Antonio Vila

Atoms in molecules interpretation of the anomeric effect in the O--C--O unit.

The conformational preferences of two model compounds for the OCH2O anomeric unit: methanediol and dimethoxymethane analyzed within the framework of the QTAIM theory provide a new interpretation of the anomeric effect. The characteristic stabilization of the gauche conformers of these compounds is accompanied by a progressive reduction of the electron population of the hydrogens of the central methylene as the number of their gauche interactions to lone pairs rises. The electron population removed from these atoms during the conformational change is gained in the gauche conformers by atoms of larger atomic number, which results in a more negative molecular energy. Also, the variations displayed by atomic populations and the QTAIM delocalization indexes are not keeping in line with the hyperconjugative model of the anomeric effect.

Transferability in alkyl monoethers. II. Methyl and methylene fragments

The transferability of the atomic and bond properties of the methyl and methylene fragments in linear unbranched alkyl monoethers was studied using the Theory of Atoms in Molecules (AIM). This theory has been applied to the analysis of the HF/6-31++G**//HF/6-31G* electron charge distributions of a series of 33 dialkyl ethers, CH3(CH2)mO(CH2)nCH3, [n=0,1(n⩽m⩽9), n=2,3(n⩽m⩽8), n=4(n⩽m⩽5)]. The results obtained indicate that the methyl and methylene fragments situated in α, β, γ, or δ positions with respect to the oxygen atom are different to those of an n-alkane. Nevertheless, CH3 and CH2 at more distant positions can be considered as standard units, whose nonenergetic properties coincide with those of the corresponding fragment in an n-alkane. On the contrary, the energetic properties of the fragments maintain a differential value with respect to the n-alkane in all of the positions studied in the series. The properties of the methyl or methylene fragments in α to the oxygen depend on the size (methyl or l...

Electron density characterisation of intermolecular interactions in the formaldehyde dimer and trimer

Abstract The electron density distributions of the diverse structures of formaldehyde dimer and trimer have been analysed within the framework of the atoms in molecules theory (AIM) with Dunnings correlation consistent basis sets aug-cc-pVXZ (X=D,T) at the B3LYP level. The angle of electrophilic attack as predicted by the Laplacian of the charge density gives a poor estimation of hydrogen bond angles in these clusters. The AIM integrated charges indicate that no charge transfer takes places between the constituent monomers in the planar clusters, whereas a sizeable flow of charge takes place in the non-planar complexes. The contribution of non-additive terms to the trimerisation energy is significant (it amounts more than 11% of the overall trimerisation energy).

A comparative AIM study of alkyl monoethers and their protonated forms

The eAects of the protonation on the atomic and bond properties of the oxygen atom were studied in a series of unbranched alkyl monoethers of formula CH3OCH2UnOOCH2UmCH3On; ma 0; 1; 2; 3; 4U using MP2/6-31++G //MP2/631G wave functions. The diAerent character of oxygen in methylethers and the remaining dialkylethers and the charge transfer dominant part in the protonation process are supported by two diAerent linear correlations (one for methoxyethers and another for the remaining ethers) between proton charges and protonation energies. The atomic energy of the proton accounts for more than 93% of the protonation energy. ” 2000 Elsevier Science B.V. All rights reserved.

Transferability of energies of atoms in organic molecules

The variation of virial-corrected energies of atoms in organic molecules (AIMs) with the lengths of the attached alkyl chains and the nature of remote substituents is shown to be largely an artifact of the correction procedure itself. Thus, it is demonstrated that the virial correction for energies of AIMs should be avoided despite the fact that it produces values that sum up to the total molecular energies. Consequently, the assessment of transferability of AIMs should be carried out with either uncorrected total energies (i.e., negative kinetic energies) or atomic properties other than energy.

On the different origin of the stabilisation of oxygen versus sulphur H-bond complexes with water

Abstract B3LYP calculations with the aug-cc-pVXZ (X=D, T) basis sets have been carried out on several hydrogen-bonded complexes involving several oxygen containing organic molecules and their sulphur analogues. These calculations were satisfactory in reproducing the experimental dipole moments. The electron densities were analysed within the framework of atoms in molecules theory (AIM). The results reveal that the sulphur containing complexes arise from the stabilisation experienced by the acceptor molecule, whereas the stabilisation of the adducts formed with oxygen compounds is provided by the donor molecule. On the contrary to what was found for complexations to hydrogen fluoride, the Laplacian based prediction of the angle of electrophilic attack gives a poor estimation of hydrogen bond angles in these clusters.

Electron density analysis of small ring ethers

Abstract Atoms in molecules theory (AIM) was employed to compute the atomic properties for a series of five protonated and neutral oxacycloalkanes (CH2)nO (n=2–6), on B3LYP/6-311++G(2d,2p) electron distributions. Atomic energies indicate that strain of oxacycloalkanes results from a destabilization of oxygen and hydrogens that is not compensated for by the stabilization of cyclic carbons. Atomic electron populations point out that cycloalkyloxonium cations are better described by an O–H+ structure than by the widespread use of the O+–H structure.

On the perfluorination of alkyl ethers. An electron density study under the AIM approach

Abstract The changes induced by perfluorination on the electron density topological properties of dimethyl ether, methyl ethyl ether, diethyl ether, and their protonated forms have been analysed under the approach of the atoms in molecules theory (AIM). Atomic electron population and bond properties of the molecules under study have been obtained from B3LYP/6-311++G(d,p) electron distributions. The integrated atomic charges indicate a strongly polarised C–O bond in the perfluorinated compounds. The topology of the electron density shows the existence of O–F and F–F closed-shell interactions in the protonated perfluorodiethyl ether. Protonation energies display a strong correlation with the integrated charges on the attached proton, supporting the consideration of protonation as a charge transfer process. The electron charge on the attached proton in the protonated perfluorinated compounds is withdrawn from all the atoms of the molecule (more than 50% is provided by the set of fluorine atoms). The values obtained for the ZPVE and BSSE corrections to the protonation energy are nearly constant along the series of compounds supporting approximations employed in previous works.

AIM study on the influence of fluorine atoms on the alkyl chain

Abstract A topological analysis of HF/6-31++G**//HF/6-31G* electron distributions on diverse conformers of 36 linear fluoroalkanes of formula CH n F 3− n (CH 2 ) m CH 3 was carried out within the atoms in molecules (AIMs) formalism. Group energy additivity of molecular energies was found in spite of lack of energy transferability. Cooperative effects due to stepwise fluorination on carbon 1 that appear to be around to 90 kJ mol −1 according to traditional analysis based upon fitted group energies, exceed 370 kJ mol −1 when obtained from AIMs energies. Mean values of atomic properties and empirical relationships between concrete atomic properties lead to a definition of transferable fragments. It was found that the effect of fluorine atom on the chain is appreciable at further carbons for trans than for gauche arrangements, whereas effects on the hydrogen atoms give rise to an oscillatory behaviour (related to F–H interatomic distances) displayed along the whole chain.

Influence of the Solvent on the Charge Distribution of Anomeric Compounds

Conformational preferences of methanediol, dimethoxymethane, methanediamine, and fluoromethanol in the presence of solvents of diverse polarity (water, acetone, and chloroform), modeled with the polarizable continuum model, were analyzed within the framework of the Quantum Theory of Atoms in Molecules. The results indicate that the hydrogens bonded to the anomeric carbon experience the largest reorganization of electron density upon conformational change, as was obtained from previous calculations in the gas phase. When the water solvation is simulated by explicit inclusion of water molecules, the electron density reorganization involved in the cluster formation is significantly different for each conformer of methanediol. As a consequence, similar depletions of electron population are displayed by the hydrogens of hydroxyl and methylene groups in the cluster obtained for the most stable conformer of methanediol, with regard to that built for the completely antiperiplanar conformer.