Importance of the Positively Charged σ-Hole in Crystal Engineering of Halogenated Polypeptoids

Crystalline nanosheets formed by amphiphilic block copolypeptoids with halogenated phenyl side chains were imaged at the atomic-scale using cryogenic transmission electron microscopy (cryo-TEM). In general, the polypeptoid molecules adopt V-shaped configurations in the crystalline state, and adjacent molecules can pack with one another in either parallel or antiparallel arrangements, depending on the chemical composition. The halogen bond, which can have characteristic energies ranging from 1 to 5 kcal/mol, is commensurate with the parallel configuration. However, cryo-TEM images show that chains in the halogenated crystals were in the antiparallel configuration. Molecular dynamics (MD) simulations show that positively charged σ-holes, which are characteristic of halogen atoms covalently bonded to carbon atoms, play an important role in determining crystal geometry. Parallel and antiparallel configurations exhibited similar stability in simulations when standard force fields that only account for the electronegativity of halogen atoms were used. However, including the σ-hole in the simulations resulted in a destabilization of the parallel configuration. This combination of imaging and simulation, which has played an important role in structural biology, has the potential to improve our understanding of factors that govern noncovalent interactions in synthetic materials.