María I. Menéndez

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.

THEORETICAL STUDY OF THE GAS-PHASE ADDITION OF HF AND HCL TO ETHYLENE: ANALYSIS OF THE CATALYTIC ACTION OF DIMERIC HALIDES

Ab initio MP2/6‐31G** calculations render the same mechanism for the gas‐phase addition of HF and HCl to ethylene in contrast with previous HF/3‐21G calculations. The leading interaction is in both cases the electrophilic attachment of the hydrogen atom in the hydrogen halide to a carbon atom in ethylene. The presence of a second molecule of hydrogen halide causes a catalytic effect by allowing an alternative mechanism for electron density rearrangement through ethylene polarization.

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.

An alternative method to assess the quality of hartree-fock-roothaan wave functions

Abstract The different contributions of the Breit Hamiltonian as well as those corresponding to the electric quadrupole and magnetic octupole interactions have been computed using several Slater-Type basis sets. These calculations allow one to assess the quality of the basis sets in regions of configuration space other than those emphasized by the operators appearing in the classical (non-relativistic) Hamiltonian. The results confirm the usefulness of the δ test (L.A.G. Bernardo and J.A. Sordo, J. Chem. Phys. 85 (1986) 1475) for measuring the quality of a given basis set.

Theoretical study of the gas-phase addition of HF and HCl to ethylene: analysis of the catalytic action of a second hydrogen halide molecule

Abstract The additions to ethylene of HF catalyzed by a HCl molecule, and of HCl catalyzed by a HF molecule, were studied by the ab initio MP2(full)/6-31G ∗ method. The addition of HCl is favored by catalysis. The formation of a new HF molecule not only provides electronic energy stabilization, but also makes possible a looser transition structure with favorable zero-point and thermal energies, and entropy.

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.

Structure, aromaticity, and bonding in subporphyrins: theoretical study of [14]tribenzosubporphine(1.1.1)hydroxyboron(III) and [14]subporphine(1.1.1)hydroxyboron(III) complexes

A theoretical analysis of the structure, aromaticity, magnetic properties and bonding in TBSPBOH and SPBOH complexes was performed. Geometry optimizations were carried out in the gas-phase at the B3LYP/6-31G(d) theory level. 1H and 13C NMR spectra of these complexes were evaluated at the B3LYP/6-311+G(2d,p)-PCM theory level in CHCl3 solution. The vector field induced by an external magnetic field was computed at the CHF/6-31G(d) theory level using the CTOCD-DZ formulation. In these cone-shaped molecules, the 14-π electron current induced in them by an external magnetic field does not follow a [14]-annulene path but the inner edge of the macrocycle. Therefore, the 14-π electron aromatic core corresponding to this induced current is constituted by the three mesoC atoms, the three N atoms, and the six C atoms directly bonded to them. The involvement of the N atoms in the 14-π aromatic core implies that one of the B-N bonds is a weaker B←N dative bond whose presence is reflected in the geometry of these complexes, which display larger average B-N bond lengths than in tripyrrolylborane. Thus, according to our analysis, structure, aromaticity and bonding in these systems are closely related. The anisotropic effect is somewhat larger in SPBOH than in TBSPBOH, and the larger curvature of the former makes larger relative shielding constants possible, not only for the hydroxyl proton but also for the outer atoms.

Theoretical study of ester enolate-imine condensation route to ?-lactams

The condensation reaction of the enolate of methyl acetate with formaldimine to afford a β‐lactam was studied using the MP2‐FC/6‐31+G* level of theory taking into account the electrostatic effect of the solvent by means of a self‐consistent reaction field continuum model. The reaction is a stepwise process with three main steps: the formation of the C3(SINGLE BOND)C4 bond, the closure of the β‐lactam ring, and the elimination of the methoxide ion. The formation of the C3(SINGLE BOND)C4 bond is rate determining and according to our calculations is not a reversible step. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1826–1833, 1998