Unveiling the Intimate Mechanism of the Crocin Antioxidant Properties by Radiolytic Analysis and Molecular Simulations.

The successive steps of the oxidation mechanism of crocin, a major compound of saffron, by the free OH• radical are investigated by pulse radiolysis, steady-state (gamma) radiolysis methods, and molecular simulations. The optical absorption properties of the transient species and their reaction rate constants are determined. The absorption spectrum of the oxidized radical of crocin resulting from the H-abstraction presents a maximum of 678 nm and a band of 441 nm, almost as intense as that of crocin. The spectrum of the covalent dimer of this radical contains an intense band at 441 nm and a weaker band at 330 nm. The final oxidized crocin, issued from radical disproportionation, absorbs weaker with a maximum of 330 nm. The molecular simulation results suggest that the OH• radical is electrostatically attracted by the terminal sugar and is scavenged predominantly by the neighbor methyl site of the polyene chain as in a sugar-driven mechanism. Based on detailed experimental and theoretical investigations, the antioxidant properties of crocin are highlighted.

Oxidation of Silver Cyanide Ag(CN)2- by the OH Radical: From Ab Initio Calculation to Molecular Simulation and to Experiment.

We investigate the oxidation of silver cyanide AgI(CN)2- in water by the OH radical in order to compare this complex with the free cation Ag+ and to measure the influence of the ligands. High-level ab initio calculations of the model species AgII(CN)2· enable the calibration of molecular simulations and the prediction of the oxidized species: AgII(CN)2(H2O)2· and its absorption spectrum, with an intense band at 292 nm and a weaker one at 390 nm. Pulse radiolysis measurements of the oxidation of AgI(CN)2- by the OH radical in water yields a transient species with a broad, intense band at 290 nm and a weaker band at 410 nm at short times after the pulse and a blue shift of the spectrum at longer times. The prediction of the simulations, that the oxidized complex AgII(CN)2(H2O)2· is formed, is confirmed by thermochemistry. Our calculations also suggest that the formation of the OH-adduct is possible only in very basic solution and that the blue shift observed at long times after the pulse is due to disproportionation of the oxidized complex. We also perform molecular simulations of the oxidation of free Ag+ cations by the OH radical. The results are compared to that of the literature and to the results obtained with the AgI(CN)2- complex.

Radiolytic Oxidation of Two Inverse Dipeptides, Methionine-Valine and Valine-Methionine: A Joint Experimental and Computational Study.

The two inverse peptides methionine-valine (Met-Val) and valine-methionine (Val-Met) are investigated in an oxidative radiolysis process in water. The OH radical yields products with very different absorption spectra and concentration effects: Met-Val yields one main product with a band at about 400 nm and other products at higher energies; there is no concentration effect. Val-Met yields at least three products, with a striking concentration effect. Molecular simulations are performed with a combination of the Monte Carlo, density functional theory, and reaction field methods. The simulation of the possible transients enables an interpretation of the radiolysis: (1) Met-Val undergoes an H atom uptake leaving mainly a neutral radical with a 2-center-3-electron (2c-3e) SN bond, which cannot dimerize. Other radicals are present at higher energies. (2) Val-Met undergoes mainly an electron uptake leaving a cation monomer with a (2c-3e) SO bond and a cation dimer with a (2c-3e) SS bond. At higher energies, neutral radicals are possible. This cation monomer can transfer a proton toward a neutral peptide, leaving a neutral radical.

Mechanism of (SCN)2·- Formation and Decay in Neutral and Basic KSCN Solution under Irradiation from a Pico- to Microsecond Range.

The detailed mechanism of the reaction between SCN- and the OH· radical and the formation of the dimer radical (SCN)2·- are studied by picosecond pulse radiolysis. First, concentrated SCN- solutions are used to observe directly the formation and decay of SCNOH·- in neutral and basic solutions. Then, the spectro-kinetic data, constituting a large matrix of data of the absorbance at different times and different wavelengths, obtained by pulse radiolysis measurements with a streak camera, in neutral and basic SCN- solutions, are analyzed simultaneously. Data analysis allowed us to deduce the absorption spectra of different radicals with their extinction coefficient and also to determine the rate constants of different reactions involved in the formation and decay of (SCN)2·-. Molecular simulations of the absorption spectra of the different species were also performed. The absorption spectrum of the radical SCN· is determined and is found to be different than that reported previously. It does not present a Gaussian shape centered at 330 nm; the absorption around 310 and 380 nm is not negligible. In addition, in a solution at pH 13, it is found that the (SCN)2·- radical is paired with an alkaline cation, inducing a blueshift of the absorption band compared to the free (SCN)2·-. Finally, the presence of K+ cations catalyzes the disproportionation reaction of (SCN)2·- and affects the kinetics.

Evaluation of Ca2+ Binding Sites in Tacrolimus by Infrared Multiple Photon Dissociation Spectroscopy.

Tacrolimus (TAC) is an efficient immunosuppressant used in organ transplantation procedures. There is an intrinsic correlation between TAC and Ca2+ because of the dependence of its action mechanism on calcium and calcineurin, and the role of ion coordination on TAC identification and quantitation. To depict the Ca2+ binding sites in TAC, this work carried out gas-phase vibrational infrared multiple photon dissociation spectroscopy of [Ca(TAC)]2+ and of three other TAC mimetic molecules (probes 1-3). Density functional theory (DFT) and Monte Carlo (MC) simulations were also used to support the experimental data assignment, and natural bond orbital (NBO) analysis was carried out to depict the coordination sphere. PM3 and B3LYP/6-31G(d) levels of theory displayed similar trends during the MC simulations, suggesting that PM3 is a viable alternative to more expensive DFT calculations, at least during the conformational analysis step. Infrared spectroscopy of the [Ca(probe X)1]2+ and [Ca(probe X)3]2+ ( X = 1-3) complexes allowed for a useful guide for building guess geometries and for the band assignment of the [Ca(TAC)]2+ complex. Nevertheless, the MC approach was particularly useful for exploring the potential energy surface. The lowest energy conformation for [Ca(TAC)]2+ was found by MC simulations and is 32.92 kJ mol-1 lower in energy than the one found by comparing the results obtained for Ca2+ coordination in probes, despite the calculated spectra being virtually identical. Both approaches are good ways to depict the coordination sites, and these results suggest that using small molecules as models is a reliable approach to depict the geometry or coordination sites of extensive ions, yielding a robust correlation between experimental and theoretical spectra. Furthermore, MC survey produced a lower energy conformation with a good match to the experimental results. Both methods depict the Ca2+ coordination sphere as a hexacoordinated environment where the main coordination centers are carbonyl groups.

Picosecond Pulse Radiolysis Study on the Radiation-Induced Reactions in Neat Tributyl Phosphate.

The ultrafast radiolytic behavior of tributyl phosphate, TBP, has been investigated using 7 ps electron pulses with 7 MeV kinetic energy, from which two key species have been observed and characterized: the TBP solvated electron (eTBP-) and the TBP triplet excited state TBP* (3a) or its fragmentation products. The eTBP- exhibits a broad absorption band in the visible and near-infrared (NIR) spectrum, with a maximum beyond our 1500 nm detection limit. Nitromethane was used to scavenge eTBP- to confirm its absorption spectrum and to determine its associated rate coefficient, 1.0 × 1010 M-1 s-1. The electron's molar extinction coefficients were found by an isosbestic method using biphenyl as a solvated electron scavenger. The time-dependent radiolytic yield of eTBP- was also determined directly from 7 ps to 7 ns and compared with those in water, tetrahydrofuran, and diethyl carbonate. In less than 10 ns, the decay is not due to the reaction with other solvent molecules and is instead predominantly due to the reactions with cations issued from the proton transfer by the TBP radical cation (TBP•+). In addition to eTBP-, another absorption band, stable up to 7 ns, was identified in the visible range. This has been attributed mainly to the TBP triplet excited state, TBP*(3a), by a combination of molecular modeling methodologies. Interestingly, we did not observe any absorption band in the visible nor in the NIR range arising from TBP•+. Calculations suggest that TBP•+ undergoes rapid proton transfer to yield a UV-absorbing species, TBP(-H+). Experimental results and supporting molecular simulations provide detailed identification of the earliest species yielded from the radiolysis of neat TBP.

Effect of the solvation state of electron in dissociative electron attachment reaction in aqueous solutions.

It is generally considered that the pre-solvated electron and the solvated electron reacting with a solute yield the same product. Silver cyanide complex, Ag(CN)2-, is used as a simple probe to demonstrate unambiguously the existence of a different reduction mechanism for pre-hydrated electrons. Using systematic multichannel transient absorption measurements at different solute concentrations from millimolar to decimolar, global data analysis and theoretical calculations, we present the dissociative electron attachment on Ag(CN)2-. The short-lived silver complex, Ag0(CN)22-, formed by hydrated electron with nanosecond pulse radiolysis, can be observed at room temperature. However, at higher temperatures only the free silver atom, Ag0, is detected, suggesting that Ag0(CN)22- dissociation is fast. Surprisingly, pulse radiolysis measurements on Ag(CN)2- reduction, performed by a 7 ps electron pulse at room temperature, show clearly that a new reduced form of silver complex, AgCN-, is produced within the pulse. This species, absorbing at 560 nm, is not formed by the hydrated electron but exclusively by its precursor. DFT calculations show that the different reactivity of the hydrated and pre-hydrated electrons can be due to the formation of different electronic states of Ag0(CN)22-: the prehydrated electron can form an excited state of this complex, which mainly dissociates into Ag0CN- + CN-.

Observation and Simulation of Transient Anion Oligomers (LiClO4)n- (n = 1-4) in Diethyl Carbonate LiClO4 Solutions.

NMR measurements show that diethyl carbonate (DEC, a solvent with a low dielectric constant) solutions of LiClO4 contain (LiClO4)n oligomers. The reduction of these species by solvated and presolvated electrons is followed by picosecond pulse radiolysis measurements. The data analysis shows that several anions absorbing in the near-infrared (NIR) and visible range are formed after the 7 ps electron pulse. In contrast with tetrahydrofuran (THF) solutions of LiClO4, the anionic monomer (LiClO4)- is not observed in DEC solutions. This is due to the fact that DEC is a nonpolar solvent favoring the clustering of monomers in the nonirradiated solution, as shown by NMR results, and also due to the instability of the anionic monomer. The absorption spectra of the anionic dimer (LiClO4)2-, trimer (LiClO4)3-, and tetramer (LiClO4)4- are clearly observed in NIR and visible ranges. Compared to the results obtained for the same system in THF and in agreement with simulated absorption spectra, the experimental results show that the absorption bands are shifted to the blue end of the spectrum when n increases. The kinetics recorded for the molar LiClO4 solution indicates that the solute is only in the form of oligomers (LiClO4)n with a large n value and that the reduced species absorb weakly in the visible region. Lastly, and contrary to what is known for well-separated ions in polar solvents, it is shown that the (LiClO4)n- anions are not stable with respect to self-reduction, leading to the decomposition of perchlorate anions. In this reaction, the perchlorate anion ClO4- is reduced by the Li atom into a chlorate anion ClO3-. This is proved by the presence of ClO3- and chlorinated species detected by mass spectrometry measurements in irradiated DEC solutions containing LiClO4.

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.

Identification of Transient Radical Anions (LiClO4)(n)(-) (n = 1-3) in THF Solutions: Experimental and Theoretical Investigation on Electron Localization in Oligomers.

Picosecond pulse radiolysis measurements of tetrahydrofuran (THF) solutions containing LiClO4 over a wide range of concentration are performed to investigate the formation of transient species. The (35)Cl NMR measurements of these solutions prior to irradiation show that the salt is in the form of (LiClO4)n oligomers. Kinetics and transient absorption spectra of intermediates in each solution are obtained on the time scale from 10 to 3800 ps. A global spectro-kinetic matrix of the data is analyzed by the multicurve resolution alternated least-squares (MCR-ALS) method. It shows the presence of 3 transient species induced by electron pulse, in addition to the solvated electron. A hybrid Monte Carlo/DFT molecular simulation method is elaborated, using the MPW1K functional for the configuration sampling and B3LYP for the spectra calculations. The maximum of the absorption band of the monomer (LiClO4)(-), dimer (LiClO4)2(-), trimer (LiClO4)3(-), and tetramer (LiClO4)4(-) anions are deduced from the simulations. They enable one to label the MCR-ALS spectra (differences are below 0.1 eV) and to interpret the kinetic data. The simulations show also that Li(I) ion catalyzes the reduction of perchlorate by excess electrons. Only the dimer anion, due to its unique structure with a stable Li2(+) core and two nonbridging perchlorates, presents higher stability toward ClO4(-) reduction into ClO3(-). It corresponds to the long-lived species observed in the experiments.

Electron-induced growth mechanism of conducting polymers: a coupled experimental and computational investigation.

Pulse radiolysis was used to study the mechanism of HO(•)-induced polymerization of poly(3,4-ethylenedioxythiophene), PEDOT, in aqueous solution. A step-by-step mechanism has been found which involves a recurrent oxidation process by HO(•) hydroxyl radicals produced by water radiolysis. Furthermore, the cation radical, EDOT(•)(+), has been proposed as the promoter of the first step of polymerization. The determination of rate constants values and the attribution of transient and stable species were confirmed by molecular simulations and spectrokinetic analysis. Moreover, applying a series of electron pulses enabled in situ PEDOT polymerization. These polymers, which were characterized in solution or after deposition, form globular self-assembled structures with interesting conducting properties. Such a synthesis initiated for the first time by an electron accelerator gives us a glimpse of future promising industrial applications in the field of conducting polymers synthesis.

Reduction of earth alkaline metal salts in THF solution studied by picosecond pulse radiolysis.

Picosecond pulse radiolysis of tetrahydrofuran (THF) solutions containing earth alkaline metal salt, M(II)(ClO4)2, at different concentrations are performed using two different supercontinua as probe pulse, one covering the visible and another the near-infrared (NIR) down to the visible. Two types of line scan detectors are used to record the absorption spectra in the range from 400 to 1500 nm. Because of the strong overlap between the spectra of the absorbing species in the present wavelength range, global matrices were built for each M(II) system, by delay-wise binding the matrix for pure THF with the available matrices for this cation. The number of absorbers was assessed by Singular Value Decomposition of the global matrix, and a MCR-ALS analysis with the corresponding number of species was performed. The analysis of the results show clearly that solvated electron reacts with the earth alkaline metal molecule and the product has an optical absorption band very different than that of solvated electron in pure THF. So, contrarily to the case of solution containing free Na(+), in the presence of Mg(II), Ca(II) and Sr(II) the observed absorption band is not only blueshifted, but its shape is also drastically changed. In fact with Na(+) solvated electron forms a tight-contact pair but with earth alkaline metal cation solvated electron is scavenged by the undissociated molecule M(II)(ClO4)2. In order to determine the structure of the absorbing species observed after the electron pulse, Monte Carlo/DFT simulations were performed in the case of Mg(II), based on a classical Monte Carlo code and DFT/PCM calculation of the solute. The UV-visible spectrum of the solute is calculated with the help of the TDDFT method. The calculated spectrum is close to the experimental one. It is due to two species, a contact pair and an anion.

Oxidation of bromide ions by hydroxyl radicals: spectral characterization of the intermediate BrOH•-.

The reaction of (•)OH with Br(-) has been reinvestigated by picosecond pulse radiolysis combined with streak camera absorption detection and the obtained spectro-kinetics data have been globally analyzed using Bayesian data analysis. For the first time, the absorption spectrum of the intermediate species BrOH(•-) has been determined. This species absorbs in the same spectral domain as Br(2)(•-): the band maximum is roughly at the same wavelength (λ(max) = 352 nm instead of 354 nm) but the extinction coefficient is smaller (ε(max) = 7800 ± 400 dm(3) mol(-1) cm(-1) compared with 9600 ± 300 dm(3) mol(-1) cm(-1)) and the band is broader (88 nm versus 76 nm). Quantum chemical calculations have also been performed and corroborate the experimental results. In contrast to Br(2)(•-), the existence of several water-BrOH(•-) configurations leading to different transition energies may account for the broadening of the absorption spectrum in addition to the higher number of degrees of freedom.

Influence of the chemical functionalities of a molecularly imprinted conducting polymer on its sensing properties: electrochemical measurements and semiempirical DFT calculations.

Starting from thiophene-based functional monomers (FM), namely, TMA, TAA, TMeOH, EDOT, and Th, bonded to atrazine (ATZ) target molecules into FM/ATZ prepolymerization dimers in acetonitrile solutions, differently functionalized molecularly imprinted conducting polymers (FM-MICP) are electrosynthesized and then washed and used as sensitive layers for ATZ recognition. Sensitivity of these layers toward ATZ, which is quantified by cyclic voltammetric measurements, decreases in the following order of functional monomers: TMA, TAA, TMeOH, EDOT, and Th. Absolute values of the FM-ATZ dimerization free energies are calculated with the help of DFT/PCM calculations and of an empirical correction of the entropy effects, using a modified Wertz formula. A strong correlation is found between FM-MICP sensitivity and the amount of FM/ATZ prepolymerization complexes.

Temperature dependent absorption spectra of Br(-), Br2(•-), and Br3(-) in aqueous solutions.

The absorption spectra of Br(2)(•-) and Br(3)(-) in aqueous solutions are investigated by pulse radiolysis techniques from room temperature to 380 and 350 °C, respectively. Br(2)(•-) can be observed even in supercritical conditions, showing that this species could be used as a probe in pulse radiolysis at high temperature and even under supercritical conditions. The weak temperature effect on the absorption spectra of Br(2)(•-) and Br(3)(-) is because, in these two systems, the transition occurs between two valence states; for example, for Br(2)(-) we have (2)Σ(u) → (2)Σ(g) transition. These valence transitions involve no diffuse final state. However, the absorption band of Br(-) undergoes an important red shift to longer wavelengths. We performed classical dynamics of hydrated Br(-) system at 20 and 300 °C under pressure of 25 MPa. The radial distribution functions (rdf's) show that the strong temperature increase (from 20 to 300 °C) does not change the radius of the solvent first shell. On the other hand, it shifts dramatically (by 1 Å) the second maximum of the Br-O rdf and introduces much disorder. This shows that the first water shell is strongly bound to the anion whatever the temperature. The first two water shells form a cavity of a roughly spherical shape around the anion. By TDDFT method, we calculated the absorption spectra of hydrated Br(-) at two temperatures and we compared the results with the experimental data.

UV-visible absorption spectra of small platinum carbonyl complexes and particles: a density functional theory study.

We investigate the influence of a carbonyl coating on the UV-visible absorption of platinum complexes and particles with the TDDFT method. We first investigate the Chini clusters [Pt(3)(CO)(6)](n)(2-), n = 1-4, for which the absorption spectra are known. We show that PBE is realistic but displays convergence issues and that B3LYP overestimates intertriangle distances and absorption intensities. We discuss the structure of the spectra and the parallel vs perpendicular character of the transition dipole with respect to the stacking axis. We then investigate the spectra of model carbonylated platinum particles: [Pt(13)(CO)(12)](2-) (with only terminal carbonyls) and [Pt(13)(CO)(24)](2-) (with only bridging carbonyls). B3LYP proves much more realistic than in the case of Chini clusters. The influence of the morphology of the platinum particle and of the carbonyl coating on the absorption spectra is discussed. The results suggest an interpretation of a spectrum, recorded in a recent synthesis.

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.

Molecular dynamics simulations of electron-alkali cation pairs in bulk water.

The structural, dynamic, and thermodynamic properties of an excess electron interacting with an alkali cation (Na+, K+, Li+) in bulk water were investigated by means of a mixed quantum-classical molecular dynamics simulation technique. This study includes a reparametrization of the electron-cation pseudopotentials. The free energy calculations for all three systems show that a contact electron-cation pair can be observed, which is either as stable as the dissociated pair (Li+) or more stable by only a few kT (Na+, K+). Given that the dissociation barrier is also quite small, we suggest that the average cation-electron distance in the experiments at room temperature will not depend on this free energy profile but rather on the minimization of the Coulombic repulsive interaction between like charges in the solvent medium. This enables us to compare the present molecular dynamics simulations with the spectroscopic data obtained for different ionic strengths. The overall trend of the UV-vis hydrated absorption spectra, namely, the shift toward shorter wavelengths at high ionic strengths, is fairly well reproduced. This confirms our hypothesis of statistical distribution of the cations and solvated electrons.

Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum.

The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the beta barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.

Molecular dynamics simulations of the Ag+ or Na+ cation with an excess electron in bulk water.

The properties of an excess electron interacting with a monovalent cation in bulk water are studied by molecular dynamics simulations. Sodium and silver cations are chosen as prototypical cases because of their very different redox properties. In both cases, mixed quantum classical molecular dynamics simulations reproduce the experimental UV-Vis spectra. In the case of silver, we observe a highly polarized neutral atom, corresponding to a dipolar excitonic state. For sodium a contact cation/electron pair is observed. Free energy curves along the cation electron coordinate are calculated using quantum Umbrella Sampling technique. The relative stability of the different chemical species is discussed.