Characterization of electronic structure and properties of a Bis(histidine) heme model complex

Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study

We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and plants, including two cytoglobins, ten hemoglobins, two myoglobins, six neuroglobins, and six phytoglobins. As a qualified measure of bond strength, we used local vibrational force constants ka (FeN) based on local mode theory developed in our group. All calculations were performed with a hybrid QM/MM ansatz. Starting geometries were taken from available x-ray structures. ka (FeN) values were correlated with FeN bond lengths and covalent bond character. We also investigated the stiffness of the axial NFeN bond angle. Our results highlight that protein effects are sensitively reflected in ka (FeN), allowing one to compare trends in diverse protein groups. Moreover, ka (NFeN) is a perfect tool to monitor changes in the axial heme framework caused by different protein environments as well as different Fe oxidation states.

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al. J. Am. Chem. Soc. 142, 10459-10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. We here explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck-Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

The Mechanism of Biochemical NO‐Sensing: Insights from Computational Chemistry

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO‐receptor in humans is soluble guanylyl cyclase (sGC) – a histidine‐ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO‐signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high‐level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H‐NOX protein from Shewanella oneidensis (So H‐NOX) homologous to the NO‐binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six‐coordinate intermediate heme‐NO complex, followed by relatively facile His decoordination yielding a five‐coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.

Insights into the Observed trans-Bond Length Variations upon NO Binding to Ferric and Ferrous Porphyrins with Neutral Axial Ligands

NO is well-known for its trans effect. NO binding to ferrous hemes of the form (por)Fe(L) (L = neutral N-based ligand) to give the {FeNO}⁷ (por)Fe(NO)(L) product results in a lengthening of the axial trans Fe-L bond. In contrast, NO binding to the ferric center in [(por)Fe(L)]⁺ to give the {FeNO}⁶ [(por)Fe(NO)(L)]⁺ product results in a shortening of the trans Fe-L bond. NO binding to both ferrous and ferric centers involves the lowering of their spin states. Density functional theory (DFT) calculations were used to probe the experimentally observed trans-bond shortening in some NO adducts of ferric porphyrins. We show that the strong σ antibonding interaction of d _{z ²} and the axial (L) ligand p orbitals present in the Fe(II) systems is absent in the Fe(III) systems, as it is now in an unoccupied orbital. This feature, combined with a lowering of spin state upon NO binding, provides a rationale for the observed net trans-bond shortening in the {FeNO}⁶ but not the {FeNO}⁷ derivatives.

Iron(II) Spin Crossover Coordination Polymers Derived From a Redox Active Equatorial Tetrathiafulvalene Schiff-Base Ligand

Two polymorphic Fe^II coordination polymers [Fe^IIL (TPPE)_0.5] 1) and [(Fe^II₃L₃ (TPPE)_1.5)] 2), were obtained from a redox-active tetrathiafulvalene (TTF) functionalized ligand [H₂L = 2,2’-(((2-(4,5-bis-(methylthio)-1,3-dithiol-2-ylidene)benzo(d) (1,3) dithiole-5,6-diyl)bis-(azanediyl))bis-(meth anylylidene)) (2E,2E')-bis(3-oxobutanoate)] and a highly luminescent connector {TPPE = 1,1,2,2-tetrakis[4-(pyridine-4-yl)phenyl]-ethene}. Complex 1 has a layered structure where the TPPE uses its four diverging pyridines from the TPPE ligand are coordinated by the trans positions to the flat TTF Schiff-base ligand, and complex 2 has an unprecedented catenation of layers within two interpenetrated frameworks. These coordination polymers reserved the redox activity of the TTF unit. Complex 1 shows gradual spin transition behavior without hysteresis. And the fluorescence intensity of TPPE in 1 changes in tandem with the spin crossover (SCO) transition indicating a possible interplay between fluorescence and SCO behavior.

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.

Multiplicity spin, structure, and charge of iron-verdohemeoxygenase complex: A comparison study by the DFT method

Recently the three-dimensional structure of verdoheme heme oxygenase complex was revealed. However, many parameters of verdoheme heme oxygenase’s complex structure and their role and function on Heme degradation were unknown. In this work the structure of iron verdoheme in complex with heme oxygenase was compared by the density functional theory (DFT)-based B3LYP method using the 6-31G basis set. Many parameters such as charge of verdoheme and iron as central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effects on verdoheme ring stabilization and their arrangement are discussed and compared for twelve different conformations of the molecules to find the most energetically stable states.

Spin Interconversion of Heme-Peroxo-Copper Complexes Facilitated by Intramolecular Hydrogen-Bonding Interactions

Synthetic peroxo-bridged high-spin (HS) heme-(μ-η2:η1-O22-)-Cu(L) complexes incorporating (as part of the copper ligand) intramolecular hydrogen-bond (H-bond) capabilities and/or steric effects are herein demonstrated to affect the complex's electronic and geometric structure, notably impacting the spin state. An H-bonding interaction with the peroxo core favors a low-spin (LS) heme-(μ-η1:η1-O22-)-Cu(L) structure, resulting in a reversible temperature-dependent interconversion of spin state (5 coordinate HS to 6 coordinate LS). The LS state dominates at low temperatures, even in the absence of a strong trans-axial heme ligand. Lewis base addition inhibits the H-bond facilitated spin interconversion by competition for the H-bond donor, illustrating the precise H-bonding interaction required to induce spin-crossover (SCO). Resonance Raman spectroscopy (rR) shows that the H-bonding pendant interacts with the bridging peroxide ligand to stabilize the LS but not the HS state. The H-bond (to the Cu-bound O atom) acts to weaken the O-O bond and strengthen the Fe-O bond, exhibiting ν(M-O) and ν(O-O) values comparable to analogous known LS complexes with a strong donating trans-axial ligand, 1,5-dicyclohexylimidazole, (DCHIm)heme-(μ-η1:η1-O22-)-Cu(L). Variable-temperature (-90 to -130 °C) UV-vis and 2H NMR spectroscopies confirm the SCO process and implicate the involvement of solvent binding. Examining a case of solvent binding without SCO, thermodynamic parameters were obtained from a van't Hoff analysis, accounting for its contribution in SCO. Taken together, these data provide evidence for the H-bond group facilitating a core geometry change and allowing solvent to bind, stabilizing a LS state. The rR data, complemented by DFT analysis, reveal a stronger H-bonding interaction with the peroxo core in the LS compared to the HS complexes, which enthalpically favors the LS state. These insights enhance our fundamental understanding of secondary coordination sphere influences in metalloenzymes.

Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4)

The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fast (ms-μs) intramolecular ET in an electrochemical environment has recently been achieved by controlling the molecular orientation of the protein assembled on a gold electrode surface. In this work we have performed computational modeling of the intramolecular ET process by a combination of density functional theory (DFT) and quantum mechanical charge transfer theory to disclose reasons for this difference. We first address the electronic structures of the model heme core with histidine and methionine axial ligands in both low- and high-spin states by structure-optimized DFT. The computations enable estimating the intramolecular reorganization energy of the ET process for different combinations of low- and high-spin heme couples. Environmental reorganization free energies, work terms ("gating") and driving force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe-Fe separations. The reactivity of low- and high-spin heme groups was notably different. The ET rate is exceedingly low for the crystallographic equilibrium orientation but increases by several orders of magnitude for thermally accessible non-equilibrium configurations. Deprotonation of the propionate carboxyl group was also found to enhance the ET rate significantly. The results are discussed in relation to the observed surface immobilization effect and support the notion of conformationally gated ET.

High- and low-spin Fe(III) complexes of various AGE inhibitors

Density functional theory calculations [CPCM/UM06/6-31+G(d,p)] were used to elucidate the structures and relative stability of Fe(III) complexes with various ligands that inhibit the formation of advanced glycation end products (AGEs) or iron overloaded disease (viz. aminoguanidine, pyridoxamine, LR-74, Amadori compounds, and ascorbic acid). EDTA was used as the free energy reference ligand. The distorted neutral octahedral complex containing one iron atom and three molecules of pyridoxamine [Fe(PM)(3)] was found to be the most stable. The stability of the complexes decreases in the following chelate sequence: pyridoxamine, Amadori complex, aminoguanidine, LR inhibitor, and ascorbic acid.

Quantum mechanical investigations of heme structure and vibrational spectra: effects of conformation, oxidation state, and electric field

Three conformers of a complex consisting of a Fe-porphyrin ring with axial imidazole groups FeP(Im)(2) that differed by orientation of axial imidazole groups were studied with quantum mechanical calculations in both reduced (neutral) and oxidized (cationic) states. In the reduced state, all three conformers correspond to local minima. On the other hand, in the oxidized state the conformer with the imidazole groups perpendicular to one another does not have a local minimum, which suggests that there could be changes in the structure of heme groups depending on oxidation state. The relative energy differences between conformers are small as well the differences of orbital energies. However, the populations of Fe 3d orbitals, and hence charge distributions, are predicted to change significantly between conformations. The orientation of heme groups can affect the kinetics of interheme electron transfer, so this electronic population redistribution will affect electron transfer kinetics. A comparison of calculated Raman spectra with measured surface-enhanced Raman spectra (Biju et al. Langmuir 2007, 23, 1333) shows excellent agreement for frequencies, but correlations of Raman intensities are less satisfactory. Possible explanations of the observed discrepancies could arise due to a problem in assignments of vibration bands in the experiment, a dependence of Raman spectra on heme complex on oxidation state, long-range protein structure, or membrane electric field are discussed. In particular, it was shown that the oxidation state does not dramatically alter the calculated Raman spectrum. However, the cell membrane electric field can significantly modify Raman spectra. An interpretation of the experimental oxidized cytochrome surface-enhanced Raman spectra is discussed.

Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment

Computer simulations of biological electron transfer reactions are reviewed with a focus on the calculation of reaction free energy (driving force) and reorganization free energy. Then a mixed quantum mechanical/molecular mechanical (QM/MM) approach is described which is designed for computation of these quantities for pure electron transfer reactions with large donor-acceptor separation distances. The method is applied to intra-protein electron transfer in Ru(bpy)(2)(im)His33 cytochrome c and the results compared to experimental data. Several modeling aspects which are important for successful calculation of free energies with QM/MM are discussed in detail.

Unravelling the intrinsic features of NO binding to iron(II)- and iron(III)-hemes

Electrospray ionization of appropriate precursors is used to deliver [Fe (III)-heme] (+) and [Fe (II)-hemeH] (+) ions as naked species in the gas phase where their ion chemistry has been examined by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. In the naked, four-coordinate [Fe (II)-hemeH] (+) and [Fe (III)-heme] (+) ions, the intrinsic reactivity of iron(II)- and iron(III)-hemes is revealed free from any influence due to axial ligand, counterion, or solvent effects. Ligand (L) addition and ligand transfer equilibria with a series of selected neutrals are attained when [Fe (II)-hemeH] (+), corresponding to protonated Fe (II)-heme, is allowed to react in the FT-ICR cell. A Heme Cation Basicity (HCB) ladder for the various ligands toward [Fe (II)-hemeH] (+), corresponding to -Delta G degrees for the process [Fe (II)-hemeH] (+) + L --> [Fe (II)-hemeH(L)] (+) and named HCB (II), can thus be established. The so-obtained HCB (II) values are compared with the corresponding HCB (III) values for [Fe (III)-heme] (+). In spite of pronounced differences displayed by various ligands, NO shows a quite similar HCB of about 67 kJ mol (-1) at 300 K toward both ions, estimated to correspond to a binding energy of 124 kJ mol (-1). Density Functional Theory (DFT) computations confirm the experimental results, yielding very similar values of NO binding energies to [Fe (II)-hemeH] (+) and [Fe (III)-heme] (+), equal to 140 and 144 kJ mol (-1), respectively. The kinetic study of the NO association reaction supports the equilibrium HCB data and reveals that the two species share very close rate constant values both for the forward and for the reverse reaction. These gas phase results diverge markedly from the kinetics and thermodynamic behavior of NO binding to iron(II)- and iron(III)-heme proteins and model complexes in solution. The requisite of either a very labile or a vacant coordination site on iron for a facile addition of NO to occur, suggested to explain the bias for typically five-coordinate iron(II) species in solution, is fully supported by the present work.

Protonated Heme

The ions formally corresponding to protonated heme [Fe(II)-hemeH](+) have been obtained by collision-induced dissociation from the electrospray ionization of microperoxidase (MP11) and their gas-phase chemistry has been studied by FTICR mass spectrometry. H/D-exchange reactions, used as a tool to gain information on the protonation sites in polyfunctional molecules, show that labile hydrogens pertain to the propionyl substituents at the periphery of the protoporphyrin IX. Several conceivable isomers for protonated heme have been evaluated by density functional theory. The most stable among the species investigated is the one corresponding to protonation at the beta carbon atom of a vinyl group, yielding a proton affinity (PA) value for [Fe(II)-heme] of 1220 kJ mol(-1). This high PA is consistent with the inertness of the hydrogen atoms at the protonation site towards H/D exchange with ND(3) and CD(3)CO(2)D. Peculiar features of this [Fe(II)-hemeH](+) isomer emerge by analysis of its electronic structure, showing that the vinyl group undergoing formal protonation has gained significant radical character due to electron transfer from the metal center. As a consequence, the iron atom acquires partial iron(III) character and none of the two formal descriptions [Fe(II)-hemeH(+)] and [Fe(III)-hemeH(.)](+) alone may adequately illustrate the protonated heme ion. In agreement with this description, the reactivity of protonated heme presents dual facets, resembling iron(III) in some aspects and iron(II) in others. On the one hand, protonated heme behaves like [Fe(III)-heme](+) ions in H/D-exchange reactions. On the other, it shows markedly decreased reactivity towards the addition of ligands with the notable exception of NO, in line with the high affinity shown by iron(II) complexes towards this molecule, NO, of key biological role.

Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation

A method for calculating the electron-transfer matrix element V(RP) using density functional theory Kohn-Sham orbitals is presented and applied to heme dimers of varying relative orientation. The electronic coupling decays with increased iron separation according to V(RP) = V(0)(RP)exp(-beta r/2) with a distance dependence parameter beta approximately 2 A(-1) for hemes with parallel porphyrins and either 1.1 or 4.0 A(-1) when the porphyrin planes are perpendicular, depending on the alignment of the iron d(pi) orbital. These findings are used to interpret the observed orientation of the hemes in tetraheme redox proteins such as Flavocytochrome c(3) fumarate reductase (Ifc(3), PDB code 1QJD) of Shewanella frigidimarina, another flavocytochrome from the same bacterium (Fcc(3), 1E39) and a small tetraheme cytochrome of Shewanella oneidensis strain MR1 (1M1P). Our results show that shifting and rotating the hemes controls the adiabaticity of the three electron hopping steps.

Correlated ab Initio Study of the Excited State of the Iron-Coordinated-Mode Noninnocent Glyoxalbis(mercaptoanil) Ligand

The intriguing and theoretically unresolved magnetic coupling in the Fe(gma)CN (1) compound [gma = glyoxalbis(mercaptoanil)] has been investigated by means of first-principle correlated ab initio calculations. The low-energy spectrum of the complex has been studied using the difference dedicated configuration interaction method, which is a dynamically correlated multiconfigurational method. In agreement with available spectroscopic information, we found that the ground-state doublet is dominated by the coupling between an iron-centered quartet and the first excited triplet on the gma ligand. The open-shell character of the electronic structure of the ligand clarifies its noninnocent nature. The low-energy spectrum reveals the presence of a first excited quartet of different symmetry lying 200 cm(-1) above. The lowest excitation energy in the ground-state symmetry is found at 4790 cm(-1), thus ruling out the simple description of the system based on a Heisenberg Hamiltonian.

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.

Computational studies on imidazole heme conformations

Density functional theory computations of heme with ionized propionic acid groups, axially coordinated with two imidazoles, were performed for different mutual orientations of the imidazole planes. Environmental influences from water or protein were considered with a continuum dielectric medium by solving the Poisson equation. In vacuum, optimized geometries yielded imidazole-heme conformations where the NH groups of imidazoles are oriented toward the heme propionic groups in agreement with data from crystal structures of heme proteins. Conformational free-energy dependencies of the mutual orientation of axially ligated imidazoles calculated in protein (epsilon=10) and water (epsilon=80) environments confirmed the vacuum results, albeit the energy difference between the preferred and the 180 degrees opposite orientations of the imidazole ligand decreased from 3.84 kcal/mol in vacuum to 2.35 and 2.40 kcal/mol in protein and water, respectively. Two main factors determine the imidazole orientation: (1) the direct intramolecular electrostatic interactions of propionic groups with the polar NH groups of imidazole and (2) the electrostatic interaction of the total dipole moment of the imidazole-heme complex with the reaction field. In vacuum, only the first type of interaction is present, while in a dielectric medium the latter effect becomes competitive at high dielectric constant, resulting in a decrease of the orientational preference. Interestingly, the orientational preference of the imidazole axially ligated to heme becomes even more pronounced, if the negatively charged propionates are neutralized by counter charges that mimic salt bridges or protonation of the propionates.

The performance of nonhybrid density functionals for calculating the structures and spin states of Fe(II) and Fe(III) complexes

The local density approximation and a range of nonhybrid gradient corrected density functionals (PW91, BLYP, PBE, revPBE, RPBE) have been assessed with respect to the prediction of geometries and spin-state energy preferences for a range of homoleptic Fe(II)L6 and Fe(III)L6 complexes, where L = Cl-, CN-, NH3, pyridine, imidazole, H2O, O=CH2 and tetrahydrofuran. While the qualitative spin-state energies from in vacuo structure optimizations are reasonable the geometries are relatively poorly treated, especially for [FeCl6]3-/4-. Structural results for all the complexes are significantly improved by including environmental effects. The best compromise between structural and spin-state predictive accuracy was obtained for the RPBE functional in combination with the COSMO solvation approach. This approach systematically overestimates the energetic preference for a low spin state, which is partly due to the well-known effect of the lack of exact exchange in nonhybrid functionals and partly due to the larger solvation stabilization of low-spin complexes that have shorter bond lengths and thus smaller molecular volumes than their high-spin partners. Calculations on low spin [Fe(bipy)3]2+ and [Fe(phen)3]2+ and their ortho methyl substituted analogs, which are high spin at room temperature but cross over to low spin at low temperature, suggest the RPBE/COSMO combination generates low spin states which are too stable by approximately 13 kcal mol(-1).

Spin and charge distribution in iron porphyrin models: A coupled cluster and density-functional study

We recently performed detailed analyses of the electronic structure of low-spin iron porphyrins using density-functional theory (DFT). Both the spin-density distributions of the oxidized, ferric forms, as well as the changes in total charge density upon reduction to the ferrous forms have been explored. Here, we compare the DFT results with wave-function theory, more specifically, with the approximate singles and doubles coupled-cluster method (CC2). Different spin states are considered by studying representative models of low spin, intermediate spin, and high spin species. The CC2 calculations corroborate the DFT results; the spin density exhibits the same amount of molecular spin polarization, and the charge delocalization is of comparable magnitude. Slight differences in the descriptions are noted and discussed.