Ana M. Graña

Do 1,2-ethanediol and 1,2-dihydroxybenzene present intramolecular hydrogen bond?

A study of the intramolecular hydrogen bond (IHB) in 1,2-ethanediol and 1,2-dihydroxybenzene (catechol) was carried out using the QTAIM theory. Atomic and bond properties defined within this theory were calculated for different donor–acceptor distances, Hd⋯Oa, in both molecules, and different H–Oa–C–C dihedral angles for 1,2-dihydroxybenzene, optimising the remaining geometry. Though no conformer of both compounds present IHB, it appears when the Hd⋯Oa distance is reduced in both molecules or when the H–Oa–C–C angle is rotated in 1,2-dihydroxybenzene. The evolution of integrated and local properties follows the criteria of Koch and Popelier for hydrogen bond formation when the interatomic distance is modified, but display the opposite trends when the IHB is formed by rotating the dihedral angle.

The transferability of the carbonyl group in aldehydes and ketones

The atomic and bond properties of the carbonyl group of a series of 42 aldehydes and ketones were calculated in order to analyze the transferability of this group. This was done by using the theory of atoms in molecules (AIM) on 6-31++G**/6-31G* wave functions. We found that the magnitudes ρ(rc), μ(O), μ(C), v(C), and λ3 differ between aldehydes and ketones, and can be said to be transferable within each of these series, with the exception of the formaldehyde molecule, which behaves in a specific way. We considered N(O), N(C), r1(O), r1(C), v(O), R, r, e, and H(rc) as transferable dividing them into three groups: Aldehydes, methylketones, and ketones of greater length; we omitted formaldehyde, acetaldehyde, and acetone molecules, which behave in a specific way. Both the total and potential energies, either absolute or by unit of population of the C and O atoms, together with their summation, varied in accordance with molecule size and, therefore, cannot be considered transferable properties of the carbony...

Transferability in aldehydes and ketones. II. Alkyl chains

An analysis of the transferability of hydrocarbon chains in aldehydes and ketones was carried out, considering the values obtained for the atomic and bond properties of these chains in a series of 42 compounds. Likewise, the differences between the n-alkane groups and the methylene and methyl groups of a chain containing a carbonyl group were established. All the properties were calculated using the theory of atoms in molecules on 6-31++G**//6-31G* wave functions. The values of the atomic properties and their evolution with L(Ω) and the size of the molecule allow the carbon atoms of an alkyl skeleton to be classified considering both their position with respect to the C=O group (α, β, γ, δ or further) and their position in relation to the end of the chain (terminal C, C previous to the terminal, and the rest). For some of the properties of the carbons in α or β dispositions to the C=O group, it is also necessary to consider the nature of the other alkyl radical bonded to the carbonyl group (H,CH3,CH2CH3 o...

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).

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.

Approximate transferability in alkanols

Abstract The approximate transferability of OH, CH2, and CH3 groups in unbranched primary alkanols has been studied by comparing several atomic and bond properties of the 12 smallest members of this series. These properties were obtained by employing the Atoms in Molecules theory on HF/6-31++G∗∗//HF/6-31G∗ and QCISD/6-31++G∗∗//QCISD/6-31G∗ wave functions. The properties computed at both levels follow parallel evolutions along the series, which allow to conclude that the OH group can be considered approximately transferable along the set of 1-alkanols larger than ethanol, whereas ethanol and methanol present specific hydroxyls. The electron population of the oxygen atom is lower than in ethers, aldehydes, and ketones. The hydroxyl affects significantly the CH3 and CH2 groups that are in positions α, β, γ, or δ, whereas those groups separated from the oxygen by more than 4 bonds can be considered similar to those included in a n-alkane. CH2 groups in the series can be classified into 6 quasi-transferable fragments taking into account their position with regard to the OH (α, β, γ, δ, or beyond (ν)), and respect to the terminal CH3 (attached to it or not). The simultaneous occurrence of both facts gives rise to four specific CH2 fragments: α-CH2 in ethanol, β-CH2 in 1-propanol, γ-CH2 in 1-butanol, and δ-CH2 in 1-pentanol. It has been found that all the CH2 and CH3 fragments that are γ or δ to the OH group do not differ significantly from the corresponding fragments of a dialkyl ether. The energy of oxygen, CH2 and CH3 fragments depend on the molecular size. The effect of the basis set size error on this quantity has been investigated, concluding that the molecular-size dependence is not an artifact due to it. The destabilization experienced by the oxygen atom for a common increase in the molecular size in alcohols is equivalent to that of ethers and smaller than the one displayed by aldehydes and ketones. It was also concluded that the effect due to the variation of the molecular size is independent on the number of alkyl chains that are increased.

How does aromaticity rule the thermodynamic stability of hydroporphyrins

Several measures of aromaticity including energetic, magnetic, and electron density criteria are employed to show how aromatic stabilization can explain the stability sequence of hydroporphyrins, ranging from porphin to octahydroporphin, and their preferred hydrogenation paths. The methods employed involve topological resonance energies and their circuit energy effects, bond resonance energies, multicenter delocalization indices, ring current maps, magnetic susceptibilities, and nuclear-independent chemical shifts. To compare the information obtained by the different methods, the results have been put in the same scale by using recently proposed approaches. It is found that all of them provide essentially the same information and lead to similar conclusions. Also, hydrogenation energies along different hydrogenation paths connecting porphin with octahydroporphin have been calculated with density functional theory. It is shown by using the methods mentioned above that the relative stability of different hydroporphyrin isomers and the observed inaccessibility of octahydroporphin both synthetically and in nature can be perfectly rationalized in terms of aromaticity.

Aromaticity in spin-polarized systems: Can rings be simultaneously alpha aromatic and beta antiaromatic?

The partition of the multicenter electron delocalization indices and the nucleus independent chemical shift indices into alpha and beta contributions in open-shell systems has been performed. In general it is shown that a full understanding of aromaticity in these systems cannot be achieved by restricting the calculations to the global properties but by dissecting these properties into alpha and beta terms. The 4n+2- and 4n-aromaticity rules for singlet and triplet annulenes, respectively, reduce to a general aromaticity rule when the alpha and beta terms are studied separately. This new rule allows us to extend the concept of conflicting aromaticities to radical systems that are simultaneously alpha-aromatic and beta-antiaromatic or vice versa. The existence of such systems is demonstrated here by means of multicenter electron delocalization indices and nucleus independent chemical shifts. Finally, the global aromatic/antiaromatic character of these radical systems is estimated by means of aromatic stabilization energy, which is shown to be either slightly positive or slightly negative, thus reflecting the small aromatic/antiaromatic character of these radicals and reinforcing the conclusions obtained with aromaticity indices.

Theoretical study of the electronic structure of CnS (n=1–6) thiocumulenes

Linear sulfur-carbon chains C(n)S (n=1-6) of astronomical interest were examined by means of several theoretical methods. The three smallest compounds of the series were chosen to evaluate the performance of several computational models, including Hartree-Fock theory, density functional theory with the Beckes three parameter exchange functional and the correlation functional of Lee, Yang, and Parr (B3LYP), and electron-correlated methods (second-order Moller-Plesset perturbation method (MP2), configuration interaction method including single and double excitations (CISD), and quadratic configuration interaction method including single and double excitations (QCISD) in combination with a large variety of basis sets. The systematic comparison between the experiment and theory indicates that the B3LYP/6-311G** method can be considered suitable for the study of the electronic structures of the C(n)S compounds. The electronic ground states of the C(n)S molecules alternate between 1Sigma and 3Sigma for odd and even values of n, respectively. The B3LYP/6-311G** wave functions for these electronic ground states were analyzed by means of the atoms in molecules (AIM) and natural bond orbital (NBO) methods. Both approaches suggest that the electronic structures for the singlet and triplet compounds must be considered separately. According to the NBO method, singlet compounds can be properly represented by acetylenic structures with alternating single and triple bonds (S[triple bond]C-C[triple bond]C...). However, triplet compounds are better described by means of double bond-double bond cumulenic structures (S=C=C=C=C...) as a consequence of the average between different alpha and beta electronic densities. AIM delocalization indexes and NBO interactions between localized orbitals also indicate that these structures are strongly pi delocalized. Finally, the different singlet and triplet structures proposed provide a consistent explanation for the geometries, dipole moments, and spin-density values of the C(n)S compounds studied.

Blue‐shifting hydrogen bond in the benzene–benzene and benzene–naphthalene complexes

Ab initio complete optimizations at MP2/6‐31++G** level have been performed in the T‐shaped geometry of the benzene–benzene and benzene–naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue‐shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems.