Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies

We have performed full atomistic molecular dynamics (MD) simulations to investigate structure and stability of bilayer membrane systems consisting of monomeric or polymeric 10,12‐pentacosadiynoic acid (PCDA) units connected with lysine groups by amide bonds. The PCDA monomer molecules show a twisted three‐rod‐domain structure with two kinks but upon polymerization, they possess more elongated conformation. The resulting polydiacetylene (PDA) membrane systems have stable membrane structures at room temperature, which is similar to biological lipid bilayer membranes and maintain their gel‐like membrane integrity even up to as high as 370 K. Structural properties such as area per monomer, membrane thickness, density profile, 2D pair distribution function, and orientational correlation function are also calculated to understand the membrane structure and check its stability upon thermal fluctuation with atomistic resolution. This study is expected to provide the understanding about PDA membrane systems in atomistic details as well as significant insights into designing new novel PDA sensors. Structure and stability of a polydiacetylene (PDA), a family of ene‐yne conjugated polymers are investigated by atomistic molecular dynamics simulations. PDAs can be easily prepared by simple UV irradiation from self‐assembled diacetylene monomers without the need for chemical initiators or catalysts and undergo dramatic colorimetric responses upon environmental stimulations such as temperature, DNA, surfactants, and so on. We study the equilibrium structural and dynamical properties of the PDA bilayer membrane such as 2‐dimensional pair distribution functions, orientational radial distribution functions, density profiles, and temperature dependence of the membrane structure.