Experimental and Theoretical Study for Core Excitation of Firefly Luciferin in Carbon K-Edge Spectra.

Carbon (C) K-edge X-ray absorption spectra for firefly luciferin were measured and assigned using time-dependent density functional theoretical calculations for luciferin anion and dianion to elucidate the effect of hydroxy-group deprotonation. It was found that the C K-edge spectra for luciferin had four characteristic peaks. The effect of deprotonation of the hydroxy group appears in the energy difference of the first and second peaks of these spectra. This energy difference is 1.0 eV at pH 7 and 2.3 eV at pH 10. The deprotonation of the hydroxy group can be distinguished based on the soft X-ray absorption spectra.

Theoretical Study of Si/C Equally Mixed Dodecahedrane Analogues.

To gain insight into the effect of Si/C arrangement on the molecular framework of strained polyhedral compounds, dodecahedrane analogues containing equal numbers of carbon and silicon (Si/C equally mixed dodecahedrane analogues) were investigated using the ab initio molecular orbital method. There are 1648 isomers for which the Si/C arrangement on the molecular framework is different. Based on the geometry optimization of all the isomers as well as the carbon and silicon analogues, the characteristics of the structure, relative energy, and strain energy of the Si/C equally mixed compounds are presented. Then, important factors controlling the relative energy, such as strain energy, are proposed through regression analysis. Also discussed is the correlation between the relative energy and the indices of Si/C dispersion, such as the number of skeletal C-Si single bonds and condensed five-membered rings constituting the polyhedral structure.

Absorption Spectra for Firefly Bioluminescence Substrate Analog: TokeOni in Various pH Solutions.

AkaLumine hydrochloride, named TokeOni, is one of the firefly luciferin analogs, and its reaction with firefly luciferase produces near-infrared (NIR) bioluminescence. Prior to studying the bioluminescence mechanism, basic knowledge about the chemical structures, electronic states, and absorption properties of TokeOni at various pH values of solution has to be acquired. In this paper, the absorption spectra for TokeOni and AkaLumine at pH 2-10 were measured. Density functional theory (DFT) calculations, time-dependent DFT calculations, and the vibrational analyses were carried out. The absorption spectra indicate that the chemical forms of TokeOni in solutions are same as those of AkaLumine. The peaks at pH 7-10 in the absorption spectra correspond to the excitation from the ground state of a carboxylate anion of AkaLumine, the peak at pH 2 corresponds to the excitation from the ground state of a carboxylate anion with an N-protonated thiazoline ring and N-protonated dimethylamino group of AkaLumine, and the peak at pH 4 corresponds to the excitation from the ground state of a carboxylate anion with an N-protonated thiazoline ring of AkaLumine.

Quantum-mechanical hydration plays critical role in the stability of firefly oxyluciferin isomers: State-of-the-art calculations of the excited states.

Stabilizing mechanisms of three possible isomers (phenolate-keto, phenolate-enol, and phenol-enolate) of the oxyluciferin anion hydrated with quantum explicit water molecules in the first singlet excited state were investigated using first-principles Born-Oppenheimer molecular dynamics simulations for up to 1.8 ns (or 3.7 × 106 MD steps), revealing that the surrounding water molecules were distributed to form clear single-layered structures for phenolate-keto and multi-layered structures for phenolate-enol and phenol-enolate isomers. The isomers employed different stabilizing mechanisms compared to the ground state. Only the phenolate-keto isomer became attracted to the water molecules in its excited state and was stabilized by increasing the number of hydrogen bonds with nearby water molecules. The most stable isomer in the excited state was the phenolate-keto, and the phenolate-enol and phenol-enolate isomers were higher in energy by ∼0.38 eV and 0.57 eV, respectively, than the phenolate-keto. This was in contrast to the case of ground state in which the phenolate-enol was the most stable isomer.

Theoretical Study of the Wavelength Selection for the Photocleavage of Coumarin-caged D-luciferin.

The equilibrium structures and optical properties of the photolabile caged luciferin, (7-diethylaminocoumarin-4-yl)methyl caged D-luciferin (DEACM-caged D-luciferin), in aqueous solution were investigated via quantum chemical calculations. The probable conformers of DEACM-caged D-luciferin were determined by potential energy curve scans and structural optimizations. We identified 40 possible conformers of DEACM-caged D-luciferin in water by comparing the Gibbs free energy of the optimized structures. Despite the difference in their structures, the conformers were similar in terms of assignments, oscillator strengths and energies of the three low-lying excited states. From the concentrations of the conformers and their oscillator strengths, we obtained a theoretical UV/Vis spectrum of DEACM-caged D-luciferin that has two main bands of shape nearly identical to the experimental UV/Vis spectrum. The absorption bands with maxima ~ 384 and 339 nm were attributed to the electronic excitations of the caged group and the luciferin moiety, respectively, by analysis of the theoretical UV/Vis spectrum. Furthermore, the analysis showed that DEACM-caged D-luciferin is excited in the caged group only by light of wavelength ranging within 400-430 nm, which is in the long-wavelength tail of the 384 nm band. This should be tested to lower damage upon photocleavage.

Photoabsorption Spectra of Aqueous Oxyluciferin Anions Elucidated by Explicit Quantum Solvent.

Experimental photoabsorption spectra of three possible isomers (phenolate-keto, phenolate-enol, and phenol-enolate) of oxyluciferin anions in aqueous solution were reproduced by first-principles time-dependent density functional theory simulations in which the entire system including the oxyluciferin anion and 64 water molecules were modeled by full quantum mechanics (full QM), unlike the conventional hybrid method, where the surrounding water molecules are modeled by molecular mechanics (MM) or a continuum solvent model. The full QM photoabsorption spectra were calculated from 1000 structures that had been obtained using the first-principles Born-Oppenheimer molecular dynamics simulations, which included the van der Waals correction, to take into account the effect of dynamical fluctuations of the hydration structure. The full QM calculation with CAM-B3LYP functional, which is the most elaborate one and is apparently the most consistent with experiment, is compared to others obtained with different levels of the functional and the solvent model. The amount of charge leakage from the oxyluciferin anions to the aqueous solution is found to differ significantly between the ground and excited states and is strongly dependent on the simulation method. The conventional solvent models do not take this into account, but the QM/MM can do it appropriately when including more than 10 water molecules into the QM region.

Synthesis and quantitative characterization of coumarin-caged D-luciferin.

Caged luciferin compounds of firefly luciferins have recently drawn much attention since firefly bioluminescence, in which D-luciferin acts as a substrate, is widely used in noninvasive gene-expression imaging, studies of in vivo cell trafficking, and the detection of enzyme activity. The objectives of this study are the development of new caged luciferins and the quantitative determination of the photophysical parameters of their photo-decomposition. We synthesized 7-(diethylaminocoumarin)-4-(yl)methyl caged D-luciferin (DEACM-caged D-luciferin) and quantitatively characterized its absorption spectrum, bioluminescence, and photoproducts using chiral HPLC chromatography, as a function of light-irradiation time. We observed that 4 min of UV irradiation generated maximum D-luciferin concentrations, which corresponds to 16.2% of the original DEACM-caged-D-luciferin concentration. Moreover, we evaluated not only the rate of photocleavage (0.20/min) from DEACM-caged D-luciferin to luciferin but also the rate of caged-luciferin degradation that did not produce luciferin (0.28/min) and the rate of luciferin decomposition (0.20/min) after exposure to irradiation with a 70 mW/cm2 high-pressure mercury lamp (254-600 nm). The formation rate of L-luciferin via DEACM-caged-D-luciferin photocleavage was smaller by a factor of 1/10 compared with that of D-luciferin. These quantitative measurements and simultaneous evaluations of photocleavage, degradation, and decomposition are the most important and original methodology presented in this study.

Theoretical insights into the effect of pH values on oxidation processes in the emission of firefly luciferin in aqueous solution.

To elucidate the emission process of firefly d-luciferin oxidation across the pH range of 7-9, we identified the emission process by comparison of the potential and free-energy profiles for the formation of the firefly substrate and emitter, including intermediate molecules such as d-luciferyl adenylate, 4-membered dioxetanone, and their deprotonated chemical species. From these relative free energies, it is observed that the oxidation pathway changes from d-luciferin → deprotonated d-luciferyl adenylate → deprotonated 4-membered dioxetanone → oxyluciferin to deprotonated d-luciferin → deprotonated d-luciferyl adenylate → deprotonated 4-membered dioxetanone → oxyluciferin with increasing pH value. This indicates that deprotonation on 6'OH occurs during the formation of dioxetanone at pH 7-8, whereas luciferin in the reactant has a 6'OH-deprotonated form at pH 9.

The effect of dynamical fluctuations of hydration structures on the absorption spectra of oxyluciferin anions in an aqueous solution.

In this study, the effect of hydration on the absorption spectra of oxyluciferin anion isomers in an aqueous solution is investigated for elucidating the influence of characteristic hydration structures. Using a canonical ensemble of hydration structures obtained from first-principles molecular dynamics simulations, the instantaneous absorption spectra of keto-, enol-, and enolate-type aqueous oxyluciferin anions at room temperature are computed from a collection of QM/MM calculations using an explicit solvent. It is demonstrated that the calculations reproduce experimental results concerning spectral shifts and broadening, for which traditional methods based on quantum chemistry and the Franck-Condon approximation fail because of the molecular vibrations of oxyluciferin anions and dynamical fluctuations of their hydration structures. Although the first absorption band associated with the lowest energy excitation corresponds to a π-π* transition for all oxyluciferin anion isomers, the changes in this band upon hydration are different among the isomers. In particular, the bands of enol- and enolate-type of oxyluciferin anions are significantly blue-shifted by hydration, whereas those of the keto-type oxylucifeion anion are shifted relatively less. Thus, the order of the first-peak positions in the aqueous solution changed relative to that in vacuo. We ascribe this to the nature of the oxyluciferin anion being more hydrophobic in the keto form as compared with the enol and enolate isomers.

Reverse Stability of Oxyluciferin Isomers in Aqueous Solutions.

We investigated the stability of oxyluciferin anions (keto, enol, and enolate isomers) in aqueous solution at room temperature by performing a nanosecond time scale first-principles molecular dynamics simulation. In contrast to all previous quantum chemistry calculations, which suggested the keto-type to be the most stable, we show that the enol-type is slightly more stable than the keto-type, in agreement with some recent experimental studies. The simulation highlights the remarkable hydrophobicity of the keto-type by the cavity formed at the oxyluciferin-water interface as well as a reduction in hydrophobicity with the number of hydrating water molecules. It is therefore predicted that the isomeric form in a hydrated cluster is size-dependent.

First-Principles Investigation of Strong Excitonic Effects in Oxygen 1s X-ray Absorption Spectra.

We calculated the oxygen 1s X-ray absorption spectra (XAS) of acetone and acetic acid molecules in vacuum by utilizing the first-principles GW+Bethe-Salpeter method with an all-electron mixed basis. The calculated excitation energies show good agreement with the available experimental data without an artificial shift. The remaining error, which is less than 1% or 2-5 eV, is a significant improvement from those of time-dependent (TD) density functional methods (5% error or 27-29 eV for TD-LDA and 2.4-2.8% error or 13-15 eV for TD-B3LYP). Our method reproduces the first and second isolated peaks and broad peaks at higher photon energies, corresponding to Rydberg excitations. We observed a failure of the one-particle picture (or independent particle approximation) from our assignment of the five lowest exciton peaks and significant excitonic or state-hybridization effects inherent in the core electron excitations.

Vibronic Structures in Absorption and Fluorescence Spectra of Firefly Oxyluciferin in Aqueous Solutions.

To elucidate the factors determining the spectral shapes and widths of the absorption and fluorescence spectra for keto and enol oxyluciferin and their conjugate bases in aqueous solutions, the intensities of vibronic transitions between their ground and first electronic excited states were calculated for the first time via estimation of the vibrational Franck-Condon factors. The major normal modes, overtones and combination tones in absorption and fluorescence spectra are similar for all species. The theoretical full widths at half maximum of absorption spectra are 0.4-0.7 eV and those for the fluorescence spectra are 0.4-0.5 eV, except for phenolate-keto that exhibits exceptionally sharp peak widths due to the dominance of the 0-0' or 0'-0 band. These spectral shapes and widths explain many relevant features of the experimentally observed spectra.

Analysis of oxyluciferin photoluminescence pathways in aqueous solutions.

We evaluated the pK(a) values of oxyluciferin and its conjugate acids and bases theoretically with the help of experimental correction values, from which free energies for the first excited and the ground states of all the species were estimated. On the basis of these results, we calculated pH-dependent absorption spectra, where the relative absorption intensities of various species strongly depend on photoexcitation energy, and we further analyzed the photoluminescence pathways of oxyluciferin in aqueous solutions with various pH. In the case of 350 nm photoexcitation, in particular, experiments have shown that dominant emission color is green and it attenuates with pH decreasing, while blue (3 < pH < 8) and red (pH < 3) emissions appear. Our present results clarify the pathways of these photoluminescence depending on the pH values and thus should be useful in further analyses of photoluminescence pathways for other photoexcitation wavelength in comparison with experiments.

First-principles investigation on Rydberg and resonance excitations: A case study of the firefly luciferin anion.

The optical properties of an isolated firefly luciferin anion are investigated by using first-principles calculations, employing the many-body perturbation theory to take into account the excitonic effect. The calculated photoabsorption spectra are compared with the results obtained using the time-dependent density functional theory (TDDFT) employing the localized atomic orbital (AO) basis sets and a recent experiment in vacuum. The present method well reproduces the line shape at the photon energy corresponding to the Rydberg and resonance excitations but overestimates the peak positions by about 0.5 eV. However, the TDDFT-calculated positions of some peaks are closer to those of the experiment. We also investigate the basis set dependency in describing the free electron states above vacuum level and the excitons involving the transitions to the free electron states and conclude that AO-only basis sets are inaccurate for free electron states and the use of a plane wave basis set is required.

Analysis of photoexcitation energy dependence in the photoluminescence of firefly luciferin.

The whole pathways for photoluminescence, which include absorption, relaxation and emission, of firefly luciferin in aqueous solutions of different pH values with different photoexcitation energies were theoretically investigated by considering protonation/deprotonation. It is experimentally known that the color of fluorescence changes from green to red with a decrease in the photoexcitation energy. We confirmed with the theoretical analysis that the peak energy shift in the fluorescence spectra with varying photoenergies is due to a change in photoluminescence pathway. When the photoexcitation energy is decreased, the red emission from a monoanion form of firefly luciferin with carboxylate and phenolate groups and N-protonated thiazoline ring occurs irrespective of the pH values. However, because the species abundant in the solution and those excited by the photon depend on the solution pH, the pathway leading to the monoanion form changes with the solution pH.

Theoretical Study of Fluorescence Spectra Utilizing the pKa Values of Acids in Their Excited States.

Assignment of the fluorescence spectrum of firefly luciferin in aqueous solutions was achieved by utilizing not only emission energies but also theoretical absorption spectra and relative concentrations as estimated by pKa values. Calculated Gibbs free energies were utilized to estimate pKa values. These pKa values were then corrected by employing the experimental results. It was previously thought that the main peak near 550 nm observed in the experimental fluorescence spectra at all pH values corresponds to emission from the first excited state of the luciferin dianion [Ando et al. (2010) Jpn. J. Appl. Phys. 49, 117002-117008]. However, we found that the peak near 550 nm at low pH corresponds to emission from the first excited state of the phenolate monoanion of luciferin. Furthermore, we found that the causes of the red fluorescence at pH 1-2 are not only the emission from phenol monoanion but also the emission from the protonated species at nitrogen atom in the thiazoline ring of dianion.

Theoretical study of firefly luciferin pKa values--relative absorption intensity in aqueous solutions.

Ground-state vibrational analyses of firefly luciferin and its conjugate acids and bases are performed. The Gibbs free energies obtained from these analyses are used to estimate pKa values for phenolic hydroxy and carboxy groups and the N-H(+) bond in the N-protonated thiazoline or benzothiazole ring of firefly luciferin. The theoretical pKa values are corrected using the experimental values. The concentrations of these chemical species in solutions with different pH values are estimated from their corrected pKa values, and the pH dependence of their relative absorption intensities is elucidated. With the results obtained we assign the experimental spectra unequivocally. Especially, the small peak near 400 nm at pH 1-2 in experimental absorption spectra is clarified to be due to the excitation of carboxylate anion with N-protonated thiazoline ring of firefly luciferin. Our results show that the pKa values of chemical species, which are contained in the aqueous solutions, are effective to assign experimental absorption spectra.

Fast time-reversible algorithms for molecular dynamics of rigid-body systems.

In this paper, we present time-reversible simulation algorithms for rigid bodies in the quaternion representation. By advancing a time-reversible algorithm [Y. Kajima, M. Hiyama, S. Ogata, and T. Tamura, J. Phys. Soc. Jpn. 80, 114002 (2011)] that requires iterations in calculating the angular velocity at each time step, we propose two kinds of iteration-free fast time-reversible algorithms. They are easily implemented in codes. The codes are compared with that of existing algorithms through demonstrative simulation of a nanometer-sized water droplet to find their stability of the total energy and computation speeds.

Theoretical study of absorption and fluorescence spectra of firefly luciferin in aqueous solutions.

The absorption and fluorescence spectra of firefly luciferin, which is an analog of oxyluciferin, are investigated by performing the density functional theory (DFT) calculations, especially focusing on the experimentally unassigned peaks. Time-dependent DFT calculations are performed for the excited states of firefly luciferin and its conjugate acids and bases. We find that (1) the peaks in the experimental absorption spectra correspond to the excited states of not only (6'O(-), 4COO(-)) and (6'OH, 4COO(-)), but also (6'OH, 4COOH) and (6'OH, 3H(+), 4COOH); (2) the peaks in the experimental fluorescence spectra correspond to the excited states of not only (6'O(-), 4COO(-)), but also (6'OH, 4COO(-)), (6'O(-), 4COOH), (6'OH, 4COOH) and (6'OH, 3H(+), 4COOH); (3) the unassigned peak near 400 nm in the experimental absorption spectra at pH 1 is assigned to the absorption from the equilibrium ground state to the first excited state of (6'OH, 3H(+), 4COOH); and (4) the unassigned peak at 610 nm in the experimental fluorescence spectra corresponds to the transition from the equilibrium first excited state to the ground state of (6'OH, 4COO(-)).

Theoretical study of electron transfer in Rhodobacter sphaeroides reaction center.

We investigate the substitution effects on electron transfer in Rhodobacter (Rb.) sphaeroides reaction center using ab initio calculations. The overlap of molecular orbitals in the X-ray structure of 1PCR of the protein data bank using Gaussian09 can qualitatively explain the tendency of the experimental transition time. The charge effects of proteins on electron transfer in Rb. sphaeroides reaction center are also investigated, by employing a simple point charge approximation for proteins. We have found that the primary effect for the route A orientation is the effect of long side chains. For the route A orientation on the electron transfer, the influence of the charges of proteins operates through the long side chains indirectly as well as directly work to increase the value of overlap integrals.