Effect of the axial ligands on the structure and reactivity of tin verdoheme in the ring opening process

Investigation of different substitutions, structure, charge and multiplicity spin of the iron verdoheme-rat heme oxygenase complex: a DFT study

Heme oxygenase-1 (HO-1) is an inducible stress protein that degrades heme to carbon monoxide, iron and biliverdin, which subsequently reduces to bilirubin. Many parameters of verdoheme–rat heme oxygenase complex structure and their role and function on heme degradation were unknown. In this work the structure of iron verdoheme in complex with rat heme oxygenase was studied by density functional theory based B3LYP method and 6-31G basis set. The main goal is to obtain structural and energetic information for various transition states and intermediates on reaction pathways. The charge of verdoheme and iron as the central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effect on the verdoheme ring stabilization and their arrangement are discussed. Gas phase computation has shown that the central metal of the five coordinated rat-verdohemeas ferrous (Fe[Formula: see text] (from 1a-1i) and ferric (Fe[Formula: see text] (from 1j–1q). The Mulliken and NBO charge and spin calculation show that iron is considered as ferrous in all of the optimized structures. Assessment results can gain valuable chemical insight into the electronic reorganization during the reactions.

Theoretical study of OH− nucleophilic attack on cobalt(II)-verdoheme complex

OH[Formula: see text] attack on a four, five and six-coordinated cobalt(II)-verdoheme-coordinated with imidazole (1 M) while the axial ligand was studied using B3LYP method. Different spin multiplicities were considered, namely doublet, quartet, and sextet. Results show the most positive charge to be concentrated at the cobalt and carbon atoms adjacent to the oxygen in the cobalt(II)-verdoheme complex. Data obtained show that a stable intermediate was formed by a nucleophilic attack on one of the latter carbon atoms. The intermediate is initially formed by a nucleophilic attack on one of the aforementioned carbon atoms. This intermediate is then directly converted to a helical open-ring complex by passing it through a transition state. It is specified that if every nucleophilic attack is considered separately, then the OH[Formula: see text] attack on cobalt(II)-verdoheme occurred at all spin multiplicity and coordination states, from a thermodynamics and kinetics point of view, all except an OH[Formula: see text] attack on five-coordinated cobalt(II)-verdoheme at quartet state. However, comparison of reaction paths with different spin in the same coordination show that such a nucleophilic attack is not proceeded, while the reactant is a four and six-coordinated cobalt(II)-verdoheme because the latter reaction spin state is not conserved. It is clear that OH[Formula: see text] attack on five-inatedcoordinated Co(II)-verdoheme at doublet spin multiplicity is the most stable reaction path. Moreover, these findings were confirmed by NBO analysis and molecular orbital calculations.

Theoretical kinetics and thermodynamics study: Peripheral substituent effects on the hydrolysis of verdoheme

The heme oxygenase (HO) enzyme is a free heme protein that binds to heme in the body. Heme acts as both a cofactor and a substrate in this enzyme. The catabolism of heme into biliverdin, monoxide carbon, and free-iron, catalyzed by heme oxygenase via three consecutive oxygenation steps, in which the heme group functions as the prosthetic group as well as the substrate. Investigations of the reactions of the peripheral substituent on the heme ring with 5-oxaporphyrin iron complexes (verdohemes) have been assumed to provide models and largely unknown for the primary step in the hydrolysis of verdohemes. In this work, a theoretical kinetics and thermodynamics study of the degradation reactions of verdohemes was performed, and calculations show that the [Formula: see text] in the hydrolysis of verdohemes with non-peripheral substituents is more negative than hydrolysis of verdohemes with peripheral substituents. In other words, the hydrolysis of verdohemes with non-peripheral substituents is more energy-efficient than verdohemes with a peripheral substituents. Equilibrium constant calculations show that hydrolysis of verdohemes with non-peripheral substituents is much faster than that of verdohemes with peripheral substituents, which is due to a more convenient nucleophilic attack on the cationic ring than the anionic ring. To acquire a good molecular understanding, peripheral substituent effects on the hydrolysis of verdoheme’s inhibitory role was studied using the DFT method.

Quantitative vibrational dynamics of the metal site in a tin porphyrin: an IR, NRVS, and DFT study

We used a newer, synchrotron-based, spectroscopic technique (nuclear resonance vibrational spectroscopy, NRVS) in combination with a more traditional one (infrared absorption, IR) to obtain a complete, quantitative picture of the metal center vibrational dynamics in a six-coordinated tin porphyrin. From the NRVS (119)Sn site-selectivity and the sensitivity of the IR signal to (112)Sn/(119)Sn isotope substitution, we identified the frequency of the antisymmetric stretching of the axial bonds (290 cm(-1)) and all the other vibrations involving Sn. Experimentally authenticated density functional theory (DFT) calculations aid the data interpretation by providing detailed normal mode descriptions for each observed vibration. These results may represent a starting point toward the characterization of the local vibrational dynamics of the metallic site in tin porphyrins and compounds with related structures. The quantitative complementariness between IR, NRVS, and DFT is emphasized.