Roles of Hydrogen, Halogen Bonding and Aromatic Stacking in a Series of Isophthalamides

Abstract

The synthesis and spectroscopic characterisation of six bis(5-X-pyridine-2-yl)isophthalamides (X = H, F, Br, Cl, I, NO2) are reported, together with five crystal structure analyses (for X = H, F to I). The isophthalamides span a range of conformations as syn/anti (H-DIP; I-DIP), anti/anti- (F-DIP; Br-DIP) and with both present in ratio 2:1 in Cl-DIP. The essentially isostructural F-DIP and Br-DIP molecules (using strong amide…amide interactions) aggregate into 2D molecular sheets that align with either F/H or Br atoms at the sheet surfaces (interfaces), respectively. Sheets are linked by weak C-H⋯F contacts in F-DIP and by Br⋯Br halogen bonding interactions as a ‘wall of bromines’ at the Br atom rich interfaces in Br-DIP. Cl-DIP is an unusual crystal structure incorporating both syn/anti and anti/anti molecular conformations in the asymmetric unit (Z’ = 3). The I-DIP•½(H2O) hemihydrate structure has a water molecule residing on a twofold axis between two I-DIPs and has hydrogen and N⋯I (Nc = 0.88) halogen bonding. The hydrate is central to an unusual synthon and involved in six hydrogen bonding interactions/contacts. Contact enrichment analysis on the Hirshfeld surface demonstrates that F-DIP, Cl-DIP and Br-DIP have especially over-represented halogen···halogen interactions. With the F-DIP, Cl-DIP and Br-DIP molecules having an elongated skeleton, the formation of layers of halogen atoms in planes perpendicular to the long unit cell axis occurs in the crystal packings. All six DIPs were analysed by ab initio calculations and conformational analysis; comparisons are made between their minimized structures and the five crystal structures. In addition, physicochemical properties are compared and assessed.

Keywords

• aggregate
• aromatic ring stacking
• crystal structure
• conformational analysis
• halogen bonding
• hydrogen bonding