Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis

Abstract

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. 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, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.

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

“…Figure 7 d, e, and f shows a separation of the molecular groups of the water cluster into their internal (or inner) and external (or outer) sub-groups. The outer molecules interact actively with FF atoms on the inner hydrophilic PNT cavity surface, namely with nitrogen and oxygen atoms due to hydrogen bonds [43]. These results are also confirmed by Visual-Differential analysis [26], which are to be published in a separate article.…”

“…These calculations require more time to proceed on a computer cluster. Nevertheless, finally, it was possible to obtain a good number of optimized structures for both D-FF and L-FF (albeit with slightly variations in their structural parameters, but sufficient to estimate reliably the effect of different + groups (short "near" inner diameter PNT) [43].…”

“…4 Schematic images of the initial water cluster embedded into the inner hydrophobic hallow cavity of the D-FF PNT: a top Z-projection images consisting from 4 unit cells of D-FF crystal structure obtained using Jmol from VASP initial data before optimization calculations (green and red lines marked the unit cell; yellow circle shows the selected atoms and molecules that form the PNT with cavity in the center filled with water cluster molecules; the colors of atoms are the same as of Fig. 1); b the same Z-projection images converted from VASP to HyperChem workspace using Cyberduck and OpenBabel software (red circle shows the same selected atoms and molecules that form the PNT with cavity in the center filled with water cluster molecules; the colors of atoms here are as follows: carbon is cyan, red is oxygen, white is hydrogen); c side Y-projection and cross-section of D-FF structures with selected water molecules formed initial water cluster [43].…”

Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

“…Открытие их пироэлектрических, пьезоэлектрических, электронных и оптических свойств [22][23][24][25][26][27][28] сделало FF PNT перспективными кандидатами для различных датчиков, исполнительных механизмов, что открывает новые возможности для разработки интеллектуальной микроэлектроники. Было показано влияние исходной хиральности дипептидов FF (L-FF, D-FF) на формирование спиральных вторичных структур разной хиральности со сменой знака хиральности, и влияние хиральности на физические свойства [30][31][32]. Есть данные о возможном применении их для адресной доставки лекарственных препаратов [33,34].…”

“…Дополнительное силовое воздействие «диаметральная растяжка».Второй тип пружин будет обеспечивать цилиндрическую связку спирали, шаг спирали, то есть соединять первую аминокислоту с 13, вторую с 14, третью с 15 и т.д. Длина пружины должна была бы составлять 5.44 Å, аналогично[29][30][31][32] (см. Рис.…”