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.
Highlights
Structural isomers are an important class of molecules with the same chemical formula but varied geometric arrangements of bonds, resulting in different physical and chemical properties [1]
While it has been empirically established that catalysts can be used to enrich one isomer over another [5,6], the role of geometry, steric interactions in intermediates and assembly pathways are not well understood
We ask the critical question: What geometric features, pathways and intermediates cause nets to self-assemble into Isomer I or II? In order to investigate the assembly pathways and intermediates that emerge from these nets we modeled the assembly using discrete geometry, extending ideas introduced earlier [16]
Summary
Structural isomers are an important class of molecules with the same chemical formula but varied geometric arrangements of bonds, resulting in different physical and chemical properties [1]. N-pentane, isopentane and neopentane all have five carbon atoms, twelve hydrogen atoms and similar interatomic bonding (tetrahedral sp carbon). Isomerization of a single amino acid such as proline can have a dramatic influence on the assembly of larger ribonuclease and cause slow folding of the molecule [3,4]. While it has been empirically established that catalysts can be used to enrich one isomer over another [5,6], the role of geometry, steric interactions in intermediates and assembly pathways are not well understood. Mechanisms and rational designs to synthetically enrich one self-assembling isomer over the other are limited
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