Intramolecular N-H···X (X = F, Cl, Br, I, and S) Hydrogen Bonding in Aromatic Amide Derivatives - The X-Ray Crystallographic Investigation

Abstract

Hydrogen bonding (H-bonding) has recently been defined by IUPAC as “an attractive interaction between a hydrogen atom from a molecule or a molecular fragment X–H in which X is more electronegative than H, and an atom or a group of atoms in the same or a different molecule, in which there is evidence of bond formation”. In most cases, the strength of an H-bond increases with the increase of the electronegativity value of the acceptor atom (Pauling, 1960). This is exactly the case for oxygen and nitrogen atoms. The H-bonds formed between them and the NH and OH groups are usually strong, which play essential roles in studies in supramolecular, crystal engineering, materials, and life sciences (Scheiner, 1997; Jeffrey,1997). As s result of their growing applications in supramolecular chemistry and crystal engineering, in the past two decades, the critical assessment of the weaker H-bonds has also become an important topic (Desiraju & Steiner, 2001). In this context, organic halogen and sulfur atoms, C-X (X = F, Cl, Br, I, S), have all been demonstrated to be weak H-bonding acceptors (Dunitz & Taylor, 1997), although their electronegativities (Pauling scale: 3.98, 3.16, 2.96, 2.66, and 2.58, respectively) are all higher than that of hydrogen (2.20). Indeed, over years it has been accepted that organic fluorine ‘‘hardly ever accepts hydrogen bonds (Dunitz, 2004),’’ presumably due to its low polarizability and tightly contracted lone pairs. For other organic heteroatoms, the increased van der Waals radius and decreased electronegativities may also weaken their capacity of forming the intramolecular electrostatic interaction, i.e., H-bonding, with the amide hydrogen and lose the competition with the amide oxygen of another molecule which forms the intermolecular N−H⋅⋅⋅O=C H-bonding. In contrast, the halogen anions are capable of forming strong intermolecular H-bonding with NH, OH or even CH protons (Harrell & McDaniel, 1964; Simonov et al., 1996; Del Bene & Jordan, 2001). This chapter summarizes recent progresses in the assessment of the weak intramolecular sixand five-membered H-bonding patterns formed by aromatic amides bearing the above five atoms. Theoretical investigations show that similar intermolecular H-bonding patterns can be formed by fluorine in DNA or RNA base analogues (Frey et al., 2006; Koller et al., 2010; Manjunatha et al., 2010), although they are difficult to be confirmed in solution