Spectroscopical UV–Vis implications of an intramolecular η²–Mg coordination in bacteriochlorophyll–a from the Fenna–Matthews–Olson complex

Abstract

Chlorophylls and their related compounds prominently feature a Mg2+ ion in the center of a porphyrine, with an intermolecular fifth coordination usually observed to place the ion out of the macrocyclic plane. Herein, we assess the role of a potential intramolecular η2–(C = C)Mg interaction and compare it to the intermolecular coordination from the Hystidine groupt to Mg2+ for Bacterichlorophyll–a (Bchl–a), the main photosynthetic pigment in the Fenna–Matthews–Olson complex present in green and purple bacteria. The influence of this fifth coordination on the UV‐Vis spectroscopy (CAM‐B3LYP/cc‐pVDZ), and the concomitant change in geometry around Mg in Bchl–a from planar to pyramidal is assessed by the quantum theory of atoms in molecules based non–covalent interactions scheme and through energetic analysis via natural bond orbital population methods at the M06‐2X/cc‐pVDZ and compared to the reference multi–hapto compound, magnesocene, Cp2Mg.

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations

“…S1 † ). While there are studies that point to the role of the phytyl chain in coordinating 91 or preventing coordination 92 to the central Mg 2+ ion, we argue that these structural effects are contained in the MD simulations. All crystal water was retained and hydrogens were added with pdb2gmx included in Gromacs 2020.1 93 or, for newly parametrized molecules, with reduce , 94 distributed with AmberTools 20 .…”

“…A list of the chlorophyll residue IDs with the standard naming convention 7,41 is available in ESI Table S5. † site energies, 91,140,141 in a temporal picture. In our model, 28 chlorophylls are coordinated axially by HIS d residues which are protonated on the d position, 14 by HIS 3 residues protonated on the 3 position and 39 by crystal water.…”

Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of Blastochloris viridis’ Light Harvesting 1-Reaction Center Complex

“…The pigment− protein interactions, such as H-bonds between pigments and their embedding surroundings, have been previously shown to be important for correctly describing the electronic spectra of photosynthetic systems, but specifically, the fifth coordination of Mg 2+ ions by a histidine residue has an important impact in the correct calculation of their UV−vis spectra, and thus those specific residues were kept to maintain the correct geometry of Mg 2+ ions. 19,27,28 To reproduce the near-IR absorption, the previous arrangement shown in Figure 1 was dissected into various pigment systems of increasing complexity. In total, seven systems were built and divided into three kinds: (A) single BChl-b pigment systems; (B) two pigments (BChl-b−DHN) systems; (C) and three pigments systems comprised of two neighboring BChl-b and the surrounding DHN molecules.…”

“…These residues were selected first by invoking a distance criterion. The pigment–protein interactions, such as H-bonds between pigments and their embedding surroundings, have been previously shown to be important for correctly describing the electronic spectra of photosynthetic systems, but specifically, the fifth coordination of Mg 2+ ions by a histidine residue has an important impact in the correct calculation of their UV–vis spectra, and thus those specific residues were kept to maintain the correct geometry of Mg 2+ ions. ,, …”

“…On these seven systems, a partial geometry optimization of hydrogen atoms and sidechain amino acids (i.e., excluding those atoms from the peptidic chain) at the PM6 semiempirical level of theory was carried out and later refined by means of a second optimization with density functional theory (DFT) calculations at the PBE0/6-31G­(d) level of theory. Electronic transitions and absorption spectra were calculated with TD-DFT at the CAM-B3LYP/cc-pVDZ level of theory, which allows a good description of the electron transitions and photophysical behavior of photosynthetic pigments. ,, Fifteen singlet excited states were requested for the B1 to B4 systems (one and two pigments systems) and 50 singlet excited states for the B5 to B7 three-pigments systems, using in all cases the SMD implicit continuum dielectric model with methanol as a solvent. A control calculation was constructed from the BChl- b pigment in the B1 model with an explicit methanol molecule coordinated to the Mg 2+ central ion fully optimized as a reference for comparing its behavior in solution with the same implicit continuum solvation model, SMD.…”