A combined Monte Carlo/DFT approach to simulate UV-vis spectra of molecules and aggregates: Merocyanine dyes as a case study.

The combination of a Monte Carlo (MC) sampling of the configurational space with time dependent-density functional theory (TD-DFT) to estimate vertical excitations energies has been applied to compute the absorption spectra of a family of merocyanine dyes in both their monomeric and dimeric forms. These results have been compared to those obtained using a static DFT/TD-DFT approach as well as to the available experimental spectra. Though suffering of the limitations related to the use of DFT and TD-DFT for this type of systems, our data clearly show that the classical MC sampling provides a suitable alternative to classical molecular dynamics to explore the structural flexibility of these donor-acceptor (D-π-A) chromophores enabling a realistic description of the potential energy surface of both their monomers and aggregates (here dimers) and thus of their spectra. Overall, the combination of MC sampling with quantum mechanics (TD-DFT) calculations, carried out in implicit dioxane solvent on random snapshots, provides a workable compromise to solve the combined challenge of accuracy and time-consuming problem not only for merocyanines momers, but also for their dimers, up to now less investigated. Indeed, the simulated absorption spectra fairly agree with the experimental ones, suggesting the general reliability of the method.

Theoretical approaches for predicting the color of rigid dyes in solution.

Aiming at developing an affordable and easily implementable computational protocol for routine prediction of spectral properties of rigid molecular dyes, density functional theory, and time-dependent density functional theory were used in conjunction with a vibronic coupling scheme for band shape estimate. To predict the perceived color of molecules in solution, a model has been setup linking the UV-vis spectra predicted at ab initio level to the L*a*b* colorimetric parameters. The results show that a mixed protocol, implying the use of a global hybrid functional for the prediction of adiabatic energy differences and a range separated hybrid for the prediction of potential energy curvature, allows perceived colors to be quantitatively predicted, as demonstrated by the comparison of L*a*b* colorimetric parameters obtained from computed and experimental spectra. © 2017 Wiley Periodicals, Inc.

Solvation Accounts for the Counterintuitive Nucleophilicity Ordering of Peroxide Anions.

The nucleophilic reactivities (N, sN ) of peroxide anions (generated from aromatic and aliphatic peroxy acids or alkyl hydroperoxides) were investigated by following the kinetics of their reactions with a series of benzhydrylium ions (Ar2 CH+ ) in alkaline aqueous solutions at 20 °C. The second-order rate constants revealed that deprotonated peroxy acids (RCO3- ), although they are the considerably weaker Brønsted bases, react much faster than anions of aliphatic hydroperoxides (ROO- ). Substitution of the rate constants of their reactions with benzhydrylium ions into the linear free energy relationship lg k=sN (N+E) furnished nucleophilicity parameters (N, sN ) of peroxide anions, which were successfully applied to predict the rates of Weitz-Scheffer epoxidations. DFT calculations with inclusion of solvent effects by means of the Integral Equation Formalism version of the Polarizable Continuum Model were performed to rationalize the observed reactivities.

Benchmarking the DFT methodology for assessing antioxidant-related properties: quercetin and edaravone as case studies.

The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported. These functionals have been chosen among those belonging to three different families of hybrid functionals, namely global, range separated, and double hybrids. Other computational parameters have also been considered, such as basis set and solvent effects. The selected parameters, namely bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) allow a mechanistic evaluation of the antioxidant activities of free radical scavengers. Our results show that all the selected functionals provide a coherent picture of these properties, predicting the same order of BDEs and PDEs. However, with respect to the reference values, the errors found at CBS-Q3 level significantly vary with the functional. Although it is difficult to evidence a global trend from the reported data, it clearly appears that LC-ωPBE, M05-2X, and M06-2X are the most suitable approaches for the considered properties, giving the lowest cumulative mean absolute errors. These methods are therefore suggested for an accurate and fast evaluation of energetic parameters related to an antioxidant activity via free radical scavenging.

D-LogP: an alignment-free 3D description of local lipophilicity for QSAR studies.

The major hurdle to overcome in the development of 3D-QSAR models using steric, electrostatic, or lipophilic "fields" is related to both conformation selection and subsequent suitable overlay (alignment) of compounds. Therefore, it is of some interest to provide a conformationally sensitive lipophilicity descriptor that is alignment-independent. In this chapter we describe the derivation and parametrization of a new descriptor called 3D-LogP and demonstrate both its conformational sensitivity and its effectiveness in QSAR analysis. The 3D-LogP descriptor provides such a representation in the form of a rapidly computable description of the local lipophilicity at points on a user-defined molecular surface.