Computational Modeling of Exciton-bath Hamiltonians for LH2 and LH3 Complexes of Purple Photosynthetic Bacteria at Room Temperature

Light harvesting 2 (LH2) complex is a primary component of the photosynthetic unit of purple bacteria that is responsible for harvesting and relaying excitons. The electronic absorption line shape of LH2 contains two major bands at 800 nm and 850 nm wavelength regions. Under low light condition, some species of purple bacteria replace LH2 with LH3, a variant form with almost the same structure as the former but with distinctively different spectral features. The major difference between the absorption line shapes of LH2 and LH3 is the shift of the 850 nm band of the former to a new 820 nm region. The microscopic origin of this difference has been subject to some theoretical/computational investigations. However, the genuine molecular level source of such difference is not clearly understood yet. This work reports a comprehensive computational study of LH2 and LH3 complexes so as to clarify different molecular level features of LH2 and LH3 complexes and to construct simple exciton-bath models with a common form. All-atomistic molecular dynamics (MD) simulations of both LH2 and LH3 complexes provide detailed molecular level structural differences of BChls in the two complexes, in particular, in their patterns of hydrogen bonding (HB) and torsional angles of the acetyl group. Time-dependent density functional theory calculation of the excitation energies of BChls for structures sampled from the MD simulations, suggests that the observed differences in HB and torsional angles cannot fully account for the experimentally observed spectral shift of LH3. Potential sources that can explain the actual spectral shift of LH3 are discussed, and their magnitudes are assessed through fitting of experimental line shapes.