Structure and stability of helices in square-well homopolymers

Abstract

Recently, it has been demonstrated [Magee, Phys. Rev. Lett. 96, 207802 (2006)] that isolated square-well homopolymers can spontaneously break chiral symmetry and "freeze" into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics combined with an optimized parallel tempering scheme to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a "window" of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature; however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.

Phase diagram for a single flexible Stockmayer polymer at zero field

“…Helicoidal states have also been found for non-magnetic chains when specific short-ranged square-well potentials were used 29 . Another issue worth to mention is the possibility that those helicoidal states could be long-lived metastable transient states as those found by Sabeur et al 30 for simple homopolymers using truncated Lennard-Jones potentials.…”

On the Pseudo Phase Diagram of Single Semi-Flexible Polymer Chains: A Flat-Histogram Monte Carlo Study

“…In one variant, chains described as thick tubes were suggested [24,25], which, upon collapse, are able to form helical ground states. In a different variant [26,27], the chains were built out of overlapping hard spheres, which, upon collapse, exhibit helical ground states for short enough chains. This model is promising for a systematic study of the effect of such steric stiffness on the single chain phase diagram [28], and we will report in the following on such a study.…”

First steps toward the construction of a hyperphase diagram that covers different classes of short polymer chains

“…It is known that any kind of anisotropic potential or a large stiffness caused by the repulsive part of the potential, can favour the local formation of secondary structures like helices. Interesting results for these kind of transitions include those of Kemp and Chen [12] and more recently those of Bannermann et al [13], Magee et al [14] and Vogel et al [15,16]. Although the transitions observed in polymer chain collapse processes are known to be of second order, the ground state is non-unique and highly depends on the potential models used in the simulations.…”