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.     

Structure and diffusion in amorphous aluminum silicate: a molecular dynamics computer simulation

The amorphous aluminum silicate (Al2O3)2(SiO2) [AS2] is investigated by means of large scale molecular dynamics computer simulations. We consider fully equilibrated melts in the temperature range 6100 K> or =T> or =2300 K as well as glass configurations that were obtained from cooling runs from T=2300 to 300 K with a cooling rate of about 10(12) K/s. Already at temperatures as high as 4000 K, most of the Al and Si atoms are fourfold coordinated by oxygen atoms. Thus, the structure of AS2 is that of a disordered tetrahedral network. The packing of AlO4 tetrahedra is very different from that of SiO4 tetrahedra in that Al is involved with a relatively high probability in small-membered rings and in triclusters in which an O atom is surrounded by four cations. We find as typical configurations two-membered rings with two Al atoms in which the shared O atoms form a tricluster. On larger length scales, the system shows a microphase separation in which the Al-rich network structure percolates through the SiO2 network. The latter structure gives rise to a prepeak in the static structure factor at a wave number q=0.5 A(-1). A comparison of experimental x-ray data with the results from the simulation shows good agreement for the structure function. The diffusion dynamics in AS2 is found to be much faster than in SiO2. We show that the self-diffusion constants for O and Al are very similar and that they are by a factor of 2-3 larger than the one for Si.     

Structure simulation of ultrathin dichloromethane layer on a solid substrate by density functional theory and molecular dynamics simulations

The method for prediction of structural properties of ultrathin liquid layers has been developed on the base of the atomistic molecular dynamics (AMD) and the density functional theory (DFT). A comparative analysis of ultrathin dichloromethane layer density profiles on three types of solid flat substrates showed that these approaches can be effectively used as mutually complementary procedures to describe the structural properties of nanometer scale surface layers. We used AMD calculations to predict the dichloromethane layer density profile on a solid substrate. However, it is difficult and computationally expensive to calculate structural and thermodynamic layers properties. At the same time, DFT can retain the microscopic details of macroscopic systems at the calculative cost significantly lower than that used in AMD. Therefore, in context of DFT, the substrate potential parameters are adjusted to reproduce AMD data. Thus, the obtained potential allows us to compute structural characteristics and, further, can be used to predict other physical properties of ultrathin films within the DFT framework. For instance, we calculated the coefficient of thermal expansion of dichloromethane in the case of three different substrates such as graphite, silicon oxide, and gold.     

Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. a molecular dynamics simulation study

The effect of physiological concentrations of different chlorides on the structure of a dipalmitoyl phosphatidylcholine (DPPC) bilayer has been investigated through atomistic molecular dynamics simulations. These calculations provide support to the concept that Li+, Na+, Ca2+, Mg2+, Sr2+, Ba2+, and Ac3+, but not K+, bind to the lipid-head oxygens. Ion binding exhibits an influence on lipid order, area per lipid, orientation of the lipid head dipole, the charge distribution in the system, and therefore the electrostatic potential across the head-group region of the bilayer. These structural effects are sensitive to the specific characteristics of each cation, i.e., radius, charge, and coordination properties. These results provide evidence aimed at shedding some light into the apparent contradictions among different studies reported recently regarding the ordering effect of ions on zwitterionic phosphatidylcholine lipid bilayers.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

Studies of translational diffusion in the smectic A phase of a Gay-Berne mesogen using molecular dynamics computer simulation

Molecular dynamics computer simulations are used to determine the self-diffusion coefficients for a Gay-Berne model mesogen GB (4.4,20,1,1) in the isotropic, nematic and smectic A phases along two isobars. The values of the parallel and perpendicular diffusion coefficients, D(parallel) and D(perpendicular), are calculated and compared in the different phases. For the phase sequence isotropic-smectic A, D(perpendicular)*> or =D(parallel)* over the whole smectic A range with the ratio D(parallel)*/D(perpendicular)* decreasing with decreasing temperature. At a higher pressure, a nematic phase is observed between these two phases and we find that D(parallel)*>D(perpendicular)* throughout the nematic region and the inequality D(parallel)*>D(perpendicular)* remains on entering the smectic A phase. However, the ratio D(parallel)*/D(perpendicular)* decreases with decreasing temperature within the smectic A range and eventually this ratio inverts such that D(perpendicular)*>D(parallel)* at low temperatures. The temperature dependence of the parallel diffusion coefficient in the smectic A phase for this model mesogen is compared to that predicted by a theoretical model for diffusion subject to a cosine potential.     

Decoupling effects in computer simulation of liquid-state molecular dynamics

Decoupling effects in liquid-state molecular dynamics are unambiguously proven by computer simulations. These can be discribed as the weakening of the dissipative interaction between the system if interest (e.g. molecular angular valocity) and its thermal bath caused by an intense external field of force. The new phenomenon may be used to confirm or challenge the validity of simple models of the liquids state of molecular matter and provide information on the microscopic time scale.     

Structure and dynamics of water at a clay surface from molecular dynamics simulation

We report a molecular dynamics study of the structure and dynamics of water at a clay surface. The negative charge of the surface and the presence of surface oxygen atoms perturbs water over two to three molecular layers, while the nature of the counterions (Na(+)or Cs(+)) has only a small effect. In the first molecular layer, approximately half of the water molecules are H-bonded to the surface. We also analyze the H-bond network between surface water molecules. The diffusion of water molecules along the surface is slowed down compared to the bulk case. As far as the orientational order and dynamics of the water dipole are concerned, only the component normal to the clay surface is perturbed. We investigate the surface H-bond formation and dissociation dynamics and their coupling to the release of molecules from the first molecular layer. We introduce a simple kinetic model in the spirit of Luzar and Chandler [Nature, 1996, 379, 55] to allow for a comparison with bulk water dynamics. This model semi-quantitatively reproduces the molecular simulation results and suggests that H-bond formation is faster with the surface than in the bulk, while H-bond dissociation is slower.     

A molecular dynamics simulation study of C60 fullerenes inside a dimyristoylphosphatidylcholine lipid bilayer

We have carried out atomistic molecular dynamics simulations of C60 fullerenes inside a dimyristoylphosphatidylcholine lipid bilayer and an alkane melt. Simulations reveal that the preferred position of a single C60 fullerene is about 6-7 A off of the center plane, allowing the fullerene to take advantage of strong dispersion interactions with denser regions of the bilayer. Further displacement (>8 A) of the fullerene away from the center plane results in a rapid increase in free energy likely due to distortion of the lipid head group layer. The effective interaction between fullerenes (direct interaction plus environment (bilayer)-induced interaction), measured as the potential of mean force (POMF) between two fullerenes as a function of their separation, was found to be significantly less attractive in the lipid bilayer than in an alkane melt of the same molecular weight as the lipid tails. Only part of this difference can be accounted for by the more favorable interaction of the fullerene with the relatively denser bilayer. Additionally, our POMF studies indicate that the bilayer is less able to accommodate the larger aggregated fullerene pair than isolated single fullerenes, again likely due to distortion of the bilayer structure. The implications of these effects on aggregation of fullerenes within lipid bilayer are considered.     

Modeling and molecular dynamics simulation of the human gonadotropin-releasing hormone receptor in a lipid bilayer

In the present study, a model for the human gonadotropin-releasing hormone receptor embedded in an explicit lipid bilayer was developed. The final conformation was obtained by extensive molecular dynamics simulations of a homology model based on the bovine rhodopsin crystal structure. The analysis of the receptor structure allowed us to detect a number of specific contacts between different amino acid residues, as well as water- and lipid-mediated interactions. These interactions were stable in six additional independent 35 ns long simulations at 310 and 323 K, which used the refined model as the starting structure. All loops, particularly the extracellular loop 2 and the intracellular loop 3, exhibited high fluctuations, whereas the transmembrane helices were more static. Although other models of this receptor have been previously developed, none of them have been subjected to extensive molecular dynamics simulations, and no other three-dimensional structure is publicly available. Our results suggest that the presence of ions as well as explicit solvent and lipid molecules are critical for the structure of membrane protein models, and that molecular dynamics simulations are certainly useful for their refinement.     

Structure and dynamics of surfactant and hydrocarbon aggregates on graphite: a molecular dynamics simulation study

We have examined the structure and dynamics of sodium dodecyl sulfate (SDS) and dodecane (C12) molecular aggregates at varying surface coverages on the basal plane of graphite via classical molecular dynamics simulations. Our results suggest that graphite-hydrocarbon chain interactions favor specific molecular orientations at the single-molecule level via alignment of the tail along the crystallographic directions. This orientational bias is reduced greatly upon increasing the surface coverage for both molecules due to intermolecular interactions, leading to very weak bias at intermediate surface coverages. Interestingly, for complete monolayers, we find a re-emergent orientational bias. Furthermore, by comparing the SDS behavior with C12, we demonstrate that the charged head group plays a key role in the aggregate structures: SDS molecules display a tendency to form linear file-like aggregates while C12 forms tightly bound planar ones. The observed orientational bias for SDS molecules is in agreement with experimental observations of hemimicelle orientation and provides support for the belief that an initial oriented layer governs the orientation of hemimicellar aggregates.     

HTPB固体推进剂增塑剂选取分子模拟研究

固体推进剂中增塑剂要求同粘合剂体系相容性良好,并提高体系的低温性能.本文采用分子动力学(MD)方法,首先计算了端羟基聚丁二烯(HTPB)粘合剂及增塑剂癸二酸二辛酯(DOS)、己二酸二辛酯(DOA)、壬酸异癸酯(TOA)、邻苯二甲酸二丁酯(DBP)和邻苯二甲酸二辛酯(DOP)的溶度参数,以此从相容性角度选取推进剂增塑剂;计算数值基本吻合实验值,表明常用的增塑剂从相容性都能满足要求.其次模拟获取了HTPB及HTPB/增塑剂混合体系的比体积-温度关系得到了体系的玻璃化转变温度(Tg),揭示增塑剂对HTPB体系低温性能的影响.结果显示:(1)HTPB的Tg模拟值为202K,基本吻合实验值196K.(2)HTPB/DOS混合体系中,当增塑剂DOS的质量含量从12%、22%、29%到36%(摩尔含量分别为50%、66%、75%和90%)增加时,体系的Tg线性降低;TOA和DOP增塑的粘合剂体系(摩尔含量为75%)Tg也降低,而增塑剂DOA和DBP对体系的Tg影响不大.因此,基于相容性及提高粘合剂低温性能考虑,DOS、DOA和DOP作为HTPB的增塑剂优于TOA和DBP.     

Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. a molecular dynamics simulation study

Understanding the lipid phase transition of lipid bilayers is of great interest from biophysical, physicochemical, and technological points of view. With the aim of elucidating the structural changes that take place in a DPPC phospholipid bilayer induced by an external isotropic surface pressure, five computer simulations were carried out in a range from 0.1 to 40 mN/m. Molecular dynamics simulations provided insight into the structural changes that took place in the lipid structure. It was seen that low pressures ranging from 0.1 to 1 mN/m had hardly any effect on the structure, electrical properties, or hydration of the lipid bilayer. However, for pressures above 40 mN/m, there was a sharp change in the lipid-lipid interactions, hydrocarbon lipid fluidity, and electrostatic potential, corresponding to the mesomorphic transition from a liquid crystalline state (L(alpha)) to its gel state (P'(beta)). The head lipid orientation remained almost unaltered, parallel to the lipid layer, as the surface pressure was increased, although a noticeable change in its angular distribution function was evident with the phase transition.     

Structure of an associating polymer melt in a narrow slit by molecular dynamics simulation

Molecular dynamics simulation has been used to study the equilibrium properties of a generic coarse-grained polymer melt with associating terminal groups, confined in a narrow slit by two atomically smooth walls. Simulations were carried out as a function of wall separation and attracting strength as well as polymer end-end interaction strength. We find that confinement has an important effect on the melt properties. In particular, strongly attracting walls can produce radical changes in chain conformation, the nature of the transient network, and the structure of the aggregates formed by the associating terminals.     

A study of molecular dynamics and phase transitions in solid MBBA

Abstract

The solid state polymorphism of liquid crystalline MBBA was investigated by temperature dependent NMR spin-lattice relaxation time measurements. The sensitivity of the method could be utilized because the correlation time of the measurement is in the correlation time region of molecular motion. Motional correlation time and activation energy values were determined and the results show some interesting changes between the different solid phases. Non-trivial variation in the end-chain rotational motion in two crystalline phases has been observed. Conclusions were drawn on the relationship between rotational molecular dynamics, intermolecular order and phase transitions.     

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.     

Diffusive dynamics of vesicles tethered to a fluid supported bilayer by single-particle tracking

We recently introduced a method to tether intact phospholipid vesicles onto a fluid supported lipid bilayer using DNA hybridization (Yoshina-Ishii, C.; Miller, G. P.; Kraft, M. L; Kool, E. T.; Boxer, S. G. J. Am. Chem. Soc. 2005, 127, 1356-1357). Once tethered, the vesicles can diffuse in two dimensions parallel to the supported membrane surface. The average diffusion coefficient, D, is typically 0.2 microm(2)/s; this is 3-5 times smaller than for individual lipid or DNA-lipid conjugate diffusion in supported bilayers. In this article, we investigate the origin of this difference in the diffusive dynamics of tethered vesicles by single-particle tracking under collision-free conditions. D is insensitive to tethered vesicle size from 30 to 200 nm, as well as a 3-fold change in the viscosity of the bulk medium. The addition of macromolecules such as poly(ethylene glycol) reversibly stops the motion of tethered vesicles without causing the exchange of lipids between the tethered vesicle and supported bilayer. This is explained as a depletion effect at the interface between tethered vesicles and the supported bilayer. Ca ions lead to transient vesicle-vesicle interactions when tethered vesicles contain negatively charged lipids, and vesicle diffusion is greatly reduced upon Ca ion addition when negatively charged lipids are present both in the supported bilayer and tethered vesicles. Both effects are interesting in their own right, and they also suggest that tethered vesicle-supported bilayer interactions are possible; this may be the origin of the reduction in D for tethered vesicles. In addition, the effects of surface defects that reversibly trap diffusing vesicles are modeled by Monte Carlo simulations. This shows that a significant reduction in D can be observed while maintaining normal diffusion behavior on the time scale of our experiments.