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?
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- 作者：L. Sreenivas Reddy ; Srinivas Basavoju ; Venu R. Vangala ; and Ashwini Nangia
- 刊名：Crystal Growth & Design
- 出版年：2006
- 出版时间：January 2006
- 年：2006
- 卷：6
- 期：1
- 页码：161 - 173
- 全文大小：509K
- 年卷期：v.6,no.1(January 2006)
- ISSN：1528-7505
文摘
The urea tape 
-network of bifurcated N-H···O hydrogen bonds is a common motif in diaryl ureas and their molecularcomplexes. We analyzed the X-ray crystal structures of N,N'-bis(3-pyridyl)urea 3 and some of its derivatives: hydrates of stoichiometry3·(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 bisN-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 isabsent in these structures because the C=O acceptor is weakened by two intramolecular C-H···Ourea interactions (synthon III) ina planar molecular conformation. Electrostatic surface potential (ESP) charges (DFT-B3LYP/6-31G*) showed that the C-H···Ointeractions 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 theplanar conformation of dipyridyl urea 3 in the solid-state persists in solution. Interestingly, even though the strong hydrogen-bondmotifs changed in structures of 3, the C-H···O interactions of synthon III (energy 4.6-5.0 kcal/mol) occurred throughout thefamily. In addition to dipyridyl urea, other electron-withdrawing diaryl ureas, e.g., those with phenylpyridyl and phenyl-nitrophenylgroups, 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 topyridyl N, nitro O, or solvent O atom instead of the urea C=O acceptor. We classify supramolecular organization in diaryl ureasinto those with the -network (twisted molecular conformation) or non-urea tape structures (stable, planar conformation) dependingon 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.
-network of bifurcated N-H···O hydrogen bonds is a common motif in diaryl ureas and their molecularcomplexes. We analyzed the X-ray crystal structures of N,N'-bis(3-pyridyl)urea 3 and some of its derivatives: hydrates of stoichiometry3·(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 bisN-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 isabsent in these structures because the C=O acceptor is weakened by two intramolecular C-H···Ourea interactions (synthon III) ina planar molecular conformation. Electrostatic surface potential (ESP) charges (DFT-B3LYP/6-31G*) showed that the C-H···Ointeractions 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 theplanar conformation of dipyridyl urea 3 in the solid-state persists in solution. Interestingly, even though the strong hydrogen-bondmotifs changed in structures of 3, the C-H···O interactions of synthon III (energy 4.6-5.0 kcal/mol) occurred throughout thefamily. In addition to dipyridyl urea, other electron-withdrawing diaryl ureas, e.g., those with phenylpyridyl and phenyl-nitrophenylgroups, 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 topyridyl N, nitro O, or solvent O atom instead of the urea C=O acceptor. We classify supramolecular organization in diaryl ureasinto those with the -network (twisted molecular conformation) or non-urea tape structures (stable, planar conformation) dependingon 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.