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?

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.分叉N−H···O氢键构成的脲α-链状结构是二芳基脲及其分子复合物中常见的超分子基元。我们对N,N'-二(3-吡啶基)脲3及其部分衍生物的X射线晶体结构进行了分析：包括化学计量比分别为3·(4/3)H₂O和3·2H₂O的水合物，分别与琥珀酸、富马酸形成的共晶体3·SA和3·FA·H₂O，双(吡啶N-氧化物)8，以及双(N-甲基吡啶鎓)碘盐9。吡啶基脲类结构的晶体堆积由N−H···N吡啶、N−H···O水、N−H···O羧酸以及N−H···I⁻氢键主导，而非常见的一维N−H···O脲链。我们提出假设，这类结构中不存在脲链，是因为平面分子构象下存在两处分子内C−H···O脲相互作用（合成子III），削弱了羰基（C=O）的受体能力。基于密度泛函理论DFT-B3LYP/6-31G*水平计算得到的静电表面电势（ESP）电荷显示，C−H···O相互作用足以降低脲氧原子的电子密度，使得吡啶氮、水、羧基以及碘离子等其他电负性原子，可作为强NH供体的适宜氢键受体。1H核磁共振差分核Overhauser效应（1H NMR difference nOe）证实，二吡啶基脲3在固态下的平面构象在溶液中得以保留。有趣的是，尽管3的结构中强氢键基元发生了改变，但合成子III的C−H···O相互作用（键能4.6~5.0 kcal/mol）在该类化合物中普遍存在。除二吡啶基脲外，其他带有吸电子取代基的二芳基脲，例如带有苯基吡啶基和硝基苯基基团的衍生物，同样偏离了经典的N−H···O脲链结构，这是因为弱C−H···O氢键的干扰。因此，当二芳基脲的一个或两个芳环带有氢键受体基团（如吡啶、硝基苯）时，NH供体优先与吡啶氮、硝基氧或溶剂氧原子结合，而非脲羰基受体。我们依据取代基类型，将二芳基脲的超分子组装分为两类：一类为带有α-链状结构的体系（对应扭曲分子构象），另一类为非脲链氢键基元结构体系（对应稳定平面构象）。我们的研究结果提出了一种调控模型：通过合理选择官能化芳基与杂环基团，可将脲晶体结构导向脲链合成子（对应苯基与给电子基团），或构建非脲氢键基元且更易发生脲···溶剂氢键作用的结构（对应吸电子基团）。