Lucas Sousa Madureira

Structural, Hirshfeld surface and theoretical analysis of two conformational polymorphs of N,N′-bis(pyridin-3-ylmethyl)oxalamide

Abstract The common feature of two conformational polymorphs of N,N′-bis(pyridin-3-ylmethyl)oxalamide is their crystallisation in the monoclinic space group P21/c with Z=4. In low symmetry form 1, the central core is effectively planar and the terminal pyridyl rings adopt a syn-periplanar conformation. In the high symmetry form, 2, there are two independent molecules in the asymmetric unit but each is located about a centre of inversion. The rings again are almost perpendicular to the central plane but, from symmetry are anti-periplanar. Computational chemistry shows that symmetric molecules with syn (two-fold) and anti (centrosymmetric) conformations have nearly identical energies. In the molecular packing of each of 1 and 2, supramolecular tapes based on amide-N–H···O(amide) hydrogen bonding are found. In 1, these are connected into layers by C–H···N(pyridyl) interactions, while in 2, the chains are linked into a three-dimensional architecture by C–H···N(pyridyl) interactions. The importance of hydrogen bonding is emphasised in the analysis of the Hirshfeld surfaces.

Crystallographic, DFT and docking (cathepsin B) studies on an organotellurium(IV) compound

Abstract Some biologically active organotellurium compounds exhibit inhibitory potency against cathepsin B. In this study, an alkyl derivative, viz. [CH3(CH2)2C(I)=C(H)](nBu)TeI2, 1, has been structurally characterised by X-ray crystallography and shown to be coordinated within a C2I2 donor set. When the stereochemically active lone pair of electrons is taken into account, a distorted trigonal bipyramidal geometry results with the iodide atoms in axial positions. Both intra- and inter-molecular Te···I interactions are also noted. If all interactions are considered, the coordination geometry is based on a Ψ-pentagonal bipyramidal geometry. An unusual feature of the structure is the curving of the functionalised C5 chain. This feature has been explored by DFT methods and shown to arise as a result of close C–H···I interactions. A docking study (cathepsin B) was performed to understand the inhibition mechanism and to compare the new results with previous observations. Notably, 1 has the same pose exhibited by analogous biologically active compounds with aryl groups. Thus, the present study suggests that (alkyl)2TeX2 compounds should also be evaluated for biological activity.

Conformational preferences for isomeric N,N′-bis(pyridin-n-ylmethyl)ethanedithiodiamides, n = 2, 3 and 4: a combined crystallographic and DFT study

Abstract Crystal structure analysis of the isomeric N,N′-bis(pyridin-n-ylmethyl)ethanedithioamides, n = 2 (1), 3 (2) and 4 (3), show a planar conformation for 1 and conformations whereby the pyridyl rings lie orthogonal and to either side of the central residue for each of 2 and 3. The universal adoption of the all ZZ conformation about the central C–N bonds, which have double bond character, is ascribed to the presence of intramolecular N–H…S hydrogen bonds that close S(5) rings. The gas-phase geometry optimised structure for 1 is the same as the experimental structure which features intramolecular amine-N–H…N(pyridyl) hydrogen bonds. The open structures found for 2 and 3 differ from the somewhat flattened optimised structures. Systematic variations in the geometric parameters characterising the central C2N2S2 residue, in particular the double-bond character of the C–N bond and the elongation of the central C–C bond are shown by theory to be due to conjugative nN → π*C=S interactions and nS → σ*C-C hyperconjugation, respectively.

4-Methyl-3-(2-phenoxy-acet-yl)-5-phenyl-1,3,4-oxadiazinan-2-one.

The 1,3,4-oxadiazinane ring in the title compound, C(18)H(18)N(2)O(4), is in a twisted boat conformation. The two carbonyl groups are orientated towards the same side of the mol-ecule. The dihedral angle between the planes of the benzene rings is 76.6 (3)°. Mol-ecules are sustained in the three-dimensional structure by a combination of C-H⋯O, C-H⋯π and π-π [shortest centroid-centroid distance = 3.672 (6) Å] inter-actions.

1-Butyl-1-chloro-3-methyl-3H-2,1λ4-benzoxatellurole: crystal structure and Hirshfeld analysis

Two chemically similar molecules comprise the asymmetric unit and these are connected via Te⋯O secondary bonding. The coordination geometry for each molecule is based on an octahedron with the lone-pair of electrons occupying a position opposite to the n-butyl group.

Structural systematics of aryl-1,3-dithiane derivatives: crystal and energy-minimised structures, and Hirshfeld surface analysis

Abstract The crystal structure analysis of three aryl-1,3-dithiane derivatives, with aryl=4-methylphenyl (1), 4-chlorophenyl (2) and 2,4-dichlorophenyl (3), shows the three molecules to have very similar conformations, with the aryl ring lying on an approximate mirror plane that bisects the dithiane ring which adopts a chair conformation; the energy-minimised structures are consistent with the experimental structures. The greater barrier to rotation about the methine-C–C(ipso) bond in 3, cf. 1 and 2, is related to unfavourable intramolecular S···Cl interactions in the putative transition state. The molecular packing in 1–3, while globally similar, are distinct, being based on combinations of identifiable C–H···π(arene), C–H···S and C–Cl···π(arene) interactions. The lack of isostructural relationships points to the significance of the identified intermolecular interactions to direct molecular packing.