Periodic density functional study of Rh and Pd interaction with the (100)MgO surface

The adsorption geometry and electronic properties of palladium and rhodium atoms deposited on the regular (100)MgO surface were analyzed by means of periodic DFT calculations using local, gradient-corrected and hybrid (B3LYP) functionals. Spin-polarized computations revealed doublet spin state of Rh atom to be the most stable electronic state for the adsorbed rhodium atom on (100)MgO. The preferred adsorption site of the metal (Pd and Rh) atoms was found to be the site on top of the surface oxygen atoms. A relatively stable geometry for the adsorption of the Pd and Rh in a bridge position above the two surface oxygens was found as well. The electronic structures suggested partly covalent bonding with contribution from electrostatic attraction between the metal and the oxygen atoms for both optimized structures. Small charge transfer was obtained from the support to the Pd and Rh metal atoms. The calculations showed that rhodium was bound stronger to the substrate probably due to stronger polarization effects

A DFT study of the NO adsorption on Pdn (n = 1–4) clusters

We report a density-functional study of some properties of the adsorption process of the NO molecule on small palladium clusters (n = 1–4). The interaction between NO and the Pdn clusters is studied on various adsorption sites. Both, NO and Pdn geometrical relaxations are taken into account. The significant conformational reconstruction of the metallic cluster upon NO adsorption induces a large decrease of the NO adsorption energy. Nevertheless, the N–O binding energy is strongly weakened when the molecule is adsorbed on the small Pdn clusters due essentially to an electrostatic repulsion between both N and O atoms. The possible dissociation process of NO on Pd4 cluster is then investigated within two processes: the NO molecule does not dissociate on Pd4 with process (i) (dissociation of the isolated gas phase NO molecule followed by the adsorption of both nitrogen and oxygen atoms on the cluster). Process (ii)which presents three successive steps (adsorption of the NO molecule, dissociation of the NO molecule adsorbed on Pd4, adsorption of the O atom on the cluster) is studied in details and we propose a reaction pathway locating transition states and intermediate species. The activation energy for process (ii) is high and the dissociation of the NO molecule on the Pd4 cluster is thus highly improbable

Theoretical Exploration of Type I/Type II Dual Photoreactivity of Promising Ru(II) Dyads for PDT Approach

Ru(II)-dyads are a class of bioactive molecules of interest as anticancer agents obtained incorporating an organic chromophore in the light-absorbing metallic scaffold. A careful DFT and TDDFT investigation of the photophysical properties of a series of Ru(II)-polypiridyl dyads containing polythiophene chains of different lengths bound to a coordinating imidazo[4,5-f][1,10]phenantroline ligand, is herein reported. The modulation of the crucial chemical and physical properties of the photosensitizer with the increasing number of thiophene units, has been accurately described investigating the UV-Vis spectra, Type I and Type II photoreactions, also including spin orbit coupling values (SOC). Results show that the low-lying 3IL states afforded as the number of the thiophene ligands increases (n=3,4) are energetically high enough to ensure the singlet oxygen production and can be also involved in electron transfer reaction, showing a dual type I/typeII photeoreactivity

The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases

A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site

22π‑Electrons [1.1.1.1.1] pentaphyrin as a new photosensitizing agent for water disinfection: experimental and theoretical characterization

In view of their promising photosensitizing features, expanded porphyrins are gaining wide attention for their potential use in both photodynamic therapy (PDT) of cancer or as likely photoactivated agent for water disinfection. Herein, we report a joint experimental and theoretical investigation on the 20-(4’-carboxyphenyl)-2,13-dimethyl-3,12-diethyl-[22]pentaphyrin complex 4. The synthesis, NMR, UV-Vis and mass characterization of the new compound together with a detailed theoretical investigation of the photophysical properties are presented. In particular, type I- and type II- photoreactions have been explored by means of DFT and its TDDFT formulation characterizing the electronic absorption spectra, providing singlet-triplet energy gap, vertical ionization potential and electron affinity. Results show that title compound is able to generate the cytotoxic singlet oxygen species supporting the application of the proposed molecule as a photoactivated agent for water disinfection

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase

The catalytic mechanism of the decarboxylation of 5-carboxyvanillate by LigW producing vanillic acid has been studied by using QM cluster and hybrid QM/MM methodologies. In the QM cluster model, the environment of a small QM model is treated with a bulky potential while two QM/MM models studies include partial and full protein with and without explicitly treated water solvent. The studied reaction involves two sequential steps: the protonation of the carbon of the 5-carboxy-vanillate substrate and the decarboxylation of the intermediate from which results deprotonated vanillic acid as product. The structures and energetics obtained by using three structural models and two density functionals are quite consistent to each other. This indicates that the small QM cluster model of the presently considered enzymatic reaction is appropriate enough and the reaction is mainly influenced by the active site