Atomistic Monte Carlo and molecular dynamics simulation of the bulk phase self-assembly of semifluorinated alkanes

Abstract

Results are presented for the conformational, thermodynamic, structural and solid-state chain organization properties of the semifluorinated alkane F(CF2)12(CH2)12H (termed perfluorododecyldodecane and abbreviated as F12H12) from detailed, atomistic-level Molecular Dynamics and Monte Carlo simulations in the isothermal–isobaric ensemble using large simulation cells containing up to 144,000 atomistic units. To cope with the large requirements in CPU time accompanying the use of super-cells in our simulations, we identified the Monte Carlo subroutines with the largest demand in computational resources and took advantage of parallelization by multithreading on NVIDIA graphics processing units (GPUs) to improve code performance by almost one order of magnitude. Consistent simulation results for the most important properties of the system have been obtained from the two methods, especially at the higher temperatures where their predictions for the density, average square chain-end-to-end distance and dihedral angle distributions are indistinguishable (practically identical). Driven by experimental data that provide evidence for two first-order phase transitions in F12H12, we have further investigated its bulk-phase assembly by carrying out gradual cooling runs from an initial configuration of randomly distributed chains. For both methods, the study of the average-squared end-to-end molecular distance indicates that F12H12 molecules prefer to be aligned in ordered zones (lamellae), whereas the dihedral distributions exhibit a favorable trans state with decreasing temperature and/or increasing pressure, verifying the tendency of perfluorododecyldodecane to undergo a structural transition at these conditions. Our simulations support a spontaneous transition of F12H12 from an isotropic phase to a smectic-like phase at a low enough temperature (close to T=315K based on cooling experiments), at a pressure P=100atm. Intermolecular pair distribution functions and atomistic configurational snapshots show that the simulated smectic phase consists of bilayer lamellae with a variety of directions, involving tilted and non-interdigitated chains. Experimentally, two solid phases are proposed for F12H12: a high-temperature one consisting of monolayer lamellae and a low temperature one consisting of bilayer lamellae with interdigitated hydrocarbon and fluorocarbon blocks. Despite that our simulations cannot unambiguously predict a second (solid-solid) phase transition, they provide convincing evidence for the co-existence of many ordered lamellae in F12H12 below its melting point Tm both in monolayer and bilayer arrangements, with the relative population of bilayer ones increasing with decreasing temperature.