Hydrogen Bonding in Crystal Structures of <i>N</i>,<i>N</i>‘-Bis(3-pyridyl)urea. Why Is the N−H···O Tape Synthon Absent in Diaryl Ureas with Electron-Withdrawing Groups?
2006-01-04T00:00:00Z (GMT) by
The urea tape α-network of bifurcated N−H···O hydrogen bonds is a common motif in diaryl ureas and their molecular complexes. We analyzed the X-ray crystal structures of <i>N</i>,<i>N</i>‘-bis(3-pyridyl)urea <b>3</b> and some of its derivatives: hydrates of stoichiometry <b>3</b>·(4/3)H<sub>2</sub>O and <b>3</b>·2H<sub>2</sub>O, cocrystals <b>3</b>·SA and <b>3</b>·FA·H<sub>2</sub>O with succinic acid and fumaric acid, bis pyridine <i>N</i>-oxide <b>8</b>, and bis <i>N</i>-methylpyridinium iodide <b>9</b>. Crystal packing in pyridyl urea structures is directed by N−H···N<sub>pyridyl</sub>, N−H···O<sub>water</sub>, N−H···O<sub>acid</sub>, and N−H···I<sup>-</sup> hydrogen bonds instead of the common one-dimensional N−H···O<sub>urea</sub> tape. We postulated that the urea tape is absent in these structures because the CO acceptor is weakened by two intramolecular C−H···O<sub>urea</sub> interactions (synthon <b>III</b>) in a planar molecular conformation. Electrostatic surface potential (ESP) charges (DFT-B3LYP/6-31G*) showed that the C−H···O interactions sufficiently reduce the electron density at the urea O, and so other electronegative atoms, such as pyridyl N, H<sub>2</sub>O, COOH, and I<sup>-</sup>, become viable hydrogen-bond acceptors for the strong NH donors. <sup>1</sup>H NMR difference nOe confirmed that the planar conformation of dipyridyl urea <b>3</b> in the solid-state persists in solution. Interestingly, even though the strong hydrogen-bond motifs changed in structures of <b>3</b>, the C−H···O interactions of synthon <b>III </b>(energy 4.6−5.0 kcal/mol) occurred throughout the family. In addition to dipyridyl urea, other electron-withdrawing diaryl ureas, e.g., those with phenylpyridyl and phenyl-nitrophenyl groups, also deviated from the prototype N−H···O tape because of the interference from weak C−H···O hydrogen bonds. Therefore, when one or both aryl rings have hydrogen-bond acceptor groups (e.g., pyridine, PhNO<sub>2</sub>), the NH donor(s) preferentially bond to pyridyl N, nitro O, or solvent O atom instead of the urea CO acceptor. We classify supramolecular organization in diaryl ureas into those with the α-network (twisted molecular conformation) or non-urea tape structures (stable, planar conformation) depending on the substituent group. Our results suggest a model to steer urea crystal structures toward the tape synthon (Ph and electron-donating groups) or with non-urea hydrogen-bond motifs and a high probability for urea···solvent hydrogen bonding (electron-withdrawing groups) by appropriate selection of functional aryl and heterocyclic groups.