纳米碳管中受限流体的分子动力学模拟
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摘要
分子动力学模拟(MD)是化工、材料和生物研究中的一种现代研究方法。采用它来研究纳米碳管中受限流体的微观结构和传递性质对建立合理的离子通道中受限分子传递机理的模型具有重要意义。
离子通道控制着水分子、离子进出细胞膜的过程，因而成为生命科学中最重要的研究对象之一。然而，各种离子通道均是由各种形状功能不同的氨基酸序列构成的，而且表面的电荷分布又极不均匀，因此不易直接建立真实的分子模型进行模拟研究。其实，无论通道的结构有多复杂，它们都遵循同样的特征：跨越细胞膜的长度约为1nm、直径≤1nm的一维孔道。
2001年Hummer等(Nature，2001，414，188)的论文标志着纳米碳管又一潜在应用的发现：设计成快速传递水的分子通道。通过适当的改性，纳米碳管可以模拟出离子通道控制小分子进出的gating机理，也就意味着纳米碳管可能成为离子通道的人工替代品。然而，Hummer等没有对受限在碳管中的水分子这一体系做过系统的研究，究竟是什么因素控制着水分子是否能够进入某种碳管?与选用的力场有关还是碳管的本性?决定碳管性质的关键参数管径和螺旋性对受限水的静态和动态行为会产生什么影响?这一系列的不确定因素是将碳管设计成分子通道过程中必不可少的研究内容。本文利用现代的MD模拟技术对分子力场、管径和螺旋性对纳米碳管中受限水的静态和动态性质的影响做了全面细致的分析。
对分子模拟的起源、发展及实际应用中的关键问题作了简要的论述。对现有的MD算法，原子、分子体系运动方程的解法，位能及其选择方法，初始构型的搭建，模拟结果的处理和分析，纳米碳管的结构和性能等作了较全面的论述。
采用新一代普遍化力场COMPASS对受限在(6，6)和(10，0)碳管中的水分子的静态性质和传递特征进行了MD模拟。验证了力场并不改变水分子进入(6，6)碳管的这一本性并发现管径和螺旋性可能会造成受限水性质的不同。
对具有类似管径的多对armchair和zigzag型碳管在水浴中的静态性质进行了MD模拟研究。结果发现静态性质主要受管径而非螺旋性的影响，这也意味着以碳管为原型进行相似受限孔道的研究具有一定的可行性。受限水分子的氢键网络相对于主体水而言都有不同程度的破坏，在较大的碳管中平均氢键数变得与管
摘要
径无关，说明特殊的受限效应只在直径一Inm的孔道内才会明显地表现出来。平
均氢键数的大幅降低对受限水的动态性质可能带来较大的影响。该部分工作在英
国皇家化学会的《PCCP》上发表之后立即引起国际同行的广泛关注，鉴于审稿
人对该项工作的高度评价该文被推荐成为《PCCP》的“Hot article”，该文在该
期刊的当月下载排名统计中位居前三名。
进一步对管径和螺旋性给受限水的动态性质带来的影响做了初步分析。定性
的结论是管径和螺旋性对受限水的动态性质均有不同程度的影响。受限在
armchair型碳管中水分子的运动要比在zigzag碳管中的更激烈、更快一些。在较
大的碳管中管径对受限水的运动起主导作用，即管径越大，运动越快;在较小的
碳管件，平均氢键数决定受限水运动的快慢，即平均氢键数越小，运动越快。水分
子运动得越快并不意味着通过碳管的传递速率就越快，水分子是否能在碳管内发
生完美的传递可能由其他的未知因素所决定。动态性质的定量分析需要纳秒级的
统计机时。
Molecular Dynamics (MD) simulation is a modern research method with applications in Chemical Engineering, Materials Designing and Biological Science. It has great significance to study microstructures and transport properties of confined fluids within carbon nanotubes (CNTs) by means of MD for establishing the reasonable conduction mechanism model of confined molecules within ion channels.
Ion channels controlling the transport of ions and associated water molecules into and out of cells have become one of the most important research objects in Biological Science. Nevertheless, ion channels with highly inhomogeneous charge distributions are composed of various amino acid sequences which fold into specific and complicated topologies. Hence, it is not easy to establish initial configurations imitating real structures of ion channels to perform simulation studies. As a matter of fact, all ion channels have a general feature, namely a pore of typical length ~1 nm and diameter <1 nm, spanning the cell membrane, whatever complex structures they have.
In 2001 the publication of Hummer et al.'s paper {Nature, 2001, 414, 188) represents the discovery of CNT's another potential application. That is, to be designed as molecular channels to transport water molecules. Properly functionalized CNTs can be used to simulate the gating mechanism of ion channels, indicating that CNTs may become the artificial ion channels. However, Hummer et al. never conducted a systematic study of confined water within CNTs. What factors on earth determine whether water molecules can enter a certain CNT or not? Is it dependent on the selected force field or just the nature of a certain CNT? What influences can diameter and helicity (two key parameters controlling properties of CNT) produce on static and dynamic properties of confined water? These uncertain issues are indispensable problems to be solved during the process of designing CNTs as molecular channels. In this dissertation, modern MD simulation techniques are utilized to fully analyze the influences of molecular force fiel
d, diameter and helicity on static and dynamic properties of confined water within CNTs.
A brief introduction and discussion about the origin, evolution and several key issues in practical application of MD simulation is reported. In particular, present MD algorithms, different kind of solution methods for atomic and molecular motion equations, potential model and its choice, construction of initial configurations, analysis of simulation results, structures and properties of CNTs are described in detail, respectively.
A new generalized force field called COMPASS is employed to perform MD simulation study on static properties and transport characteristics of confined water within (6,6) and (10,0) CNTs. We approved the fact that water molecules are able to enter (6,6) CNT which is independent of force field and found that different diameter and helicity may cause different behavior of confined water.
Further MD simulations are performed to study the properties of several pairs of armchair and zigzag CNTs with similar diameters dissolved in water bath. The results show that the static properties of confined water are dominated by diameter rather than helicity, indicating a certain feasibility that CNT can serve as prototypes to study similar confined channels. The hydrogen bond network of confined water has been destroyed to different extents relative to that of bulk water. In larger CNTs the average number of hydrogen bonds has become independent of tube diameter, denoting that special confinement effect can only be obviously seen in channels with diameter ~1 nm. The steep decrease of the average number of hydrogen bonds may bring significant influences on dynamic properties of confined water. This work immediately attracted a lot of attention from international colleagues after its publication on PCCP (a journal of Royal Society of Chemistry). Because of the excellent response by the referees, this paper has been selected as a "hot article" by PCCP. In addition, it
离子通道控制着水分子、离子进出细胞膜的过程，因而成为生命科学中最重要的研究对象之一。然而，各种离子通道均是由各种形状功能不同的氨基酸序列构成的，而且表面的电荷分布又极不均匀，因此不易直接建立真实的分子模型进行模拟研究。其实，无论通道的结构有多复杂，它们都遵循同样的特征：跨越细胞膜的长度约为1nm、直径≤1nm的一维孔道。
2001年Hummer等(Nature，2001，414，188)的论文标志着纳米碳管又一潜在应用的发现：设计成快速传递水的分子通道。通过适当的改性，纳米碳管可以模拟出离子通道控制小分子进出的gating机理，也就意味着纳米碳管可能成为离子通道的人工替代品。然而，Hummer等没有对受限在碳管中的水分子这一体系做过系统的研究，究竟是什么因素控制着水分子是否能够进入某种碳管?与选用的力场有关还是碳管的本性?决定碳管性质的关键参数管径和螺旋性对受限水的静态和动态行为会产生什么影响?这一系列的不确定因素是将碳管设计成分子通道过程中必不可少的研究内容。本文利用现代的MD模拟技术对分子力场、管径和螺旋性对纳米碳管中受限水的静态和动态性质的影响做了全面细致的分析。
对分子模拟的起源、发展及实际应用中的关键问题作了简要的论述。对现有的MD算法，原子、分子体系运动方程的解法，位能及其选择方法，初始构型的搭建，模拟结果的处理和分析，纳米碳管的结构和性能等作了较全面的论述。
采用新一代普遍化力场COMPASS对受限在(6，6)和(10，0)碳管中的水分子的静态性质和传递特征进行了MD模拟。验证了力场并不改变水分子进入(6，6)碳管的这一本性并发现管径和螺旋性可能会造成受限水性质的不同。
对具有类似管径的多对armchair和zigzag型碳管在水浴中的静态性质进行了MD模拟研究。结果发现静态性质主要受管径而非螺旋性的影响，这也意味着以碳管为原型进行相似受限孔道的研究具有一定的可行性。受限水分子的氢键网络相对于主体水而言都有不同程度的破坏，在较大的碳管中平均氢键数变得与管
摘要
径无关，说明特殊的受限效应只在直径一Inm的孔道内才会明显地表现出来。平
均氢键数的大幅降低对受限水的动态性质可能带来较大的影响。该部分工作在英
国皇家化学会的《PCCP》上发表之后立即引起国际同行的广泛关注，鉴于审稿
人对该项工作的高度评价该文被推荐成为《PCCP》的“Hot article”，该文在该
期刊的当月下载排名统计中位居前三名。
进一步对管径和螺旋性给受限水的动态性质带来的影响做了初步分析。定性
的结论是管径和螺旋性对受限水的动态性质均有不同程度的影响。受限在
armchair型碳管中水分子的运动要比在zigzag碳管中的更激烈、更快一些。在较
大的碳管中管径对受限水的运动起主导作用，即管径越大，运动越快;在较小的
碳管件，平均氢键数决定受限水运动的快慢，即平均氢键数越小，运动越快。水分
子运动得越快并不意味着通过碳管的传递速率就越快，水分子是否能在碳管内发
生完美的传递可能由其他的未知因素所决定。动态性质的定量分析需要纳秒级的
统计机时。
Molecular Dynamics (MD) simulation is a modern research method with applications in Chemical Engineering, Materials Designing and Biological Science. It has great significance to study microstructures and transport properties of confined fluids within carbon nanotubes (CNTs) by means of MD for establishing the reasonable conduction mechanism model of confined molecules within ion channels.
Ion channels controlling the transport of ions and associated water molecules into and out of cells have become one of the most important research objects in Biological Science. Nevertheless, ion channels with highly inhomogeneous charge distributions are composed of various amino acid sequences which fold into specific and complicated topologies. Hence, it is not easy to establish initial configurations imitating real structures of ion channels to perform simulation studies. As a matter of fact, all ion channels have a general feature, namely a pore of typical length ~1 nm and diameter <1 nm, spanning the cell membrane, whatever complex structures they have.
In 2001 the publication of Hummer et al.'s paper {Nature, 2001, 414, 188) represents the discovery of CNT's another potential application. That is, to be designed as molecular channels to transport water molecules. Properly functionalized CNTs can be used to simulate the gating mechanism of ion channels, indicating that CNTs may become the artificial ion channels. However, Hummer et al. never conducted a systematic study of confined water within CNTs. What factors on earth determine whether water molecules can enter a certain CNT or not? Is it dependent on the selected force field or just the nature of a certain CNT? What influences can diameter and helicity (two key parameters controlling properties of CNT) produce on static and dynamic properties of confined water? These uncertain issues are indispensable problems to be solved during the process of designing CNTs as molecular channels. In this dissertation, modern MD simulation techniques are utilized to fully analyze the influences of molecular force fiel
d, diameter and helicity on static and dynamic properties of confined water within CNTs.
A brief introduction and discussion about the origin, evolution and several key issues in practical application of MD simulation is reported. In particular, present MD algorithms, different kind of solution methods for atomic and molecular motion equations, potential model and its choice, construction of initial configurations, analysis of simulation results, structures and properties of CNTs are described in detail, respectively.
A new generalized force field called COMPASS is employed to perform MD simulation study on static properties and transport characteristics of confined water within (6,6) and (10,0) CNTs. We approved the fact that water molecules are able to enter (6,6) CNT which is independent of force field and found that different diameter and helicity may cause different behavior of confined water.
Further MD simulations are performed to study the properties of several pairs of armchair and zigzag CNTs with similar diameters dissolved in water bath. The results show that the static properties of confined water are dominated by diameter rather than helicity, indicating a certain feasibility that CNT can serve as prototypes to study similar confined channels. The hydrogen bond network of confined water has been destroyed to different extents relative to that of bulk water. In larger CNTs the average number of hydrogen bonds has become independent of tube diameter, denoting that special confinement effect can only be obviously seen in channels with diameter ~1 nm. The steep decrease of the average number of hydrogen bonds may bring significant influences on dynamic properties of confined water. This work immediately attracted a lot of attention from international colleagues after its publication on PCCP (a journal of Royal Society of Chemistry). Because of the excellent response by the referees, this paper has been selected as a "hot article" by PCCP. In addition, it
引文
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