Redox-Dependent Structural Transformations of the [4Fe-3S] Proximal Cluster in O2-Tolerant Membrane-Bound [NiFe]-Hydrogenase: A DFT Study

Substrate-Dependent Conformational Switch of the Noncubane [4Fe-4S] Cluster in Heterodisulfide Reductase HdrB

The noncubane [4Fe-4S] cluster identified in the active site of heterodisulfide reductase (HdrB) displays a unique geometry among Fe-S cofactors found in metalloproteins. Here we employ resonance Raman (RR) spectroscopy and density functional theory (DFT) calculations to probe structural, electronic, and vibrational properties of the noncubane cluster in HdrB from a non-methanogenic Desulfovibrio vulgaris (Dv) Hildenborough organism. The immediate protein environment of the two neighboring clusters in DvHdrB is predicted using homology modeling. We demonstrate that in the absence of substrate, the oxidized [4Fe-4S]³⁺ cluster adopts a "closed" conformation. Upon substrate coordination at the "special" iron center, the cluster core translates to an "open" structure, facilitated by the "supernumerary" cysteine ligand switch from iron-bridging to iron-terminal mode. The observed RR fingerprint of the noncubane cluster, supported by Fe-S vibrational mode analysis, will advance future studies of enzymes containing this unusual cofactor.

Antiferromagnetic Exchange and Metal-Metal Bonding in Roussin's Black Sulfur and Selenium Salts

Atom-efficient syntheses of the tetraethylammonium Roussin black sulfur and selenium salts ((Et₄N)[Fe₄E₃(NO)₇], E = S, Se) as well as their ¹⁵N-labeled counterparts are described herein. Broken-symmetry DFT calculations were conducted on both complexes to model an antiferromagnetic interaction between the apical {FeNO}⁷ unit, S_ap = 3/2, and the three basal {Fe(NO)₂}⁹ units, S_bas = 1/2. The calculated J values are -1813 and -1467 cm^-1 for the sulfur and selenium compounds, respectively. The mechanism for antiferromagnetic exchange in both compounds was deduced to be direct exchange on the basis of the partially overlapping magnetic orbitals with orbital density only residing on the Fe-centers. The obtained Mössbauer parameters are most consistent with the calculated M_S = 0 broken-symmetry state for both complexes. The values for J have been determined with variable-temperature ¹⁵N NMR experiments. Values of -1660 and -1430 cm^-1 for the sulfur and selenium compounds, respectively, were obtained by fits to the variable-temperature NMR data, further validating the broken-symmetry M_S = 0 model of the electronic structure.

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.

Theoretical Studies of Nickel-Dependent Enzymes

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.

Proton Transfer Pathways between Active Sites and Proximal Clusters in the Membrane-Bound [NiFe] Hydrogenase

[NiFe] hydrogenases are enzymes that catalyze the splitting of molecular hydrogen according to the reaction H₂ → 2H⁺ + 2e^-. Most of these enzymes are inhibited even by low traces of O₂. However, a special group of O₂-tolerant hydrogenases exists. A member of this group is the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha ( ReMBH). The ReMBH harbors an unusual iron sulfur cluster with composition 4Fe3S(6Cys) that is able to undergo structural changes triggering the flow of two electrons to the [NiFe] active site. These electrons promote oxygen reduction at the active site, preventing, in this way, aerobic inactivation of the enzyme. In the superoxidized state, the [4Fe3S] cluster binds to a hydroxyl group that originates from either molecular oxygen or water reaching the site. Both reactions, oxygen reduction to water at the [NiFe]- or [4Fe3S]-centers and oxygen evolution from water at the proximal cluster, require the delivery of protons regulated by a subtle communication mechanism between these metal centers. In this work, we sequentially apply multiscale modeling techniques as quantum mechanical/molecular mechanics methods and classical molecular dynamics simulations to investigate the role of two distinct proton transfer pathways connecting the [NiFe] active site and the [4Fe3S] proximal cluster of ReMBH in the protection mechanism against an oxygen attack. Although the "glutamate" pathway is preferred by protons migrating toward the active site to avoid inactivation by O₂, the "histidine" pathway plays an essential role in delivering protons for O₂ reduction at the proximal cluster. The results obtained in this work not only provide new pieces to the puzzling catalytic mechanisms governing O₂-tolerant hydrogenases but also highlight the relevance of dynamics in the proper description of biochemical reactions in general.

X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster

The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.

Quantum chemical approaches to [NiFe] hydrogenase

The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.

Characterization of the [3Fe-4S](0/1+) cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses

The D14C variant of Pyrococcus furiosus ferredoxin provides an extraordinary framework to investigate a [3Fe-4S] cluster at two oxidation levels and compare the results to its physiologic [4Fe-4S] counterpart in the very same protein. Our spectroscopic and computational study reveals vibrational property changes related to the electronic and structural aspects of both Fe-S clusters.

How does ammonia bind to the oxygen-evolving complex in the S2state of photosynthetic water oxidation? Theoretical support and implications for the W1 substitution mechanism

The mechanistic study shows that NH₃substitutes W1 rather than O5 of the OEC in the S₂state and leaves in the S₄′ state.

The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study

An unprecedented [4Fe-3S] cluster proximal to the regular [NiFe] active site has recently been found to be responsible for the ability of membrane-bound hydrogenases (MBHs) to oxidize dihydrogen in the presence of ambient levels of oxygen. Starting from proximal cluster models of a recent DFT study on the redox-dependent structural transformation of the [4Fe-3S] cluster, ⁵⁷Fe Mössbauer parameters (electric field gradients, isomer shifts, and nuclear hyperfine couplings) were calculated using DFT. Our results revise the previously reported correspondence of Mössbauer signals and iron centers in the [4Fe-3S]³⁺ reduced-state proximal cluster. Similar conflicting assignments are also resolved for the [4Fe-3S]⁵⁺ superoxidized state with particular regard to spin-coupling in the broken-symmetry DFT calculations. Calculated ⁵⁷Fe hyperfine coupling (HFC) tensors expose discrepancies in the experimental set of HFC tensors and substantiate the need for additional experimental work on the magnetic properties of the MBH proximal cluster in its reduced and superoxidized redox states.

The [NiFe]-Hydrogenase of Pyrococcus furiosus Exhibits a New Type of Oxygen Tolerance

We report the first direct electrochemical characterization of the impact of oxygen on the hydrogen oxidation activity of an oxygen-tolerant, group 3, soluble [NiFe]-hydrogenase: hydrogenase I from Pyrococcus furiosus (PfSHI), which grows optimally near 100 °C. Chronoamperometric experiments were used to probe the sensitivity of PfSHI hydrogen oxidation activity to both brief and prolonged exposure to oxygen. For experiments between 15 and 80 °C, following short (<200 s) exposure to 14 μM O2 under oxidizing conditions, PfSHI always maintains some fraction of its initial hydrogen oxidation activity; i.e., it is oxygen-tolerant. Reactivation experiments show that two inactive states are formed by interaction with oxygen and both can be quickly (<150 s) reactivated. Analogous experiments, in which the interval of oxygen exposure is extended to 900 s, reveal that the response is highly temperature-dependent. At 25 °C, under sustained 1% O2/ 99% H2 exposure, the H2oxidation activity drops nearly to zero. However, at 80 °C, up to 32% of the enzyme's oxidation activity is retained. Reactivation of PfSHI following sustained exposure to oxygen occurs on a much longer time scale (tens of minutes), suggesting that a third inactive species predominates under these conditions. These results stand in contrast to the properties of oxygen-tolerant, group 1 [NiFe]-hydrogenases, which form a single state upon reaction with oxygen, and we propose that this new type of hydrogenase should be referred to as oxygen-resilient. Furthermore, PfSHI, like other group 3 [NiFe]-hydrogenases, does not possess the proximal [4Fe3S] cluster associated with the oxygen tolerance of some group 1 enzymes. Thus, a new mechanism is necessary to explain the observed oxygen tolerance in soluble, group 3 [NiFe]-hydrogenases, and we present a model integrating both electrochemical and spectroscopic results to define the relationships of these inactive states.

Theoretical investigation of the interaction between aromatic sulfur compounds and [BMIM](+)[FeCl4](-) ionic liquid in desulfurization: A novel charge transfer mechanism

In this work, interaction nature between a group of aromatic sulfur compounds and [BMIM](+)[FeCl4](-) have been investigated by density functional theory (DFT). A coordination structure is found to be critical to the mechanism of extractive desulfurization. Interaction energy and extractive selectivity follow the order: thiophene (TH)<dibenzothiophene (DBT)≈benzothiophene (BT). Alkylation of TH or BT (e.g. 3-methylthiophene, and 3-methylbenzothiophene) leads to a stronger interaction with ionic liquid, but steric hindrance effects of some alkylic derivatives (e.g. 2,7-dimethylbenzothiophene) lead to a weaker interaction with ionic liquid. The mechanism of extractive desulfurization is attributed to the charge transfer effect. During extractive desulfurization, electrons on aromatic sulfur compounds transfer into the Lewis part of ionic liquid, namely, [FeCl4](-). Furthermore, it is better to consider the Lewis acidity of Fe-containing ionic liquid by the whole unit (such as [FeCl4](-) and aromatic sulfur compounds (X)) rather than only Fe or S atom.

What is the trigger mechanism for the reversal of electron flow in oxygen-tolerant [NiFe] hydrogenases?

A new mechanistic model is developed for the sequence of events by which oxygen-tolerant [NiFe] hydrogenase enzymes respond to O₂.

The [NiFe] hydrogenases use an electron transfer relay of three FeS clusters – proximal, medial and distal – to release the electrons from the principal reaction, H₂ → 2H⁺ + 2e^–, that occurs at the Ni–Fe catalytic site. This site is normally inactivated by O₂, but the subclass of O₂-tolerant [NiFe] hydrogenases are able to counter this inactivation through the agency of an unusual and unprecedented proximal cluster, with composition [Fe₄S₃(S^cys)₆], that is able to transfer two electrons back to the Ni–Fe site and effect crucial reduction of O₂-derived species and thereby reactivate the Ni–Fe site. This proximal cluster gates both the direction and the number of electrons flowing through it, and can reverse the normal flow during O₂ attack. The unusual structures and redox potentials of the proximal cluster are known: a structural change in the proximal cluster causes changes in its electron-transfer potentials. Using protein structure analysis and density functional simulations, this paper identifies a closed protonic system comprising the proximal cluster, some contiguous residues, and a proton reservoir, and proposes that it is activated by O₂-induced conformational change at the Ni–Fe site. This change is linked to a key histidine residue which then causes protonation of the proximal cluster, and migration of this proton to a key μ₃-S atom. The resulting SH group causes the required structural change at the proximal cluster, modifying its redox potentials, and leads to the reversed electron flow back to the Ni–Fe site. This cycle is reversible, and the protons involved are independent of those used or produced in reactions at the active site. Existing experimental support for this model is cited, and new testing experiments are suggested.

Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom

The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.