Structure and conformation of photosynthetic pigments and related compounds. Conformation analysis of chlorophyll derivatives

Abstract

The computational program, Normal-Coordinate Structural Decomposition (NSD), provides meaningful information that allows a comparative analysis about the conformation of tetrapyrroles. Their conformation has an intrinsic effect on their physiochemical properties and the NSD program uses known crystal structures to display the tetrapyrroles deviation from the mean D4h plane. This deviation describes the molecules 3D structure in terms of their out-of-plane and in-plane deviations from the 24-atom macrocyclic mean plane. There is no known crystal structure of chlorophyll a (Chl a) at an atomic, high resolution level. Therefore, a conformational analysis of crystal structures of Chl a-related structures is conducted using the NSD program to understand how this compounds conformation influences its role in nature. The NSD program is first validated by conducting a conformational analysis on well-studied porphyrins and chlorins, followed by the conformational analysis of the Chl a-related structures. In terms of the 3D structure, it was found that the non-planarity and the macrocyclic in-plane distortion of these structures depends on the presence of a metal in the core of the macrocycle, different metals give different conformations, axial ligands, solvent, and peripheral substituents, which is representative of the protein?s environment in nature.