title: Modeling an electronic conductor based on natural peptide sequences.
abstract: In this work we used quantum mechanical calculations, molecular dynamics simulations, and QM/MM methods to examine the formation of a pi-stacking ladder and the existence of charge transfer processes in a tubular nanostructure constructed using protein building blocks. Initially, the conformational properties of beta-3-thienylalanine, a synthetic amino acid with an aromatic side group, were studied using quantum mechanical calculations. Next, this amino acid was used to substitute the natural residues at selected positions of the nanotube. Molecular dynamics simulations showed that a rational design of the targeted replacements enhances the stability of the tubular nanostructure and forms a pi-stacking ladder in the inner core of the tube. Finally, QM/MM calculations on the oxidized nanotube evidenced the delocalization of the pi-electron deficiency between the thienyl side groups of the different synthetic residues. The overall results reflected that the system under study is a potential candidate to be used as a nanowire.
authors: Departament d'Enginyeria Quimica, ETS d'Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona E-08028, Spain. francisco.rodriguez-ropero@upc.edu
authors: Francisco
authors: F
authors: Rodríguez-Ropero
authors: David
authors: D
authors: Zanuy
authors: Xavier
authors: X
authors: Assfeld
authors: Carlos
authors: C
authors: Alemán
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry*; D000595:Amino Acid Sequence; D001696:Biomechanical Phenomena; D003198:Computer Simulation; D004583:Electrons; D008432:Mathematical Computing; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D045333:Nanotubes, Peptide / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry* / Q000235:genetics; D011789:Quantum Theory
chemical_list: D045333:Nanotubes, Peptide; D010446:Peptide Fragments; D000409:Alanine