Miyabi Hiyama

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.

Theoretical assignment of the vibronic bands in the photoelectron spectra of N2 below 30 eV

Abstract The high-resolution photoelectron spectra of N 2 up to 30 eV are analyzed with ab initio MO CI calculations. The potential energy curves of the highly excited states of the molecular nitrogen N + 2 , are drawn to near the dissociation limit, and then the Franck—Condon factors (FCF) for the neutral ground state are evaluated. By comparing the vibrational progression and band shapes of the experimental photoelectron spectra with the theoretical FCF distribution, the observed bands between 23 and 30 eV are assigned, and the vibrational quantum numbers of the spectra are identified.

Ab initio R-matrix/multichannel quantum defect theory study of nitric oxide

Ab initio R-matrix techniques are combined with multi-channel quantum defect theory to determine the properties of arbitrarily highly excited electronic states of nitric oxide. Results are obtained for l = 0-4 channels associated with the four lowest NO+ target channels, namely 1Σ+, 3Σ+, 3Π and 3Δ. Energy and bond length variations of the quantum defect functions for all target states are reported. Certain small surface amplitude R-matrix poles also serve to determine the energies of valence states. Diabatic potential curves for Rydberg states converging to the 1Σ+ and 3Σ+ target states and for the valence states are presented. Systematic jumps in the pσ quantum defects for all target states as the bond length increases beyond R = 2.5 au are attributed to Rydbergization of the antibonding 2pσ* molecular orbital.

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.

Angular Momentum Form of Verlet Algorithm for Rigid Molecules

A new simple algorithm is presented for solving the equations of motion for rigid molecules. These equations are integrated using a Verlet framework in the angular momentum form. This simple algorithm is named “the angular momentum Verlet algorithm”. For obtaining a high accuracy in molecular dynamics (MD) simulations, we introduce the scaling method with the constraint by Lagranges method of undetermined multipliers. The results of MD simulations for carbon tetrachloride using the angular momentum Verlet algorithm are reported. The relative total energy fluctuations for carbon tetrachloride using the angular momentum Verlet algorithm are compared with those using the standard leap-frog and Gear predictor–corrector algorithms. The energy drift using the angular momentum Verlet algorithm is smaller than that using the leap-frog or Gear predictor–corrector algorithm, particularly for large time intervals. The MD simulations for A X n Y 4- n -type models having different moments of inertia are also carried ...

Superexcited states of CO near the first ionization threshold

Abstract Characteristics of the superexcited states of CO which dominate the various dynamic processes near the first ionization potential are determined by using quantum chemical calculations and multi-channel quantum defect theoretical analyses. Quantum defects are obtained as functions of the internuclear distance for the sσ, pσ, pπ, dσ, dπ and dδ symmetries. Two dissociative states ( 1 Σ + and 1 Π ) which cross the ionic potential curve near the equilibrium internuclear distance of CO+ are also determined.

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 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.

Assignment of the photoelectron spectrum of HCl above 20 eV

Abstract The photoelectron spectrum of HCl up to 32 eV is analyzed with ab initio MO Cl calculations. The potential energy curves of most of the highly excited states of the ion HCl+ are correctly drawn to near the dissociation limit, and the Franck-Condon factors (FCF) from the neutral ground state are evaluated. By comparing the experimental spectrum with the theoretical FCF distribution, six observed bands between 20 and 32 eV are assigned. One of them turns out to be a Rydberg state converged to the ground state of HCl2+.

Analysis of Oxyluciferin Photoluminescence Pathways in Aqueous Solutions

We evaluated the pKa 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.