Solvophobic and Steric Effects of Side Groups on Polymer Folding:  Molecular Modeling Studies of Amine-Functionalized m-Poly(phenyleneethynylene) Foldamers in Aqueous Solution

Abstract

The folding behavior of five different amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomers containing 24 phenyl rings (12 residues, where a residue includes 2 phenyl rings) in water was examined by using a combination of molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulation techniques. The REMD method employed the highly parallelized GROMACS MD software and a modified OPLS-AA force field to simulate 44 replicas of each solvated system in parallel, with temperatures ranging from 300 to 577 K. Our results showed that the REMD method was more effective in predicting the helical conformation of the m-PPE in water, from an extended structure, than canonical MD methods in the same simulation time. Furthermore, we observed from canonical MD simulations of the explicitly solvated helical m-PPEs at 300 K that the radius of gyration, average helix inner diameter, and average helix pitch of the helical structure all pass through a minima when the side group is R = OC(2)H(5) as R is changed from R = H through OC(4)H(9).

Recent advances in arylene ethynylene folding systems: Toward functioning

“…Ever since the folding behaviors of m-phenylene ethynylene (mPE) oligomers were first reported by Moore and coworkers in 1997 [26], mPE and related arylene ethynylene foldamer systems have been extensively developed and investigated [27][28][29][30][31][32][33][34][35][36][37][38][39]. Compared with many other foldamer systems containing non-natural, aromatic units, such as aromatic oligoamides [15,16,[40][41][42][43], arylene polymer/oligomers [21,24,25,[44][45][46][47][48][49][50][51][52][53][54][55], poly(phenylacetylene)s [21,23,[56][57][58], iso-polydiacetylenes [59,60], poly(N-propargylamides) [61], poly(N-octylcarbazole ethylene) [62], polydiacetylene [63], etc., arylene ethynylene foldable systems (AEFS) exhibit a distinct feature that they mainly rely on weak, noncovalent interactions among non-adjacent backbone units to realize folding.…”

Preparation and characterization of zeolite beta–polyurethane composite membranes

“…meta ‐Poly(phenylene ethynylene)s (mPPEs) are a class of macromolecules that are able to fold into stable helical conformations under suitable conditions 1–14. This biomimetic property makes them ideal for a variety of applications, including self‐assembled nanostructures for sensor, drug delivery, and other biological applications.…”

Effect of solvents on polymerization of N-propargylamide monomer and secondary structure of polymer

“…39,40 Adisa and colleagues also explored the solvophobic effect on polymeric folding. 41 More recently, Mikami and coworkers reported the helical folding prompted by solvophobic effect in poly(naphthalenecarboxamide). 42 Similar effects were also observed in conjugated oligo(o-phenyleneethynylene-alt-p-phenyleneethynylene) systems.…”