Molecular orbital study of polypeptides. Conformational and electronic structure of polyglycine

Abstract

Approximate ob inifio molecular orbital calculations are presented for the di-, tri-, tetra-, and pentapeptides of glycine. Six key conformations of polyglycine were considered: fully extended, parallel chain-pleated sheet, antiparallel chain-pleated sheet, a helix, 3-10 helix, and polyglycine 11. Beyond the pentapeptide level the a-helix and 3-10-helix conformations were predicted to be the most stable. The stability of the latter pair of conformations is attributed to hydrogen bonding, an effect which is confirmed by a detailed population analysis of the wave function. Additional evidence for hydrogen bond formation is provided by the localized molecular orbitals which are reported for several conformations studied here. An analysis of the eigenvalue spectrum of these molecules reveals a band structure that is characteristic of periodic systems. All calculations were performed using the partial retention of diatomic differential overlap (PRDDO) approximation. Comparisons of the PRDDO results with experiment and with other molecular orbital techniques are also made.

Aggregation of Capped Hexaglycine Strands into Hydrogen-Bonding Motifs Representative of Pleated and Rippled β-Sheets, Collagen, and Polyglycine I and II Crystal Structures. A Density Functional Theory Study

“…Recent Hartree-Fock and DFT calculations have found small models of infinite strands of polyglycine9 and antiparallel β-sheets to be essentially planar 10,11. Earlier MO calculations were based upon pleated sheet structures without geometry optimization 12–15…”

“…Of the natural amino acids, only glycine (which is enantiomorphic) can assume such a structure. Recent Hartree−Fock and density functional theory (DFT) calculations have found small models of infinite strands of polyglycine and antiparallel β-sheets to be essentially planar. , Earlier MO calculations were based upon pleated sheet structures without geometry optimization. − …”

“…10,11 Earlier MO calculations were based upon pleated sheet structures without geometry optimization. [12][13][14][15] Polyglycine is the only short peptide that can form H-bonding motifs that resemble all the H-bonding motifs studied here. As such, it is the only short peptide that can be used to compare the "natural" relative energies of all of these motifs without the influence of the side chains that differentiate between the amino acids.…”