Ab initio periodic study of the conformational behavior of glycine helical homopeptides.
Representative helicoidal conformations of polyglycine infinite chains have been investigated by using periodic boundary conditions, the B3LYP hybrid functional, and large basis sets, by means of the CRYSTAL code. The exploitation of the helix roto-translational symmetry permits to optimize at a relatively low cost the structure of systems whose unit cell contains more than 300 atoms, much larger than the one investigated till now. In the present calculations, the helix symmetry is exploited at three levels. First, for the automatic generation of the structure. Second, for the calculation of the one- and two-electron integrals that enter into the Fock matrix definition. Only the irreducible wedge of the Fock matrix is computed. Finally, for the diagonalization of the Fock matrix, where each irreducible representation is separately treated. The efficiency and accuracy of the computational scheme are documented, by considering cells containing up to 47 glycine residues. Results are compared with previous calculations and available experimental data. The role of hydrogen bonding in stabilizing polyglycine conformers is also addressed.
Ferrari
Anna Maria
AM
Dipartimento di Chimica IFM, Università di Torino and NIS (Nanostructured Interfaces and Surfaces), Centre of Excellence, Via P. Giuria 7, 10125 Torino, Italy. anna.ferrari@unito.it
Civalleri
Bartolomeo
B
Dovesi
Roberto
R
D003198:Computer Simulation; D006860:Hydrogen Bonding; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory
D010455:Peptides; C011080:polyglycine