Theoretical investigation of five-coordinated manganese(III) oxophlorin with different axial ligands at various spin states using different DFT methods

2022 ◽  
pp. A-S
Author(s):  
Pezhman Mirmarghabi ◽  
Homayoon Bahrami
Keyword(s):  
Nbo Analysis ◽  
Axial Ligand ◽  
Spin States ◽  
Dft Methods ◽  
Quintet State ◽  
Axial Ligands ◽  
Pyramid Structure ◽  
Stability Of Complexes ◽  
D Orbitals ◽  
Optimized Geometries

The Mn(III)-oxophlorin complexes with imidazole, pyridine and t-butylcyanide as axial ligands have been studied using B3LYP, Bv86p, and M06-2X methods. All of the possible optimized geometries are specified, while the M06-2X is employed. Results obtained show that the isomers of Mn(III)-oxophlorin with imidazole or pyridine are the most stable at quintet state, compared to singlet and triplet spin states. Besides, there are two and four [Formula: see text]-electrons on manganese in each of these complexes at triplet and quintet states, respectively. Also, Mn(III)-oxophlorin with t-butylcyanide as axial ligand is only stable at singlet state. Non-specific solvent effects show that dispersion and London forces have the basic role in stability of complexes in a solvent. Note that latter interactions can occur in medium with dielectric constant ([Formula: see text]) of [Formula: see text]8, such as [Formula: see text] for position of oxophlorin in heme oxygenase enzyme. NBO analysis show that there is no degeneracy between d orbitals of Mn in the five-coordinated Mn(III)-oxophlorin at singlet and triplet spin states, but two d orbitals of manganese are degenerated in latter complexes at quintet state. Such degeneracy of d orbitals is observed in a complex with square pyramid structure. Then five-coordinated Mn(III)-oxophlorin with imidazole or pyridine is the most stable at quintet spin state, because of its geometry corresponding to square pyramid configuration of atoms. Also, nonbounding interaction between Mn and the ring of oxophlorin or Mn and ligand are more effective in Mn(III)-oxophlorin with imidazole as axial ligand, compared to pyridine and t-butylcyanide.

Proximal ligand effects on electronic structure and spectra of compound I of peroxidases

2001 ◽  
Vol 05 (03) ◽  
pp. 334-344 ◽  
Author(s):  
DANNI L. HARRIS ◽  
GILDA H. LOEW
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Axial Ligand ◽  
Compound I ◽  
Imidazole Ligand ◽  
Axial Ligands ◽  
Transient Spectra ◽  
Main Determinants ◽  
And Function ◽  
Optimized Geometries

Computational studies exploring the extent to which differences in proximal axial ligands modulate structure, spectra, and function of peroxidases have been performed. To this end, three heme models of compound I were characterized differing only in the axial ligand. The axial ligands considered were L = ImH , Im -, that are alternative protonation models for a typical peroxidase with an imidazole ligand such as horseradish peroxidase (HRP-I), and L = SCH - that is a model for an unsual peroxidase, chloroperoxidase (CPO-I). Density functional calculations (DFTs) were performed to determine the optimized geometries and electronic structure of each of these three species. Their electronic spectra were also calculated at the DFT optimized geometries, using the INDO/S/CI method. The results of these studies led to the following conclusions: (1) the presence of the nearby Asp in a typical peroxidase does indeed decrease the energy required to deprotonate the imidazole making the two forms essentially degenerate, (2) neither the state of protonation of the imidazole ligand nor the change in axial ligand from an imidazole in typical peroxidases such as HRP to a mercaptide in CPO significantly alters the characteristics of the lowest energy spin state or the electronic structure of compound I in a way that can obviously affect function, (3) both the Im - and ImH forms of the peroxidase compound I (HRP-I) lead to the same dramatic reduction in intensity relative to the ferric resting form observed experimentally. However, only in the ImH form of HRP-I does the calculated relative shift of one component of the Soret bands relative to CPO-I agree with that observed in the transient spectra of HRP-I compared to CPO-I. These results taken together strongly indicate that factors other than the nature of the proximal axial ligand are the main determinants of function.

scholarly journals Synthesis, Spectroscopy and Electrochemistry of Cobalt(III) Schiff Base Complexes

2005 ◽  
Vol 2005 (3) ◽  
pp. 190-193 ◽  
Author(s):  
Ali Hossein Sarvestani ◽  
Abdollah Salimi ◽  
Sajjad Mohebbi ◽  
Rahman Hallaj
Keyword(s):  
Schiff Base ◽  
Structural Model ◽  
Ligand Substitution ◽  
Axial Ligand ◽  
Schiff Base Complexes ◽  
H Nmr ◽  
Reduction Potentials ◽  
Axial Ligands ◽  
D Orbitals ◽  
Equatorial Ligand

Three Co(III) complexes of the type [Co(chel)(PBu3)]ClO4.H2O, (chel = 5-BrSalen, 5-MeOSalen and 4-MeOSalen), were synthesised and characterised by elemental analysis, IR, UV-Vis and 1H NMR spectroscopy. In their electronic spectra, the absorptions between 550 and 750 nm of these complexes are attributable to the lowest d–d transition. The axial ligands affect this transition through a σ-intraction with the dz2 orbital and the equatorial ligands affect it by π-interaction with populated d-orbitals. On the basis of an electronic structural model, in which the dz2 orbital is populated in forming cobalt(II), it is suggested that equatorial ligand substitution affects the reduction potentials less than axial ligand substitution.

Conformational Stability, FMO, NMR, MEP and NBO Analysis of 2,5-Di-methyl-2,5-bis(methylthio)-1,4-dithiane and Dimethoxy compounds by DFT Approach

2021 ◽  
Vol 17 ◽  
Author(s):  
Nasrin Masnabadi
Keyword(s):  
Computational Methods ◽  
Electrostatic Potential ◽  
Conformational Stability ◽  
Nbo Analysis ◽  
Dft Methods ◽  
Geometrical Properties ◽  
Stereoelectronic Effect ◽  
Nmr Parameters ◽  
Electron Transfers ◽  
Stability Energy

Abstract: Conformational behaviors of 2,5-dimethoxy-2,5-dimethyl-1,4-dithiane (compound 1) and 2,5-dimethyl-2,5-bis (methylthio)-1,4-dithiane (compound 2) investigated by computational methods including B3LYP/6-311+G** and M06-2X/6-311+G** levels of theory and NBO analysis. The stereoelectronic effect of axial, axial (ax, ax) and equatorial, equa-torial (eq, eq) conformations were studied using NBO analysis. Using NBO analysis, the values of the stereoelectronic effects were calculated through the energy of stability associated with the electron transfers of compounds 1 and 2. The results showed that the eq, eq conformations of the studied compounds were more stable than their corresponding ax, ax conformations, and LP2X→σS1-C2 and LP2S→σ*C2-X electron transfers play important roles in the conformational be-havior of the studied compounds. The main purpose of the present work was to study the effects of stereoelectronic inter-actions and steric on the conformational superiority of the di-methoxy (compound 1) and di-thiomethyl compounds (com-pound 2). Thus, the values of resonance stability energy, non-diagonal elements, and orbital populations were investigated. Also, active electrophilic and nucleophilic centers were identified using fronting orbitals analysis obtained by DFT methods. The electrostatic potential maps of the title compounds were investigated at the B3LYP/6-311+G* level of theory. All of the NMR parameters and geometrical properties of both compounds were determined in this study.

scholarly journals Temperature dependence of the spin state and geometry in tricobalt paddlewheel complexes with halide axial ligands

2018 ◽  
Vol 47 (46) ◽  
pp. 16798-16806
Author(s):  
Anandi Srinivasan ◽  
Xiaoping Wang ◽  
Rodolphe Clérac ◽  
Mathieu Rouzières ◽  
Larry R. Falvello ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Spin State ◽  
Spin Crossover ◽  
Molecular Geometry ◽  
Axial Ligand ◽  
Paddlewheel Complexes ◽  
Axial Ligands

A series of tricobalt EMACs with halide axial ligands demonstrate diverse spin-crossover behaviors as a function of the molecular geometry and the nature of the axial ligand.

scholarly journals One Pathway Can Incorporate either Adenine or Dimethylbenzimidazole as an α-Axial Ligand of B12 Cofactors in Salmonella enterica

2007 ◽  
Vol 190 (4) ◽  
pp. 1160-1171 ◽  
Author(s):  
Peter J. Anderson ◽  
Jozsef Lango ◽  
Colleen Carkeet ◽  
Audrey Britten ◽  
Bernhard Kräutler ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Axial Ligand ◽  
Vitamin B ◽  
Wild Type ◽  
Aerobic Growth ◽  
Anaerobic Conditions ◽  
Aerobic Conditions ◽  
Axial Ligands ◽  
And Control ◽  
Coenzyme B

ABSTRACT Corrinoid (vitamin B12-like) cofactors contain various α-axial ligands, including 5,6-dimethylbenzimidazole (DMB) or adenine. The bacterium Salmonella enterica produces the corrin ring only under anaerobic conditions, but it can form “complete” corrinoids aerobically by importing an “incomplete” corrinoid, such as cobinamide (Cbi), and adding appropriate α- and β-axial ligands. Under aerobic conditions, S. enterica performs the corrinoid-dependent degradation of ethanolamine if given vitamin B12, but it can make B12 from exogenous Cbi only if DMB is also provided. Mutants isolated for their ability to degrade ethanolamine without added DMB converted Cbi to pseudo-B12 cofactors (having adenine as an α-axial ligand). The mutations cause an increase in the level of free adenine and install adenine (instead of DMB) as an α-ligand. When DMB is provided to these mutants, synthesis of pseudo-B12 cofactors ceases and B12 cofactors are produced, suggesting that DMB regulates production or incorporation of free adenine as an α-ligand. Wild-type cells make pseudo-B12 cofactors during aerobic growth on propanediol plus Cbi and can use pseudo-vitamin B12 for all of their corrinoid-dependent enzymes. Synthesis of coenzyme pseudo-B12 cofactors requires the same enzymes (CobT, CobU, CobS, and CobC) that install DMB in the formation of coenzyme B12. Models are described for the mechanism and control of α-axial ligand installation.

The effect of the trans axial ligand of cobalt corroles on water oxidation activity in neutral aqueous solutions

2017 ◽  
Vol 19 (15) ◽  
pp. 9755-9761 ◽  
Author(s):  
Liang Xu ◽  
Haitao Lei ◽  
Zongyao Zhang ◽  
Zhen Yao ◽  
Jianfeng Li ◽  
...  
Keyword(s):  
Aqueous Solutions ◽  
Water Oxidation ◽  
Axial Ligand ◽  
Oxidation Activity ◽  
Axial Ligands

Co corroles containing electron-donating trans axial ligands are more active than those containing electron-withdrawing trans axial ligands in catalyzing water oxidation.

Axial Ligand Effects in Sterically Strained Porphyrins: A Crystallographic Study of Five- and Six-coordinated Metal Complexes of 2,3,7,8,12,13,17,18-Octaethyl-5,10,15,20-tetranitroporphyrin

1998 ◽  
Vol 02 (02) ◽  
pp. 107-121 ◽  
Author(s):  
MATHIAS O. SENGE
Keyword(s):  
High Spin ◽  
Mutual Influence ◽  
Structural Data ◽  
Axial Ligand ◽  
The Novel ◽  
X Ray Crystallography ◽  
Axial Ligands ◽  
Metal Derivatives ◽  
Ligand Orientation ◽  
Derivatives Of

Porphyrins with steric hindrance at the periphery are known to exhibit severely non-planar macrocycle conformations. Among other dodecasubstituted porphyrins, the title compound has been studied widely and shows a typical saddle-distorted macrocycle. The specific conformation of the porphyrin leads to the formation of distinct cavities on both sides of the macrocycle. Compared to planar porphyrins this should increase steric interactions between the macrocycle and axial ligands in five- and six-coordinated metal derivatives. In order to study the influence of different axial ligands on the conformation (or vice versa) a variety of five- and six-coordinated metal derivatives of 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetranitroporphyrin (oetnp) were prepared and their conformation investigated by X-ray crystallography. Structural data for Zn II oetnp (L) where L is imidazole, 1-methylimidazole, 2-methylimidazole, 4-methylimidazole and 3,5-lutidine clearly indicated that a mutual influence exists between axial ligands and non-planar porphyrins. An asymmetric macrocycle distortion and axial ligand orientation was found in the sterically hindered 2- and 4-methylimidazole derivatives. The presence of four electron-withdrawing nitro-groups led to the formation of the novel polymeric porphyrins ( Zn II oetnp )n and ( Co II oetnp )n where polymer formation was achieved via the utilization of nitro oxygen atoms as axial ligands to the metal centre of neighbouring porphyrins. The structure of the six-coordinated Ni II oetnp ( pyr )2 (where pyr is pyridine) yielded first structural data on neutral, non-planar, high-spin Ni ( II ) porphyrins. A comparison with the respective low-spin Ni II oetnp clearly showed that a change to the high-spin form leads to a less non-planar macrocycle conformation further proving that spin state changes can have a profound effect on the conformation in distorted porphyrins.

scholarly journals Versatility in Corrinoid Salvaging and Remodeling Pathways Supports Corrinoid-Dependent Metabolism in Dehalococcoides mccartyi

2012 ◽  
Vol 78 (21) ◽  
pp. 7745-7752 ◽  
Author(s):  
Shan Yi ◽  
Erica C. Seth ◽  
Yu-Jie Men ◽  
Sally P. Stabler ◽  
Robert H. Allen ◽  
...  
Keyword(s):  
De Novo ◽  
Chlorinated Solvents ◽  
Axial Ligand ◽  
Content Type ◽  
Dehalococcoides Mccartyi ◽  
Axial Ligands ◽  
The Common ◽  
Enzyme Cofactors ◽  
Lower Ligand ◽  
Insight Into

ABSTRACTCorrinoids are cobalt-containing molecules that function as enzyme cofactors in a wide variety of organisms but are produced solely by a subset of prokaryotes. Specific corrinoids are identified by the structure of their axial ligands. The lower axial ligand of a corrinoid can be a benzimidazole, purine, or phenolic compound. Though it is known that many organisms obtain corrinoids from the environment, the variety of corrinoids that can serve as cofactors for any one organism is largely unstudied. Here, we examine the range of corrinoids that function as cofactors for corrinoid-dependent metabolism inDehalococcoides mccartyistrain 195.Dehalococcoidesbacteria play an important role in the bioremediation of chlorinated solvents in the environment because of their unique ability to convert the common groundwater contaminants perchloroethene and trichloroethene to the innocuous end product ethene. All isolatedD. mccartyistrains require exogenous corrinoids such as vitamin B12for growth. However, like many other corrinoid-dependent bacteria, none of the well-characterizedD. mccartyistrains has been shown to be capable of synthesizing corrinoidsde novo. In this study, we investigate the ability ofD. mccartyistrain 195 to use specific corrinoids, as well as its ability to modify imported corrinoids to a functional form. We show that strain 195 can use only specific corrinoids containing benzimidazole lower ligands but is capable of remodeling other corrinoids by lower ligand replacement when provided a functional benzimidazole base. This study of corrinoid utilization and modification byD. mccartyiprovides insight into the array of strategies that microorganisms employ in acquiring essential nutrients from the environment.

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