Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes)

Alik S. Widge, Yoky Matsuoka, Maria Kurnikova

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10 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)34-44
Number of pages11
JournalJournal of Molecular Graphics and Modelling
Issue number1
StatePublished - Aug 2008
Externally publishedYes

Bibliographical note

Funding Information:
ASW was funded during this research by a Ruth L. Kirchstein National Research Service Award (grant number F30 NS051866-01) from the National Institutes of Health. The simulations reported here were carried out using the Cray XT3 machine of the Pittsburgh Supercomputing Center, and we thank PSC for its generous grants of computer time to MK (NSF PACI CHE030007P) and YM. MK's research is also supported by NIH (GM067962-01).


  • Conductive polymer
  • Force field
  • Implicit solvent
  • Molecular dynamics
  • Polythiophene


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