title: Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes).
abstract: Conductive polymers from the polythiophene (PT) family have attracted interest in numerous domains, including potential applications in biosensing. Despite this, atomistic simulations of PTs have tended to use general organic force fields without well-tuned PT parameters, and there exists no optimized and well-validated PT force field that is compatible and consistent with existing biomolecular simulation suites. We present here the development of a new PT forcefield following the AMBER approach, using the program ANTECHAMBER and ab initio calculations at the HF/6-31G* level of theory to assign partial charges and parameterize the critical backbone torsion potential. The optimized geometries and force field potentials match well with both empirical data and previous investigators' calculations. Initial testing of these parameters through a series of replica exchange simulations of two PT derivatives in aqueous and organic implicit solvents demonstrates that the parameters can match empirical expectations within the limits of an implicit solvent model. This new force field forms a framework for modeling of proposed PT-based devices and sensors, and is expected to accelerate device design and eventual deployment.
authors.affiliation: Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States.
authors.forename: Alik S
authors.initials: AS
authors.lastname: Widge
authors.forename: Yoky
authors.initials: Y
authors.lastname: Matsuoka
authors.forename: Maria
authors.initials: M
authors.lastname: Kurnikova
mesh_terms: D002625:Chemistry, Organic / Q000379:methods*; D003198:Computer Simulation; D019281:Dimerization; D008958:Models, Molecular; D011108:Polymers / Q000737:chemistry*; D012984:Software; D012997:Solvents; D013876:Thiophenes / Q000737:chemistry*
chemical_list: D011108:Polymers; D012997:Solvents; D013876:Thiophenes; C066730:polythiophene