Effect of Perturbing Strata on Chain Conformations and Ordering in Closely Packed Layered Structures of Chain Molecules

Two-dimensional assemblies of packed alkyl chains can be viewed as stacks of microlayers or strata, where each stratum is comprised of closely packed atomic groups with intrachain bonding constraints between the strata. A perturbing stratum can be introduced by imposing spacing, symmetry, and size constraints in one of the strata that are incommensurate with close-packing requirements of the other strata. Using molecular mechanics and dynamics simulations, we study two concrete examples: a chemisorption potential incompatible with planar close-packing and a mid-chain bulky group. We find a progressive rearrangement from the packing at the perturbing stratum toward a lower energy-packing, at the expense of progressive distortions of the chains that increase their total bond angle energy. The experimental implications of such rearrangements are discussed briefly.