On the Simulation of Two‐dimensional Electronic Spectroscopy of Indole‐containing Peptides

Abstract

A benchmark study of low-cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near-ultraviolet (UV) pump visible (VIS) probe (i.e. two-color) two-dimensional electronic spectra (2DES) of homo- and hetero-aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited-state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm . The 18-24 k cm spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge-transfer signatures in stacked aggregates. The small peptide Trp-cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge-transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near-UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra-short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited-state absorption signals can be correlated to the polarity of the relevant states.

The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations

“…To reduce costs, two different approaches have been followed: the use of artificial level shifts and of larger restricted active space schemes. In a series of benchmarks on aromatic systems [24,64,65] we have documented that the RASPT2 protocol using schemes with small active spaces or featuring a moderate number of CSFs can dramatically underestimate transition energies as it overestimates the dynamic correlation of ionic (in valence bond terms) states. In the search for a cost-effective protocol to counteract (or at least damp) this effect we observe that real and imaginary shift parameters (originally introduced to solve intruder state problem) invoke a non-uniform decrease of the correlation contribution, much more pronounced for ionic that for covalent states.…”

Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules

“…This SOS//QM/MM 77 protocol was applied to simulate 2DUV maps of folding/unfolding in small peptides, 80,103 p-stacking in a dinucleoside homo-dimer 88 and non-adiabatic dynamics in a dinucleoside hetero-dimer. 87 This approach is particularly appealing due to its simplicity and affordable computational cost and it is suitable for obtaining spectral ngerprints of photo-intermediates, in systems where the underlying conformational dynamics is slow, i.e.…”

Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy

“…This makes their use well suited for our purposes, even if we need to resort to larger values than suggested in the literature (a detailed argumentation can be found in ref. [83]). However, the choice of shift parameter is chromophoredependent and its application, while simpler with respect to orbital removal procedure, is limited to systems where transition energies of different chromophores can be corrected with the similar shift parameter, such as homodimeric systems.…”

“…A successful benchmark study aimed at identifying efficient multiconfigurational/multireference approaches in terms computational cost/accuracy ratio has been showed in details here for benzene and phenol chromophores involved in proteic systems. Analogous studies have been performed for indole [83] and adenine [57] chromophores, while the remaining nucleobases are currently under investigation. Overall, we believe that such theoretical benchmark studies are going to provide a full set of parameters and computational recipes that will allow building excitonic model Hamiltonians for applications in large systems (such full proteins or large DNA/RNA sequences) and simulating 2DUV spectra of dimeric and small oligomeric systems in realistic conditions with unprecedented accuracy.…”

“…In another example we benchmarked low-cost methods for indole. [83] The first two (ππ*) excited states (L b and L a ) of indole (see Figure 5) have essentially opposite character: L b is covalent, apolar, with low oscillator strength, while L a is ionic, polar and bright. Thus, indole represents a more intricate challenge compared to benzene and phenol that possess a single (covalent) state absorbing in the near-UV.…”