Excited-State Decay Pathways of Flavin Molecules in Five Redox Forms: The Role of Conical Intersections

Electronic Structure Methods for Simulating Flavin's Spectroscopy and Photophysics: Comparison of Multi-reference, TD-DFT, and Single-Reference Wave Function Methods

The use of flavins and flavoproteins in photocatalytic, sensing, and biotechnological applications has led to a growing interest in computationally modeling the excited-state electronic structure and photophysics of flavin. However, there is limited consensus regarding which computational methods are appropriate for modeling flavin's photophysics. We compare the energies of low-lying excited states of flavin computed with time-dependent density functional theory (TD-DFT), equation-of-motion coupled cluster (EOM-EE-CCSD), scaled opposite-spin configuration interaction [SOS-CIS(D)], multiconfiguration pair-density functional theory (MC-PDFT), and several multireference perturbation theory (MR-PT2) methods. In the first part, we focus on excitation energies of the first singlet excited state (S1) of five different redox and protonation states of flavin, with the goal of finding a suitable active space for MR-PT2 calculations. In the second part, we construct two sets of one-dimensional potential energy surfaces connecting the S0 and S1 equilibrium geometries (S0-S1 path) and the S1 (π,π*) and S2 (n,π*) equilibrium geometries (S1-S2 path). The first path therefore follows a Franck-Condon active mode of flavin while the second path maps crossings points between low-lying singlet and triplet states in flavin. We discuss the similarities and differences in the TD-DFT, EOM-EE-CCSD, SOS-CIS(D), MC-PDFT and MR-PT2 energy profiles along these paths. We find that (TD-)DFT methods are suitable for applications such as simulating the spectra of flavins but are inconsistent with several other methods when used for some geometry optimizations and when describing the energetics of dark (n,π*) states. MR-PT2 methods show promise for the simulation of flavin's low-lying excited states, but the selection of orbitals for the active space and the number of roots used for state averaging must be done carefully to avoid artifacts. Some properties, such as the intersystem crossing geometry and energy between the S1 (π,π*) and T2 (n,π*) states, may require additional benchmarking before they can be determined quantitatively.

Flavin-induced charge separation in transmembrane model peptides

Hydrophobic peptide models derived from the α-helical transmembrane segment of the epidermal growth factor receptor were synthetically modified with a flavin amino acid as a photo-inducible charge donor and decorated with tryptophans along the helix as charge acceptors. The helical conformation of the peptides was conserved despite the modifications, notably also in lipid vesicles and multibilayers. Their ability to facilitate photo-induced transmembrane charge transport was examined by means of steady-state and time-resolved optical spectroscopy. The first tryptophan next to the flavin donor plays a major role in initiating the charge transport near the N-terminus, while the other tryptophans might promote charge transport along the transmembrane helix. These artificially modified, but still naturally derived helical peptides are important models for studying transmembrane electron transfer and the principles of photosynthesis.

Lightening flavin by amination for fluorescent sensing

Monitoring of reactive oxygen species (ROS), such as O2˙-, etc., in organisms is of great significance, not only for their essential role in biological processes, but their excessive production may also result in many diseases. Flavin (FL) is a fluorophore that naturally exists in flavoenzymes, and its fluorescent emission (FE) becomes negligible when reduced. This enables the application of FL derivatives as fluorescent sensors for ROS. We presented a theoretical investigation to address the impact of amino substitution on the photophysical properties of aminoflavins (AmFLs). Resulting from the interplay of electronic and positional effects, amination at C8 enhances the electronic coupling between the ground state and the first singlet excited state by enlarging the adiabatic energy change of the electronic transitions and the emission transition dipole moments, weakens the vibronic coupling by decreasing the contribution of isoalloxazine to the frontier molecular orbitals, redshifts the absorption band, and enhances the fluorescent emission drastically in 8AmFL. The theoretically estimated fluorescent emission intensity of 8AmFL is ∼40 times that of FL, suggesting its potential application as a fluorescent sensor.

Systematic Theoretical Study on the pH-Dependent Absorption and Fluorescence Spectra of Flavins

Flavins are a class of organic compounds with the basic structure of 7,8-dimethy-10-alkyl isoalloxazine. They are ubiquitous in nature and participate in many biochemical reactions. Due to various existing forms, there is a lack of systematic research on the absorption and fluorescence spectra of flavins. In this study, employing the density functional theory (DFT) and time-dependent (TD) DFT, we calculated the pH-dependent absorption and fluorescence spectra of flavin of three redox states (quinone, semiquinone, and hydroquinone) in solvents. The chemical equilibrium of three redox states of flavins and the pH effect on the absorption spectra and fluorescence spectra of flavins were carefully discussed. The conclusion helps with identifying the existing forms of flavins in solvent with different pH values.

Ultrafast Dynamics of Fatty Acid Photodecarboxylase in Anionic Semiquinone State

Fatty acid photodecarboxylase is a newly identified blue-light driven photoenzyme that catalyzes decarboxylation of fatty acids. The catalytic reaction involves a transient anionic semiquinone of flavin cofactor (FAD^•-) as an intermediate, but photochemical properties of this anionic radical are largely unknown. Here, we have anaerobically produced the wild-type FAP in the FAD^•- state and conducted femtosecond-resolved fluorescence and absorption measurements. We have observed the multiphasic deactivation dynamics of excited states on multiple time scales from a few picoseconds even to a few nanoseconds through conical intersections between various electronic states. Interestingly, the nanosecond components can only be observed from higher electronic excited states. Our results show the complexity of the energy landscapes of various excited states and rule out the occurrence of electron or proton transfer with nearby residue(s) in the active site.

Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX

Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH^-) as prosthetic group and (6R)-N₅,N₁₀-methylene-5,6,7,8-tetrahydrofolate (CH₂THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH^- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH^- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH^- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH^- in ThyX is only mildly more constrained than that of free FADH^- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH^- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH^- photophysics to the constraints exerted by its immediate surroundings.

Intermolecular conical intersections in molecular aggregates

Conical intersections (CoIns) of multidimensional potential energy surfaces are ubiquitous in nature and control pathways and yields of many photo-initiated intramolecular processes. Such topologies can be potentially involved in the energy transport in aggregated molecules or polymers but are yet to be uncovered. Here, using ultrafast two-dimensional electronic spectroscopy (2DES), we reveal the existence of intermolecular CoIns in molecular aggregates relevant for photovoltaics. Ultrafast, sub-10-fs 2DES tracks the coherent motion of a vibrational wave packet on an optically bright state and its abrupt transition into a dark state via a CoIn after only 40 fs. Non-adiabatic dynamics simulations identify an intermolecular CoIn as the source of these unusual dynamics. Our results indicate that intermolecular CoIns may effectively steer energy pathways in functional nanostructures for optoelectronics.

Directed Electron Transfer in Flavin Peptides with Oligoproline-Type Helical Conformation as Models for Flavin-Functional Proteins

To mimic the charge separation in functional proteins we studied flavin-modified peptides as models. They were synthesized as oligoprolines that typically form a polyproline type-II helix, because this secondary structure supports the electron transfer properties. We placed the flavin as photoexcitable chromophore and electron acceptor at the N-terminus. Tryptophans were placed as electron donors to direct the electron transfer over 0-3 intervening prolines. Spectroscopic studies revealed competitive photophysical pathways. The reference peptide without tryptophan shows dominant non-specific ET dynamics, leading to an ion pair formation, whereas peptides with tryptophans have weak non-specific ET and intensified directed electron transfer. By different excitation wavelengths, we can conclude that the corresponding ion pair state of flavin within the peptide environment has to be energetically located between the S1 and S4 states, whereas the directed electron transfer to tryptophan occurs directly from the S1 state. These photochemical results have fundamental significance for proteins with flavin as redoxactive cofactor.

UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein

Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.

Investigating the Photochemistry of C7 and C8 Functionalized N(5)-Ethyl-flavinium Cation: A Computational Study

Flavins are a diverse set of compounds with a wide variety of biological and nonbiological applications. Applications of flavins receiving attention recently consist of electro- and photocatalytic oxidation of substrates for organic synthesis, bioengineered nanotechnology, and water splitting catalysts, among others. While there is vast knowledge regarding the structure-property relationships of flavins and their electrochemistry, there is much less work elucidating the structure property relationships as they pertain to flavinium photochemistry. Herein, we report the effect of molecular tailoring on the molecular properties of N(5)-ethyl-flavinium cation (Et-Fl⁺), a derivative of the biocatalytic coenzyme riboflavin, by incorporating electron withdrawing and donating groups at the C7 and C8 position of the isoalloxazine ring. The presence of electron withdrawing groups at the C8 position caused a red shift in the absorption spectrum, while the electron donating groups caused a blue shift. Functionalization at the C7 position had the opposite effect on the absorption spectrum. The effects of single substitution were relatively negated with simultaneous functionalization at both the C8 and C7 positions. Difference density plots indicate no change in the nature of the S₁ excited state, which was confirmed by optimization of the excited state geometries. The results presented in this study indicate that functionalization of the isoalloxazine unit affects the photophysical properties of N(5)-ethyl-flavinium cations.

Fluorescence Properties of Flavin Semiquinone Radicals in Nitronate Monooxygenase

Fluorescent cofactors like flavins can be exploited to probe their local environment with spatial and temporal resolution. Although the fluorescence properties of the oxidized and two-electron-reduced states of flavins have been studied extensively, this is not the case for the one-electron-reduced state. Both the neutral and anionic semiquinones have proven particularly challenging to examine, as they are unstable in solution and are transient, short-lived species in many catalytic cycles. Here, we report that the nitronate monooxygenase (NMO) from Pseudomonas aeruginosa PAO1 is capable of stabilizing both semiquinone forms anaerobically for hours, thus enabling us to study their spectroscopy in a constant protein environment. We found that in the active site of NMO, the anionic semiquinone exhibits no fluorescence, whereas the neutral semiquinone radical shows a relatively strong fluorescence, with a behavior that violates the Kasha-Vavilov rule. These fluorescence properties are discussed in the context of time-dependent density functional theory calculations, which reveal low-lying dark states in both systems.

Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment

This study discusses how UV/vis absorption spectra of flavin in different redox and protonation states are shifted by the nearby electrostatic microenvironment.