Iron porphyrins with different imidazole ligands. A theoretical comparative study

Binding of Carbon Monoxide to Hemoglobin in an Oxygen Environment: Force Field Development for Molecular Dynamics

Carbon monoxide (CO) is a byproduct of the incomplete combustion of carbon-based fuels, such as wood, coal, gasoline, or natural gas. As incomplete combustion in a fire accident or in an engine, massively produced CO leads to a serious life threat because CO competes with oxygen (O2) binding to hemoglobin and makes people suffer from hypoxia. Although there is hyperbaric O2 therapy for patients with CO poisoning, the nanoscale mechanism of CO dissociation in the O2-rich environment is not completely understood. In this study, we construct the classical force field parameters compatible with the CHARMM for simulating the coordination interactions between hemoglobin, CO, and O2, and use the force field to reveal the impact of O2 on the binding strength between hemoglobin and CO. Density functional theory and Car-Parrinello molecular dynamics simulations are used to obtain the bond energy and equilibrium geometry, and we used machine learning enabled via a feedforward neural network model to obtain the classical force field parameters. We used steered molecular dynamics simulations with a force field to characterize the mechanical strength of the hemoglobin-CO bond before rupture under different simulated O2-rich environments. The results show that as O2 approaches the Fe2+ of heme at a distance smaller than ∼2.8 Å, the coordination bond between CO and Fe2+ is reduced to 50% bond strength in terms of the peak force observed in the rupture process. This weakening effect is also shown by the free energy landscape measured by our metadynamics simulation. Our work suggests that the O2-rich environment around the hemoglobin-CO bond effectively weakens the bonding, so that designing of O2 delivery vector to the site is helpful for alleviating CO binding, which may shed light on de novo drug design for CO poisoning.

Aromatic heterobicycle-fused porphyrins: impact on aromaticity and excited state electron transfer leading to long-lived charge separation

A new synthetic method to fuse benzo[4,5]imidazo[2,1-a]isoindole to the porphyrin periphery at the β,β-positions has been developed, and its impact on the aromaticity and electronic structures is investigated. Reactivity investigation of the fused benzoimidazo-isoindole component reveals fluorescence quenching of a zinc porphyrin (AMIm-2) upon treatment with a Brønsted acid. The reaction of the zinc porphyrin (AMIm-2) with methyl iodide initiated a new organic transformation, resulting in the ring-opening of isoindole with the formation of an aldehyde and dimethylation of the benzoimidazo component. The fused benzoimidazo-isoindole component acted as a good ligand to bind platinum(ii), forming novel homobimetallic and heterobimetallic porphyrin complexes. The fusion of benzoimidazo-isoindole on the porphyrin ring resulted in bathochromically shifted absorptions and emissions, reflecting the extended conjugation of the porphyrin π-system. Time-resolved emission and transient absorption spectroscopy revealed stable excited state species of the benzoimidazo-isoindole fused porphyrins. Zinc porphyrin AMIm-2 promoted excited state electron transfer upon coordinating with an electron acceptor, C60, generating a long-lived charge-separated state, in the order of 37.4 μs. The formation of the exceptionally long-lived charge-separated state is attributed to the involvement of both singlet and triplet excited states of AMIm-2, which is rarely reported in porphyrins.

Resonance Raman Spectroscopy and Density Functional Theory Calculations on Ferrous Porphyrin Dioxygen Adducts with Different Axial Ligands: Correlation of Ground State Wave Function and Geometric Parameters with Experimental Vibrational Frequencies

A dioxygen adduct of ferrous porphyrin is an important chemical species in nature as it is a common intermediate in all oxygen transfer, storage, reducing, and activating heme enzymes. The ground state (GS) wave function of this complex has been investigated using several techniques like resonance Raman (rR), Mossbauer, and X-ray absorption spectroscopies. The Fe-O and O-O vibrations of these six-coordinated diamagnetic species show a positive correlation with each other in contrast to analogous ferrous carbonyl complexes where the Fe-CO vibration correlates negatively with the C-O vibration due to a synergistic effect. In this Article, three Fe-porphyrins with different axial ligands (imidazole, phenolate, and thiolate) are investigated using rR spectroscopy and density functional theory (DFT) calculations. The GS wave functions of these species are analyzed, and the contribution of the three primary bonding interactions in the Fe-O₂ unit (a σ interaction from the in-plane π* of the superoxide to the vacant d_z² of Fe, a π donation from the out of plane (oop) π* to the d_π orbital of Fe, and a π back bonding interaction from the d_π orbital of Fe to the oop π* of the superoxide) to the calculated Fe-O and O-O vibrations and bond lengths are deconvoluted using a MO theory framework. The GS wave function provides a basis for the correlations observed between different vibrational and geometric parameters of these dioxygen adducts. Furthermore, the correlations obtained allows estimation of the GS wave function and geometry of these species (both natural and artificial) using their experimentally observed Fe-O/O-O vibrations. The wave functions thus extracted from the experimental vibrational data reported offer insight into the role of the axial ligand and hydrogen bonding on the geometric and electronic structures of these crucial chemical species in different protein active sites.

Resonant inelastic X-ray scattering determination of the electronic structure of oxyhemoglobin and its model complex

Hemoglobin and myoglobin are oxygen-binding proteins with S = 0 heme {FeO₂}⁸ active sites. The electronic structure of these sites has been the subject of much debate. This study utilizes Fe K-edge X-ray absorption spectroscopy (XAS) and 1s2p resonant inelastic X-ray scattering (RIXS) to study oxyhemoglobin and a related heme {FeO₂}⁸ model compound, [(pfp)Fe(1-MeIm)(O₂)] (pfp = meso-tetra(α,α,α,α-o-pivalamido-phenyl)porphyrin, or TpivPP, 1-MeIm = 1-methylimidazole) (pfpO₂), which was previously analyzed using L-edge XAS. The K-edge XAS and RIXS data of pfpO₂ and oxyhemoglobin are compared with the data for low-spin Fe^II and Fe^III [Fe(tpp)(Im)₂]^0/+ (tpp = tetra-phenyl porphyrin) compounds, which serve as heme references. The X-ray data show that pfpO₂ is similar to Fe^II, while oxyhemoglobin is qualitatively similar to Fe^III, but with significant quantitative differences. Density-functional theory (DFT) calculations show that the difference between pfpO₂ and oxyhemoglobin is due to a distal histidine H bond to O₂ and the less hydrophobic environment in the protein, which lead to more backbonding into the O₂ A valence bond configuration interaction multiplet model is used to analyze the RIXS data and show that pfpO₂ is dominantly Fe^II with 6-8% Fe^III character, while oxyhemoglobin has a very mixed wave function that has 50-77% Fe^III character and a partially polarized Fe-O₂ π-bond.

The dramatic effect of N-methylimidazole on trans axial ligand binding to ferric heme: experiment and theory

The binding energy of CO, O2 and NO to isolated ferric heme, [FeIIIP]+, was studied in the presence and absence of a σ donor (N-methylimidazole and histidine) as the trans axial ligand. This study combines the experimental determination of binding enthalpies by equilibrium measurements in a low temperature ion trap using the van't Hoff equation and high level DFT calculations. It was found that the presence of N-methylimidazole as the axial ligand on the [FeIIIP]+ porphyrin dramatically weakens the [FeIIIP-ligand]+ bond with an up to sevenfold decrease in binding energy owing to the σ donation by N-methylimidazole to the FeIII(3d) orbitals. This trans σ donor effect is characteristic of ligation to iron in hemes in both ferrous and ferric redox forms; however, to date, this has not been observed for ferric heme.

On the structures, spin states, and optical properties of titanium, platinum, and iron azacalixphyrins: a DFT study

Azacalixphyrins (ACP) constitute a new class of macrocycles isoelectronic and isostructural to porphyrins. Herein, we report the first theoretical investigation of the properties of the ACP macrocycles metallated at their centre by titanium, platinum, and iron ions. We considered both the original phenyl-type ACP and new pyridyl-type forms. Our results indicate that the metallation greatly impacts the global structure of the macrocycle through pseudo Jahn-Teller effects, giving rise to a possible conformational transition between D_2d and S₄ structures. Such an effect could not be found in the metal-free ACPs. In addition, we find that, in contrast to the purely singlet platinum ACPs, and the purely triplet iron ACPs, several spin states are energetically close in the titanium ACPs, especially when weak field ligands are bound in axial positions to the metallic centre. According to TD-DFT calculations, metallation also tunes the optical properties. In particular, the absorption band in the near infrared region undergoes a hypsochromic shift of ca. 100-200 nm when going from the D_2d to the S₄ structures. We quantify how the addition of electroactive ligands in the axial position can increase or tune down these spectral changes. This contribution therefore supports the development of ACP coordination complexes.

Influence of mutations at the proximal histidine position on the Fe-O2 bond in hemoglobin from density functional theory

Four mutated hemoglobin (Hb) variants and wild type hemoglobin as a reference have been investigated using density functional theory methods focusing on oxygen binding. Dispersion-corrected B3LYP functional is used and found to provide reliable oxygen binding energies. It also correctly reproduces the spin distribution of both bound and free heme groups as well as provides correct geometries at their close vicinity. Mutations in hemoglobin are not only an intrigued biological problem and it is also highly important to understand their effects from a clinical point of view. This study clearly shows how even small structural differences close to the heme group can have a significant effect in reducing the oxygen binding of mutated hemoglobins and consequently affecting the health condition of the patient suffering from the mutations. All of the studied mutated Hb variants did exhibit much weaker binding of molecular oxygen compared to the wild type of hemoglobin.

Correlated ligand dynamics in oxyiron picket fence porphyrins: structural and Mössbauer investigations

Disorder in the position of the dioxygen ligand is a well-known problem in dioxygen complexes and, in particular, those of picket fence porphyrin species. The dynamics of Fe-O2 rotation and tert-butyl motion in three different picket fence porphyrin derivatives has been studied by a combination of multitemperature X-ray structural studies and Mössbauer spectroscopy. Structural studies show that the motions of the dioxygen ligand also require motions of the protecting pickets of the ligand binding pocket. The two motions appear to be correlated, and the temperature-dependent change in the O2 occupancies cannot be governed by a simple Boltzmann distribution. The three [Fe(TpivPP)(RIm)(O2)] derivatives studied have RIm = 1-methyl-, 1-ethyl-, or 2-methylimidazole. In all three species there is a preferred orientation of the Fe-O2 moiety with respect to the trans imidazole ligand and the population of this orientation increases with decreasing temperature. In the 1-MeIm and 1-EtIm species the Fe-O2 unit is approximately perpendicular to the imidazole plane, whereas in the 2-MeHIm species the Fe-O2 unit is approximately parallel. This reflects the low energy required for rotation of the Fe-O2 unit and the small energy differences in populating the possible pocket quadrants. All dioxygen complexes have a crystallographically required 2-fold axis of symmetry that limits the accuracy of the determined Fe-O2 geometry. However, the 80 K structure of the 2-MeHIm derivative allowed for resolution of the two bonded oxygen atom positions and provided the best geometric description for the Fe-O2 unit. The values determined are Fe-O = 1.811(5) Å, Fe-O-O = 118.2(9)°, O-O = 1.281(12) Å, and an off-axis tilt of 6.2°. Demonstration of the off-axis tilt is a first. We present detailed temperature-dependent simulations of the Mössbauer spectra that model the changing value of the quadrupole splitting and line widths. Residuals to fits are poorer at higher temperature. We believe that this is consistent with the idea that population of the two conformers is related to the concomitant motions of both Fe-O2 rotations and motions of the protecting tert-butyl pickets.

Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study

The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron-histidine (Fe-His) binding. The Heme-AB (AB = O2, NO) and Fe-His binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX(AB), and Tyr140 → Phe mutated H-NOX[Y140F(AB)] were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than that in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN , where the Trp9 and Asn74 residues do not form a hydrogen-bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe-His binding strength, but a dispersion contribution to Ebind(Fe-His) may be significant, depending on the crystal structure used. We speculate that the Fe-His binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.

Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies

The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.

Electronic structure and ligand vibrations in FeNO, CoNO, and FeOO porphyrin adducts

The gaseous ligands, CO, NO, and O2 interact with the Fe ion in heme proteins largely via backbonding of Fe electrons to the π* orbitals of the XO (X = C, N, O) ligands. In these FeXO adducts, the Fe-X stretching frequency varies inversely with the X-O stretching frequency, since increased backbonding strengthens the Fe-X bond while weakening the X-O bond. Inverse frequency correlations have been observed for all three ligands, despite differing electronic and geometric structures, and despite variable composition of the "FeX" vibrational mode, in which Fe-X stretching and Fe-X-O coordinates are mixed for bent FeXO adducts. We report experimental data for 5-coordinate Co(II)(NO) porphyrin adducts (isoelectronic with Fe(II)(OO) adducts), and the results of density functional theory (DFT) modeling for 5-coordinate Fe(II)(NO), Co(II)(NO), and Fe(II)(OO) adducts. Inverse ν(MX)/ν(XO) correlations are obtained computationally, using model porphyrins with graded electron-donating and -withdrawing substituents to modulate the backbonding. Computed slopes agree satisfactorily with experiment, provided nonhybrid functionals are used, which avoid overemphasizing high-spin states. The BP86 functional gives correct ground states, a closed-shell singlet for Co(II)(NO) and an open-shell singlet for the isoelectronic Fe(II)(OO), as corroborated by structural data for Co(II)(NO), and the ν(MX)/ν(XO) slope agreement with experiment for both adducts. However, for Fe(II)(OO) adducts, the computed inverse ν(MX)/ν(XO) correlation applies only to porphyrins with electron-donating and withdrawing substituents of moderate strength. For substituents more donating than -CH3, a direct correlation is obtained, the Fe-O and O-O bonds weakening in concert. This effect is ascribed to the dominance of σ bonding via the in-plane dxz(+dz(2))-π* orbital, when electron-donating substituents raise the d orbital energies sufficiently to render backbonding (dyz-π*) unimportant.

CO, NO and O2 as Vibrational Probes of Heme Protein Interactions

The gaseous XO molecules (X = C, N or O) bind to the heme prosthetic group of heme proteins, and thereby activate or inhibit key biological processes. These events depend on interactions of the surrounding protein with the FeXO adduct, interactions that can be monitored via the frequencies of the Fe-X and X-O bond stretching modes, νFeX and νXO. The frequencies can be determined by vibrational spectroscopy, especially resonance Raman spectroscopy. Backbonding, the donation of Fe dπ electrons to the XO π* orbitals, is a major bonding feature in all the FeXO adducts. Variations in backbonding produce negative νFeX/νXO correlations, which can be used to gauge electrostatic and H-bonding effects in the protein binding pocket. Backbonding correlations have been established for all the FeXO adducts, using porphyrins with electron donating and withdrawing substituents. However the adducts differ in their response to variations in the nature of the axial ligand, and to specific distal interactions. These variations provide differing vantages for evaluating the nature of protein-heme interactions. We review experimental studies that explore these variations, and DFT computational studies that illuminate the underlying physical mechanisms.

Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study

DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX. The natural tendency of the heme is to be planar. The strong structural distortion in H-NOX is mainly brought about by the intermolecular interactions between the whole heme molecule (heme ring plus its peripheral substituents) and the surrounding residues, among which the polar residues (Tyr140, Pro115, Mse98) play major roles in distorting the heme structure. The two peripheral propionate substituents that are oriented on the same side of the heme plane can also make the molecule distort, but the distortion caused by this factor is not significant. In Mb, the surrounding residues considered are all nonpolar and do not cause a structural distortion. The different structural features of the heme macrocycle in the different proteins (H-NOX and Mb) are reproduced by the calculations. The dispersion correction is necessary, since it improves the calculated structures. The effects of the distortion on the binding affinity of the axial ligand to the heme were also examined.

Electronic structure, spin-states, and spin-crossover reaction of heme-related Fe-porphyrins: a theoretical perspective

The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).

New perspectives on iron-ligand vibrations of oxyheme complexes

We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations.

FeP(Im)-AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O(2))

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (E(bond)) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). The results indicate that an accurate prediction of E(bond) for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield E(bond) values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O(2), respectively, which are in reasonable agreement with experimental data (0.78 - 0.85 eV for CO, 0.99 eV for NO, and 0.44 - 0.53 eV for O(2)). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined.

The structures and stabilities of the complexes of biologically available ligands with Fe(III)-porphine: an ab initio study

Fe(III) porphine complexes and a limited number of Fe(II) porphine complexes were investigated at the 'MP2/LB'//B3LYP/SB level of theory, where SB and LB represent small and large basis sets, 6-31+G(d) and 6-311+G(2df,2p), respectively. Solvation effects were incorporated by the IEFPCM procedure. Most of the ligands whereby the heme prosthetic group is bound in biological systems were modeled in the study. These include H(2)O, Im (imidazole), CH(3)NH(2), CH(3)CO(2)(-), CH(3)S(-), CH(3)PhO(-), OH(-), and Cl(-). Fe(III) porphine, 2(+), and the pentacoordinated complexes, 2(+)(Im), 2(+)(CH(3)NH(2)), and 2(+)(H(2)O), have quartet ground states. The pentacoordinated complexes with negatively charged ligands all have high spin hextet ground states. All of the hexacoordinated complexes have low spin doublet ground states, with the exception of 2(+)(H(2)O)(2) and 2(+)(H(2)O)(Im) which have intermediate spin quartet ground states. None of the pentacoordinated complexes, 2(+)(OH(-)), 2(+)(CH(3)PhO(-)), and 2(+)(CH(3)S(-)), are predicted to form stable hexacoordinated complexes in water with any of the ligands of the present study. The most stable species in water is 2(+)(OH(-)). The hydroxide may be displaced by CH(3)PhOH and CH(3)SH at physiological pH, and by Cl(-), CH(3)CO(2)(-), and Im under acidic conditions, but not by CH(3)NH(3)(+). The relevance of the present results for the pH-dependent transitions of cytochrome c and the fragments, NAcMP8, and NAcMP11, the resting state of cytochrome P450, and the bonding interactions between heme and Aβ, is discussed.