受限于不同螺旋性的纳米碳管中水的分子动力学模拟

近年来将纳米碱米碳管引入到与生命过程息息相关的离子通道膜的研究逐渐成 为热点，而其中的关键就是要了解受限于膜孔道（碳管）中水分子的行为。采用分 子动力学模拟在300 K和1.01 * 10~5 Pa下对受限于（6，6）armchair型和（10， 0）zigzag型纳米碳管中的水进行了研究，得到了水分子在碳管中的局部密度分布 等静态性质以及水分子在碳管中的传递等动态性质，并对不同势能模型的模拟结果 作了比较。结果表明选择不同的势能模型并没有改变此体系的固有性质，即水分子 不仅能够进入到憎水性的（6，6）碳管中而且能形成一条稳定的由氢键相连的纵列 （single file），而且在管中以纵列的形式进行同歇传递。此外，碳管螺旋性对 受限水的静态性质影响不大但对动态性质则有一定程度的影响，水分子在（10，0 ）zigzag型碳管中的传递能力要强于在（6，6）armchair型碳管中的能力。     

Kinetics of water filling the hydrophobic channels of narrow carbon nanotubes studied by molecular dynamics simulations

The kinetics of water filling narrow single-walled carbon nanotubes was studied using molecular dynamics simulations. The time required to fully fill a nanotube was linear with respect to the tube length. We observed that water molecules could enter into nanotubes of different lengths, either from one end or from both ends. The probability of having a nanotube filled completely from both ends increased exponentially with the tube length. For short tubes, filling usually proceeded from only one end. For long tubes, filling generally proceeded from both tube ends over three stages, i.e., filling from one end, filling from both ends, and filling from both ends with the dipole reorientation of water molecules to give a concerted ordering within the fully filled tube. The water molecules in the partially filled nanotube were hydrogen bonded similarly to those in the fully filled nanotube. Simulations for the reference Lennard-Jones fluid without hydrogen bonds were also performed and showed that the filling behavior of water molecules can be attributed to strong intermolecular hydrogen bonding.     

CO2 adsorption by nitrogen-doped carbon nanotubes predicted by density-functional theory with dispersion-correcting potentials

The interaction of CO(2) to the interior and exterior walls of pristine and nitrogen-doped single-walled carbon nanotubes (SWNT) has been studied using density-functional theory with dispersion-correcting potentials (DCPs). Our calculations predict Gibbs energies of binding between SWNT and CO(2) of up to 9.1 kcal mol(-1), with strongest binding observed for a zigzag [10,0] nanotube, compared to armchair [6,6] (8.3 kcal mol(-1)) and chiral [8,4] (7.0 kcal mol(-1)). Doping of the [10,0] tube with nitrogen increases the Gibbs energies of binding of CO(2) by ca. 3 kcal mol(-1), but slightly reduced binding is found when [6,6] and [8,4] SWNT are doped in similar fashion. The Gibbs energy of binding of CO(2) to the exterior of the tubes is quite small compared to the binding that occurs inside the tubes. These findings suggest that the zigzag SWNT show greater promise as a means of CO(2) gas-capture.     

Hierarchical multiscale simulation of electrokinetic transport in silica nanochannels at the point of zero charge

Effects of nanoscale confinement and partial charges that stem from quantum calculations are investigated in silica slit channels filled with 1 M KCl at the point of zero charge by using a hierarchical multiscale simulation methodology. Partial charges of both bulk and surface atoms from ab initio quantum calculations that take into account bond polarization and electronegativity are used in molecular dynamics (MD) simulations to obtain ion and water concentration profiles for channel widths of 1.1, 2.1, 2.75, and 4.1 nm. The interfacial electron density profiles of simulations matched well with that of recent X-ray reflectivity experiments. By simulating corresponding channels with no partial charges, it was observed that the partial charges affect the concentration profiles and transport properties such as diffusion coefficients and mobilities up to a distance of about 3 sigma(O)(-)(O) from the surface. Both in uncharged and partially charged cases, oscillations in concentration profiles of K(+) and Cl(-) ions give rise to an electro-osmotic flow in the presence of an external electric field, indicating the presence of an electric double layer at net zero surface charge, contrary to the expectations from classical continuum theory. I-V curves in a channel-bath system using ionic mobilities from MD simulations were significantly different for channels with and without partial charges for channel widths less than 4.1 nm.     

Ni adsorption on Stone-Wales defect sites in single-wall carbon nanotubes

Ni adsorption on Stone-Wales defect sites in (10,0) zigzag and (5,5) armchair single-wall carbon nanotubes was studied using the density functional theory. The stable adsorption sites and their binding energies on different Stone-Wales defect types were analyzed and compared to those on perfect side walls. It was determined that the sites formed via fusions of 7-7 and 6-7 rings are the most exothermic in the cases of (10,0) and (5,5) defective tubes. In addition C-C bonds associated with Stone-Wales defects are more reactive than the case for a perfect hexagon, thus enhancing the stability of the Ni adsorption. Moreover, the Ni adsorption was found to show a noticeable relationship to the orientation of the Stone-Wales defects with respect to the tube axis. The nature of the Ni adsorption on Stone-Wales defects that have the similar orientation is identical, in spite of the different chiralities.     

Electrochemical doping of chirality-resolved carbon nanotubes

Raman spectra of electrochemically charged single-wall carbon nanotubes (HiPco) were studied by five different laser photon energies between 1.56 and 1.92 eV. The bands of radial breathing modes (RBM) were assigned to defined chiralities by using the experimental Kataura plot. The particular (n,m) tubes exhibit different sensitivity to electrochemical doping, monitored as the attenuation of the RBM intensities. Tubes which are in good resonance with the exciting laser exhibit strong doping-induced drop of the RBM intensity. On the other hand, tubes whose optical transition energy is larger than the energy of an exciting photon show only small changes of their RBM intensities upon doping. This rule presents a tool for analysis of mixtures of single-walled carbon tubes of unknown chiralities. It also asks for a re-interpretation of some earlier results which were reported on the diameter-selectivity of doping. The radial breathing mode in strongly n- or p-doped nanotubes exhibited a blue-shift. A suggested interpretation follows from the charging-induced structural changes of SWCNTs bundles, which also includes a partial de-bundling of tube ropes.     

Ion permeation dynamics in carbon nanotubes

Molecular dynamics simulations are carried out to investigate the permeation of ions and water in a membrane consisting of single wall carbon nanotubes possessing no surface charges connecting two reservoirs. Our simulations reveal that there are changes in the first hydration shell of the ions upon confinement in tubes of 0.82 or 0.90 nm effective internal diameter. Although the first minimum in the g(r) is barely changed in the nanotube compared to in the bulk solution, the hydration number of Na(+) ion is reduced by 1.0 (from 4.5 in bulk to 3.5 in the 0.90 nm tube) and the hydration number is reduced further in the 0.82 nm tube. The changes in the hydration shell of Cl(-) ion are negligible, within statistical errors. The water molecules of the first hydration shell of both ions exchange less frequently inside the tube than in the bulk solution. We compare ion trajectories for ions in the same tube under identical reservoir conditions but with different numbers of ions in the tubes. This permits investigation of changes in structure and dynamics which arise from multiple ion occupancy in a carbon nanotube possessing no surface charges. We also investigated the effects of tube flexibility. Ions enter the tubes so as to form a train of ion pairs. We find that the radial distribution profiles of Na(+) ions broaden significantly systematically with increasing number of ion pairs in the tube. The radial distribution profiles of Cl(-) ions change only slightly with increasing number of ions in the tube. Trajectories reveal that Na(+) ions do not pass each other in 0.90 nm tubes, while Cl(-) ions pass each other, as do ions of opposite charge. An ion entering the tube causes the like-charged ions preceding it in the tube to be displaced along the tube axis and positive or negative ions will exit the tube only when one or two other ions of the same charge are present in the tube. Thus, the permeation mechanism involves multiple ions and Coulomb repulsion among the ions plays an essential role.     

Charge asymmetries in hydration of polar solutes

We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.     

异型碳纳米管储氢性能的分子动力学模拟研究

采用分子动力学(MD)方法对三种理想的Y型碳纳米管[记为Y(4,4), Y(6,6), Y(10,0)]和三种L型碳纳米管[记为L(9,0), L(6,6), L(10,0)]之储氢性能进行了模拟研究, 并与相应的直线型碳纳米管的储氢能力进行了比较, 同时考察了温度、碳纳米管的直径和螺旋性以及缺陷的位置和大小对异型碳纳米管储氢性能的影响. 结果表明, 在室温和低温条件下, 异型碳纳米管的储氢量高于直线型碳纳米管的储氢量, 且其储氢量大小随温度的降低和碳管直径的增大而增加, 椅式碳纳米管的储氢性能优于齿式碳纳米管, 而缺陷的位置和大小对异型碳管之储氢性能的影响则因碳管的形貌和直径的大小不同而存在差异.     

Molecular simulation study of water mobility in aerosol-OT reverse micelles

In this work, we present results from molecular dynamics simulations on the single-molecule relaxation of water within reverse micelles (RMs) of different sizes formed by the surfactant aerosol-OT (AOT, sodium bis(2-ethylhexyl)sulfosuccinate) in isooctane. Results are presented for RM water content w(0) = [H(2)O]/[AOT] in the range from 2.0 to 7.5. We show that translational diffusion of water within the RM can, to a good approximation, be decoupled from the translation of the RM through the isooctane solvent. Water translational mobility within the RM is restricted by the water pool dimensions, and thus, the water mean-squared displacements (MSDs) level off in time. Comparison with models of diffusion in confined geometries shows that a version of the Gaussian confinement model with a biexponential decay of correlations provides a good fit to the MSDs, while a model of free diffusion within a sphere agrees less well with simulation results. We find that the local diffusivity is considerably reduced in the interfacial region, especially as w(0) decreases. Molecular orientational relaxation is monitored by examining the behavior of OH and dipole vectors. For both vectors, orientational relaxation slows down close to the interface and as w(0) decreases. For the OH vector, reorientation is strongly affected by the presence of charged species at the RM interface and these effects are especially pronounced for water molecules hydrogen-bonded to surfactant sites that serve as hydrogen-bond acceptors. For the dipole vector, orientational relaxation near the interface slows down more than that for the OH vector due mainly to the influence of ion-dipole interactions with the sodium counterions. We investigate water OH and dipole reorientation mechanisms by studying the w(0) and interfacial shell dependence of orientational time correlations for different Legendre polynomial orders.     

Accounting for electronic polarization in non-polarizable force fields

The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole μ～ 3D reported in recent ab initio and experimental studies with the value μ(eff)～ 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value μ(eff) = μ/√ε(el), where ε(el) = 1.78 is the electronic (high-frequency) dielectric constant of water. This simple theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes.     

Electronic transport in Z-junction carbon nanotubes

In this paper, the electronic transport in different Z-shape carbon nanotubes containing double knee junction structures on the same tube is studied. One consists of (5,5)-(9,0)-(5,5) double knee nano-metal-metal-metal junctions and another consists (6,6)-(10,0)-(6,6) double knee nano-metal-semiconductor-metal junctions. With the nearest-neighbor pi-orbital tight-binding model, quantum conductances of these double knee junctions are calculated using the Landauer formula. The interesting conductance curves are provided to exhibit a potential application in the arena of molecular electronics.     

Entropy of single-file water in (6,6) carbon nanotubes

We used molecular dynamics simulations to investigate the thermodynamics of filling of a (6,6) open carbon nanotube (diameter D = 0.806 nm) solvated in TIP3P water over a temperature range from 280 K to 320 K at atmospheric pressure. In simulations of tubes with slightly weakened carbon-water attractive interactions, we observed multiple filling and emptying events. From the water occupancy statistics, we directly obtained the free energy of filling, and from its temperature dependence the entropy of filling. We found a negative entropy of about -1.3 k(B) per molecule for filling the nanotube with a hydrogen-bonded single-file chain of water molecules. The entropy of filling is nearly independent of the strength of the attractive carbon-water interactions over the range studied. In contrast, the energy of transfer depends strongly on the carbon-water attraction strength. These results are in good agreement with entropies of about -0.5 k(B) per water molecule obtained from grand-canonical Monte Carlo calculations of water in quasi-infinite tubes in vacuum under periodic boundary conditions. Overall, for realistic carbon-water interactions we expect that at ambient conditions filling of a (6,6) carbon nanotube open to a water reservoir is driven by a favorable decrease in energy, and opposed by a small loss of water entropy.     

手性和尺寸对受限于单壁碳纳米管内的硝基甲烷热解反应的影响

采用组合的量子化学ONIOM(B3LYP/6-311++G**:UFF)方法, 研究了不同直径的扶手椅型(CNT(5,5)、CNT(6,6)、CNT(8,8))和锯齿型(CNT(9,0)、CNT(10,0)、CNT(11,0))单壁碳纳米管(CNTs)的限制作用对硝基甲烷分子结构和热解反应的影响. 分子结构分析表明, 与单体硝基甲烷相比, 受限于直径较小的CNT(5,5)和CNT(9,0)碳纳米管内的硝基甲烷构型发生扭转, Cs对称性消失, C—N键长略微缩短; 而受限于CNT(6,6)、CNT(8,8)、CNT(10,0)和CNT(11,0)内的硝基甲烷结构变化不明显. 热解势能面计算发现, 与硝基甲烷单体的热解是一个无过渡态的解离过程明显不同: 硝基甲烷在CNT(5,5)和CNT(9,0)碳纳米管内沿C—N键的解离经历过渡态结构, 所需克服的活化能比单体的解离能分别下降了约71和58 kJ·mol-1; 在CNT(6,6)和CNT(10,0)碳纳米管内, 硝基甲烷的热解活化能略有下降; 而在直径较大的CNT(8,8)和CNT(11,0)碳纳米管内, 热解活化能基本不变. 研究结果表明, 直径小的碳纳米管的限制作用对硝基甲烷热解活化能影响显著, 碳纳米管的手性对硝基甲烷热解反应影响不明显.     

Theoretical study of the 13C NMR spectroscopy of single-walled carbon nanotubes

The 13C NMR spectroscopy of armchair and zigzag single-walled carbon nanotubes has been investigated theoretically. Spectra for (4,4), (5,5), (6,6), (6,0), (9,0), and (10,0) nanotubes have been simulated based on ab initio calculations of model systems. The calculations predict a dominant band arising from the carbon atoms in the "tube" with smaller peaks at higher chemical shifts arising from the carbon atoms of the caps. The dominant band lies in the range of 128 and 138 ppm. Its position depends weakly on the length, width, and chirality of the tubes. The calculations demonstrate how structural information may be gleaned from relatively low-resolution nanotube 13C NMR spectra.     

Shapes and dynamics of miscible liquid/liquid interfaces in horizontal capillary tubes

We report optical observations of the dissolution behaviour of glycerol/water, soybean oil/hexane, and isobutyric acid (IBA)/water binary mixtures within horizontal capillary tubes. Tubes with diameters as small as 0.2mm were initially filled with one component of the binary mixture (solute) and then immersed into a solvent-filled thermostatic bath. Both ends of the tubes were open, and no pressure difference was applied between the ends. In the case of glycerol/water and soybean oil/hexane mixtures, we managed to isolate the dissolution (the interfacial mass transfer) from the hydrodynamic motion. Two phase boundaries moving from the ends into the middle section of the tube with the speeds v～D(1/3)t(-2/3)d(2) (D,t and d are the coefficient of diffusion, time and the diameter of the tube, respectively) were observed. The boundaries slowly smeared but their smearing occurred considerably slower than their motion. The motion of the phase boundaries cannot be explained by the dependency of the diffusion coefficient on concentration, and should be explained by the effect of barodiffusion. The shapes of the solute/solvent boundaries are defined by the balance between gravity and surface tension effects. The contact line moved together with the bulk interface: no visible solute remained on the walls after the interface passage. Changes in temperature and in the ratio between gravity and capillary forces altered the apparent contact angles. The IBA/water system had different behaviour. Below the critical (consolute) point, no dissolution was observed: IBA and water behaved like two immiscible liquids, with the IBA phase being displaced from the tube by capillary pressure (the spontaneous imbibition process). Above the critical point, two IBA/water interfaces could be identified, however the interfaces did not penetrate much into the tube.     

Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution

We probe the urea-denaturation mechanism using molecular dynamics simulations of an elementary "folding" event, namely, the formation of end-to-end contact in the linear hydrocarbon chain (HC) CH(3)(CH(2))(18)CH(3). Electrostatic effects are examined using a model HC in which one end of the chain is positively charged (+0.2e) and the other contains a negative charge (-0.2e). For these systems multiple transitions between "folded" (conformations in which the chain ends are in contact) and "unfolded" (end-to-end contact is broken) can be observed during 4 ns molecular dynamics simulations. In water and 6 M aqueous urea solution HC and the charged HC fluctuate between collapsed globular conformations and a set of expanded structures. The collapsed conformation adopted by the HC in water is slightly destablized in 6 M urea. In contrast, the end-to-end contact is disrupted in the charged HC only in aqueous urea solution. Despite the presence of a large hydrophobic patch, on length scales on the order of approximately 8-10 A "denaturation" (transition to the expanded unfolded state) occurs by a direct interaction of urea with charges on the chain ends. The contiguous patch of hydrophobic moieties leads to "mild dewetting", which becomes more pronounced in the charged HC in 6 M aqueous urea solution. Our simulations establish that the urea denaturation mechanism is most likely electrostatic in origin.     

Flow structure of water in carbon nanotubes: poiseuille type or plug-like?

We have conducted molecular dynamics simulations of water flow in carbon nanotubes (CNTs) for (6,6) to (20,20) CNTs at a streaming velocity of 100 ms. The fluidized piston model (FPM) and the ice piston model (IPM) are employed to drive flow through the CNTs. The results show that the single-file water flow inside (6,6) CNT has a convex upward streaming velocity profile, whereas the velocity profiles in (10,10) to (20,20) CNTs are flat except near the tube wall. The flow structure of cylindrical water in the (8,8) CNT is intermediate between that for the (6,6) CNT and the larger CNTs. The flow parameters are found not to exhibit any dependence on streaming velocity at up to 300 ms in the (12,12) CNT. The hydrogen bond lifetimes of water flowing in CNTs tend to be longer than for the corresponding equilibrium states, and nonzero flow does not reduce the microscopic structure or structural robustness (hydrogen bond lifetime). Although the atomic density profile varies with tube diameter, reflecting the change in static microscopic structure of flow from single file to cylindrical, tube diameter does not induce a clear transition in streaming velocity, temperature, or hydrogen bond lifetime over this diameter range. The results suggest that water flow in CNTs of this size is more pluglike than Poiseuille type, although the flow structure does not strictly accord with either definition.     

The reactivity of defects at the sidewalls of single-walled carbon nanotubes: the Stone-Wales defect

The reactivity of 5/7/7/5 (Stone-Wales, SW) defects is compared to that of the pristine sidewalls of (5,5) and (10,0) carbon nanotubes (CNTs) using density functional theory (PBE). Infinite tube models (periodic boundary conditions) are used to investigate the reaction energy for CH(2) addition to the ten [5,6], [5,7], [6,7], and [7,7] C-C junctions resulting from SW rotations of the two unique bonds in (5,5) and (10,0) CNTs. In all cases, at least one of the junctions associated with the SW defects is more highly reactive than the pristine tubes. The orientation of these junctions with respect to the tube axis mainly determines the exothermicity. The [7,7] junctions are not the most reactive sites in SW defects of (5,5) and (10,0) CNTs.