Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.
PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States.
J Phys Chem B. 2018 Apr 12;122(14):3815-3825. doi: 10.1021/acs.jpcb.8b00358. Epub 2018 Mar 30.
Light harvesting 2 (LH2) complex is the 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 and 850 nm wavelength regions. Under low light conditions, some species of purple bacteria replace LH2 with light harvesting 3 (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 the subject of some theoretical/computational investigations. However, the genuine molecular level source of such a 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 simulations of both LH2 and LH3 complexes provide detailed molecular level structural differences of bacteriochlorophylls (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 the 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. These results demonstrate the feasibility of developing simple exciton-bath models for both LH2 and LH3, which can be employed for large-scale exciton quantum dynamics in their aggregates.
光捕获 2（LH2）复合物是负责收集和传递激子的紫色细菌光合单位的主要成分。LH2 的电子吸收谱线形状包含两个主要带，分别在 800nm 和 850nm 波长区域。在低光照条件下，一些紫色细菌用光捕获 3（LH3）代替 LH2，后者是一种结构几乎与前者相同但光谱特征明显不同的变体。LH2 和 LH3 的吸收谱线形状的主要区别在于前者的 850nm 带移至新的 820nm 区域。这种差异的微观起源一直是一些理论/计算研究的主题。然而，这种差异的真正分子水平来源尚不清楚。这项工作报告了对 LH2 和 LH3 复合物的全面计算研究，以澄清 LH2 和 LH3 复合物的不同分子水平特征，并构建具有共同形式的简单激子-浴模型。LH2 和 LH3 复合物的全原子分子动力学模拟提供了这两个复合物中细菌叶绿素（BChls）的详细分子水平结构差异，特别是在它们的氢键（HB）模式和乙酰基的扭转角度方面。从 MD 模拟中采样的结构的 BChls 激发能的含时密度泛函理论计算表明，观察到的 HB 和扭转角度的差异不能完全解释 LH3 实验观察到的光谱位移。讨论了可以解释 LH3 实际光谱位移的潜在来源，并通过拟合实验谱线评估了它们的大小。这些结果表明，对于 LH2 和 LH3 都可以开发简单的激子-浴模型，这可以用于它们聚集体中的大规模激子量子动力学。
