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.

QM/MM calculations on a newly synthesised oxyluciferin substrate: new insights into the conformational effect.

In this publication we conduct calculations on a newly synthesised red-shifted emitter of luciferin in order to understand what are the main contributions to the colour-shifting emission. Indeed the bioluminescent system, especially from fireflies, is one of the main resources for medical imaging but its efficiency greatly depends on the wavelength of the emission. We performed classical molecular dynamics followed by quantum mechanics/molecular mechanics (QM/MM) calculations, with either density functional theory or multiconfigurational reference second-order perturbation theory on different emitters to obtain bioluminescence emission. We analysed the calculations and investigated the effects which play a non-negligible role in the emission, like the effect of the surroundings or the effect of the conformation of the emitter. Finally, in the absence of crystallographic structures, we proposed the most likely conformation for the emitter in the bioluminescence process.

Luminescence and single-molecule magnet behavior in lanthanide complexes involving a tetrathiafulvalene-fused dipyridophenazine ligand.

The reaction between the TTF-fused dipyrido[3,2-a:2',3'-c]phenazine (dppz) ligand (L) and 1 equiv of Ln(hfac)3·2H2O (hfac(-) = 1,1,1,5,5,5-hexafluoroacetyacetonate) or 1 equiv of Ln(tta)3·2H2O (tta(-) = 2-thenoyltrifluoroacetonate) (Ln(III) = Dy(III) or Yb(III)) metallic precursors leads to four mononuclear complexes of formula [Ln(hfac)3(L)]·C6H14 (Ln(III) = Dy(III) (1), Yb(III) (2)) and [Ln(tta)3(L)]·C6H14 (Ln(III) = Dy(III) (3), Yb(III) (4)), respectively. Their X-ray structures reveal that the Ln(III) ion is coordinated to the bischelating nitrogenated coordination site and adopts a D4d coordination environment. The dynamic magnetic measurements show a slow relaxation of the Dy(III) magnetization for 1 and 3 with parameters highlighting a slower relaxation for 3 than for 1 (τ0 = 4.14(±1.36) × 10(-6) and 1.32(±0.07) × 10(-6) s with Δ = 39(±3) and 63.7(±0.7) K). This behavior as well as the orientation of the associated magnetic anisotropy axes have been rationalized on the basis of both crystal field splitting parameters and ab initio SA-CASSCF/RASSI-SO calculations. Irradiation of the lowest-energy HOMO → LUMO ILCT absorption band induces a (2)F5/2 → (2)F7/2 Yb-centered emission for 2 and 4. For these Yb(III) compounds, Stevens operators method has been used to fit the thermal variation of the magnetic susceptibilities, and the resulting MJ splittings have been correlated with the emission lines.

Redesigning donor-acceptor Stenhouse adduct photoswitches through a joint experimental and computational study.

Many studies have recently explored a new class of reversible photoswitching compounds named Donor-Acceptor Stenhouse Adducts (DASAs). Upon light irradiation, these systems evolve from a coloured open-chain to a colourless closed-ring form, while the thermal back-reaction occurs at room temperature. In order to fulfill the requirements for different applications, new molecules with specific properties need to be designed. For instance, shifting the activation wavelength towards the red part of the visible spectrum is of relevance to biological applications. By using accurate computational calculations, we have designed new DASAs and predicted some of their photophysical properties. Starting from well-studied donor and acceptor parts, we have shown that small chemical modifications can lead to substantial changes in both photophysical and photoswitching properties of the resulting DASAs. Furthermore, we have also analysed how these substitutions impact the electronic structure of the systems. Finally, some pertinent candidates have been successfully synthesized and their photoswitching properties have been characterized experimentally.

Unveiling the Photophysical Properties of Boron-dipyrromethene Dyes Using a New Accurate Excited State Coupled Cluster Method.

Boron-dipyrromethene (BODIPY) molecules form a class of fluorescent dyes known for their exceptional photoluminescence properties. Today, they are used extensively in various applications from fluorescent imaging to optoelectronics. The ease of altering the BODIPY core has allowed scientists to synthesize dozens of analogues by exploring chemical substitutions of various kinds or by increasing the length of conjugated groups. However, predicting the impact of any chemical change accurately is still a challenge, especially as most computational methods fail to describe correctly the photophysical properties of BODIPY derivatives. In this study, the recently developed coupled cluster method called "domain-based local pair natural orbital similarity transformed equation of motion-coupled cluster singles and doubles" (DLPNO-STEOM-CCSD) is employed to compute the lowest vertical excitation energies of more than 50 BODIPY molecules. The method performs remarkably well yielding an accuracy of about 0.06 eV compared to the experimental absorption maxima. We also provide an estimate to the error made by neglecting vibronic effects in the computed spectra. The dyes selected for investigation here span a large range of molecular sizes and chemical functionalities and are embedded in solvents with different polarities. We have also investigated if the method is able to correctly reproduce the impact of a single chemical modification on the absorption energy. To characterize the method in more specific terms, we have studied four large BODIPY analogues used in real-life applications due to their interesting chemical properties. These examples should illustrate the capacity of the DLPNO-STEOM-CCSD procedure to become a method of choice for the study of photophysical properties of medium to large organic compounds.

Accurate Computation of the Absorption Spectrum of Chlorophyll a with Pair Natural Orbital Coupled Cluster Methods.

The ability to accurately compute low-energy excited states of chlorophylls is critically important for understanding the vital roles they play in light harvesting, energy transfer, and photosynthetic charge separation. The challenge for quantum chemical methods arises both from the intrinsic complexity of the electronic structure problem and, in the case of biological models, from the need to account for protein-pigment interactions. In this work, we report electronic structure calculations of unprecedented accuracy for the low-energy excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD) in combination with sufficiently large and flexible basis sets. The results of our DLPNO-STEOM-CCSD calculations are compared with more approximate approaches. The results demonstrate that, in contrast to time-dependent density functional theory, the DLPNO-STEOM-CCSD method provides a balanced performance for both absorption bands. In addition to vertical excitation energies, we have calculated the vibronic spectrum for the Q and B bands through a combination of DLPNO-STEOM-CCSD and ground-state density functional theory frequency calculations. These results serve as a basis for comparison with gas-phase experiments.

Computational Design of Near-Infrared Fluorescent Organic Dyes Using an Accurate New Wave Function Approach.

The extensive research focusing on fluorescent organic dyes for bioimaging has made this in vivo method available for a diverse range of applications. One way to enhance this method is to tune the absorption and emission wavelengths of dyes to the near-infrared region where better light penetration and imaging resolution can be achieved. For this purpose, the well-known BODIPY dyes and their derivatives called aza-BODIPY have been the subject of extensive synthetic efforts. The interest in these systems stems from their excellent photophysical properties. Despite numerous studies, the rational design of near-infrared active dyes with desirable properties remains difficult. Here, we present a new wave function-based method for modeling excited states of large molecules, which has numerous theoretical advantages over the most commonly used electronic structure methods. This method is employed to suggest candidates for new dyes with the desired properties and to predict the absorption and fluorescence maxima and luminescence spectra of aza-BODIPY dyes with possible applications in fluorescence imaging.

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.

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

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.

Beetle luciferases with naturally red- and blue-shifted emission.

The different colors of light emitted by bioluminescent beetles that use an identical substrate and chemiexcitation reaction sequence to generate light remain a challenging and controversial mechanistic conundrum. The crystal structures of two beetle luciferases with red- and blue-shifted light relative to the green yellow light of the common firefly species provide direct insight into the molecular origin of the bioluminescence color. The structure of a blue-shifted green-emitting luciferase from the firefly Amydetes vivianii is monomeric with a structural fold similar to the previously reported firefly luciferases. The only known naturally red-emitting luciferase from the glow-worm Phrixothrix hirtus exists as tetramers and octamers. Structural and computational analyses reveal varying aperture between the two domains enclosing the active site. Mutagenesis analysis identified two conserved loops that contribute to the color of the emitted light. These results are expected to advance comparative computational studies into the conformational landscape of the luciferase reaction sequence.

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.