Medium- to long-chain alkanes can form upon cooling intermediate phases between isotropic liquid and solid crystalline, called rotator phases, where relative freedom of the molecules to rotate about their long axis is combined with long range translational order. Rotator phases are well documented experimentally but the mechanism of their formation at the molecular level is still not fully explained. In a previous work, we have shown that molecular dynamics simulations can produce rotator phases upon cooling of hexadecane [S. Iliev et al., J. Col. Int. Sci., 2023, 638, 743]. The aim of the current work is to develop a procedure to identify the specific ordered phase obtained in the simulations. The influence of the cooling rate on the freezing process of hexadecane (bulk and surfactant-interfaced to water) is tested as well. Several parameters are combined to quantify the degree of ordering and the type of phase in the studied systems. These are the tilt angle of the molecules with respect to the crystallite plane, the radial distribution function of the centre of mass of the molecules in the crystallite, the percentage of the gauche torsion angles in the molecules, the angle of the second principal axis of each molecule with respect to the x axis of the coordinate system, and estimates from Voronoi analysis. The results show that the systems form a rotator phase, which transitions gradually towards the thermodynamically most stable triclinic crystal, and the transformation progresses to different extent depending on the system. The influence of the cooling rate is related only to the size of the largest crystallite formed, the other parameters of the freezing process remain unaffected. The work also presents a robust procedure for obtaining and identifying different types of ordered phases in alkane-containing systems with thoroughly tested computational protocol and a comprehensive set of structural analyses. Several key characteristics are advanced, compared to previous research [Ryckaert et al., Mol. Phys., 1989, 67, 957; Wentzel et al., J. Chem. Phys. 2011, 134, 224504], namely, a new methodology is proposed to compute the unit cell deformation parameter and azimuthal angle from MD simulation trajectories of the freezing process in alkane-containing systems. The suggested structural analysis, which is independent of the coordinate system, is applicable to any linear-chain system with polycrystalline structure.

Hypothesis: Upon cooling, alkanes can form intermediate phases between liquid and crystal. They are called “rotator” or “plastic” phases and have long-range positional order with rotational freedom around the long molecular axis which gives them non-trivial and useful visco-plastic properties. We expect that the formation and structure of rotator phases formed in freezing alkanes can be understood much deeper by tracking the process at molecular level with atomistic molecular dynamics. Simulations: We defined an appropriate CHARMM36-based computational protocol for simulating the freezing of hexadecane, which contained a sufficiently long (500 ns) equilibrium sampling of the frozen states. We employed it to simulate successfully the freezing of bulk and interface-contacting hexadecane and to provide a pioneering clarification of the effect of surfactant on the crystallization mechanism and on the type of intermolecular ordering in the crystallites. Findings: The devised computational protocol was able to reproduce the experimentally observed polycrystalline structure formed upon cooling. However, different crystallization mechanisms were established for the two types of models. Crystallites nucleate at random locations in the bulk and start growing rapidly within tens of nanoseconds. In contrast, the surfactants freeze first during the fast cooling (<1 ns), followed by rapid hexadecane freezing, with nucleation starting along the entire surfactant adsorption layer. Thereby, the hexadecane molecules form rotator phases which transition into a more stable ordered phase. This collective transition is first-time visualized directly. The developed robust computational protocol creates a foundation for future in-depth modelling and analysis of solid-state alkane-containing, incl. lipid, structures.

In the current work, a comprehensive procedure for structural analysis of quasilinear organic molecules arranged in a polycrystalline sample generated by molecular dynamics is developed. A linear alkane, hexadecane, is used as a test case because of its interesting behavior upon cooling. Instead of a direct transition from isotropic liquid to the solid crystalline phase, this compound forms first a short-lived intermediate state known as a “rotator phase”. The rotator phase and the crystalline one are distinguished by a set of structural parameters. We propose a robust methodology to evaluate the type of ordered phase obtained after a liquid-to-solid phase transition in a polycrystalline assembly. The analysis starts with the identification and separation of the individual crystallites. Then, the eigenplane of each of them is fit and the tilt angle of the molecules relative to it is computed. The average area per molecule and the distance to the nearest neighbors are estimated by a 2D Voronoi tessellation. The orientation of the molecules with respect to each other is quantified by visualization of the second molecular principal axis. The suggested procedure may be applied to different quasilinear organic compounds in the solid state and to various data compiled in a trajectory.

The saponin escin, extracted from horse chestnut seeds, forms adsorption layers with high viscoelasticity and low gas permeability. Upon deformation, escin adsorption layers often feature surface wrinkles with characteristic wavelength. In previous studies, we investigated the origin of this behavior and found that the substantial surface elasticity of escin layers may be related to a specific combination of short-, medium-, and long-range attractive forces, leading to tight molecular packing in the layers. In the current study, we performed atomistic molecular dynamics simulations of 441 escin molecules in a dense adsorption layer with an area per molecule of 0.49 nm2 . We found that the surfactant molecules are less submerged in water and adopt a more upright position when compared to the characteristics determined in our previous simulations with much smaller molecular models. The number of neighbouring molecules and their local orientation, however, remain similar in the different-size models. To maintain their preferred mutual orientation, the escin molecules segregate into well-ordered domains and spontaneously form wrinkled layers. The same specific interactions (H-bonds, dipole–dipole attraction, and intermediate strong attraction) define the complex internal structure and the undulations of the layers. The analysis of the layer properties reveals a characteristic wrinkle wavelength related to the surface lateral dimensions, in qualitative agreement with the phenomenological description of thin elastic sheets.