular S therefore X two-center three-electron bond (X = S, N, O). This stabilization was investigated computationally in the radical cations of three peptides, methionine glycine (Met Gly) and its reverse sequence Gly Met, and Met Met. Geometry optimizations were done at the BH&HLYP/6-31G(d) level of theory and the effect of solvation was taken into account using a continuum model (CPCM). Up to seven stable conformations were considered for each peptide, with formation of 5-10 member cycles involving nitrogen from the peptidic bond or from the amine, oxygen from the peptidic bond or from the carboxylate group, or sulfur from the other residue for Met Met. The absorption wavelengths corresponding to the sigma --> sigma* transition calculated for each complex at the TD-BH&HLYP/6-311+G(d,p)//BH&HLYP/6-31G(d) level of theory vary from the near-UV for the S therefore O bonds to the green visible for the S therefore S bonds. For X = N, they increase with the SN distance as expected for a 2c-3e bond, whereas for X = O they slightly decrease. Characterization of these 2c-3e bonds as a function of the sequence, using the ELF and the AIM topological analyses, shows the different natures of the S therefore X bonds, which is purely 2c-3e for X = S, mainly 2c-3e with a part of electrostatic interaction for X = N and mainly electrostatic for X = O.

The protein residue methionine (Met) is one of the main targets of oxidizing free radicals produced in oxidative stress. Despite its biological importance, the mechanism of the oxidation of this residue is still partly unknown. In particular the one-electron redox potentials of the couple Met(•+)/Met have not been measured. In this work, two approaches, experimental as well as theoretical, were applied for three dipeptides L-Met L-Gly, L-Gly L-Met and L-Met L-Met. Measurements by electrochemistry indicated differences in the ease of oxidation. Two DFT methods (BH&HLYP and PBE0) with two basis sets (6-31G(d) and 6-311+G(2d,2p)) were used to determine the redox potentials of Met in these peptides present in different conformations. In agreement with experimental results, we show that they vary with the sequence and the spatial structure of the peptide, most of the values being higher than 1 V (up to 2 V) vs NHE.

The "inverse hydration" of neutral complexes of Pt(II) by an axial water molecule, whose one OH-bond is oriented toward Pt, has been the subject of recent works, theoretical as well as experimental. To study the influence of the ligands on this non-conventional H-bond, we extend here our previous energy calculations, using the second-order Moeller-Plesset perturbation theory (MP2) method together with the Dolg-Pélissier pseudopotential for platinum, to various neutral complexes including the well-known chemotherapeutic agent "cisplatin". The stabilization energy, depending on the nature and the configuration of platinum ligands, is dominated by the same important dispersive component, for all the investigated complexes. For a further characterization of this particular H-bond, we used the atoms in molecules theory (AIM) and the topological analysis of the electron localization function (ELF). The charge transfer occurring from the complex to the water molecule and the Laplacian of the density at the bond critical point between water and Pt are identified as interesting AIM descriptors of this non-conventional H-bond. Beyond this AIM analysis, we show that the polarization of the ELF bonding O-H basin involved in the non-conventional H-bond is enhanced during the approach of the water molecule to the Pt complexes. When the water medium, treated in an implicit solvation model, is taken into account, the interaction energies become independent on the nature and configuration of platinum ligands. However, the topological descriptors remain qualitatively unchanged.

The three-electron bond in radical anions of the H n XYH m - type, with X, Y = Cl, S, P, Si, F, O, N, C and n, m = 0−2, has been investigated from the topological analysis of the electron localization function (ELF) at the BH&HLYP level. It is shown that the topological modifications arising within the bonding region upon vertical electron attachment are of three different types, according to the vertical electron affinity (vEA) of the neutral compound:  for vEA smaller than −16 kcal mol-1 the bonding population remains unchanged, as in H4P2, for negative vEA greater than −16 kcal mol-1 the bonding population decreases, as in H2S2, and for positive vEA the bonding population disappears, as in Cl2. However, after relaxation of the geometry, the formation of the three-electron bond is accompanied in all cases by the disappearance of the X−Y bonding basin (which is the signature of the covalent bond in the neutral parent molecule). From a quantitative point of view, the topological approach also allows us to characterize the transfer of charge and spin densities that arises upon these processes toward the lone pairs basins of the X and Y atoms. Finally, to quantify the electron fluctuation between the two moieties, an index of delocalization has been defined from the analysis of the variance of the lone pairs population. This index increases approximately linearly with the dissociation energy D e of the radical anions, provided that they are separated into a group of weakly bonded ones (D e < 18 kcal mol-1) and a group of strongly 3e-bonded ones (D e > 18 kcal mol-1).