碳纳米管基载体的药物输运相关性质研究
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摘要
碳纳米管(CNT)以其特殊的管状结构,独特的力学、化学、电学和光学性质,被广泛应用到生物传感和生物医学领域。分子动力学模拟研究表明碳纳米管可以作为分子的载体,有效的传输一系列具有生物活性分子(蛋白质、DNA和药物分子等)到达细胞中,但目前仍没有明确的理论说明不同生物活性分子与碳纳米管相互作用机理以及不同的活性分子对碳纳米管的影响。本文主要围绕单壁碳纳米管作为分子载体在输运药物过程中所涉及到的药物分子与纳米管之间的耦合方式及相关作用,同时探讨外界环境的改变对纳米管-药物分子体系的影响。本文采用量子化学计算和分子动力学模拟相结合的方法深入研究碳纳米管作为载体的输运药物分子的机理,表征其相互作用模式,探讨微环境调控、结构因素等对碳纳米管的输运机制及其性质的影响,探究部分药物分子在纳米管中的插入或者缠绕的影响,开发诸过程的能量因素,为认识碳纳米管在生命科学方面的应用提供必要的理论信息。主要的研究成果与创新简述如下：
(1)钙通道抑制剂尼非地平与Ca2+的耦合特征
我们首先先定性的研究钙离子与一个单独的药物分子(尼非地平)之间的相互作用。详细的相互作用模式的探讨有助于了解尼非地平在生命过程中的作用。因此,在本论文中,我们首先系统考察了尼非地平分子与Ca2+在气相中的相互作用。密度泛函理论的研究结果表明,在气相中,存在25种尼非地平-Ca2+异构体,分别对应着尼非地平分子与Ca2+的三齿、双齿和单齿耦合的结构特征。其中,最稳定的构象是是三齿耦合的形式,尼非地平分子通过两个羰基氧原子和一个硝基氧原子与Ca2+耦合。能量次稳定的也是一个三齿耦合的形式,它的能量比最稳定的复合物1高18.77kcal/mol,其中Ca2+分别与一个羰基氧原子一个硝基氧原子和一个酯基氧原子耦合。这说明,复合物1在气相中是非常稳定的。另外,我们发现双齿耦合物5和6比许多三齿耦合物更稳定,这说明,配位数与耦合物的相对稳定性并没有直接的关系。我们从复合物的耦合形式、相对能、静电相互作用、形变能、电荷布局分析、空间位阻和分子内氢键等方面分析所有复合物的构型特征和能量特点。结果表明,尼非地平的不同电负性原子与Ca2+的结合能力大小排序如下：硝基氧>羰基氧>酯基氧>亚胺氮。尼非地平分子总是以尽可能多的活性基团与Ca2+耦合。由于构型和能量上的相似性,不同复合物之间的相互转化也非常容易发生。另一方面,由于在实际的生命体环境中,反应都是在溶液或蛋白环境中进行的。而在溶剂分子的作用下,金属离子-配体的作用模式会与气相中有所区别。为了更好的接近于真实的生命过程,我们考察了水分子对尼非地平-Ca2+体系的影响。通过计算我们发现,无论配体水分子数目的多少,六配位的耦合模式是相对稳定的结合方式,而尼非地平-Ca2+在水溶液中的分子动力学模拟也证明了这点。在静电作用、电荷转移和离子-配体、配体-配体排斥力的共同影响下,配体水分子数目的增加逐渐削弱了Ca2+与尼非地平中氧原子的静电吸引力。当内层结合的水分子数达到6或7时,逐步拉长的Ca-O(nifedipine)键将会断裂,从而导致新引入的水分子部分或全部地取代尼非地平的位置,使尼非地平由内层耦合模式转变为外层耦合模式。同时,六配位的水合物的分子动力学模拟也证明了水分子可以通过形成分子间氢键的形式从内层向外层的转移。因此,我们认为对于nifedipine-Ca2+(H20) n (n＞6)体系而言,随着水分子数目的增加,内层配体-配体间的排斥作用逐渐增大,导致“n+m”型的异构体将更稳定。
(2)单壁碳纳米管与尼非地平的结合特征及其动力学行为
首先,我们采用一种新型的密度泛函方法MPWB1K分别研究尼非地平分子在(10,10)单壁碳纳米管内部空腔与外表面吸附的情况。其中,我们讨论了两种不同大小的单壁碳纳米管,分别考虑了碳纳米管终端的悬挂键用氢原子饱和与悬挂键不饱和的两种情况(C200H40和C280)。我们发现尼非地平分子在纳米管内部的构型比其在外表面吸附的构型更稳定,两者能量相差大约为5.3-7.8 kcal/mol,这也表明了尼非地平分子更容易吸附到纳米管内部,这也说明用氢原子饱和纳米管终端的悬挂键对计算结果没有明显影响。另一方面,我们也研究了碳纳米管-尼非地平体系在气相中与液相中的分子动力学模拟。我们发现在这两种情况下,尼非地平分子均能自动进入的纳米管内部空腔,但是在水分子存在的情况下,尼非地平分子进入纳米管的过程明显的减缓了。无论是在气相还是液相中,我们都发现了一个有趣的现象：尼非地平分子可以在纳米管内部做来回往返的振荡运动。同样在水分子的影响下,出现振荡现象的时间也大大的推迟了。在整个动力学过程中,范德华吸引作用与水分子的疏水作用共同影响着尼非地平分子进入纳米管的过程,其中,范德华作用是主要的影响因素,决定了尼非地平分子能够进入到纳米管内部并且做往返的振荡运动。另外,我们研究水分子在纳米管内部的结构时发现,水分子在尼非地平的影响下,在纳米管的内部空腔中呈现一种不规则的单分子层结构。
(3)Ca2+吸附对碳纳米管-尼非地平复合物的影响
在本章中,我们用密度泛函方法分别计算了Ca2+与尼非地平分子对(10,10)扶手椅型单壁碳纳米管(SWCNT)的结构和性质的影响。首先,我们讨论了Ca2+吸附对碳纳米管的影响。当单个Ca2+在纳米管表面吸附时我们考虑了其在纳米管内与管外共8种情况(Ca2+分别位于六元环的中心位置,与轴向倾斜的桥位,轴向垂直的桥位,一个碳原子的顶部),计算结果表明,最稳定的SWCNT-Ca2+复合物是Ca2+吸附在碳纳米管外表面的六元环中心,这主要是由于Ca2+与碳纳米管之间的阳离子-π相互作用。其中,Ca2+到碳纳米管表面的距离约为2.3A。其次,我们分析了尼非地平分子与碳纳米管的耦合作用模式。结果表明,当尼非地平分子内嵌在纳米管内部,且其二氢吡啶环平行于纳米管表面,苯环垂直于纳米管的轴向位置是最稳定的结构。这主要是因为二氢吡啶环与碳纳米管的六元环之间的π…π相互作用以及二者之间的X-H…π(X=C、N)相互作用抵消了因为药物分子内嵌引起的空间位阻的影响。最后,探讨了Ca2+对最稳定的SWCNT/N复合物(复合物1)的影响。我们发现尽管钙离子的初始位置有所不同,但经过优化后,钙离子均吸附在六元环的中心位置,说明Ca2+结合在六元环中心位置的趋势变大。另一方面,我们也计算了Ca2+与尼非地平分子的吸附对于碳纳米管的HOMO、LUMO轨道能级与电子态密度等性质的影响。计算结果表明,Ca2+吸附能极大的降低单壁碳纳米管的HOMO-LUMO的能级差,改变了体系在费米能级(Fermi Levely)附近的态密度,使体系的金属性增强。而尼非地平分子的吸附则使碳纳米管的HOMO-LUMO的能级差增大,在费米能级附近带隙变宽,导电性减弱。而SWCNT-N-Ca2+体系的金属性也较纯碳纳米管有所提高,说明Ca2+对纳米管电子性质的影响要远大于尼非地平分子的影响。另外,我们也发现了一个有趣的现象,与纯碳纳米管的电子云均匀粉笔相比,由于Ca2+与尼非地平分子的吸附,复合物体系的电子云分布出现了非常明显的偏移现象,说明我们可以根据电子传导性等性质开发新型的电化学器件和纳米电子器件等。
(4)单壁碳纳米管与阿霉素的动力学特征与结合模式
本章中,一方面我们采用分子动力学模拟的方法分别讨论了抗癌药阿霉素分子与(10,10)单壁碳纳米管在中性与酸性水溶液中的动力学行为。我们发现,在中性环境下阿霉素分子能自动的进入的纳米管的内部,并且在水分子的作用下,药物分子的进入过程明显的被延迟了。在这个过程中,碳纳米管与阿霉素分子之间的范德华作用是主要的驱动力。而在酸性环境下,阿霉素分子通过蒽环与碳纳米管的外壁形成π…π相互作用的方式结合在碳纳米管的外表面,这主要是由于H+的存在导致阿霉素分子与周围水分子结合作用更强,不足以进入到相对较小的纳米管空腔中。我们用密度泛函方法进一步讨论了气相中碳纳米管一阿霉素复合物的主要结合方式、相对稳定性、电荷转移以及电子性质等。我们发现阿霉素分子结合在纳米管的外表面的结构时最稳定的,这说明蒽环与纳米管的六元环之间的π…π相互作用和X-H…π(X=O、N和C)作用是影响复合物稳定性的主要因素。另外,药物分子阿霉素的吸附对碳纳米管的电子态密度与电子传导性的影响很小,纳米管仍然保持导体的特性。
Carbon nanotubes (CNTs) have been recognized as one of the most fascinating materials because of their unique tubular structural and consequently excellent mechanical, chemical, electronic and optical properties and have already been widely employed in physical, biotechnological, biomedical and biochemical fields. The molecular dynamic simulations (MD) have proved that the carbon nanotubes have emerged as a new alternative and efficient tool for transporting and translocating bioactive molecules (peptides, proteins, nucleic acids and drugs), for CNT can be functionalized with bioactive molecules, and used to deliver their cargos to cells and organs. Because functionalized CNT (f-CNT) display low toxicity and are not immunogenic, such systems hold great potential in the field of nanobiotechnology and nanomedicine. However, the mechanism of transport is far from clearly. Thus, in the present doctoral dissertation, by using density function theory calculations (DFT) and molecular dynamic simulations (MD), we have studied the interaction between single-walled carbon nanotube and two widely used drugs (nifedipine, the calcium channel antagonist and doxorubicin, the anti-cancer drug). As a result, some significant progresses have been made, which can be described as follows.
(1) Exploration of the Ca2+-interaction Modes of the Nifedipine Calcium Channel Antagonist
To pave the way for how the calcium cations bind to the proteins in the presence of the drug (nifedipine) that regulate the channels and how they transfer through the channels, we begin with accumulating a quantitative knowledge of how calcium ion interacts with the single drug molecule. Detailed studies of the interaction between them are essential for understanding the role of nifedipine in the biophysical course though the biological processes occur in solution. A good knowledge of geometries and relative energies in the gas phase can be useful for application to condensed-phase by computational techniques. This allows us to perceptively predict and understand the effect of the antagonists on the calcium channels. This work offers a discussion of the chelating structures of Ca2+ with the most important class of the calcium channel antagonists with density functional theory calculations and molecular dynamic simulations. Although the real interaction between the metal ions and nifedipine is much more intricacy because of the complexity of the drug and the surroundings, the performed analyses have also presented a comprehensive understanding about the affinity. There are 25 minima on the PES. The favorable isomer of nifedipine-Ca2+ system without water molecules is a tridentate one in which the Ca2+ interacting with two carboxyl oxygen atoms and one nitryl oxygen atom. The next one is 18.77kcal mol-1 higher than isomer 1 in energy, where Ca2+ cheated with one etheric oxygen atom substituting for the carbonyl oxygen atom. This indicated that the isomer 1 was extremely stable in the gas phase on this theoretical level. Furthermore, the bidentate isomers 5 and 6 are found to be more stable than the tridentate ones 7, implying that the coordination number has no directly connection with the stability of isomers. The chelating structures and energy characters of the first 15 isomers have been investigated from chelating sites, electrostatics and polarizations, steric repulsions, charge distributions and intramolecular H-bond. The bonding ability of the negative atoms is the nitryl O＞the carbonyl O＞the etheric O＞the imine N, and the main binding character is that Ca2+ couples with nifedipine as in the multidentate form as possible. Because of the similarity of the geometric character and relative energy, the interconversions may occur among some structures in gas phase. Furthermore, in vivo, the complexes exist in the bulk solvent. Considering the effect of water, some different phenomena may take place for the nifedipine-Ca2+ complexes. To approach the real biological processes, the hydration effect on the nifedipine-Ca2+ complexes have been investigated systematically. We found that the hexa-coordination is the favorable hydrated geometry no matter how many water molecules are contained at this level of theory, which can be supported by the MD simulations for the nifedipine-Ca2+ system in aqueous solution. Influenced by the ion-ligand electrostatic interaction, charge transfer from ligand to ion, ion-ligand and ligand-ligand repulsions, the increase of the water molecules in the first shell has weakened the interaction between nifedipine and Ca2+, and the hexahydrated complexes are the most stable ones due to the hydration energy. On the other hand, the MD simulations for hexahydrated complexes have also verified that water molecule can transfer from the inner-to the outer-shell because of the formation of H-bond between the two shells ligands. So it can be expected that the "n+m" clusters will play a significant role for nifedipine-Ca2+(H2O) n system (n＞6), when the ligands in the inner shell become too crowed.
(2) Interaction Site Preference between Carbon Nanotube and Nifedipine:A Combined Density Functional Theory and Classical Molecular Dynamics Study
Using a novel DFT, MPWB1K, both internal and external adsorptions of a nifedipine, one of the calcium channel antagonist, on a (10,10) type of single-walled carbon nanotube (SWCNT) were investigated with both C200H40 and C280 cluster models for the SWCNT. The internal adsorption is more stable than the external adsorption in a range of 5.3-7.8 kcal/mol, which indicates that a nifedipine has a preference to internally adsorb on the (10,10) SWCNT. It also proved that the passviated nanotube by hydrogen atoms has no obvious influence for the SWCNT-nifedipine system. Furthermore, molecular dynamics simulations (MD) were then done on the system consisting of nifedipine and the SWCNT (10, 10) in the absence and in the presence of water molecules. The spontaneous encapsulations of nifedipine into the SWCNT channel were observed in both cases; however this process was significantly delayed by including water molecules in the simulation. The nifedipine for both cases also demonstrates an oscillation behavior inside the (10,10) SWCNT, which again occurs later for the system including water than without water. The two competing effects, van der Waals and the hydrophobic forces caused by water molecules, should be responsible for the encapsulation process, yet the van der Waals attraction plays a dominant role on the encapsulation process of nifedipine into the nanotube and the oscillation behavior of nifedipine. In addition, it was found that the water molecules absorbed inside the channel is an irregular monolayer interacting with the nanotube interior surface.
(3) Effects of adsorption of Ca2+ on SWCNT-Nifedipine system
This work offers an exploration of the affection of Ca2+ on the SWCNT-Nifedipine system using density functional theory calculations. First of all, we calculated the interaction between the single-walled carbon nanotube and Ca2+. There are four distinct symmetry sites related to the relative position of Ca2+ with respect to the nanotube carbon rings, which is the center of the carbon rings, the center of the C-C bond along the radical direction of the tube, the center of the C-C bond parallel to the axis of the tube, and the site on the top of a carbon atom. We designed two different situations containing the Ca2+ on the external sidewall of the nanotube and in the internal of the nanotube channel. The most favorable isomer of SWCNT-Ca2+ system is the one that Ca2+ binding to the external sidewall of the nanotueb above the center of the carbon ring, due to the cation-πinteraction between the Ca2+ and the nanotube. The distance of Ca2+ to the surface of the carbon nanotube is 2.3 (?). Then we calculated the effection of nifedipine to the carbon nanotube. We found that the most stable isomer is the one that nifedipine molecule encapsulated into the nanotube channel with the dihydropyridine ring parallel to nanotube surface. Theπ…πstacking interaction between the dihydropyridine ring and the carbon rings and the X-H…π(X=C, N) interaction are overcompensate the steric repulsions caused by the encapsulation of the drug. Finally, four complexes of the SWCNT-N-Ca2+ system are investigated to exploration the affection of Ca2+ to the most stable SWCNT-N complex (complex 1). It is interesting that the Ca2+ is above the center of the carbon rings after optimized in all cases. On the other hand, we discuss the change of the HOMO-LUMO gap and the electron density of states (DOS) of carbon nanotube caused by the adsorption of Ca2+ and nifedipine molecule. It is found that the adsorption of Ca2+ can reduce the HOMO-LUMO gap of the nanotube, and change the DOS around the Fermi level dramatically. Compared with the intrinsic carbon nanotube, the conductivity of the SWCNT-Ca2+ system is improved obviously. However, the adsorption of nifedipine molecule reduced the conductivity of the SWCNT-N system unexpectly. Similar with the SWCNT-Ca2+ system, the reducing HOMO-LUMO gap and the improved conductivity are also found in SWCNT-N-Ca2+ system.
(4) Interaction between Single-Walled Carbon Nanotube and Doxorubicin, a very widely used anti-cancer drug
To quantify approximately the thermodynamics of binding, and to obtain putative binding structures, we simulated interaction between the widely used anticancer drug, doxorubicin molecule and the (10,10) armchair carbon nanotube in neutral and in acidic aqueous solutions. The drug could spontaneously encapsulate into the nanotube channel and the process was significantly delayed by the presence of water molecules in neutral solution, The van der Waals attraction plays a dominant role on the encapsulation process. On the other hand, the doxorubicin molecule adsorbed on the external wall of the nanotube in acidic aqueous solution throughπ…πstacking interaction between the aromatic rings and the carbon rings. The present study suggests that the nanotube network could be used as an efficient tool for transporting this kind of anti-cancer drug. Furthermore, the equilibrium distances, adsorption energies, charge transfer, and density of states characteristics are investigated about SWCNT-DOX system in gas phase. The results show that the main contribution comes from theπ…πstacking and X-H…πinteraction (X=O, N, and C) between the doxorubicin and the nanotube. In addition, the presence of the doxorubicin molecule would neither modify the DOS of the SWCNT nor lead to significant changes in the conductivity of the nanotube. The fact that the electronic properties of the SWCNT are preserved upon doxorubicin adsorption is found to be a general feature.
(1)钙通道抑制剂尼非地平与Ca2+的耦合特征
我们首先先定性的研究钙离子与一个单独的药物分子(尼非地平)之间的相互作用。详细的相互作用模式的探讨有助于了解尼非地平在生命过程中的作用。因此,在本论文中,我们首先系统考察了尼非地平分子与Ca2+在气相中的相互作用。密度泛函理论的研究结果表明,在气相中,存在25种尼非地平-Ca2+异构体,分别对应着尼非地平分子与Ca2+的三齿、双齿和单齿耦合的结构特征。其中,最稳定的构象是是三齿耦合的形式,尼非地平分子通过两个羰基氧原子和一个硝基氧原子与Ca2+耦合。能量次稳定的也是一个三齿耦合的形式,它的能量比最稳定的复合物1高18.77kcal/mol,其中Ca2+分别与一个羰基氧原子一个硝基氧原子和一个酯基氧原子耦合。这说明,复合物1在气相中是非常稳定的。另外,我们发现双齿耦合物5和6比许多三齿耦合物更稳定,这说明,配位数与耦合物的相对稳定性并没有直接的关系。我们从复合物的耦合形式、相对能、静电相互作用、形变能、电荷布局分析、空间位阻和分子内氢键等方面分析所有复合物的构型特征和能量特点。结果表明,尼非地平的不同电负性原子与Ca2+的结合能力大小排序如下：硝基氧>羰基氧>酯基氧>亚胺氮。尼非地平分子总是以尽可能多的活性基团与Ca2+耦合。由于构型和能量上的相似性,不同复合物之间的相互转化也非常容易发生。另一方面,由于在实际的生命体环境中,反应都是在溶液或蛋白环境中进行的。而在溶剂分子的作用下,金属离子-配体的作用模式会与气相中有所区别。为了更好的接近于真实的生命过程,我们考察了水分子对尼非地平-Ca2+体系的影响。通过计算我们发现,无论配体水分子数目的多少,六配位的耦合模式是相对稳定的结合方式,而尼非地平-Ca2+在水溶液中的分子动力学模拟也证明了这点。在静电作用、电荷转移和离子-配体、配体-配体排斥力的共同影响下,配体水分子数目的增加逐渐削弱了Ca2+与尼非地平中氧原子的静电吸引力。当内层结合的水分子数达到6或7时,逐步拉长的Ca-O(nifedipine)键将会断裂,从而导致新引入的水分子部分或全部地取代尼非地平的位置,使尼非地平由内层耦合模式转变为外层耦合模式。同时,六配位的水合物的分子动力学模拟也证明了水分子可以通过形成分子间氢键的形式从内层向外层的转移。因此,我们认为对于nifedipine-Ca2+(H20) n (n＞6)体系而言,随着水分子数目的增加,内层配体-配体间的排斥作用逐渐增大,导致“n+m”型的异构体将更稳定。
(2)单壁碳纳米管与尼非地平的结合特征及其动力学行为
首先,我们采用一种新型的密度泛函方法MPWB1K分别研究尼非地平分子在(10,10)单壁碳纳米管内部空腔与外表面吸附的情况。其中,我们讨论了两种不同大小的单壁碳纳米管,分别考虑了碳纳米管终端的悬挂键用氢原子饱和与悬挂键不饱和的两种情况(C200H40和C280)。我们发现尼非地平分子在纳米管内部的构型比其在外表面吸附的构型更稳定,两者能量相差大约为5.3-7.8 kcal/mol,这也表明了尼非地平分子更容易吸附到纳米管内部,这也说明用氢原子饱和纳米管终端的悬挂键对计算结果没有明显影响。另一方面,我们也研究了碳纳米管-尼非地平体系在气相中与液相中的分子动力学模拟。我们发现在这两种情况下,尼非地平分子均能自动进入的纳米管内部空腔,但是在水分子存在的情况下,尼非地平分子进入纳米管的过程明显的减缓了。无论是在气相还是液相中,我们都发现了一个有趣的现象：尼非地平分子可以在纳米管内部做来回往返的振荡运动。同样在水分子的影响下,出现振荡现象的时间也大大的推迟了。在整个动力学过程中,范德华吸引作用与水分子的疏水作用共同影响着尼非地平分子进入纳米管的过程,其中,范德华作用是主要的影响因素,决定了尼非地平分子能够进入到纳米管内部并且做往返的振荡运动。另外,我们研究水分子在纳米管内部的结构时发现,水分子在尼非地平的影响下,在纳米管的内部空腔中呈现一种不规则的单分子层结构。
(3)Ca2+吸附对碳纳米管-尼非地平复合物的影响
在本章中,我们用密度泛函方法分别计算了Ca2+与尼非地平分子对(10,10)扶手椅型单壁碳纳米管(SWCNT)的结构和性质的影响。首先,我们讨论了Ca2+吸附对碳纳米管的影响。当单个Ca2+在纳米管表面吸附时我们考虑了其在纳米管内与管外共8种情况(Ca2+分别位于六元环的中心位置,与轴向倾斜的桥位,轴向垂直的桥位,一个碳原子的顶部),计算结果表明,最稳定的SWCNT-Ca2+复合物是Ca2+吸附在碳纳米管外表面的六元环中心,这主要是由于Ca2+与碳纳米管之间的阳离子-π相互作用。其中,Ca2+到碳纳米管表面的距离约为2.3A。其次,我们分析了尼非地平分子与碳纳米管的耦合作用模式。结果表明,当尼非地平分子内嵌在纳米管内部,且其二氢吡啶环平行于纳米管表面,苯环垂直于纳米管的轴向位置是最稳定的结构。这主要是因为二氢吡啶环与碳纳米管的六元环之间的π…π相互作用以及二者之间的X-H…π(X=C、N)相互作用抵消了因为药物分子内嵌引起的空间位阻的影响。最后,探讨了Ca2+对最稳定的SWCNT/N复合物(复合物1)的影响。我们发现尽管钙离子的初始位置有所不同,但经过优化后,钙离子均吸附在六元环的中心位置,说明Ca2+结合在六元环中心位置的趋势变大。另一方面,我们也计算了Ca2+与尼非地平分子的吸附对于碳纳米管的HOMO、LUMO轨道能级与电子态密度等性质的影响。计算结果表明,Ca2+吸附能极大的降低单壁碳纳米管的HOMO-LUMO的能级差,改变了体系在费米能级(Fermi Levely)附近的态密度,使体系的金属性增强。而尼非地平分子的吸附则使碳纳米管的HOMO-LUMO的能级差增大,在费米能级附近带隙变宽,导电性减弱。而SWCNT-N-Ca2+体系的金属性也较纯碳纳米管有所提高,说明Ca2+对纳米管电子性质的影响要远大于尼非地平分子的影响。另外,我们也发现了一个有趣的现象,与纯碳纳米管的电子云均匀粉笔相比,由于Ca2+与尼非地平分子的吸附,复合物体系的电子云分布出现了非常明显的偏移现象,说明我们可以根据电子传导性等性质开发新型的电化学器件和纳米电子器件等。
(4)单壁碳纳米管与阿霉素的动力学特征与结合模式
本章中,一方面我们采用分子动力学模拟的方法分别讨论了抗癌药阿霉素分子与(10,10)单壁碳纳米管在中性与酸性水溶液中的动力学行为。我们发现,在中性环境下阿霉素分子能自动的进入的纳米管的内部,并且在水分子的作用下,药物分子的进入过程明显的被延迟了。在这个过程中,碳纳米管与阿霉素分子之间的范德华作用是主要的驱动力。而在酸性环境下,阿霉素分子通过蒽环与碳纳米管的外壁形成π…π相互作用的方式结合在碳纳米管的外表面,这主要是由于H+的存在导致阿霉素分子与周围水分子结合作用更强,不足以进入到相对较小的纳米管空腔中。我们用密度泛函方法进一步讨论了气相中碳纳米管一阿霉素复合物的主要结合方式、相对稳定性、电荷转移以及电子性质等。我们发现阿霉素分子结合在纳米管的外表面的结构时最稳定的,这说明蒽环与纳米管的六元环之间的π…π相互作用和X-H…π(X=O、N和C)作用是影响复合物稳定性的主要因素。另外,药物分子阿霉素的吸附对碳纳米管的电子态密度与电子传导性的影响很小,纳米管仍然保持导体的特性。
Carbon nanotubes (CNTs) have been recognized as one of the most fascinating materials because of their unique tubular structural and consequently excellent mechanical, chemical, electronic and optical properties and have already been widely employed in physical, biotechnological, biomedical and biochemical fields. The molecular dynamic simulations (MD) have proved that the carbon nanotubes have emerged as a new alternative and efficient tool for transporting and translocating bioactive molecules (peptides, proteins, nucleic acids and drugs), for CNT can be functionalized with bioactive molecules, and used to deliver their cargos to cells and organs. Because functionalized CNT (f-CNT) display low toxicity and are not immunogenic, such systems hold great potential in the field of nanobiotechnology and nanomedicine. However, the mechanism of transport is far from clearly. Thus, in the present doctoral dissertation, by using density function theory calculations (DFT) and molecular dynamic simulations (MD), we have studied the interaction between single-walled carbon nanotube and two widely used drugs (nifedipine, the calcium channel antagonist and doxorubicin, the anti-cancer drug). As a result, some significant progresses have been made, which can be described as follows.
(1) Exploration of the Ca2+-interaction Modes of the Nifedipine Calcium Channel Antagonist
To pave the way for how the calcium cations bind to the proteins in the presence of the drug (nifedipine) that regulate the channels and how they transfer through the channels, we begin with accumulating a quantitative knowledge of how calcium ion interacts with the single drug molecule. Detailed studies of the interaction between them are essential for understanding the role of nifedipine in the biophysical course though the biological processes occur in solution. A good knowledge of geometries and relative energies in the gas phase can be useful for application to condensed-phase by computational techniques. This allows us to perceptively predict and understand the effect of the antagonists on the calcium channels. This work offers a discussion of the chelating structures of Ca2+ with the most important class of the calcium channel antagonists with density functional theory calculations and molecular dynamic simulations. Although the real interaction between the metal ions and nifedipine is much more intricacy because of the complexity of the drug and the surroundings, the performed analyses have also presented a comprehensive understanding about the affinity. There are 25 minima on the PES. The favorable isomer of nifedipine-Ca2+ system without water molecules is a tridentate one in which the Ca2+ interacting with two carboxyl oxygen atoms and one nitryl oxygen atom. The next one is 18.77kcal mol-1 higher than isomer 1 in energy, where Ca2+ cheated with one etheric oxygen atom substituting for the carbonyl oxygen atom. This indicated that the isomer 1 was extremely stable in the gas phase on this theoretical level. Furthermore, the bidentate isomers 5 and 6 are found to be more stable than the tridentate ones 7, implying that the coordination number has no directly connection with the stability of isomers. The chelating structures and energy characters of the first 15 isomers have been investigated from chelating sites, electrostatics and polarizations, steric repulsions, charge distributions and intramolecular H-bond. The bonding ability of the negative atoms is the nitryl O＞the carbonyl O＞the etheric O＞the imine N, and the main binding character is that Ca2+ couples with nifedipine as in the multidentate form as possible. Because of the similarity of the geometric character and relative energy, the interconversions may occur among some structures in gas phase. Furthermore, in vivo, the complexes exist in the bulk solvent. Considering the effect of water, some different phenomena may take place for the nifedipine-Ca2+ complexes. To approach the real biological processes, the hydration effect on the nifedipine-Ca2+ complexes have been investigated systematically. We found that the hexa-coordination is the favorable hydrated geometry no matter how many water molecules are contained at this level of theory, which can be supported by the MD simulations for the nifedipine-Ca2+ system in aqueous solution. Influenced by the ion-ligand electrostatic interaction, charge transfer from ligand to ion, ion-ligand and ligand-ligand repulsions, the increase of the water molecules in the first shell has weakened the interaction between nifedipine and Ca2+, and the hexahydrated complexes are the most stable ones due to the hydration energy. On the other hand, the MD simulations for hexahydrated complexes have also verified that water molecule can transfer from the inner-to the outer-shell because of the formation of H-bond between the two shells ligands. So it can be expected that the "n+m" clusters will play a significant role for nifedipine-Ca2+(H2O) n system (n＞6), when the ligands in the inner shell become too crowed.
(2) Interaction Site Preference between Carbon Nanotube and Nifedipine:A Combined Density Functional Theory and Classical Molecular Dynamics Study
Using a novel DFT, MPWB1K, both internal and external adsorptions of a nifedipine, one of the calcium channel antagonist, on a (10,10) type of single-walled carbon nanotube (SWCNT) were investigated with both C200H40 and C280 cluster models for the SWCNT. The internal adsorption is more stable than the external adsorption in a range of 5.3-7.8 kcal/mol, which indicates that a nifedipine has a preference to internally adsorb on the (10,10) SWCNT. It also proved that the passviated nanotube by hydrogen atoms has no obvious influence for the SWCNT-nifedipine system. Furthermore, molecular dynamics simulations (MD) were then done on the system consisting of nifedipine and the SWCNT (10, 10) in the absence and in the presence of water molecules. The spontaneous encapsulations of nifedipine into the SWCNT channel were observed in both cases; however this process was significantly delayed by including water molecules in the simulation. The nifedipine for both cases also demonstrates an oscillation behavior inside the (10,10) SWCNT, which again occurs later for the system including water than without water. The two competing effects, van der Waals and the hydrophobic forces caused by water molecules, should be responsible for the encapsulation process, yet the van der Waals attraction plays a dominant role on the encapsulation process of nifedipine into the nanotube and the oscillation behavior of nifedipine. In addition, it was found that the water molecules absorbed inside the channel is an irregular monolayer interacting with the nanotube interior surface.
(3) Effects of adsorption of Ca2+ on SWCNT-Nifedipine system
This work offers an exploration of the affection of Ca2+ on the SWCNT-Nifedipine system using density functional theory calculations. First of all, we calculated the interaction between the single-walled carbon nanotube and Ca2+. There are four distinct symmetry sites related to the relative position of Ca2+ with respect to the nanotube carbon rings, which is the center of the carbon rings, the center of the C-C bond along the radical direction of the tube, the center of the C-C bond parallel to the axis of the tube, and the site on the top of a carbon atom. We designed two different situations containing the Ca2+ on the external sidewall of the nanotube and in the internal of the nanotube channel. The most favorable isomer of SWCNT-Ca2+ system is the one that Ca2+ binding to the external sidewall of the nanotueb above the center of the carbon ring, due to the cation-πinteraction between the Ca2+ and the nanotube. The distance of Ca2+ to the surface of the carbon nanotube is 2.3 (?). Then we calculated the effection of nifedipine to the carbon nanotube. We found that the most stable isomer is the one that nifedipine molecule encapsulated into the nanotube channel with the dihydropyridine ring parallel to nanotube surface. Theπ…πstacking interaction between the dihydropyridine ring and the carbon rings and the X-H…π(X=C, N) interaction are overcompensate the steric repulsions caused by the encapsulation of the drug. Finally, four complexes of the SWCNT-N-Ca2+ system are investigated to exploration the affection of Ca2+ to the most stable SWCNT-N complex (complex 1). It is interesting that the Ca2+ is above the center of the carbon rings after optimized in all cases. On the other hand, we discuss the change of the HOMO-LUMO gap and the electron density of states (DOS) of carbon nanotube caused by the adsorption of Ca2+ and nifedipine molecule. It is found that the adsorption of Ca2+ can reduce the HOMO-LUMO gap of the nanotube, and change the DOS around the Fermi level dramatically. Compared with the intrinsic carbon nanotube, the conductivity of the SWCNT-Ca2+ system is improved obviously. However, the adsorption of nifedipine molecule reduced the conductivity of the SWCNT-N system unexpectly. Similar with the SWCNT-Ca2+ system, the reducing HOMO-LUMO gap and the improved conductivity are also found in SWCNT-N-Ca2+ system.
(4) Interaction between Single-Walled Carbon Nanotube and Doxorubicin, a very widely used anti-cancer drug
To quantify approximately the thermodynamics of binding, and to obtain putative binding structures, we simulated interaction between the widely used anticancer drug, doxorubicin molecule and the (10,10) armchair carbon nanotube in neutral and in acidic aqueous solutions. The drug could spontaneously encapsulate into the nanotube channel and the process was significantly delayed by the presence of water molecules in neutral solution, The van der Waals attraction plays a dominant role on the encapsulation process. On the other hand, the doxorubicin molecule adsorbed on the external wall of the nanotube in acidic aqueous solution throughπ…πstacking interaction between the aromatic rings and the carbon rings. The present study suggests that the nanotube network could be used as an efficient tool for transporting this kind of anti-cancer drug. Furthermore, the equilibrium distances, adsorption energies, charge transfer, and density of states characteristics are investigated about SWCNT-DOX system in gas phase. The results show that the main contribution comes from theπ…πstacking and X-H…πinteraction (X=O, N, and C) between the doxorubicin and the nanotube. In addition, the presence of the doxorubicin molecule would neither modify the DOS of the SWCNT nor lead to significant changes in the conductivity of the nanotube. The fact that the electronic properties of the SWCNT are preserved upon doxorubicin adsorption is found to be a general feature.
引文
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