Simulations of stochastic sensing of proteins

We have performed Langevin dynamics and Poisson-Nernst-Planck calculations to simulate detection of proteins by genetically engineered alpha-hemolysin channels. In the recent stochastic sensing experiments, one end of a flexible polymer chain is permanently anchored inside the protein channel at a specified location, and the other end undergoes complexation with an analyte. Our simulations, using coarse-grained modeling, reproduce all essential qualitative results of the electrophysiology measurements of stochastic sensing. In addition, the underlying macromolecular mechanisms behind stochastic sensing are revealed in vivid details. The entropic fluctuations of the conformations of the tethered polymer chain dictate crucially the unique signatures of the ionic current trace of the channel and provide design rules for successful stochastic sensing. The origin of strong fluctuations in the ionic current of the channel is found to arise from the obstruction of the entrance at the beta-barrel of the channel by the fluctuating segments of the tether. Silencing of the pore is due to the suppression of conformational fluctuations of the chain, and the permanent blockade of ionic current is due to the threading of the tether through the channel. The onset of silencing and permanent blockade of the channel current cannot necessarily be attributed to the capture of analytes. In order for detection events to be timed accurately, the length and anchoring location of the tether must be tuned appropriately.     

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.     

DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model

We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 μm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 μm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.     

Temperature dependence of the electrical conductivity of imidazolium ionic liquids

The electrical conductivities of 1-alkyl-3-methylimidazolium tetrafluoroborate ionic liquids and of 1-hexyl-3-methylimidazolium ionic liquids with different anions were determined in the temperature range between 123 and 393 K on the basis of dielectric measurements in the frequency range from 1 to 10(7) Hz. Most of the ionic liquids form a glass and the conductivity values obey the Vogel-Fulcher-Tammann equation. The glass transition temperatures are increasing with increasing length of the alkyl chain. The fragility is weakly dependent on the alkyl chain length but is highly sensitive to the structure of the anion.     

表面活性离子液体参与构筑的胶束体系

离子液体(ILs)的可设计性,使得新型表面活性离子液体(SAILs)不断涌现,从而将具有不同功能基团的ILs引入到了传统的有序分子聚集体中,这也将有助于实现有序分子聚集体的可控性和功能化。本文综述了SAILs在水溶液及离子液体中的胶束化行为,重点总结了烷基碳链长度、阴离子类型和阳离子结构对SAILs聚集行为的影响,分类归纳了SAILs与传统表面活性剂复配体系的协同增效作用,并探讨了SAILs构建的胶束体系的发展方向。     

Spatial correlations of a flexible-chain oligomer in an ionic liquid

The effect of the length of the cationic tail of an ionic liquid on the dependence of the scale of structural heterogeneities of a flexible-chain oligomer dissolved in the liquid on the oligomer concentration is studied in terms of the integral equation theory. The structure of the ionic-liquid-oligomer mixture is analyzed with the use of the calculated partial structure factors. The effect of the alkyl chain length of the cation on the dependence of the characteristic scale of ordering of the oligomer chains on their concentration in the solution is the most significant for an ionic liquid with medium-length and long cationic tails. It is shown that the behavior of this dependence is affected by the type of ordering of the ionic-liquid ions. For comparison, a similar dependence for an oligomer in a molecular solvent is calculated and analyzed.     

A systematic molecular simulation study of ionic liquid surfaces using intrinsic analysis methods

In this paper, we apply novel intrinsic analysis methods, coupled with bivariate orientation analysis, to obtain a detailed picture of the molecular-level structure of ionic liquid surfaces. We observe pronounced layering at the interface, alternating non-polar with ionic regions. The outermost regions of the surface are populated by alkyl chains, which are followed by a dense and tightly packed layer formed of oppositely charged ionic moieties. We then systematically change the cation chain length, the anion size, the temperature and the molecular model, to examine the effect of each of these parameters on the interfacial structure. Increasing the cation chain length promotes orientations in which the chain is pointing into the vapor, thus increasing the coverage of the surface with alkyl groups. Larger anions promote a disruption of the dense ionic layer, increasing the orientational freedom of cations and increasing the amount of free space. The temperature had a relatively small effect on the surface structure, while the effect of the choice of molecular model was clearly significant, particularly on the orientational preferences at the interface. Our study demonstrates the usefulness of molecular simulation methods in the design of ionic liquids to suit particular applications.     

A polymer in an ionic liquid: Effect of the length of the cationic nonpolar tail on the character of interchain correlations

On the basis of the integral equation theory, we examine spatial correlations of flexible polymer chains dissolved in an ionic liquid. The effect of the concentration of a polymer on its structural properties is studied for different lengths of the nonpolar tail of the solvent cation. The structure of a polymer-containing ionic liquid is analyzed in the reciprocal space on the basis of calculated partial structure factors. In a wide range of polymer concentrations, for all the selected values of length of the cationic nonpolar tail, long-range liquid ordering and intermediate-range liquid ordering of polymer chains are observed. The dependences of the characteristic scale of ordering of macromolecules on their number density in solution are different for ionic liquids with different lengths of the cationic nonpolar tail.     

二茂铁在几种离子液体中的迁移行为

采用循环伏安法研究了二茂铁(Fc)在几种离子液体中的迁移行为. 计算了Fc在各离子液体中的扩散系数和粘度系数,探讨了离子液体粘度与离子液体结构之间的关系. 实验结果表明, 离子液体的粘度随阳离子取代基碳链长度的增加而增加, 随阴离子对称性的增加而增加.     

Single walled carbon nanotube length determination by asymmetrical-flow field-flow fractionation hyphenated to multi-angle laser-light scattering

Asymmetrical flow field-flow fractionation (AFlFFF) hyphenated to multi-angle laser-light scattering (MALS) was evaluated in order to determine single walled carbon nanotube (SWCNT) length distribution. Fractionation conditions were investigated by examining mobile phase ionic strength and pH, channel components and cross-flow rate. Ammonium nitrate-based mobile phase with 10(-5)molL(-1) ionic strength and pH 6 allows the highest sample recovery (89±3%) to be obtained and the lowest loss of the longest SWCNT. A cross-flow rate of 0.9mLmin(-1) leads to avoid any significant membrane-sample interaction. Length was evaluated from gyration radius measured by MALS by comparing SWCNT to prolate ellipsoid. In order to validate the fractionation and the length determination obtained by AFlFFF-MALS, different SWCNT aliquots were collected after fractionation and measured by dynamic light scattering (DLS). AFlFFF is confirmed to operate in normal mode over 100-2000nm length. MALS length determination after fractionation is found to be accurate with 5% RSD. Additionally, a shape analysis was performed by combining gyration and hydrodynamic radii.     

Molecular dynamics simulation of polymer electrolytes based on poly(ethylene oxide) and ionic liquids. I. Structural properties

Molecular dynamics (MD) simulations have been performed for prototype models of polymer electrolytes in which the salt is an ionic liquid based on 1-alkyl-3-methylimidazolium cations and the polymer is poly(ethylene oxide), PEO. The MD simulations were performed by combining the previously proposed models for pure ionic liquids and polymer electrolytes containing simple inorganic ions. A systematic investigation of ionic liquid concentration, temperature, and the 1-alkyl- chain length, [1,3-dimethylimidazolium]PF6, and [1-butyl-3-methylimidazolium]PF6, effects on resulting equilibrium structure is provided. It is shown that the ionic liquid is dispersed in the polymeric matrix, but ionic pairs remain in the polymer electrolyte. Imidazolium cations are coordinated by both the anions and the oxygen atoms of PEO chains. Probability density maps of occurrences of nearest neighbors around imidazolium cations give a detailed physical picture of the environment experienced by cations. Conformational changes on PEO chains upon addition of the ionic liquid are identified. The equilibrium structure of simulated systems is also analyzed in reciprocal space by using the static structure factor, S(k). Calculated S(k) display a low wave-vector peak, indicating that spatial correlation in an extended-range order prevail in the ionic liquid polymer electrolytes. Long-range correlations are assigned to nonuniform distribution of ionic species within the simulation box.     

离子液体溶胀对煤直接液化残渣结构及热解性能的影响

采用四种相同阴离子不同有机链长阳离子的离子液体([EMIM][MeSO_4]、[BMIM][MeSO_4]、[HMIM][MeSO_4]和[OMIM][MeSO_4])对煤直接液化残渣(DCLR)进行溶胀处理,通过SEM、FT-IR和TG-DTG表征,分析了各离子液体溶胀对煤直接液化残渣溶胀效果、表面形貌、官能团分布、主体结构和热解性能的影响。溶胀结果表明,不同链长离子液体对煤直接液化残渣具有不同的溶胀效果,[HMIM][MeSO_4]对残渣溶胀效果最好,其溶胀度高达1.78。FT-IR表明,不同链长离子液体会不同程度地破坏煤中C-H键,使得脂肪族和芳香族类化合物的相对含量有所差异。由TG-DTG可知,不同链长离子液体溶胀对残渣热解性能的影响具有较大差异,其中,以离子液体[OMIM][MeSO_4]溶胀对残渣的热解最为有利,失重率高达47.5%;而离子液体[BMIM][MeSO_4]溶胀在一定程度上抑制了残渣的热解,其失重率低于未经溶胀处理的残渣。基于Coats-Redfern法的热解动力学分析表明,煤直接液化残渣及其溶胀残渣在低温段(180-480℃)的热解过程均符合二级反应动力学,高温段(480-825℃)均以三级和四级反应动力学为宜。另外,不同链长离子液体溶胀处理明显改变了残渣的热解活化能,其链越长残渣的热解活化能越高。     

Ionic Liquids: Not only Structurally but also Dynamically Heterogeneous

In recent years, the complex and heterogeneous structure of ionic liquids has been demonstrated; however, the consequences on the dynamics have remained elusive. Here, we use femtosecond IR spectroscopy to elucidate the local structural dynamics in protic alkylammonium‐based ionic liquids. The structural relaxation after an ultrafast temperature increase, following vibrational excitation and subsequent relaxation of the N‐D (or N‐H) stretching vibration, is found to vary substantially between the ionic and hydrophobic subdomains. The dynamics in the ionic domains are virtually unaffected by the alkyl chain length and is, therefore, decoupled from viscosity. Equilibration within the hydrophobic subdomains, as evident from the dynamics of the C‐H stretching vibration, is faster than that in the ionic domains and shows a remarkably low thermal activation.     

Ionic conductivities of the complexes of LiClO4 and alternating copolymers of oligomeric poly(ethylene oxide) having biphenyl units in the backbone

A series of copolymers of predominantly poly(ethylene oxide) (PEO) with biphenyl (BP) units in the backbone were synthesized. The solid polymer electrolytes (SPEs) were prepared from these copolymers (BP-PEG) employing lithium perchlolate (LiClO₄) as a lithium salt and their ionic conductivities were investigated to exploit the structure–ionic conductivity relationships as a function of chain length ratio between the flexible PEO chains and rigid BP units. The ionic conductivity increases with increasing PEO length in BP-PEG. The salt concentrations in BP-PEG/LiClO₄ complexes were also changed and the results show that maximum conductivity is obtained at [EO]/[Li⁺]≈8. The reasons for these findings are discussed in terms of the number of charge carriers and the mobility of the polymer chain.     

Local structure of ionic liquid–monohydric alcohol solutions

The method of molecular dynamics is used to investigate the effect of monohydric alcohols on the formation of the local structure of ionic liquids based on the dimethylimidazolium cation at T = 400 K. The intermolecular interaction energies are analyzed to find that the increase in the length of the alkyl chain in the alcohol molecule reduces the influence of the solute molecule on the formation of the local structure of the dmim⁺/Cl^––solute molecule systems. An analysis of the radial distribution function shows that the change in the structure and physical characteristics of the solute molecule does not affect the interaction between the hydroxyl group proton of the alcohol molecule and the ionic liquid anions, whose interactions form the hydrogen bond H^alcohol…Cl^– with a length of 2.3 Å.     

两亲性嵌段共聚物的合成及其在离子液体中的自组装行为

采用阴离子开环聚合法合成了两亲性嵌段共聚物PLA-PEG-PLA.用FT-IR,1H NMR和GPC等手段对嵌段共聚物的结构组成进行了表征.两亲性嵌段共聚物在离子液体1-丁基-3-甲基咪唑六氟磷酸盐中能自组装成胶束,用透射电子显微镜观察了聚合物在离子液体中形成胶束的纳米结构.当疏水链长固定时,胶束的自组装形状主要依赖于亲水链的长度.两亲性共聚物在离子液体中可自组装成可控制结构的纳米胶束,这种纳米结构胶束在很多领域具有广泛的应用前景.     

离子液体表面活性剂在水溶液中的自组装及其调控研究进展

离子液体表面活性剂在化学合成、材料制备和环境污染控制等方面的应用与它们在水溶液中的自组装及其微观结构密切相关。因此,研究离子液体表面活性剂在水溶液中的自组装行为具有重要的意义。本文重点综述了阳离子的结构、阴离子的类型、外加电解质、有机添加剂、环境因素(温度、溶液pH值和光)等对离子液体表面活性剂在水中的自组装行为以及对组装体结构影响的研究进展,总结了这些因素对离子液体表面活性剂在水中自组装的调控规律,展望了该领域的发展方向及面临的挑战。     

Electrokinetics in nanochannels: part I. Electric double layer overlap and channel-to-well equilibrium

In this paper a new model is described for calculating the electric potential field in a long, thin nanochannel with overlapped electric double layers. Electrolyte concentration in the nanochannel is predicted self-consistently via equilibrium between ionic solution in the wells and within the nanochannel. Differently than published models that require detailed iterative numerical solutions of coupled differential equations, the framework presented here is self-consistent and predictions are obtained solving a simple one-dimensional integral. The derivation clearly shows that the electric potential field depends on three new parameters: the ratio of ion density in the channel to ion density in the wells; the ratio of free-charge density to bulk ion density within the channel; and a modified Debye-Hückel thickness, which is the relevant scale for shielding of surface net charge. For completeness, three wall-surface boundary conditions are analyzed: specified zeta-potential; specified surface net charge density; and charge regulation. Predictions of experimentally observable quantities based on the model proposed here, such as depth-averaged electroosmotic flow and net ionic current, are significantly different than results from previous overlapped electric double layer models. In this first paper of a series of two, predictions are presented where channel depth is varied at constant well concentration. Results show that under conditions of electric double layer overlap, electroosmosis contributes only a small fraction of the net ionic current, and that most of the measurable current is due to ionic conduction in conditions of increased counterion density in the nanochannel. In the second of this two-paper series, predictions are presented where well-concentration is varied and the channel depth is held constant, and the model described here is employed to study the dependence of ion mobility on ionic strength, and compare predictions to measurements of ionic current as a function of channel depth and ion density.     

Control of phase behavior and properties of vesicle gels by admixing ionic surfactants to the nonionic surfactant Brij 30

The effect of the addition of two cationic surfactants of different chain length (decyl and dodecyl trimethylammonium bromide, DeTMABr and DTMABr, respectively) and one anionic surfactant of identical chain length (sodium dodecyl sulfate, SDS) on phase behavior, structure, and macroscopic properties of a bilayer forming nonionic surfactant (Brij 30) has been investigated by means of phase studies, rheology, turbidity measurements, dynamic light scattering, and freeze-fracture transmission electron microscopy. We concentrated on DTMABr because of the generically similar behavior for the other ionic surfactants. It is found that already very small amounts of added ionic surfactant have a very pronounced effect on the phase behavior of these systems. The pure nonionic surfactant forms bilayers and has a tendency for the formation of vesicles which becomes enhanced by charging the bilayer through the incorporation of the ionic surfactant. The presence of the ionic surfactant leads to much more viscous systems, which already at a total surfactant concentration of 150 mM become gel-like. For a given surfactant concentration, the elastic properties of the gels increase largely upon the addition of ionic surfactant. This effect is strongly synergistic, requiring only very small amounts of added ionic surfactant, and the elastic properties pass through a maximum for a content of ionic surfactant of about 3-5 mol %. This behavior can be explained in a self-consistent way by a simple rheological model and by combining it with light scattering data. For the addition of larger amounts, the elastic properties decrease again and the formed vesicles become structurally less defined as one is leaving the range of conditions for forming well-defined vesicles, which are required for forming elastic vesicle gels.     

Modeling of electrokinetic transport in silica nanofluidic channels

We present a theoretical and numerical modeling study of the multiphysicochemical process in electrokinetic transport in silica nanochannels. The electrochemical boundary condition is solved by considering both the chemical equilibrium on solid-liquid interfaces and the salt concentration enrichment caused by the double layer interaction. The transport behavior is modeled numerically by solving the governing equations using the lattice Poisson-Boltzmann method. The framework is validated by good agreements with the experimental data for all range of ionic concentrations. The modeling results suggest that when the double layers interact, the bulk salt concentration enrichment results in the saturation of conductances for low ionic concentrations. Both the streaming conductance and the electrical conductance are enhanced by the double layer interaction, and such enhancements diminish when the channel size is larger than 10 times of the Debye length. The streaming conductance increases with pH almost linearly when pH < 8, while the electrical conductance increases with pH exponentially.