Regulation Mechanism of Spin−Orbit Coupling in Charge-Transfer-Induced Luminescence of Imidazopyrazinone Derivatives

Optical Image Sensors for Smart Analytical Chemiluminescence Biosensors

Optical biosensors have emerged as a powerful tool in analytical biochemistry, offering high sensitivity and specificity in the detection of various biomolecules. This article explores the advancements in the integration of optical biosensors with microfluidic technologies, creating lab-on-a-chip (LOC) platforms that enable rapid, efficient, and miniaturized analysis at the point of need. These LOC platforms leverage optical phenomena such as chemiluminescence and electrochemiluminescence to achieve real-time detection and quantification of analytes, making them ideal for applications in medical diagnostics, environmental monitoring, and food safety. Various optical detectors used for detecting chemiluminescence are reviewed, including single-point detectors such as photomultiplier tubes (PMT) and avalanche photodiodes (APD), and pixelated detectors such as charge-coupled devices (CCD) and complementary metal-oxide-semiconductor (CMOS) sensors. A significant advancement discussed in this review is the integration of optical biosensors with pixelated image sensors, particularly CMOS image sensors. These sensors provide numerous advantages over traditional single-point detectors, including high-resolution imaging, spatially resolved measurements, and the ability to simultaneously detect multiple analytes. Their compact size, low power consumption, and cost-effectiveness further enhance their suitability for portable and point-of-care diagnostic devices. In the future, the integration of machine learning algorithms with these technologies promises to enhance data analysis and interpretation, driving the development of more sophisticated, efficient, and accessible diagnostic tools for diverse applications.

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.

Investigation of the Chemiluminescent Reaction of a Fluorinated Analog of Marine Coelenterazine

Bioluminescence (BL) and chemiluminescence (CL) are remarkable processes in which light is emitted due to (bio)chemical reactions. These reactions have attracted significant attention for various applications, such as biosensing, bioimaging, and biomedicine. Some of the most relevant and well-studied BL/CL systems are that of marine imidazopyrazine-based compounds, among which Coelenterazine is a prime example. Understanding the mechanisms behind efficient chemiexcitation is essential for the optimization and development of practical applications for these systems. Here, the CL of a fluorinated Coelenterazine analog was studied using experimental and theoretical approaches to obtain insight into these processes. Experimental analysis revealed that CL is more efficient under basic conditions than under acidic ones, which could be attributed to the higher relative chemiexcitation efficiency of an anionic dioxetanone intermediate over a corresponding neutral species. However, theoretical calculations indicated that the reactions of both species are similarly associated with both electron and charge transfer processes, which are typically used to explain efficiency chemiexcitation. So, neither process appears to be able to explain the relative chemiexcitation efficiencies observed. In conclusion, this study provides further insight into the mechanisms behind the chemiexcitation of imidazopyrazinone-based systems.

Practical Guidance for Developing Small-Molecule Optical Probes for In Vivo Imaging

The WMIS Education Committee (2019-2022) reached a consensus that white papers on molecular imaging could be beneficial for practitioners of molecular imaging at their early career stages and other scientists who are interested in molecular imaging. With this consensus, the committee plans to publish a series of white papers on topics related to the daily practice of molecular imaging. In this white paper, we aim to provide practical guidance that could be helpful for optical molecular imaging, particularly for small molecule probe development and validation in vitro and in vivo. The focus of this paper is preclinical animal studies with small-molecule optical probes. Near-infrared fluorescence imaging, bioluminescence imaging, chemiluminescence imaging, image-guided surgery, and Cerenkov luminescence imaging are discussed in this white paper.

De novo design of luciferases using deep learning

De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds1,2, but has been limited by a lack of suitable protein structures and the complexity of native protein sequence-structure relationships. Here we describe a deep-learning-based 'family-wide hallucination' approach that generates large numbers of idealized protein structures containing diverse pocket shapes and designed sequences that encode them. We use these scaffolds to design artificial luciferases that selectively catalyse the oxidative chemiluminescence of the synthetic luciferin substrates diphenylterazine3 and 2-deoxycoelenterazine. The designed active sites position an arginine guanidinium group adjacent to an anion that develops during the reaction in a binding pocket with high shape complementarity. For both luciferin substrates, we obtain designed luciferases with high selectivity; the most active of these is a small (13.9 kDa) and thermostable (with a melting temperature higher than 95 °C) enzyme that has a catalytic efficiency on diphenylterazine (kcat/Km = 106 M-1 s-1) comparable to that of native luciferases, but a much higher substrate specificity. The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes.

Multi- and single-reference methods for the analysis of multi-state peroxidation of enolates

In spite of being spin-forbidden, some enzymes are capable of catalyzing the incorporation of O₂(Σg-3) to organic substrates without needing any cofactor. It has been established that the process followed by these enzymes starts with the deprotonation of the substrate forming an enolate. In a second stage, the peroxidation of the enolate formation occurs, a process in which the system changes its spin multiplicity from a triplet state to a singlet state. In this article, we study the addition of O₂ to enolates using state-of-the-art multi-reference and single-reference methods. Our results confirm that intersystem crossing is promoted by stabilization of the singlet state along the reaction path. When multi-reference methods are used, large active spaces are required, and in this situation, semistochastic heat-bath configuration interaction emerges as a powerful method to study these multi-configurational systems and is in good agreement with PNO-LCCSD(T) when the system is well-represented by a single-configuration.

Deciphering the unusual fluorescence in weakly coupled bis-nitro-pyrrolo[3,2-b]pyrroles

Electron-deficient π-conjugated functional dyes lie at the heart of organic optoelectronics. Adding nitro groups to aromatic compounds usually quenches their fluorescence via inter-system crossing (ISC) or internal conversion (IC). While strong electronic coupling of the nitro groups with the dyes ensures the benefits from these electron-withdrawing substituents, it also leads to fluorescence quenching. Here, we demonstrate how such electronic coupling affects the photophysics of acceptor-donor-acceptor fluorescent dyes, with nitrophenyl acceptors and a pyrrolo[3,2-b]pyrrole donor. The position of the nitro groups and the donor-acceptor distance strongly affect the fluorescence properties of the bis-nitrotetraphenylpyrrolopyrroles. Concurrently, increasing solvent polarity quenches the emission that recovers upon solidifying the media. Intramolecular charge transfer (CT) and molecular dynamics, therefore, govern the fluorescence of these nitro-aromatics. While balanced donor-acceptor coupling ensures fast radiative deactivation and slow ISC essential for large fluorescence quantum yields, vibronic borrowing accounts for medium dependent IC via back CT. These mechanistic paradigms set important design principles for molecular photonics and electronics.

A detailed mechanism of the oxidative half-reaction of d-amino acid oxidase: another route for flavin oxidation

d-Amino acid oxidase (DAAO) is a flavoenzyme whose inhibition is expected to have therapeutic potential in schizophrenia. DAAO catalyses hydride transfer from the substrate to the flavin in the reductive half-reaction, and the flavin is reoxidized by O2 in the oxidative half-reaction. Quantum mechanical/molecular mechanical calculations were performed and their results together with available experimental information were used to elucidate the detailed mechanism of the oxidative half-reaction. The reaction starts with a single electron transfer from FAD to O2, followed by triplet-singlet transition. FAD oxidation is completed by a proton coupled electron transfer to the oxygen species and the reaction terminates with H2O2 formation by proton transfer from the oxidized substrate to the oxygen species via a chain of water molecules. The substrate plays a double role by facilitating the first electron transfer and by providing a proton in the last step. The mechanism differs from the oxidative half-reaction of other oxidases.

Theoretical Analysis of the Effect Provoked by Bromine-Addition on the Thermolysis and Chemiexcitation of a Model Dioxetanone

Chemi-/bioluminescence are phenomena in which chemical energy is converted into electronically excited singlet states, which decay with light emission. Given this feature, along with high quantum yields and other beneficial characteristics, these systems have gained numerous applications in bioanalysis, in biomedicine, and in the pharmaceutical field. Singlet chemiexcitation is made possible by the formation of cyclic peroxides (as dioxetanones) as thermolysis provides a route for a ground state reaction to produce singlet excited states. However, such thermolysis can also lead to the formation of triplet states. While triplet states are not desired in the typical applications of chemi-/bioluminescence, the efficient production of such states can open the door for the use of these systems as sensitizers in photocatalysis and triplet-triplet annihilation, among other fields. Thus, the goal of this study is to assess the effect of heavy atom addition on the thermolysis and triplet chemiexcitation of a model dioxetanone. Monobromination does not affect the thermolysis reaction but can improve the efficiency of intersystem crossing, depending on the position of monobromination. Addition of bromine atoms to the triplet state reaction product has little effect on its properties, except on its electron affinity, in which monobromination can increase between 3.1 and 8.8 kcal mol−1.

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.

Theoretical Study on the Reaction Mechanism of Ti with CH3CN in the Gas Phase

To gain a deeper understanding of the reaction mechanisms of Ti with acetonitrile molecules, the triplet and singlet spin-state potential energy surfaces (PESs) has been investigated at B3LYP level of density functional theory (DFT). Crossing points between the different PESs and possible spin inversion processes are discussed by spin-orbit coupling (SOC) calculation. In addition, the bonding properties of the species along the reaction were analyzed by electron localization function (ELF), atoms in molecules (AIM) and natural bond orbital (NBO). The results showed that acetonitrile activation by Ti is a typical spin-forbidden process; larger SOC (by 220.12 cm(-1)) and the possibility of crossing between triplet and singlet imply that intersystem crossing (ISC) would occur near the minimum energy crossing point (MECP) during the transfer of the hydrogen atom.

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.

Solvent viscosity influence on the chemiexcitation efficiency of inter and intramolecular chemiluminescence systems

Efficiency of electron transfer catalyzed chemiluminescence systems is subject to differential solvent viscosity effects; unexpectedly, intermolecular transformations show lower sensitivity than an intramolecular system.

Water oxidation chemistry of a synthetic dinuclear ruthenium complex containing redox-active quinone ligands

We investigated theoretically the catalytic mechanism of electrochemical water oxidation in aqueous solution by a dinuclear ruthenium complex containing redox-active quinone ligands, [Ru2(X)(Y)(3,6-tBu2Q)2(btpyan)](m+) [X, Y = H2O, OH, O, O2; 3,6-tBu2Q = 3,6-di-tert-butyl-1,2-benzoquinone; btpyan =1,8-bis(2,2':6',2″-terpyrid-4'-yl)anthracene] (m = 2, 3, 4) (1). The reaction involves a series of electron and proton transfers to achieve redox leveling, with intervening chemical transformations in a mesh scheme, and the entire molecular structure and motion of the catalyst 1 work together to drive the catalytic cycle for water oxidation. Two substrate water molecules can bind to 1 with simultaneous loss of one or two proton(s), which allows pH-dependent variability in the proportion of substrate-bound structures and following pathways for oxidative activation of the aqua/hydroxo ligands at low thermodynamic and kinetic costs. The resulting bis-oxo intermediates then undergo endothermic O-O radical coupling between two Ru(III)-O(•) units in an anti-coplanar conformation leading to bridged μ-peroxo or μ-superoxo intermediates. The μ-superoxo species can liberate oxygen with the necessity for the preceding binding of a water molecule, which is possible only after four-electron oxidation is completed. The magnitude of catalytic current would be limited by the inherent sluggishness of the hinge-like bending motion of the bridged μ-superoxo complex that opens up the compact, hydrophobic active site of the catalyst and thereby allows water entry under dynamic conditions. On the basis of a newly proposed mechanism, we rationalize the experimentally observed behavior of electrode kinetics with respect to potential and discuss what causes a high overpotential for water oxidation by 1.

Dynamic chirality determines critical roles for bioluminescence in symplectin-dehydrocoelenterazine system

Symplectin is a photoprotein containing the dehydrocoelenterazine (DCL) chromophore, which links to a cysteine residue through a covalent bond with the emission of blue light. This study focuses on the stereochemical process of the emerging stereogenic centers. Two isomeric fluorinated DCL analogs (2,4-diF- and 2,6-diF-DCL) were employed owing to their different bioluminescence activities, these being 200% and 20% compared to natural DCL, respectively. Each of these diF-DCLs was found to exchange with the natural DCL in symplectin at pH 6.0. The emerging stereogenic carbons were racemic at the binding sites. Changing the pH of this storage form to the protein's optimum solubility pH (pH 7.8) resulted in 2,4-diF-DCL-bound symplectin luminescence, and the spent solutions were then analyzed and coelenteramide-390-CGLK-peptide and coelenteramine were detected after a peptidase digestion. The same analysis of the 2,6-diF-DCL-bound symplectin, on the other hand, afforded coelenteramine only but no coelenteramide. When the racemic storage diF-DCLs moved to the active site at pH 7.8, a change in the chirality with the 390-Cys residue resulted. Model experiments using L-cysteine-containing CGLK-peptide supported two diastereoisomers from each diF-DCL. The significant difference in the luminescence from these two chromophores is attributed to a plausible mechanism including the dynamically variable stereogenic center emerging at the storage and then the active site on the symplectin. It is concluded that such dynamic chirality plays a significant role in the symplectoteuthis bioluminescence.

Intermediate-assisted multifunctional catalysis in the conversion of flavin to 5,6-dimethylbenzimidazole by BluB: a density functional theory study

BluB is a distinct flavin destructase that catalyzes a complex oxygen-dependent conversion of reduced flavin mononucleotide (FMNH(2)) to form 5,6-dimethylbenzimidazole (DMB), the lower ligand of vitamin B(12). The catalyzed mechanism remains a challenge due to the discrepancy between the complexity of the conversion and the relative simplicity of the active site of BluB. In this study, we have explored the detailed conversion mechanism by using the hybrid density functional method B3LYP on an active site model of BluB consisting of 144 atoms. The results indicate that the conversion involves more than 14 sequential steps in two distinct stages. In the first stage, BluB catalyzes the incorporation of dioxygen, and the fragmentation of the isoalloxazine ring of FMNH(2) to form alloxan and the ribityl dimethylphenylenediimine (DMPDI); in the second stage, BluB exploits alloxan as a multifunctional cofactor, such as a proton donor, a proton acceptor, and a hydride acceptor, to catalyze the remaining no fewer than 10 steps of the reaction. The retro-aldol cleavage of the C1'-C2' bond of DMPDI is the rate-determining step with a barrier of about 21.6 kcal/mol, which produces D-erythrose 4-phosphate (E4P) and the ring-closing precursor of DMB. The highly conserved residue Asp32 plays critical roles in multiple steps of the conversion by serving as a proton acceptor or a proton shuttle, and another conserved residue Ser167 plays its catalytic role mainly in the rate-determining step by stabilizing the protonated retro-aldol precursor. These results are consistent with the available experimental observations. More significantly, the novel intermediate-assisted mechanism not only provides significant insights into understanding the mechanism underlying the power of the simple BluB catalyzing the complex conversion of FMNH(2) to DMB, but also represents a new type of intermediate-assisted multifunctional catalysis in an enzymatic reaction.