碳纳米管非共价功能化的理论研究
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摘要
碳纳米管(carbon nanotube, CNT)具有卓越的电学、机械和结构特性,在基因运载、生物成像等领域具有广泛的应用价值。但是,CNT难溶于水和普通的有机溶剂,极大地限制了其在分子水平上的进一步操控和应用。CNT非共价功能化既能够克服CNT水溶性和分散性差的缺陷,又不破坏其独特的π电子体系。此外,结合生物分子功能化还能增加CNT的生物兼容性,从而降低CNT的生理毒性。然而,CNT非共价功能化过程中许多微观细节诸如结构、作用机制及能量等尚不清楚。因此,本论文采用分子模拟方法从本质上理解CNT非共价功能化体系的自组装机制,旨在为新型CNT复合材料的设计提供理论依据与指导。主要内容如下：
(1)多糖缠绕CNT是一种新兴的非共价功能化方式,借助分子动力学和自由能计算分别对海藻酸、壳聚糖和淀粉三种多糖缠绕CNT的动力学行为进行了系统地研究。结果表明,在范德华吸引作用和疏水作用的驱动下,三种多糖在水环境中均能自发地缠绕在CNT表面。其中,海藻酸和壳聚糖因骨架结构张力较大,形成疏松的螺旋结构,而淀粉则形成紧密的螺旋结构,分子内氢键是稳定紧密螺旋结构的主要因素。同时,海藻酸在模拟中重现了“长城”式结构重排的典型特征。两条海藻酸长链在Ca2+交联下通过静电吸引作用能够形成稳定的双螺旋结构,从而解释了可逆缠绕现象。另外,计算了壳聚糖缠绕过程的自由能变化曲线,得到了两个自由能最优的螺旋结构及相应的螺距,并预测了缠绕结构的稳定性,为设计功能化缠绕剂提供了一个潜在途径。最后,证实了CNT的末端效应,即CNT末端能够诱导淀粉发生缠绕行为,而CNT中端则不具有类似的效应,揭示了超短CNT在合成新型纳米材料领域的良好应用前景。
(2)疏水蛋白HFBI吸附CNT表面能够有效地改善CNT的水溶性,并形成三维有序的纳米复合材料。通过分子动力学模拟和自由能计算研究了HFBI在3种取向下吸附CNT表面的动力学行为。结果表明,由于HFBI含有4个二硫键,在吸附过程中自身结构变化不大,主要的二级结构均得以保留。在不同的吸附取向下,分别得到了不同的吸附模式。其中,当HFBI的直接与CNT表面相互作用且最大限度地被掩埋时,形成了最稳定的吸附结构,结合自由能最为有利；反之,当疏水端完全暴露在水溶液环境中,吸附模式最为不利。溶剂化作用是吸附的主要驱动力。另外,比较了HFBI在聚二甲基硅氧烷固体基底上的吸附行为,得到了同样的吸附机制,残基Leu12、Leu24、Leu26、Ile27、Ala66及Leu68是导致疏水蛋白能够吸附在不同疏水表面上的关键残基。该研究合理地解释了实验现象,为设计新型生物活性表面提供了理论基础。
(3)Smith-Lemli-Opitz综合症是一种由7-脱氢胆固醇-△7还原酶缺陷导致的胆固醇代谢异常的遗传性疾病,具体表现为患者体内血浆中低胆固醇及高7-脱氢胆固醇浓度。采用分子动力学模拟结合两种分子力场探索了不同浓度下胆固醇及7-脱氢胆固醇对细胞膜结构性质的影响,旨在从理论计算的角度阐述该综合症的病因,进而开展基于CNT功能化体系的基因运载研究。结果表明,两种固醇的浓缩效应与有序效应主要取决于浓度,即浓度越大,效应越明显。然而,在相同浓度下,两种固醇在对细胞膜的浓缩和有序能力上并无显著差异。
Carbon nanotubes (CNTs) have attracted enormous interest on account of their remarkable electrical, mechanical, and structural properties, offering a wide spectrum of applications in a variety of fields that range from gene delivery to bioimaging. However, their poor solubility and dispersity in aqueous and organic solvents have imposed great limitations to the wide usage of CNTs. Noncovalent functionalization of CNTs can not only overcome this shortcoming, but also potentially preserve the π-conjugated system. Furthermore, noncovalent functionalization can decrease toxicity of CNTs by combining biomolecules as a function of their biocompatibility. However, many aspects of the interactions involved in noncovalent functionalization of CNTs remain poorly understood owing to the lack of atomic-level information. In this dissertation, therefore, noncovalent functionalization of CNTs was probed with the help of molecular simulations to understand the nature of the underlying interactions and the processes of self-assembly. The main contents of the present dissertation include:
(1) Helical wrapping of CNTs by polysaccharides is a new strategy of noncovalent functionalization. The wrapping processes of alginic acid, chitosan, and amylose around CNTs was systematically investigated by means of molecular dynamics simulations and free energy calculations. The results show that these polysaccharide chains can spontaneously wrap around CNTs by virtue of van der Waals attractions and hydrophobic interactions. Alginic acid and chitosan form loose helical structures due to the big rigidity while amylose forms compact helical conformation stabilized by an interlaced hydrogen-bond network. Documented experimentally and coined "Great Wall of China" motif, the typical arrangement of alginic acid residues around the tubular structure, is observed in the present simulations. Investigation of metal cations binding to alginic acid suggests that calcium ions can mediate aggregation of alginic acid chains by interacting strongly with the carboxylate groups, thereby leading to reverse unwrapping. Furthermore, the free-energy landscape characterizing the wrapping process of the chitosan chain from a straight conformation to a tight helical one brings to light two energetically favored helical conformations corresponding to distinct pitches. This method can be employed to estimate the pitch of the most stable helical structure, as well as to predict its stability with respect to an extended conformation, which provides a possible route for designing functionalized polymers wrapped on CNTs. At last, the simulations prove that amylose can wrap spontaneously around the tubular surface, starting from the end of the CNTs. Conversely, if wrapping proceeds from the middle of the CNTs, self-organization into a helical structure is not observed. The results reported herein shed meaningful light on the potential of short SWNTs for building ordered and innovative nanostructures.
(2) The adsorption of hydrophobin protein named HFBI on the CNT surface can effectively increase the solubility of CNTs, leading to the architecture of ordered and novel nanoscale materials. Atomistic molecular dynamics simulations have been conducted to elucidate the adsorption mechanism of HFBI on the CNT surface in an aqueous environment. Independent simulations starting from three representative initial orientations of HFBI toward the tubular surface were performed, resulting in different adsorption modes. The main secondary structures of the protein in each mode are found to be preserved in the entire course of adsorption due to the four disulfide bonds. The relative binding free energies of the different adsorption modes were calculated, showing that the mode, in which the binding residues of HFBI fully come from its hydrophobic patch, is most energetically favored. Meanwhile, the adsorption behavior of HFBI on polydimethylsiloxane substrates was explored and the same adsorption mechanism was obtained. Moreover, a set of residues consisting of Leul2, Leu24, Leu26, Ile27, Ala66, and Leu68are found to play an important role in the adsorption of HFBI on different hydrophobic substrates, irrespective of the structural features of the surfaces. The results reported herein are consistent with experiments, and provide the theoretical basis for the design of bioactive surfaces.
(3) Smith-Lemli-Opitz syndrome, a congenital and developmental malformation disease, is typified by abnormal accumulation of7-dehydrocholesterol (7DHC), the immediate precursor of cholesterol (CHOL), and depletion thereof. Knowledge of the effect of7DHC on the biological membrane is, however, still fragmentary. Large-scale atomistic molecular dynamics simulations have been conducted to elucidate differences in the structural properties of a bilayer membrane due to CHOL and7DHC, which is envisioned to probe the pathogeny of Smith-Lemli-Opitz syndrome from the perspective of computer simulations and provide a preliminary exploration for gene delivery by functionalized CNTs. The present series of results indicate that CHOL and7DHC possess virtually the same ability to condense and order membranes. Furthermore, the condensing and ordering effects are shown to be strengthened at increasing sterol concentrations.
(1)多糖缠绕CNT是一种新兴的非共价功能化方式,借助分子动力学和自由能计算分别对海藻酸、壳聚糖和淀粉三种多糖缠绕CNT的动力学行为进行了系统地研究。结果表明,在范德华吸引作用和疏水作用的驱动下,三种多糖在水环境中均能自发地缠绕在CNT表面。其中,海藻酸和壳聚糖因骨架结构张力较大,形成疏松的螺旋结构,而淀粉则形成紧密的螺旋结构,分子内氢键是稳定紧密螺旋结构的主要因素。同时,海藻酸在模拟中重现了“长城”式结构重排的典型特征。两条海藻酸长链在Ca2+交联下通过静电吸引作用能够形成稳定的双螺旋结构,从而解释了可逆缠绕现象。另外,计算了壳聚糖缠绕过程的自由能变化曲线,得到了两个自由能最优的螺旋结构及相应的螺距,并预测了缠绕结构的稳定性,为设计功能化缠绕剂提供了一个潜在途径。最后,证实了CNT的末端效应,即CNT末端能够诱导淀粉发生缠绕行为,而CNT中端则不具有类似的效应,揭示了超短CNT在合成新型纳米材料领域的良好应用前景。
(2)疏水蛋白HFBI吸附CNT表面能够有效地改善CNT的水溶性,并形成三维有序的纳米复合材料。通过分子动力学模拟和自由能计算研究了HFBI在3种取向下吸附CNT表面的动力学行为。结果表明,由于HFBI含有4个二硫键,在吸附过程中自身结构变化不大,主要的二级结构均得以保留。在不同的吸附取向下,分别得到了不同的吸附模式。其中,当HFBI的直接与CNT表面相互作用且最大限度地被掩埋时,形成了最稳定的吸附结构,结合自由能最为有利；反之,当疏水端完全暴露在水溶液环境中,吸附模式最为不利。溶剂化作用是吸附的主要驱动力。另外,比较了HFBI在聚二甲基硅氧烷固体基底上的吸附行为,得到了同样的吸附机制,残基Leu12、Leu24、Leu26、Ile27、Ala66及Leu68是导致疏水蛋白能够吸附在不同疏水表面上的关键残基。该研究合理地解释了实验现象,为设计新型生物活性表面提供了理论基础。
(3)Smith-Lemli-Opitz综合症是一种由7-脱氢胆固醇-△7还原酶缺陷导致的胆固醇代谢异常的遗传性疾病,具体表现为患者体内血浆中低胆固醇及高7-脱氢胆固醇浓度。采用分子动力学模拟结合两种分子力场探索了不同浓度下胆固醇及7-脱氢胆固醇对细胞膜结构性质的影响,旨在从理论计算的角度阐述该综合症的病因,进而开展基于CNT功能化体系的基因运载研究。结果表明,两种固醇的浓缩效应与有序效应主要取决于浓度,即浓度越大,效应越明显。然而,在相同浓度下,两种固醇在对细胞膜的浓缩和有序能力上并无显著差异。
Carbon nanotubes (CNTs) have attracted enormous interest on account of their remarkable electrical, mechanical, and structural properties, offering a wide spectrum of applications in a variety of fields that range from gene delivery to bioimaging. However, their poor solubility and dispersity in aqueous and organic solvents have imposed great limitations to the wide usage of CNTs. Noncovalent functionalization of CNTs can not only overcome this shortcoming, but also potentially preserve the π-conjugated system. Furthermore, noncovalent functionalization can decrease toxicity of CNTs by combining biomolecules as a function of their biocompatibility. However, many aspects of the interactions involved in noncovalent functionalization of CNTs remain poorly understood owing to the lack of atomic-level information. In this dissertation, therefore, noncovalent functionalization of CNTs was probed with the help of molecular simulations to understand the nature of the underlying interactions and the processes of self-assembly. The main contents of the present dissertation include:
(1) Helical wrapping of CNTs by polysaccharides is a new strategy of noncovalent functionalization. The wrapping processes of alginic acid, chitosan, and amylose around CNTs was systematically investigated by means of molecular dynamics simulations and free energy calculations. The results show that these polysaccharide chains can spontaneously wrap around CNTs by virtue of van der Waals attractions and hydrophobic interactions. Alginic acid and chitosan form loose helical structures due to the big rigidity while amylose forms compact helical conformation stabilized by an interlaced hydrogen-bond network. Documented experimentally and coined "Great Wall of China" motif, the typical arrangement of alginic acid residues around the tubular structure, is observed in the present simulations. Investigation of metal cations binding to alginic acid suggests that calcium ions can mediate aggregation of alginic acid chains by interacting strongly with the carboxylate groups, thereby leading to reverse unwrapping. Furthermore, the free-energy landscape characterizing the wrapping process of the chitosan chain from a straight conformation to a tight helical one brings to light two energetically favored helical conformations corresponding to distinct pitches. This method can be employed to estimate the pitch of the most stable helical structure, as well as to predict its stability with respect to an extended conformation, which provides a possible route for designing functionalized polymers wrapped on CNTs. At last, the simulations prove that amylose can wrap spontaneously around the tubular surface, starting from the end of the CNTs. Conversely, if wrapping proceeds from the middle of the CNTs, self-organization into a helical structure is not observed. The results reported herein shed meaningful light on the potential of short SWNTs for building ordered and innovative nanostructures.
(2) The adsorption of hydrophobin protein named HFBI on the CNT surface can effectively increase the solubility of CNTs, leading to the architecture of ordered and novel nanoscale materials. Atomistic molecular dynamics simulations have been conducted to elucidate the adsorption mechanism of HFBI on the CNT surface in an aqueous environment. Independent simulations starting from three representative initial orientations of HFBI toward the tubular surface were performed, resulting in different adsorption modes. The main secondary structures of the protein in each mode are found to be preserved in the entire course of adsorption due to the four disulfide bonds. The relative binding free energies of the different adsorption modes were calculated, showing that the mode, in which the binding residues of HFBI fully come from its hydrophobic patch, is most energetically favored. Meanwhile, the adsorption behavior of HFBI on polydimethylsiloxane substrates was explored and the same adsorption mechanism was obtained. Moreover, a set of residues consisting of Leul2, Leu24, Leu26, Ile27, Ala66, and Leu68are found to play an important role in the adsorption of HFBI on different hydrophobic substrates, irrespective of the structural features of the surfaces. The results reported herein are consistent with experiments, and provide the theoretical basis for the design of bioactive surfaces.
(3) Smith-Lemli-Opitz syndrome, a congenital and developmental malformation disease, is typified by abnormal accumulation of7-dehydrocholesterol (7DHC), the immediate precursor of cholesterol (CHOL), and depletion thereof. Knowledge of the effect of7DHC on the biological membrane is, however, still fragmentary. Large-scale atomistic molecular dynamics simulations have been conducted to elucidate differences in the structural properties of a bilayer membrane due to CHOL and7DHC, which is envisioned to probe the pathogeny of Smith-Lemli-Opitz syndrome from the perspective of computer simulations and provide a preliminary exploration for gene delivery by functionalized CNTs. The present series of results indicate that CHOL and7DHC possess virtually the same ability to condense and order membranes. Furthermore, the condensing and ordering effects are shown to be strengthened at increasing sterol concentrations.
引文
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