title: Self-assembly of mesoscale isomers: the role of pathways and degrees of freedom.
abstract: The spontaneous self-organization of conformational isomers from identical precursors is of fundamental importance in chemistry. Since the precursors are identical, it is the multi-unit interactions, characteristics of the intermediates, and assembly pathways that determine the final conformation. Here, we use geometric path sampling and a mesoscale experimental model to investigate the self-assembly of a model polyhedral system, an octahedron, that forms two isomers. We compute the set of all possible assembly pathways and analyze the degrees of freedom or rigidity of intermediates. Consequently, by manipulating the degrees of freedom of a precursor, we were able to experimentally enrich the formation of one isomer over the other. Our results suggest a new approach to direct pathways in both natural and synthetic self-assembly using simple geometric criteria. We also compare the process of folding and unfolding in this model with a geometric model for cyclohexane, a well-known molecule with chair and boat conformations.
authors.affiliation: Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Shivendra
authors.initials: S
authors.lastname: Pandey
authors.affiliation: Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Daniel
authors.initials: D
authors.lastname: Johnson
authors.affiliation: Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Ryan
authors.initials: R
authors.lastname: Kaplan
authors.affiliation: Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Joseph
authors.initials: J
authors.lastname: Klobusicky
authors.affiliation: Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Govind
authors.initials: G
authors.lastname: Menon
authors.affiliation: Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: David H
authors.initials: DH
authors.lastname: Gracias
mesh_terms: D007536:Isomerism; D008954:Models, Biological; D008968:Molecular Conformation