Firefly bioluminescence has been applied in several fields. However, the absorption and fluorescence spectra of the substrate, luciferin, have not been observed at the vibrational level. In this study, the vibrationally resolved absorption and fluorescence spectra of firefly luciferin (neutral form LH₂, phenolate ion form LH⁻ and dianion form L²⁻) are simulated using the density functional method and convoluted by a Gaussian function, with displacement, distortion and Duschinsky effects in the framework of the Franck–Condon approximation. Both neutral and anionic forms of the luciferin are considered in the gas phase and in solution. The simulated spectra have desired band maxima with the experimental ones. The vibronic structure analysis reveals that the features of the most contributive vibrational modes coincide with the key geometry-changing region during transition between the ground state and the first singlet excited state.

Investigation of the relative reactivity of bonds in fullerenes will provide fundamental theory for the design of fullerene-based materials. We have theoretically investigated the reactivity of the Diels–Alder (DA) cycloaddition of cis-1,3-butadiene to all types of bonds in C₆₀ and C₇₀ using the M06-2X hybrid density functional theory (DFT) calculations (J. Phys. Org. Chem. 2012, 25 850–855) and have pointed out that the DA cycloadditions of cis and trans forms of 1,3-butadiene to ethylene have a specially intimate relationship (J. Phys. Org. Chem. 2014, 27 652–660). For the aim of telling a whole story of the DA cycloaddition concerning C₆₀ and C₇₀, the DA cycloadditions of trans-1,3-butadiene to all types of bonds in C₆₀ and C₇₀ were explored at the same theoretical level as those of the cis-1,3-butadiene. The calculated results related with the trans- and cis-1,3-butadienes were compared. The potential energy curves of DA cycloadditions of trans- and cis-1,3-butadiene to C₆₀ and C₇₀ were discussed. The distortion–interaction energy model was employed to elucidate the origin of different reactivity of all kinds of CC bonds. The solvent effects were examined using the continuum solvent model. These current results, along with our previous research, will help to obtain an overall view of the DA cycloadditions of 1,3-butadiene to C₆₀ and C₇₀. Copyright © 2014 John Wiley & Sons, Ltd.

A reversible wetting/dewetting procedure is reported for an open-cage fullerene with an 18-membered orifice. In a homogeneous mixture of H₂O/EtOH/CHCl₃, water was encapsulated into the cavity of the open-cage compound quantitatively at 80 °C. Addition of aqueous hydrogen fluoride into the water-encapsulated complex removed the encapsulated water completely at room temperature. H-bonding between the trapped water and fluoride is shown to play a key role for the water release process.

The Diels–Alder (DA) reaction is one of the most important reactions in organic chemistry. The controversy surrounding this reaction as to whether it follows a concerted or stepwise mechanism has existed for a long time. The reaction of 1,3-butadiene and ethylene is the paradigmatic example of the DA reaction. We have reinvestigated the mechanism of this reaction using density functional theory. The theoretical study considered all types of possible pathways for the reaction of 1,3-butadiene and ethylene using six functionals at different rungs of Jacob's ladder. Therefore, a complete picture is given for a thorough understanding of the iconic DA reaction, and a new stationary point during the reaction processes has been reported for the first time. The calculated results indicated that three functionals, ωB97X-D, M06-2X, and B2-PLYP, of the fourth and fifth rungs of Jacob's ladder performed well in the investigation of the mechanism of this reaction and that the reliable basis set should be larger than 6-311+G(2d,p). The cis-1,3-butadiene more easily reacted with ethylene compared with 1,3-butadiene in the trans conformation. The concerted mechanism was found to be energetically favorable, whose energy barrier is around 10 kcal/mol lower than that of the stepwise mechanism. Two investigated solvents, toluene and CH₃CN, had little impact on this simple DA reaction. Copyright © 2014 John Wiley & Sons, Ltd.

The 1,3-dipolar cycloaddition (1,3-DPCA) reaction plays a crucial role during the functionalization of fullerenes, which have broad applications in the materials and pharmaceutical fields. In concert with previous experiments, we theoretically investigated the mechanisms of 1,3-DPCA of diphenyldiazomethane (DDMf) to two fullerenes (C₆₀ and C₇₀) using the M06-2X density functional method under vacuum and in solvents. To understand the influence of the dipolarophile on these reactions, the 1,3-DPCA of DDMf to three common acceptors, specifically tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and chloranil (CA), was also studied at the same computational level. The substituent effects on the five reactions were investigated by modeling 1,3-DPCA reactions with 12 different substituted DDMf (DDMs) with five dipolarophiles, totaling 60 reactions. Including the five unsubstituted DDMf reactions, 65 1,3-DPCA reactions were studied. The stereoselectivity, relative reactivity, solvent effects, and distortion/interaction energy model were carefully considered and analyzed based on their corresponding electronic structures, electrostatic potential surfaces, interaction models, solvent models, and thermodynamic data. An intermediate was identified for each of the 65 reactions. A possible biradical pathway for the reactions between DDMf and the two fullerenes was also investigated. The calculated results corroborate and enrich the experimental observations. The conclusion and detailed discussion are generally important for understanding the 1,3-DPCA reactions to fullerenes. Copyright © 2014 John Wiley & Sons, Ltd.

The chemical complexity of oxyluciferin (OxyLH₂), the light-emitting molecule in the bioluminescence of fireflies, originates from the possibility of keto/enol tautomerism and single or double deprotonation. Herein, we present detailed infrared spectroscopic analysis of OxyLH₂ and several of its chemical isomers and isotopomers. To facilitate the future characterization of its biogenic forms, we provide accurate assignments of the solid-state and solution FTIR spectra of OxyLH₂ based on comparison to six isotopically labeled variants ([2-¹³C]-OxyLH₂, [3-¹⁵N]-OxyLH₂, [4-¹³C]-OxyLH₂, [5-¹³C]-OxyLH₂, [2′-¹³C]-OxyLH₂, [3′-¹⁵N]-OxyLH₂), five closely related structural analogues, and theoretically computed spectra. The computed DFT harmonic vibrational force fields (B3LYP and M06 functionals with basis sets of varying flexibility up to 6-311++G**) reproduce well the observed shifts in the IR spectra of both isotopically labeled and structurally related analogues.

Bacterial bioluminescence (BL) has been successfully applied in water-quality monitoring and in vivo imaging. The attention of researchers has been attracted for several decades, but the mechanism of bacterial BL is still largely unknown due to the complexity of the multistep reaction process. Debates mainly focus on three key questions: How is the bioluminophore produced? What is the exact chemical form of the bioluminophore? How does the protein environment affect the light emission? Using quantum mechanics (QM), combined QM and molecular mechanics (QM/MM) and molecular dynamic (MD) calculations in gas-phase, solvent and protein environments, the entire process of bacterial BL was investigated, from flavin reduction to light emission. This investigation revealed that: 1) the chemiluminescent decomposition of flavin peroxyhemiacetal does not occur through the intramolecular chemical initiated electron exchange luminescence (CIEEL) or the “dioxirane” mechanism, as suggested in the literature. Instead, the decomposition occurs according to the charge-transfer initiated luminescence (CTIL) mechanism for the thermolysis of dioxetanone. 2) The first excited state of 4a-hydroxy-4a,5-dihydroFMN (HFOH) was affirmed to be the bioluminophore of bacterial BL. This study provides details regarding the mechanism by which bacterial BL is produced and is helpful in understanding bacterial BL in general.

Aequorea victoria is a type of jellyfish that is known by its famous protein, green fluorescent protein (GFP), which has been widely used as a probe in many fields. Aequorea has another important protein, aequorin, which is one of the members of the EF-hand calcium-binding protein family. Aequorin has been used for intracellular calcium measurements for three decades, but its bioluminescence mechanism remains largely unknown. One of the important reasons is the lack of clear and reliable knowledge about the light emitters, which are complex. Several neutral and anionic forms exist in chemiexcited, bioluminescent, and fluorescent states and are connected with the H-bond network of the binding cavity in the protein. We first theoretically investigated aequorin chemiluminescence, bioluminescence, and fluorescence in real proteins by performing hybrid quantum mechanics and molecular mechanics methods combined with a molecular dynamics method. For the first time, this study reported the origin and clear differences in the chemiluminescence, bioluminescence and fluorescence of aequorin, which is important for understanding the bioluminescence not only of jellyfish, but also of many other marine organisms (that have the same coelenterazine caved in different coelenterazine-type luciferases).

All possible types of Diels–Alder cycloadditions of 1,3-cis-butadiene to C₆₀ (2 in total) and to C₇₀ (8 in total) were theoretically investigated by the M06-2X density functional method in gas phase and solutions. An intermediate between the reactant and the transition state was located for each reaction. These intermediates except one have not been experimentally or theoretically reported before. The reactivities of the 10 reactions in both the gas phase and solutions were systematically compared based on the calculated results. The present conclusion agrees with the experimental observations and partly disagrees with the previously theoretical conclusion. Copyright © 2012 John Wiley & Sons, Ltd.