Hydrogen bonding in crystal structures of N,N'-bis(3-pyridyl)urea. Why is the N-H···O tape synthon absent in diaryl ureas with electron-withdrawing groups?

Reddy, L. Sreenivas ; Basavoju, Srinivas ; Vangala, Venu R. ; Nangia, Ashwini (2006) Hydrogen bonding in crystal structures of N,N'-bis(3-pyridyl)urea. Why is the N-H···O tape synthon absent in diaryl ureas with electron-withdrawing groups? Crystal Growth & Design, 6 (1). pp. 161-173. ISSN 1528-7483

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Official URL: http://pubs.acs.org/doi/abs/10.1021/cg0580152

Related URL: http://dx.doi.org/10.1021/cg0580152

Abstract

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 N,N'-bis(3-pyridyl)urea 3 and some of its derivatives: hydrates of stoichiometry 3·(4/3)H2O and 3·2H2O, cocrystals 3·SA and 3·FA·H2O with succinic acid and fumaric acid, bis pyridine N-oxide 8, and bis N-methylpyridinium iodide 9. Crystal packing in pyridyl urea structures is directed by N-H···Npyridyl, N-H···Owater, N-H···Oacid, and N-H···I- hydrogen bonds instead of the common one-dimensional N-H···Ourea tape. We postulated that the urea tape is absent in these structures because the C=O acceptor is weakened by two intramolecular C-H···Ourea interactions (synthon III) 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, H2O, COOH, and I-, become viable hydrogen-bond acceptors for the strong NH donors. 1H NMR difference nOe confirmed that the planar conformation of dipyridyl urea 3 in the solid-state persists in solution. Interestingly, even though the strong hydrogen-bond motifs changed in structures of 3, the C-H···O interactions of synthon III (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, PhNO2), the NH donor(s) preferentially bond to pyridyl N, nitro O, or solvent O atom instead of the urea C=O 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.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:24573
Deposited On:29 Nov 2010 08:30
Last Modified:04 Mar 2011 05:30

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