Ramón López

Effect of the Nature of the Substituent in N-Alkylimidazole Ligands on the Outcome of Deprotonation: Ring Opening versus the Formation of N-Heterocyclic Carbene Complexes

Complexes [Re(CO)(3)(N-RIm)(3)]OTf (N-RIm=N-alkylimidazole, OTf=trifluoromethanesulfonate; 1a-d) have been straightforwardly synthesised from [Re(OTf)(CO)(5)] and the appropriate N-alkylimidazole. The reaction of compounds 1a-d with the strong base KN(SiMe(3))(2) led to deprotonation of a central C-H group of an imidazole ligand, thus affording very highly reactive derivatives. The latter can evolve through two different pathways, depending on the nature of the substituents of the imidazole ligands. Compound 1a contains three N-MeIm ligands, and its product 2a features a C-bound imidazol-2-yl ligand. When 2a is treated with HOTf or MeOTf, rhenium N-heterocyclic carbenes (NHCs) 3a or 4a are afforded as a result of the protonation or methylation, respectively, of the non-coordinated N atom. The reaction of 2a with [AuCl(PPh(3))] led to the heterobimetallic compound 5, in which the N-heterocyclic ligand is once again N-bound to the Re atom and C-coordinated to the gold fragment. For compounds 1b-d, with at least one N-arylimidazole ligand, deprotonation led to an unprecedented reactivity pattern: the carbanion generated by the deprotonation of the C2-H group of an imidazole ligand attacks a central C-H group of a neighbouring N-RIm ligand, thus affording the product of C-C coupling and ring-opening of the imidazole moiety that has been attacked (2c, d). The new complexes featured an amido-type N atom that can be protonated or methylated, thus obtaining compounds 3c, d or 4c, d, respectively. The latter reaction forces a change in the disposition of the olefinic unit generated by the ring-opening of the N-RIm ligand from a cisoid to a transoid geometry. Theoretical calculations help to rationalise the experimental observation of ring-opening (when at least one of the substituents of the imidazole ligands is an aryl group) or tautomerisation of the N-heterocyclic ligand to afford the imidazol-2-yl product.

Theoretical analysis of the role of the solvent on the reaction mechanisms: one-step versus two-step ketene-imine cycloaddition

The effect of correlation energy, basis set size, zero‐point energy (ZPE) correction, and solvation on the reaction mechanism of the ketene–imine cycloaddition reaction has been investigated. The electrostatic solvent effect was studied with a self‐consistent reaction field method in which the solvation energy is obtained using a multipole expansion of the molecular charge distribution. The ab initio results have been analyzed by means of a theoretical method based on the expansion of the MOs of the supermolecule in terms of those of the reactants and the performance of the configuration analysis. In gas phase, due to the correlation energy and/or the ZPE corrections, the reaction is predicted to be a one‐step process. In solution, the stabilization of the charge‐transferred configurations results in the occurrence of a very stable, Zwitterionic intermediate giving a two‐step mechanism.

ANACAL: a program to carry out a configurational analysis of the wave function of reactive systems

Abstract A method to analyze the wave function of a closed-shell composed system in terms of the electronic configuration of its closed-shell components is presented. The molecular orbitals of a supersystem A-B (or A-B-C) are presented as linear combinations of the molecular orbitals of the fragments A, B (or A, B, and C), thus allowing the wave function of a two-fragment (A-B) or a three-fragment (A-B-C) composed system to be interpreted in terms of the electronic configurations of the reactants ( ABC, A + B - C,…,A ∗ BC,… ).

Theoretical Study of the Oxidation of Histidine by Singlet Oxygen

Herein we present a theoretical study of the reaction of singlet oxygen with histidine performed both in the gas phase and in aqueous solution. The potential energy surface of the reactive system was explored at the B3LYP/cc-pVTZ level of theory and the electronic energies were refined by means of single-point CCSD(T)/cc-pVTZ(-f) calculations. Solvent effects were taken into account by using a solvent continuum model (COSMO) and by adding explicit water molecules. The results show that the first step in the reaction mechanism corresponds to a nearly symmetric Diels-Alder addition of the singlet oxygen molecule to the imidazole ring to yield an endoperoxide, in agreement with experimental evidence. The intermediate formed can evolve along two different reaction paths leading to two isomeric hydroperoxides and, eventually, to open-chain or internally cyclised oxidised products. Water plays a significant role in stabilising the reaction structures by solvation and by acting as a bifunctional catalyst in the elimination/addition reaction steps. Our results explain why substituents at the N1-imidazole ring can hamper the evolution of the initial endoperoxide and result in Gibbs energy barriers in solution similar to those experimentally measured and suggest a likely route to the formation of peptide aggregates during the oxidation of histidine by singlet molecular oxygen.

Unmasking the Action of Phosphinous Acid Ligands in Nitrile Hydration Reactions Catalyzed by Arene–Ruthenium(II) Complexes

The catalytic hydration of benzonitrile and acetonitrile has been studied by employing different arene-ruthenium(II) complexes with phosphinous (PR2OH) and phosphorous acid (P(OR)2OH) ligands as catalysts. Marked differences in activity were found, depending on the nature of both the P-donor and η(6)-coordinated arene ligand. Faster transformations were always observed with the phosphinous acids. DFT computations unveiled the intriguing mechanism of acetonitrile hydration catalyzed by these arene-ruthenium(II) complexes. The process starts with attack on the nitrile carbon atom of the hydroxyl group of the P-donor ligand instead of on a solvent water molecule, as previously suggested. The experimental results presented herein for acetonitrile and benzonitrile hydration catalyzed by different arene-ruthenium(II) complexes could be rationalized in terms of such a mechanism.

Taste for chiral guests: investigating the stereoselective binding of peptides to β-cyclodextrins.

Obtaining compounds of diastereomeric purity is extremely important in the field of biological and pharmaceutical industry, where amino acids and peptides are widely employed. In this work, we theoretically investigate the possibility of chiral separation of peptides by β-cyclodextrins (β-CDs), providing a description of the associated interaction mechanisms by means of molecular dynamics (MD) simulations. The formation of host/guest complexes by including a model peptide in the macrocycle cavity is analyzed and discussed. We consider the terminally blocked phenylalanine dipeptide (Ace-Phe-Nme), in the L- and D-configurations, to be involved in the host/guest recognition process. The CD-peptide free energies of binding for the two enantiomers are evaluated through a combined approach that assumes: (1) extracting a set of independent molecular structures from the MD simulation, (2) evaluating the interaction energies for the host/guest complexes by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations carried out on each structure, for which we also compute, (3) the solvation energies through the Poisson-Boltzmann surface area method. We find that chiral discrimination by the CD macrocycle is of the order of 1 kcal/mol, which is comparable to experimental data for similar systems. According to our results, the Ace-(D)Phe-Nme isomer leads to a more stable complex with a β-CD compared to the Ace-(L)Phe-Nme isomer. Nevertheless, we show that the chiral selectivity of β-CDs may strongly depend on the secondary structure of larger peptides. Although the free energy differences are relatively small, the predicted selectivities can be rationalized in terms of host/guest hydrogen bonds and hydration effects. Indeed, the two enantiomers display different interaction modes with the cyclodextrin macrocavity and different mobility within the cavity. This finding suggests a new interpretation for the interactions that play a key role in chiral recognition, which may be exploited to design more efficient and selective chiral separations of peptides.

Peptide Binding to β-Cyclodextrins: Structure, Dynamics, Energetics, and Electronic Effects

Peptide-cyclodextrin and protein-cyclodextrin host-guest complexes are becoming more and more important for industrial applications, in particular in the fields of pharmaceutical and food chemistry. They have already deserved many experimental investigations although the effect of complex formation in terms of peptide (or protein) structure is not well-known yet. Theoretical calculations represent a unique tool to analyze such effects, and with this aim we have carried out in the present investigation molecular dynamics simulations and combined quantum mechanics-molecular mechanics calculations. We have studied complexes formed between the model Ace-Phe-Nme peptide and the β-cyclodextrin (β-CD) macromolecule, and our analysis focuses on the following points: (1) how is the peptide structure modified in going from bulk water to CD environment (backbone torsion angles), (2) which are the main peptide-CD interactions, in particular in terms of hydrogen bonds, (3) which relative peptide-CD orientation is preferred and which are the structural and energetic differences between them, and (4) how the electronic properties of the peptide changes under complex formation. Overall, our calculations show that in the most stable configuration, the backbone chain lies in the narrow rim of the CD. Strong hydrogen bonds form between the H atoms of the peptidic NH groups and oxygen atoms of the secondary OH groups in the CD. These and other (weaker) hydrogen bonds formed by the carbonyl groups reduce considerably the flexibility of the peptide structure, compared to bulk water, and produce a marked increase of the local dipole moment by favoring configurations in which the two C═O bonds point toward the same direction. This effect might have important consequences in terms of the peptide secondary structure, although this hypothesis needs to be tested using larger peptide models.

Theoretical Study on the Electronic Excitations of a Porphyrin-Polypyridyl Ruthenium(II) Photosensitizer

In this work, we investigated the UV-vis spectra of the [Ru(bipy)(2)(MPyTPP)Cl](+) (MPyTPP = 5-pyridyl-15,20,25-triphenylporphyrin) complex and its related species [Ru(bipy)(2)(py)Cl](+) and MPyTPP, by using time-dependent density functional theory and a set of functionals (B3LYP, M05, MPWB1K, and PBE0) in chloroform with the basis set 6-31++G(d,p) for nonmetal atoms and the pseudopotential LANL2DZ for Ru. Practically no geometrical changes are observed in the Ru environment when py ligand is replaced by MPyTPP. This replacement favors the electronic redistribution from bipy ligands to Ru, and from the metal to MPyTPP ligand, as indicated by NBO analysis. We found that M05 functional predicts very well the UV-vis spectra, as it shows a low deviation with respect to the experimental data, with a maximum error of 0.19 eV (11 nm). M05 theoretical electronic spectrum of [Ru(bipy)(2)(MPyTPP)Cl](+) complex indicates that the presence of the Ru complex does not alter Q porphyrin bands, while charge transfer bands from Ru to bipy and porphyrin ligands mixes up in the region close to the porphyrin Soret band. Theoretical analysis allows the decomposition of this broad experimental band into specific ones identifying the Soret band and new metal to ligand charge transfers toward porphyrin at 425 and 478 nm, which were not possible in none of the moieties MPyTPP and [Ru(bipy)(2)(Py)Cl](+) complex. In the UV region, the most intense intraligand band of bipy ligands becomes slightly blue-shifted both in the experimental and in the theoretical spectrum of [Ru(bipy)(2)(MPyTPP)Cl](+) complex compared to that in [Ru(bipy)(2)(py)Cl](+) complex. Some of the bands of [Ru(bipy)(2)(MPyTPP)Cl](+) showed in this theoretical study may have practical applications. That is the case for the band at 478 nm, with potential use in PDT, and those more energetic at 348 and 329 nm, which could help in the cleavage mechanism of DNA performed by this ruthenium complex.

Unraveling the Reaction Mechanism on Nitrile Hydration Catalyzed by [Pd(OH2)4]2+: Insights from Theory

Density functional theory methodologies combined with continuum and discrete-continuum descriptions of solvent effects were used to investigate the [Pd(OH2)4](2+)-catalyzed acrylonitrile hydration to yield acrylamide. According to our results, the intramolecular hydroxide attack mechanism and the external addition mechanism of a water molecule with rate-determining Gibbs energy barriers in water solution of 27.6 and 28.3 kcal/mol, respectively, are the most favored. The experimental kinetic constants of the hydration started by hydroxide, k(OH), and water, k(H2O), attacks for the cis-[Pd(en)(OH2)2](2+)-catalyzed dichloroacetonitrile hydration rendered Gibbs energy barriers whose energy difference, 0.7 kcal/mol, is the same as that obtained in the present study. Our investigation reveals the nonexistence of the internal attack of a water ligand for Pd-catalyzed nitrile hydration. At the low pHs used experimentally, the equilibrium between [Pd(OH2)3(nitrile)](2+) and [Pd(OH2)2(OH)(nitrile)](+) is completely displaced to [Pd(OH2)3(nitrile)](2+). Experimental studies in these conditions stated that water acts as a nucleophile, but they could not distinguish whether it was a water ligand, an external water molecule, or a combination of both possibilities. Our theoretical explorations clearly indicate that the external water mechanism becomes the only operative one at low pHs. On the basis of this mechanistic proposal it is also possible to ascribe an (1)H NMR signal experimentally detected to the presence of a unidentate iminol intermediate and to explain the influence of nitrile concentration reported experimentally for nitriles other than acrylonitrile in the presence of aqua-Pd(II) complexes. Therefore, our theoretical point of view on the mechanism of nitrile hydration catalyzed by aqua-Pd(II) complexes can shed light on these relevant processes at a molecular level as well as afford valuable information that can help in designing new catalysts in milder and more efficient conditions.

Understanding regioselective cleavage in peptide hydrolysis by a palladium(II) aqua complex: a theoretical point of view.

Hydrolytic cleavage of the oligopeptides Ace-Ala-Lys-Tyr-Gly approximately Gly-Met-Ala-Ala-Arg-Ala and Ace-Lys-Gly-Gly-Ala-Gly approximately Pro-Met-Ala-Ala-Arg-Gly by [Pd(H(2)O)(4)](2+) was theoretically investigated by using molecular dynamics simulations and quantum mechanical calculations. The Pd anchorage to the peptide sequence is crucial to provoke the cleavage of the second bond upstream from the anchored methionine. For both cases, the most favorable reaction mechanism is a three-step route. The first step coincides with the experimental suggestion found for the Gly approximately Pro-Met sequence on a cleavage caused by an external attack of a water molecule to a complex in trans conformation of the scissile Gly approximately Gly and Gly approximately Pro peptide bonds. However, our results uncover the important role played by the presence of a Pd-coordinated water molecule, which simultaneously interacts with the carbonyl oxygen atom of the Gly amino acid in the Gly approximately Gly and Gly approximately Pro bonds. In accordance with experimental facts, the rise of the hydrolysis reaction rate when the Pro amino acid is located in the scissile peptide bond was also corroborated. The findings obtained at a molecular level from the present computations not only are relevant to rationalize the previously reported experiments but also could be of importance in designing new Pd(II) complexes for the regioselective cleavage of peptides and proteins.