Asha Haritha, Green James A, Esposito Luciana, Martinez-Fernandez Lara, Santoro Fabrizio, Improta Roberto
Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.
Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany.
J Phys Chem B. 2022 Dec 22;126(50):10608-10621. doi: 10.1021/acs.jpcb.2c05688. Epub 2022 Dec 12.
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC) sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
在此，我们完善并评估了两种计算程序，旨在纳入热涨落对多发色团系统电子光谱和超快激发态动力学的影响，重点关注DNA双链体。我们的方法基于一种片段 diabatic 化程序，该程序从给定的量子力学（QM）参考方法出发，能够基于孤立片段为纯电子激子哈密顿量（FrDEx）或线性振子耦合哈密顿量（FrD-LVC）提供参考 diabatic 态的参数（能量和耦合）。在为两个较小片段上的DNA双链体定义了最具成本效益的程序后，FrDEx 被用于模拟（GC）序列的吸收光谱和电子圆二色性（ECD）光谱，包括与电荷转移（CT）态的耦合，这些光谱是在从经典分子动力学（MD）模拟中提取的多个结构上计算得到的。计算得到的光谱与参考的 TD-DFT 计算结果相近，且与实验结果完全一致。然后，我们将 MD 模拟与 FrD-LVC 相结合，以模拟当包含在寡聚 GC 或寡聚 AT DNA 序列中的 GC 和 CG 步中，局部激发与链内和链间 CT 跃迁之间的相互作用。我们预测，对于这两个序列，G 和 C 上光激发群体的很大一部分会在50 - 100飞秒内衰减到相应的链内 CT 态。这种转移对于 GC 步更为有效，因为平均而言，GC 步的堆积比 CG 步更紧密。
