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.

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.

DFT insight into axial ligand effects on electronic structure and mechanistic reactivity of oxoiron(iv) porphyrin

2020 ◽  
Vol 22 (21) ◽  
pp. 12173-12179
Author(s):  
Zhifeng Ma ◽  
Naoki Nakatani ◽  
Hiroshi Fujii ◽  
Masahiko Hada
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Axial Ligand ◽  
Functional Theory ◽  
Ligand Effects ◽  
Insight Into

The nature of axial ligand effects is revealed by density functional theory calculations, the ability of axial ligand bound to iron is strong, and the reaction is more reactive.

scholarly journals How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by Nδ-Methyl Histidine Affect Its Properties and Functions? A Computational Study

2020 ◽  
Vol 21 (19) ◽  
pp. 7133
Author(s):  
Calvin W. Z. Lee ◽  
M. Qadri E. Mubarak ◽  
Anthony P. Green ◽  
Sam P. de Visser
Keyword(s):  
Cytochrome C ◽  
Oxygen Atom ◽  
Density Functional ◽  
Computational Study ◽  
Cytochrome C Peroxidase ◽  
Electronic Configuration ◽  
Axial Ligand ◽  
Atom Transfer ◽  
Compound I ◽  
Oxygen Atom Transfer

Heme peroxidases have important functions in nature related to the detoxification of H2O2. They generally undergo a catalytic cycle where, in the first stage, the iron(III)–heme–H2O2 complex is converted into an iron(IV)–oxo–heme cation radical species called Compound I. Cytochrome c peroxidase Compound I has a unique electronic configuration among heme enzymes where a metal-based biradical is coupled to a protein radical on a nearby Trp residue. Recent work using the engineered Nδ-methyl histidine-ligated cytochrome c peroxidase highlighted changes in spectroscopic and catalytic properties upon axial ligand substitution. To understand the axial ligand effect on structure and reactivity of peroxidases and their axially Nδ-methyl histidine engineered forms, we did a computational study. We created active site cluster models of various sizes as mimics of horseradish peroxidase and cytochrome c peroxidase Compound I. Subsequently, we performed density functional theory studies on the structure and reactivity of these complexes with a model substrate (styrene). Thus, the work shows that the Nδ-methyl histidine group has little effect on the electronic configuration and structure of Compound I and little changes in bond lengths and the same orbital occupation is obtained. However, the Nδ-methyl histidine modification impacts electron transfer processes due to a change in the reduction potential and thereby influences reactivity patterns for oxygen atom transfer. As such, the substitution of the axial histidine by Nδ-methyl histidine in peroxidases slows down oxygen atom transfer to substrates and makes Compound I a weaker oxidant. These studies are in line with experimental work on Nδ-methyl histidine-ligated cytochrome c peroxidases and highlight how the hydrogen bonding network in the second coordination sphere has a major impact on the function and properties of the enzyme.

Effect of axial ligands on electronic structure and O2 reduction by iron porphyrin complexes: Towards a quantitative understanding of the "push effect"

2015 ◽  
Vol 19 (01-03) ◽  
pp. 92-108 ◽  
Author(s):  
Subhra Samanta ◽  
Pradip Kumar Das ◽  
Sudipta Chatterjee ◽  
Abhishek Dey
Keyword(s):  
Electronic Structure ◽  
Active Sites ◽  
Reduction Reaction ◽  
Axial Ligand ◽  
Iron Porphyrin ◽  
Axial Ligands ◽  
O2 Reduction ◽  
Thiolate Complexes ◽  
Quantitative Understanding ◽  
Iron Porphyrin Complexes

Axial ligands play a dominating role in determining the electronic structure and reactivity of iron porphyrin active sites and synthetic models. Several properties unique to the cysteine bound heme enzyme, cytochrome P450, is attributed to the "push effect" of the thiolate axial ligand. In this mini-review the ground state electronic structure of iron porphyrins with imidazole, phenolate and thiolate complexes, derived using a combination of spectroscopy and DFT calculations, are discussed. The differences in kinetics and selectivity of oxygen reduction reaction (ORR), catalyzed by these iron porphyrin complexes with different axial ligands, help elucidate the varying push effects of the different axial ligands on oxygen activation by ferrous porphyrin. The spectroscopic and kinetic data help to develop a quantitative understanding of the "push effect" and, in particular, the electrostatic and covalent contributions to it.

Doping effects on the geometric and electronic structure of tin clusters

2019 ◽  
Vol 21 (44) ◽  
pp. 24478-24488 ◽  
Author(s):  
Martin Gleditzsch ◽  
Marc Jäger ◽  
Lukáš F. Pašteka ◽  
Armin Shayeghi ◽  
Rolf Schäfer
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Beam Deflection ◽  
Functional Theory ◽  
Doping Effects ◽  
Depth Analysis ◽  
Trajectory Simulations

In depth analysis of doping effects on the geometric and electronic structure of tin clusters via electric beam deflection, numerical trajectory simulations and density functional theory.

Electronic Structure Benchmark Calculations of Inorganic and Biochemical Carboxylation Reactions

2018 ◽  
Author(s):  
Oscar A. Douglas-Gallardo ◽  
David A. Sáez ◽  
Stefan Vogt-Geisse ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electronic Structure ◽  
Chemical Reactions ◽  
Density Functional ◽  
Correlation Energy ◽  
Electronic Energy ◽  
Basis Sets ◽  
Electronic Correlation ◽  
Correct Description ◽  
Carbon Dioxide Co2 ◽  
High Level

<div><div><div><p>Carboxylation reactions represent a very special class of chemical reactions that is characterized by the presence of a carbon dioxide (CO2) molecule as reactive species within its global chemical equation. These reactions work as fundamental gear to accomplish the CO2 fixation and thus to build up more complex molecules through different technological and biochemical processes. In this context, a correct description of the CO2 electronic structure turns out to be crucial to study the chemical and electronic properties associated with this kind of reactions. Here, a sys- tematic study of CO2 electronic structure and its contribution to different carboxylation reaction electronic energies has been carried out by means of several high-level ab-initio post-Hartree Fock (post-HF) and Density Functional Theory (DFT) calculations for a set of biochemistry and inorganic systems. We have found that for a correct description of the CO2 electronic correlation energy it is necessary to include post-CCSD(T) contributions (beyond the gold standard). These high-order excitations are required to properly describe the interactions of the four π-electrons as- sociated with the two degenerated π-molecular orbitals of the CO2 molecule. Likewise, our results show that in some reactions it is possible to obtain accurate reaction electronic energy values with computationally less demanding methods when the error in the electronic correlation energy com- pensates between reactants and products. Furthermore, the provided post-HF reference values allowed to validate different DFT exchange-correlation functionals combined with different basis sets for chemical reactions that are relevant in biochemical CO2 fixing enzymes.</p></div></div></div>

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

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