Molecular Dynamics Simulations of Helix-Forming, Amine-Functionalizedm-Poly(phenyleneethynylene)s

Abstract

We present here the results of all-atom and united-atom molecular dynamics (MD) simulations that were used to examine the folding behavior of an amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomer in aqueous environment. The parallelized GROMACS MD simulation code and OPLS force field were used for multiple MD simulations of m-PPE oligomers containing 24 phenyl rings in extended, coiled and helix conformations separately in water to determine the minimum energy conformation of the oligomer in aqueous solvent and what interactions are most important in determining this structure. Simulation results showed that the helix is the preferred minimum energy conformation of a single oligomer in water and that Lennard-Jones interactions are the dominant forces for the stabilization of the helix. In addition, these solvophobic interactions are strong enough to maintain the helix conformation at temperatures up to 523 K.

Conformational Space of a Polyphilic Molecule with a Fluorophilic Side Chain Integrated in a DPPC Bilayer

“…As these parameters already cover the side chains of the polyphilic molecule in Figure , only some additional parameters were needed for proper coverage of the molecule. For them, we strictly followed the CHARMM parametrization procedure, as discussed in the Supporting Information, where the resulting parameters as well as technical details are listed. For all calculations, SHAKE constraints have been used for the water molecules only.…”

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.…”