1-甲基-5-硝基尿嘧啶一水化合物的晶体结构

Stephan L Ginell, R Parthasarathy
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引用次数: 2

摘要

1-甲基-5-硝基尿嘧啶一水化合物的晶体结构显示出一种新颖的水分子嵌入在间距为6.2 Å的嘧啶碱基之间。在单个基团上没有直接的氢键,但是一个基团中的一个水分子与相邻基团中的三个相邻碱基形成了氢键。这三个碱基与水分子位于同一平面上,它们与水分子形成氢键。这种氢键模式导致在y≈0和12层上的碱和水分子的平行片的无限平面,而片间没有氢键。基于这种嵌入和我们的模型构建研究,我们认为,如果由于DNA螺旋的动态波动或非互补的碱基对立而导致碱基转向外部,水分子在立体化学上可能充当“间隔剂”并稳定DNA螺旋。该化合物晶体为单斜晶,空间群为C2,胞常数a = 14.676(1), b = 6.243(1), c = 8.363(1) a, β = 100.88(2)°,Z = 4。利用950个衍射仪数据,通过直接检查(|E|2−1)Patterson函数确定了1-甲基-5-硝基尿嘧啶一水合物的晶体结构,并将其细化为R = 0.062。
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Intercalation of water molecules between pyrimidine bases Crystal structure of 1-methyl-5-nitrouracil monohydrate

The crystal structure of 1-methyl-5-nitrouracil monohydrate exhibits a novel intercalation of water molecules between pyrimidine bases that are stacked 6.2 Å apart. There is no direct hydrogen bonding along individual stacks, but a water molecule in one stack is hydrogen-bonded to three neighboring bases from adjacent stacks. These three bases are located in the same plane as the water molecule to which they are hydrogen-bonded. This mode of hydrogen bonding leads to infinite planes of parallel sheets of bases and water molecules at layers y ≈ 0 and 12 with no inter-sheet hydrogen bonding. On the basis of this intercalation and our model building studies, it is suggested that it would be stereochemically possible for a water molecule to act as a ‘spacer’ and stabilize the DNA helix, should a base be turned outside due to dynamical fluctuations of the DNA helix or non-complementary base opposition. Crystals of the title compound are monoclinic, space group C2, with cell constants a = 14.676(1), b = 6.243(1), c = 8.363(1)A, β = 100.88(2)°, Z = 4. Using 950 diffractometer data, the crystal structure of 1-methyl-5-nitrouracil monohydrate was determined by a direct inspection of the (|E|2 − 1) Patterson function and refined to an R of 0.062.

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