Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes

Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system. However, when Cu+ interacts with thymine, through the O2 carbonyl atom, the single proton transfer from thymine to adenine becomes thermodynamically spontaneous, and thus rare forms of the DNA bases may spontaneously appear. For Cu2+ cation, important effects on proton-transfer processes appear due to oxidation of the base pair, which stabilizes the different single proton-transfer products. Results for hydrated systems show that the presence of the water molecules interacting with the metal cation (and their mode of coordination) can strongly influence the ability of Cu2+ to induce oxidation on the base pair.     

Mechanistic insights into ring-closing enyne metathesis with the second-generation Grubbs-Hoveyda catalyst: a DFT study

The full catalytic process (precatalyst activation, propagating cycle and active-species interconversion) of the ring-closing enyne metathesis (RCEYM) reaction of 1-allyloxy-2-propyne with the Grubbs-Hoveyda complex as catalyst was studied by B3LYP density functional theory. Both the ene-then-yne and yne-then-ene pathways are considered and, for the productive catalytic cycle, the feasibility of the endo-yne-then-ene route is also explored. Calculations predict that the ene-then-yne and yne-then-ene pathways proceed through equivalent steps, the only major difference being the order in which they take place. In this way, all alkene metathesis processes studied here involve four steps: olefin coordination, cycloaddition, cycloreversion and olefin decoordination. Among them, the two more energetically demanding ones are the olefin coordination and decoordination steps. The reaction of the alkyne fragment consists of two steps: alkyne coordination and alkyne skeletal reorganization, the latter of which has the highest Gibbs energy barrier. Comparison between the ene-then-yne and yne-then-ene pathways shows that there is no clear energetic preference for either of the two processes, and thus both should be operative when unsubstituted enynes are involved. In addition, although the endo orientation is computed to be slightly disfavored, it is not ruled out for 1-allyloxy-2-propyne, and thus calculations seem to indicate that the exo versus endo selectivity is strongly influenced by the presence of substituents in the reagent.     

Influence of ionization on the conformational preferences of peptide models. Ramachandran surfaces of N‐formyl‐glycine amide and N‐formyl‐alanine amide radical cations

Ramachandran maps of neutral and ionized HCO–Gly–NH₂ and HCO–Ala–NH₂ peptide models have been built at the B3LYP/6‐31++G(d,p) level of calculation. Direct optimizations using B3LYP and the recently developed MPWB1K functional have also been carried out, as well as single‐point calculations at the CCSD(T) level of theory with the 6‐311++G(2df,2p) basis set. Results indicate that for both peptide models ionization can cause drastic changes in the shape of the PES in such a way that highly disallowed regions in neutral PES become low‐energy regions in the radical cation surface. The structures localized in such regions, and are highly stabilized due to the formation of 2‐centre‐3‐electron interactions between the two carbonyl oxygens. Inclusion of solvent effects by the conductor‐like polarizable continuum model (CPCM) shows that the solute‐solvent interaction energy plays an important role in determining the stability order. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

What is the structure of FeC5H6?

Calculations performed using both density functional theory (DFT) and the modified coupled-pair functional (MCPF) approach show that FeC₅H₆⁺ is more stable than HFeC₅H₅⁺ by about 10 kcal/mol. The ground state of FeC₅H₆⁺ is a quartet state derived from the 3d⁷ occupation of Fe⁺. For HFeC₅H₅⁺, the MCPF approach yields a sextet ground state while DFT yields a quartet; however, these two states are close in energy at both levels of theory.     

Diastereoselective synthesis of allosecurinine and viroallosecurinine from menisdaurilide

A new and versatile synthetic route to Securinega alkaloids is reported. The first synthesis of allosecurinine has been accomplished in seven steps and 40% yield, starting from (+)-menisdaurilide, using a vinylogous Mannich reaction as the key transformation. Similarly, viroallosecurinine has been synthesized from (-)-menisdaurilide.     

Binding properties of Cu(+/2+)-(glycyl)n glycine complexes (n = 1-3)

The structure, relative energies, and binding energies of the complexes formed by the interaction of Cu+ (d10,1S) and Cu2+ (d9,2D) cations with the (glycyl)n glycine (n = 1-3) oligomers have been theoretically determined by means of density functional methods. The most stable structures of the Cu+ systems present linear dicoordination geometries, in agreement with a recent X-ray absorption spectroscopic study of Cu(I) interacting with model dipeptides. This is attributed to an efficient reduction of metal-ligand repulsion through sd sigma hybridization in dicoordinated linear structures. In contrast, for Cu2+ systems the lowest energy structures are tricoordinated (n = 1), tetracoordinated (n = 2), and pentacoordinated (n = 3). For both copper cations, binding energy values show that the interaction energies increase when the peptide chain is elongated. Differences on the coordination properties of the ligands are discussed according to their length as well as to the electronic configuration of the metal cations, which are compared to the Cu+/2+-glycine systems.     

DFT Study on the Recovery of Hoveyda–Grubbs‐Type Catalyst Precursors in Enyne and Diene Ring‐Closing Metathesis

DFT (B3LYP‐D) calculations have been used to better understand the origin of the recovered Hoveyda–Grubbs derivative catalysts after ring‐closing diene or enyne metathesis reactions. For that, we have considered the activation process of five different Hoveyda–Grubbs precursors in the reaction with models of usual diene and enyne reactants as well as the potential precursor regeneration through the release/return mechanism. The results show that, regardless of the nature of the initial precursor, the activation process needs to overcome relatively high energy barriers, which is in agreement with a relatively slow process. The precursor regeneration process is in all cases exergonic and it presents low energy barriers, particularly when compared to those of the activation process. This indicates that the precursor regeneration should always be feasible, unlike the moderate recoveries sometimes observed experimentally, which suggests that other competitive processes that hinder recovery should take place. Indeed, calculations presented in this work show that the reactions between the more abundant olefinic products and the active carbenes usually require lower energy barriers than those that regenerate the initial precatalyst, which could prevent precursor regeneration. On the other hand, varying the precursor concentration with time obtained from the computed energy barriers shows that, under the reaction conditions, the precursor activation is incomplete, thereby suggesting that the origin of the recovered catalyst probably arises from incomplete precursor activation.     

Cation-pi Interactions and oxidative effects on Cu+ and Cu2+ binding to Phe, Tyr, Trp, and His amino acids in the gas phase. Insights from first-principles calculations

The coordination properties of the four natural aromatic amino acids (AA(arom) = Phe, Tyr, Trp, and His) to Cu+ and Cu2+ have been exhaustively studied by means of ab initio calculations. For Cu+-Phe, Cu+-Tyr and Cu+-Trp, the two charge solvated tridentate N/O/ring and bidentate N/ring structures, with the metal cation interacting with the pi system of the ring, were found to be the lowest ones, relative DeltaG(298K) energies being less than 0.5 kcal/mol. The Cu+-His ground-state structure has the metal cation interacting with the NH2 group and the imidazole N. For these low-lying structures vibrational features are also discussed. Unlike Cu+ complexes, the ground-state structure of Cu2+-Phe, Cu2+-Tyr, and Cu2+-Trp does not present cation-pi interactions due to the oxidation of the aromatic ring induced by the metal cation. The ground-state structure of Cu2+-His does not present oxidation of the amino acid, the coordination to Cu2+ being tridentate with the oxygen of the carbonyl group, the nitrogen of the amine, and the N of the imidazole. Other less stable isomers, however, show oxidation of His, particularly of the imidazole ring, which can induce spontaneous proton-transfer reactions from the NH of the imidazole to the NH2 of the backbone. Finally, the computed binding energies for Cu+-AA(arom) and Cu2+-AA(arom) systems have been computed, the order found for the single charged systems being Cu+-His > Cu+-Trp > Cu+-Tyr > Cu+-Phe, in very good agreement with the experimental data.