PubMed · 15628515
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Tokio Yamaguchi, Akiko Sugimoto. 2004. [Biliverdin].. https://pubmed.ncbi.nlm.nih.gov/15628515/
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Conversion of iron(II) verdoheme to iron biliverdin in the presence of OH(-) was investigated using B3LYP method. Both 3-21G and 6-31G* basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Calculation at 6-31G* level was found necessary for a correct spin state estimation of the iron complexes. Two possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In one path the iron was six-coordinate while in the other it was considered to be five-coordinate. In the six-coordinated pathway, the ground state of bis imidazole iron verdoheme is singlet while that for open chain iron biliverdin it is triplet state with 4.86 kcal/mol more stable than the singlet state. The potential energy surface suggests that a spin inversion take place during the course of reaction after TS. The ring opening process in the six-coordinated pathway is in overall -2.26 kcal/mol exothermic with a kinetic barrier of 9.76 kcal/mol. In the five-coordinated pathway the reactant and product are in the ground triplet state. In this path, hydroxyl ion attacks the iron center to produce a complex, which is only 1.59 kcal/mol more stable than when OH(-) directly attacks the macrocycle. The activation barrier for the conversion of iron hydroxy species to the iron biliverdin complex by a rebound mechanism is estimated to be 32.68 kcal/mol. Large barrier for rebound mechanism, small barrier of 4.18 kcal/mol for ring opening process of the hydroxylated macrocycle, and relatively same stabilities for complexes resulted by the attack of nucleophile to the iron and macrocycle indicate that five-coordinated pathway with direct attack of nucleophile to the 5-oxo position of macrocycle might be the path for the conversion of verdoheme to biliverdin.
We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn --> C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn --> C15-E,syn (photochemical), C15-E,syn --> C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.
This is a first density functional theory survey of transition-metal biliverdines (Blv), where we have chosen to focus on key Mn, Fe, Co, and Cu complexes. According to the calculations, the complexes are invariably noninnocent, featuring Blv*2- ligand radicals. In this, biliverdine complexes resemble metallocorroles, but the parallels are only approximate. Briefly, metallobiliverdines exhibit a much greater tendency to adopt noninnocent electronic structures than analogous metallocorroles. The O...O nonbonded contacts in biliverdines apparently preclude the formation of short metal-N bonds that, in turn, could stabilize high-valent metal ions. Thus, while most copper corroles (Cor) exhibit diamagnetic CuIII ground states, copper biliverdines are clearly Cu(II)Blv*2- species. In the same spirit, while chloroiron corroles are best described as FeIII(S = 3/2)Cor*2-,the analogous biliverdine derivative seems best described as Fe(III)(S = 5/2)Blv*2-, i.e., featuring a high-spin FeIII center with long (>2.0 A) Fe-N bond distances. Overall, the results highlight the important role that steric effects may play in modulating the electronic structures and the potentially noninnocent nature of transition-metal complexes.