Role of weak C-H...O and strong N-H...O intermolecular interactions on the high-symmetry molecular packing of trans-cyclohexane-1,4-dicarboxamide.

An unpredicted fourfold screw N-H...O hydrogen bond C(4) motif in a primary dicarboxamide (trans-cyclohexane-1,4-dicarboxamide, C8H14N2O2) was investigated by single-crystal X-ray diffraction and IR and Raman spectroscopies. Electron-density topology and intermolecular energy analyses determined from ab initio calculations were employed to examine the influence of weak C-H...O hydrogen-bond interactions on the peculiar arrangement of molecules in the tetragonal P43212 space group. In addition, the way in which the co-operative effects of those weak bonds might modify their relative influence on molecular packing was estimated from cluster calculations. Based on the results, a structural model is proposed which helps to rationalize the unusual fourfold screw molecular arrangement.

A combined crystallographic, thermal, Raman and computational study on polymorphism and phase transition in 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

The crystal structure of the triclinic polymorph of 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3, differs markedly from that of the orthorhombic polymorph [Manzano et al. (2015). Acta Cryst. C71, 1022-1027]. The two molecular structures are alike with respect to their bond lengths and angles, but differ in their spatial arrangement. This gives rise to quite different packing schemes, even if built up by similar chains having the hydroxy-ethanone O-H...O hydrogen-bond synthon in common. Both phases were found to be related by a first-order thermally driven phase transformation at 338-340 K, which is discussed in detail. The relative stabilities of both polymorphs are explained on the basis of both the noncovalent interactions operating in each structure and quantum chemical calculations. The polymorphic phase transition has also been studied experimentally by means of differential scanning calorimetry (DSC) experiments, conducted on individual single crystals, Raman spectroscopy and controlled heating under a microscope of individual single crystals, which were further characterized by powder and single-crystal X-ray diffraction.

Polymorphism of a widely used building block for halogen-bonded assemblies: 1,3,5-trifluoro-2,4,6-triiodobenzene.

After reporting the structure of a new polymorph of 1,3,5-trifluoro-2,4,6-triiodobenzene (denoted BzF3I3), C6F3I3, (I), which crystallized in the space group P21/c, we perform a comparative analysis with the already reported P21/n polymorph, (II) [Reddy et al. (2006). Chem. Eur. J. 12, 2222-2234]. In polymorph (II), type-II I...I halogen bonds and I...π interactions connect molecules in such a way that a three-dimensional structure is formed; however, the way in which molecules are connected in polymorph (I), through type-II I...I halogen bonds and π-π interactions, gives rise to an exfoldable lamellar structure, which looks less tightly bound than that of (II). In agreement with this structural observation, both the melting point and the melting enthalpy of (I) are lower than those of (II).

Understanding the conformational changes and molecular structure of furoyl thioureas upon substitution.

1-Acyl thioureas [R1C(O)NHC(S)NR2R3] are shown to display conformational flexibility depending on the degree of substitution at the nitrogen atom. The conformational landscape and structural features for two closely related thioureas having R1=2-furoyl have been studied. The un-substituted 2-furoyl thiourea (I) and its dimethyl analogue, i.e. 1-(2-furoyl)-3,3-dimethyl thiourea (II), have been synthesized and fully characterized by spectroscopic (FT-IR, 1H and 13C NMR) and elemental analysis. According to single crystal X-ray diffraction analysis, compounds I and II crystallize in the monoclinic space group P21/c. In the compound I, the trans-cis geometry of the almost planar thiourea unit is stabilized by intramolecular NH⋯OC hydrogen bond between the H atom of the cis thioamide and the carbonyl O atom. In compound II, however, the acyl thiourea group is non-planar, in good agreement with the potential energy curve computed at the B3LYP/6-31+G(d,p) level of approximation. Centrosymmetric dimers generated by intermolecular NH⋯SC hydrogen bond forming R22(8) motif are present in the crystals. Intermolecular interactions have been rationalized in terms of topological partitions of the electron distributions and Hirshfeld surface analysis, which showed the occurrence of S⋯H, O⋯H and H⋯H contacts that display an important role to crystal packing stabilization of both thiourea derivatives.

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach.

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, (1)H and (13)C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···O=C hydrogen bond occurring between the carbonyl (-C=O) and the hydrazone -C=N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1→σ*(N2-H) remote interaction between the C2=O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.

Intra- and intermolecular hydrogen bonding and conformation in 1-acyl thioureas: an experimental and theoretical approach on 1-(2-chlorobenzoyl)thiourea.

The vibrational analysis (FT-IR and FT-Raman) for the new 1-(2-chlorobenzoyl)thiourea species suggests that strong intramolecular interactions affect the conformational properties. The X-ray structure determination corroborates that an intramolecular N-H⋯OC hydrogen bond occurs between the carbonyl (-CO) and thioamide (-NH2) groups. Moreover, periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Extended N-H⋯SC hydrogen-bonding networks between both the thioamide (N-H) and carbamide (NH2) groups and the thiocarbonyl bond (CS) determine the crystal packing. The Natural Bond Orbital (NBO) population analysis demonstrates that strong hyperconjugative remote interactions are responsible for both, intra and intermolecular interactions. The Atom in Molecule (AIM) results also show that the N-H⋯Cl intramolecular hydrogen bond between the 2-Cl-phenyl ring and the amide group characterized in the free molecule changes to an N⋯Cl interaction as a consequence of crystal packing.

Conformational preference of chlorothioformate species: molecular structure of ethyl chlorothioformate, ClC(O)SCH2CH3, in the solid phase and NBO analysis.

The molecular structure of ethyl chlorothioformate, ClC(O)SCH(2)CH(3), has been investigated in the solid phase by X-ray diffraction analysis at low temperature using a miniature zone-melting procedure and IR laser radiation. The crystalline solid consists exclusively of molecules with the synperiplanar conformation with respect to the C=O double bond and the S-C single bond, and gauche orientation of the ethyl group (syn-gauche). These results coincide with previous studies devoted to gas-phase conformational properties. The conformational preference for the ClC(O)SY (Y = Cl, CF(3), CH(3) and CH(2)CH(3)) series of molecules was rationalized using the natural bond orbital (NBO) scheme. It was found that both resonance (mesomeric) and anomeric (hyperconjugation) intermolecular charge-transfer interactions are important for describing the syn ↔ anti equilibrium, also illustrating the effect of electronegativity of the substituent in the conformation preference of the ClC(O)S- moiety. On the basis of the atoms in molecules (AIM) theory, intermolecular interactions have been characterized in the B3LYP/6-31G** periodic boundary electron density.

On the electron density topology and electrostatic properties of nitroanilines. A theoretical investigation on m-nitroaniline and 2-methyl-5-nitroaniline crystals.

On the basis of the AIM theory, intermolecular interactions have been characterized in the B3LYP/6-31G** periodic electron density of the title compounds. Although the set of bond paths identified in each system is not fully equivalent to its experimental counterpart, agreement is reasonable with regard to the nature and relative importance of the intermolecular interactions at play. Within the AIM partition scheme, the molecular dipole moment of the in-crystal molecule was determined for the title compounds and the two closely related crystals of 2-methyl-4-nitroaniline and p-nitroaniline. Using a method that relies only on molecular calculations and a mean electric field approximation, it was possible to reproduce within 6% the values of the molecular dipole moment modulus obtained directly from the periodic electron densities. This result reveals that, for this kind of molecular crystal, enhancement of the dipole moment in going from the isolated molecule to the in-crystal one is an almost exclusively inductive effect.