Study of ortho-Phenylene Foldamers using Molecular Dynamics Simulation

In nature, the folding of oligomers and polymers is used to generate complex threedimensional structures, yielding macromolecules with diverse functions in catalysis, recognition, transport, and charge- and energy-transfer. The ortho-phenylenes are a simple class of foldamers, with the formation of helices driven by offset aromatic stacking interactions parallel to the helical axis. The conformational behavior of o-phenylene 8-mers solvated in a series of linear alkane solvents by means of classical molecular dynamics and firstprinciples calculations was studied. We carried out a theoretical study on the conformational behavior of o-phenylene using molecular dynamics (MD) techniques. The canonical ensemble (NVT) was used to simulate a single o-phenylene molecule in the gas phase, whereas the NPT ensemble was used to model ophenylene/ solvent systems to allow for control over pressure. Molecular geometries and intermolecular interactions were described by adopting the parameterization of the OPLS allatom force field optimized for accurate reproduction of density, latent heat of vaporization, and torsional angle distribution for liquid hydrocarbons. we next carried out 16 ns MD simulations of the gas-phase o-phenylene 8-mer at 300 K starting from the coiled configuration. The systematic studies of o-phenylene 8-mers showed that they reliably fold into helices in solution, and the effects of factors such as solvent, the electron-withdrawing substituent and electron-releasing substituent on the aromatic ring, and … on the structure of this foldamer.