Beatrix M.
Bold
a,
Monja
Sokolov
a,
Sayan
Maity
b,
Marius
Wanko
c,
Philipp M.
Dohmen
a,
Julian J.
Kranz
ad,
Ulrich
Kleinekathöfer
b,
Sebastian
Höfener
a and
Marcus
Elstner
*ad
aInstitute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany. E-mail: marcus.elstner@kit.edu
bDepartment of Physics and Earth Science, Jacobs University Bremen, 28759 Bremen, Germany
cNano-Bio Spectroscopy Group and ETSF, Dpto. Material Physics, Universidad del País Vasco, 20018 San Sebastiàn, Spain
dInstitute of Biological Interfaces (IBG2), Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany
First published on 6th June 2023
Correction for ‘Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes’ by Beatrix M. Bold et al., Phys. Chem. Chem. Phys., 2020, 22, 10500–10518, https://doi.org/10.1039/C9CP05753F.
In brief, the most important changes are: (i) the ZINDO site energies for the individual pigments are closer to each other and the ZINDO site energy fluctuations are smaller; (ii) the couplings are smaller and now in better agreement with reference data; and (iii) as a consequence, the exciton splitting is decreased. These errors do not change the conclusions of the study but only lead to small corrections of the reported results, as detailed below.
Prior to the calculations of site energies and couplings along the trajectory, the coordinates of the system were processed as follows: the protein complex was centered in the simulation box with Gromacs tools in two steps. First, the protein and the chromophores were clustered using the pbc cluster option of trjconv; second, they were centered in the box using the pbc mol option of trjconv. However, it was not recognized that some counterions were placed outside the simulation box erroneously. Consequently, the MM point charges corresponding to these counterions had wrong coordinates in the QM/MM calculations of the site energies and couplings, leading to an incorrect description of the QM–MM electrostatics.
These calculations of site energies and couplings were repeated using a corrected procedure for the processing of the MM point charges. Specifically, the trajectory was centered using the Gromacs tools in a more appropriate way: in the first step, any appearing error due to the periodic boundary conditions were corrected, and the protein was centered in the box using the pbc atom option of trjconv in the second step.
Additionally, the authors have recognized an error in a script that was used to compute the Coulomb couplings. The coordinates were not converted to atomic units as needed, which resulted in a significant overestimation of the coupling values reported in the original publication. The corrected couplings are now in much better agreement with the reference data.
The authors recalculated only a selection and comment on the expected changes for the other figures and tables. In the following, they start with the benchmark of the couplings on the BChl a dimer models, followed by exemplary couplings in the LH2 complex. Thereafter, they continue with the new site energies, couplings and the resulting exciton energies of the FMO complex. Previous results are shown in parentheses, while the new results are shown in bold. The figures and tables carry the same numbers as in the published version of the article. The corrections to the ESI have been discussed here. Please refer to revised version of the ESI (https://www.rsc.org/suppdata/c9/cp/c9cp05753f/c9cp05753f1.pdf) for the corrected tables and figures.
Distance [Å] | 7 | 8 | 9 | 10 | |
---|---|---|---|---|---|
TrESP | B3LYP | 0.050 | 0.038 | 0.029 | 0.023 |
CAM-B3LYP | 0.056 | 0.043 | 0.033 | 0.026 | |
Tr-Mulliken | B3LYP | 0.047 | 0.036 | 0.028 | 0.022 |
CAM-B3LYP | 0.054 | 0.041 | 0.032 | 0.025 | |
— | LC-DFTB | 0.041 | 0.031 | 0.024 | 0.019 |
(0.082) | (0.063) | (0.049) | (0.039) |
Fig. 12 depicts a slightly different trend for the corrected TD-LC-DFTB site energies compared to the ones shown in the original publication, while the range between the lowest and largest values remains basically the same (Table 9). The results in Fig. 12b were computed with the same parameter set as in the original publication and reveal the changes due to the corrected electrostatics. Fig. 12c shows the almost constant shift to lower excitation energies when the new parameter set is applied for the computations with a correct representation of the electrostatics.
Max | Min | Shift | |
---|---|---|---|
Vacuum | 1.738 (1.865) | 1.716 (1.841) | −0.022 (−0.024) |
Protein | 1.754 (1.882) | 1.698 (1.827) | −0.056 (−0.055) |
Coupled chromophores | |||
LC-DFTB | 1.811 (1.979) | 1.659 (1.775) | −0.152 (−0.204) |
TrESP | 1.876 | 1.777 | −0.099 |
Experimental | 1.563 | 1.503 | −0.060 |
The ZINDO/S approach now predicts a smaller range of the excitation energies along the MD trajectory (Fig. S7 and Table S20). It is remarkable that the excitation energy of BChl 5 is no longer overestimated as previously reported. Nonetheless, the large excitation energy of BChl 3 in the QM/MM optimized structure as well as the large energetic change in BChl 5 indicate a strong sensitivity to the electrostatics.
The corrected couplings of the BChl a pairs in the FMO complex are presented in Table S19. Their values are roughly half of those previously presented in the published version of the article.
Finally, the excitonic energies were recalculated using the corrected excitation energy and coupling values (Table S21). The range of the excitonic energies is smaller due to the smaller couplings.
The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.
Footnote |
† Corrections have also been made to the ESI, which can be reached using the following link, https://www.rsc.org/suppdata/c9/cp/c9cp05753f/c9cp05753f1.pdf |
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