Theoretical Study of the Chemiluminescent Decomposition of Dioxetanone

Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm

Molecular discovery is central to the field of chemical informatics. Although optimization approaches have been developed that target-specific molecular properties in combination with machine learning techniques, optimization using databases of limited size is challenging for efficient molecular design. We present a molecular design method with a Gaussian process regression model and a graph-based genetic algorithm (GB-GA) from a data set comprising a small number of compounds by introducing mutation probability control in the genetic algorithm to enhance the optimization capability and speed up the convergence to the optimal solution. In addition, we propose reducing the number of parameters in the conventional GB-GA focusing on efficient molecular design from a small database. We generated a target-specific database by combining active learning and iterative design in the evolutionary methodologies and chose Gaussian process regression as the prediction model for molecular properties. We show that the proposed scheme is more efficient for optimization toward the target properties from goal-directed benchmarks with several drug-like molecules compared to the conventional GB-GA method. Finally, we provide a demonstration whereby we designed D-luciferin analogues with near-infrared fluorescence for bioimaging, which is desirable for effective in vivo light sources, from a small-size data set.

Chemiluminescence of a Firefly Luciferin Analogue Reveals that Formation of the Key Intermediate Responsible for Excited State Generation Occurs on a Fully Concerted Step

The chemiluminescence (CL) reaction of eight different 2-(4-hydroxyphenyl)-4,5-dihydrothiazole-4-carboxylate esters with an organic superbase and oxygen was investigated through a kinetic and computational study. These esters are all analogues to the luciferin substrate involved in efficient firefly bioluminescence. The kinetic data obtained from CL emission and light absorption assays were used in the context of linear free energy relationships (LFER); we obtained the Hammett reaction constant ρ = +1.62 ± 0.09 and the Brønsted constant βlg = -0.39 ± 0.04. These observations from LFER, together with activation parameters obtained from Arrhenius plots, suggest that the formation of the high-energy intermediate (HEI) 1,2-dioxetanone occurs via a concerted mechanism during the rate-determining step of the reaction. Calculations performed using density functional theory support a late transition state for HEI formation within the reaction mechanism pathway, which was described considering geometric parameters, Wiberg bond indices from natural bond order analysis, and the atomic charges derived from the electrostatic potential.

Theoretical investigation on triphenylamine coelenteramide for bioinspired OLED application using thiophene rings in π-bridge

As light emitter of most marine organisms bioluminescence, coelenteramide (CLM) received much attention due to some exciting application in the field of bioinspired organic light-emitting devices (OLED). Nevertheless, native CLM only emit bright blue light. In order to obtain light of different colors, two CLM analogues, TPA-CLM and TPA-TP-CLM were designed by introduction of triphenylamine group and (thiophene) π-bridge. On the other hand, because the light emitter, CLM was produced by the chemical reaction which originates from the oxidation of bioluminescent substrate, coelenterazine (CLZ), it must be evaluated if and how substituent group tune the chemiluminescent (CL) reaction mechanism, firstly. In this article, the complete chemiluminescent reaction mechanism of TPA-CLZ and TPA-TP-CLZ and the photophysical properties of light emitters, TPA-CLM and TPA-TP-CLM were investigated by (time-dependent) density functional theory, (TD) DFT calculations. The calculations indicate that the introduction of triphenylamine and π-bridge minimally affect the complete reaction process. For the light emitters, TPA-CLM and TPA-TP-CLM, the calculation results indicate that the injection abilities of hole and electron can be largely improved by introduction of triphenylamine and π-bridge. The absorption and emission spectra appeared at longer wavelengths than native CLM. These results illustrate that TPA-CLM and TPA-TP-CLM are good candidates for bioinspired OLED application.

Theoretical Understanding on the Facilitated Photoisomerization of a Carbonyl Supported Borane System

Boron compound BOMes2 containing an internal B-O bond undergoes highly efficient photoisomerization, followed by sequential structural transformations, resulting in a rare eight-membered B, O-heterocycle (S. Wang, et al. Org. Lett. 2019, 21, 5285-5289). In this work, the detailed reaction mechanisms of such a unique carbonyl-supported tetracoordinate boron system in the first excited singlet (S1 ) state and the ground (S0 ) state were investigated by using the complete active space self-consistent field and its second-order perturbation (MS-CASPT2//CASSCF) method combined with time-dependent density functional theory (TD-DFT). Moreover, an imine-substituted tetracoordinated organic boron system (BNMes2 ) was selected for comparative study to explore the intrinsic reasons for the difference in reactivity between the two types of compounds. Steric factor was found to influence the photoisomerization activity of BNMes2 and BOMes2 . These results rationalize the experimental observations and can provide helpful insights into understanding the excited-state dynamics of heteroatom-doped tetracoordinate organoboron compounds, which facilitates the rational design of boron-based materials with superior photoresponsive performances.

Theoretical Study on the Formation and Decomposition Mechanisms of Coelenterazine Dioxetanone

Bioluminescence has been drawing broad attention due to its high signal-to-noise ratio and high bioluminescence quantum yields, which has been widely applied in the fields of biomedicine, bioanalysis, and so on. Among numerous bioluminescent substrates, coelenterazine is famous for its wide distribution. However, the oxygenation reaction mechanism of coelenterazine is far from being completely understood. In this paper, the formation and decomposition mechanisms of coelenterazine dioxetanone were investigated via density functional theory (DFT) and time-dependent (TD) DFT approaches. The results showed that the oxygenation reaction first occurred along the triplet-state potential energy surface (PES), after the intersystem crossing (ISC), second jumped to the diradical-state PES, and ultimately formed coelenterazine dioxetanone. For the decomposition mechanism of dioxetanone, the computational results showed that the chemiexcitation of neutral dioxetanone was more efficient than that of other dioxetanone species. Moreover, the diradical properties and the degree of ionic character are modified by the counter ions.

The Molecular Basis of Organic Chemiluminescence

Bioluminescence (BL) and chemiluminescence (CL) are interesting and intriguing phenomena that involve the emission of visible light as a consequence of chemical reactions. The mechanistic basis of BL and CL has been investigated in detail since the 1960s, when the synthesis of several models of cyclic peroxides enabled mechanistic studies on the CL transformations, which led to the formulation of general chemiexcitation mechanisms operating in BL and CL. This review describes these general chemiexcitation mechanisms-the unimolecular decomposition of cyclic peroxides and peroxide decomposition catalyzed by electron/charge transfer from an external (intermolecular) or an internal (intramolecular) electron donor-and discusses recent insights from experimental and theoretical investigation. Additionally, some recent representative examples of chemiluminescence assays are given.

Conical Intersection in Chemiluminescence of Cyclic Peroxides

Chemiluminescence (CL) utilizing chemiexcitation for energy transformation is one of the most highly sensitive and useful analytical techniques. The chemiexcitation is a chemical process of a ground-state reactant producing an excited-state product, in which a nonadiabatic event is facilitated by conical intersections (CIs), the specific molecular geometries where electronic states are degenerated. Cyclic peroxides, especially 1,2-dioxetane/dioxetanone derivatives, are the iconic chemiluminescent substances. In this Perspective, we concentrated on the CIs in the CL of cyclic peroxides. We first present a computational overview on the role of CIs between the ground (S₀) state and the lowest singlet excited (S₁) state in the thermolysis of cyclic peroxides. Subsequently, we discuss the role of the S₀/S₁ CI in the CL efficiency and point out misunderstandings in some theoretical studies on the singlet chemiexcitations of cyclic peroxides. Finally, we address the challenges and future prospects in theoretically calculating S₀/S₁ CIs and simulating the dynamics and chemiexcitation efficiency in the CL of cyclic peroxides.

Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs

Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.

Analytic First-Order Derivatives of (X)MS, XDW, and RMS Variants of the CASPT2 and RASPT2 Methods

Crossings between states involve complex electronic structures, making the accurate characterization of the crossing point difficult. In this study, the analytic derivatives of three complete active space second-order perturbation theory (CASPT2) variants as well as an extension of the restricted active space (RASPT2) are developed. These variants are applied to locating minimum energy conical intersections. Our results demonstrate that the three CASPT2 variants predict qualitatively similar results, but a recently developed variant, the rotated multistate CASPT2 (RMS-CASPT2), is least sensitive to the number of states considered in the calculation. We demonstrate that CASPT2 and the reference self-consistent field calculations predict qualitatively different energetics and bond lengths.

H2O-Bridged Proton-Transfer Channel in Emitter Species Formation in Obelin Bioluminescence

Bioluminescence of a number of marine organisms is conditioned by Ca²⁺-regulated photoprotein (CaRP) with coelenterazine as the reaction substrate. The reaction product, coelenteramide, at the first singlet excited state (S₁) is the emitter of CaRP. The S₁-state coelenteramide is produced via the decomposition of coelenterazine dioxetanone. Experiments suggested that the neutral S₁-coelenteramide is the primary emitter species. This supposition contradicts with theoretical calculations showing that the anionic S₁-coelenteramide is a primary product of the decomposition of coelenterazine dioxetanone. In this study, applying molecular dynamic (MD) simulations and the hybrid quantum mechanics/molecular mechanics (QM/MM) method, we investigated a proton-transfer (PT) process taking place in CaRP obelin from Obelia longissima for emitter formation. Our calculations demonstrate a concerted PT process with a water molecule as a bridge between anionic S₁-coelenteramide and the nearest histidine residue. The low activation barrier as well as the strong hydrogen-bond network between the proton donor and the proton acceptor suggests a fast PT process comparable with that of the lifetime of excited anionic S₁-coelenteramide. The existence of the PT process eliminates the discrepancy between experimental and theoretical studies. The fast PT process at emitter formation can also take place in other CaRPs.

Three S0/S1 Conical Intersections Control Electron-Transfer-Catalyzed Chemiluminescence of 1,2-Dioxetanedione

Chemiluminescence (CL) utilizing four-membered cyclic peroxides is one of the most useful analytical techniques. Up to now, the CL mechanisms for nonketone (1,2-dioxetanes) and monoketone (1,2-dioxetanones) derivatives of four-membered cyclic peroxides have been intensively studied experimentally and theoretically in the past several decades, but no general mechanism has been concluded to rationalize the origin of high-efficiency singlet chemiexcitation. In contrast, as the only diketone derivative of four-membered cyclic peroxide, the electron-transfer (ET)-catalyzed CL of 1,2-dioxetanedione (DDO), which is most suggested as a critical step in the well-known peroxyoxalate CL (POCL), has never been theoretically investigated and uncovered yet. In this work, we theoretically investigated the rubrene-catalyzed decomposition of DDO for the first time, with a hybrid quantum mechanical/molecular mechanical model and nonadiabatic molecular dynamics simulation. The computation shows a stepwise ET-catalyzed decomposition and three S₀/S₁ conical intersection (CI)-controlled singlet chemiexcitation. The three universal S₀/S₁ CIs play different roles in the high-efficiency singlet chemiexcitation in ET-catalyzed CL of DDO and should be the true origin of the high-efficiency singlet CL. We believe that the current work could not only provide a further understanding for high-efficiency singlet CL but also provide some general clues to designed new high-efficient CL systems.

The elusive relationship between structure and colour emission in beetle luciferases

In beetles, luciferase enzymes catalyse the conversion of chemical energy into light through bioluminescence. The principles of this process have become a fundamental biotechnological tool that revolutionized biological research. Different beetle species can emit different colours of light, despite using the same substrate and highly homologous luciferases. The chemical reasons for these different colours are hotly debated yet remain unresolved. This Review summarizes the structural, biochemical and spectrochemical data on beetle bioluminescence reported over the past three decades. We identify the factors that govern what colour is emitted by wild-type and mutant luciferases. This topic is controversial, but, in general, we note that green emission requires cationic residues in a specific position near the benzothiazole fragment of the emitting molecule, oxyluciferin. The commonly emitted green-yellow light can be readily changed to red by introducing a variety of individual and multiple mutations. However, complete switching of the emitted light from red to green has not been accomplished and the synergistic effects of combined mutations remain unexplored. The minor colour shifts produced by most known mutations could be important in establishing a 'mutational catalogue' to fine-tune emission of beetle luciferases, thereby expanding the scope of their applications.

The role of CO2 detachment in fungal bioluminescence: thermally vs. excited state induced pathways

Different fungi lineages are known to emit light on Earth, mainly in tropical climates. Although the preparation of bioluminescent cell-free extracts allowed one to characterize the enzymatic requirements, the molecular mechanism underlying luminescence is still largely unknown and is based on the experimental putative assumption that a high-energy intermediate should be formed by reaction with O2 and formation of an endoperoxide. Here, we aim at determining, through state-of-the-art multiconfigurational quantum chemistry, the full mechanistic landscape leading from the endoperoxide to the emitting species, envisaging different possible pathways and proposing their viability. Especially, thermal CO2 detachment followed by excited-state peroxide opening (thermal-chemiluminescence) can compete with a parallel pathway, i.e., first excited-state endoperoxide opening, followed by CO2 detachment on the same excited-state (excited state-chemiluminescence). Clear differences in the energy supplies, as well as the possibility to directly populate the emitting species from the intersection seam between ground and excited states, land credence to a kinetically efficient thermal-chemiluminescent pathway, establishing for the first time a detailed description of fungal bioluminescence.

Computational Insights on the Mechanism of the Chemiluminescence Reaction of New Group of Chemiluminogens-10-Methyl-9-thiophenoxycarbonylacridinium Cations

Immunodiagnostics, in which one of the promising procedures is the chemiluminescent labelling, is essential to facilitate the detection of infections in a human organism. One of the standards commonly used in luminometric assays is luminol, which characterized by low quantum yield in aqueous environments. Acridinium esters have better characteristics in this topic. Therefore, the search for new derivatives, especially those characterized by the higher quantum yield of chemiluminescence, is one of the aims of the research undertaken. Using the proposed mechanism of chemiluminescence, we examined the effect of replacing a single atom within a center of reaction on the efficient transformation of substrates into electronically excited products. The density functional theory (DFT) and time dependent (TD) DFT calculated thermodynamic and kinetic data concerning the chemiluminescence and competitive dark pathways suggests that some of the scrutinized derivatives have better characteristics than the chemiluminogens used so far. Synthesis of these candidates for efficient chemiluminogens, followed by studies of their chemiluminescent properties, and ultimately in chemiluminescent labelling, are further steps to confirm their potential applicability in immunodiagnostics.

Multimodal Imaging Iridium(III) Complex for Hypochlorous Acid in Living Systems

Biomolecule tracing with different imaging methods is of great significance for more accurately unravelling the fundamental processes in living systems. However, considering the different principles of each imaging method for probe design, it is still a great challenge to apply one molecular probe to achieve two or even more imaging analyses for biomarkers. In general, traditional oxime was reported as a recognition group for fluorescence imaging of HOCl. Herein, for the first time, we designed the oxime decorated iridium(III) complex, which can be directly used for chemiluminescence as well as two-photon luminescence and photoluminescence lifetime imaging of HOCl in living systems. Moreover, the novel chemiluminescence mechanism of Ir-CLFLPLIM for HOCl was also proposed and explored by continuously monitoring chemiluminescence peak shapes and mass spectra, inferring the reaction intermediate and calculating the chemical reaction energy range of the reaction process. This strategy could lead us to expand the chemiluminescence application of transition metal complexes and develop more multimodal imaging probes.

Quantum yields of singlet and triplet chemiexcitation of dimethyl 1,2-dioxetane: ab initio nonadiabatic molecular dynamic simulations

The global nonadiabatic switching on-the-fly trajectory surface hopping simulation at the 8SA-CASSCF quantum level has been performed to estimate the quantum yield of chemiexcitation for the uncatalyzed decomposition reaction of the open-shell biradical trans-3,4-dimethyl-1,2-dioxetane system. The present ab initio nonadiabatic molecular dynamic simulation involving both conical intersection and intersystem crossing is to compute for the first time the population evolution of quantum yields at the four lowest singlet and four lowest triplet states. The simulated results demonstrate not only the stepwise dissociation of O-O and C-C bond breaking, but also confirm the existence of a biradical entropic trap which is responsible for chemiexcitation. The simulated quantum yield of the triplet chemiexcitation ΦT1 = 0.266 ± 0.096 agrees with the experimental value of 0.20 ± 0.04 very well. The present nonadiabatic molecular dynamic simulation of dimethyl 1,2-dioxetanes provides a further advanced understanding and stepping stone for future studies on chemi- and bio-luminescence.

Elucidating the multi-configurational character of the firefly dioxetanone anion and its prototypes in the biradical region using full valence active spaces

We analyzed the near-degenerate states of the firefly dioxetanone anion (FDO-) and its prototypes, especially in the biradical region, using multi-configurational approaches. The importance of utilizing full valence active spaces by means of density-matrix renormalization group self-consistent field (DMRG-SCF) calculations was described. Our results revealed that the neglect of some valence orbitals can affect the quantitative accuracy in later multi-reference calculations or the qualitative conclusion when optimizing conical intersections. Using all of the relevant valence orbitals of FDO-, we confirmed that there were two conical intersections, as reported in previous work, and that the intersecting states were changed when the active space was enlarged. Beyond these, we found that there were strong interactions between states in the biradical regions, in which the changes in entanglements can be used to visualize the interacting state evolution.

Approximate Analytical Gradients and Nonadiabatic Couplings for the State-Average Density Matrix Renormalization Group Self-Consistent-Field Method

We present an approximate scheme for analytical gradients and nonadiabatic couplings for calculating state-average density matrix renormalization group self-consistent-field wave function. Our formalism follows closely the state-average complete active space self-consistent-field (SA-CASSCF) ansatz, which employs a Lagrangian, and the corresponding Lagrange multipliers are obtained from a solution of the coupled-perturbed CASSCF (CP-CASSCF) equations. We introduce a definition of the matrix product state (MPS) Lagrange multipliers based on a single-site tensor in a mixed-canonical form of the MPS, such that a sweep procedure is avoided in the solution of the CP-CASSCF equations. We apply our implementation to the optimization of a conical intersection in 1,2-dioxetanone, where we are able to fully reproduce the SA-CASSCF result up to arbitrary accuracy.

Firefly-Inspired Approach to Develop New Chemiluminescence Materials

Bioluminescence, wherein marine and terrestrial organisms chemically produce light for communication, is a burgeoning area of research. Herein, we demonstrate a new series of artificial chemiluminescent compounds inspired by the enol-degradation reaction of natural bioluminescent molecules, luciferins. Based on systematic optical experiments, isotope labeling, and theoretical calculations, the chemiluminescent mechanism of these new materials and the relationship of enol-degradation reaction and chemiluminescence are fully discussed. The color and efficiency of the artificial chemiluminescent materials can be easily adjusted, and blue (486 nm), yellow (565 nm), and near-infrared (756 nm) luminescence can thus be obtained. The findings and in-depth understanding herein may accelerate the development of bio/chemiluminescent materials for analytical applications and non-invasive bioluminescence imaging.

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New chemiluminescent materials inspired by bioluminescence have been designed

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A way to design new chemiluminescent materials is reported

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The relationship of enol-degradation and chemiluminescence is methodically discussed

Mechanism of the Chemiluminescent Reaction between Nitric Oxide and Ozone

The gas phase reaction of nitric oxide with ozone to give chemiluminescence is used extensively for detection of nitrogen oxides. The molecular mechanism of chemiluminescence in this reaction is not known. So far, the only chemiluminescent systems studied in depth are certain cycloperoxides, which emit light following decomposition. Given our understanding of the mechanism of chemiluminescence in those molecules, one would expect by extension that in the NO + O₃ reaction the chemiluminescent species (NO₂ in this case) is formed in the excited state through a reaction pathway that diverges from the ground state pathway near the transition state. A systematic search for such a pathway leads us to conclude that such a mechanism is unlikely. Instead, our study suggests that chemiluminescence in the NO + O₃ reaction is due to emission from the NO₂ vibronic states associated with the ground (X̃ ²A₁) and first excited (à ²B₂) electronic states, which are populated in the nascent NO₂ produced in the reaction. The vibronic coupling between the X̃ ²A₁ and à ²B₂ states of NO₂ is due to a conical intersection (CI), which is geometrically and energetically close to the à ²B₂ minimum energy geometry and only 1.3 eV higher than ground state NO₂. Further, the CI is 1.2 eV lower than the energy of the NO + O₃ reactants and therefore thermodynamically accessible following the reaction. An analysis of the product energy distribution indicates that the major fraction of the reaction energy is channeled into the vibrational modes of NO₂, sufficient to populate the vibronic states of NO₂ around the X̃/à CI. These vibronic states show dipole-allowed emission in a frequency range that is consistent with the observed broad chemiluminescence spectrum.

Theoretical Development of Near-Infrared Bioluminescent Systems

The luciferin/luciferase system of the firefly has been used in bioluminescent imaging to monitor biological processes. In order to enhance the efficiency and expand the application range, some efforts have been made to tune the light emission, especially the effort to obtain NIR light. However, those case-by-case studies have not together revealed the nature and mechanism of the color tuning. In this paper, we theoretically investigated the fluorescence of all kinds of typical oxyluciferin analogues. The present systematical modifications of both oxyluciferin and luciferase indicate that the essential factor affecting the emission color is the charge distribution (or the electric dipole moment) on the oxyluciferin, which impacts on the charge transfer to form the light emitter and, subsequently, influence the strength and wavelength of the emission light. More negative charge distributed on the "thiazolone moiety" of the oxyluciferin or its analogues leads to a redshift. Based on this conclusion, we theoretically designed optimal pairs of luciferin analogue and luciferase for emitting NIR light, which could inspire new synthetic procedures and practical applications.

Chemi- and Bioluminescence of Cyclic Peroxides

Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.

Mechanism of activated chemiluminescence of cyclic peroxides: 1,2-dioxetanes and 1,2-dioxetanones

The supermolecule model explains low quantum efficiency of the catalyzed decomposition of 1,2-dioxetanones.

Theoretical modulation of singlet/triplet chemiexcitation of chemiluminescent imidazopyrazinone dioxetanone via C8-substitution

DFT analysis of the thermolysis of C₈-substituted imidazopyrazinone dioxetanone allows the rational tuning of the activation barrier and singlet/triplet chemiexcitation.

A combined theoretical and experimental study on the mechanism of spiro-adamantyl-1,2-dioxetanone decomposition

Our study on the unimolecular decomposition of a relatively stable 1,2-dioxetanone derivative, model compound for bioluminescence processes, indicates the existence of different reaction pathways for ground and excited state formation.

Excited-State Dynamics of Oxyluciferin in Firefly Luciferase

The color variations of light emitted by some natural and mutant luciferases are normally attributed to collective factors referred to as microenvironment effects; however, the exact nature of these interactions between the emitting molecule (oxyluciferin) and the active site remains elusive. Although model studies of noncomplexed oxyluciferin and its variants have greatly advanced the understanding of its photochemistry, extrapolation of the conclusions to the real system requires assumptions about the polarity and proticity of the active site. To decipher the intricate excited-state dynamics, global and target analysis is performed here for the first time on the steady-state and time-resolved spectra of firefly oxyluciferin complexed with luciferase from the Japanese firefly (Luciola cruciata). The experimental steady-state and time-resolved luminescence spectra of the oxyluciferin/luciferase complex in solution are compared with the broadband time-resolved firefly bioluminescence recorded in vivo. The results demonstrate that de-excitation of the luminophore results in a complex cascade of photoinduced proton transfer processes and can be interpreted by the pH dependence of the emitted light. It is confirmed that proton transfer is the central event in the spectrochemistry of this system for which any assignment of the pH-dependent emission to a single chemical species would be an oversimplification.

Perspectives on Bioluminescence Mechanisms

The molecular mechanisms of the bioluminescence systems of the firefly, bacteria and those utilizing imidazopyrazinone luciferins such as coelenterazine are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography and computational chemistry. The chemical structures of all reactants are well defined, and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high-energy species that undergoes decarboxylation to form directly the product in its S₁ state, the bioluminescence emitter. More work is still needed to establish the structure of the products completely. In spite of the bacterial system receiving the most research attention, the chemical pathway for excitation remains mysterious except that it is clearly not by a decarboxylation. Both the coelenterazine and bacterial systems have in common of being able to employ "antenna proteins," lumazine protein and the green-fluorescent protein, for tuning the color of the bioluminescence. Spatial structure information has been most valuable in informing the mechanism of the Ca²⁺ -regulated photoproteins and the antenna protein interactions.

Mechanistic insight into marine bioluminescence: photochemistry of the chemiexcited Cypridina (sea firefly) lumophore

Cypridina hilgendorfii (sea firefly) is a bioluminescent crustacean whose bioluminescence (BL) reaction is archetypal for a number of marine organisms, notably other bioluminescent crustaceans and coelenterates. Unraveling the mechanism of its BL is paramount for future applications of its strongly emissive lumophore. Cypridina produces light in a three-step reaction: First, the cypridinid luciferin is activated by an enzyme to produce a peroxide intermediate, cypridinid dioxetanone (CDO), which then decomposes to generate excited oxyluciferin (OxyCLnH*). Finally, OxyCLnH* deexcites to its ground state along with emission of bright blue light. Unfortunately, the detailed mechanism of the critical step, the thermolysis of CDO, remains unknown, and it is unclear whether the light emitter is generated from a neutral form (CDOH) or anionic form (CDO(-)) of the CDO precursor. In this work, we investigated the key step in the process by modeling the thermal decompositions of both CDOH and CDO(-). The calculated results indicate that the decomposition of CDO(-) occurs via the gradually reversible charge transfer (CT)-initiated luminescence (GRCTIL) mechanism, whereas CDOH decomposes through an entropic trapping mechanism without an obvious CT process. The thermolysis of CDO(-) is sensitive to solvent effects and is energetically favorable in polar environments compared with the thermolysis of CDOH. The thermolysis of CDO(-) produces the excited oxyluciferin anion (OxyCLn(-)*), which combines with a proton from the environment to form OxyCLnH*, the actual light emitter for the natural system.

A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins

Photobleaching and photostability of proteins of the green fluorescent protein (GFP) family are crucially important for practical applications of these widely used biomarkers. On the basis of simulations, we propose a mechanism for irreversible bleaching in GFP-type proteins under intense light illumination. The key feature of the mechanism is a photoinduced reaction of the chromophore with molecular oxygen (O2) inside the protein barrel leading to the chromophore's decomposition. Using quantum mechanics/molecular mechanics (QM/MM) modeling we show that a model system comprising the protein-bound Chro(-) and O2 can be excited to an electronic state of the intermolecular charge-transfer (CT) character (Chro(•)···O2(-•)). Once in the CT state, the system undergoes a series of chemical reactions with low activation barriers resulting in the cleavage of the bridging bond between the phenolic and imidazolinone rings and disintegration of the chromophore.

The Theoretical Estimation of the Bioluminescent Efficiency of the Firefly via a Nonadiabatic Molecular Dynamics Simulation

The firefly is famous for its high bioluminescent efficiency, which has attracted both scientific and public attention. The chemical origin of firefly bioluminescence is the thermolysis of the firefly dioxetanone anion (FDO(-)). Although considerable theoretical research has been conducted, and several mechanisms were proposed to elucidate the high efficiency of the chemi- and bioluminescence of FDO(-), there is a lack of direct experimental and theoretical evidence. For the first time, we performed a nonadiabatic molecular dynamics simulation on the chemiluminescent decomposition of FDO(-) under the framework of the trajectory surface hopping (TSH) method and theoretically estimated the chemiluminescent quantum yield. The TSH simulation reproduced the gradually reversible charge-transfer initiated luminescence mechanism proposed in our previous study. More importantly, the current study, for the first time, predicted the bioluminescence efficiency of the firefly from a theoretical viewpoint, and the theoretical prediction efficiency is in good agreement with experimental measurements.