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Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates

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Department of Chemical Engineering and Materials Science and Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
Cite this: J. Phys. Chem. B 2015, 119, 35, 11459–11465
Publication Date (Web):August 21, 2015
https://doi.org/10.1021/acs.jpcb.5b03874
Copyright © 2015 American Chemical Society

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    Abstract

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    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.

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    Cited By

    This article is cited by 10 publications.

    1. Jeffrey Gorman, Sarah R. E. Orsborne, Akshay Sridhar, Raj Pandya, Peter Budden, Alexander Ohmann, Naitik A. Panjwani, Yun Liu, Jake L. Greenfield, Simon Dowland, Victor Gray, Seán T. J. Ryan, Sara De Ornellas, Afaf H. El-Sagheer, Tom Brown, Jonathan R. Nitschke, Jan Behrends, Ulrich F. Keyser, Akshay Rao, Rosana Collepardo-Guevara, Eugen Stulz, Richard H. Friend, Florian Auras. Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides. Journal of the American Chemical Society 2022, 144 (1) , 368-376. https://doi.org/10.1021/jacs.1c10241
    2. Nadjib Kihal, Ali Nazemi, Steve Bourgault. Supramolecular Nanostructures Based on Perylene Diimide Bioconjugates: From Self-Assembly to Applications. Nanomaterials 2022, 12 (7) , 1223. https://doi.org/10.3390/nano12071223
    3. Arpita Srivastava, Avinash Garg, Debapratim Das, Ananya Debnath. Molecular dynamics simulations of a stacked $$\uppi $$-conjugated soft material: binding energy and preferential geometry for self-assembly. Bulletin of Materials Science 2020, 43 (1) https://doi.org/10.1007/s12034-020-2053-4
    4. Andrew Bartlett, Cade B. Markegard, David J. Dibble, Alon A. Gorodetsky, Sahar Sharifzadeh, Hung D. Nguyen. Molecular dynamics simulations of DNA-inspired macromolecules from perylenediimide base surrogates. Synthetic Metals 2019, 253 , 146-152. https://doi.org/10.1016/j.synthmet.2019.04.012
    5. Kuo‐Yao Lin, Anthony Burke, Nolan B. King, Dimithree Kahanda, Amir Mazaheripour, Andrew Bartlett, David J. Dibble, Marc A. McWilliams, David W. Taylor, Jonah‐Micah Jocson, Majid Minary‐Jolandan, Alon A. Gorodetsky, Jason D. Slinker. Enhancement of the Electrical Properties of DNA Molecular Wires through Incorporation of Perylenediimide DNA Base Surrogates. ChemPlusChem 2019, 84 (4) , 416-419. https://doi.org/10.1002/cplu.201800661
    6. Pascal Röthlisberger, Fabienne Levi-Acobas, Ivo Sarac, Rémy Ricoux, Jean-Pierre Mahy, Piet Herdewijn, Philippe Marlière, Marcel Hollenstein. Incorporation of a minimal nucleotide into DNA. Tetrahedron Letters 2018, 59 (48) , 4241-4244. https://doi.org/10.1016/j.tetlet.2018.10.036
    7. Amir Mazaheripour, Gregor Kladnik, Jonah-Micah Jocson, Austin G. Wardrip, Cade B. Markegard, Nathan Frey, Albano Cossaro, Luca Floreano, Alberto Verdini, Andrew Bartlett, Anthony M. Burke, Nina Hüsken, Kelsey Miller, Katarina Van Wonterghem, Robert Lopez, Michelle Lu, Amrita Masurkar, Mary N. Dickson, Sahar Sharifzadeh, Hung D. Nguyen, Ioannis Kymissis, Dean Cvetko, Alberto Morgante, Alon A. Gorodetsky. Unexpected length dependence of excited-state charge transfer dynamics for surface-confined perylenediimide ensembles. Materials Horizons 2017, 4 (3) , 437-441. https://doi.org/10.1039/C6MH00465B
    8. Austin G. Wardrip, Amir Mazaheripour, Nina Hüsken, Jonah‐Micah Jocson, Andrew Bartlett, Robert C. Lopez, Nathan Frey, Cade B. Markegard, Gregor Kladnik, Albano Cossaro, Luca Floreano, Alberto Verdini, Anthony M. Burke, Mary N. Dickson, Ioannis Kymissis, Dean Cvetko, Alberto Morgante, Sahar Sharifzadeh, Hung D. Nguyen, Alon A. Gorodetsky. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angewandte Chemie 2016, 128 (46) , 14479-14483. https://doi.org/10.1002/ange.201605411
    9. Austin G. Wardrip, Amir Mazaheripour, Nina Hüsken, Jonah‐Micah Jocson, Andrew Bartlett, Robert C. Lopez, Nathan Frey, Cade B. Markegard, Gregor Kladnik, Albano Cossaro, Luca Floreano, Alberto Verdini, Anthony M. Burke, Mary N. Dickson, Ioannis Kymissis, Dean Cvetko, Alberto Morgante, Sahar Sharifzadeh, Hung D. Nguyen, Alon A. Gorodetsky. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angewandte Chemie International Edition 2016, 55 (46) , 14267-14271. https://doi.org/10.1002/anie.201605411
    10. Riccardo Concu, Manuel Azenha, M Cordeiro. Molecular Dynamics Simulations and Comparison of Two New and High Selective Imprinted Xerogels. 2016, 339-361. https://doi.org/10.1201/9781315368863-15

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