Organic nanowires represent idealized model systems for understanding the interactions between organic semiconductor building blocks. We have synthesized nanowires consisting of pi-conjugated DNA-base surrogates covalently attached to a DNA-like backbone and studied the properties of these constructs with molecular dynamics simulations. The DNA base surrogates were first parametrized through quantum mechanics calculations to create an atomistic model. Subsequently, constant-temperature molecular dynamics simulations provided an improved understanding of the kinetics of stacking between adjacent DNA base surrogates. In turn, replica-exchange simulations yielded the atomic structures of our nanowires at equilibrium. By examining the lowest energy structures obtained from our simulations, we gained insight into the geometry of our nanowires that would not be readily available through experimental techniques.

Molecular dynamics simulations of stacked DNA base surrogates

251st National Meeting (2016)

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