Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diph
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ORIGINAL PAPER
Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules Vladimir S. Bystrov 1 & Jose Coutinho 2 & Pavel S. Zelenovskiy 3,4 & Alla S. Nuraeva 3 & Svitlana Kopyl 5 & Sergei V. Filippov 1 & Olga A. Zhulyabina 6 & Vsevolod A. Tverdislov 6 Received: 9 July 2020 / Accepted: 7 October 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. Keywords Diphenylalanine . Peptide nanotube . Water molecules . Molecular modeling . DFT . Semi-empirical methods . Self-assembly . Polarization . Chirality
Introduction Self-assembly of complex molecular structures based on amino acids (AA) is one of the most important phenomena both in living nature and in artificial biomimetics [1, 2]. At the same time, the chirality of the initial molecules also plays an
* Vladimir S. Bystrov [email protected] 1
Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Moscow region, Russia
2
Department of Physics & I3N, University of Aveiro, Campus Santiago, 3810-193 Aveiro, Portugal
3
School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia
4
Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
5
Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
6
Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia
important role in self-assembly processes [3, 4]. All this is important both for our understanding of wildlife and the basic principles of the emergence of life, and for numerous practical applications [5–7], including for biomedicine and targeted drug delivery [8, 9]. A necessary research approach here is computer molecular modeling of the processes of self-organization of molecular systems at the different levels and by different methods [10–12]. All AA have their own dipole moments [13], which interact with each other and self-organize into more complex molecular and crystalline structures, such as peptide nanotubes (PNT) and similar nanostructures [14]. Many of these structures have piezoelectric and ferroelectric properties [15–20]. This has been shown and investigated in detail in our work [20–26]. Self-ass
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