Molecular dynamics simulation of crystalline poly(ethylene oxide)
01 Dec 1994-Journal of Chemical Physics (American Institute of Physics)-Vol. 101, Iss: 11, pp 10064-10073
TL;DR: In this paper, a molecular dynamics model for the crystalline phase of the widely used host-polymer poly(ethylene oxide) (PEO) was presented, where force field and computational parameters were optimized to give realistic behavior for crystalline PEO.
Abstract: Molecular dynamics (MD) simulation holds great promise as a source of otherwise elusive information concerning ionic conduction mechanisms occurring in the amorphous phases of polymer electrolytes. However, most polymer/salt complexes have a multiphase character at temperatures of interest. Insights into crystalline phases may thus prove meaningful in the subsequent design of strategies to decrease the degree of crystallinity in these systems. We report here the full details of a molecular dynamics model (‘‘md’’ model) for the crystalline phase of the widely used host‐polymer poly(ethylene oxide) (PEO). Force‐field and computational parameters are optimized to give realistic behavior for crystalline PEO. Analyses of the structure and dynamics obtained from the MD simulations performed at 300 K include mean‐square displacements, x‐ray powder diffractograms, distributions of bond and torsion angles, and radial distribution functions. These are compared with experimental data, the static x‐ray determined PEO structure and that obtained using a ‘‘tethered’’ model, in which the atoms are attached by springs to their initial crystalline positions, and allowed to move according to their experimental mean‐square displacements. Agreement is good, but the reliability of the x‐ray refined positions is questioned.
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TL;DR: In this article, the authors present a review of recent developments that increase the time and distance scales accessible in the simulations of specific polymers by replacing a model expressed in fully atomistic detail with a coarse-grained model of the same polymer.
Abstract: Recent developments that increase the time and distance scales accessible in the simulations of specific polymers are reviewed. Several different techniques are similar in that they replace a model expressed in fully atomistic detail with a coarse-grained model of the same polymer, atomistic → coarse-grained (and beyond!), thereby increasing the time and distance scales accessible within the expenditure of reasonable computational resources. The bridge represented by the right-pointing arrow can be constructed via different procedures, which are reviewed here. The review also considers the status of methods which reverse this arrow, atomistic ← coarse-grained. This “reverse-mapping” recovers a model expressed in fully atomistic detail from an arbitrarily chosen replica generated during the simulation of the coarse-grained system. Taken in conjunction with the efficiency of the simulation when the system is in its coarse-grained representation, the overall process Open image in new window permits a much more complete equilibration of the system (larger effective size of Δt) when that equilibration is performed with the coarse-grained replicas (II → III) than if it were attempted with the fully atomistic replicas (I → IV).
353 citations
TL;DR: In this article, a poly(oxyethylene) (POE) chain with 15 ethylene oxide (EO) units have been performed in an aqueous solution for 2 ns at 300 K and for 1 ns at 373 K, a cloud point for POE.
Abstract: Molecular dynamics simulations of a poly(oxyethylene) (POE) chain with 15 ethylene oxide (EO) units have been performed in an aqueous solution for 2 ns at 300 K and for 1 ns at 373 K, a cloud point for POE. The conformation and the hydration structure of POE and the structure and the dynamics of water molecules in the vicinity of POE were examined. The conformation of POE was transformed from a collapsed chain in the gas phase to a helix in water which was maintained for 2 ns. After a simulated annealing at 1000 K, POE still showed a preference for a helix. An extended network of POE−water and water−water hydrogen bonds was found throughout inside the helix, stabilizing the helix backbone. The same helical conformation was maintained even at 373 K. The pair distribution functions for water oxygen atoms near POE indicated significantly enhanced water structures in the hydrophilic region of POE, and to a lesser extent in the hydrophobic region, at both 300 and 373 K. Considerably reduced translational movem...
338 citations
TL;DR: It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around O EG chains and the rapid mobility of hydrated SAM chains.
Abstract: Molecular simulations were performed to study a system consisting of protein (e.g., lysozyme) and self-assembled monolayers (SAMs) terminating with different chemical groups in the presence of explicit water molecules and ions. Mixed SAMs of oligo (ethylene glycol) [S(CH2)4(OCH2CH2)4OH, (OEG)] and hydroxyl-terminated SAMs [S(CH2)4OH] with a mole fraction of OEG at χOEG = 0.2, 0.5, 0.8, and 1.0 were used in this study. In addition, methyl-terminated SAMs [S(CH2)11CH3] were also studied for comparison. The structural and dynamic behavior of hydration water, the flexibility and conformation state of SAMs, and the orientation and conformation of protein were examined. Simulation results were compared with those of experiments. It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around OEG chains and the rapid mobility of hydrated SAM chains.
293 citations
TL;DR: In this paper, the system of lithium iodide dissolved in poly(ethylene oxide), which are prototypes of polymer electrolytes used, for example, in batteries, was studied by means of molecular dynamics simulations.
Abstract: Systems of lithium iodide dissolved in poly(ethylene oxide), which are prototypes of polymer electrolytes used, for example, in batteries were studied by means of molecular dynamics simulations. Investigations were aimed at the molecular driving force behind the salt uptake, the mechanism of ion transport, participation of the polymer in ion transport, ion clustering, change of polymer properties by the presence of ions, and ionic conductivity. Particular attention has been given to the differences in behavior between (previously studied) neutral and ionic species dissolved in polymers.
229 citations
TL;DR: Polymer electrolytes have been a focus of the scientific community for a quarter century and have been used to construct electrochemical devices such as sensors, batteries, and fuel cells.
Abstract: Polymer electrolytes have been a focus of the scientific community for a quarter century. They extend the realm of traditional solid-state ionics from hard materials to include soft materials and, in doing so, pose issues both fundamental (e.g., how are structure and transport defined in a concentrated electrolyte with an immobile solvent?) and technological (e.g., how can polymer ionics be used to construct electrochemical devices such as sensors, batteries, and fuel cells?)
191 citations
References
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TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath
25,256 citations
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11 Feb 1988TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Abstract: Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.
21,073 citations
TL;DR: In this paper, a structure refinement method was described which does not use integrated neutron powder intensities, single or overlapping, but employs directly the profile intensities obtained from step-scanning measurements of the powder diagram.
Abstract: A structure refinement method is described which does not use integrated neutron powder intensities, single or overlapping, but employs directly the profile intensities obtained from step-scanning measurements of the powder diagram. Nuclear as well as magnetic structures can be refined, the latter only when their magnetic unit cell is equal to, or a multiple of, the nuclear cell. The least-squares refinement procedure allows, with a simple code, the introduction of linear or quadratic constraints between the parameters.
14,360 citations
TL;DR: In this paper, a new parametric quantum mechanical molecular model, AM1 (Austin Model l), based on the NDDO approximation, is described, in which the major weaknesses of MNDO, in particular failure to reproduce hydrogen bonds, have been overcome without any increase in computing time.
Abstract: A new parametric quantum mechanical molecular model, AM1 (Austin Model l), based on the NDDO approximation, is described. In it the major weaknesses of MNDO, in particular failure to reproduce hydrogen bonds, have been overcome without any increase in computing time. Results for 167 molecules are reported. Parameters are currently available for C, H, 0, and N.
12,452 citations
TL;DR: The DREIDING force field as discussed by the authors uses general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants or geometric parameters that depend on the particular combination of atoms involved in the bond, angle, or torsion terms.
Abstract: We report the parameters for a new generic force field, DREIDING, that we find useful for predicting structures and dynamics of organic, biological, and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants and geometric parameters that depend on the particular combination of atoms involved in the bond, angle, or torsion terms. Thus all bond distances are derived from atomic radii, and there is only one force constant each for bonds, angles, and inversions and only six different values for torsional barriers. Parameters are defined for all possible combinations of atoms and new atoms can be added to the force field rather simply. This paper reports the parameters for the "nonmetallic" main-group elements (B, C, N, 0, F columns for the C, Si, Ge, and Sn rows) plus H and a few metals (Na, Ca, Zn, Fe). The accuracy of the DREIDING force field is tested by comparing with (i) 76 accurately determined crystal structures of organic compounds involving H, C, N, 0, F, P, S, CI, and Br, (ii) rotational barriers of a number of molecules, and (iii) relative conformational energies and barriers of a number of molecules. We find excellent results for these systems.
5,380 citations