A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. The method is applied towards a study of the highly flexible water-solvated adenine–adenine monophosphate (ApA), a system featuring two interacting adenine moieties that display various intermolecular arrangements, known to deeply affect their photochemical outcome. Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the complexity of the flexible ApA conformational space. By using our sum-over-states (SOS) approach to obtain the 2DES spectra for each of these selected conformations, we can discern spectral changes and relate them to specific nuclear arrangements: close lying π-stacked bases exhibit a splitting of their respective ¹L_a signal traces; T-stacked bases exhibit the appearance of charge transfer states in the low-energy Vis probing window while displaying no ¹L_a splitting, being particularly favoured when promoting amino to 5-ring interactions; unstacked and distant adenine moieties exhibit signals similar to those of the adenine monomer, as is expected for non-interacting nucleobases. 2DES maps reveal the spectral fingerprints associated with specific molecular conformations, and are thus a promising option to enable their quantitative spectroscopic detection beyond standard 1D pump-probe techniques. This is expected to aid the understanding of how nucleobase aggregation controls and modulates the photostability and photo-damage of extended DNA/RNA systems.

中文翻译：

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二维电子光谱作为追踪DNA / RNA聚集体中分子构象的工具

介绍了一种模拟二维电子光谱（2DES）的计算策略，它使我们能够分析基态动力学，并采样和测量溶液中柔性分子系统获得的不同构象。显式的混合量子力学/分子力学（QM / MM）方法用于评估必要的电子激发态能量和跃迁偶极矩。该方法用于研究高度灵活的水溶腺嘌呤-单磷酸腺嘌呤（ApA）系统，该系统具有两个相互作用的腺嘌呤部分，显示出不同的分子间排列，已知会深深影响其光化学结果。分子动力学模拟和聚类分析已用于选择分子构象，降低了灵活的ApA构象空间的复杂性。通过使用状态总和（SOS）方法获得这些选定构象中每个构象的2DES光谱，我们可以辨别光谱变化并将其与特定的核排列相关：紧密堆积的π堆积碱基表现出它们各自的分裂¹ L _a信号迹线；T堆积的碱基在低能Vis探测窗口中表现出电荷转移状态，而没有¹ L _a分裂，当促进氨基与5环的相互作用时尤其受青睐；如非相互作用核碱基所预期的那样，未堆叠且相距较远的腺嘌呤部分表现出与腺嘌呤单体相似的信号。2DES图谱揭示了与特定分子构象相关的光谱指纹，因此是使它们的定量光谱检测超出标准1D泵浦探针技术的有前途的选择。预期这将有助于理解核碱基的聚集如何控制和调节扩展的DNA / RNA系统的光稳定性和光损伤。