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In this discussion we present a methodology to describe spectral lineshape from first principles, providing insight into the solvent-solute molecular interactions in terms of static and dynamic disorder and how these shape the signals recorded experimentally in linear and nonlinear optical spectroscopies, including two-dimensional electronic spectroscopy (2DES). Two different strategies for simulating the lineshape are compared: both rely on the same evaluation of the coupling between the electronic states and the intra-molecular vibrations, while they differ in describing the influence exerted by the diverse water configurations attained along a molecular dynamics (MD) simulation. The first method accounts for such water arrangements as first order perturbations on the adenine energies computed for a single reference (gas phase) quantum calculation. The second method requires computation of the manifold of excited states explicitly at each simulation snapshot, employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. Both approaches are applied to a large number of states of the adenine singlet excited manifold (chosen because of its biological role), and compared with available experimental data. They give comparable results but the first approach is two orders of magnitude faster. We show how the various contributions (static/dynamic disorder, intra-/inter-molecular interactions) sum up to build the total broadening observed in experiments.

X-ray spectroscopy is gaining a growing interest in the scientific community, as it represents a versatile and powerful experimental toolbox for probing the dynamics of both core and valence electronic excitations, nuclear motions and material structure, with element and site specificity. Among the various X-ray based techniques, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, which investigates the energy and probability of resonant core-to-valence transitions, has started to be applied to organic molecules: a recent UV-pump X-ray probe time-resolved NEXAFS experiment [Wolf et al., Nat. Commun., 2017, 8, 1] has shown the capability of the technique to provide information about the ultrafast internal conversion between the bright ππ* and the dark nπ* electronic states of the nucleobase thymine. In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case. The electronic structure calculations, which provide both energy levels and transition probabilities of core-to-valence excitations, were here performed with a high level multiconfigurational method, the restricted active space self consistent field (RASSCF/RASPT2). GS- and nπ*-NEXAFS spectra were obtained on the top of key molecular geometries (as the optimized cis, trans and conical intersection(s) structures) as well as along the fundamental isomerization coordinates (namely, symmetric and asymmetric bendings of the phenyl rings, and torsion around the central dihedral). We eventually characterize and explain the origin of the simulated signals, highlighting the specific signatures that make it possible to follow the excited state evolution from the nπ* Franck-Condon point, towards the conical intersection(s).

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 1La signal traces; T-stacked bases exhibit the appearance of charge transfer states in the low-energy Vis probing window while displaying no 1La 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.

The UVB-induced photomechanism leading the carbonyl group of a thymine nucleobase to react with the carbon-carbon double bond of a consecutive thymine nucleobase in a DNA strand to form the thymine-thymine (6-4) photodamage adduct remains poorly understood. Key questions remain unanswered, concerning both the intrinsic features of the photoreaction (such as the contribution (or not) of triplet states, the nature of the involved states and the time-scale of the photoprocess) and the role played by the non-reactive surroundings of the two reactive pyrimidine nucleobases (such as the nature of the flanked nucleobases and the flexibility of the whole DNA molecule). A small number of theoretical studies have been carried out on the title photoreaction, most of which have used reduced model systems of DNA, consequently neglecting potential key parameters for the photoreaction such as the constraints due to the double strain structure and the presence of paired and stacked nucleobases. In the present contribution the photoactivation step of the title reaction has been studied in a DNA system, and in particular for a specific DNA hairpin for which the quantum yield of photodamage formation has been recently experimentally measured. The reaction has been characterized by carrying out high-level QM/MM computations, combining the CASPT2//CASSCF approach for the study of the reactive part (i.e. the two thymine molecules) with an MM-Amber treatment of the surrounding environment. The possibility of a reaction path along both the singlet and triplet manifolds has been characterized, the nature of the reactive states has been analyzed, and the role played by the flexibility of the whole system, which in turn determines the initial accessible geometrical conformations, has been evaluated, thus substantially contributing towards the elucidation of the photoreaction mechanism. On the basis of the obtained results, it can be observed that a charge-transfer state can decay from a pro-reactive initial structure towards a region of energy degeneracy with the ground state, from which the subsequent decay along the ground state hypersurface can lead to the photoreaction.

The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.

In this paper we employ a CASSCF/AMBER quantum-mechanics/molecular-mechanics tool to map the intersection space (IS) of a protein. In particular, we provide evidence that the S1 excited-state potential-energy surface of the visual photoreceptor rhodopsin is spanned by an IS segment located right at the bottom of the surface. Analysis of the molecular structures of the protein chromophore (a protonated Schiff base of retinal) along IS reveals a type of geometrical deformation not observed in vacuo. Such a structure suggests that conical intersections mediating different photochemical reactions reside along the same intersection space. This conjecture is investigated by mapping the intersection space of the rhodopsin chromophore model 2-Z-hepta-2,4,6-trieniminium cation and of the conjugated hydrocarbon 3-Z-deca-1,3,5,6,7-pentaene.