ArticleThe journal of physical chemistry. B2021
Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- Multiscale Machine Learning Prediction of Infrared Spectra of Solvated Molecules.Journal of chemical theory and computation · 2026Article
- Article
- Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2023Article
- Recent progress in atomistic modeling of light-harvesting complexes: a mini review.Photosynthesis research · 2023Review
- Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor.The journal of physical chemistry letters · 2023Article
- Time-resolved infrared absorption spectroscopy applied to photoinduced reactions: how and why.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2022Review
- Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics.The journal of physical chemistry. B · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.