Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study.

ABSTRACT: DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH₂ group or seven CH₂ groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.

SUBMITTER: Parra RD 

PROVIDER: S-EPMC10488343 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature