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Center for Nonlinear Studies |
Studies on the nature of decay in the DNA nucleobases and larger oligomers are essential in order to further our understanding of the complex photochemical and photophysical processes which lead to cell degradation and mutation which are two of the major causes of skin cancer. In this work the algebraic diagrammatic construction through second order level of theory method (ADC(2)) is utilized to describe the excited states of a pi-stacked adenine dimer embedded in a 20 base pair DNA duplex through a combination of Quantum Mechanical and classical methods (QM/MM). Inclusion of the environmental interaction dramatically alters the shape of the potential energy surfaces due to steric interactions from the backbone and interactions with the surrounding bases and environment. This work examines the complete picture of photophysical processes occuring in adenine oligonucleotides within the environment of the DNA helix: the nature of initial absorption and the subsequent radiative and non-radiative decay.1,2,3 The results of our studies reveal that geometries with increased excitonic coupling due to pi-stacking interactions contribute to the additional features present in the first absorption band when comparing polynucleotides to the monomer bases. Within the Franck Condon region we find that the photoexcitation of conformations with a mix of excitonic and charge transfer character may decay to excimers and bonded excimers. Analysis of the physical properties of these conformations in relation to experimental findings reveals that these species undergo photophysical deactivation processes on longer timescales and are responsible for long-lived signals evidenced in Transient Absorption and Fluorescence experiments.4 1. V. A. Spata, W. Lee, and S. Matsika, “Excimers and Exciplexes in Photoinitiated Processes in Oligonucleotides.” J. Phys. Chem. Lett., 7, 976-984 (2016) http://dx.doi.org/10.1021/acs.jpclett.5b02756 2. V. A. Spata and S. Matsika, “Photophysical Deactivation Pathways in Adenine Oligonucleotides.” Phys. Chem. Chem. Phys., 17, 31073-31083 (2015) http://dx.doi.org/10.1039/C5CP04254B 3. V. A. Spata and S. Matsika, “Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations.” J. Phys. Chem. A, 118, 12021-12030 (2014) http://dx.doi.org/10.1021/jp507520c 4. Middleton, C. T.; de La Harpe, K.; Su, C.; Law, Y. K.; Crespo-Hernández, C. E.; Kohler, B. Annu. Rev. Phys. Chem. 2009, 60, 217-239. If you would like to meet with Vincent, please contact Sergei Tretiak (serg@lanl.gov)
Host: Sergei Tretiak