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We introduce the basic concepts of two-dimensional electronic spectroscopy (2DES) and a general theoretical framework adopted to calculate, from first principles, the nonlinear response of multi-chromophoric systems in realistic environments. Specifically, we focus on UV-active chromophores representing the building blocks of biological systems, from proteins to nucleic acids, describing our progress in developing computational tools and protocols for accurate simulation of their 2DUV spectra. The roadmap for accurate 2DUV spectroscopy simulations is illustrated starting with benchmarking of the excited-state manifold of the chromophoric units in a vacuum, which can be used for building exciton Hamiltonians for large-scale applications or as a reference for first-principles simulations with reduced computational cost, enabling treatment of minimal (still realistic) multi-chromophoric model systems. By adopting a static approximation that neglects dynamic processes such as spectral diffusion and population transfer, we show how 2DUV is able to characterize the ground-state conformational space of dinucleosides and small peptides comprising dimeric chromophoric units (in their native environment) by tracking inter-chromophoric electronic couplings. Recovering the excited-state coherent vibrational dynamics and population transfers, we observe a remarkable agreement between the predicted 2DUV spectra of the pyrene molecule and the experimental results. These results further led to theoretical studies of the excited-state dynamics in a solvated dinucleoside system, showing that spectroscopic fingerprints of long-lived excited-state minima along the complex photoinduced decay pathways of DNA/RNA model systems can be simulated at a reasonable computational cost. Our results exemplify the impact of accurate simulation of 2DES spectra in revealing complex physicochemical properties of fundamental biological systems and should trigger further theoretical developments as well as new experiments.

The Siberian hamster ultraviolet (SHUV) visual pigment has an unprotonated Schiff-base (SB) retinyl chromophore in the dark state, which becomes protonated after photoexcitation during the early stages of the photobleaching cycle. While the photochemical relaxation processes of the SHUV remain poorly understood, they are expected to show significant differences when compared to those of the protonated SB (PSB) chromophore in visual rhodopsin. Here, we report a study of the photophysical properties of the SHUV unprotonated SB (SHUV-USB), based on multiconfigurational and multireference perturbative methods within a hybrid quantum mechanics/molecular mechanics scheme. Comparisons of multireference and time-dependent density functional theory results indicate that both methodologies predict an ionic excited state (S1), similar to the PSB of rhodopsin, although its minimum has even bond-lengths in the central region of the retinyl polyene chain. The analysis of excited-state manifolds at the Franck–Condon region and S1 minimum configuration indicates that the skeletal relaxation initiated in the S1 surface is likely to involve S1/S2 surface crossing. These results provide valuable insights for future studies of the SHUV-USB photoisomerization mechanism.