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Updated: Apr 17, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
Published on: May 13, 2020
Theoretical study of the molecular ordering, paracrystallinity, and charge mobilities of oligomers in different
Ilhan Yavuz1, Blanton N Martin, Jiyong Park
1Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States.
Abstract:
Molecular ordering and charge transport have been studied computationally for 22 conjugated oligomers fabricated as crystal or thin-film semiconductors. Molecular dynamics (MD) simulations are employed to equilibrate crystal morphologies at 300 K. The paracrystalline order parameter, g, is calculated to characterize structural order in the materials. Charge-transport dynamics are predicted using kinetic Monte Carlo methods based on a charge-hopping mechanism described by the Marcus theory of electron transfer to calculate charge-transfer rates using the VOTCA package. We introduce an error function to assess the reliability of our computed values to reproduce experimental hole mobilities in both crystalline and thin-film morphologies of the 22 conjugated oligomers. For each of the oligomers, we compute hole mobility with three different theoretical models incorporating increasing measures of disorder: (1) a perfect crystal, based on the experimentally derived crystal structure, with no disorder, (2) an MD-equilibrated structure incorporating thermal disorder into the crystal structure, and (3) model 2 above but also incorporating energetic disorder arising from variations in site energies. For the series of known crystals with long-range order, we find that the perfect crystal model produces hole mobilities giving the best fit to experimental data. For the series of thin-film morphologies with short-range order, we observe that the presence of both thermal and energetic disorder is essential for accurate calculation. We also discuss the interplay between hole mobility and other charge-transport parameters in these morphologies, such as reorganization energy and energetic disorder.
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