Unraveling the contributions to the spectral shape of flexible dyes in solution: insights on the absorption spectrum of an oxyluciferin analogue

Abstract

We present a computational investigation of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH), an analogue of the emitter compound responsible for the bioluminescence in fireflies. Several factors concur to...

The protein environment restricts the intramolecular charge transfer character of the luciferine/luciferase complex

“…Summarizing, although the QM/MM vertical energy calculations based on both classical and QM/MM trajectories provide emission spectra that compare well with the experimental data, it seems that the classical trajectories underestimate the vibrational torsion of OLU, resulting in narrow angle distributions, as reported by Cerezo et al . 83 Therefore, even if energetically accurate, the classical MD protocol alone would produce a not accurate enough conformational distribution of the chromophore in the biological environment, which can be then reached once the molecule is allowed to move in a QM/MM potential.…”

“…Moreover, the electrostatic charges were computed by using the Merz–Singh–Kollman scheme 80 at the B3LYP/6-(2d,p) level of theory, according to previous studies. 53,81,82 While it is true that some parameterization effort has been previously done for an OLU analogue, 83 this was only carried out for the electronic ground state. However, our parameters, which are listed in Tables S1–S6 of the ESI,† not only aim at describing the electronic ground state but also the first excited state.…”

Environmentally Driven Symmetry Breaking Quenches Dual Fluorescence in Proflavine

“…In this work, a simple (quasi)-diabatization scheme based on the transition dipole moments of the two adiabatic electronic excited states is used (see section 1.3 of the Supporting Information). Importantly, the MD sampling of the fully solvated system encodes all coupling to the nuclear degrees of freedom of the solute and the solvent in the continuous spectral densities, in contrast to approaches based on parametrizing the LVC Hamiltonian from static calculations of the chromophore in a frozen (decoupled) solvent environment sampled from MD. ,, …”

“…Nonadiabatic effects due to the interactions of multiple electronic excited states are ubiquitous in many molecular systems, ranging from biological light-harvesting complexes to quantum dots and organic optoelectronic materials. − They arise when nuclear motion mixes adiabatic electronic states, the true eigenstates of the electronic Hamiltonian, representing a breakdown of the Born–Oppenheimer approximation. , Signatures of such nonadiabatic effects , can be commonly observed in linear and nonlinear optical spectra of molecules and molecular assemblies, with prominent examples such as dark (dipole-forbidden) transitions contributing to spectral line shapes through intensity borrowing effects, − anomalous emission properties like those observed for molecules undergoing twisted intramolecular charge transfer (TICT), − or molecules violating Kasha’s rule. ,− First-principles modeling of these effects is highly challenging, as it must account for explicit couplings between the electronic and nuclear degrees of freedom. , Additionally, most systems of interest are embedded in condensed-phase environments such as solvents or proteins, and understanding how environmental degrees of freedom influence energy relaxation processes in multiple coupled electronic states poses a major theoretical challenge. − In this work, we introduce a first-principles approach, based on combining molecular dynamics (MD) sampling of vibronic couplings with tensor network methods, ,− that is capable of capturing environmental interactions on several coupled excited states in absorption, fluorescence, and time-resolved spectroscopy experiments. We showcase the strengths of the approach by uncovering the origin of the recently reported dual fluorescence in the proflavine molecule …”

Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure

“…Due to these challenges, a vast majority of previous studies that sample chromophore-environment excitation energies have used time-dependent density functional theory (TDDFT) , to treat the electronic excitations since it serves as a practical compromise between computational efficiency and accuracy. However, although for a range of chromophores in solution TDDFT has been shown to produce accurate linear spectra, − in particular when combined with approaches that account for vibronic effects that are not present in ensemble methods, ,− challenging cases remain where a higher-level treatment of the electronic structure is essential.…”