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. 2020 Nov 2;26(11):326. doi: 10.1007/s00894-020-04564-5.

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: Chirality; DFT; Diphenylalanine; Molecular modeling; Peptide nanotube; Polarization; Self-assembly; Semi-empirical methods; Water molecules.

MeSH terms

  • Computer Simulation*
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular*
  • Nanotubes, Peptide / chemistry*
  • Phenylalanine / chemistry
  • Thermodynamics
  • Water / chemistry*

Substances

  • Nanotubes, Peptide
  • diphenylalanine
  • Water
  • Phenylalanine