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, <i>k</i>(OH), and water, <i>k</i>(H₂O), attacks for the <i>cis</i>-[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 ¹H 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

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

Understanding the Hydrolysis Mechanism of Ethyl Acetate Catalyzed by an Aqueous Molybdocene: A Computational Chemistry Investigation

A thoroughly mechanistic investigation on the [Cp₂Mo­(OH)­(OH₂)]⁺-catalyzed hydrolysis of ethyl acetate has been performed using density functional theory methodology together with continuum and discrete–continuum solvation models. The use of explicit water molecules in the PCM-B3LYP/aug-cc-pVTZ (aug-cc-pVTZ-PP for Mo)//PCM-B3LYP/aug-cc-pVDZ (aug-cc-pVDZ-PP for Mo) computations is crucial to show that the intramolecular hydroxo ligand attack is the preferred mechanism in agreement with experimental suggestions. Besides, the most stable intermediate located along this mechanism is analogous to that experimentally reported for the norbornenyl acetate hydrolysis catalyzed by molybdocenes. The three most relevant steps are the formation and cleavage of the tetrahedral intermediate immediately formed after the hydroxo ligand attack and the acetic acid formation, with the second one being the rate-determining step with a Gibbs energy barrier of 36.7 kcal/mol. Among several functionals checked, B3LYP-D3 and M06 give the best agreement with experiment as the rate-determining Gibbs energy barrier obtained only differs 0.2 and 0.7 kcal/mol, respectively, from that derived from the experimental kinetic constant measured at 296.15 K. In both cases, the acetic acid elimination becomes now the rate-determining step of the overall process as it is 0.4 kcal/mol less stable than the tetrahedral intermediate cleavage. Apart from clarifying the identity of the cyclic intermediate and discarding the tetrahedral intermediate formation as the rate-determining step for the mechanism of the acetyl acetate hydrolysis catalyzed by molybdocenes, the small difference in the Gibbs energy barrier found between the acetic acid formation and the tetrahedral intermediate cleavage also uncovers that the rate-determining step could change when studying the reactivity of carboxylic esters other than ethyl acetate substrate specific toward molybdocenes or other transition metal complexes. Therefore, in general, the information reported here could be of interest in designing new catalysts and understanding the reaction mechanism of these and other metal-catalyzed hydrolysis reactions

Influence of the N–N Coligand: C–C Coupling Instead of Formation of Imidazol-2-yl Complexes at {Mo(η³‑allyl)(CO)₂} Fragments. Theoretical and Experimental Studies

New <i>N</i>-methylimidazole (N-MeIm) complexes of the {Mo­(η³-allyl)­(CO)₂(N–N)} fragment have been prepared, in which the N,N-bidentate chelate ligand is a 2-pyridylimine. The addition of a strong base to the new compounds deprotonates the central CH group of the imidazole ligand and subsequently forms the C–C coupling product that results from the nucleophilic attack to the imine C atom. This reactivity contrasts with that previously found for the analogous 2,2′-bipyridine compounds [Mo­(η³-allyl)­(CO)₂­(bipy)­(N-RIm)]­OTf [N-RIm = N-MeIm, <i>N</i>-mesitylimidazole (N-MesIm, Mes= 2,4,6-trimethylphenyl); OTf = trifluoromethanesulfonate) which afforded imidazol-2-yl complexes upon deprotonation. Density Functional Theory (DFT) computations uncover that the reactivity of the imine C atom along with its ability to delocalize electron density are responsible for the new reactivity pattern found for the kind of molybdenum complexes reported herein

Unveiling the Reactivity of Propargylic Hydroperoxides under Gold Catalysis

Controlled gold-catalyzed reactions of primary and secondary propargylic hydroperoxides with a variety of nucleophiles including alcohols, phenols, 2-hydroxynaphthalene-1,4-dione, and indoles allow the direct and efficient synthesis of β-functionalized ketones. Moreover, the utility of some of the resulting products for the selective preparation of fused polycycles has been demonstrated. In addition, density functional theory (DFT) calculations and ¹⁸O-labeling experiments were performed to obtain an insight into various aspects of the controlled reactivity of propargylic hydroperoxides with external nucleophiles under gold catalysis

Insights on the Reactivity of Terminal Phosphanido Metal Complexes toward Activated Alkynes from Theoretical Computations

Herein we present a theoretical study on the reaction of [Re­(PPh₂) (CO)₃(phen)] (phen = 1,10-phenanthroline) and [Re­(PPh₂) (CO)₃(bipy)] (bipy = 2,2′-bipyridine) toward methyl propiolate. In agreement with experimental results for the phen ligand, the coupling of the substituted acetylenic carbon with the nonsubstituted <i>ortho</i> carbon of the phen ligand is the preferred route from both kinetic and thermodynamic viewpoints with a Gibbs energy barrier of 18.8 kcal/mol and an exoergicity of 11.1 kcal/mol. There are other two routes, the insertion of the acetylenic fragment into the P–Re bond and the coupling between the substituted acetylenic carbon and a carbonyl ligand in <i>cis</i> disposition, which are kinetically less favorable than the preferred route (by 2.8 and 1.9 kcal/mol, respectively). Compared with phen, the bipy ligand shows less electrophilic character and also less π electron delocalization due to the absence of the fused ring between the two pyridine rings. As a consequence, the route involving the coupling with a carbonyl ligand starts to be kinetically competitive, whereas the product of the attack to bipy is still the most stable and would be the one mainly obtained after spending enough time to reach thermal equilibrium