Influence of Deuteration and Fluorination on the Supramolecular Architecture of Pyridine N‐Oxide Crystals

Abstract

To understand how deuterium and fluorine substituents influence the supramolecular architecture of pyridine N-oxide crystals, the crystal structure of 3-fluoropyridine N-oxide (PNO-3F) was determined and the crystal packing motives of non-deuterated pyridine-N-oxide (PNO), partial-deuterated pyridine-N-oxide (PNO-D) and PNO-3F were analyzed based on ab initio quantum-chemical calculations of the intermolecular interaction energy, using the MP2/6-311G(d,p) method. The appearance of the weak-directing substituents deuterium and fluorine leads to significant changes in the crystal organization of the isotropic packing of PNO molecules.

Crystal structures of 2-chloropyridine and 2-fluoropyridine: Isostructural crystal packing or not?

“…The C-HÁÁÁp and pÁÁÁp interactions (dimers [3][4]8) lead to the formation of shifted columns. Combining these two elements results in a twodimensional network, a layered structure, a double-layered structure in particular, based on the dimers with the highest intermolecular interaction energies.…”

“…The question of the nature of short FÁÁÁF intermolecular distances is still not fully understood, and a controversial discussion is attributed to the importance of short FÁÁÁF intermolecular distances on the non-covalent synthesis of molecular arrangements [5]. Our own studies have shown that, comparable to halogenated benzonitriles and phenols, the substitution pattern on the benzene backbone of fluoro-substituted pyridines influences the formation of packing motifs in crystal structures [6][7][8]. Noteworthy is the structural similarity between 2,4,6-trifluoropyridine, 1,3,5-trifluorobenzene and 1,3,5-triazine.…”

“…In continuation of our investigations on aggregation phenomena of small organic compounds [3,4,[6][7][8], we have performed the crystal structure of the low-melting compound 2-chloropyridine. The crystal packing of 2-chloropyridine (1) was analyzed and compared with the crystal packing of 2-fluoropyridine (2) by experimental and theoretical methods.…”

Distortions of a flexible metal-organic framework from substituted pendant ligands

“…The 3-bromopyridine groups are parallel but the Br substituents force the pyridine rings away from each other so that they are offset, preventing anyinteractions. Interestingly, in the crystal structure of pyridine-N-oxide itself there are apparently nointeractions but instead one intermolecular interaction is characterized by a CHÁ Á Á distance of 2.72 Å from the one pyridine-N-oxide to the centroid of the aromatic ring of the next (in addition to C-HÁ Á ÁO interactions not possible in the metal-organic frameworks; Shishkin et al, 2013). In the metal-organic framework, the neighbouring 3-bromo-pyridine-N-oxides are too far apart for such an interaction; instead there is evidence for a CHÁ Á Á interaction between H16 and a centroid of the aromatic ring of the closest 1,4-benzenedicarboxylate linker (3.19 Å ).…”

Deuterium Perturbs the Molecular Arrangement in the Solid State

“…Extensive IR studies of pyridine and d 5 -pyridine by Verderamew et al in 1969revealed the different arrangements of the molecules in the solid state45 . Pyridine crystallizes in the space group P2 1 2 1 2 1 and has an unusual crystal structure with four independent molecules in the asymmetric unit (Z'=4)50 . In contrast, Boese et al(2009) discovered that the isotopic polymorph of d 5 -pyrinde crystallizes at about -85 °C with a crystal structure (Pna2 1 with Z'=1) which differs from the structure which is usually adopted by pyridine.…”