Methylene Blue Adsorption on a DMPA Lipid Langmuir Monolayer

Adsorption of methylene blue (MB) onto a dimyristoylphosphatidic acid (DMPA) Langmuir air/water monolayer is studied by molecular dynamics (MD) simulations, UV reflection spectroscopy and surface potential measurements. The free‐energy profile associated with MB transfer from water to the lipid monolayer shows two minima of ?66 and ?60 kJ mol^?1 for its solid and gas phase, respectively, corresponding to a spontaneous thermodynamic process. From the position of the free‐energy minima, it is possible to predict the precise location of MB in the interior of the DMPA monolayer. Thus, MB is accommodated in the phosphoryl or carbonyl region of the DMPA Langmuir air/water interface, depending on the isomorphic state (solid or gas phase, respectively). Reorientation of MB, measured from the bulk solution to the interior of the lipid monolayer, passes from a random orientation in bulk solution to an orientation parallel to the surface of the lipid monolayer when MB is absorbed.     

Determining the Local Shear Viscosity of a Lipid Bilayer System by Reverse Non‐Equilibrium Molecular Dynamics Simulations

The parallel shear viscosity of a dipalmitoylphosphatidylcholine (DPPC) bilayer system is studied by reverse non‐equilibrium molecular dynamics simulations (RNEMD) with two different united‐atom force fields. The results are related to diffusion coefficients and structural distributions obtained by equilibrium molecular simulations. We investigate technical issues of the algorithm in the bilayer setup, namely, the dependence of the velocity profiles on the imposed flux and the influence of the thermostat on the calculated shear viscosity. We introduce the concept of local shear viscosity and investigate its dependence on the slip velocity of the monolayers and the particle density at the headgroup–water interface and the tail–tail interface. With this we demonstrate that the lipid bilayer is more viscous than the surrounding water phase, and that slip takes place near the headgroup region and in the centre of the bilayer where the alkyl tails meet. We also quantify the apparent increase in viscosity of the water molecules entangled at the water–headgroup interface.     

Investigation of Thermal Expansion of Polyimide/SiO2 Nanocomposites by Molecular Dynamics Simulations

In this paper, an atomistic model for PI/SiO₂ hybrid nanocomposites was designed for the investigation of physical properties of this material on the base of molecular dynamics simulations. The thermal properties of a reference pure PI matrix in the temperature range of 300–650 K were first investigated. The results for the CTE and the glass transition temperature showed good agreement with the experimental data. Then, the thermal expansion of the model of PI/silica composite material with different SiO₂ fractions was investigated at normal conditions. The CTE of the composite model decreases with the increase in the SiO₂ content in agreement with experimental studies. The results show a threshold for the SiO₂ loading beyond which the material model exhibits ultra‐low thermal expansion.

     

Molecular Dynamics Simulation of Mg2+ and Ca2+ Ions in Water

Molecular dynamics simulations of single Mg²⁺ and Ca²⁺ ions in water have been carried out. Different ion-water potentials from the literature have been used, whereas the same water potential, a rigid simple point charged model, has been considered in all the simulations. Structural, thermodynamic, and dynamic properties have been calculated, and the results for different potentials have been compared with available experimental data. The study includes ion–water radial distribution functions, coordination numbers, solution enthalpies, hydration free energies, self-diffusion coefficients, and reorientational times of water molecules in the hydration shells.     

离子通过碳纳米管的拉伸分子动力学模拟

采用拉伸分子动力学模拟研究了Na⁺, K⁺和Cl^－通过(6,6), (7,7), (8,8), (9,9)和(10,10)碳纳米管的过程, 利用伞形取样法计算了离子通过碳管的平均力势能, 并对离子在管中和本体相中的水化作了比较. 结果表明, 离子通过管径较窄的碳管时, 在入口处遇到较大的阻力, 从出口进入本体相较容易|而通过管径相对较宽的碳管则几乎无阻碍. 离子通过碳管的能垒随管径的增大而降低, 不同离子的能垒各不相同, 表明碳管具有固有的离子选择性|离子通过碳管时, 不仅其配位数改变了, 而且配位层中水分子的取向也有所改变, 这两者共同决定了离子进入碳管时的去水化能, 进而影响离子通过碳管的能垒和碳管的离子选择性. 本工作将有助于理解离子通道蛋白中疏水区域的功能作用, 并可以为基于碳纳米管的纳流控系统的设计提供指导.     

Tetrathiophene on Graphite: Molecular Dynamics Simulations

Summary: We describe molecular dynamics simulations of α‐tetrathiophene molecules deposited on a flat graphite substrate, at two different temperatures (300 K and 400 K) and several degrees of coverage (from approximately one to three molecular layers). The simulations employ a modified version of the CFF91 force field, with the torsion parameters tailored on high‐level ab initio calculations on 2,2′‐bithiophene. We found that the molecules in the first layer were relatively planar and packed against the underlying surface, while those outside it were not arranged in well‐defined layers and were more conformationally disordered. On the time scale of the simulation, the molecules did not crystallize but rather achieved a liquid crystalline‐like state with their average director parallel to the surface.

Side view of the final configuration in the simulation of 24 tetrathiophenes at 300 K. Molecules are depicted with different shades of gray according to their z coordinate (first, second or third layer).     

Atomistic Simulations of Dopamine Diffusion Dynamics on a Pristine Graphene Surface**

Carbon microelectrodes enable in vivo detection of neurotransmitters, and new electrodes aim to optimize the carbon surface. However, atomistic detail on the diffusion and orientation of neurotransmitters near these surfaces is lacking. Here, we employ molecular dynamics simulations to investigate the surface diffusion of dopamine (DA), its oxidation product dopamine-o-quinone (DOQ), and their protonated forms on the pristine basal plane of flat graphene. We find that all DA species rapidly adsorb to the surface and remain adsorbed, even without a holding potential or graphene surface defects. We also find that the diffusivities of the adsorbed and the fully solvated DA are similar and that the protonated species diffuse more slowly on the surface than their corresponding neutral forms, while the oxidized species diffuse more rapidly. Structurally, we find that the underlying graphene lattice has little influence over the molecular adsorbate's lateral position, and the vertical placement of the amine group on dopamine is highly dependent upon its charge. Finally, we find that solvation has a large effect on surface diffusivities. These first results from molecular dynamics simulations of dopamine at the aqueous-graphene interface show that dopamine diffuses rapidly on the surface, even without an applied potential, and provide a basis for future simulations of neurotransmitter structure and dynamics on advanced carbon materials electrodes.     

Representation of Hydrogen Atoms in Molecular Dynamics Simulations: The Influence on the Computed Properties of Thin Polystyrene Films

The united atoms (UA) and dummy hydrogen atom (DHA) approaches for molecular dynamics simulations of the interface between oxidized atactic polystyrene (aPS) thin films and water are compared. For both oxidized and non‐oxidized aPS films the polymer density profile decays steepest when using the UA model. The surface roughness of the aPS film and the ordering of the phenyl rings near the surface decrease upon changing from vacuum to water for the UA, but not for the DHA model. This also supports the fact that the non‐oxidized aPS films modeled in DHA representation become less hydrophobic. The water structure close to the interface also suggests that the aPS films modeled using UA are more hydrophobic compared to the aPS films modeled with DHA in the phenyl rings.

     

Switching Ca2+/Ba2+ to Ba2+/Ca2+ Potentiometric Selectivities of Podands with Phosphoryl-containing Terminal Groups: A Molecular Modelling Study

It has been shown experimentally that theCa²⁺/Ba²⁺ potentiometric selectivity ofphosphoryl-containing podandR–-O–-(CH₂–-CH₂–-O)_nndash;-R,R = –-C₆H₄–-P(O)Ph₂, n = 3 (I),switches to Ba²⁺/Ca²⁺ when the ligand containsthe longer polyether chain, n = 5 (II). Here, we reportmolecular dynamics and free energy perturbation simulationsperformed using the amber 4.1 program on the complexesL ^.M²⁺ (M²⁺ = Ca²⁺, Sr²⁺ andBa²⁺, L = I and II) in the gas phase inorder to gain a microscopic insight into structural and energy bindingproperties of podands as a function of n. Mixed QM/MM (PM3/ amber) calculations were performed toanalyse the role of polarisation effects on the complexation selectivityof podands. It isshown that an increase of n does not affect the interactions ofM²⁺ with phosphine oxide groups,but leads to less efficient interactions of small cations with the polyether chain. Calculatedpotentiometric selectivities of I (Ca²⁺ > Ba²⁺)and II (Ba²⁺ > Ca²⁺) are in agreement with the experimental data.     

First and Second Hydration Shell of Ni2+ Studied by Molecular Dynamics Simulations

Molecular dynamics simulations of a Ni²⁺ ion in water have been carried out to investigate the structure and dynamics of water molecules around the nickel, extending the analysis to the second hydration shell. The structural parameters as well as the motions of water molecules in various sub-structures of the solution have been evaluated giving a detailed picture of the motional modes of water molecules     

Effect of Na+, Mg2+, and Zn2+ chlorides on the structural and thermodynamic properties of water/n-heptane interfaces

The effect on the structural and thermodynamic properties in water/n-heptane interfaces on addition of NaCl, MgCl(2), and ZnCl(2) has been examined through five independent 100-ns molecular dynamics simulations. Results indicate that the interfacial thickness within the framework of the capillary-wave model decreases on addition of electrolytes in the order Na(+) < Mg(2+) < Zn(2+), whereas the interfacial tension increases in the same order. Ionic density profiles and self-diffusion coefficients are strongly influenced by the strength of the first hydration shell, which varies in the order Na(+) < Mg(2+) < Zn(2+). On the other hand, the Cl(-) behavior, that is, diffusion and solvation sphere, is influenced by its counterion. Accordingly, cations are strongly expelled from the interface, which is especially remarkable for the small divalent cations. This fact alters the water geometry near the interface and in a lesser extent n-heptane order and number of hydrogen bonds per water molecule close to the interface.     

Characterisation of N‐(Octadecyl)‐1,8‐naphthalimide Monolayer Compression Using Molecular Dynamics and Experimental Approaches

The development of luminescent surfaces is an active area of supramolecular chemistry, particularly for the development of new sensing platforms. One particularly useful surface deposition method is the Langmuir–Blodgett technique where organic amphiphilic fluorophores (e.g. 1,8‐naphthalimides) can form ordered monolayers at an air–water interface before being deposited onto solid supports. The ability to simulate monolayer formation and consequently develop predictability over film formation would allow for significant advances in the luminescent materials field where synthesis might be directed by simulation data. Here, we compare pressure‐area isotherms of N‐(octadecyl)‐1,8‐naphthalimide determined experimentally, using the Langmuir–Blodgett technique, and computationally, using three different simulation techniques. We find that all three simulation techniques are able to describe the liquid‐condensed/liquid‐expanded region of the isotherm, and that the isotherms are highly similar in this region, although the NγT ensemble performs best. Experimental isotherms showed film formation properties that align with the simulation data, suggesting that simulations are a viable means to direct synthesis. Investigation of the underlying structural details disclosed by the simulations reveals the compression‐induced ordering at atomic‐level detail, which will allow prediction of how functionalisation of the naphthalimides will alter the monolayer compression and mounting process.     

Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis

Summary: The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square end‐to‐end distances, glycosidic link torsion correlations, ring puckering and hydrogen bonding. The cellulose oligomer melts were relaxed at 800 K with molecular dynamics, and then cooled down in three different ways to obtain dense amorphous systems at 500 K and at room temperature. The sample resulting from the quench (step) shows too much similarity with the melt at 800 K. The two other cooling schemes (ramp, 2ramps) give very similar results for all quantities investigated. The relevance of previous single molecule calculations with respect to the dense amorphous systems is called into question. Comparisons between the chains in the dense systems and those in the gas phase reveal that, even for these relatively short stiff chains, differences exist in the preferred conformations. At high temperatures, where both systems are in equilibrium, the distribution of square end‐to‐end distances are both fairly smooth, but the gas phase clearly prefers more compact conformations. At 300 K, the differences are exacerbated as the equilibrium distribution for the gas phase shows a high proportion of folded conformers, whereas the nonequilibrium quenched systems necessarily retain the extended envelope of the higher temperature. Differences are also evident in the puckering, the rotation of the hydroxymethyl groups and the pattern of hydrogen bonds.

The probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.     

Effect of gramicidin on phospholipid-modified monolayers and on ion transfer at a liquid-liquid interface.

The interaction of hybrid lipid/gramicidin A (gA) monolayers with dextran sulfate (DS) and the effect of this interaction on ion transfer at a liquid-liquid interface is reported. The interfacial and physicochemical properties are studied with Langmuir-Blodgett (LB) and electrochemical techniques. The results obtained from compression isotherms demonstrate that the interactions between the different species in the hybrid monolayer vary according to the chemical nature of the lipid (hydrocarbon region and charge of the head group). Interfacial capacitance measured with AC voltammetry indicates that the DS chains form a rather flat and compact layer when adsorbed to either zwitterionic or negatively charged phospholipid monolayers, and that calcium, even at low concentrations, interacts with the monolayers. These results are successfully described by a model based on the solution of the Poisson-Boltzmann equation in the interfacial region. Ion transfer and interactions with the lipid/gA/DS-modified monolayers were also studied with electrochemical techniques. Admittance data show that although the studied ions are not using gA channels for the transfer through the lipid membranes, the incorporation of gA in the lipid domain and the adsorption of DS at the interface have a significant effect on ion transfer across the monolayers. This effect can be explained as a consequence of the modified surface charge and of the compactness of the lipid domain due to its interaction with gA and to calcium and DS adsorption at the interface. The ion-transfer rate, therefore, depends on the composition of the monolayer and the chemical nature of the ion.     

An Electrically Driven and Readable Molecular Monolayer Switch Based on a Solid Electrolyte

The potential application of molecular switches as active elements in information storage has been demonstrated through numerous works. Importantly, such switching capabilities have also been reported for self‐assembled monolayers (SAMs). SAMs of electroactive molecules have recently been exploited as electrochemical switches. Typically, the state of these switches could be read out through their optical and/or magnetic response. These output reading processes are difficult to integrate into devices, and furthermore, there is a need to use liquid environments for switching the redox‐active molecular systems. In this work, both of these challenges were overcome by using an ionic gel as the electrolyte medium, which led to an unprecedented solid‐state device based on a single molecular layer. Moreover, electrochemical impedance has been successfully exploited as the output of the system.     

胰岛素六聚体在水溶液中的稳定性研究

用分子动力学（MD）模拟方法设计了两个模拟时间为600ps的对比计算机模拟 实验,研究了R6态的胰岛素六聚体在水溶液中的稳定性以及苯酚和锌离子对结构稳 定性的影响。通过对MD模拟所得到的轨迹的分析发现,在维系胰岛素六聚体稳定性 的因素中,静电相互作用和氢键起着主要的作用。对于包含锌离子和苯酚的体系。 胰岛素六聚体的稳定性得到了增强;对不含锌离子和苯酚的关系,胰岛素六聚体的 稳定性明显减弱,在这种情况下,胰岛素六聚体还表现出解聚的倾向。这些模拟结 果与实验观测结果相吻合。     

Influence of K+, Na+ or Ca2+ Ions on the Interaction Between AmB and Saturated Phospholipids by Langmuir Technique

Interaction between amphotericin B(AmB) and cell membrane is influenced by different metal cations. In the presence of K⁺, Na⁺ or Ca²⁺ ions, the surface pressure-area isotherms and the elastic modulus of an amphotericindipalmitoylphosphatidylcholine(AmB-DPPC) mixed monolayer were discussed. And the excess free energy and entropies of mixing were calculated according to the surface pressure-area isotherms. The phase transition of the mixed monolayer needed a higher concentration of AmB in the sequence Na⁺ > pure buffer > K⁺ > Ca²⁺. When the molar fraction of AmB(x_AmB) was 0.5, the molecular interaction changed from attraction to repulsion and the mixed monolayer turned to ordered state from disorder state under the induction of K⁺ or Ca²⁺ ions at all surface pressure in our experiment. At high surface pressure, the disorder of monolayer enhanced in the presence of Na⁺ ions at x_AmB > 0.1. At different molar ratios of AmB, the influences of these metal cations were discrepant. These cations may influence AmB molecules to form pores on the monolayer. It is helpful to understand the reduction of AmB's toxicity as theoretical reference.     

分子动力学模拟多巴在自组装膜上的黏附性

为了更好地理解贻贝在表面的黏附机理,实现水下胶黏,采用分子动力学方法研究了多巴在自组装膜上的黏附性:采用伞形取样和加权柱状图分析方法计算了多巴在不同自组装膜表面的黏附自由能,使用拉伸分子动力学模拟研究了多巴在不同自组装膜表面上黏附后的脱附力.结果表明,多巴在带负电的羧基自组装膜上的黏附能比在带正电的氨基自组装膜上的大,多巴更容易黏附到带负电表面;多巴在带电表面的黏附能比未带电表面的黏附能更强,表明在带电表面黏附更稳定.进一步分析了多巴在不同表面的取向分布,发现多巴与不同表面相互作用的方式不同:与疏水表面主要通过苯环相互作用;与亲水表面主要通过羟基相互作用;与负电表面主要通过氨基相互作用;与正电表面主要通过羧基相互作用.通过模拟比较了多巴在不同自组装膜上的脱附力,发现多巴在带电表面的脱附力比在未带电表面的大,与黏附能的趋势一致.对比4种非带电表面的脱附力,发现多巴在疏水性甲基自组装膜表面的脱附力最大,黏附更稳定,随着表面疏水性的增加,脱附力增大,黏附稳定性增强.本工作可为研发新型水下胶黏剂提供理论指导.