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Article

QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra

Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
*
Author to whom correspondence should be addressed.
Current address: Physics Department, Universität Paderborn, 33098 Paderborn, Germany.
Academic Editors: Antonio Monari, Elise Dumont and Marco Marazzi
Molecules 2019, 24(9), 1720; https://doi.org/10.3390/molecules24091720
Received: 4 April 2019 / Revised: 28 April 2019 / Accepted: 30 April 2019 / Published: 3 May 2019
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes. View Full-Text
Keywords: phytochrome; cyanobacteriochrome; Slr1393g3; spectral tuning; QM/MM; molecular dynamics; photochemistry; excited states phytochrome; cyanobacteriochrome; Slr1393g3; spectral tuning; QM/MM; molecular dynamics; photochemistry; excited states
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MDPI and ACS Style

Wiebeler, C.; Schapiro, I. QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra. Molecules 2019, 24, 1720. https://doi.org/10.3390/molecules24091720

AMA Style

Wiebeler C, Schapiro I. QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra. Molecules. 2019; 24(9):1720. https://doi.org/10.3390/molecules24091720

Chicago/Turabian Style

Wiebeler, Christian, and Igor Schapiro. 2019. "QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra" Molecules 24, no. 9: 1720. https://doi.org/10.3390/molecules24091720

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