Density functional theory of biologically relevant metal centers

The cytochrome b6f complex: plastoquinol oxidation and regulation of electron transport in chloroplasts

In oxygenic photosynthetic systems, the cytochrome b6f (Cytb6f) complex (plastoquinol:plastocyanin oxidoreductase) is a heart of the hub that provides connectivity between photosystems (PS) II and I. In this review, the structure and function of the Cytb6f complex are briefly outlined, being focused on the mechanisms of a bifurcated (two-electron) oxidation of plastoquinol (PQH2). In plant chloroplasts, under a wide range of experimental conditions (pH and temperature), a diffusion of PQH2 from PSII to the Cytb6f does not limit the intersystem electron transport. The overall rate of PQH2 turnover is determined mainly by the first step of the bifurcated oxidation of PQH2 at the catalytic site Qo, i.e., the reaction of electron transfer from PQH2 to the Fe2S2 cluster of the high-potential Rieske iron-sulfur protein (ISP). This point has been supported by the quantum chemical analysis of PQH2 oxidation within the framework of a model system including the Fe2S2 cluster of the ISP and surrounding amino acids, the low-potential heme b6L, Glu78 and 2,3,5-trimethylbenzoquinol (the tail-less analog of PQH2). Other structure-function relationships and mechanisms of electron transport regulation of oxygenic photosynthesis associated with the Cytb6f complex are briefly outlined: pH-dependent control of the intersystem electron transport and the regulatory balance between the operation of linear and cyclic electron transfer chains.

Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation

Photosynthetic water oxidation is catalyzed by a manganese–calcium oxide cluster, which experiences five “S-states” during a light-driven reaction cycle. The unique “distorted chair”-like geometry of the Mn₄CaO₅₍₆₎ cluster shows structural flexibility that has been frequently proposed to involve “open” and “closed”-cubane forms from the S₁ to S₃ states. The isomers are interconvertible in the S₁ and S₂ states, while in the S₃ state, the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples. In this work, using density functional theory calculations, we go beyond the S₃⁺Y_z state to the S₃ⁿY_z^• → S₄⁺Y_z step, and report for the first time that the reversible isomerism, which is suppressed in the S₃⁺Y_z state, is fully recovered in the ensuing S₃ⁿY_z^• state due to the proton release from a manganese-bound water ligand. The altered coordination strength of the manganese–ligand facilitates formation of the closed-cubane form, in a dynamic equilibrium with the open-cubane form. This tautomerism immediately preceding dioxygen formation may constitute the rate limiting step for O₂ formation, and exert a significant influence on the water oxidation mechanism in photosystem II.

The importance of exact exchange-A methodological investigation of NO reduction in heme-copper oxidases

Significant improvements of the density functional theory (DFT) methodology during the past few decades have made DFT calculations a powerful tool in studies of enzymatic reaction mechanisms. For metalloenzymes, however, there are still concerns about the reliability in the DFT-results. Therefore, a systematic study is performed where the fraction of exact exchange in a hybrid DFT functional is used as a parameter. By varying this parameter, a set of different but related functionals are obtained. The various functionals are applied to one of the reactions occurring in the enzyme family heme-copper oxidases, the reduction of nitric oxide (NO) to nitrous oxide (N₂O) and water. The results show that, even though certain parts of the calculated energetics exhibit large variations, the qualitative pictures of the reaction mechanisms are quite stable. Furthermore, it is found that the functional with 15% exact exchange (B3LYP^*) gives the best agreement with experimental data for the particular reactions studied. An important aspect of the procedure used is that the computational results are carefully combined with a few more general experimental data to obtain a complete description of the entire catalytic cycle of the reactions studied.

Spin-Orbit Coupling Changes the Identity of the Hyper-Open-Shell Ground State of Ce+, and the Bond Dissociation Energy of CeH+ Proves to Be Challenging for Theory

Cerium (Ce) plays important roles in catalysis. Its position in the sixth period of the periodic table leads to spin-orbit coupling (SOC) and other open-shell effects that make the quantum mechanical calculation of cerium compounds challenging. In this work, we investigated the low-lying spin states of Ce⁺ and the bond energy of CeH⁺, both by multiconfigurational methods, in particular, SA-CASSCF, MC-PDFT, CASPT2, XMS-PDFT, and XMS-CASPT2, and by single-configurational methods, namely, Hartree-Fock theory and unrestricted Kohn-Sham density functional theory with 34 choices of the exchange-correlation functional. We found that only CASPT2, XMS-CASPT2, and SA-CASSCF (among the five multiconfigurational methods) and GAM, HCTH, SOGGA11, and OreLYP (among the 35 single-configuration methods) successfully predict that the SOC-free ground spin state of Ce⁺ is a doublet state, and CASPT2 and GAM give the most accurate multireference and single-reference calculations, respectively, of the excitation energy of the first SOC-free excited state for Ce⁺. We calculated that the ground doublet state of Ce⁺ is an intra-atomic hyper-open-shell state. We calculated the spin-orbit energy (E^SO) of Ce⁺ by the five multiconfigurational methods and found that E^SO calculated by CASPT2 is the closest to the experimental value. Taking advantage of the availability of an experimental D₀ for CeH⁺ as a way to provide a unique test of theory, we showed that all the multiconfigurational methods overestimate D₀ by at least 246 meV (5.7 kcal/mol), and only three functionals, namely, SOGGA, MN15, and GAM, have an error of D₀ that is less than 200 meV (5 kcal/mol).

A quantum chemical approach for the mechanisms of redox-active metalloenzymes

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes. In our group we have developed an approach that has been applied to a large number of such systems. Hybrid density functional theory (hybrid DFT) has from the start of these investigations been the leading electronic structure tool. An understanding of how the method works in practice has significantly improved the accuracy and applicability. During the past ten years, it has been found that the results for redox enzymes mainly depend on the chosen fraction of exact exchange in the functional, and that a choice of 15% has worked best. The idea has therefore been to vary that fraction over a reasonable range and study the relative energy dependence. For modeling the enzymes, a cluster approach has been developed. In the present review the development of the method we used is described from its start in work on photosystem II, fifteen years ago. Examples from a few recent applications are described, where the metals have been iron, nickel, copper, cobalt or manganese. The results are in excellent agreement with available experiments, and a large number of new predictions have been made.

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes.

Noncollinear Relativistic Two-Component X2C Calculations of Hyperfine Couplings Using Local Hybrid Functionals. Importance of the High-Density Coordinate Scaling Limit

Local hybrid functionals with position-dependent exact-exchange admixture have been implemented in the noncollinear spin form into a two-component X2C code and are evaluated for the hyperfine coupling tensors of a series of 3d, 4d, and 5d transition-metal complexes. One aim is to see if the potential of local hybrid functionals toward an improved balance between core-shell and valence-shell spin polarization, recently identified in nonrelativistic computations on 3d complexes (Schattenberg, C.; Maier, T. M.; Kaupp, M. J. Chem. Theory Comput. 2018, 14, 5653-5672), can be extended to the hyperfine couplings of heavier metal centers. The correctness of the two-component implementation is first established by comparison to previous computations for 3d systems with or without notable spin-orbit contributions to their hyperfine tensors, and the good performance of a standard "t-LMF" local mixing function is confirmed. However, when moving to 4d and 5d metal centers, the performance of such local mixing functions deteriorates. This is likely due to their violation of the homogeneous coordinate scaling condition in the high-density limit, which is particularly important for the core shells of heavier atoms. A local mixing function that respects this high-density limit performs notably better for heavier metal centers. However, it brings in much too high exact-exchange admixtures for the 3d systems and is too inflexible to simultaneously provide reasonable chemical accuracy in other areas. These results point to the ongoing need to develop improved local mixing functions and local hybrid functionals that exhibit favorable properties in different areas of space defined by very high and much lower electron densities.

Theoretical study of aromatic hydroxylation of the [Cu2(H-XYL)O2]2+ complex mediated by a side-on peroxo dicopper core and Cu-ligand effects

In this work, the aromatic hydroxylation mechanism of the [Cu₂(H-XYL)O₂]²⁺ complex mediated by a peroxo dicopper core and Cu-ligand effects are investigated by using hybrid density functional theory (DFT) and the broken symmetry B3LYP method. Based on the calculated free-energy profiles, we proposed two available mechanisms. The first reaction steps of both mechanisms involve concerted O-O bond cleavage and C-O bond formation and the second step involves the Wagner-Meerwein rearrangement of the substrate by a [1,2] H shift (H_A shift from C_A to C_C) or (H_A shift from C_A to O_A) across the phenyl ring to form stable dienone intermediates, and this is followed by the protonation of bridging oxygen atoms to produce the final hydroxylated dicopper(ii) product. The H_A shift from C_A to C_C mechanism is the energetically most favorable, in which the first reaction step is the rate-limiting reaction, with a calculated free-energy barrier of 19.0 kcal mol^-1 and a deuterium kinetic isotope effect of 1.0, in agreement with experimental observations. The calculation also shows that the reaction started from the P-type species of [Cu₂(H-XYL)O₂]²⁺ which is capable of mediating the direct hydroxylation of aromatic substrates without the intermediacy of an O-type species. Finally, we designed some new complexes with different Cu-ligands and found the complex that computationally possesses a higher activity in mediating the hydroxylation of the ligand based aromatic substrate; here, Cu loses a pyridyl ligand donor by dissociation, compared to the [Cu₂(H-XYL)O₂]²⁺ complex.

Bio-mimetic self-assembled computationally designed catalysts of Mo and W for hydrogenation of CO2/dehydrogenation of HCOOH inspired by the active site of formate dehydrogenase

Density functional theory modelling has been used to design Mo and W-based catalysts MoIII(tBu)(CO) and WIII(tBu)(CO) for CO2 hydrogenation and HCOOH dehydrogenation, which are bio-mimics of the active site of formate dehydrogenase. Based on DFT calculations, the molybdenum and tungsten based complexes are good catalysts in the +3 oxidation state for CO2 hydrogenation with free energies of 24.03 and 21.31 kcal mol-1, respectively. Such a low barrier indicates that our newly designed Mo and W-based complexes are very efficient for CO2 hydrogenation or HCOOH dehydrogenation catalysis. Overall, our computational results provide in depth insights that can serve as a great tool for the design and development of new and efficient molybdenum and tungsten based catalysts for CO2 hydrogenation or HCOOH dehydrogenation.

Reassessment of the Mechanisms of Thermal C-H Bond Activation of Methane by Cationic Magnesium Oxides: A Critical Evaluation of the Suitability of Different Density Functionals

The mechanisms of the thermal reactions of the two iconic magnesium oxide cations MgO^.+ and Mg₂ O₂ ^.+ with methane have been re-evaluated at the CCSD(T)/CBS//CCSD/def2-TZVP level of theory. For the reaction of MgO^.+ with CH₄ , only the classical hydrogen-atom transfer (HAT) was found; in contrast, for the Mg₂ O₂ ^.+ /CH₄ couple, both HAT and proton-coupled electron-transfer (PCET) exist as mechanistic variants. In order to evaluate the suitability of density functional theory (DFT) methods, the reactions were computed by using 27 density functionals. The results obtained demonstrate that the various DFT methods often deliver rather different results for both geometric and energetic features. As to the prediction of the apparent barriers, pure functionals give the largest mean absolute errors. BMK, ωB97XD, and the double-hybrid functional mPW2PLYP were confirmed to come closest to the results provided by CCSD(T)/CBS. Thus, mechanistic conclusions based on a single DFT method should be viewed with great caution. In summary, this study may assist in the selection of a suitable quantum chemical method to unravel the mechanistic details of C-H bond activation by charged metal oxides.

Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems

We applied our analysis, based on a linear response function of density and spin density, to two typical transition metal complex systems-the reaction centers of P450, and oxygen evolving center in Photosystem II, both of which contain open-shell transition metal ions. We discuss the relationship between LRF of electron density and spin density and the types of units and interactions of the systems. The computational results are discussed in relation to quantum mechanics (QM) cluster and quantum mechanics/molecular mechanics (QM/MM) modeling that are employed to compute the reaction centers of enzymes.

Computational Understanding of the Selectivities in Metalloenzymes

Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.

A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations

Heme degradation by heme oxygenase enzymes is important for maintaining iron homeostasis and prevention of oxidative stress.

QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase

Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.

Selectivity of Cobalt Corrole for CO vs. O2 and N2 in Indoor Pollution

Coal combustion causes indoor pollution of CO. In this work, DFT calculations on cobalt corrole (Co(Cor)) with three most common indoor gas molecules (N₂, O₂ and CO) were performed. The Mulliken spin densities show that the ground states of Co(N₂)(Cor), Co(CO)(Cor) and Co(OC)(Cor) have an anti-ferromagnetic coupling fashion of the electrons on the Co 3d _z² orbital and the π orbital of the corrole ring. However, Co(O₂)(Cor) has a triplet ground state. With the spin contamination corrections, the Co(N₂)(Cor) binding energy was obtained at -50.6 kcal mol^-1 (B3LYP-D3). While CO can interact with Co(Cor) in two different ways, and their binding energies were -22.8 and -10.9 kcal mol^-1 (B3LYP-D3) for Co(CO)(Cor) and Co(OC)(Cor), respectively. The natural bond orbital charges on the axial ligands (NO, CO, OC) are increased upon the chemical bond formation. These are the cause of the shorten metal-ligand bond and the increase of the wavenumber of the metal-ligand bond vibrational transitions. While the charges for O₂ are decreased, leading to bond elongation as well as the decrease of the wavenumber upon complexation. Overall, O₂ was found to be hardly coordinated with Co(Cor). This study provides a detailed molecular understanding of interactions between a gas sensor and gaseous indoor air-pollutants.

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.

Noncovalent interactions between the second coordination sphere and the active site of [NiFeSe] hydrogenase

QM/MM studies on seven truncated models of the oxidized as-isolated state of the [NiFeSe] Hases reveal the influence of the residues in the second coordination sphere on the active site.

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic Reactions

In this chapter, we discuss the influence of an anisotropic protein environment on the reaction mechanisms of saccharopine reductase and uroporphyrinogen decarboxylase, respectively, via the use of a quantum mechanical and molecular mechanical (QM/MM) approach. In addition, we discuss the importance of selecting a suitable DFT functional to be used in a QM/MM study of a key intermediate in the mechanism of 8R-lipoxygenase, a nonheme iron enzyme. In the case of saccharopine reductase, while the enzyme utilizes a substrate-assisted catalytic pathway, it was found that only through treating the polarizing effect of the active site, via the use of an electronic embedding formalism, was agreement with experimental kinetic data obtained. Similarly, in the case of uroporphyrinogen decarboxylase, the effect of the protein environment on the catalytic mechanism was found to be such that the calculated rate-limiting barrier is in good agreement with related experimentally determined values for the first decarboxylation of the substrate. For 8R-lipoxygenase, it was found that the geometries and energies of the multicentered open-shell intermediate complexes formed during the mechanism are quite sensitive to the choice of the density functional theory method. Thus, while density functional theory has become the method of choice in QM/MM studies, care must be taken in the selection of a particular high-level method.

Enzymatic mechanism of copper-containing nitrite reductase

Copper-containing nitrite reductases (CuNiRs) catalyze the reduction of nitrite to nitric oxide, a key step in the denitrification process that maintains balance between organic and inorganic nitrogen. Despite their importance, their functioning is not well understood. In this work, we carry out first-principles calculations and show that the available structural data are consistent only with a single mechanism. For this mechanism, we determine the activation energies, transition states, and minimum energy pathways of CuNiR. The calculations lead to an updated enzymatic mechanism and resolve several controversial issues. In particular, our work identifies the origins of the two protons necessary for the enzymatic function and shows that the transformation from the initial O-coordination of substrate to the final N-coordination of product is achieved by electron transfer from T1 copper to T2 copper, rather than by the previously reported side-on coordination of a NO intermediate, which only takes place in the reduced enzyme. We also examine the role of structural change in the critical residue Asp(98), reported in one experimental study, and find that while the structural change affects the energetics of substrate attachment and product release at the T2 copper reaction center, it does not significantly affect the activation energy and reaction pathways of the nitrite reduction process.

Modeling nuclear resonance vibrational spectroscopic data of binuclear non-heme iron enzymes using density functional theory

Nuclear resonance vibrational spectroscopy (NRVS) is a powerful technique that can provide geometric structural information on key reaction intermediates of Fe-containing systems when utilized in combination with density functional theory (DFT). However, in the case of binuclear non-heme iron enzymes, DFT-predicted NRVS spectra have been found to be sensitive to truncation method used to model the active sites of the enzymes. Therefore, in this study various-level truncation schemes have been tested to predict the NRVS spectrum of a binuclear non-heme iron enzyme, and a reasonably sized DFT model that is suitable for employing the NRVS/DFT combined methodology to characterize binuclear non-heme iron enzymes has been developed.

Proton pumping in cytochrome c oxidase: energetic requirements and the role of two proton channels

Cytochrome c oxidase is a superfamily of membrane bound enzymes catalyzing the exergonic reduction of molecular oxygen to water, producing an electrochemical gradient across the membrane. The gradient is formed both by the electrogenic chemistry, taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each reduction step, which is surprising considering the fact that two of the reduction steps most likely are only weakly exergonic. Based on a combination of quantum chemical calculations and experimental information, it is here shown that from both a thermodynamic and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the reduction steps, at least up to half the maximum gradient. A previously suggested pumping mechanism is developed further to suggest a reason for the use of two proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox dependent, it might become too slow for the steps with low exergonicity. Therefore, a second channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility is also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase is also suggested. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.

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.

Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II

The influence of electrostatic interactions on the free energy of proton coupled electron transfer in biomimetic oxomanganese complexes inspired by the oxygen-evolving complex (OEC) of photosystem II (PSII) are investigated. The reported study introduces an enhanced multiconformer continuum electrostatics (MCCE) model, parametrized at the density functional theory (DFT) level with a classical valence model for the oxomanganese core. The calculated pKa's and oxidation midpoint potentials (E(m)'s) match experimental values for eight complexes, indicating that purely electrostatic contributions account for most of the observed couplings between deprotonation and oxidation state transitions. We focus on pKa's of terminal water ligands in [Mn(II/III)(H2O)6](2+/3+) (1), [Mn(III)(P)(H2O)2](3-) (2, P = 5,10,15,20-tetrakis(2,6-dichloro-3-sulfonatophenyl)porphyrinato), [Mn2(IV,IV)(μ-O)2(terpy)2(H2O)2](4+) (3, terpy = 2,2':6',2″-terpyridine), and [Mn3(IV,IV,IV)(μ-O)4(phen)4(H2O)2](4+) (4, phen = 1,10-phenanthroline) and the pKa's of μ-oxo bridges and Mn E(m)'s in [Mn2(μ-O)2(bpy)4] (5, bpy = 2,2'-bipyridyl), [Mn2(μ-O)2(salpn)2] (6, salpn = N,N'-bis(salicylidene)-1,3-propanediamine), [Mn2(μ-O)2(3,5-di(Cl)-salpn)2] (7), and [Mn2(μ-O)2(3,5-di(NO2)-salpn)2] (8). The analysis of complexes 6-8 highlights the strong coupling between electron and proton transfers, with any Mn oxidation lowering the pKa of an oxo bridge by 10.5 ± 0.9 pH units. The model also accounts for changes in the E(m)'s by ligand substituents, such as found in complexes 6-8, due to the electron withdrawing Cl (7) and NO2 (8). The reported study provides the foundation for analysis of electrostatic effects in other oxomanganese complexes and metalloenzymes, where proton coupled electron transfer plays a fundamental role in redox-leveling mechanisms.

Hybrid dynamics simulation engine for metalloproteins

Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins' structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca(2+) form of the enzyme catechol O-methyl transferase, which, unlike the native Mg(2+) form, is catalytically inactive. The Mg(2+) site is ochtahedral, but the Ca(2+) is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight.

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.