Molecular simulation study of temperature effect on ionic hydration in carbon nanotubes

Molecular dynamics simulations have been performed to investigate the hydration of Li(+), Na(+), K(+), F(-), and Cl(-) inside the carbon nanotubes at temperatures ranging from 298 to 683 K. The structural characteristics of the coordination shells of ions are studied, including the ion-oxygen radial distribution functions, the coordination numbers, and the orientation distributions of the water molecules. Simulation results show that the first coordination shells of the five ions still exist in the nanoscale confinement. Nevertheless, the first coordination shell structures of cations change more significantly than those of anions because of the preferential orientation of the water molecules induced by the carbon nanotube. The first coordination shells of cations are considerably less ordered in the nanotube than in the bulk solution, whereas the change of the first coordination shell structures of the anions is minor. Furthermore, the confinement induces the anomalous behavior of the coordination shells of the ions with temperature. The first coordination shell of K(+) are found to be more ordered as the temperature increases only in the carbon nanotube with the effective diameter of 1.0 nm, implying the enhancement of the ionic hydration with temperature. This is contrary to that in the bulk solution. The coordination shells of the other four ions do not have such behavior in the carbon nanotube with the effective diameter ranging from 0.73 to 1.00 nm. The easier distortion of the coordination shell of K(+) and the match of the shell size and the nanotube size may play roles in this phenomenon. The exchange of water molecules in the first coordination shells of the ions with the solution and the ion diffusion along the axial direction of the nanotube are also investigated. The mobility of the ions and the stability of the coordination shells are greatly affected by the temperature in the nanotube as in the bulk solutions. These results help to understand the biological and chemical processes at the high temperature.     

Hydration of alkali ions from first principles molecular dynamics revisited

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.     

Hydration shell exchange dynamics during ion transfer across the liquid/liquid interface

We examine using molecular dynamics simulations the rate and mechanism of water molecules exchange around the Li(+) and Na(+) ions during ion transfer across the interface between water and nitrobenzene. As the ions are transferred from the water to the organic phase, they keep their first hydration shell and an incomplete second shell. The rate of water exchange between the first shell and the rest of the interfacial water molecule decreases during the transfer, which is consistent with an increase in the barrier along the ion-water potential of mean force. While in bulk water the exchange of water molecules around the Li(+) follows an associative (A) or associative interchange (I(a)) type mechanism, the fraction of exchange events of type A increases at the interface. In contrast, while in bulk water the exchange of water molecules around the six coordinated Na(+) hydrated species mainly follows a dissociative mechanism, the situation at the interface involves an equilibrium interchange between the four- and five-coordinated hydrated ion. Simulation of the reversed process, in which the hydrated Li(+) ion is transferred to the aqueous phase, shows the same general behavior as a function of location from the interface.     

Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.     

Molecular dynamics simulation of glycine zwitterion in aqueous solution

A classical molecular dynamics method was used to study the modifications of the solution structure and the properties of glycine zwitterion in aqueous solution due to the increase of glycine zwitterion concentration and the incorporation of Na(+) and Cl(-) ions to the solution. The glycine zwitterion had fundamentally a hydrophilic behavior at infinite dilution, establishing around six hydrogen bonds with the water molecules that surrounded it, which formed a strong hydration layer. Because of the increase of glycine zwitterion concentration, the hydration structure became more compact and the quantity of water molecules bound to this molecule decreased. The Na(+) ion bound to the CO(2) group of glycine, while the Cl(-) ion bound mainly to the NH(3) group of this molecule. The integration of the ions to the hydration layer of the glycine zwitterion produced modifications in the orientational correlation between atoms of glycine zwitterion and water that surrounded them and an increase of the approaches between the glycine zwitterion molecules. The incorporation of ions to the solution also produced changes in the water-water orientational correlation. Decreases of the water-water hydrogen bonds and diffusion coefficient of all molecules were observed when the glycine zwitterion concentration increased and when the ions were incorporated to the solution.     

Incidence of partial charges on ion selectivity in potassium channels

Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter model of KcsA of about 300 atoms at the Hartree-Fock level of theory. Partial charges were derived from the quantum mechanically determined electrostatic potential either with Merz-Kollman or Hinsen-Roux schemes. Large polarization and/or charge transfer occur on potassium ions located in the filter, while the charges on sodium ions remain closer to unity. As a result, a weaker binding is obtained for K(+) ions. Using a simplified version of a permeation model based on the concerted-motion mechanism for ion translocation within the single-file ion channel [P. H. Nelson, J. Chem. Phys. 117, 11396 (2002)], we discuss how differences in polarization effects in the adducts with K(+) and Na(+) can play a role as for ionic selectivity and conductance.     

Atomistic nature of NaCl nucleation at the solid-liquid interface

The early stage of heterogeneous nucleation of NaCl from supersaturated NaCl aqueous solution at the water-NaCl (001) interface has been investigated by molecular dynamics simulations. The critical size of the nuclei for spontaneous growth was found to be as small as two atoms (a Na(+)-Cl(-) ion pair) at high supersaturation. Due to the presence of a relatively stable water network and the effect of the hydration force at the interface, the stable nuclei formed on the NaCl (001) are found to contain more Na(+) ions than Cl(-) ions. The different deposition characteristics of the Na(+) and Cl(-) solutes lead to a positively charged substrate and thus may introduce another driving force for nucleation besides the level of solution supersaturation. The role of water was further confirmed by comparison with NaCl epitaxy growth in the vacuum.     

Free energy of solvation of simple ions: molecular-dynamics study of solvation of Cl- and Na+ in the ice/water interface

Molecular-dynamics simulations of Cl(-) and Na(+) ions are performed to calculate ionic solvation free energies in both bulk simple point-charge/extended water and ice 1 h at several different temperatures, and at the basal ice 1 h/water interface. For the interface we calculate the free energy of "transfer" of the ions across the ice/water interface. For the ions in bulk water in the NPT ensemble at 298 K and 1 atm, results are found to be in good agreement with experiments, and with other simulation results. Simulations performed in the NVT ensemble are shown to give equivalent solvation free energies, and this ensemble is used for the interfacial simulations. Solvation free energies of Cl(-) and Na(+) ions in ice at 150 K are found to be approximately 30 and approximately 20 kcal mol(-1), respectively, less favorable than for water at room temperature. Near the melting point of the model the solvation of the ions in water is the same (within statistical error) as that measured at room temperature, and in the ice is equivalent and approximately 10 kcal mol(-1) less favorable than the liquid. The free energy of transfer for each ion across ice/water interface is calculated and is in good agreement with the bulk observations for the Cl(-) ion. However, for the model of Na(+) the long-range electrostatic contribution to the free energy was more negative in the ice than the liquid, in contrast with the results observed in the bulk calculations.     

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+)

Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.     

Structure of the hydration shell of the Na+ ion in a planar nanopore with hydrophobic walls

The effect of steric hindrances in extremely narrow planar pores on the structure of the hydration shell of the single-charged sodium cation in water vapors at room temperature was studied by computer simulation. The deficiency of empty space for the motion in the slit-like pore was shown to slightly affect the radial distribution of molecules around the ion. The integrated (over the directions) numbers of ion-oxygen atom bonds of molecules in the ion’s hydration shell did not change despite the change in the shape of the hydration cluster from three- to two-dimensional. It was concluded that the changes in the positions of molecules relative to the ion were mainly reduced to azimuthal displacements; as a result, the local bulk density of molecules in the pore was higher than at the same distances outside the pore for the same total number of molecules. The distribution of molecules over layers inside the pore demonstrates the effect of molecules spread over the walls. The effect of ion displacement from its own hydration shell found earlier for the free chloride ion is steadily reproduced under the pore conditions. An alternative explanation to this effect was proposed that does not suggest high ion polarizability.     

A new surface structural approach to ion adsorption: tracing the location of electrolyte ions

Electrolyte ions differ in size leading to the possibility that the distance of closest approach to a charged surface differs for different ions. So far, ions bound as outersphere complexes have been treated as point charges present at one or two electrostatic plane(s). However, in a multicomponent system, each electrolyte ion may have its own distance of approach and corresponding electrostatic plane with an ion-specific capacitance. It is preferable to make the capacitance of the compact part of the double layer a general characteristic of the solid-solution interface. A new surface structural approach is presented that may account for variation in size of electrolyte ions. In this approach, the location of the charge of the outersphere surface complexes is described using the concept of charge distribution in which the ion charge is allowed to be distributed over two electrostatic planes. It was shown that the concept can successfully describe the pH dependent proton binding and the shift in the isoelectric point (IEP) in the presence of variety of monovalent electrolyte ions, including Li(+), Na(+), K(+), Cs(+), Cl(-), NO(-)(3), and ClO(-)(4) with a common set of parameters. The new concept also sheds more light on the degree of hydration of the ions when present as outersphere complexes. Interpretation of the charge distribution values obtained shows that Cl(-) ions are located relatively close to the surface. The large alkali ions K(+), Cs(+), and Rb(+) are at the largest distance. Li(+), Na(+), NO(-)(3), and ClO(-)(4) are present at intermediate positions.     

Formation and interaction of hydrated alkali metal ions at the graphite-water interface

Ion hydration at a solid surface ubiquitously exists in nature and plays important roles in many natural processes and technological applications. Aiming at obtaining a microscopic insight into the formation of such systems and interactions therein, we have investigated the hydration of alkali metal ions at a prototype surface-graphite (0001), using first-principles molecular dynamics simulations. At low water coverage, the alkali metal ions form two-dimensional hydration shells accommodating at most four (Li, Na) and three (K, Rb, Cs) waters in the first shell. These two-dimensional shells generally evolve into three-dimensional structures at higher water coverage, due to the competition between hydration and ion-surface interactions. Exceptionally K was found to reside at the graphite-water interface for water coverages up to bulk water limit, where it forms an "umbrellalike" surface hydration shell with an average water-ion-surface angle of 115 degrees . Interactions between the hydrated K and Na ions at the interface have also been studied. Water molecules seem to mediate an effective ion-ion interaction, which favors the aggregation of Na ions but prevents nucleation of K. These results agree with experimental observations in electron energy loss spectroscopy, desorption spectroscopy, and work function measurement. In addition, the sensitive dependence of charge transfer on dynamical structure evolution during the hydration process, implies the necessity to describe surface ion hydration from electronic structure calculations.     

Path integral Monte Carlo study of 4He clusters doped with alkali and alkali-earth ions

Path integral Monte Carlo calculations of (4)He nanodroplets doped with alkali (Na(+), K(+) and Cs(+)) and alkali-earth (Be(+) and Mg(+)) ions are presented. We study the system at T = 1 K and between 14 and 128 (4)He atoms. For all studied systems, we find that the ion is well localized at the center of the droplet with the formation of a "snowball" of well-defined shells of localized (4)He atoms forming solid-like order in at least the first surrounding shell. The number of surrounding helium shells (two or three) and the number of atoms per shell and the degree of localization of the helium atoms are sensitive to the type of ion. The number of (4)He atoms in the first shell varies from 12 for Na(+) to 18 for Mg(+) and depends weakly on the size of the droplet. The study of the density profile and of the angular correlations shows that the local solid-like order is more pronounced for the alkali ions with Na(+) giving a very stable icosahedral order extending up to three shells.     

Ions in water: the microscopic structure of concentrated hydroxide solutions

Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45 degrees from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.     

高斯多峰拟合在径向分布函数中的应用

利用同步辐射X射线散射法测定了盐水摩尔比分别为1:30和1:14的Rb2SO4和Cs2SO4的水溶液结构. 通过对散射数据的处理, 获得了两种溶液的径向分布函数. 采用多峰拟合中的Gaussian法对径向分布函数中金属离子第一水合层附近的叠加峰进行了处理, 多峰拟合结果与实验结果吻合得很好. 通过将拟合数据与已报道的溶液结构和晶体结构对比分析, 确定了每个拟合峰的归属.多峰拟合结果分析表明, Rb+和Cs+第一水合层配位数为6, 为变形的八面体构型. 两种溶液中都存在着金属离子和硫酸根离子接触离子对: Rb—S 和Cs—S 的特征距离分别为0.407和0.427 nm. 研究证实, 多峰拟合有助于阐述溶液中离子的水合结构.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.     

The effects of charge transfer on the aqueous solvation of ions

Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and -0.775 for Na(+), K(+), and Cl(-), respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.     

纳米受限下溶质水化结构的分子模拟

利用分子动力学模拟研究了五种不同种类的溶质分子(K+, Mg2+, Cl-, K-和K0)在直径为0.60-1.28 nm的纳米碳管内的水化结构. 模拟结果揭示了单电荷溶质、双电荷溶质和中性溶质在受限条件下具有不同的水化行为. 单价溶质的配位数只有在直径不大于0.73 nm的纳米碳管内才会明显减少. 和带有电荷的溶质不同, 中性溶质的配位数对纳米碳管直径的改变非常敏感, 并且随着管径的减小而迅速减少. 模拟结果还表明带单价正电荷的溶质(K+)第一配位层水分子的取向结构会随着纳米碳管直径的改变发生变化, 而其他溶质配位层取向结构在本文所涉及的纳米碳管内都几乎和体相中一致. 在直径大于1.0 nm的纳米碳管中, K+的配位层取向结构有序度随着管径的减小而单调下降, 但是在直径小于1.0 nm的纳米碳管中, 随着碳管管径的减小而迅速上升. 在两个最窄的纳米碳管内, 其结构有度甚至高于体相. 双电荷溶质的水化结构在本文所研究的碳管直径范围内和体相完全一致, 即使在直径只有0.6 nm的碳管内也无任何改变.