Adsorption of a single polymer chain on a surface: A molecular dynamics simulation study

We performed simulations of the physical adsorption of a single globular chain on a surface of hemispherical shape by means of molecular dynamics simulations. For the chain, we took advantage of a united atom model. Interactions within the chain were limited to stretching, bending, and torsional as well as nonbonded interactions between the nonadjacent atoms. The interaction between each chain element and the surface formation are reigned by a Lennard–Jones potential. In this article, we focused on differences in the behavior of the adsorbed globule to the free unadsorbed one particularly in two different zones of the immediate vicinity of the surface. There were strong indications for a localized acceleration of the dynamics as compared with the bulk that appears in an increase of trans–gauche switches. For explanation we came up with an adsorption scenario. Special attention was given to the shift of the percentage of trans and gauche conformations within the globule in dependence on the strength of the adsorption potential that might be related to crystallization or glass transition. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2333–2339, 2001     

Structure and dynamics of short chain molecules in disordered porous materials: a molecular dynamics simulation study

The static and dynamic properties of short polymer chains in disordered materials are studied using discontinuous molecular dynamics simulations. The polymers are modeled as chains of hard spheres and the matrix is a collection of fixed hard spheres. The simulations show that the chain size is a nonmonotonic function of the matrix concentration for all polymer concentrations. The dependence of polymer diffusion D on the degree of polymerization N becomes stronger as the matrix concentration is increased. At high matrix concentrations we observe a decoupling between translational and rotational diffusion, i.e., the rotational relaxation time becomes very large but the translational diffusion is not affected significantly. We attribute this to the trapping of a small number of polymers. Under these conditions the polymer chains diffuse via a hopping mechanism.     

Kinetics of the shear-induced isotropic-to-lamellar transition of an amphiphilic model system: a nonequilibrium molecular dynamics simulation study

The shear-induced isotropic-to-lamellar phase transition in the amphiphilic systems in the vicinity of the quiescent order-to-disorder transition point is investigated by the large-scale parallel nonequilibrium molecular dynamics simulations of simple amphiphilic model systems. There is a shear-induced upward shift of the ordering temperature. The initial isotropic phase orders into a lamellar phase perpendicular to the shear vorticity. The phase diagram as a function of temperature and shear rate is established. The dependency of the ordering transition on interaction strength and shear rate is rationalized by the competition between shear rate and chain relaxation. The time evolution of morphology reveals that the shear-induced ordering proceeds via nucleation and growth, a signature of a first-order phase transition. At low shear rate, a single ordered domain grows after an incubation period. With increasing shear rate ordering speeds up, but eventually develops in a lamellar system with disordered shear bands. The time dependence of the order parameter follows that of the mean-squared end-to-end distance, shear viscosity, and bulk pressure, and follows an Avrami scheme with an Avrami exponent between 2 and 4.     

Molecular dynamics simulation study on adsorption and diffusion processes of a hydrophilic chain on a hydrophobic surface

Molecular dynamics simulations are applied to investigate the adsorption and diffusion processes of a single hydrophilic poly(vinyl alcohol) (PVA) chain with different chain lengths on a hydrophobic graphite surface. It is expected that the chain and the surface "dislike" each other because one is hydrophilic and the other is hydrophobic. But surprisingly, a short PVA chain is well adsorbed on the surface, accompanied by large changes in the chain configuration. With increasing degree of polymerization (N), the chain turns gradually from two-dimensional adsorption to possessing certain height in the direction perpendicular to the surface. Moreover, the adsorption energy increases and the diffusion coefficient decreases with increasing N. In particular, for N = 20 in equilibrium, the hydroxyls of this short chain are close to the graphite surface in the stable adsorption configuration. In addition, we change the effective dielectric constant to 76.0 to mimic good solvent condition. The chain configurations and the diffusion coefficients both vary in contrast to the foregoing results.     

Thermophoresis in liquids: a molecular dynamics simulation study

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.     

A molecular dynamics computer simulation study of room-temperature ionic liquids. II. Equilibrium and nonequilibrium solvation dynamics

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M. Y. Choi and H. J. Kim, J. Chem. Phys. 122, 044510 (2005)] is extended to investigate dynamic properties of these liquids. Solvent fluctuation dynamics near equilibrium are studied via MD and associated time-dependent friction is analyzed via the generalized Langevin equation. Nonequilibrium solvent relaxation following an instantaneous change in the solute charge distribution and accompanying solvent structure reorganization are also investigated. Both equilibrium and nonequilibrium solvation dynamics are characterized by at least two vastly different time scales--a subpicosecond inertial regime followed by a slow diffusive regime. Solvent regions contributing to the subpicosecond nonequilibrium relaxation are found to vary significantly with initial solvation configurations, especially near the solute. If the solvent density near the solute is sufficiently high at the outset of the relaxation, subpicosecond dynamics are mainly governed by the motions of a few ions close to the solute. By contrast, in the case of a low local density, solvent ions located not only close to but also relatively far from the solute participate in the subpicosecond relaxation. Despite this difference, linear response holds reasonably well in both ionic liquids.     

Semi-classical generalized Langevin equation for equilibrium and nonequilibrium molecular dynamics simulation

Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matter in different phases. Normally, the atomic dynamics are described by classical equations of motion and the effect of the environment is taken into account through the fluctuating and frictional forces. Generally, the nuclear quantum effects and their coupling to other degrees of freedom are difficult to include in an efficient way. This could be a serious limitation on its application to the study of dynamical properties of materials made from light elements, in the presence of external driving electrical or thermal fields. One example of such system is single molecule dynamics on metal surface, an important system that has received intense study in surface science. In this review, we summarize recent effort in extending the Langevin MD to include nuclear quantum effect and their coupling to flowing electrical current. We discuss its applications in the study of adsorbate dynamics on metal surface, current-induced dynamics in molecular junctions, and quantum thermal transport between different reservoirs.     

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study

A method for performing implicit-solvent molecular dynamics simulations at constant pH was applied to a pentapeptide acetyl-Ala-Asp-Ala-Lys-Ala-amide at pH 4. As a reference, molecular dynamics simulations were done for the same peptide with two variants of its fixed protonation patterns expected to dominate at pH 4, i.e., with a protonated and a deprotonated side chain of the Asp residue and the protonated Lys residue in both cases. The dynamic trajectories of the peptide were used to discuss the problem of the significance of the solute-solvent proton exchange phenomena for the dynamics and structural distributions of the polypeptide chain. The Asp-Lys distance was used as a probe of the overall molecular structure of the investigated pentapeptide. To characterize the dynamics, distributions of the "waiting" times for a transition from a "short" distance conformation to a "long" distance conformation were constructed, based on the generated molecular dynamics trajectories. We show that the relaxation time for the transitions, derived from the constant-pH simulations, is very close to the relaxation time characterizing a permanently protonated molecule, although the average protonation probability of the short-distance conformation is close to zero. However, the distribution of the Asp-Lys distances obtained from constant-pH simulations cannot be reproduced as a linear combination of the distributions resulting from the simulations with fixed protonation states.     

A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

 In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA–DNA attractions. Received: 30 November 2000 / Accepted: 7 February 2001 / Published online: 22 May 2001     

Local chain dynamics of a model polycarbonate near glass transition temperature: A molecular dynamics simulation

Constant pressure constant temperature molecular dynamics method is employed to investigate the atomistic scale dynamics of a model Bisphenol A polycarbonate in the vicinity of its glass transition temperature. First, the glass transition temperature and the thermal expansion coefficients of the polymer are predicted by performing simulations at different temperatures. To explore the significance of different modes of motion, various types of time correlation functions are utilized in analyzing the trajectories. In these nanosecond scale simulations, the motion of the chain segments is found to be highly localized with little reorientation of the vectors representing these segments. Detailed analysis of trajectories and the correlation functions of the backbone dihedrals and side methyl groups indicates that they exhibit numerous conformational transitions. The activation energies of the conformational transitions obtained from the simulation are generally larger than the potential barriers for the rotations of these dihedrals, however, both show the same trend. We also have estimated the phenylene ring flip activation energy as 12.6 kcal/mol and the flip frequency as 0.77 MHz at 300 K. These values fall either fall within the range determined by various NMR spectroscopy experiments or slightly out of the range. The study shows that the conformational transitions between the adjacent dihedrals are strongly correlated. Three basic cooperative modes are identified from the simulation. They are: a positive synchronous rotation of two phenylene rings, a negative synchronous rotation of two phenylene rings, and a carbonate group rotation. Above the glass transition temperature, the large scale cooperative motions become much more significant.     

Reverse nonequilibrium molecular dynamics simulation of thermal conductivity in nanoconfined polyamide-6,6

A new molecular dynamics simulation method, with coupling to external baths, is used to perform equilibrium simulations on polyamide-6,6 trimers nanoconfined between graphene surfaces, in equilibrium with the bulk polymer. The method is coupled with the reverse nonequilibrium molecular dynamics simulation technique to exchange heat in the direction normal to the surfaces. To be able to study the effect of confinement on the heat conductance in nanoconfined pores, in this work a number of simulations on systems with different pore sizes are done. It is concluded that the coefficient of heat conductivity depends on the degree of polymer layering between the surfaces and on the pore width. Our results further indicate a considerable temperature drop at the interface between the surfaces and polymer. The calculated Kapitza lengths depend on the intersurface distance and on the layering of the polymer nanoconfined between the surfaces.     

A study on the structural transition of a single polymer chain by parallel tempering molecular dynamics simulation

The structural transition of a single polymer chain with chain length of 100,200 and 300 beads was investigated by parallel tempering MD simulation.Our simulation results can capture the structural change from random coil to orientationally ordered structure with decreasing temperature.The clear transition was observed on the curves of radius of gyration and global orientational order parameter P as the function of temperature,which demonstrated structural formation of a single polymer chain.The linear relationships between three components of square radius of gyration R_gx²,R_gx²,R_gz² and global orientational order P can be obtained under the structurally transformational process.The slope of the linear relationship between x（or y-axis） component R_gx²(or R_gy²) and P is negative,while that of RL as the function of P is positive.The absolute value of slope is proportional to the chain length.Once the single polymer chain takes the random coil or ordered configuration,the linear relationship is invalid.The conformational change was also analyzed on microscopic scale.The polymer chain can be treated as the construction of rigid stems connecting by flexible loops.The deviation from exponentially decreased behavior of stem length distribution becomes prominent,indicating a stiffening of the chain arises leading to more and more segments ending up in the trans state with decreasing temperature.The stem length N_tr is about 21 bonds indicating the polymer chain is ordered with the specific fold length.So,the simulation results,which show the prototype of a liquid-crystalline polymer chain,are helpful to understand the crystallization process of crystalline polymers.     

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.     

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.     

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.     

Temperature-induced crystallization in concentrated suspensions of multiarm star polymers: a molecular dynamics study

In this work, we study temperature-induced crystallization in dense suspensions of multiarm star polymers. This is a continuation of a previous study, which identified and studied the emergence of "glassy" amorphous states, in accordance with experimental observations. We performed molecular dynamics simulations on two types of star polymers: 128-arm stars and 64-arm stars dissolved in n-decane in the temperature range of 20-60 degrees C. These supramolecules are modeled as "soft spheres" interacting via a theoretically developed potential of mean field. Both systems attain a crystalline structure with the characteristics of a face-centered-cubic (fcc) crystal beyond a certain temperature. Kinetics is sensitive on initial configuration. Interestingly, kinetic trapping in "temporary" energy wells leads to highly crystalline structures, yet less ordered than their genuine equilibrium fcc structure. This complication illustrates the difficulty in reaching the equilibrium state, which is crystalline at high temperatures. A structural analysis of the final conformations is presented. The effect of size dispersity and star functionality of soft spheres on microstructure is also examined. Both factors influence crystallization and their effect is quantified by our study.     

Anisotropic heat transport in nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation

While polymers are known as thermal insulators, recent studies show that stretched single chains of polymers have a very high thermal conductivity. In this work, our new simulation scheme for simulation of heat flow in nanoconfined fluids [H. Eslami, L. Mohammadzadeh, and N. Mehdipour, J. Chem. Phys. 135, 064703 (2011)] is employed to study the effect of chain ordering (stretching) on the rate of heat transfer in polyamide-6,6 nanoconfined between graphene surfaces. Our results for the heat flow in the parallel direction (the plane of surfaces) show that the coefficient of thermal conductivity depends on the intersurface distance and is much higher than that of the bulk polymer. A comparison of results in this work with our former findings on the heat flow in the perpendicular direction, with the coefficient of heat conductivity less than the bulk sample, reveal that well-organized polymer layers between the confining surfaces show an anisotropic heat conduction; the heat conduction in the direction parallel to the surfaces is much higher than that in the perpendicular direction. The origin of such anisotropy in nanometric heat flow is shown to be the dramatic anisotropy in chain conformations (chain stretching) beside the confining surfaces. The results indicate that the coefficients of heat conductivity in both directions, normal and parallel to the surfaces, depend on the degree of polymer layering between the surfaces and the pore width.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

Adsorption states of amphipatic solutes at the surface of naturally hydrophobic minerals: a molecular dynamics simulation study

An initial molecular dynamics simulation study regarding interfacial phenomena at selected naturally hydrophobic surfaces is reported. Simulation results show that, due to the natural hydrophobicity of graphite and talc basal planes, the cationic surfactant dodecyltrimethylammonium bromide preferentially adsorbs at these surfaces through hydrophobic interactions. When a model dextrin molecule is considered, the simulation results suggest that the hydrophobic interaction between the naturally hydrophobic surfaces of graphite, talc basal plane, and sulfur and the hydrophobic moieties (C-H and methylene groups) in the dextrin molecule plays a significant role in dextrin adsorption at these surfaces. The hydroxyl group in the dextrin molecule also contributes to its adsorption at the talc basal plane surface. In contrast, dextrin was not found to adsorb at talc edge surfaces.     

Glass transition in single poly(ethylene oxide) chain: A molecular dynamics simulation study

Local dynamics of single poly(ethylene oxide) chain in various environments (bulk, film, and isolated systems) has been characterized by the reorientation functions of various backbone bond vectors. Within any observation time, the variations of these reorientation functions with the temperature can be well described by the Kohlrausch?Williams?Watts (KWW) like equation, in which the fitted temperature parameter is identified as the glass transition temperature (T _g). The so‐obtained T _g for that polymer faithfully reveals the effects of the observation time, chain flexibility and vector range on the local dynamics. Furthermore, it is found that the KWW like relation is also applicable to the temperature‐dependence of the fraction of frozen atoms or torsions defined by the trajectory radii of gyration or the conformational transitions. Consequently, different motions lead to different values of T _g for the same system. Despite all, the consistent trend can be yielded, namely, T _g (bulk) > T _g (film) > T _g (isolated), which captures the effects of free surfaces on enhanced dynamics. In addition, dynamics heterogeneity in the systems can be quantitatively revealed. The newly proposed method holds a bright promise to predict the T _g values of complex polymers especially for comparisons. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 178–188