On similarity of structure of icosahedral viral capsids and shells of metallic nanoclusters

Abstract

TOPOS software has been applied for searching for topological types of viral capsids—virus shells generated by self-assembly of proteins into geometrically ordered structure (VIPERdb database). Three topological capsid types that characterize packing of capsomeres (1) in the form of 12-vertex icosahedron (its vertex are occupied with pentamers), (2) in the form of 32-vertex polyhedron (12-pentamers + 20-hexamers), and (3) in the form of 62-vertex polyhedron (12-pentamers + 50-hexamers) have been outlined. The three mentioned polyhedral shells have been presented in the form of graphs of edge nets and applied for searching for relevant nanocluster fragments in the developed database of intermetallic compounds (25808 structures). It has been established that local structures in the form of icosahedral shells can be met in 6403 (27.1%) intermetallic compounds. Thirty-two atom shells have been found in 469 (2.0%) intermetallic compounds; furthermore, they are always the second shells of Bergman nanoclusters where the first shell is icosahedron. Sixty-two atom polyhedral shells in intermetallic compounds have not been found in intermetallic compounds; however, a modified 110-atom shell has been obtained on its basis, which is a polyhedron with 72 pentagonal faces. Such a shell has been established in 18 intermetallic compounds, including quasicrystal approximants AlCa3Cd17, CaCd6, Eu3Cd19, HfNi2.15Ca3.85, etc.