Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared, [linear span]R(g)(2)[linear span], was found to scale as N(4/5) for an intermediate regime and N(2/3) for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are "surface beads" interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the next paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204905 (2011)]. Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models.     

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics

Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ～ N(-2.4) scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension [linear span]R(g)(2)[linear span], neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η(0) ～ N(1.4 ± 0.2) which is much weaker than the N(3.4) behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)].     

Molecular dynamics simulation of nanoparticle self-assembly at a liquid-liquid interface

We have used molecular dynamics simulations to investigate the in situ self-assembly of modified hydrocarbon nanoparticles (mean diameter of 1.2 nm) at a water-trichloroethylene (TCE) interface. The nanoparticles were first distributed randomly in the water phase. The MD simulation shows the in situ formation of nanoparticle clusters and the migration of both single particles and clusters from the water phase to the trichloroethylene phase, possibly due to the hydrophobic nature of the nanoparticles. Eventually, the single nanoparticles or clusters equilibrate at the water-TCE interface, and the surrounding liquid molecules pack randomly when in contact with the nanoparticle surfaces. In addition, the simulations show that the water-TCE interfacial thickness analyzed from density profiles is influenced by the presence of nanoparticles either near or in contact with the interface but is independent of the number of nanoparticles present. The nanoparticles, water molecules, and TCE molecules all exhibit diffusion anisotropy.     

Molecular dynamics simulation of amphiphilic dimers at a liquid-vapor interface

Molecular dynamics simulations are utilized to simulate a model liquid-vapor-amphiphile system. Amphiphilic surfactant molecules are modeled as dimers composed of a hydrophilic head and a hydrophobic tail. Three dimer models with three different head sizes and two different head-to-tail size ratios are studied. The surfactant molecules distribute preferentially at the interfaces at low concentrations and form micelles in the bulk liquid phase as the concentration increases. We find that the surface tension decreases as molecular concentration increases, with a reduction in the rate of decrease after micellization occurs. The extent to which a surfactant can reduce the surface tension at a given concentration is found to depend on the head size. Furthermore, the head size and concentration dependence of the surfactant tilt-angle distribution is studied and compared to experimental data.     

Molecular dynamics simulation of the kinetics of nucleation of supercooled NaCl melt clusters

Approaches to describing the structure of metastable liquids are considered. A criterion for the classification of particles in a supercooled NaCl melt is suggested. The criterion is based on the Q₆ method and structural features of salt crystals. It was applied to analyze the configurations of clusters calculated by the molecular dynamics method. The results were interpreted using classic nucleation theory and the probabilistic approach. It was shown that crystalline phase nuclei with subcritical sizes existed in a metastable liquid. The evolution of nucleus sizes follows a complex mechanism. Along with monomer attachment and detachment reactions, collective structural fluctuations play a noticeable role.     

Molecular dynamics simulation of the thermodynamic properties of mercury at pressures below 2.5 GPa and temperatures below 10000 K

Models of mercury were constructed by molecular dynamics using the interparticle potential of the embedded atom model (EAM) at temperatures below 10 000 K and pressures below 2.5 GPa. The thermodynamic properties of the models were presented on the isobars of 0.5, 1.0, 1.5, 2.0, and 2.5 GPa. The compressibility factors Z = pV/(RT) were calculated; the coordinates of the inversion points of the Joule–Thomson coefficient below 5600 K were found from the positions of minima on the Z(p, T) isobars. At densities above 8–9 g/cm³, the results of simulation agreed well with experiment; at lower densities there were discrepancies associated with a loss of metal properties by real mercury. The behavior of the models was analyzed in the region of the van der Waals loop. The calculated critical temperature of mercury was found to be significantly overestimated relative to the experiment. Modeling the “meta-mercury” with the EAM potential with excluded embedded potential contribution gave better agreement with the equation of state of mercury at lower densities. The states with Z = 1 can be observed below 1.0 GPa. The calculated temperature of the inversion of the Joule–Thomson coefficient increased monotonically to 5600 K as the pressure increased to 2.5 GPa.     

Molecular dynamics simulation study of the dynamics of fluids at solid-liquid interfaces

The dynamics of fluids at solid-liquid interfaces is investigated. In particular, we consider a simple Lennard-Jones fluid as well as a melt of hexadecane chains. For the Lennard-Jones fluid, the numerical results are compared with analytical calculations based on the diffusion equation, which shows that the numerical results can very well by described by the solution of the diffusion equation for reflecting surfaces. The diffusion coefficient is practically independent of the position within the film, although the fluid is inhomogeneous perpendicular to the surface. In contrast, the dynamics of the centers of mass of hexadecane molecules perpendicular to repulsive surfaces is severely slowed down due to their extended and anisotropic nature and cannot be described by a single particle diffusion equation.     

Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement

The oxy-Cope rearrangement reaction in the antibody AZ28 is investigated using ab initio molecular orbital calculations and molecular mechanical molecular dynamics simulations. This antibody, AZ28, is known as one of the few systems where the mature catalytic antibody shows a negative correlation between the transition state analogue (TSA) binding affinity and the catalytic rate of the oxy-Cope rearrangement compared to the germ line catalytic antibody. The ab initio optimized structure shows that the transition state structure has a more planar configuration than the TSA. The favorable electrostatic interactions between AZ28 and the transition state analogue overcome the unfavorable van der Waals interactions; thus, AZ28 shows higher binding affinity for the TSA than the germ line. However, the AZ28 is not flexible enough to accept the relatively planar transition state structure. Because the lower flexibility causes poorer antibody-hapten interaction energies, the activation free energy of the oxy-Cope rearrangement becomes larger in the mature antibody than the germ line. We show that the differences in flexibility between the germ line and the mature form and the differences in structure between TSA and the transition state are the origin of the negative correlation in AZ28-catalyzed oxy-Cope rearrangement. The mutation of residue 34 of the light chain, 34(L), affects the binding free energies through the interresidue interaction because it is the closest to the hapten among the six mutatable residues. However, it does not affect the negative correlation.     

Rapid solidification of cobalt melt by molecular dynamics simulation

Molecular dynamics simulation was applied to investigating the evolvement rule of cobalt melt microstructure during solidification at different cooling rates. The cooling rate for the formation of amorphous phase is determined by analyzing the radial distribution function, the H–A bond-type index and the mean square displacement. The simulation results showed that the nucleation undercooling increases with the initial temperature, and in the undercooling versus temperature curve, there are two inflection points. Besides, when the initial temperature reaches 2450 K, the undercooling will be stabilized at 1061 K. As the cooling rate is less than 1.0?×?10^11.0 K s^?1, the FCC and HCP crystal structures will be obtained. Amorphous structure will be obtained if the cooling rate is more than 1.0?×?10^13.0 K s^?1. If the cooling rate of the Co melt is between 1.0?×?10^11.0 and 1.0?×?10^13.0 K s^?1, the crystal and amorphous structures will be coexistent, which indicates that the critical cooling rate of crystal–amorphous transition is 1.0?×?10^11.0 K s^?1.

     

分子动力学模拟研究荧光分子芘在磺基甜菜碱胶束中的增溶

采用分子动力学模拟研究了荧光分子芘在磺基甜菜碱两性表面活性剂聚集体中的增溶现象．结果表明,芘分子自发地自溶液中增溶进入胶束疏水内核的栅栏层区域．当胶束溶液中芘分子的局部浓度增大时,两个芘分子可以同时增溶进胶束的栅栏层区域,此时两个芘分子形成π-π共轭堆积的激发态络合物．但是由于荧光分子之间的弱兀．兀相互作用,激发态络合物在胶束中是不稳定的,表现为两个芘分子的多次结合和分离．模拟表明,分子动力学方法可以在分子水平上研究荧光探针分子在表面活性剂胶束中的增溶位点,解释荧光分子在胶束中的动力学现象．     

Molecular dynamics simulation of cellobiose in water

The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.     

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.     

Molecular dynamics simulation of a water/metal interface

First results of a molecular dynamics study of a water/metal interface, lasting 3.3 ps at an average temperature of 294 K, are reported. The basic periodic box contains 216 water molecules and a crystal slab of 550 platinum atoms with (100) surface planes. A combination of a Lennard-Jones potential between centers of mass and a Coulomb potential arising from dielectric interactions of the water charge distribution with the metal is employed for the water-wall interaction, the ST2 model for the water-water, and a nearest-neighbour harmonic potential for the platinum-platinum interactions. Considerable adsorption at the interface together with a drastic change of the water structure is observed.     

Molecular dynamics simulation of semirigid polymers

The chain rigidity of poly(p-hydroxybenzoate) was estimated through the theoretical evaluation of its persistence length (L_p). A non-Brownian molecular dynamics (MD) simulation of an isolated chain with 20 monomeric units was performed. The sampled conformational population was analyzed and the orientational correlation function between monomeric units along the chain was calculated. An algorithm based on the worm-like chain model was applied to evaluate the persistence length. The results were compared with those obtained from equilibrium models like the freely-rotating-chain and the rotational-matrix method with fluctuations. Equilibrium models give different results depending on the degree of accuracy used in describing the monomeric unit. The inclusion of thermal fluctuations is crucial to obtain realistic results. These coincide with those given by MD simulation when only nearest-neighbour orientational correlations are taken into account: inclusion of higher-order correlation terms leads to lower values of the persistence length. The origin of this discrepancy was investigated. The MD simulation results are characterized by an overrepresentation of conformations with a short end-to-end distance resulting from an anomalous energy concentration in the first bending mode of the chain. In analogy with previous simulation results from systems characterized by a week coupling amoung their degrees of freedom, failure in the energy equipartition is proposed as a likely explanation of the anomalous dynamical behaviour.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.     

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.