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-.

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.

Transferable force field for alcohols and polyalcohols.

A new force field has been developed for alcohol and polyalcohol molecules. Based on the anisotropic united-atom force field AUA4 developed for hydrocarbons, it only introduces one new anisotropic united atom corresponding to the hydroxyl group OH. In the case of polyalcohols and complex molecules, the calculation of the intramolecular electrostatic energy is revisited. These interactions are calculated between charges belonging to the different local dipoles of the molecule, one dipole being defined as a group of consecutive charges globally neutral. This new method allows avoiding the use of empirical scaling parameters commonly introduced to calculate 1-4 electrostatic interactions. The transferability of the proposed potential is demonstrated through the simulation of a wide variety of alcohol families: primary alcohols (methanol, ethanol, propan-1-ol, hexan-1-ol, octan-1-ol), secondary alcohols (propan-2-ol), tertiary alcohols (2-methylpropan-2-ol), phenol, and diols (1,2-ethanediol, 1,3-propanediol, 1,5-pentanediol). Monte Carlo simulations carried out in the Gibbs ensemble lead to a good agreement between calculated and experimental data for the thermodynamic properties along the liquid/vapor saturation curve, for the critical point coordinates and for the liquid structure at room temperature. Additional simulations were performed on the methanol + n-butane system showing the capability of the proposed potential to reproduce the azeotropic behavior of such mixtures with a good agreement.

Thermodynamic behavior of the CO2 + NO2/N2O4 mixture: a Monte Carlo simulation study.

The thermodynamic behavior of the carbon dioxide + nitrogen dioxide (CO2 + NO2) mixture was investigated using a Monte Carlo molecular simulation approach. This system is a particularly challenging one because nitrogen dioxide exists as a mixture of monomers (NO2) and dimers (N2O4) under certain pressure and temperature conditions. The chemical equilibrium between N2O4 and 2NO2 and the vapor-liquid equilibrium of CO2 + NO2/N2O4 mixtures were simulated using simultaneously the reaction ensemble and the Gibbs ensemble Monte Carlo (RxMC and GEMC) methods. Rigid all atoms molecular potentials bearing point charges were proposed to model both NO2 and N2O4 species. Liquid-vapor coexistence properties of the reacting NO2/N2O4 system were first investigated. The calculated vapor pressures and coexisting densities were compared to experimental values, leading to an average deviation of 10% for vapor pressures and 6% for liquid densities. The critical region was also addressed successfully using the subcritical Monte Carlo simulation results and some appropriate scaling laws. Predictions of CO2 + NO2/N2O4 phase diagrams at 300, 313, and 330 K were then proposed. Derivative properties calculations were also performed in the reaction ensemble at constant pressure and temperature for both NO2/N2O4 and CO2 + NO2/N2O4 systems. The calculated heat capacities show a maximum in the temperature range where N2O4 dissociation occurs, in agreement with available experimental data.

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.

Simulating Electron Dynamics in Polarizable Environments.

We propose a methodology for simulating attosecond electron dynamics in large molecular systems. Our approach is based on the combination of real time time-dependent-density-functional theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol) with the point-charge-dipole model of electrostatic induction. We implemented this methodology in the software deMon2k that relies heavily on auxiliary fitted densities. In the context of RT-TDDFT/MMpol simulations, fitted densities allow the cost of the calculations to be reduced drastically on three fronts: (i) the Kohn-Sham potential, (ii) the electric field created by the (fluctuating) electron cloud which is needed in the QM/MM interaction, and (iii) the analysis of the fluctuating electron density on-the-fly. We determine conditions under which fitted densities can be used without jeopardizing the reliability of the simulations. Very encouraging results are found both for stationary and time-dependent calculations. We report absorption spectra of a dye molecule in the gas phase, in nonpolarizable water, and in polarizable water. Finally, we use the method to analyze the distance-dependent response of the environment of a peptide perturbed by an electric field. Different response mechanisms are identified. It is shown that the induction on MM sites allows excess energy to dissipate from the QM region to the environment. In this regard, the first hydration shell plays an essential role in absorbing energy. The methodology presented herein opens the possibility of simulating radiation-induced electronic phenomena in complex and extended molecular systems.

Low-temperature vapor-liquid equilibria from parallelized molecular dynamics simulations. Application to 1- and 2-methylnaphthalene.

A parallelized sampling version of the Gibbs Ensemble (Mol. Phys. 2000, 98, 1887) has been implemented to predict low-temperature vapor-liquid equilibria of 1- and 2-methylnaphthalene modeled by anisotropic united atom potentials. The simulation were performed at the low temperature of 364.2 K at which common direct simulation methods fail due to particle transfer problems. The simulation results are compared with published results obtained from the Gibbs-Duhem integration method and with experimental data. Both methods are compared and discussed in terms of computational efficiency and with respect to their future use at other thermodynamic conditions.

Optimized intermolecular potential for aromatic hydrocarbons based on anisotropic united atoms. III. Polyaromatic and naphthenoaromatic hydrocarbons.

In this third article of the series, a new anisotropic united atoms (AUA) intermolecular potential parameter set has been proposed for the carbon force centers connecting the aromatic rings of polyaromatic hydrocarbons to predict thermodynamic properties using both the Gibbs ensemble and NPT Monte Carlo simulations. The model uses the same parameters as previous AUA models used for the aromatic CH force centers. The optimization procedure is based on the minimization of a dimensionless error criterion incorporating various thermodynamic data of naphthalene at 400 and 550 K. The new model has been evaluated on a series of polyaromatic and naphthenoaromatic hydrocarbons over a wide range of temperatures up to near-critical conditions. Vaporization enthalpy, liquid density, and normal boiling temperature are reproduced with good accuracy. The new potential parameters have also been tested successfully on toluene, 1,3,5-trimethylbenzene, styrene, m-xylene, n-hexylbenzene, and n-dodecylbenzene to demonstrate their transferability to alkylbenzenes.

Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale.

We have introduced a new algorithm in the parallel processing PMEMD module of the AMBER suite that allows MD simulations with a potential involving two coupled torsions. We have used this modified module to study the green fluorescent protein. A coupled torsional potential was adjusted on high accuracy quantum chemical calculations of the anionic chromophore in the first excited state, and several 15-ns-long MD simulations were performed. We have obtained an estimate of the fluorescence lifetime (2.2 ns) to be compared to the experimental value (3 ns), which is, to the best of our knowledge, the first theoretical estimate of that lifetime.