Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Molecular dynamics study of surfactant monolayers adsorbed at the oil/water and air/water interfaces

Atomistic molecular dynamics (MD) simulations have been carried out to investigate the physical properties of monolayers of monododecyl diethylene glycol (C(12)E(2)) surfactants adsorbed at the oil/water and air/water interfaces. The study shows that the surfactant molecules exhibit more extended conformations with a consequent increase of the thickness of the monolayer in the presence of the oil medium. It is noticed that the hydrocarbon tails of the surfactants are more vertically oriented at the oil/water interface. Interestingly, we notice that the presence of the oil medium has a strong influence in restricting both the translational and reorientational motions of the water molecules present in the hydration layer close to the surfactant headgroups.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

Solvation of xyloglucan in water/alcohol systems by molecular dynamics simulation

Xyloglucan in water solution turns into a gel with addition of alcohol such as methanol and ethanol. In regard to this phenomenon, we investigated the adhesive property of alcohol to xyloglucan and proposed the mechanism of the gelation by molecular dynamics (MD) simulation of a xyloglucan in water, water/methanol, and water/ethanol solution for 10 ns. The alcohol molecules showed its adhesive property to the xyloglucan and made the swelling-shrinking motion of the xyloglucan slow. Alcohol molecules solvated to the xyloglucan mainly in hydrophobic way so as to fill the void of water hydration shell, resulting in reformation of the hydrogen-bond network of water molecules around the solute. We also found that alcohol molecules have strong tendency to hydrogen-bond on xylose O3 in xyloglucan. According to these results, we proposed the gelation mechanism of xyloglucan in water/alcohol solution.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

Molecular dynamics studies on octadecylammonium chloride at the air/liquid interface

Molecular dynamics simulations on surfactant octadecylammonium chloride at the air/liquid interface were performed. It was found that the alkyl chains of octadecylammonium would change to order with increasing the concentration of octadecylammonium at the air/liquid interface. Some functions, such as the concentration distributions, the radial distribution function and the mean squared displacement (MSD) were evaluated to investigate the structural properties of interface. We found that the salts can affect octadecylammonium aggregate at the interface: (1) univalent ions, such as chloride and sodium ions, affect slightly the structure of monolayer and (2) bivalent ions, such as sulfate or calcium ions, affect greatly, especially for the bivalent negative ions.     

The phenomenon of water penetration into sodium octanoate micelles studied by molecular dynamics computer simulation

 In this publication we have studied the penetration process of water molecules into the hydrophobic core of a sodium octanoate micelle. The analysis of this phenomenon was based on a molecular dynamics computer simulation. We calculated the probability to find water molecules within a specific sphere which was adjusted in the center of the micelle. It turned out that the position of the micellar mass and geometry center was not too different, so that this reference point was well characterized. Water penetration was observed within the whole aggregate but if the radius is smaller than 300 pm, polar solvent molecules are very rarely observed. The results of our computer simulations suggest that significant water diffusion into the micelle occurs at larger distances from the micellar center with a lower threshold value of about 400 pm. In addition to these calculations, we used the Connolly algorithm in order to determine the solvent accessible surfaces of different micellar equilibrium structures. We observed large dynamical fluctuations with the formation of pores and channels. These structures are occasionally filled with water molecules. Received: 29 April 1998 Accepted: 27 May 1998     

Molecular dynamics simulation of the aggregation of colloidal particles

The spontaneous time evolution of systems containing N colloidal particles (N = 12, 24, 100) in a spherical cell of volume V at a constant volume fraction φ=0.1 was studied by a molecular dynamics method in the NVT ensemble. The starting velocities of the particles are allocated according to the Maxwell distribution at T=273 K.

Pairwise interaction of the particles was specified by molecular, electrostatic and elastic forces. The changes in the potential energy of the systems were calculated during the establishment of dynamic equilibrium. Coagulation takes place at sufficiently high values of the Hamaker constant. The value of the coefficient of Brownian diffusion, which is calculated from the half-time of coagulation, is found to be close to the known value for aqueous dispersions. The inclusion of electrostatic forces prevents coagulation.

The results obtained are in agreement with those obtained using theories of aggregate formation. Some structural characteristics of aggregates and stable systems are discussed.     

Phase behavior of amphiphiles at liquid crystals/water interface: A coarse-grained molecular dynamics study

We present a coarse-grained molecular dynamics simulation study of phase behavior of amphiphilic monolayers at the liquid crystal （LC）/water interface. The results revealed that LCs at interface can influence the lateral ordering of amphiphiles. Particularly, the amphiphile tails along with perpendicularly penetrated LCs between tails undergo a two-dimension phase transition from liquid-expanded into a liquid-condensed phase as their area density at interface reaches 0.93. While, the liquid-condensed phase of the monolayer never appears at oil/water interface with isotropic shape oil particles. These findings reveal the penetration of anisotropic LC can promote ordered lateral organization of amphiphiles. Moreover, we find the phase transition point is shifted to lower surface coverage of amphiphiles when the LCs have larger affinity to the amphiphile tails.     

Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation

The present study investigates the variation of static contact angle of a water droplet in equilibrium with a solid surface in the absence of a body force and the dynamic contact angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation. With increasing characteristic energy, the static contact angle in equilibrium with a solid surface in the absence of a body force decreases because the hydrophobic surface changes its characteristics to the hydrophilic surface. In order to consider the effect of moving water droplet on the dynamic contact angles, we apply the constant acceleration to an individual oxygen and hydrogen atom. In the presence of a body force, the water droplet changes its shape with larger advancing contact angle than the receding angle. The dynamic contact angles are compared with the static contact angle in order to see the effect of the presence of a body force.     

Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution

Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared deviations from experimental structures and now provide believable structural insight into a variety of processes such as the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald methods are becoming the de facto standard. Received: 9 April 1998 / Accepted: 21 May 1998 / Published online: 13 August 1998     

A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex：Exploring the closing mechanism of the substrate pocket

To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.     

Molecular dynamics simulation of four typical surfactants at oil/water interface

In the present study, we have performed molecular dynamics simulations to describe the microscopic behaviors of the anionic, nonionic, zwitterion, and gemini surfactants at oil/water interface. The abilities of reducing the interfacial tension and forming the stable interfacial film of the four surfactants have been investigated through evaluating interfacial thickness, interface formation energy and radial distribution function. The results show that the four kinds of surfactants can form in stable oil/water interface of monolayer, and the gemini surfactant can form the more stable monolayer. The results of the above three parameters demonstrate that the gemini surfactant has the best simulation effect in the four surfactants. From the calculated interfacial tension values, the gemini surfactant possess the more powerful ability of reducing the interfacial tension than others, so it is more suitable to be used as the surfactant for flooding. In addition, the effects of different electric field intensities on surfactants were calculated, through the radial distribution function of the hydrophilic group in the surfactant and the oxygen atom in the water. We have found that the adding of the periodic electric field can significantly affect the diffusion behavior of the molecules, and nonionic surfactant has stronger demulsification capability than others.     

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Molecular theory on dielectric constant at interfaces: a molecular dynamics study of the water/vapor interface

Though the local dielectric constant at interfaces is an important phenomenological parameter in the analysis of surface spectroscopy, its microscopic definition has been uncertain. Here, we present a full molecular theory on the local field at interfaces with the help of molecular dynamics simulation, and thereby provide microscopic basis for the local dielectric constant so as to be consistent to the phenomenological three-layer model of interface systems. To demonstrate its performance, we applied the theory to the water/vapor interface, and obtained the local field properties near the interface where the simple dielectric model breaks down. Some computational issues pertinent to Ewald calculations of the dielectric properties are also discussed.     

Tetracyclines adsorption onto alumina: A comparative experimental and molecular dynamics simulation study

Using alumina (Al₂O₃) as the adsorbent, a static adsorption experiment was carried out in this study. It comprehensively evaluated the factors including Al₂O₃ dosage, adsorption temperature, and pH that influence the adsorption capability of three tetracyclines (TCs), namely, tetracycline hydrochloride (TC), chlortetracycline hydrochloride (CTC) and oxytetracycline hydrochloride (OTC). The results demonstrate that the adsorption efficiency increases with Al₂O₃ dosage. In addition, low-acid or natural solution is benefit for the adsorption. The adsorption behavior is more reasonably described with the Freundlich isotherm, and fits well with the pseudo-second-order kinetic model (R²?>?0.999). The results of molecular dynamics (MD) simulation show that the structures of TCs deformed during the combining process. The values of binding energy of TCs follow the order as: CTC (88.45?kcal/mol)?>?OTC (73.54?kcal/mol)?>?TC (54.28?kcal/mol). The MD simulation results agree well with the adsorption experimental results, which indicates that the MD simulation is reliable and reasonable. The MD simulation will provide theoretical knowledge in understanding the adsorption mechanism and environmental behavior of TCs.     

Interfacial rheology of natural silk fibroin at air/water and oil/water interfaces

The interfacial viscoelastic behavior of natural silk fibroin at both the air/water and oil/water interfaces is reported. This natural multiblock copolymer is found to be strongly amphiphilic and forms stable films at these interfaces. The result is an interfacial layer that is rheologically complex with strong surface elastic moduli that are only slightly frequency-dependent. The kinetics of surface viscoelastic evolution are reported as functions of time for various concentrations of the spread films. Films deposited by Langmuir-Blodgett deposition were studied by scanning electron microscopy (SEM) to reveal a fibrous structure at the interface. The production of stable O/W emulsions by silk fibroin further confirms the generation of the elastic films at the oil/water interfaces.