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The Q y and B x excitation energy transfer (EET) in the minor light-harvesting complex CP29 (LHCII B4.1) antenna complex of Pisum sativum was characterized using a computational approach. We applied Forster resonance energy transfer (FRET) and the transition density cube (TDC) method to estimate the Coulombic coupling, based on a combination of classical molecular dynamics and quantum mechanics/molecular mechanics calculations. Employing TDC instead of FRET mostly affects the EET between chlorophylls (Chls) and carotenoids (Crts), as expected due to the Crts being spatially more challenging for FRET. Only between Chls, effects are found to be small (about only 0.1 EET efficiency change when introducing TDC instead of FRET). Effects of structural sampling were found to be small, illustrated by a small average standard deviation for the Q y state coupling elements (FRET/TDC: 0.97/0.94 cm −1 ). Due to the higher flexibility of the B x state, the corresponding deviations are larger (FRET/TDC between Chl−Chl pairs: 17.58/22.67 cm −1 , between Crt−Chl pairs: 62.58/31.63 cm −1 ). In summary, it was found for the Q band that the coupling between Chls varies only slightly depending on FRET or TDC, resulting in a minute effect on EET acceptor preference. In contrast, the coupling in the B band spectral region is found to be more affected. Here, the S 2 (1B u ) states of the spatially challenging Crts may act as acceptors in addition to the B states of the Chls. Depending on FRET or TDC, several Chls show different Chl-to-Crt couplings. Interestingly, the EET between Chls or Crts in the B band is found to often outcompete the corresponding decay processes. The individual efficiencies for B band EET to Crts vary however strongly with the chosen coupling scheme (e.g., up to 0.29/0.99 FRET/TDC efficiency for the Chl a604/ neoxanthin pair). Thus, the choice of the coupling scheme must involve a consideration of the state of interest.

The Qy and Bx excitation energy transfer (EET) in the minor light harvesting complex CP29 (LHCII B4.1) antenna complex of Pisum sativum was characterized using a computational approach. We applied Förster theory (FRET) and the transition density cube (TDC) method estimating the Coulombic coupling, based on a combination of classical molecular dynamics and QM/MM calculations. Employing TDC instead of FRET mostly affects the EET between chlorophylls (Chls) and carotenoids (Crts), as expected due to the Crts being spatially more challenging for FRET. Only between Chls, effects are found to be small (about only 0.1 EET efficiency change when introducing TDC instead of FRET). Effects of structural sampling were found to be small, illustrated by a small average standard deviation for the Qy state coupling elements (FRET/TDC: 0.97/0.94 cm-1). Due to the higher flexibility of the Bx state, the corresponding deviations are larger (FRET/TDC between Chl-Chl pairs: 17.58/22.67 cm-1, between Crt-Chl pairs: 62.58/31.63 cm-1). In summary, it was found for the Q band that the coupling between Chls varies only slightly depending on FRET or TDC, resulting in a minute effect on EET acceptor preference. In contrast, the coupling in the B band spectral region is found to be more affected. Here, the S2 (1Bu) states of the spatially challenging Crts may act as acceptors in addition to the Chl B states. Depending on FRET or TDC, several Chls show different Chl-to-Crt couplings. Interestingly, the EET between Chls or Crts in the B band is found to often outcompete the corresponding decay processes. The individual efficiencies for B band EET to Crts vary however strongly with the chosen coupling scheme (e.g., up to 0.29/0.99 FRET/TDC efficiency for the Chl a604/neoxanthin pair). Thus, the choice of coupling scheme must involve a consideration of the state of interest.

We introduce a Python 2.7 software called gmx2qmmm, which provides an interface between the Gaussian and Gromacs software packages in an additive quantum mechanics/molecular mechanics (QM/MM) scheme. Other QM packages will be added in future releases. The main advantage of gmx2qmmm is its simplicity in terms of input setup and configuration as it maintains the Gromacs file formats, as well as input conventions. It is also designed such that users do not need to reconfigure or recompile any of the interfaced programs. While our main goal was to provide a simplified transition from Gromacs to QM/MM using Gromacs directly as the basis for the MM part, we considered alternative ways to treat the QM/MM boundary. Our software was also developed to test a previously considered way to account for the presence of link atoms, which we term here link atom correction functions (LCFs). We show that LCFs can be good candidates to improve the forces at the QM/MM junction; however, from our data, it is also apparent that LCFs will not necessarily improve energy barriers, likely due to them being tailored to improve the situation close to potential minima. LCFs are, however, trivial to set up and can be used in the future to support the accuracy of QM/MM optimizations and dynamics. We present data on how our interface compares to a full QM description of small polypeptides; furthermore, we investigate the UV/vis spectroscopy of chlorophyll-containing proteins depending on the employed potentials and geometries.