---
_id: '17077'
abstract:
- lang: eng
  text: <jats:p>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.</jats:p>
article_number: '1720'
author:
- first_name: Christian
  full_name: Wiebeler, Christian
  last_name: Wiebeler
- first_name: Igor
  full_name: Schapiro, Igor
  last_name: Schapiro
citation:
  ama: Wiebeler C, Schapiro I. QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3
    Absorption Spectra. <i>Molecules</i>. 2019. doi:<a href="https://doi.org/10.3390/molecules24091720">10.3390/molecules24091720</a>
  apa: Wiebeler, C., &#38; Schapiro, I. (2019). QM/MM Benchmarking of Cyanobacteriochrome
    Slr1393g3 Absorption Spectra. <i>Molecules</i>. <a href="https://doi.org/10.3390/molecules24091720">https://doi.org/10.3390/molecules24091720</a>
  bibtex: '@article{Wiebeler_Schapiro_2019, title={QM/MM Benchmarking of Cyanobacteriochrome
    Slr1393g3 Absorption Spectra}, DOI={<a href="https://doi.org/10.3390/molecules24091720">10.3390/molecules24091720</a>},
    number={1720}, journal={Molecules}, author={Wiebeler, Christian and Schapiro,
    Igor}, year={2019} }'
  chicago: Wiebeler, Christian, and Igor Schapiro. “QM/MM Benchmarking of Cyanobacteriochrome
    Slr1393g3 Absorption Spectra.” <i>Molecules</i>, 2019. <a href="https://doi.org/10.3390/molecules24091720">https://doi.org/10.3390/molecules24091720</a>.
  ieee: C. Wiebeler and I. Schapiro, “QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3
    Absorption Spectra,” <i>Molecules</i>, 2019.
  mla: Wiebeler, Christian, and Igor Schapiro. “QM/MM Benchmarking of Cyanobacteriochrome
    Slr1393g3 Absorption Spectra.” <i>Molecules</i>, 1720, 2019, doi:<a href="https://doi.org/10.3390/molecules24091720">10.3390/molecules24091720</a>.
  short: C. Wiebeler, I. Schapiro, Molecules (2019).
date_created: 2020-06-04T07:27:03Z
date_updated: 2022-01-06T06:53:04Z
doi: 10.3390/molecules24091720
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
  name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Molecules
publication_identifier:
  issn:
  - 1420-3049
publication_status: published
status: public
title: QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra
type: journal_article
user_id: '61189'
year: '2019'
...