Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?

Kjellgren, Erik; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

doi:10.1021/acs.jctc.8b00202

Cited by 27 publications

(28 citation statements)

References 73 publications

(94 reference statements)

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“…This improves the agreement with experiments, where the second absorption band of both forms also appears broad without much fine structure [13,14]. Overall, the photoproduct tuning might be already described with one or few selected structures, whereas sampling is necessary to describe the shape of the absorption bands and their broadening due to temperature effects, which was also stated in a recent study investigating chromophores in solution with QM/MM [89]. We note that with the approaches employed by us, it is not possible to describe vibronic effects as reviewed recently [90,91].…”

Section: Resultssupporting

confidence: 68%

QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra

Wiebeler

Schapiro

2019

Molecules

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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.

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Section: Resultssupporting

confidence: 68%

QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra

Wiebeler

Schapiro

2019

Molecules

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“…The large discrepancy between the experimental and the theoretical absorption spectra obtained with classical MD followed by QM/MM excited-state calculations ( Figure 1 ) could be attributed to a failure of the force field that describes the vibrational motion of the chromophore during the classical sampling [ 46 ]. To investigate whether this is the case, the classical MD sampling is refined with subsequent QM/MM-MD simulations, where mTHPC is treated at QM level with the B3LYP functional.…”

Section: Resultsmentioning

confidence: 99%

Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States

et al. 2018

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The absorption properties of Temoporfin, a second-generation photosensitizer employed in photodynamic therapy, are calculated with an electrostatic-embedding quantum mechanics/molecular mechanics (QM/MM) scheme in methanol. The suitability of several ensembles of geometries generated by different sampling techniques, namely classical-molecular-dynamics (MD) and QM/MM-MD thermal sampling, Wigner quantum sampling and a hybrid protocol, which combines the thermal and quantum approaches, is assessed. It is found that a QM description of the chromophore during the sampling is needed in order to achieve a good agreement with respect to the experimental spectrum. Such a good agreement is obtained with both QM/MM-MD and Wigner samplings, demonstrating that a proper description of the anharmonic motions of the chromophore is not relevant in the computation of the absorption properties. In addition, it is also found that solvent organization is a rather fast process and a long sampling is not required. Finally, it is also demonstrated that the same exchange-correlation functional should be employed in the sampling and in the computation of the excited states properties to avoid unphysical triplet states with relative energies close or below 0 eV.

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“…Indeed, an accurate modelisation of the optical properties in principle requires taking into account the different molecular states, their possible conformations, thermal fluctuations, and the effects of the solvent. Previous works have gone as far as taking into account thermal fluctuations in the minimum energy conformer, 9,10,20,21 however realistically many conformers will coexist in solution, and each of their contributions to the final color should be taken into account. Such a systematic study is lacking, and the present work intends to be a first step in this direction by applying a multi-scale simulation protocol to the simulation of anthocyanins.…”

Section: Introductionmentioning

confidence: 99%