高等学校化学学报 ›› 2015, Vol. 36 ›› Issue (11): 2211.doi: 10.7503/cjcu20150620

• 物理化学 • 上一篇    下一篇

链状结构的疏水性对溶剂控制的轮烷穿梭行为的影响

汪双双1,2, 刘鹏2, 蔡文生1, 邵学广1,2()   

  1. 1. 南开大学化学学院分析科学研究中心, 天津市生物传感与分子识别重点实验室,天津化学化工协同创新中心, 天津 300071
    2. 药物化学生物学国家重点实验室, 天津 300071
  • 收稿日期:2015-08-06 出版日期:2015-11-10 发布日期:2015-10-10
  • 作者简介:联系人简介: 邵学广, 男, 博士, 教授, 博士生导师, 主要从事化学信息学研究. E-mail:xshao@nankai.edu.cn
  • 基金资助:
    国家自然科学基金(批准号: 21373117)资助

Effect of Hydrophobicity of Threads on the Solvent-controlled Shuttling in Rotaxanes

WANG Shuangshuang1,2, LIU Peng2, CAI Wensheng1, SHAO Xueguang1,2,*()   

  1. 1. Research Center for Analytical Sciences, College of Chemistry,Tianjin Key Laboratory of Biosensing and Molecular Recognition,Collaborative Innovation Center of Chemical Science and Engineering(Tianjin), Nankai University, Tianjin 300071, China
    2. State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
  • Received:2015-08-06 Online:2015-11-10 Published:2015-10-10
  • Contact: SHAO Xueguang E-mail:xshao@nankai.edu.cn
  • Supported by:
    † Supported by the National Natural Science Foundation of China(No.21373117)

摘要:

研究了3种由α-环糊精(α-CD)、 不同线性结构及中间连接基团组成的轮烷的穿梭行为, 其中, 线性结构为烷基链(ALK)或聚乙二醇链(PEG), 中间连接基团为联吡啶或联苯. 采用分子动力学模拟方法对室温下这些轮烷在水或二甲基亚砜(DMSO)溶液中α-CD的穿梭过程进行了研究; 利用自适应偏置力(ABF)和多副本ABF(MW-ABF)方法计算了穿梭过程的自由能变化. 结果表明, 由PEG链组成的轮烷在2种溶剂中穿梭所需克服的能垒均比由ALK链组成的轮烷低, 并且前者在DMSO中穿梭所需克服的能垒比在水中的能垒要低. 由联苯基团组成的轮烷比由联吡啶基团组成的轮烷的能垒要低很多. 通过对自由能曲线进行分解表明, 破坏联吡啶基团的溶剂化层是穿梭过程能垒形成的主要原因, 因此采用疏水的联苯基团可大大降低该能垒高度; 另一方面, 由于PEG链比ALK链具有更强的亲水性, 也导致穿梭过程能垒降低. 此外, 通过对2种计算方法进行比较发现, MW-ABF能够明显改善对构象空间的采样效率, 加快收敛速度.

关键词: 轮烷, 穿梭, 疏水性, 自由能计算, 多副本自适应偏置力(MW-ABF)方法

Abstract:

In order to investigate the hydrophobic effect of chain-like structures on shuttling in further, three similar rotaxanes are studied in this work. The rotaxanes are formed by an α-CD, two dodecamethylene chains(ALK) or two poly(ethylene glycol)(PEG) for stations, one bipyridinium moiety(PY) or one biphenyl moiety(PH) for linkers and large end groups at both sides. The shuttling of the rotaxanes was studied by means of molecular dynamics simulations(MD) combined with free-energy calculations in water and DMSO at room temperature. Two methods, the adaptive biasing force(ABF) method and the multiple walker ABF(MW-ABF) method, a modified version of ABF, are adopted for calculating the free-energy change characte-rizing the shuttling process. The potentials of mean force(PMFs) for the three rotaxanes are determined. The free-energy barriers of the PMFs for the PEG-rotaxane are lower than those for the the ALK-rotaxane both in water and DMSO. Furthermore, the barriers for the PEG-rotaxanes in DMSO are lower than that in water, which is in accordance with the ALK-rotaxanes. The barriers for the PH-rotaxanes are significantly lower than those for the PY-rotaxanes. Partitioning the PMFs into free-energy components suggests that change of the the charged group by an hydrophobic biphenyl moiety or decrease of the hydrophobicity of the chain-like structure in two stations from ALK to PEG reduces the free-energy barrier with respect to the stable states in the stations. In addition, comparison of the two free-energy calculation methods shows that the MW-ABF method can significantly improve the uniformity of sampling and hence increase the computational efficiency.

Key words: Rotaxane, Shuttling, Hydrophobicity, Free-energy calculation, Multiple walker adaptive biasing force(MW-ABF)

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