Equilibrium Geometries and Electronic Structure of Iron−Porphyrin Complexes: A Density Functional Study

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.

Identification of catalytic sites for oxygen reduction in iron- and nitrogen-doped graphene materials

While platinum has hitherto been the element of choice for catalysing oxygen electroreduction in acidic polymer fuel cells, tremendous progress has been reported for pyrolysed Fe-N-C materials. However, the structure of their active sites has remained elusive, delaying further advance. Here, we synthesized Fe-N-C materials quasi-free of crystallographic iron structures after argon or ammonia pyrolysis. These materials exhibit nearly identical Mössbauer spectra and identical X-ray absorption near-edge spectroscopy (XANES) spectra, revealing the same Fe-centred moieties. However, the much higher activity and basicity of NH3-pyrolysed Fe-N-C materials demonstrates that the turnover frequency of Fe-centred moieties depends on the physico-chemical properties of the support. Following a thorough XANES analysis, the detailed structures of two FeN4 porphyrinic architectures with different O2 adsorption modes were then identified. These porphyrinic moieties are not easily integrated in graphene sheets, in contrast with Fe-centred moieties assumed hitherto for pyrolysed Fe-N-C materials. These new insights open the path to bottom-up synthesis approaches and studies on site-support interactions.

Role of Spin States in Nitric Oxide Binding to Cobalt(II) and Manganese(II) Porphyrins. Is Tighter Binding Always Stronger?

Binding of nitric oxide (NO) to metalloporphyrins and heme groups is important in biochemistry while challenging to describe accurately by density functional theory (DFT) calculations. Here, the structural and thermochemical aspect of NO binding to Co(II) and Mn(II) porphyrins is investigated by DFT and DFT-D (dispersion-corrected) calculations, supported by reliable coupled-cluster methodology (CCSD(T)), and critically correlated with the experimental data. It is argued that whereas the bonding of NO to Co(II) porphyrin is a simple radical recombination, the bonding of NO to Mn(II) porphyrin is accompanied by a crossing of spin states. For this reason, the spin-state conversion energy contributes to the Mn-NO bond energy, and the paradigmatic correlation between bond length and bond energy is violated for the considered nitrosyl complexes: the Mn-NO bond is (structurally) shorter by ∼0.2 Å, albeit (energetically) weaker by a few kcal/mol, compared with the Co-NO bond. Moreover, none of the many tested DFT methods can reproduce the Co-NO and Mn-NO bond energies simultaneously, except for calculations with B3LYP*-D3, TPSSh-D3, and M06-D3 methods supplemented with the proposed spin-state energy correction (to compensate for an error on the calculated spin-state conversion energy). The results of this study are important to appreciate the role of spin-state changes in ligand binding properties of heme-related models. They also highlight the need for accurate calculations for correct interpretation of experimental data, including the qualitative structure-energy relationship.

Geometric and electronic structures of five-coordinate manganese(ii) “picket fence” porphyrin complexes

The X-ray structural investigation rationalized the variable axial ligand distances. EPR revealed five resonance positions and the simulations gave reasonable zero field splitting parameters.

Observation in the gas phase of the ligation of 1-methylimidazole to hemoprotein mimics

Hemoprotein mimics, cobalt picket fence porphyrins have been prepared in the gas phase as neutral molecules for the first time. Their ligation properties have been studied with 1-methylimidazole and compared with those of other cobalt porphyrins, tetraphenyl porphyrin, and cobalt protoporphyrin IX chloride, in view of studying the sterical properties of the ligation. It is shown that the cobalt picket fence porphyrin can only accept one 1-methylimidazole ligand in contrast to less sterically crowded porphyrins like cobalt tetraphenylporphyrin that present two accessible ligation sites. The femtosecond dynamics of these ligated systems have been studied after excitation at 400 nm, in comparison with the unligated ones. The observed transients are formed in much shorter times, 30 fs for the ligated species, as compared to free species (100 fs), supporting the porphyrin to metal charge transfer nature of these transients. The similar decays of the ligated transients <1 ps reveal the absence of photodissociation of the cobalt-1-methylimidazole bond at this step of evolution.

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks

BACKGROUND

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled.

METHODS

All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics.

RESULTS

Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites.

CONCLUSIONS

Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion.

GENERAL SIGNIFICANCE

Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Revisiting the role of exact exchange in DFT spin-state energetics of transition metal complexes

Sensitivity of DFT spin-state energetics to exact exchange is rooted in the description of metal–ligand bonding.

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.

Symmetry-induced quantum interference effects in metalloporphyrin wires

We calculate the electronic and transport properties of a series of metalloporphyrin molecules sandwiched between gold electrodes using a combination of density functional theory and scattering theory. The impact of strong correlations at the central metallic atom is gauged by comparing our results obtained using conventional DFT and DFT + U approaches. The zero- and finite-bias transport properties may or may not show spin-filtering behavior, depending on the nature of the d state closest to the Fermi energy. The type of d state depends on the metallic atom and gives rise to interference effects that produce different Fano features. The inclusion of the U term opens a gap between the d states and changes the conductance and spin-filtering behavior qualitatively in some of the molecules. We explain the origin of the quantum interference effects found as due to the symmetry-dependent coupling between the d states and other molecular orbitals and propose the use of these systems as nanoscale chemical sensors. We also demonstrate that an adequate treatment of strong correlations is really necessary to correctly describe the transport properties of metalloporphyrins and similar molecular magnets.

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.

Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin

The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane-wave pseudopotential framework; however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate-ligated Cpd I is performed using several generalized-gradient approximation (GGA) functionals in the Martins-Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized-basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.

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.

Small ligand-globin interactions: reviewing lessons derived from computer simulation

In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin

High-valent oxo-metal complexes exhibit correlated electronic behavior on dense, low-lying electronic state manifolds, presenting challenging systems for electronic structure methods. Among these species, the iron-oxo (IV) porphyrin denoted Compound I occupies a privileged position, serving a broad spectrum of catalytic roles. The most reactive members of this family bear a thiolate axial ligand, exhibiting high activity toward molecular oxygen activation and substrate oxidation. The default approach to such systems has entailed the use of hybrid density functionals or multi-configurational/multireference methods to treat electronic correlation. An alternative approach is presented based on the GGA+U approximation to density functional theory, in which a generalized gradient approximation (GGA) functional is supplemented with a localization correction to treat on-site correlation as inspired by the Hubbard model. The electronic structure of thiolate-ligated iron-oxo (IV) porphyrin and corresponding Coulomb repulsion U are determined both empirically and self-consistently, yielding spin-distributions, state level splittings, and electronic densities of states consistent with prior hybrid functional calculations. Comparison of this detailed electronic structure with model Hamiltonian calculations suggests that the localized 3d iron moments induce correlation in the surrounding electron gas, strengthening local moment formation. This behavior is analogous to strongly correlated electronic systems such as Mott insulators, in which the GGA+U scheme serves as an effective single-particle representation for the full, correlated many-body problem.

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.

Weak coordination of neutral S- and O-donor proximal ligands to a ferrous porphyrin nitrosyl. Characterization of 6-coordinate complexes at low T

The interaction of the S- and O-donor ligands tetrahydrothiophen (THT) and tetrahydrofuran (THF) with the ferrous nitrosyl complex Fe(TTP)(NO) (TTP(2-) is meso-tetra-p-tolyl-porphyrinatodianion) was studied at various temperatures both in solid state and solution using electronic and infrared absorption spectroscopy. Upon addition of these ligands to a cryostat containing sublimed layers of Fe(TTP)(NO), no complex formation was detected at room temperature. However, upon lowering the temperature, spectral changes were observed that are consistent with ligand binding in axial position trans to the NO (the proximal site) and formation of the six-coordinate adducts. Analogous behavior was observed in solution. In both media, the six-coordinate adducts are stable only at low temperature and dissociate to the 5-coordinate nitrosyl complexes upon warming. The NO stretching frequencies of the six-coordinate thioether and ether complexes were recorded and binding constants for the weak bonding of proximal THF and THT ligands were determined from the spectral changes. These parameters are compared with those obtained for the N-donor ligand pyrrolidine.

Oxygen migration pathways in NO-bound truncated hemoglobin

Atomistic simulations of dioxygen (O(2)) dynamics and migration in nitric oxide-bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O(2) ligand is built and analyzed. It is found that channel I is the primary entrance point for O(2) whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O(2) a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O(2) can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O(2) docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a "hub" and free energy barriers between the different metastable states are ≈1.5 kcal mol(-1) which allows facile O(2) migration within the protein.

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.

Catalases versus peroxidases: DFT investigation of H₂O₂ oxidation in models systems and implications for heme protein engineering

Catalases and peroxidases are ubiquitous heme enzymes that catalyze the removal of hydrogen peroxide (H(2)O(2)). Both enzymes use one molecule of hydrogen peroxide to form a high valent iron intermediate named Compound I (Cpd I). However, whereas catalase Cpd I oxidizes a second H(2)O(2) molecule to oxygen, peroxidases use this intermediate to oxidize other substrates rather than H(2)O(2). The origin of the different reactivity of peroxidases and catalases is not known, but it is likely to be related to structural differences between the two heme active sites. Recent modeling studies suggest that the oxidation of H(2)O(2) by catalase Cpd I may take place by two hydrogen atom transfer steps. In this work, we investigate how catalases and peroxidases compare along the same hydrogen transfer steps to give hints into the question why peroxidases cannot efficiently oxidize H(2)O(2). The use of simplified models allows us to probe the direct effect of the proximal ligand (tyrosinate in catalases and histidine in peroxidases) without masking from the protein environment. We show that the nature of the fifth ligand (His in peroxidase and Tyr in catalase) has little effect on the energy barriers of the hydrogen transfer steps. On the contrary, the Cpd I-hydrogen peroxide (O(Fe)-O(peroxide)) distance affects significantly the reaction barriers. We propose that the distal side architecture of peroxidases do not allow to attain short O(Cpd I)-O(peroxide) distances, thus resulting in a lower efficiency towards H(2)O(2) oxidation.

Ambidentate H-bonding of NO and O2 in heme proteins

The affinity and reactivity of the gaseous molecules CO, NO and O(2) (XO) in heme protein adducts are controlled by secondary interactions, especially by H-bonds donated from distal protein residues. Vibrational spectroscopy, supported by DFT (Density Functional Theory) modeling, has revealed that for NO and O(2), but not for CO, a critical issue is whether the H-bond is donated to the outer or inner atom of the bound diatomic ligand. DFT modeling shows that bound NO and O(2) are ambidentate, both atoms separately acting as H-bond acceptors. This is not the case for CO, whose π* orbital acts as a delocalized H-bond acceptor. Vibrational spectra of heme-XO adducts reveal a general pattern of backbonding variations, marked by families of negative correlations between frequencies associated with FeX and XO bond stretches. For heme-CO adducts, H-bonding increases backbonding, the νFeX/νXO points moving up the backbonding correlation established with model compounds. For NO and O(2) adducts, however, increased backbonding is only observed when the outer atom is the H-bond acceptor. H-bonding to the inner (X) atom instead produces a positive νFeX/νXO correlation. This effect can be reproduced by DFT modeling. Its mechanism is polarization of the sp(2) orbital on the X atom, on the back side of the bent FeXO unit, drawing electrons from both the FeX and XO bonds and weakening them together. Thus, the positioning of H-bond donors in the protein differentially affects bonding and reactivity in heme adducts of NO and O(2).

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).

NMR, IR, Mössbauer and quantum chemical investigations of metalloporphyrins and metalloproteins

We review contributions made towards the elucidation of CO and O2binding geometries in respiratory proteins. Nuclear magnetic resonance, infrared spectroscopy, Mössbauer spectroscopy, X-ray crystallography and quantum chemistry have all been used to investigate the Fe –ligand interactions. Early experimental results showed linear correlations between17O chemical shifts and the infrared stretching frequency (νCO) of the CO ligand in carbonmonoxyheme proteins and between the17O chemical shift and the13CO shift. These correlations led to early theoretical investigations of the vibrational frequency of carbon monoxide and of the13C and17O NMR chemical shifts in the presence of uniform and non-uniform electric fields. Early success in modeling these spectroscopic observables then led to the use of computational methods, in conjunction with experiment, to evaluate ligand-binding geometries in heme proteins. Density functional theory results are described which predict57Fe chemical shifts and Mössbauer electric field gradient tensors,17O NMR isotropic chemical shifts, chemical shift tensors and nuclear quadrupole coupling constants (e2qQ/h) as well as13C isotropic chemical shifts and chemical shift tensors in organometallic clusters, heme model metalloporphyrins and in metalloproteins. A principal result is that CO in most heme proteins has an essentially linear and untilted geometry (τ = 4 °, β = 7 °) which is in extremely good agreement with a recently published X-ray synchrotron structure. CO / O2discrimination is thus attributable to polar interactions with the distal histidine residue, rather than major Fe–C–O geometric distortions.

Steric contributions to CO binding in heme proteins: a density functional analysis of FeCO vibrations and deformability

Non-local Density Functional Theory (DFT) is applied to the calculation of geometry and vibrational frequencies of FeII (porphine)(imidazole)(CO), a model for CO adducts of heme proteins. Bond distances and angles are in agreement with crystallographic data, and frequencies are correctly calculated for C–O and Fe–C stretching and for Fe–C - O bending. This last mode is actually the out-of-phase combination of Fe–C–O bending and Fe–C tilting coordinates, which are heavily mixed because of a large bend–tilt interaction force constant. The in-phase combination is predicted at a very low frequency, 73 cm-1, and to have a low infrared intensity; attempts to detect it in far-IR spectra via 13 C 18 O isotope sensitivity have been unsuccessful. The stretch–bend interaction lowers the energy required for FeCO distortion. A soft potential may account for the wide range of crystallographically determined Fe–C–O displacements and orientations in myoglobin ( Mb ). The minimum energy path for displacement of the O atom from the heme normal was calculated by relaxing the structure while constraining only the O atom displacement from the heme normal. Energies of 0.2 to 3.5 kcal mol-1 are required for the range of reported displacement, 0.3–1.3 Å. However, vibrational spectroscopy limits the allowable displacement to the low end of this range. The O atom displacement is computed via DFT to be 0.6 Å for a 7 ° angle of the C–O stretching IR dipole relative to the heme normal, the maximum value compatible with IR polarization measurements on MbCO . FeCO distortion is predicted to diminish both ν CO and ν FeC , thereby producing deviations from the well-established backbonding correlation; the scatter of the data permits a maximum displacement of 0.5 Å. This displacement would cost about 1.6 kcal mol-1 of steric energy. A small distortion energy is consistent with the CO affinity changes produced by mutations of the distal histidine residue in Mb . Taking the leucine mutant as reference, we estimate the 1.6 kcal mol-1 affinity loss in the wild-type protein to be the resultant of a 0.0–1.6 kcal steric inhibition, a 0.5 kcal mol-1 attraction of the distal histidine sidechain for the bound CO [weak H -bond], and a 0.5–2.1 kcal mol-1 attraction of the same side-chain for a water molecule in the deoxy protein. The observed 2.3 kcal mol-1 O 2 affinity increase in the wild-type protein relative to the leucine mutant then implies a 2.8–4.4 kcal mol-1 attraction of the histidine sidechain for bound O 2, consistent with a substantial H -bond interaction with the distal histidine. Thus steric inhibition can account for only a minor fraction of the discrimination factor against CO and in favor of O 2 which is produced by the heme–myoglobin interaction.

Z-scan studies and quantum chemical calculations of meso-tetrakis(p-sulfonatophenyl)porphyrin and meso-tetrakis(4-N-methyl-pyridiniumyl)porphyrin and their Fe(III) and Mn(III) complexes

Optical self-defocusing, characterized by the non-linear refractive index n2, was investigated by the Z-scan technique in water solutions of two porphyrins (PPhs), negatively charged meso-tetrakis(p-sulfonatophenyl)porphyrin ( TPPS 4) and positively charged meso-tetrakis(4-N-methyl-pyridiniumyl)porphyrin ( TMPyP ), in their free base forms and as Fe (III) and Mn (III) complexes. Significant n2 values were observed only for the TMPyP metal complexes, while for the other porphyrins the n2 values were negligible. The effect is explained by the reorientation of the porphyrin molecule due to interaction of its permanent dipole moment perpendicular to the molecular ring plane with the electromagnetic field of the exciting light pulse. The permanent dipole moment is due to the shift of the metal atom out of the molecular plane. The electrostatic interaction between the metal atom and charged substituents increases (repulsion) or decreases (attraction) the shift of the metal atom and consequently affects the dipole moment value. Ligand binding to the metal atoms also increases the out-of-plane metal shift and hence the dipole moment and n2 value. pH changes were shown to modify the Fe (III)-ligand structure, thus changing n2. The experimental data correlate well with the metal shift and dipole moment values calculated for simplified PPh structures by the ZINDO method.

Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins

Density functional calculations have been used to compare the geometric, electronic, and functional properties of the three important tetrapyrrole systems in biology, heme, coenzyme B 12, and coenzyme F430, formed from iron porphyrin ( Por ), cobalt corrin ( Cor ), and nickel hydrocorphin ( Hcor ). The results show that the flexibility of the ring systems follows the trend Hcor > Cor > Por and that the size of the central cavity follows the trend Cor < Por < Hcor . Therefore, low-spin Co I, Co II, and Co III fit well into the Cor ring, whereas Por seems to be more ideal for the higher spin states of iron, and the cavity in Hcor is tailored for the larger Ni ion, especially in the high-spin Ni II state. This is confirmed by the thermodynamic stabilities of the various combinations of metals and ring systems. Reduction potentials indicate that the +I and +III states are less stable for Ni than for the other metal ions. Moreover, Ni – C bonds are appreciably less stable than Co - C bonds. However, it is still possible that a Ni – CH 3 bond is formed in F 430 by a heterolytic methyl transfer reaction, provided that the donor is appropriate, e.g. if coenzyme M is protonated. This can be facilitated by the adjacent SO 3− group in this coenzyme and by the axial glutamine ligand, which stabilizes the Ni III state. Our results also show that a Ni III– CH 3 complex is readily hydrolysed to form a methane molecule and that the Ni III hydrolysis product can oxidize coenzyme B and M to a heterodisulphide in the reaction mechanism of methyl coenzyme M reductase.