The role of solvation models on the computed absorption and emission spectra: the case of fireflies oxyluciferin

García‐Iriepa, Cristina; Zemmouche, Madjid; Ponce-Vargas, Miguel; Navizet, Isabelle

doi:10.1039/c8cp07352j

Cited by 23 publications

(27 citation statements)

References 42 publications

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“…Vibrationally resolved absorption spectra have been computed on the basis of the TD‐DFT vibrational signatures by using the Franck‐Condon‐Herzberg‐Teller (FCHT) approximation and the Adiabatic Hessian method as implemented in Gaussian 16 . A comparison of the FranckCondon (FC) and FCHT vibrationally resolved absorption and emission spectra of oxyluciferin has been already discussed in a previous study, showing that the FCHT spectra resemble the FC ones. For this reason, only the FCHT spectra are simulated in this study.…”

Section: Methodsmentioning

confidence: 82%

pH‐Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate

et al. 2019

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The photophysical properties of oxyluciferin, the light emitter responsible for firefly bioluminescence, are pH-dependent. One of the potential proton acceptor/donor is adenosine monophosphate (AMP). We have studied three oxyluciferin synthetic analogues with or without AMP, in water, in the pH = 5 to 11 range, using both experimental steady-state absorption spectroscopy or the recently developed computational protocol that uses constant pH molecular dynamics and then hybrid QM/MM calculations (CpHMD-then-QM/MM). The latter features a sys-tematic investigation of all the protonation microstates using molecular dynamics simulations coupled to thousands hybrid QM/MM vertical excitation energies. Our results demonstrate that AMP does not significantly modify the visible light absorption of the analogues, whatever the pH value. We also show that CpHMD-then-QM/MM is capable to qualitatively reproduce the pH-dependent absorption spectrum of the analogues, despite the employed low QM level of theory.

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Section: Methodsmentioning

confidence: 82%

pH‐Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate

et al. 2019

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“…(As discussed in Section 5.2, the cLR formalism encountered in some of these studies is really a ptSS‐PCM approach, and typically outperforms true LR methods for excitations with charge‐transfer character.) Even for states that are not dominated by charge transfer, the SS‐PCM approach generally affords smaller errors for solvatochromatic shifts in the absorption spectrum as compared to LR‐PCM calculations, 586,597,631 although it is worth bearing in mind that the experimental λ max need not correspond to the origin (0–0) transition, due to vibrational structure 664–666 . The ptSS‐PCM approach also affords more accurate results for emission energies, 667 though it is found that the accuracy is largely unaffected if the LR‐PCM procedure is used for the excited‐state geometry optimization, followed by a ptSS‐PCM single‐point calculation, which simplifies the procedure 667 .…”

Section: Nonequilibrium Solvationmentioning

confidence: 99%

Dielectric continuum methods for quantum chemistry

Herbert

2021

WIREs Comput Mol Sci

135

195

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This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular boundary‐element approach to the problem defined by the Poisson or Poisson–Boltzmann equation, but that moniker belies the diversity of available methods. This work reviews the current state‐of‐the art, with emphasis on theory and methods rather than applications. The basics of continuum electrostatics are described, including the nonequilibrium polarization response upon excitation or ionization of the solute. Nonelectrostatic interactions, which must be included in the model in order to obtain accurate solvation energies, are also described. Numerical techniques for implementing the equations are discussed, including linear‐scaling algorithms that can be used in classical or mixed quantum/classical biomolecular electrostatics calculations. Anisotropic models that can describe interfacial solvation are briefly described. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Molecular and Statistical Mechanics > Free Energy Methods

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“…The nature of the emitter depends on the pH and the "local" pH inside the cavity is not an experimentally measurable. Joint experimental and computational studies of solvated emitters and of analogous systems in which the key reactions like the keto-enol tautomerization of the thiazolone moiety or the deprotonation of the phenolate group are blocked show that the experimental observations can be reproduced by protocols, which take into account dynamics of the protein, and that the use of analogues helps to better understand the nature of the light emitter (35)(36)(37). Nevertheless, accounting for fluctuating protonation states of the protein residues still needs to be improved.…”

Section: Challenges In Modeling Bioluminescent Systemsmentioning

confidence: 99%

Frontiers in Multiscale Modeling of Photoreceptor Proteins

Mroginski

Adam

Amoyal

et al. 2021

Photochem & Photobiology

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This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

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The role of solvation models on the computed absorption and emission spectra: the case of fireflies oxyluciferin

Abstract: Absorption and emission energies calculation covering both implicit and explicit solvation models using oxyluciferin as the case of study.

Cited by 23 publications

References 42 publications

pH‐Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate

pH‐Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate

Dielectric continuum methods for quantum chemistry

Frontiers in Multiscale Modeling of Photoreceptor Proteins

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