链状结构的疏水性对溶剂控制的轮烷穿梭行为的影响

doi:10.7503/cjcu20150620

摘要/Abstract

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)

中图分类号:

O641

TrendMD:

汪双双, 刘鹏, 蔡文生, 邵学广. 链状结构的疏水性对溶剂控制的轮烷穿梭行为的影响. 高等学校化学学报, 2015, 36(11): 2211.

WANG Shuangshuang, LIU Peng, CAI Wensheng, SHAO Xueguang. Effect of Hydrophobicity of Threads on the Solvent-controlled Shuttling in Rotaxanes^†. Chem. J. Chinese Universities, 2015, 36(11): 2211.

图/表 9

Fig.1 Structures of rotaxanes formed by α-CD and 2,4-dinitrophenyl moieties (A) 4,4'-Bipyridinium moieties and decametrylene moieties; (B) 4,4'-bipyridinium moieties and triethylene glycol moieties; (C) 4,4'-biphenyl moiety, 4,4'-bipyridinium moieties and decametrylene moieties; (D) 4,4'-biphenyl moiety, 4,4'-bipyridinium moieties and triethylene glycol moieties. ξ is the model reaction coordinate, r is the distance between the center of the left bipyridi-nium moieties and that of the middle bipyridinium or biphenyl moiety.

Fig.2 Number of α-CD samples of rotaxane B along ξ by the methods of MW-ABF(A) and ABF(B)

Fig.3 Free-energy profiles of rotaxane B characterizing the shuttling process along ξ by the methods of ABF(a) and MW-ABF(b) respectively

Fig.4 Free-energy profiles of rotaxanes A and B delineating the shuttling process along ξ in water and DMSO(a—d) and rotaxanes C and D delineating the shuttling process along ξ in water(e, f) a. A in water; b. A in DMSO; c. B in water; d. B in DMSO; e. C in water; f. C in DMSO.

Fig.5 Radial distribution function of the water molecules along the radius from the center of mass of the central PY(PH) moiety a. PY in rotaxane B; b. PH in rotaxane D.

Fig.6 Volumetric map of the water density around rotaxane B(A1—A3) and rotaxane D(B1—B3) (A1—A3) Rotaxane B in its left free-energy minimum, energy barrier, and right free-energy minimum, respectively;(B1—B3) rotaxane D in its left free-energy minimum, energy barrier, and right free-energy minimum, respectively.

Table 1 Activation free energies and shuttling time throw-over the barriers at 303 K and 373 K*

Condition	ΔG_forward/(kJ·mol^-1)	Δ $G backward$ /(kJ·mol^-1)	ΔG^≠/(kJ·mol^-1)	T_shuttling/s
Condition	ΔG_forward/(kJ·mol^-1)	Δ $G backward$ /(kJ·mol^-1)	ΔG^≠/(kJ·mol^-1)	303 K	373 K
Rotaxane A in water	121.4	111.0	116.2	1.3×10⁷
Rotaxane B in water	111.4	108.0	109.7	1.4×10⁶
Rotaxane A in DMSO	104.7	92.1	98.4	2.7×10²	0.502
Rotaxane B in DMSO	85.4	80.0	82.7	61.6	0.105
Rotaxane C in water	46.5	42.3	44.4	7.5×10^-6
Rotaxane D in water	31.8	31.0	31.4	4.3×10^-8

Table 1 Activation free energies and shuttling time throw-over the barriers at 303 K and 373 K*

Condition	ΔG_forward/(kJ·mol^-1)	Δ $G backward$ /(kJ·mol^-1)	ΔG^≠/(kJ·mol^-1)	T_shuttling/s
Condition	ΔG_forward/(kJ·mol^-1)	Δ $G backward$ /(kJ·mol^-1)	ΔG^≠/(kJ·mol^-1)	303 K	373 K
Rotaxane A in water	121.4	111.0	116.2	1.3×10⁷
Rotaxane B in water	111.4	108.0	109.7	1.4×10⁶
Rotaxane A in DMSO	104.7	92.1	98.4	2.7×10²	0.502
Rotaxane B in DMSO	85.4	80.0	82.7	61.6	0.105
Rotaxane C in water	46.5	42.3	44.4	7.5×10^-6
Rotaxane D in water	31.8	31.0	31.4	4.3×10^-8

Fig.7 Decomposition of the total free-energy profile into CD-chain and CD-sol contributions for the shuttling process along ξ: rotaxanes A and B in water(A) and in DMSO(B)

Fig.8 Interaction of the central bipyridinium moiety with the solvent(BIPY-sol)(A) and interaction of the chain-like moiety with the solvent(ALK/PEG-sol)(B)

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