Application of vibrational correlation formalism to internal conversion rate: case study of Cu(n) (n = 3, 6, and 9) and H2/Cu3.

This work reports non-radiative internal conversion (IC) rate constants obtained for Cun with n = 3, 6, and 9 and H2 on Cu3. The Time-Dependent Density Functional Theory (TDDFT) method was employed with three different functionals in order to investigate the electronic structures and the absorption spectra. The performance of the generalized gradient approximation of Perdew, Burke and Ernzerhof (PBE) and the hybrid B3LYP and PBE0 exchange correlation functionals in combination with the SVP and the def2-TZVP basis sets was examined. TDDFT results were used as input data to compute internal conversion rate constants. For this purpose, we have developed a program package. A description of the theoretical background used in our numerical implementation and the program input file is presented. In view of future applications of this program package in photoinduced catalysis, we present the analysis of the IC rate processes for the photodissociation of H2 on Cu3. These results showed the applicability of the method and the computational program to identify the vibrational modes in transition metal clusters giving rise to the largest IC rate constant due to their interactions with the excited electronic states occurring in the hot-electron induced dissociation phenomena.

Antioxidant efficiency of oxovitisin, a new class of red wine pyranoanthocyanins, revealed through quantum mechanical investigations.

Oxovitisin is a natural antioxidant present in aged wine and comes from the chemical transformation undergone by anthocyanins and pyranoanthocyanins. Its antioxidant radical scavenging capacity was theoretically explored by density functional theory (DFT)/B3LYP methods. The O-H bond dissociation energy (BDE), the ionization potential (IP), the proton affinity (PA), and the metal-oxovitisin binding energy (BE) parameters were computed in the gas-phase and in water and benzene solutions. Results provided molecular insight into factors that influence radical scavenging potential of this new class of anthocyanins.

A TDDFT investigation of bay substituted perylenediimides: absorption and intersystem crossing.

The conformational structure and electronic spectra properties of a series of bay substituted perylenediimides (PDI) derivatives have been investigated by means of density functional theory (DFT) and time-dependent DFT. The B3LYP and PBE0 hybrid exchange-correlation functionals were applied in conjunction with the double-ζ quality SVP basis set. These compounds are interesting for organic materials science and as photosensitizers in cancer phototherapy (PDT), because of their intense absorption in the visible region. Results show that the substitution at the bay position of the PDI parent molecule with N-alkyl groups shifts the absorption maxima towards the red part of the visible spectrum (around 650-700 nm) as required for the applications in PDT. The main PDT action mechanisms have been investigated by computing of electron affinities, ionization potentials, triplet energies and spin-orbit matrix elements between singlet and triplet excited states.

Detailed Investigation of the OH Radical Quenching by Natural Antioxidant Caffeic Acid Studied by Quantum Mechanical Models.

The effectiveness of naturally occurring antioxidant caffeic acid in the inactivation of the very damaging hydroxyl radical has been theoretically investigated by means of hybrid density functional theory. Three possible pathways by which caffeic acid may inactivate free radicals were analyzed: hydrogen abstraction from all available hydrogen atoms, hydroxyl radical addition to all carbon atoms in the molecule, and single electron transfer. The reaction paths were traced independently, and the respective thermal rate constants were calculated using variational transition-state theory including the contribution of tunneling. The more reactive sites in caffeic acid are the C4OH phenolic group and the C4 carbon atom, for the hydrogen abstraction and radical addition, respectively. The single electron transfer process seems to be thermodynamically unfavored, in both polar and nonpolar media. Both hydrogen abstraction and radical addition are very feasible, with a slight preference for the latter, with a rate constant of 7.29 × 10(10) M(-1) s(-1) at 300 K. Tunnel effects are found to be quite unimportant in both cases. Results indicate caffeic acid as a potent natural antioxidant in trapping and scavenging hydroxyl radicals.

The inactivation of lipid peroxide radical by quercetin. A theoretical insight.

The effectiveness of naturally occurring antioxidant quercetin in the inactivation of the damaging lipid peroxide radical was investigated by means of hybrid density functional based approach, using the direct dynamics method, where the thermal rate constants were calculated using variational transition-state theory with multidimensional tunneling. H-atom abstraction in quercetin by CH(3)OO peroxide occurs preferentially at the 4'OH phenolic site, from both kinetic and thermodynamic points of view. In principle, the narrowness of the obtained adiabatic potential-energy profile makes the occurrence of a significant tunnelling contribution possible. In fact, this contribution enhances the value of the computed rate constant at 300 K from 1.94 x 10(1) to 9.63 x 10(3) M(-1) s(-1) indicating that quercetin is a potent natural antioxidant in trapping and scavenging free radicals.

A Theoretical Study of Brominated Porphycenes: Electronic Spectra and Intersystem Spin-Orbit Coupling.

In this paper, a time-dependent density functional theoretical study (TDDFT) has been carried out for brominated 2,7,12,17-tetra-n-propylporphycenes. Their potential therapeutic use in photodynamic therapy (PDT), a noninvasive medical treatment of cancer diseases, is due to the strong absorbance in the red part of the visible spectrum and the presence of heavy atoms (bromine). The prediction of electronic spectra for photosensitizer molecules can be a valuable tool in the design of drugs for application in PDT. Singlet and triplet vertical excitation energies have been calculated by means of the nonempirical hybrid functional PBE0 in conjunction with a split valence basis set (SVP), on previously optimized, at the density functional level of theory, ground state geometries. In particular, the quantum-chemical simulation of their absorption electronic spectra, both in vacuo and in solvent environments (dichloromethane and bromobenzene), has evidenced the red shift maxima wavelengths for the Q bands (or lower energy bands) with an increasing number of bromine atoms, in agreement with experimental results. The mean absolute deviation for the Q-electronic bands is about 0.3 eV. Calculated vertical triplet energies are between 1.04 (for tetra-brominated derivative) and 1.20 eV (for dibrominated derivative). The influence of bromine atoms on intersystem spin crossing has been investigated by applying a computational code which calculates spin-orbit matrix elements between singlet and triplet excited state wave functions weighted by the TDDFT transition coefficients.

One-electron spin-orbit contribution by effective nuclear charges.

Effective nuclear charges of the main group elements from the second up to the fifth row have been developed for the one-electron part of the spin-orbit (SO) coupling Hamiltonian. These parameters, suitable to be used for SO calculations of large molecular systems, provide a useful and remarkably good approximation to the full SO Hamiltonian. We have derived atomic effective nuclear charges by fitting procedure. Computed fine-structure splitting (FSS) of the doublet and triplet II states of AH species (A is one of the abovementioned elements) have been chosen for this purpose. We have adopted the noniterative scheme, previously reported, according to which SO contributions can be calculated through direct coupling between the II states. The latter have been optimized at B3LYP level using DZVP basis sets. As surrogates for a large number of possible applications, we have widely employed the empirical parameters to compute II-FSSs of diatomic species for which experimental data are available.

Reaction mechanism of molybdoenzyme formate dehydrogenase.

Formate dehydrogenase is a molybdoenzyme of the anaerobic formate hydrogen lyase complex of the Escherichia coli microorganism that catalyzes the oxidation of formate to carbon dioxide. The two proposed mechanisms of reaction, which differ in the occurrence of a direct coordination or not of a SeCys residue to the molybdenum metal during catalysis were analyzed at the density functional level in both vacuum and protein environments. Some DF functionals, in addition to the very popular B3LYP one, were employed to compute barrier heights. Results revealed the role played by the SeCys residue in performing the abstraction of the proton from the formate substrate. The computation of the energetic profiles for both mechanisms indicated that the reaction barriers are higher when the selenium is directly coordinated to the metal, whereas less energy is required when SeCys is not a ligand at the molybdenum site.

Hydration of ionic species studied by the reference interaction site model with a repulsive bridge correction.

We have tested the reference interaction site model (RISM) for the case of the hypernetted chain (HNC) and the partially linearized hypernetted chain (PLHNC) closures improved by a repulsive bridge correction (RBC) for ionic hydrated species. We have analyzed the efficiency of the RISM/HNC+RBC and RISM/PLHNC+RBC techniques for decomposition of the electrostatic and the nonpolar hydration energies on the energetic and the enthalpic parts for polyatomic ions when the repulsive bridge correction is treated as a thermodynamic perturbation, and investigate the repulsive bridge effect on the electrostatic potential induced by solvent on solute atoms. For a number of univalent and bivalent atomic ions, molecular cations, and anions, the method provides hydration energies deviating only by several percents from the experimental data. In most cases, the enthalpic contributions to the free energies are also close to the experimental results. The above models are able to satisfactory predict the hydration energies as well as the electrostatic potential around the ionic species. For univalent atomic ions, they also provide qualitative estimates of the Samoilov activation energies.

Determination of spin-orbit coupling contributions in the framework of density functional theory.

We present a noniterative method to calculate spin-orbit coupling by means of a theoretical approach that provides the use of the full Breit-Pauli operator. This method was applied to compute one and two-electron spin-orbit coupling contributions between singlet and triplet, and doublet and doublet states, respectively. These states have been represented by monodeterminantal wave functions and optimized using the PW91 gradient-corrected exchange-correlation functional and the hybrid B3LYP one. They have been supplied by the conventional density functional theory packages, and thus coupled by our spin-orbit coupling code. Different size basis sets have been employed and the obtained results have been compared with the corresponding ones provided by some of the already existing methods and with the experimental data. They have been found to be in good quantitative agreement.

Activation of methane by the iron dimer cation. A theoretical study.

A detailed investigation of the reaction mechanisms underlying the observed reactivity of the iron dimer cation with respect to methane has been performed by density functional hybrid (B3LYP) and nonhybrid (BPW91) calculations. Minima and transition states have been fully optimized and characterized along the potential energy surfaces leading to three different exit channels for both the ground and the first excited states of the dimer. A comparison with our previous work covering the reactivity of the Fe(+) monomer was made to underline similarities and differences of the reaction mechanisms. Results show that geometric arrangements corresponding to bridged positions of the ligands with respect to iron atoms are always favored and stabilize intermediates, transition states and products, facilitating their formation. Binding energies of reaction products have been computed and compared with experimental measurements, and ELF analysis of the bond has been performed to rationalize trends as a function of the structure.

Iron chelation by the powerful antioxidant flavonoid quercetin.

Chelation of the bare and hydrated iron(II) cation by quercetin has been investigated at the DF/B3LYP level in the gas phase. Several complexed species arising from neutral and anionic forms of the ligand have been taken into account. Both 1:1 and 1:2 metal/flavonoid stoichiometries have been considered. Results indicate that among the potential sites of chelation present on quercetin, the oxygen atoms belonging to the 3-hydroxy and 4-oxo, and to the 5-hydroxy and 4-oxo groups, are the preferred ones. Time-dependent density functional theory (TDDFT) calculations, used to reproduce the electronic UV-vis spectra of isolated quercetin and its complexes with Fe2+, were also performed in methanol and dimethylsulfoxide.

Reaction of bare VO+ and FeO+ with ammonia: a theoretical point of view.

The potential energy surfaces corresponding to the dehydration reaction of NH(3) by VO(+) ((3)Sigma, (1)Delta, (5)Sigma) and FeO(+) ((6)Sigma, (4)Delta) metal oxide cations have been investigated within the framework of the density functional theory in its B3LYP formulation and by employing new optimized basis sets for iron and vanadium. The reaction is proposed to occur through two hydrogen shifts from the nitrogen to the oxygen atom giving rise to multicentered transition states. Possible spin crossing between surfaces at different spin multiplicities has been considered. The energy profiles are compared with the corresponding ones for the insertion of bare cations to investigate the influence on reactivity of the presence of the oxygen ligand. The topological analysis of the gradient field of the electron localization function has been used to characterize the nature of the bonds for all the minima and transition states along the paths.