碳纳米材料与生物小分子间相互作用及保护机理的理论研究
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摘要
过去的十多年中,碳纳米材料与生物分子相互作用的研究已经引起人们的极大关注。其中,人们比较关心的碳纳米材料的生物安全性、活性以及相容性等问题又与纳米材料的药物输送以及生物医学领域的应用前景紧密相关,然而至今关于在原子分子层次上对于其理论的基础研究尚很欠缺,受限于实验手段以及体系本身的复杂性,通过理论手段研究这方面的问题就显得尤为重要。本文采用密度泛函以及色散力校正的密度泛函等方法重点讨论了碳纳米管、富勒烯及其衍生物在氨基酸分子探针、输运、封装以及DNA碱基保护方面起到的作用,从而逐步达到设计应用于生物医学领域的新型功能材料的目的。围绕这一主题我们开展了一系列工作并取得了一些有意义的研究成果,主要成果和创新简介如下：
(1)通过密度泛函方法对甘氨酸以及自由基在未掺杂／硼掺杂(8,0)单壁碳纳米管管壁(SWNT)上的吸附作用进行了研究。通过研究发现甘氨酸分子在SWNT上表现为物理吸附形式,而在硼掺杂SWNT管壁上则为化学吸附,即甘氨酸上具有富电子特性氮原子与硼掺杂SWNT管上具有缺电子特性硼原子之间形成了化学键。对于甘氨酸自由基来说,无论是以氮原子为中心还是以碳原子为中心的自由基在两种(8,0)单壁碳纳米管管壁上都表现为化学吸附,我们的研究结果对已被报道的结果进行了比较和讨论(J. Phys. Chem. B 2006,110,6048-6050)。当甘氨酸自由基分子和硼掺杂纳米管作用时,管上的硼原子和同轴向方向上临近的碳原子表现出对于吸附物的竞争。我们也讨论了甘氨酸在不同管径的单壁碳纳米管中的封装,研究表明单壁碳纳米管对于甘氨酸分子的封装过程的临界直径应该为7.83A。
(2)使用密度泛函方法,我们以一系列周期性的扶手椅型纳米管、折叠型纳米管以及双壁纳米管为模型,对其电离势(IP)、电子亲和势(EA)、电负性(χ)以及费米能(Ef)进行了研究。结果表明,这些性质是由纳米管管径直接决定的,并且由于纳米管手性不同,其变化规律也并不一致。随着管径增大,扶手椅型纳米管的电离势单调降低,而其电子亲和势单调升高；尽管折叠型纳米管的电离势总体上随直径增大而降低,但其表现为一种“三个一组”的锯齿形特征,也就是每三个相邻的管组成一组。和扶手椅型纳米管不同的是,折叠型纳米管的电子亲和势随着直径增加而迅速减小,至(10,0)管后再缓慢增大。折叠型纳米管的电子亲和势也表现为三个一组的变化趋势,但是其“组”与电离势中“组”并不同步。随直径增大,两种纳米管的电离势和电子亲和势分别趋近于4.7eV和3.9eV。对于扶手椅型纳米管,电负性和费米能随直径变化不明显,而对于折叠型纳米管其变化表现为先降低后共振趋势。研究的几种双壁纳米管的变化趋势和单壁扶手椅型纳米管变化趋势一致,并且其氧化还原性质要优于构成它们的单壁纳米管。这些有趣的研究发现对于纳米管氧化还原性的研究以及分离纳米管都提出了一种新的思路。
(3)通过包括GGA/PW91、两种新的meta-GGA泛函：M05-2X和M06-2X以及色散力校正的密度泛函理论方法(DFT-D)在内的多种理论方法,考察了DNA四种碱基与C60的相互作用,并对四种碱基的结合能排序,以澄清当前对于此顺序的认识。研究结果表明结合顺序为G>A>T>C,这与先前报道的NAB与其它碳纳米材料,如单壁碳纳米管、石墨的结合顺序相同。结果证实对于A@C60与C@C60结合能大小顺序的争议来源于PW91和M05-2X以及M06-2X方法对于体系中电子相关作用的处理不足。通过这一体系对不同计算方法的对比和评价为今后处理类似体系提供了方法上的指导。另外为了讨论C60的存在是否能保护NAB免于氧化损伤,我们研究了单体以及复合物的电离势、中性体系以及阳离子体系复合物的前线轨道等性质。这些电子性质表明,当体系失去一个电子后形成的空穴会倾向于离域在两个分子片上,从这种意义上说C60的存在一定程度上保护了NAB免于氧化损伤,而如果想得到更好的保护效果,我们建议使用电离势明显小于鸟嘌呤的C60衍生物作为保护剂。
(4)我们考察了不同溶剂的溶剂化效应对于NAB-C60构型以及电子性质的影响,并进一步讨论了C60作为NAB氧化损伤保护剂的可行性。结果表明水相环境中C60的电离势高于四种碱基的电离势,如果NAB-C60体系电离掉一个电子,则空穴定域在碱基片上,使得C60不再起到保护作用,这个重要的结论不仅是对之前工作的有力补充也为下一步我们基于C60衍生物设计抗电离辐射保护剂提供了思路。另外我们还讨论了不同的溶剂对于NAB-C60体系电离势的影响规律,结果表明随着溶剂介电常数增加,无论是单体还是复合物的电离势都会逐渐降低,变得更加容易电离。
(5)我们在M06-2X/6-311G**水平上考察了四种DNA碱基与Li@C60复合物在不同氧化态以及气/水相环境下的构型以及电子性质。结果表明,内嵌Li原子对表面吸附的影响。另外我们对溶剂化效应的研究表明,溶剂会弱化静电作用使阳离子体系的构型,尤其是C-Li@C60阳离子体系构型从σ-π构型转变为π-π构型。同时我们还指出对于类似体系的研究,ESP电荷布局分布方法得到的结果是比较可信的。除此之外,我们还使用杨伟涛课题组新发展的方法实现了对非键相互作用的可视化,对这种作用有了更为直观的认识和理解。最为重要的是由于Li@C60分子的电离势(尤其是在水相环境中)要明显低于四种碱基中电离势最低的鸟嘌呤,所以其可以设计为良好的DNA氧化损伤的保护剂。
这一系列系统的研究为基于碳纳米管的分子器件设计、碳纳米管电化学应用、多种碳纳米管分离以及富勒烯及其衍生物的生物医学应用等领域的相关问题的研究提出了新的思路。
The interaction of biomolecules with carbon-based nanomaterials has generated a great deal of interest in the past few years. There are concerns about the biological safety, activity and compatibility of carbon-based nanomaterials. Such issues are relevant to the proposed applications of nanomaterials in drug or gene delivery and protective agent. However, fundamental understanding of how the nanomaterial interacts with a biomolecule at atomic/molecular level still remains as an open question. Given the complexity of the interested systems, it is challenging to probe these properties by experiment. A promising alternative approach is theoretical modeling. Thus, in the present dissertation, density functional theory and dispersion-corrected DFT methods have been performed to investigate the interactions such as glycine with intrinsic/B-doped single walled carbon nanotubes, and nucleic acid bases with C60 and its derivatives. We expect that these findings would offer new strategy for designing new functional nanodevices. We carried out a series of significative work and obtained some valuable results on these issues. The primary innovations are related as follows.
(1) Interaction between glycine molecule/radical and intrinsic/B-doped SWCNT. The adsorptions of a glycine molecule as well as dehydrogenated radicals on the side walls of both intrinsic and boron-doped (B-doped) single-walled (8,0) carbon nanotubes (SWCNTs) were investigated by a density functional theory. A glycine molecule tends to physically adsorb on intrinsic SWCNT, yet chemically adsorb on B-doped SWCNT as a result of a somewhat chemical bond between the electron-rich nitrogen atom of the glycine molecule and the electron-scarce boron atom of the doped SWCNT. Opposite to the previous report (J. Phys. Chem. B 2006, 110,6048-6050), it is found in the present study that both the N-centered and C-centered glycine radicals can form quite stable complexes with intrinsic as well as B-doped (8,0) SWCNTs. When the B-doped SWCNT interacts with glycine radicals, although there is a competition between B and the neighbour C in the nanotube axis direction, glycine radicals preferentially bind to the C site. The encapsulations of a glycine molecule into SWCNTs with various diameters are also discussed. We find that the encapsulation process is endothermic for (8,0) and (9,0) SWCNTs, while it is exothermic for (10,0) SWCNT, indicating that the critical diameter of the zigzag SWCNT for the encapsulation is 7.83 A, the diameter of (10,0).
(2).Redox properties of nanotubes. Density functional theory was used to investigate redox properties, such as ionization potentials (IP), electron affinities (EA), electronegativities (x) and Fermi levels (Ef) for infinite length armchair single-walled carbon nanotubes (SWNT) (n, n) (n=3-16), zigzag SWNT (n,0) (n=5-16), as well as double-walled carbon nanotubes (DWNT) (n, n)@(n+5, n+5) (n=3,5 and 6). These properties show a strong and different diameter dependence. With increasing diameters, IPs of armchair SWNTs (n, n) decrease monotonically, while EAs increase monotonically. Although IPs of zigzag SWNTs (n,0) also generally decrease, there is an increase occurring just after (3k,0) (k=2,3,4, and 5) and shows a group behaviour, in which every three neighbourhood (3k,0), (3k-1,0) and (3k-2,0) form a group. However, opposite to the armchair SWNTs, the EAs of zigzag SWNTs decrease rapidly with increasing diameter till (11,0) and then gently increase. EAs of the zigzag SWNTs also exhibit a group behaviour, yet are not synchronous with IPs. With increasing diameters, the IPs and EAs of both the armchair and zigzag SWNTs approach to approximately 4.7 and 3.9eV. For the armchair SWNTs electronegativity (x) and Fermi level (-Ef) change very slightly with diameters, while for the zigzag they decrease rapidly till (9,0) and then gently oscillate to the similar levels to those of the armchair. The IPs and EAs for (n, n)@ (n+5, n+5) DWNTs have the same trend as armchair SWNTs. It was also found that these DWNTs characterize better redox properties than their constituents. These interesting findings are important for redox chemistry based on NTs and may offer a new strategy for separation of NTs.
(3). Interaction between NAB and C60 in the gas phase. The major objective of this part is to address a controversial binding sequence between nucleic acid bases (NABs) and C6o by investigating adsorptions of NABs and their cations on C6o fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2X and M06-2X, as well as a dispersion-corrected density functional, PBE-D. PBE-D provides result in the following sequence, G>A>T>C, which is the same as the hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2X or even the M06-2X method. The results indicated that PDE-D performs better than M06-2X for the observed NAB@C60π-stacked complexes. To discuss whether C6o could prevent NABs from oxidative damage, ionization potentials of NABs and C6o, and frontier molecular orbitals of the complexes NABs@C6o and (NABs@C6o)+ are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C6o for T and C complexes, while for G and A the hole delocalized over the entire complex, rather than a localization on the C6o moiety. The interesting finding might open a new strategy for protecting DNA from oxidative damage and offer a new idea for designing C60-based antioxidative drugs.
(4). Solvation effect on the interaction between NAB and C6o. Solvation effect was involved to investigate the feasibility of C6o act as the protective agent. Results indicated that in the aqueous phase, C6o has a larger IP value than NAB. These results revealed that when an electron escapes from the complexes, the hole was preferentially created in NAB parts, not in C60 moiety. In this sense, the absent of C6o in the aqueous phase could not protect NAB from oxidative damage. This part is not only a supplement to the former exploration, but also offers a new strategy of designing new C60-based protective agent.
(5). Interaction between NAB and Li/Na@C60.The binding trend of neutral NAB and Li@C6o decreases in the sequence G>C>A>T, while the binding in cationic state exhibit a distinct sequence of C>G>A>T. These two binding trends are different with their counterparts in NAB-C60 complexes, indicating that the encapsulating of Li atom could affect the binding orders. Regarding its lower IP, Li@C6o could protect NABs from oxidative damage, which produces a better performance than intrinsic C60. We also investigated the performance of different charge population scheme upon our complexes. It was suggested that ESP could obtain reasonable charge population results in the describing of intermolecular properties of these complexes. Besides providing detailed information of the equilibrium distances, binding energies, charge transfer and frontier orbitals about the interaction, the noncovalent interaction was also identifying and visualization based on Yang's approach. Since Li@C6o has a lower IP than NAB, especially in the aqueous phase, it could protect NAB from oxidative damage both in the gas and aqueous phase.
The series of systemic investigations will offer new statregies for the fields such as the CNT-based molecular device design, the application of CNT in electrochemistry, the separation of CNTs and the biomedical engineering application of fullerene-based materials.
(1)通过密度泛函方法对甘氨酸以及自由基在未掺杂／硼掺杂(8,0)单壁碳纳米管管壁(SWNT)上的吸附作用进行了研究。通过研究发现甘氨酸分子在SWNT上表现为物理吸附形式,而在硼掺杂SWNT管壁上则为化学吸附,即甘氨酸上具有富电子特性氮原子与硼掺杂SWNT管上具有缺电子特性硼原子之间形成了化学键。对于甘氨酸自由基来说,无论是以氮原子为中心还是以碳原子为中心的自由基在两种(8,0)单壁碳纳米管管壁上都表现为化学吸附,我们的研究结果对已被报道的结果进行了比较和讨论(J. Phys. Chem. B 2006,110,6048-6050)。当甘氨酸自由基分子和硼掺杂纳米管作用时,管上的硼原子和同轴向方向上临近的碳原子表现出对于吸附物的竞争。我们也讨论了甘氨酸在不同管径的单壁碳纳米管中的封装,研究表明单壁碳纳米管对于甘氨酸分子的封装过程的临界直径应该为7.83A。
(2)使用密度泛函方法,我们以一系列周期性的扶手椅型纳米管、折叠型纳米管以及双壁纳米管为模型,对其电离势(IP)、电子亲和势(EA)、电负性(χ)以及费米能(Ef)进行了研究。结果表明,这些性质是由纳米管管径直接决定的,并且由于纳米管手性不同,其变化规律也并不一致。随着管径增大,扶手椅型纳米管的电离势单调降低,而其电子亲和势单调升高；尽管折叠型纳米管的电离势总体上随直径增大而降低,但其表现为一种“三个一组”的锯齿形特征,也就是每三个相邻的管组成一组。和扶手椅型纳米管不同的是,折叠型纳米管的电子亲和势随着直径增加而迅速减小,至(10,0)管后再缓慢增大。折叠型纳米管的电子亲和势也表现为三个一组的变化趋势,但是其“组”与电离势中“组”并不同步。随直径增大,两种纳米管的电离势和电子亲和势分别趋近于4.7eV和3.9eV。对于扶手椅型纳米管,电负性和费米能随直径变化不明显,而对于折叠型纳米管其变化表现为先降低后共振趋势。研究的几种双壁纳米管的变化趋势和单壁扶手椅型纳米管变化趋势一致,并且其氧化还原性质要优于构成它们的单壁纳米管。这些有趣的研究发现对于纳米管氧化还原性的研究以及分离纳米管都提出了一种新的思路。
(3)通过包括GGA/PW91、两种新的meta-GGA泛函：M05-2X和M06-2X以及色散力校正的密度泛函理论方法(DFT-D)在内的多种理论方法,考察了DNA四种碱基与C60的相互作用,并对四种碱基的结合能排序,以澄清当前对于此顺序的认识。研究结果表明结合顺序为G>A>T>C,这与先前报道的NAB与其它碳纳米材料,如单壁碳纳米管、石墨的结合顺序相同。结果证实对于A@C60与C@C60结合能大小顺序的争议来源于PW91和M05-2X以及M06-2X方法对于体系中电子相关作用的处理不足。通过这一体系对不同计算方法的对比和评价为今后处理类似体系提供了方法上的指导。另外为了讨论C60的存在是否能保护NAB免于氧化损伤,我们研究了单体以及复合物的电离势、中性体系以及阳离子体系复合物的前线轨道等性质。这些电子性质表明,当体系失去一个电子后形成的空穴会倾向于离域在两个分子片上,从这种意义上说C60的存在一定程度上保护了NAB免于氧化损伤,而如果想得到更好的保护效果,我们建议使用电离势明显小于鸟嘌呤的C60衍生物作为保护剂。
(4)我们考察了不同溶剂的溶剂化效应对于NAB-C60构型以及电子性质的影响,并进一步讨论了C60作为NAB氧化损伤保护剂的可行性。结果表明水相环境中C60的电离势高于四种碱基的电离势,如果NAB-C60体系电离掉一个电子,则空穴定域在碱基片上,使得C60不再起到保护作用,这个重要的结论不仅是对之前工作的有力补充也为下一步我们基于C60衍生物设计抗电离辐射保护剂提供了思路。另外我们还讨论了不同的溶剂对于NAB-C60体系电离势的影响规律,结果表明随着溶剂介电常数增加,无论是单体还是复合物的电离势都会逐渐降低,变得更加容易电离。
(5)我们在M06-2X/6-311G**水平上考察了四种DNA碱基与Li@C60复合物在不同氧化态以及气/水相环境下的构型以及电子性质。结果表明,内嵌Li原子对表面吸附的影响。另外我们对溶剂化效应的研究表明,溶剂会弱化静电作用使阳离子体系的构型,尤其是C-Li@C60阳离子体系构型从σ-π构型转变为π-π构型。同时我们还指出对于类似体系的研究,ESP电荷布局分布方法得到的结果是比较可信的。除此之外,我们还使用杨伟涛课题组新发展的方法实现了对非键相互作用的可视化,对这种作用有了更为直观的认识和理解。最为重要的是由于Li@C60分子的电离势(尤其是在水相环境中)要明显低于四种碱基中电离势最低的鸟嘌呤,所以其可以设计为良好的DNA氧化损伤的保护剂。
这一系列系统的研究为基于碳纳米管的分子器件设计、碳纳米管电化学应用、多种碳纳米管分离以及富勒烯及其衍生物的生物医学应用等领域的相关问题的研究提出了新的思路。
The interaction of biomolecules with carbon-based nanomaterials has generated a great deal of interest in the past few years. There are concerns about the biological safety, activity and compatibility of carbon-based nanomaterials. Such issues are relevant to the proposed applications of nanomaterials in drug or gene delivery and protective agent. However, fundamental understanding of how the nanomaterial interacts with a biomolecule at atomic/molecular level still remains as an open question. Given the complexity of the interested systems, it is challenging to probe these properties by experiment. A promising alternative approach is theoretical modeling. Thus, in the present dissertation, density functional theory and dispersion-corrected DFT methods have been performed to investigate the interactions such as glycine with intrinsic/B-doped single walled carbon nanotubes, and nucleic acid bases with C60 and its derivatives. We expect that these findings would offer new strategy for designing new functional nanodevices. We carried out a series of significative work and obtained some valuable results on these issues. The primary innovations are related as follows.
(1) Interaction between glycine molecule/radical and intrinsic/B-doped SWCNT. The adsorptions of a glycine molecule as well as dehydrogenated radicals on the side walls of both intrinsic and boron-doped (B-doped) single-walled (8,0) carbon nanotubes (SWCNTs) were investigated by a density functional theory. A glycine molecule tends to physically adsorb on intrinsic SWCNT, yet chemically adsorb on B-doped SWCNT as a result of a somewhat chemical bond between the electron-rich nitrogen atom of the glycine molecule and the electron-scarce boron atom of the doped SWCNT. Opposite to the previous report (J. Phys. Chem. B 2006, 110,6048-6050), it is found in the present study that both the N-centered and C-centered glycine radicals can form quite stable complexes with intrinsic as well as B-doped (8,0) SWCNTs. When the B-doped SWCNT interacts with glycine radicals, although there is a competition between B and the neighbour C in the nanotube axis direction, glycine radicals preferentially bind to the C site. The encapsulations of a glycine molecule into SWCNTs with various diameters are also discussed. We find that the encapsulation process is endothermic for (8,0) and (9,0) SWCNTs, while it is exothermic for (10,0) SWCNT, indicating that the critical diameter of the zigzag SWCNT for the encapsulation is 7.83 A, the diameter of (10,0).
(2).Redox properties of nanotubes. Density functional theory was used to investigate redox properties, such as ionization potentials (IP), electron affinities (EA), electronegativities (x) and Fermi levels (Ef) for infinite length armchair single-walled carbon nanotubes (SWNT) (n, n) (n=3-16), zigzag SWNT (n,0) (n=5-16), as well as double-walled carbon nanotubes (DWNT) (n, n)@(n+5, n+5) (n=3,5 and 6). These properties show a strong and different diameter dependence. With increasing diameters, IPs of armchair SWNTs (n, n) decrease monotonically, while EAs increase monotonically. Although IPs of zigzag SWNTs (n,0) also generally decrease, there is an increase occurring just after (3k,0) (k=2,3,4, and 5) and shows a group behaviour, in which every three neighbourhood (3k,0), (3k-1,0) and (3k-2,0) form a group. However, opposite to the armchair SWNTs, the EAs of zigzag SWNTs decrease rapidly with increasing diameter till (11,0) and then gently increase. EAs of the zigzag SWNTs also exhibit a group behaviour, yet are not synchronous with IPs. With increasing diameters, the IPs and EAs of both the armchair and zigzag SWNTs approach to approximately 4.7 and 3.9eV. For the armchair SWNTs electronegativity (x) and Fermi level (-Ef) change very slightly with diameters, while for the zigzag they decrease rapidly till (9,0) and then gently oscillate to the similar levels to those of the armchair. The IPs and EAs for (n, n)@ (n+5, n+5) DWNTs have the same trend as armchair SWNTs. It was also found that these DWNTs characterize better redox properties than their constituents. These interesting findings are important for redox chemistry based on NTs and may offer a new strategy for separation of NTs.
(3). Interaction between NAB and C60 in the gas phase. The major objective of this part is to address a controversial binding sequence between nucleic acid bases (NABs) and C6o by investigating adsorptions of NABs and their cations on C6o fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2X and M06-2X, as well as a dispersion-corrected density functional, PBE-D. PBE-D provides result in the following sequence, G>A>T>C, which is the same as the hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2X or even the M06-2X method. The results indicated that PDE-D performs better than M06-2X for the observed NAB@C60π-stacked complexes. To discuss whether C6o could prevent NABs from oxidative damage, ionization potentials of NABs and C6o, and frontier molecular orbitals of the complexes NABs@C6o and (NABs@C6o)+ are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C6o for T and C complexes, while for G and A the hole delocalized over the entire complex, rather than a localization on the C6o moiety. The interesting finding might open a new strategy for protecting DNA from oxidative damage and offer a new idea for designing C60-based antioxidative drugs.
(4). Solvation effect on the interaction between NAB and C6o. Solvation effect was involved to investigate the feasibility of C6o act as the protective agent. Results indicated that in the aqueous phase, C6o has a larger IP value than NAB. These results revealed that when an electron escapes from the complexes, the hole was preferentially created in NAB parts, not in C60 moiety. In this sense, the absent of C6o in the aqueous phase could not protect NAB from oxidative damage. This part is not only a supplement to the former exploration, but also offers a new strategy of designing new C60-based protective agent.
(5). Interaction between NAB and Li/Na@C60.The binding trend of neutral NAB and Li@C6o decreases in the sequence G>C>A>T, while the binding in cationic state exhibit a distinct sequence of C>G>A>T. These two binding trends are different with their counterparts in NAB-C60 complexes, indicating that the encapsulating of Li atom could affect the binding orders. Regarding its lower IP, Li@C6o could protect NABs from oxidative damage, which produces a better performance than intrinsic C60. We also investigated the performance of different charge population scheme upon our complexes. It was suggested that ESP could obtain reasonable charge population results in the describing of intermolecular properties of these complexes. Besides providing detailed information of the equilibrium distances, binding energies, charge transfer and frontier orbitals about the interaction, the noncovalent interaction was also identifying and visualization based on Yang's approach. Since Li@C6o has a lower IP than NAB, especially in the aqueous phase, it could protect NAB from oxidative damage both in the gas and aqueous phase.
The series of systemic investigations will offer new statregies for the fields such as the CNT-based molecular device design, the application of CNT in electrochemistry, the separation of CNTs and the biomedical engineering application of fullerene-based materials.
引文
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