Related Experiment Video
Updated: Jan 19, 2026

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins
Published on: June 4, 2021
Photoabsorption Spectra of Aqueous Oxyluciferin Anions Elucidated by Explicit Quantum Solvent
Yoshifumi Noguchi1, Miyabi Hiyama2, Motoyuki Shiga3
1Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering , Shizuoka University , Johoku 3-5-1 , Hamamatsu, Shizuoka 432-8561 , Japan.
Abstract:
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.
More Related Videos
Related Concept Videos
UV–Vis Spectrum
The UV–Vis spectrum of a molecule is the plot of its absorbance versus wavelength. The plot is drawn by taking molar...
UV–Vis Spectrometers
UV–Vis Spectroscopy of Conjugated Systems
One of the factors influencing λmax is the extent of conjugation in...
IR and UV–Vis Spectroscopy of Carboxylic Acids
However, the stretching absorptions for the C=O bond vary depending on the structure of carboxylic acids. The C=O bond of the free carboxylic acids shows a higher stretching frequency, 1760 cm−1, while H-bonded carboxylic acids (dimers) exhibit stretching absorptions at a lower frequency,...
UV–Vis Spectroscopy: Beer–Lambert Law
Ultraviolet and Visible (UV–Vis) Spectroscopy: Overview

