title: Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.
abstract: Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Cade B
authors: CB
authors: Markegard
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Amir
authors: A
authors: Mazaheripour
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Jonah-Micah
authors: JM
authors: Jocson
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Anthony M
authors: AM
authors: Burke
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Mary N
authors: MN
authors: Dickson
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Alon A
authors: AA
authors: Gorodetsky
authors: Department of Chemical Engineering and Materials Science and ‡Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
authors: Hung D
authors: HD
authors: Nguyen
mesh_terms: D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D007094:Imides / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010569:Perylene / Q000031:analogs & derivatives* / Q000737:chemistry; D013057:Spectrum Analysis; D013696:Temperature
chemical_list: D007094:Imides; C521332:perylenediimide; D010569:Perylene; D004247:DNA