Synthesis, Spectroscopy and Crystal Structure Analysis of N1,N3-dicyclohexyl-N1-(all-trans-retinoyl)urea,Journal of Chemical Crystallography

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Synthesis, Spectroscopy and Crystal Structure Analysis of N1,N3-dicyclohexyl-N1-(all-trans-retinoyl)urea
Journal of Chemical Crystallography ( IF 0.4 ) Pub Date : 2022-01-05 , DOI: 10.1007/s10870-021-00917-x
Eleanna Vachlioti ₁ , Stefania Kalantzi ₁ , Dionissios Papaioannou ₁ , Vassilios Nastopoulos ₁

Affiliation

The title compound, C₃₃H₅₀N₂O₂, is a side product in the reaction of all-trans-retinoic acid (atRA) with N-hydroxysuccinimide, in the presence of the coupling agent N,N′-dicyclohexylcarbodiimide, which produces the ‘active’ ester succinimidyl all-trans-retinoate as the product. It crystallizes in the orthorhombic Pbca space group. The compound was characterized by ¹H-NMR, ¹³C-NMR, ESI–MS and IR spectroscopy and its structure was determined by single-crystal X-ray diffraction. For example in the ¹³C-NMR spectrum, diagnostic peaks are those of the two amide carbonyl C atoms at δ 169.5 and 154.2 ppm, the ten olefinic C atoms of the unsaturated chain of atRA moiety at δ 149.0, 139.3, 137.7, 137.3, 134.9, 130.2, 130.0, 129.4, 128.5 and 121.5 ppm and the two methine C atoms of the N,N′-dicyclohexylurea moiety at δ 57.9 and 49.5 ppm. Detailed analysis of its molecular and supramolecular structure showed that close-packing principles (elongated shape/large hydrophobic region of the molecule) together with chemical factors (N–H⋯O and C–H⋯O intermolecular interactions) direct the 3D self-assembly process in the crystalline state. Hirshfeld surface analysis was employed, a powerful approach to quickly and easily gain insight into molecular environments in the crystalline state.

Graphical Abstract

The synthesis and X-ray structure of 1-((2E, 4E, 6E, 8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-enyl)nona-2,4,6,8-tetraenoyl)-1,3-dicyclohexylurea, a side product in the synthesis of succinimidyl all-trans-retinoate, is reported; Hirshfeld surface analysis was employed to identify intermolecular interactions.

中文翻译：

N1,N3-二环己基-N1-(全反式-视黄酰基)脲的合成、光谱和晶体结构分析

标题化合物 C ₃₃ H ₅₀ N ₂ O ₂是全反式视黄酸 (atRA) 与N-羟基琥珀酰亚胺在偶联剂N , N'-二环己基碳二亚胺存在下反应的副产物，其产生“活性”酯琥珀酰亚胺全反式视黄酸酯作为产物。它在正交Pbca空间群中结晶。该化合物通过¹ H-NMR、¹³ C-NMR、ESI-MS 和 IR 光谱进行表征，并通过单晶 X 射线衍射确定其结构。例如在¹³C-NMR谱，诊断峰是δ 169.5和154.2 ppm处的两个酰胺羰基C原子，atRA部分不饱和链的十个烯属C原子δ 149.0、139.3、137.7、137.3、134.9、1300 , 129.4, 128.5 和 121.5 ppm 以及N , N '-二环己基脲部分在δ处的两个次甲基 C 原子57.9 和 49.5 ppm。对其分子和超分子结构的详细分析表明，紧密堆积原理（分子的细长形状/大疏水区域）与化学因素（N-H⋯O 和 C-H⋯O 分子间相互作用）共同指导了 3D 自组装结晶状态的过程。采用 Hirshfeld 表面分析，这是一种强大的方法，可以快速轻松地深入了解结晶状态下的分子环境。