Ignasi Mata

Universal Features of the Electron Density Distribution in Hydrogen-Bonding Regions: A Comprehensive Study Involving H⋅⋅⋅X (X=H, C, N, O, F, S, Cl, π) Interactions

Topological analyses of the theoretically calculated electron densities for a large set of 163 hydrogen-bonded complexes show that HX interactions can be classified in families according to X (X=atom or pi orbital). Each family is characterised by a set of intrinsic dependencies between the topological and energetic properties of the electron density at the hydrogen-bond critical point, as well as between each of them and the bonding distance. Comparing different atom-acceptor families, these dependencies are classified as a function of the van der Waals radius r(X) or the electronegativity chi(X), which can be explained in terms of the molecular orbitals involved in the interaction. According to this ordering, the increase of chi(X) leads to a larger range of HX distances for which the interaction is of pure closed-shell type. Same dependencies observed for HO interactions experimentally characterised by means of high-resolution X-ray diffraction data show a good agreement with those obtained from theoretical calculations, in spite of a larger dispersion of values around the expected fitting functions in the experimental case. Theoretical dependencies can thus be applied to the analysis of the experimental electron density for detecting either unconventional hydrogen bonds or problems in the modelling of the experimental electron density.

Synthesis, structure and nuclease properties of several ternary copper(II) peptide complexes with 1,10-phenanthroline.

Three new ternary peptide-Cu(II)-1,10-phenanthroline (phen) complexes, [Cu(L-ala-gly)(phen)].3.5H(2)O 1, [Cu(L-val-gly)(phen)] 2 and [Cu(gly-L-trp)(phen)].2H(2)O 3, have been prepared and structurally characterised. These compounds exist as distorted square pyramidal complexes with the five co-ordination sites occupied by the tridentate peptide dianion and the two heterocyclic nitrogens of the phenanthroline ligand. The bulk of the lateral chain in the peptide moiety determines the relative disposition of the phen ligand. Thus, in [Cu(L-val-gly)(phen)] 2, the phenanthroline plane is deviated towards the opposite side of the isopropyl group of the L-valine moiety. On the other hand, in [Cu(gly-L-trp)(phen)].2H(2)O 3 the absence of stacking interactions between phen and indole rings and the presence of an intramolecular CH...pi interaction should be pointed out. These complexes exhibit significant differences in their nuclease activity which depends on the nature of the peptidic moiety, the complex [Cu(gly-L-trp) (phen)].2H(2)O 3 being the most active.

CRYSTAL STRUCTURES OF THE N-SALICYLIDENE-L-SERINATOAQUACOPPER(II) MONOHYDRATE AND ITS TERNARY DERIVATIVE WITH 2-AMINOPYRIDINE

Abstract The complexes [Cu(Sal–( L -Ser))H2O]⋅H2O 1 and [Cu(Sal–Ser)(2-amino pyridine)] 2 have been prepared and their crystal structures determined. In 1 the copper(II) has a square-pyramidal geometry, being coordinated to the tridentate Sal–( L -Ser) Schiff base ligand and the oxygen atom (O(16)) of one water molecule occupying the corners of a square. The coordination sphere about the copper is completed by an axial O(12) atom of an hydroxyl group belonging to an adjacent complex unit. In the racemic ternary complex 2 the metal atom has a square-planar coordination with O,N,O atoms of the tridentate Sal–Ser dianion and the heterocyclic N atom of the 2-aminopyridine. Spectroscopic data are discussed.

Experimental and theoretical study of uracil derivatives: the crucial role of weak fluorine–fluorine noncovalent interactions

We have recently communicated the important role of lone pair–π, π–π and hydrophobic interactions in the solid architecture of 5-fluoro-1-hexyluracil and 1-hexyluracil (CrystEngComm, 2010, 12, 362–365). As a matter of fact, the simple substitution of a hydrogen atom by a fluorine atom has an enormous consequence in the solid state structure. It has been demonstrated that this is due to an increase in the π-acidity of the ring. In this article we extend the study to other uracil derivatives, where we have changed the hydrophobicity of the hexyl chain by introducing hydrophilic groups in the substituent, such as hydroxyl or carboxylic groups. The latter compounds, i.e. (N1-(3-hydroxypropyl)-5-fluorouracil and N1-(4-hydroxycarbonylbutyl)-5-fluorouracil monohydrate present interesting fluorine–fluorine interactions that are very important in determining the crystal packing.

Effect of an external electric field on the dissociation energy and the electron density properties: The case of the hydrogen bonded dimer HF...HF.

The effect of a homogeneous external electric field parallel to the hydrogen bond in the FH...FH dimer has been studied by theoretical methods. The quantum theory of atoms in molecules methodology has been used for analyzing the electron distribution of the dimer, calculated with different hydrogen bond distances and external field magnitudes. It is shown that an electric field in the opposite direction to the dipole moment of the system strengthens the interaction due to a larger mutual polarization between both molecules and increases the covalent character of the hydrogen bond, while an external field in the opposite direction has the inverse effect. The properties of the complex at its equilibrium geometry with applied field have been calculated, showing that dependencies between hydrogen bond distance, dissociation energy, and properties derived from the topological analysis of the electron distribution are analogous to those observed in families of XDH...AY complexes. The application of an external field appears as a useful tool for studying the effect of the atomic environment on the hydrogen bond interaction. In the case of FH...FH, both the kinetic energy density and the curvature of the electron density along the hydrogen bond at the bond critical point present a surprisingly good linear dependence on the dissociation energy. The interaction energy can be modeled by the sum of two exponential terms that depend on both the hydrogen bond distance and the applied electric field. Moreover, as indicated by the resulting interaction energy observed upon application of different external fields, the equilibrium distance varies linearly with the external field, and the dependence of the dissociation energy on either the hydrogen bond distance or the external electric field is demonstrated to be exponential.

Synthesis of Zn N-salicylidene-l-aminoacidatos: X-ray structure of [(N-salicylidene-l-alaninato)(aqua)zinc(II)]·0.25H2O and [(N-salicylidene-l-valinato)(aqua)zinc(II)]

Abstract The synthesis in aqueous ethanol solution of eight Zn(II) compounds of salicylaldehyde-amino acid Schiff bases together with their spectral characterisation is reported. Two of the complexes, [( N -salicylidene- l -alaninato)(aqua)zinc(II)]·0.25H 2 O ( 1 ) and [( N -salicylidene- l -valinato)(aqua)zinc(II)] ( 2 ), have been obtained in the form of crystals suitable for X-ray crystallography. The coordination geometry about the zinc in both structures is between distorted trigonal bipyramidal and distorted square pyramidal with the iminic nitrogen N(4) ( 1 =2.020(3) and 2 =2.015(7) A), the phenolic O(8) ( 1 =1.991(2) and 2 =1.997(6) A) and the carboxylic O(1) ( 1 =2.160(2) and 2 =2.156(5) A) of the N -salicylidene-aminoacidato base ligand. Another carboxylic O(1)* of an adjacent unit ( 1 =2.033(2) and 2 =2.033(5) A), curiously shorter than the bond from the ligand itself, and a water molecule ( 1 =2.006(3) and 2 =1.999(6) A) comprise the fourth and fifth coordination positions. The crystals are constituted by polymeric [( N -salicylidene- l -aminoacidato)zinc(II)] moieties forming helical arrays about three-fold screw axes. To our knowledge these are the first two structures of binary complexes of the type [( N -salicylidene- l -aminoacidato)Zn(II)]. The NMR studies, in DMSO, agree with a general endo disposition between the side chain of the amino acid and the aromatic ring of the salicylidene moiety.

The Paradox of Hydrogen-Bonded Anion–Anion Aggregates in Oxoanions: A Fundamental Electrostatic Problem Explained in Terms of Electrophilic···Nucleophilic Interactions

A theoretical study of anionic complexes formed by two partly deprotonated oxoacids joined by hydrogen bonds has been carried out at the MP2 computational level. In spite of the ionic repulsion, local energy minima are found both in the gas phase and in aqueous solution. Electrostatic potential and electron density topologies, and the comparison with neutral complexes formed by oxoacids, reveal that the ionization has no significant effect on the properties of the hydrogen bonds. The stability of the complexes in the gas phase is explained by attractive forces localized in a volume situated in the hydrogen bond and defined as the electrostatic attraction region (EAR) and determined by the topological analyses of the electron density and the electrostatic potential, and by the electric field lines. In solution, the strong anionic repulsion is mostly screened by the effect of the surrounding polar solvent, which only leads to a weak destabilizing interaction in the hydrogen bond region and finally favors the overall stability of the complexes. The anion-anion complexes have been compared with the corresponding neutral ones (as salts or protonated forms), showing that EAR remains unchanged along the series.

Stereochemistry of Phenylα-Nitronyl Nitroxide Radicals

An extensive investigation of the conformations adopted by the family of phenyl alpha-nitronyl nitroxides has been carried out. A database containing 110 crystal structures was used in a statistical study of the solid-state geometries and conformations of these radicals. This study revealed that the favoured conformations involve a twisted distortion in the imidazolyl rings and a twist between the aromatic and heterocyclic rings in the molecules. As a consequence, these radicals show two types of preferred conformations in the solid state: the pseudo-anti enantiomeric pair and the pseudo-eclipsed pair, the latter type being the most statistically probable. A new chiral member of this group of radicals that bears a lactate moiety, (R)-1, and its corresponding racemic compound, (R,S)-1, have been prepared in order to study the influence of chiral induction from the stereogenic centre on the torsion angle between the aromatic and heterocyclic rings of the alpha-nitronyl nitroxides. The X-ray crystal structures of the enantiopure and racemic compounds, which both reveal chains of molecules sustained by strong O-H...O hydrogen bonds between the carboxylic acid group and the ON group of the radical in the solid, as well as their magnetic properties have been determined. Remarkably, the molecules with a given stereogenic centre have a single helical sense between their component rings, even in the racemic crystal. Chiral induction from the stereogenic centre to the radical unit has also been proved by CD spectroscopy in the solid state. The results of these experiments have been rationalised by ab initio calculations of the spectra.

Crystal structure of the copper(II) ternary complex of N-salicylidene-l-serinato with 2,6-diaminopyridine.: Toxicity studies against Drosophila melanogaster

Abstract The ternary [Cu(Sal-( l -Ser))(2,6-diaminopyridine)H2O] (1b) complex has been prepared and the crystal structure determined. The copper(II) cation has a square pyramidal geometry, being coordinated to the tridentate Sal-( l -Ser) Schiff base ligand and the heterocyclic nitrogen atom N(11) of the 2,6-diaminopyridine molecule which occupying the corners of the square base. The coordination sphere about the copper is completed by an axial O(W) atom of a water molecule. Spectroscopic data are discussed. Preliminary toxicity studies [larva-to-adult viability (V) and developmental time (in days) (DT)] of several copper(II) compounds including complex 1 and other related previously described complexes [Cu(Sal-( l -Ser))H2O]·H2O (2) and [Cu(Sal-Ser)(2-aminopyridine)] (3) against Drosophila melanogaster (Or-R) show that these copper(II) complexes display less toxicity than simple copper(II) salts.

The chiral structure of 1H-indazoles in the solid state: a crystallographic, vibrational circular dichroism and computational study

A survey of the Cambridge Crystallographic Database reveals that there are 17 1H-indazoles forming dimers (7), trimers (4) and catemers or chains (6). Amongst the catemers there is one centrosymmetric compound and five non-centrosymmetric ones that crystallize in chiral helices, either M or P, including indazole itself, whose structure has been determined anew. An explanation will be provided for how an achiral molecule crystallizes in a chiral space group. The second part of the paper is devoted to the use of Vibrational Circular Dichroism (VCD) for determining the absolute configuration of a crystal of indazole. This previously needs the complete assignment of its IR and Raman spectra in solution and in the solid-state based on B3LYP/6-31G(d) calculations of indazole dimers and trimers, which are already chiral.