| 1. |
- Berraud-Pache, Romain, et al.
(författare)
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QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion
- 2018
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 122:20, s. 5173-5182
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
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| 3. |
- Chen, Shu-Feng, et al.
(författare)
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Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide : A Systematic Theoretical Study
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:8, s. 2796-2807
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Tidskriftsartikel (refereegranskat)abstract
- 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 ab initio results [Roca-Sanjuan et al J. Chem. Theory Comput. 2011, 7, 4060] Because the chemiluminescence state appears to be completely dark, a new mechanism is tentatively introduced for this process.
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| 4. |
- Chen, Shu-Feng, et al.
(författare)
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Systematic theoretical investigation on the light emitter of firefly
- 2011
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:3, s. 798-803
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Tidskriftsartikel (refereegranskat)abstract
- This is a systematic theoretical investigation on all the possible light emitters of firefly using multireference method. Six chemical forms of oxyluciferin (OxyLH2) molecules/anions were studied by a multi-state complete active space second order perturbation (MS-CASPT2) method in vacuum and DMSO. The calculated results and subsequent analysis excluded enol-OxyLH2, keto-OxyLH2 and enolate-OxyLH- as possible light emitters. The remaining three candidates, phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2-, were further investigated in protein by a MS-CASPT2/molecular mechanics (MM) study to explain the natural bioluminescence of firefly. By comparison of the MS-CASPT2/MM calculated results of phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2- with the experimental observation and detailed analysis, we concluded that the direct decomposition excited-state product of firefly dioxetanone in vivo and the only light emitter of firefly in natural bioluminescence is the first singlet exited state (S1) of phenolate-keto-OxyLH-.
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| 5. |
- Chen, Shufeng, et al.
(författare)
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Hybrid QM/MM Simulations of the Obelin Bioluminescence and Fluorescence Reveal an Unexpected Light Emitter
- 2014
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 118:11, s. 2896-2903
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Farahani, Pooria, 1985-
(författare)
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Theoretical Studies of Ground and Excited State Reactivity
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- To exemplify how theoretical chemistry can be applied to understand ground and excited state reactivity, four different chemical reactions have been modeled. The ground state chemical reactions are the simplest models in chemistry. To begin, a route to break down halomethanes through reactions with ground state cyano radical has been selected. Efficient explorations of the potential energy surfaces for these reactions have been carried out using the artificial force induced reaction algorithm. The large number of feasible pathways for reactions of this type, up to eleven, shows that these seemingly simple reactions can be quite complex. This exploration is followed by accurate quantum dynamics with reduced dimensionality for the reaction between Cl− and PH2Cl. The dynamics indicate that increasing the dimensionality of the model to at least two dimensions is a crucial step for an accurate calculation of the rate constant. After considering multiple pathways on a single potential energy surface, various feasible pathways on multiple surfaces have been investigated. As a prototype of these reactions, the thermal decomposition of a four-membered ring peroxide compound, called 1,2-dioxetane, which is the simplest model of chemi- and bioluminescence, has been studied. A detailed description of this model at the molecular level can give rise to a unified understanding of more complex chemiluminescence mechanisms. The results provide further details on the mechanisms and allow to rationalize the high ratio of triplet to singlet dissociation products. Finally, a thermal decomposition of another dioxetane-like compound, called Dewar dioxetane, has been investigated. This study allows to understand the effect of conjugated double bonds adjacent to the dioxetane moiety in the chemiluminescence mechanism of dioxetane. Our studies illustrate that no matter how complex a system is, theoretical chemistry can give a level of insight into chemical processes that cannot be obtained from other methods.
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| 7. |
- Fernández Galván, Ignacio, et al.
(författare)
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S0 → S3 transition in recombination products of photodissociated dihalomethanes
- 2014
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 112:5-6, s. 575-582
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Tidskriftsartikel (refereegranskat)abstract
- Species of the form CH2X–Y (X, Y = Br, I) have been proposed and identified as recombination products of the photodissociation of the parent dihalomethanes. Second-order complete active space perturbation theory (CASPT2) calculations of the vertical absorption energies considerably overestimate the experimental transient absorption band maxima, while the computationally cheaper time-dependent density functional theory (TD-DFT) method yields results with a reasonable agreement. In this work, we try to find the reason for this unexpected performance difference. In an initial study of the I2 molecule, we establish that CASPT2 is capable of providing quantitatively accurate results and that the TD-DFT values are only valid at first sight, but are qualitatively flawed. In the CASPT2 calculations for the CH2X–Y molecules, we include relativistic corrections, spin–orbit coupling, vibrational and thermal effects, and the solvent polarisation. Unfortunately, the results do not improve appreciably compared to the experimental measurements. We conclude that the good agreement of TD-DFT results is very likely fortuitous in this case as well, and that further theoretical and experimental investigations are probably needed to resolve the current discrepancy between CASPT2 and experiments.
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| 8. |
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| 9. |
- Marazzi, Marco, et al.
(författare)
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Photostability Mechanisms in Human gamma B-Crystallin : Role of the Tyrosine Corner Unveiled by Quantum Mechanics and Hybrid Quantum Mechanics/Molecular Mechanics Methodologies
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:4, s. 1351-1359
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Tidskriftsartikel (refereegranskat)abstract
- The tyrosine corner is proposed as a featured element to enhance photostability in human gamma B-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 gamma B-crystallin.
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| 10. |
- Navizet, Isabelle, et al.
(författare)
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Are the Bio- and Chemiluminescence States of the Firefly Oxyluciferin the Same as the Fluorescence State?
- 2013
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Ingår i: Photochemistry and Photobiology. - : Wiley. - 0031-8655 .- 1751-1097. ; 89:2, s. 319-325
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Tidskriftsartikel (refereegranskat)abstract
- A usual strategy in both experimental and theoretical studies on bio- and chemiluminescence is to analyze the fluorescent properties of the bio- and chemiluminescence reaction product. Recent findings in a coelenteramide and Cypridina oxyluciferin model arise a concern on the validity of this procedure, showing that the light emitters in each of these luminescent processes might differ. Here, the thermal decomposition path of the firefly dioxetanone and the light emission states of the Firefly oxyluciferin responsible for the bio-, chemiluminescence, and fluorescence of the molecule are characterized using ab initio quantum chemistry and hybrid quantum chemistry/molecular mechanics methods to determine if the scenario found in the coelenteramide and Cypridina oxyluciferin study does also apply to the Firefly bioluminescent systems. The results point out to a unique emission state in the bio-, chemiluminescence, and fluorescence phenomena of the Firefly oxyluciferin and, therefore, using fluorescence properties of this system is reasonable.
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