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Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules

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Abstract

DFT (VASP) and semi-empirical (HyperChem) calculations for the l- and d-chiral diphenylalanine (l-FF and d-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type l-FF and d-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as l-FF and d-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside l-FF and d-FF PNT and total l-FF and d-FF PNT with embedded water/ice cluster are discussed.

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Acknowledgments

This work was partially supported by the Fundacão para a Ciência e a Tecnologia(FCT, Portugal) through project UID/CTM/50025/2013 and UIDB/50011/2020 & UIDP/50011/2020. P.Z. and S.K. are grateful to the FCT (Portugal) through the project “BioPiezo,” PTDC/CTM–CTM/31679/2017 (CENTRO-01-0145-FEDER-031679). The computational parts of the study was completed within the framework of the non-commercial Agreement on scientific-technical cooperation between Institute of Mathematical Problems of Biology (IMPB) of the Keldysh Institute of Applied Mathematics RAS (KIAM RAS) and Department of Physics and I3N Institution of the University of Aveiro, Portugal.

Funding

This work was supported by Russian Foundation for Basic Research (RFBR No. 19-01-00519-a and No. 18-07-00354-a (S.V. Filippov)).

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Authors and Affiliations

  1. Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290, Pushchino, Moscow region, Russia

    Vladimir S. Bystrov & Sergei V. Filippov

  2. Department of Physics & I3N, University of Aveiro, Campus Santiago, 3810-193, Aveiro, Portugal

    Jose Coutinho

  3. School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia

    Pavel S. Zelenovskiy & Alla S. Nuraeva

  4. Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal

    Pavel S. Zelenovskiy

  5. Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal

    Svitlana Kopyl

  6. Faculty of Physics, Lomonosov Moscow State University, 119991, Moscow, Russia

    Olga A. Zhulyabina & Vsevolod A. Tverdislov

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  1. Vladimir S. Bystrov
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Correspondence to Vladimir S. Bystrov.

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Bystrov, V.S., Coutinho, J., Zelenovskiy, P.S. et al. Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules. J Mol Model 26, 326 (2020). https://doi.org/10.1007/s00894-020-04564-5

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