Bidimensional electronic spectroscopy on indole in gas phase and in water from first principles

Abstract

a b s t r a c tThe electronic transitions of indole, the aromatic UV chromophore of the amino acid tryptophan, are characterized by using state-of-the-art multiconfigurational methods in gas-phase and aqueous solution, revealing the electronic spectrum up to 10 eV. Bidimensional near-ultraviolet (2D-NUV) electronic spectra of indole are simulated using the sum-over-states approach, based on ab initio calculations, accounting for different experimental set-ups, including rephasing ðKI ¼ Àk 1 þ k 2 þ k 3 ), quasi-absorptive (PP) and double quantum coherence ðKIII ¼ k 1 þ k 2 À k 3 ) signals, and both one-color (2D-NUV) and two-colors (2D-NUV/Vis) regimes. In order to obtain accurate energies of high lying excited states and reliable 2DES spectra, extravalence virtual orbitals have been included using the restricted active space technique. The 2D-NUV spectrum of indole shows off-diagonal signals due to the correlation of the GS ? L b and GS ? L a transitions, an indole ''fingerprint'' in the NUV region that differentiate it from other aromatic chromophores in proteins. Further indole-specific transitions are resolved in the whole Vis-NUV range. A background-free region bellow the ionization potential, which shows no absorption signals in the monomer, can be used to resolve charge transfer states in coupled chromophore aggregates with a two-color 2D-NUV/Vis experimental set-up. Fundamental information for design of the 2DES experiments of indole is provided, including possible experimental pulse configurations that improve spectral resolution, revealing anharmonicities and selecting transitions. The proposed 2DES experiments could provide unprecedented level of detail for tracking indole electronic transitions in proteins, laying the groundwork for the use of nonlinear ultrafast optical spectroscopy for the study of protein structure and dynamics in solution.

Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy

“…Different levels of theory based on the RASSCF/RASPT2 framework have been tested in order to get the best compromise between accuracy and computational efforts for the simulation of nonlinear electronic spectroscopy experiments of the adenine monomer and homodimer. Following a previously reported recipe, 26 which takes into account valence-Rydberg mixing problems, the active space of adenine has been progressively enlarged yielding the most accurate estimate within the RASSCF/RASPT2 framework corresponding to a RAS(0,0| 12,10|2,12)/SS-RASPT2, which is here used as a reference. The computed transition energies and dipole moments here provided can be used for building parameterized exciton models for DNA/RNA nucleobases, similarly to what has been done in the past for aminoacids.…”

“…We have tested the ability of the reduced computations to reproduce the correct energy differences and TDMs (which are the required quantities in order to build the spectra within the sum-over-states approach) 26,30 so to properly account for the relevant spectral ranges Vis-NUV. The reduction of the level of theory can be operated in different ways employing either (a) a smaller active space, (b) the less expensive RAS scheme (see computational method Sec.…”

“…[19][20][21][22] Nevertheless, parameterized exciton models are commonly applied to study molecular aggregates as they allow for increasing the aggregate size at virtually no cost. In order to obtain more accurate estimates, we have recently introduced a computational protocol based on a sum-overstates approach 23 where ab initio calculations for dimeric and multimeric systems within a quantum mechanics/molecular mechanics (QM/MM) scheme 18,[24][25][26][27] are coupled with nonlinear response theory, 28 so as to give a better account of the inter-monomer and monomer-solvent interaction effects simultaneously. Within this approach, the dimeric or multimeric system is treated at an ab initio level, thus including the interaction between monomers giving rise to mixed doubly excited and CT states, providing unique fingerprints arising from these interactions that allow disentangling the spectral signals to differentiate specific conformations along folding and unfolding protein processes, 18,27 or to those signals arising due to stacking interactions in a DNA/RNA double-stranded chain.…”

Spectral lineshapes in nonlinear electronic spectroscopy

“…[1][2][3][4] Another essential requirement for modeling nonlinear spectra of photoexcited molecules is the incorporation of higher lying ES. This is desirable for two reasons: first, absorptions to these states (excited state absorptions, ESA) dominate the spectra due to the high spectral density in the visible (Vis) and ultraviolet (UV) region; [5][6][7] second, ESA, together with the stimulated emission (SE) represent characteristic signatures of each photophysical or photochemical decay channel, and hence, their proper description will allow us to recognize electronic structural changes during the dynamics, as well as to disentangle dynamics occurring via competing channels. 8 However, the higher ES also exhibits fluctuations coupled to the dynamics on the states on which the relevant photophysics and photochemistry occur (i.e.…”

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations

“…The SOS//QM/MM protocol is the first method which couples quantum-mechanics / molecular mechanics (QM/MM) calculations, multi-configurational excited state calculations with non-linear spectroscopy to generate time-resolved 2D electronic spectra 34 . It allows for the characterization of the vertical 1D and 2D electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy 27,35,36 . Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as CT excimer states are revealed.…”