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CHARMM force field generation for a cationic thiophene oligomer with ffTK

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Abstract

In the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field.

Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.

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Acknowledgments

The numerical calculations reported in this paper were fully performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). We would like to give thanks to Ümit Hakan Yıldız for inspirations to this study.

Funding

This work was supported by the “Scientific and Technological Research Council of Turkey,” TUBITAK, under the project numbers 119Z100.

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Authors and Affiliations

  1. Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey

    Erman Kıbrıs, Nehir Nalıncı Barbak & Nuran Elmacı Irmak

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  1. Erman Kıbrıs
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  2. Nehir Nalıncı Barbak
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  3. Nuran Elmacı Irmak
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Correspondence to Nuran Elmacı Irmak.

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Kıbrıs, E., Barbak, N.N. & Irmak, N.E. CHARMM force field generation for a cationic thiophene oligomer with ffTK. J Mol Model 27, 34 (2021). https://doi.org/10.1007/s00894-020-04610-2

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