School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, Perth, Australia.
J Am Chem Soc. 2011 Nov 23;133(46):18880-8. doi: 10.1021/ja206962f. Epub 2011 Oct 28.
Molecular dynamics provides a means to examine the mechanism of reorientation of hydrogen bond networks that are present in a range of biological and crystalline materials. Simulations of hydroxyl reorientation in the six-membered hydrogen bonded rings in crystalline clathrates of Dianin's compound (DC) and hydroquinone (HQ) reveal that in the clathrate of Dianin's compound with ethanol (DC:ethanol), hydroxyl groups perform single independent flips, and occasionally all six hydroxyls in a ring reorient following a sequential mechanism with participation of the guest ethanol molecule. The free energy estimated for this process agrees well with experimental results. The simulations suggest that hydroxyl reorientation occurs in the empty DC lattice as well, but at a higher energy cost, from which we conclude that it is the participation of ethanol that lowers the barrier of reorientation. Single independent flips of hydroxyl groups are observed to be more frequent in the hydroquinone clathrate with methanol (HQ:methanol) than in DC:ethanol, but reorientation of all six hydroxyls does not occur. This is attributed to the larger difference in energy between the original and reoriented positions of hydroxyl hydrogen atoms in HQ:methanol compared to DC:ethanol.
分子动力学为研究存在于一系列生物和结晶材料中的氢键网络重取向机制提供了一种手段。对 Dianin 化合物（DC）和对苯二酚（HQ）的六元氢键环中羟基重取向的模拟表明，在 Dianin 化合物与乙醇（DC：乙醇）的包合物中，羟基基团进行单独立体翻转，偶尔情况下，在客体乙醇分子参与下，环中的所有六个羟基按照顺序机制进行重取向。该过程的自由能估计与实验结果吻合良好。模拟表明，羟基重取向也发生在空的 DC 晶格中，但能量成本更高，由此我们得出结论，是乙醇的参与降低了重取向的势垒。在与甲醇形成的对苯二酚包合物（HQ：甲醇）中，羟基基团的单独立体翻转比在 DC：乙醇中更为频繁，但不会发生所有六个羟基的重取向。这归因于 HQ：甲醇中羟基氢原子原始位置和重取向位置之间的能量差异比 DC：乙醇更大。
