QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion

The bioluminescence emission from fireflies is an astounding tool to mark and view cells. However, the bioluminescent mechanism is not completely deciphered, limiting the comprehension of key processes. We use a theoretical approach to study for the first time the arrival of a dioxygen molecule inside the fireflies protein and one path of the formation of the dioxetanone ring, the high-energy intermediate precursor of the bioluminescence. To describe this reaction step, a joint approach combining classical molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations is used. The formation of the dioxetanone ring has been studied for both singlet and triplet states with the help of MS-CASPT2 calculations. We also emphasize the role played by the proteinic environment in the formation of the dioxetanone ring. The results obtained shed some light on an important reaction step and give new insights concerning the bioluminescence in fireflies

DataSheet1_Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems.PDF

<p>In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modeling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.</p

Photostability Mechanisms in Human γB-Crystallin: Role of the Tyrosine Corner Unveiled by Quantum Mechanics and Hybrid Quantum Mechanics/Molecular Mechanics Methodologies

The tyrosine corner is proposed as a featured element to enhance photostability in human γB-crystallin when exposed to UV irradiation. Different ultrafast processes were studied by multiconfigurational quantum chemistry coupled to molecular mechanics: photoinduced singlet–singlet energy, electron and proton transfer, as well as population and evolution of triplet states. The minimum energy paths indicate two possible UV photoinduced events: forward–backward proton-coupled electron transfer providing to the system a mechanism for ultrafast internal conversion, and energy transfer, leading to fluorescence or phosphorescence. The obtained results are in agreement with the available experimental data, being in line with the proposed photoinduced processes for the different tyrosine environments within γB-crystallin

Hybrid QM/MM Simulations of the Obelin Bioluminescence and Fluorescence Reveal an Unexpected Light Emitter

Obelia longissima, a tiny hydrozoan living in temperate and cold seas, features the Obelin photoprotein, which emits blue light. The Obelin bioluminescence and the Ca²⁺-discharged Obelin fluorescence spectra show multimodal characteristics that are currently interpreted by the concomitant participation of several light emitters. Up to now, the coelenteramide luminophore is thought to exist in different protonation states, one of them engaged in an ion-pair with the nearby residue, His22. Using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, we demonstrate that such an ion-pair cannot exist as a stable light emitter. However, when His22 electric neutrality is maintained by means of another proton transfer, the phenolate state of coelenteramide exhibits emission properties in agreement with experiment. Finally, an alternative nonradiative decay pathway, involving the formation of a diradical excited state, is postulated for the first time

Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide: A Systematic Theoretical Study

A systematic investigation of the structural and spectroscopic properties of coelenteramide has been performed at the TD-CAM-B3LYP/6-31+G­(d,p) level of theory, including various fluorescence and chemiluminescence states. The influence of geometric conformations, solvent polarity, protonation state, and the covalent character of the O–H bond of the hydroxyphenyl moiety were carefully studied. Striking differences in geometries and electronic structures among the states responsible for light emission were characterized. All fluorescence states can be described as a limited charge transfer process for a planar amide moiety. However, the chemiluminescence state is characterized by a much larger charge transfer that takes place over a longer distance. Moreover, the chemiluminescent coelenteramide structure exhibits an amide moiety that is no longer planar, in agreement with recent, more accurate <i>ab initio</i> results [Roca-Sanjuán et al. <i>J. Chem. Theory Comput.</i> <b>2011</b>, <i>7</i>, 4060]. Because the chemiluminescence state appears to be completely dark, a new mechanism is tentatively introduced for this process

The Synthesis of a Corrole Analogue of Aquacobalamin (Vitamin B_12a) and Its Ligand Substitution Reactions

The synthesis of a Co­(III) corrole, [10-(2-[[4-(1<i>H</i>-imidazol-1-ylmethyl)­benzoyl]­amino]­phenyl)-5,15-diphenylcorrolato]­cobalt­(III), DPTC-Co, bearing a tail motif terminating in an imidazole ligand that coordinates Co­(III), is described. The corrole therefore places Co­(III) in a similar environment to that in aquacobalamin (vitamin B_12a, H₂OCbl⁺) but with a different equatorial ligand. In coordinating solvents, DPTC-Co is a mixture of five- and six-coordinate species, with a solvent molecule occupying the axial coordination site trans to the proximal imidazole ligand. In an 80:20 MeOH/H₂O solution, allowed to age for about 1 h, the predominant species is the six-coordinate aqua species [H₂O–DPTC-Co]. It is monomeric at least up to concentrations of 60 μM. The coordinated H₂O has a p<i>K</i>_a = 9.76(6). Under the same conditions H₂OCbl⁺ has a p<i>K</i>_a = 7.40(2). Equilibrium constants for the substitution of coordinated H₂O by exogenous ligands are reported as log <i>K</i> values for neutral N-, P-, and S-donor ligands, and CN^–, NO₂^–, N₃^–, SCN^–, I^–, and Cys in 80:20 MeOH/H₂O solution at low ionic strength. The log <i>K</i> values for [H₂O–DPTC-Co] correlate reasonably well with those for H₂OCbl⁺; therefore, Co­(III) displays a similar behavior toward these ligands irrespective of whether the equatorial ligand is a corrole or a corrin. Pyridine is an exception; it is poorly coordinated by H₂OCbl⁺ because of the sterically hindered coordination site of the corrin. With few exceptions, [H₂O–DPTC-Co] has a higher affinity for neutral ligands than H₂OCbl⁺, but the converse is true for anionic ligands. Density functional theory (DFT) models (BP86/TZVP) show that the Co–ligand bonds tend to be longer in corrin than in corrole complexes, explaining the higher affinity of the latter for neutral ligands. It is argued that the residual charge at the metal center (+2 in corrin, 0 in corrole) increases the affinity of H₂OCbl⁺ for anionic ligands through an electrostatic attraction. The topological properties of the electron density in the DFT-modeled compounds are used to explore the nature of the bonding between the metal and the ligands

Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water

Firefly bioluminescence is a quite efficient process largely used for numerous applications. However, some fundamental photochemical properties of the light emitter are still to be analyzed. Indeed, the light emitter, oxyluciferin, can be in six different forms due to interexchange reactions. In this work, we present the simulation of the absorption and emission spectra of the possible natural oxyluciferin forms in water and some of their analogues considering both the solvent/oxyluciferin interactions and the dynamical effects by using MD simulations and QM/MM methods. On the one hand, the absorption band shapes have been rationalized by analyzing the electronic nature of the transitions involved. On the other hand, the simulated and experimental emission spectra have been compared. In this case, an ultrafast excited state proton transfer (ESPT) occurs in oxyluciferin and its analogues, which impairs the detection of the emission from the protonated state by steady-state fluorescence spectroscopy. Transient absorption spectroscopy was used to evidence this ultrafast ESPT and rationalize the comparison between simulated and experimental steady-state emission spectra. Finally, this work shows the suitability of the studied oxyluciferin analogues to mimic the corresponding natural forms in water solution, as an elegant way to block the desired interexchange reactions allowing the study of each oxyluciferin form separately