Influence of Water on the Oxidation of Dimethyl Sulfide by the ·OH Radical.

Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to the formation of adduct intermediates that are too short-lived to be experimentally detectable. In this study we have modeled the simplest of such oxidative reactions: the attack of dimethyl sulfide (DMS) by a hydroxyl radical (·OH) to form a radical adduct, whose subsequent heterolytic dissociation leads to a radical cation (DMS+) that is important for further reactions. We have modeled the aqueous environment with a limited number of discrete water molecules, selected after an original multistep procedure, and further embedded in a polarizable continuum model, to observe the impact of the water configuration on the heterolytic dissociation of the radical adduct. Molecular dynamics and quantum chemical methods (DFT, MP2, and CCSD) were used to elucidate the lowest energy structures resulting from the ·OH attack on DMS. Subsequent high level ab initio valence bond (BOVB) calculations revealed the possibility for the occurrence of subsequent heterolytic dissociation.

Radical Cations of the Monomer and van der Waals Dimer of a Methionine Residue as Prototypes of (2 Center-3 Electron) SN and SS Bonds. Molecular Simulations of Their Absorption Spectra in Water.

Oxidation of peptides or proteins by the OH(•) radicals produced by pulse radiolysis yields species identified by their absorption spectra in the UV-visible domain. However, the case of methionine (Met) in peptides is complex because its oxidation can lead to various free radicals with 2 center-3 electron (2c-3e) bonds. We have performed Monte Carlo/density functional theory molecular simulations of the radical cation of the methylated methionine aminoacid, Met(•+), taken as a model of the methonine residue of peptides, and of the radical cation of its van der Waals dimer, Met2(•+). The cation of the methionine residue displays a 2c-3e SN bond. The cation of dimer Met2(•+) displays three quasidegenerate conformers, one stabilized by a 2c-3e SS bond and the other two stabilized by ion-molecule interactions and made up of a neutral and a cationic unit. These conformers are characterized by their charge and spin density localization and their UV-visible absorption spectra. These spectra enable a discussion of the absorption spectra of the literature; in particular, we emphasize the role of dimers before and after the oxidation process.

Toward an Understanding of the Oxidation Process of Methionine Enkephalin: A Combined Electrochemistry, Quantum Chemistry and Quantum Chemical Topology Analysis.

Recent experimental results about the oxidation of methionine enkephalin by ·OH radicals indicated an intramolecular electron transfer between the C-terminal methionine radical cation and the tyrosine N-terminus too fast to be observed. We have investigated the thermodynamic possibility of this intramolecular electron transfer by calculating the one-electron redox potentials of both residues for several conformations of the peptide, extracted from the experimental data of the Protein Data Bank (1PLW). Using a QM/MM approach, we show that the redox potential of the Met(•+)/Met couple is higher than that of the TyrOH(•+)/TyrOH one (tyrosine is denoted as TyrOH) for all conformations. The intramolecular electron transfer between both residues (from TyrOH to Met(•+)) is thus always thermodynamically allowed. Previously, we had performed topological studies on the intramolecular electron transfer which predicted this charge transfer. A study by cyclic voltammetry pointed out that the wave belonging to methionine is not present when methionine enkephalin is oxidized and only the direct involvement of the tyrosine residue is observed.

Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin.

We have studied electron transfers (ET) between electron donors and acceptors, taking as illustrative example the case of ET in methionine enkephalin. Recent pulse and gamma radiolysis experiments suggested that an ultrafast ET takes place from the C-terminal tyrosine residue to the N-terminal, oxidized, methionine residue. According to standard theoretical frameworks like the Marcus theory, ET can be decomposed into two successive steps: i) the achievement through thermal fluctuations, of a set of nuclear coordinates associated with degeneracy of the two electronic states, ii) the electron tunneling from the donor molecular orbital to the acceptor molecular orbital. Here, we focus on the analysis of the time-dependent electronic dynamics during the tunneling event. This is done by extending the approaches based on the topological analyses of stationary electronic density and of the electron localization function (ELF) to the time-dependent domain. Furthermore, we analyzed isosurfaces of the divergence of the current density, showing the paths that are followed by the tunneling electron from the donor to the acceptor. We show how these functions can be calculated with constrained density functional theory. Beyond this work, the topological tools used here can open up new opportunities for the electronic description in the time-dependent domain.

Quantum chemical topology study of the water-platinum(II) interaction.

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 one-electron reduction potential of methionine-containing peptides depends on the sequence.

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.

Structural and topological studies of methionine radical cations in dipeptides: electron sharing in two-center three-electron bonds.

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.

Energies, stability and structure properties of radicals derived from organic sulfides containing an acetyl group after the *OH attack: ab initio and DFT calculations vs experiment.

The mutual location of the sulfur atom and the acetyl group was found to affect significantly the (*)OH-induced oxidation mechanism of the organic sulfides containing either an alpha- or beta-positioned acetyl group. This phenomenon was reflected in formation of different intermediate products observed in pulse radiolysis experiments (Varmenot et al. J. Phys. Chem. A. 2004, 108, 6331-6346). In order to obtain a better support for the earlier interpretation of the experimental data, quantum mechanical calculations were performed using a density functional theory method (DFT-B3LYP) and the ab initio method (Møller-Plesset perturbation theory MP2) for optimizations and energy calculations of the parent molecules and radicals and radical cations derived from them. In accordance with experiments, it was found that the alpha-positioned acetyl group in S-ethylthioacetate (SETAc) destabilizes hydroxysulfuranyl radicals and monomeric sulfur radical cations. Instead, formation of stable C-centered radicals of the alpha-(alkylthio)alkyl-type was found energetically favorable, the H3C-(*)CH-S-C(=O)CH3 radical, in particular. On the other hand, the beta-positioned acetyl group in S-ethylthioacetone (SETA) does not destabilize hydroxysulfuranyl radicals, monomeric sulfur radical cations, and dimeric sulfur radical cations. Moreover, the alpha-(alkylthio)alkyl radicals of the type -S-(*)CH-C(=O)- were found to be particularly stabilized. The calculated transition states pointed toward the efficient direct conversion of the hydroxysulfuranyl radicals derived from SETAC and SETA radicals into the respective C-centered radicals. This reaction pathway, important in neutral solutions, is responsible for the absence of the dimeric radical cations of SETAc at low and high concentrations and of the dimeric radical cations of SETA at relatively low concentrations of the solute.

Ab initio and QM/MM study of electron addition on the disulfide bond in thioredoxin.

Thioredoxin controls the intracellular redox potential through a disulfide/dithiol couple. Under conditions of oxidative stress, this protein functions via one-electron exchange, in which formation of the disulfide radical anion occurs. Combined quantum mechanical (QM) and molecular mechanical (MM) calculations using two- and three-level ONIOM schemes were performed on the thioredoxin (Trx) protein of Chlamydomonas reinhardtii in its oxidized-disulfide and one-electron-reduced forms. In both cases, the active site disulfide moiety was described at the MP2(fc)/6-31+G(d) level, and larger regions of varying sizes around the active site were described at the B3LYP/6-31+G(d) level. The remainder of the 112 residues and 33 water molecules of the crystal structure (PDB entry 1EP7) were described by the AMBER force field. Adiabatic electron affinities were calculated for the disulfide bond in all systems. Separate QM or QM/QM calculations were performed on the QM regions to establish the role of the remainder of the protein on the active site properties. The radical anion species becomes more stable as the number of amide groups in the vicinity increases. One-electron reduction potentials were calculated for the small molecule models, and approximated for the protein for which the values are similar to the experimental one (approximately 0 V). This high reduction potential is due to interaction with the charged end of Lys40, as indicated by mutation in silico to norleucine. The inclusion of the protonated Asp30 side chain and a water molecule in the QM region leads to an increase in the electron affinity. Proton transfer from the Asp30 side chain to the Cys39 sulfur in the radical anion species is strongly disfavored. The radical anion is more stable than the protonated form, which is consistent with experimental results.

EPR spectroscopy and theoretical study of gamma-irradiated asparagine and aspartic acid in solid state.

Aspartic acid (Asp) and asparagine (Asn) are vulnerable amino acids. One-electron addition or withdrawal reactions initiate many deleterious processes involving these amino acids. To study these redox processes we have irradiated by gamma-rays asparagine or aspartic acid in the solid state. The nature of the resulting free radicals was determined by electron paramagnetic resonance (EPR) and by calculations using DFT methods in various environments. Reactions initiated by electron transfer are different for both amino acids: Asn anion loses hydrogen atom whereas the cation undergoes decarboxylation. Conversely, Asp cation loses hydrogen atom from amine group, which triggers decarboxylation.

Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation.

Irradiation of proteins with intense X-ray radiation produced by third-generation synchrotron sources generates specific structural and chemical alterations, including breakage of disulfide bonds and decarboxylation. In this paper, disulfide bond lengths in irradiated crystals of the enzyme Torpedo californica acetylcholinesterase are examined based on quantum simulations and on experimental data published previously. The experimental data suggest that one disulfide bond elongates by approximately 0.7 A upon X-ray irradiation as seen in a series of nine data sets collected on a single crystal. Simulation of the same bond suggests elongation by a similar value if a disulfide-radical anion is formed by trapping an electron. The absorption spectrum of a crystal irradiated under similar conditions shows a peak at approximately 400 nm, which in aqueous solution has been attributed to disulfide radicals. The results suggest that the formation of disulfide radicals in protein crystals owing to X-ray irradiation can be observed experimentally, both by structural means and by absorption spectroscopy.