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

Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase

The transsulfuration pathway plays a key role in mammals for maintaining the balance between cysteine and homocysteine, whose concentrations are critical in several biochemical processes. Human cystathionine β-synthase is a heme-containing, pyridoxal 5'-phosphate (PLP)-dependent enzyme found in this pathway. The heme group does not participate directly in catalysis, but has a regulatory function, whereby CO or NO binding inhibits the PLP-dependent reactions. In this study, we explore the detailed structural changes responsible for inhibition using quantum chemical calculations to validate the experimentally observed bonding patterns associated with heme CO and NO binding and molecular dynamics simulations to explore the medium-range structural changes triggered by gas binding and propagating to the PLP active site, which is more than 20 Å distant from the heme group. Our results support a previously proposed mechanical signaling model, whereby the cysteine decoordination associated with gas ligand binding leads to breaking of a hydrogen bond with an arginine residue on a neighbouring helix. In turn, this leads to a shift in position of the helix, and hence also of the PLP cofactor, ultimately disrupting a key hydrogen bond that stabilizes the PLP in its catalytically active form.

Mechanism of Peroxynitrite Interaction with Ferric M. tuberculosis Nitrobindin: A Computational Study

Nitrobindins (Nbs) are all-β-barrel heme proteins present along the evolutionary ladder. They display a highly solvent-exposed ferric heme group with the iron atom being coordinated by the proximal His residue and a water molecule at the distal position. Ferric nitrobindins (Nb(III)) play a role in the conversion of toxic peroxynitrite (ONOO-) to harmless nitrate, with the value of the second-order rate constant being similar to those of most heme proteins. The value of the second-order rate constant of Nbs increases as the pH decreases; this suggests that Nb(III) preferentially reacts with peroxynitrous acid (ONOOH), although ONOO- is more nucleophilic. In this work, we shed light on the molecular basis of the ONOO- and ONOOH reactivity of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) by dissecting the ligand migration toward the active site, the water molecule release, and the ligand binding process by computer simulations. Classical molecular dynamics simulations were performed by employing a steered molecular dynamics approach and the Jarzynski equality to obtain ligand migration free energy profiles for both ONOO- and ONOOH. Our results indicate that ONOO- and ONOOH migration is almost unhindered, consistent with the exposed metal center of Mt-Nb(III). To further analyze the ligand binding process, we computed potential energy profiles for the displacement of the Fe(III)-coordinated water molecule using a hybrid QM/MM scheme at the DFT level and a nudged elastic band approach. These results indicate that ONOO- exhibits a much larger barrier for ligand displacement than ONOOH, suggesting that water displacement is assisted by protonation of the leaving group by the incoming ONOOH.

Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation

Nitrobindins (Nbs) represent an evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom, coordinated by a proximal His residue. Interestingly, even if the distal side is exposed to the solvent, the value of the second order rate constants for ligand binding to the ferrous derivative is almost one order of magnitude lower than those reported for myoglobins (Mbs). Noteworthy, nitric oxide binding to the sixth coordination position of the heme-Fe(II)-atom causes the cleavage or the severe weakening of the proximal His-Fe(II) bond. Here, we provide a computer simulation investigation to shed light on the molecular basis of ligand binding kinetics, by dissecting the ligand binding process into the ligand migration and the bond formation steps. Classical molecular dynamics simulations were performed employing a steered molecular dynamics approach and the Jarzinski equality to obtain ligand migration free energy profiles. The formation of the heme-Fe(II)-NO bond took into consideration the iron atom displacement from the heme plane. The ligand migration is almost unhindered, and the low rate constant for NO binding is due to the large displacement of the Fe(II) atom with respect to the heme plane responsible for the barrier for the Fe(II)-NO bond formation. In addition, we investigated the weakening and breaking of the proximal His-Fe(II) bond, observed experimentally upon NO binding, by means of a combination of classical molecular dynamics simulations and quantum-classical (QM-MM) optimizations. In both human and M. tuberculosis Nbs, a stable alternative conformation of the proximal His residue interacting with a network of water molecules was observed.

Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin

Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pK_a values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.

Electron Correlation in the Iron(II) Porphyrin by Natural Orbital Functional Approximations

The relative stability of the singlet, triplet, and quintet spin states of iron(II) porphyrin (FeP) represents a challenging problem for electronic structure methods. While it is currently accepted that the ground state is a triplet, multiconfigurational wave function-based methods predict a quintet, and density functional approximations vary between triplet and quintet states, leading to a prediction that highly depends on the features of the method employed. The recently proposed Global Natural Orbital Functional (GNOF) aims to provide a balanced treatment between static and dynamic correlation, and together with the previous Piris Natural Orbital Functionals (PNOFs), allowed us to explore the importance of each type of correlation in the stability order of the states of FeP with a method that conserves the spin of the system. It is noteworthy that GNOF correlates all electrons in all available orbitals for a given basis set; in the case of the FeP with a double-ζ basis set as used in this work, this means that GNOF can properly correlate 186 electrons in 465 orbitals, significantly increasing the sizes of systems amenable to multiconfigurational treatment. Results show that PNOF5, PNOF7s, and PNOF7 predict the quintet to have a lower energy than the triplet state; however, the addition of dynamic correlation via second-order Møller-Plesset corrections (NOF-MP2) turns the triplet state to be lower than the quintet state, a prediction also reproduced by GNOF that incorporates much more dynamic correlation than its predecessors.

Reliably assessing the electronic structure of cytochrome P450 on today's classical computers and tomorrow's quantum computers

Chemical simulation is one of the most promising applications for future quantum computers. It is thought that quantum computers may enable accurate simulation for complex molecules that are otherwise impossible to simulate classically; that is, it displays quantum advantage. To better understand quantum advantage in chemical simulation, we explore what quantum and classical resources are required to simulate a series of pharmaceutically relevant molecules. Using classical methods, we show that reliable classical simulation of these molecules requires significant resources and therefore is a promising candidate for quantum simulation. We estimate the quantum resources, both in overall simulation time and the size. The insights from this study pave the way for future quantum simulation of complex molecules.

An accurate assessment of how quantum computers can be used for chemical simulation, especially their potential computational advantages, provides important context on how to deploy these future devices. To perform this assessment reliably, quantum resource estimates must be coupled with classical computations attempting to answer relevant chemical questions and to define the classical algorithms simulation frontier. Herein, we explore the quantum computation and classical computation resources required to assess the electronic structure of cytochrome P450 enzymes (CYPs) and thus define a classical–quantum advantage boundary. This is accomplished by analyzing the convergence of density matrix renormalization group plus n-electron valence state perturbation theory (DMRG+NEVPT2) and coupled-cluster singles doubles with noniterative triples [CCSD(T)] calculations for spin gaps in models of the CYP catalytic cycle that indicate multireference character. The quantum resources required to perform phase estimation using qubitized quantum walks are calculated for the same systems. Compilation into the surface code provides runtime estimates to compare directly to DMRG runtimes and to evaluate potential quantum advantage. Both classical and quantum resource estimates suggest that simulation of CYP models at scales large enough to balance dynamic and multiconfigurational electron correlation has the potential to be a quantum advantage problem and emphasizes the important interplay between classical computations and quantum algorithms development for chemical simulation.

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.

Revisiting the Orbital Energy-Dependent Regularization of Orbital-Optimized Second-Order Møller-Plesset Theory

Optimizing orbitals in the presence of electron correlation, as in orbital-optimized second-order Møller-Plesset perturbation theory (OOMP2), can remove artifacts associated with mean-field orbitals such as spin contamination and artificial symmetry-breaking. However, OOMP2 is known to suffer from divergent correlation energies in regimes of small orbital energy gaps. To address this issue, several approaches to amplitude regularization have been explored, with those featuring energy-gap-dependent regularizers appearing to be most transferable and physically justifiable. For instance, κ-OOMP2 was shown to address the energy divergence issue in, for example, bond-breaking processes while offering a significant improvement in accuracy for the W4-11 thermochemistry data set, and a parameter of κ = 1.45 was recommended. A more recent investigation of regularized MP2 with Hartree-Fock orbitals revealed that stronger regularization (i.e., smaller values of κ) than what had previously been recommended for κ-OOMP2 may offer huge improvements in certain cases such as noncovalent interactions while retaining a high level of accuracy for main-group thermochemistry data sets. In this study, we investigate the transferability of those findings to κ-OOMP2 and assess the implications of stronger regularization on the ability of κ-OOMP2 to diagnose strong static correlation. We found similar results using κ-OOMP2 for several main-group thermochemistry, barrier height, and noncovalent interaction data sets including both closed shell and open shell species. However, stronger regularization yielded substantially higher accuracy for open-shell transition-metal (TM) thermochemistry and is necessary to provide qualitatively correct spin symmetry breaking behavior for several large and electrochemically relevant TM systems. We therefore find a single κ value insufficient to treat all systems using κ-OOMP2.

On the Sensitivity to Density-Functional Approximations for CO Binding Energies of Single-Atom Catalysts in Nitrogen-Doped Graphene

Density functional theory (DFT) methods are the working horse in screening new catalytic materials. They are widely used to predict trends in binding energies, which are then used to compare the activity of different materials. The binding strength of CO is an important descriptor to the CO₂ reduction catalytic activity of the single transition metal atoms embedded on nitrogen-doped graphene (TM/NG). In this work, however, we show that CO binding strengths in different TM/NG has very different sensitivity to DFT methods. Specifically, Fe/NG CO binding energy changes dramatically with the percentage of exact exchange in the functional; Co/NG does less so, while Ni/NG nearly has no change. Such varying behaviors is a direct result of different local spin configurations, similar to the performance of DFT methods for metal porphyrin complexes. Therefore, caution should be exercised when using DFT binding energies for quantitative predictions in TM/NG single atom catalysis.

Insights into the effect of distal histidine and water hydrogen bonding on NO ligation to ferrous and ferric heme: a DFT study

The effect of distal histidine on ligation of NO to ferrous and ferric-heme, has been investigated with the high-level density functional theoretical (DFT) method. It has been predicted that the distal histidine significantly stabilizes the interaction of NO ferrous-heme (by −2.70 kcal mol⁻¹). Also, water hydrogen bonding is quite effective in strengthening the Fe–NO bond in ferrous heme. In contrast in ferric heme, due to the large distance between the H₂O and O(NO) and lack of hydrogen bonding, the distal histidine exhibits only a slight effect on the binding of NO to the ferric analogue. Concerning the bond nature of Fe^II–NO and Fe^III–NO in heme, a QTAIM analysis predicts a partially covalent and ionic bond nature in both systems.

The effect of distal histidine on ligation of NO to ferrous and ferric-heme, has been investigated with the high-level density functional theoretical (DFT) method.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

An out of box thinking: the changes of iron-porphyrin during meat processing and gastrointestinal tract and some methods for reducing its potential health hazard

Iron-porphyrin is a very important substance in organisms, especially in animals. It is not only the source of iron in human body, but is also the catalytic center of many reactions. Previous studies suggested that adequate intake of iron was important for the health of human, especially for children and pregnant women. However, associated diseases caused by iron over-intake and excessive meat consumption suggested its potential harmfulness for human health. During meat processing, Iron-porphyrin will cause the oxidation of proteins and fatty acids. In the gastrointestinal tract, iron-porphyrin can induce the production of malondialdehyde, fats oxidation, and indirectly cause oxidation of amino acids and nitrates etc. Iron-porphyrin enters the intestinal tract and disturbs the balance of intestinal flora. Finally, some common measures for inhibiting its activity are introduced, including the use of chelating agent, antioxidants, competitive inhibitor, etc., as well as give the hypothesis that sodium chloride increases the catalytic activity of iron-porphyrin. The purpose of this review is to present an overview of current knowledge about the changes of iron-porphyrin in the whole technico- and gastrointesto- processing axis and to provide ideas for further research in meat nutrition.

A detailed analysis of the spin-crossover reaction of H2S binding to heme and the six-coordinated FeP(Im)-HS- porphyrin complex

The potential energy surfaces of the H₂S binding to iron-porphyrin (FeP) with the imidazole (Im) ligand via intersystem crossings are investigated by using density functional theory. The minimum energy intersystem crossing point (MEISCP) between the quintet and triplet states (MEISCP_TQ) for the Fe(II)P(Im)-H₂S complex is located at a Fe-S distance of 3.39 Å with only 1.1 kcal/mol above the quintet state minimum. The second spin-crossover point, where a change from the triplet to the singlet state occurs, comes at a much shorter Fe-S distance of 2.79 Å, and the MEISCP_ST is located at 3.7 kcal/mol above the triplet state minimum. The nature of the chemical bonding along the Fe-S reaction coordinate from the ground state singlet to the quintet state along the path to the separated species is analyzed. An inspection of the vibrational modes reveals that the largest contribution to the triplet-quintet transition around the quintet and triplet state minimum comes from the symmetric shrinking of the pyrrole units of the porphyrin ring, indicating that the related reaction coordinate plays a main role in the intersystem crossing. The fully optimized structures of the Fe(II)P(Im)-HS^- complex corresponding to three different spin multiplicities (M = 1, 3, 5) are characterized by a bent Fe-H-S conformation. The binding of the hydrosulfide anion to Fe(II)P(Im) in the quintet state induces a 0.2 Å displacement of the Fe atom out of the nitrogen porphyrin (N_pyr) plane. The fully optimized structure of the ground state of Fe(II)P(Im)-HS^- agrees well with experimental data for the corresponding heme models.

Second-order MCSCF optimization revisited. I. Improved algorithms for fast and robust second-order CASSCF convergence

A new improved implementation of the second-order multiconfiguration self-consistent field optimization method of Werner and Knowles [J. Chem. Phys. 82, 5053 (1985)] is presented. It differs from the original method by more stable and efficient algorithms for minimizing the second-order energy approximation in the so-called microiterations. Conventionally, this proceeds by alternating optimizations of the orbitals and configuration (CI) coefficients and is linearly convergent. The most difficult part is the orbital optimization, which requires solving a system of nonlinear equations that are often strongly coupled. We present a much improved algorithm for solving this problem, using an iterative subspace method that includes part of the orbital Hessian explicitly, and discuss different strategies for performing the uncoupled optimization in a most efficient manner. Second, we present a new solver in which the orbital-CI coupling is treated explicitly. This leads to quadratic convergence of the microiterations but requires many additional evaluations of reduced (transition) density matrices. In difficult optimization problems with a strong coupling of the orbitals and CI coefficients, it leads to much improved convergence of both the macroiterations and the microiterations. Third, the orbital-CI coupling is treated approximately using a quasi-Newton approach with Broyden-Fletcher-Goldfarb-Shanno updates of the orbital Hessian. It is demonstrated that this converges almost as well as the explicitly coupled method but avoids the additional effort for computing many transition density matrices. The performance of the three methods is compared for a set of 21 aromatic molecules, an Fe(ii)-porphine transition metal complex, as well as for the [Cu₂O₂(NH₃)  ₆]²⁺, FeCl₃, Co₂(CO)₆C₂H₂, and Al₄O₂ complexes. In all cases, faster and more stable convergence than with the original implementation is achieved.

Local Energy Decomposition of Open-Shell Molecular Systems in the Domain-Based Local Pair Natural Orbital Coupled Cluster Framework

Local energy decomposition (LED) analysis decomposes the interaction energy between two fragments calculated at the domain-based local pair natural orbital CCSD(T) (DLPNO-CCSD(T)) level of theory into a series of chemically meaningful contributions and has found widespread applications in the study of noncovalent interactions. Herein, an extension of this scheme that allows for the analysis of interaction energies of open-shell molecular systems calculated at the UHF-DLPNO-CCSD(T) level is presented. The new scheme is illustrated through applications to the CH₂···X (X = He, Ne, Ar, Kr, and water) and heme···CO interactions in the low-lying singlet and triplet spin states. The results are used to discuss the mechanism that governs the change in the singlet–triplet energy gap of methylene and heme upon adduct formation.

Dynamic Characterization of the Human Heme Nitric Oxide/Oxygen (HNOX) Domain under the Influence of Diatomic Gaseous Ligands

Soluble guanylate cyclase (sGC) regulates numerous physiological processes. The β subunit Heme Nitric Oxide/Oxygen (HNOX) domain makes this protein sensitive to small gaseous ligands. The structural basis of the activation mechanism of sGC under the influence of ligands (NO, O₂, CO) is poorly understood. We examine the effect of different ligands on the human sGC HNOX domain. HNOX systems with gaseous ligands were generated and explored using Molecular Dynamics (MD). The distance between heme Fe²⁺ and histidine in the NO-ligated HNOX (NO-HNOX) system is larger compared to the O₂, CO systems. NO-HNOX rapidly adopts the conformation of the five-group metal coordination system. Loops α, β, γ and helix-f exhibit increased mobility and different hydrogen bond networks in NO-HNOX compared to the other systems. The removal of His from the Fe coordination sphere in NO-HNOX is assisted by interaction of the imidazole ring with the surrounding residues which in turn leads to the release of signaling helix-f and activation of the sGC enzyme. Insights into the conformational dynamics of a human sGC HNOX domain, especially for regions which are functionally critical for signal transduction, are valuable in the understanding of cardiovascular diseases.

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.

Applications of the Marcus cross relation to inner sphere reduction of O2: implications in small-molecule activation

The Marcus cross relation is demonstrated to be applicable to inner sphere electron transfer from iron to molecular oxygen by incorporation of the Fe(iii)–O₂to Fe(iii) + superoxide BDFE inK_eq. A few case-studies are provided as working examples.

Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins

With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.

The surprisingly high ligation energy of CO to ruthenium porphyrins

A combined theoretical and experimental approach has been used to investigate the binding energy of a ruthenium metalloporphyrin ligated with CO, ruthenium tetraphenylporphyrin [RuII TPP], in the RuII oxidation degree. Measurements performed with VUV ionization using the DESIRS beamline at Synchrotron SOLEIL led to adiabatic ionization energies of [RuII TPP] and its complex with CO, [RuII TPP-CO], of 6.48 ± 0.03 eV and 6.60 ± 0.03 eV, respectively, while the ion dissociation threshold of [RuII TPP-CO]+ is measured to be 8.36 ± 0.03 eV using the ground-state neutral complex. These experimental data are used to derive the binding energies of the CO ligand in neutral and cationic complexes (1.88 ± 0.06 eV and 1.76 ± 0.06 eV, respectively) using a Born-Haber cycle. Density functional theory calculations, in very satisfactory agreement with the experimental results, help to get insights into the metal-ligand bond. Notably, the high ligation energies can be rationalized in terms of the ruthenium orbital structure, which is singular compared to that of the iron atom. Thus, beyond indications of a strengthening of the Ru-CO bond due to the decrease in the CO vibrational frequency in the complex as compared to the Fe-CO bond, high-level calculations are essential to accurately describe the metal ligand (CO) bond and show that the Ru-CO bond energy is strongly affected by the splitting of triplet and singlet spin states in uncomplexed [Ru TPP].

Using porphyrin–amino acid pairs to model the electrochemistry of heme proteins: experimental and theoretical investigations

Deconstructing the complex electrochemistry of heme proteins into simpler heme–amino acid interactions.

The dioxygen adducts of iron and manganese porphyrins: electronic structure and binding energy

The electronic structures of adducts of O₂ and metal porphyrins were thoroughly investigated by highly accurate DMRG-CASPT2.

Hydration of iron-porphyrins: ab initio quantum mechanical charge field molecular dynamics simulation study

The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe²⁺-P and Fe³⁺-P in water to evaluate their structural, dynamical and energetic properties. Based on the structural data, it was found that Fe²⁺-P accommodates one water molecule in the first coordination sphere of the Fe²⁺ ion including the four nitrogen atoms of the porphyrin system coordinating with central metal species. On the other hand, two water molecules were coordinated to Fe³⁺-P, thus forming a hexa-coordinated species. Comparison of dynamical properties such as the vibrational power spectrum and ligand mean residence times to other metal-free porphyrin systems demonstrate the ions' influence on the hydration structure, enabling a characterisation of the strong interaction of the ions which greatly reduces the hydrogen bonding potential of the complex. The association of water molecules with the metal ions in both solutes was quantified by computing the free energy of binding obtained via the potential of mean force. This further confirmed the strong association of water to the metal ions which was conversely weak as inferred from the energetic data for the Fe²⁺-P system.

A unified understanding of the direct coordination of NO to first-transition-row metal centers in metal-ligand complexes

The binding of nitric oxide (NO) to heme-proteins is an important biochemical process involved in a variety of physiological functions. Here, using hybrid density-functional calculations, we systematically investigate the adsorption of NO to first-transition-row metal centers in metal-ligand complexes. Through the comparative study for different transition metal (TM) centers, we provide a unified understanding of the microscopic interactions of NO with the TM centers and related chemical trends. We found that as the atomic number of the TM center increases, the binding strength of NO is largely reduced from 207 kJ mol^-1 to near zero due to the low d-orbital energies for late TM centers. The intermolecular spin coupling between the localized spins at the TM center and the NO molecule is generally antiferromagnetic, except for the case of Sc. The spin-spin coupling is determined in such a way to avoid the energy penalty associated with the electron occupation in the antibonding states of the NO-bound complex. The adsorption strength of NO is generally larger than of CO because the unpaired electron of NO occupies the associated bonding state.

Cleavage mechanism of the aliphatic C–C bond catalyzed by 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP: a QM/MM study

Calculations suggest that the reactant complex may firstly undergo a triplet–quintet crossing to initiate the reaction and then the subsequent chemistry occurs on the multiple-states surfaces. The key C–C bond cleavage is accompanied by an insertion reaction of oxygen radical.

Six-Coordinate Ferrous Nitrosyl Complex FeII(TTP)(PMe3)(NO) (TTP = meso-Tetra-p-tolylporphyrinato Dianion)

Low-temperature in situ Fourier transform infrared and UV-vis measurements show that trimethylphosphine (PMe₃) reacts with microporous layers of Fe^II(TTP)(NO) (TTP = meso-tetra-p-tolylporphyrinato dianion; NO = nitric oxide) to form the previously unknown six-coordinate complex Fe^II(TTP)(PMe₃)(NO). Upon warming this compound to room temperature in the presence of excess phosphine, the NO ligand is completely replaced by phosphine, resulting in formation of the bis(trimethylphosphine) complex Fe^II(TTP)(PMe₃)₂. Simultaneously, the NO released oxidizes free PMe₃ to the corresponding phosphine oxide (OPMe₃) with concomitant formation of nitrous oxide (N₂O).

A mononuclear non-heme-iron dioxygen-carrying protein?

The ability of mononuclear non-heme iron complexes to function as molecular oxygen transporters is investigated by density functional theory. The factors governing the efficiency of the reversible binding of dioxygen at the active site of the dinuclear non-heme iron enzyme hemerythrin, including antiferromagnetic coupling and the conversion of dioxygen to hydroperoxo by a proton coupled 2-electron transfer mechanism, are revisited and considered as possible tools in mononuclear non-heme complexes. Several mononuclear non-heme model complexes, including active sites of enzymes already known to interact with dioxgenic ligands, are constructed and the molecular oxygen transportation capabilities of these complexes are examined computationally. The high-spin nature of the ground state of these complexes implies an intrinsic kinetic lability of the oxy structures, as also evident from potential energy surface calculations towards iron-dioxygen cleavage. Proton affinities as calibrated with reference compounds showed that these complexes are highly unlikely to undergo protonation to form hydroperoxo-like adducts. Mixed superoxo descriptions of the dissociated dioxygenic ligands in all complexes add to the overall conclusion that these model structures are significantly disadvantaged in any attempt to be employed for molecular oxygen transportation.

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.

Computation Sheds Insight into Iron Porphyrin Carbenes' Electronic Structure, Formation, and N-H Insertion Reactivity

Iron porphyrin carbenes constitute a new frontier of species with considerable synthetic potential. Exquisitely engineered myoglobin and cytochrome P450 enzymes can generate these complexes and facilitate the transformations they mediate. The current work harnesses density functional theoretical methods to provide insight into the electronic structure, formation, and N-H insertion reactivity of an iron porphyrin carbene, [Fe(Por)(SCH3)(CHCO2Et)](-), a model of a complex believed to exist in an experimentally studied artificial metalloenzyme. The ground state electronic structure of the terminal form of this complex is an open-shell singlet, with two antiferromagnetically coupled electrons residing on the iron center and carbene ligand. As we shall reveal, the bonding properties of [Fe(Por)(SCH3)(CHCO2Et)](-) are remarkably analogous to those of ferric heme superoxide complexes. The carbene forms by dinitrogen loss from ethyl diazoacetate. This reaction occurs preferentially through an open-shell singlet transition state: iron donates electron density to weaken the C-N bond undergoing cleavage. Once formed, the iron porphyrin carbene accomplishes N-H insertion via nucleophilic attack. The resulting ylide then rearranges, using an internal carbonyl base, to form an enol that leads to the product. The findings rationalize experimentally observed reactivity trends reported in artificial metalloenzymes employing iron porphyrin carbenes. Furthermore, these results suggest a possible expansion of enzymatic substrate scope, to include aliphatic amines. Thus, this work, among the first several computational explorations of these species, contributes insights and predictions to the surging interest in iron porphyrin carbenes and their synthetic potential.

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.

Local changes in arterial oxygen saturation induced by visible and near-infrared light radiation

In this study, we investigate the efficiency of laser radiation on oxyhemoglobin (HbO2) rate in blood vessels and its wavelength dependence. The results of in vivo experimental measurements of the laser-induced photodissociation of HbO2 in cutaneous blood vessels in the visible and near-infrared (IR) spectral range are presented. Arterial oxygen saturation (SpO2) was measured by a method of fingertip pulse oximetry, which is based on the measurement of the modulated pulse wave of the blood. The light irradiating the finger was provided by corresponding light-emitting diodes (LED) at 15 wavelengths in the 400-940 nm spectrum range. Statistical results with a value of p < 0.05 were viewed as being significant for all volunteers. The results show that there is a decrease in SpO2 in the blood under the influence of the transcutaneous laser irradiation. Three maxima in the spectral range (530, 600, and 850 nm) are revealed, wherein decrease in the relative concentration of SpO2 reaches 5 % ± 0.5 %. Near-IR radiation plays a dominant role in absorption of laser radiation by oxyhemoglobin in deeper layers of tissue blood vessels. The obtained data correlate with the processes of light propagation in biological tissue. The observed reduction in SpO2 indicates the process of photodissociation of HbO2 in vivo and may result in local increase in O2 in the tissue. Such laser-induced enrichment of tissue oxygenation can be used in phototherapy of pathologies, where the elimination of local tissue hypoxia is critical.