Rhodium-catalyzed hydroformylation of ketal-masked β-isophorone: computational explanation for the unexpected reaction evolution of the tertiary Rh-alkyl via an exocyclic β-elimination derivative.

Ketal-masked β-isophorone (7,9,9-trimethyl-1,4-dioxaspiro[4.5]dec-7-ene) is an interesting case study of Rh-catalyzed hydroformylations not only for the competition between secondary and tertiary rhodium alkyls but also for the unexpected isomerization of the tertiary Rh-alkyl to the exocyclic olefin which undergoes hydroformylation, yielding the acetaldehyde derivative (2) of 7,9,9-trimethyl-1,4-dioxaspiro[4.5]decane.

Computational prediction of selectivities in nonreversible and reversible hydroformylation reactions catalyzed by unmodified rhodium-carbonyls.

The regio- and stereoselectivities of the hydroformylation reaction catalyzed by an unmodified Rh catalyst have been investigated at the B3P86/6-31G* level with Rh described by effective core potentials in the LANL2DZ valence basis set for a number of either mono- or (1,1-, 1,2-, 1,3-) di-substituted substrates and compared with a variety of earlier results of ours, supplemented with free energy results when not already available. The computational prediction of regio- and stereoselectivities in nonreversible hydroformylations performed under mild reaction conditions is seemingly possible provided a careful conformational search for TS structures is carried out and all the low energy conformers are taken into account. The internal energy can be used to compute both the regio- and stereoselectivities in the hydroformylation of 1,1- and 1,3-substituted substrates with satisfactory results, whereas for 1,2-substituted substrates the regioselectivity determined from the internal energy is in good agreement with the experiment in the case of aliphatic olefins just for the lowest terms in the series (i.

The catalytic effect of water on the keto-enol tautomerism. Pyruvate and acetylacetone: a computational challenge.

The catalytic effect of explicit water molecules on the keto-enol tautomerism in a system of biological interest (enolpyruvate) has been investigated at the B3LYP/6-31++G** level by exploring the potential energy surface in the presence of 1 or 2 water molecules and comparing the energy profiles to the direct tautomerisation one. The water-assisted mechanisms turned out to be more favourable than the direct ones, in agreement with what occurred for the acetylacetone tautomerism in the presence of a single water molecule. To compare the behaviour of water in pyruvate and in acetylacetone, the two-water-assisted mechanism has been also examined for the latter at the B3LYP/6-31G* level.

Antioxidant properties of pterocarpans through their copper(II) coordination ability. A DFT study in vacuo and in aqueous solution.

The antioxidant activity of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) and 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C) is supposed to be related to their copper coordination ability. Therefore several complexes with Cu(2+) of low-energy conformers of these two prenylated pterocarpans, whose conformational landscape was the subject of a prior B3LYP/6-31G* study (Alagona, Ghio, Monti Phys. Chem.

Plicatin B conformational landscape and affinity to copper (I and II) metal cations. A DFT study.

The conformational landscape of the prenylchalcone plicatin B and some of its tautomers has been investigated at the B3LYP/6-31G* level in analogy to prior studies of ours on two structurally related prenylated pterocarpans. Since the antioxidant activity of these natural compounds is supposed to be related to their copper chelation ability, several complexes with Cu(i) and Cu(ii) metal cations, Cu(+) and Cu(2+), have been taken into account with the metal ions described by effective core potentials in the LANL2DZ valence basis set. The preferred binding sites on low-energy conformers of E and Z plicatin B have been determined and their metal ion affinity (MIA) values have been compared.

Theoretical Investigation of Tautomeric Equilibria for Isonicotinic Acid, 4-Pyridone, and Acetylacetone in Vacuo and in Solution.

Tautomeric equilibria have been theoretically calculated for isonicotinic acid (neutral and zwitterionic forms), the 4-pyridone/4-hydroxypyridine system, and the keto-enol transformation for acetylacetone in vacuo and in tetrahydrofuran, methanol, and water solvents. Solvent, basis set, and cavity model effects have been studied in the integral equation formalism for the polarizable continuum model (IEF-PCM)/B3LYP framework, as well as the effect of the procedure, CHELPG or RESP, applied in fitting atomic charges to the in-solution molecular electrostatic potential (ELPO). The in-solution optimized geometries obtained at the IEF-PCM/B3LYP/6-31G* and 6-311++G** levels differ moderately but deviate from their gas-phase counterparts.

Computational prediction of the regio- and diastereoselectivity in a rhodium-catalyzed hydroformylation/cyclization domino process.

The regioselectivity of the hydroformylation reaction of 2-methyl-3-(3-acetylpyrrol-1-yl)prop-1-ene catalyzed by an unmodified Rh catalyst has been investigated at the B3LYP/6-31G* level with Rh described by effective core potentials in the LANL2DZ valence basis set. Considering the population of all the H-Rh(CO)3-olefin transition state complexes, a regioselectivity ratio (B:L) of 12:88 has been obtained, in satisfactory agreement with the experiment producing the chiral linear aldehyde as the only product. The aldehyde, after complete diastereoselective cyclization, yields a 1:1 mixture of 1-acetyl-6R(S)-methyl-8R(S)-hydroxy-5,6,7,8-tetrahydroindolizine (having the same configuration on both stereogenic carbon atoms) and 2-acetyl-6-methyl-5,6-dihydroindolizine [Lett Org Chem (2006) 3:10-12].

Caco-2 cell permeability modelling: a neural network coupled genetic algorithm approach.

The ability to cross the intestinal cell membrane is a fundamental prerequisite of a drug compound. However, the experimental measurement of such an important property is a costly and highly time consuming step of the drug development process because it is necessary to synthesize the compound first. Therefore, in silico modelling of intestinal absorption, which can be carried out at very early stages of drug design, is an appealing alternative procedure which is based mainly on multivariate statistical analysis such as partial least squares (PLS) and neural networks (NN).

Structure and dynamics of the hydrogen-bond network around (R,R)-pterocarpans with biological activity in aqueous solution.

Molecular dynamics simulations were carried out in the presence of 2380 water molecules (TIP3P) to explore the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) and 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C) and the H-bond network around them, using the empirical general AMBER force field (GAFF). Specific angle and torsional parameters have been improved in order to match the geometries of the minimum energy structures obtained from an earlier DFT/ab initio study in vacuo, taking into account a few configurations [Alagona, G.; Ghio, C.

Conformational landscape of (R,R)-pterocarpans with biological activity in vacuo and in aqueous solution (PCM and/or water clusters).

All possible combinations of stable dihedral values have been considered in vacuo at the B3LYP/6-31G level for 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C), whose hydroxy out-out conformation had been examined earlier together with the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) at the same level (Phys. Chem. Chem.

Theoretical Conformational Analysis for Neurotransmitters in the Gas Phase and in Aqueous Solution. Serotonin.

Conformational analyses have been performed for protonated serotonin in the gas phase, aqueous solution, and in the binding cavity of a 5-HT2A receptor model. DFT geometry optimizations have been performed in the gas phase at the B3LYP/6-31G* levels. Optimized calculations up to the B3LYP/6-311++G** level find two low-energy gauche conformations separated by 8-10 kcal/mol barriers from a trans conformation with relative energy of about 6 kcal/mol.

Quantum mechanical study of stereoselectivity in the oxazaborolidine-catalyzed reduction of acetophenone.

Chiral oxazaborolidines, known as CBS catalysts after the work of Corey, Bakshi and Shibata, are used for the stereoselective reduction of prochiral ketones to secondary chiral alcohols. Due to their relative low cost, ease of use, and high selectivity, their popularity has remarkably grown in the last 15 years. Oxazaborolidine-catalyzed reductions have been much studied, both experimentally and computationally, by means of semiempirical methods.

Cholic acid derivatives containing both 2-naphthylcarbamate and 3,5-dinitrophenylcarbamate groups: a combined circular dichroism-molecular mechanics approach to the definition of their molecular conformation.

CD spectra of the chiral auxiliaries for enantioselective HPLC N-allyl-N'-methyl-3,12-bis(2-naphthyl)carbamoyloxy-7-(3,5-dinitrophenyl)carbamoyloxycholan-24-amide (1), N-allyl-N'-methyl-3-(3,5-dinitrophenyl)carbamoyloxy-7,12-bis(2-naphthyl)carbamoyloxycholan-24-amide (2), N-allyl-N'-methyl-3,7-bis(2-naphthyl)carbamoyloxy-12-(3,5-dinitrophenyl)carbamoyloxycholan-24-amide (3), and N-allyl-N'-methyl-3,7,12-tris(2-naphthyl)carbamoyloxycholan-24-amide (4) are presented. To determine the preferred conformations of those chiral auxiliaries, a random search based on the aromatic side-chain conformational degrees of freedom was performed and the energy was minimized using two different molecular mechanics force fields. The low energy structures presenting common features were arranged in groups and selected exploiting appropriate filters.

Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine.

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries.

The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach.

The intramolecular mechanism we earlier proposed [Alagona, G.; Desmeules, P.; Ghio, C.