Theoretical Studies of Nickel-Dependent Enzymes

How Geometric Constraints Control the Hydride Position and Activity in [NiFe]-Hydrogenases and Their Biomimetic Complexes

The Ni-R active site in [NiFe]-hydrogenase features a bridging hydride between the Ni and Fe, displaced toward the Ni. However, all synthetic Ni-R models reported to date exhibit a hydride displaced toward Fe and display low turnover frequencies for H2 evolution. Understanding the factors governing the hydride position and activity of Ni-R and biomimetic complexes is crucial for developing efficient hydrogen-evolving catalysts. By utilizing the CCSD theory, DFT, NBO, and QTAIM analysis, we investigated these factors in a Ni-R active-site model (1), and two representative biomimetic complexes, 2* and 3. Our results reveal that the Ni site of 1 inherently prefers a square-planar [S2NiSH] configuration with an apically positioned thiolate and that hydride positioning is governed by the strength of [Ni-H-Fe] three-center two-electron bonding, which is modulated by the geometric torsion between the Ni terminal ligands and the bridging thiolates. By modifying the linkers between the Ni terminal ligands and bridging thiolate ligands of 2* and 3, we designed virtual biomimetic complexes (4-10). These complexes exhibit improved hydride nucleophilicity and increased potential for H2 formation, providing valuable insights into how geometric and electronic factors influence hydride activity and informing the design of more effective biomimetic hydrogenase models.

Mechanism of Methyl Transfer Reaction between CH3Co(dmgBF2)2py and PPh3Ni(Triphos)

DFT calculations were performed for the methyl group transfer reaction between CH3Co (dmgBF2)py and PPh3Ni(Triphos). The reaction mechanism and its energetics were investigated. This reaction is relevant to the catalytic mechanism of the enzyme acetyl coenzyme A synthase. BP86 and PBE functionals and dispersion corrections were used. It was found that intermolecular interactions are very important for this reaction. The influence of the solvent on the reaction was studied.

Spectroscopic, crystal structure and DFT-assisted studies of some nickel(II) chelates of a heterocyclic-based NNO donor aroylhydrazone: in vitro DNA binding and docking studies

Five new nickel(II) complexes have been synthesised with an NNO donor tridentate aroylhydrazone (HFPB) employing the chloride, nitrate, acetate and perchlorate salts, and all the complexes are physiochemically characterized. Elemental analyses suggested stoichiometries as Ni(FPB)(NO3)]·2H2O (1), [Ni(HFPB)(FPB)]Cl (2), [Ni(FPB)(OAc)(DMF)] (3), [Ni(FPB)(ClO4)]·DMF (4), [Ni(FPB)2] (5). Aroylhydrazone is found coordinating in deprotonated iminolate form in four of the complexes (1, 3, 4, 5) however in one case (complex 2), two aroylhydrazone moieties are binding to the metal centre in the neutral and anionic forms. The structure of the bisligated complex 5, found using single crystal X ray diffraction studies confirmed that the metal has a distorted octahedral N4O2 coordination environment, with each of the two deprotonated ligands coordinating through the pyridine nitrogen, imino-hydrazone nitrogen and the enolate oxygen of the hydrazone moiety. To compare and study, the electronic interactions and stabilities of the metal complexes, various quantum chemical parameters were calculated. Moreover, Hirshfeld surface analysis was carried out for complex 5 to determine the intermolecular interactions. The biophysical attributes of the ligand and complex 5 have been investigated with CT-DNA and experimental outcomes show that the Ni(II) complex exhibited higher binding propensity towards DNA as compared to ligand. Furthermore, to specifically understand the type of interactions of the metal complexes with DNA, molecular docking studies were effectuated. In addition, the electronic and related reactivity behaviors of the ligand and five Ni(II) complexes were studied using B3LYP/6-31 +  + G**/LANL2DZ level. As expected, the obtained results from Natural Bond Orbital (NBO) computations displayed that the resonance interactions (n → π* and π → π*) play a determinant role in evaluating the chemical attributes of the reported compounds.

Novel Bidentate Amine Ligand and the Interplay between Pd(II) and Pt(II) Coordination and Biological Activity

Pt(II) and Pd(II) coordinating N-donor ligands have been extensively studied as anticancer agents after the success of cisplatin. In this work, a novel bidentate N-donor ligand, the N-[[4-(phenylmethoxy)phenyl]methyl]-2-pyridinemethanamine, was designed to explore the antiparasitic, antiviral and antitumor activity of its Pt(II) and Pd(II) complexes. Chemical and spectroscopic characterization confirm the formation of [MLCl2 ] complexes, where M=Pt(II) and Pd(II). Single crystal X-ray diffraction confirmed a square-planar geometry for the Pd(II) complex. Spectroscopic characterization of the Pt(II) complex suggests a similar structure. 1 H NMR, 195 Pt NMR and HR-ESI-MS(+) analysis of DMSO solution of complexes indicated that both compounds exchange the chloride trans to the pyridine for a solvent molecule with different reaction rates. The ligand and the two complexes were tested for in vitro antitumoral, antileishmanial, and antiviral activity. The Pt(II) complex resulted in a GI50 of 10.5 μM against the NCI/ADR-RES (multidrug-resistant ovarian carcinoma) cell line. The ligand and the Pd(II) complex showed good anti-SARS-CoV-2 activity with around 65 % reduction in viral replication at a concentration of 50 μM.

Intramolecular Proton-Coupled Hydride Transfers with Relatively Low Activation Barriers

We report that bifunctional molecules containing hydroxyl and carbonyl functional groups can undergo an effective transfer hydrogenation via an intramolecular proton-coupled hydride transfer (PCHT) mechanism. In this reaction mechanism, a hydride transfer between two carbon atoms is coupled with a proton transfer between two oxygen atoms via a cyclic bond rearrangement transition structure. The coupled transfer of the two hydrogens as H^δ+ and H^δ- is supported by atomic polar tensor charges. The activation energy for the PCHT reaction is strongly dependent on the length of the alkyl chain between the hydroxyl and carbonyl functional groups but relatively weakly dependent on the functional groups attached to the hydroxyl and carbonyl carbons. We investigate the PCHT reaction mechanism using the Gaussian-4 thermochemical protocol and obtain high activation energy barriers (ΔH^‡₂₉₈) of 210.5-228.3 kJ mol^-1 for chain lengths of one carbon atom and 160.2-163.9 kJ mol^-1 for chain lengths of two carbon atoms. However, for longer chain lengths containing 3-4 carbon atoms, we obtain ΔH^‡₂₉₈ values as low as 101.9 kJ mol^-1. Importantly, the hydride transfer between two carbon atoms proceeds without the need for a catalyst or hydride transfer activating agent. These results indicate that the intramolecular PCHT reaction provides an effective avenue for uncatalyzed, metal-free hydride transfers at ambient temperatures.

Flavonol dioxygenase chemistry mediated by a synthetic nickel superoxide

Nature exploits transition metal centers to enhance and tune the oxidizing power of natural oxidants such as O₂ and H₂O₂. The design and interrogation of synthetic metallocomplexes with similar reactivity to metalloproteins provides one strategy for gaining insight into the mechanistic underpinnings of oxygen-activating enzymes such as oxidases, oxygenases, and dioxygenases like Ni-quercetinase (Ni-QueD). Ni-QueD catalyzes the oxidative ring opening of the polyphenol quercetin, a natural product with antioxidant properties. Herein, we report the synthesis and characterization of Ni(13-DOB), a Ni(II) species complexed by an N4-macrocycle that has been characterized by single crystal X-ray crystallography. Ni(13-DOB) forms a Ni-superoxide intermediate (Ni(13-DOB)O₂^•-) upon treatment with H₂O₂ and Et₃N, as verified by resonance Raman spectroscopy. We demonstrate through UV/vis and LCMS that Ni(13-DOB)O₂^•- is capable of the 1-electron oxidation of flavonols, including both 3-hydroxyflavone (3-HF, the simplest flavonol) and quercetin itself. Incorporation of two O-atoms into the flavonol radical via superoxide from Ni(13-DOB)O₂^•- precedes oxidative cleavage of the flavonol scaffold in each case, consistent with quercetinase ring cleavage by Ni-QueD in Streptomyces sp. FLA. Conversion of 3-HF into 2-hydroxybenzoylbenzoic acid was accomplished with catalytic turnover of Ni(13-DOB) at ambient temperature, as confirmed by HPLC timecourses and GCMS analysis of isotopic labeling studies. The Ni(13-DOB)-mediated oxidative cleavage of quercetin to the corresponding biomimetic phenolic ester was also verified through ¹⁸O-isotopic labeling studies. Through the HPLC characterization of both on- and off-pathway products of flavonol dioxygenation by Ni(13-DOB)O₂^•-, the stringent reaction pathway control provided by enzyme active sites is highlighted.

Reaction mechanism of the PuDddK dimethylsulfoniopropionate lyase and cofactor effects of various transition metal ions

The microbial cleavage of dimethylsulfoniopropionate (DMSP) produces volatile dimethyl sulfide (DMS) via the lyase pathway, playing a crucial role in the global sulfur cycle. Herein, the DMSP decomposition catalyzed by PuDddK (a DMSP lyase) devised with various transition metal ion cofactors are investigated using density functional calculations. The PuDddK reaction has been demonstrated to employ a concerted β-elimination mechanism, where the substrate α-proton abstraction by the deprotonated Tyr64 occurs simultaneously with the C_β-S bond cleavage and C_α = C_β double bond formation. The PuDddK enzymes with diverse divalent metal ions (Ni²⁺, Mn²⁺, Fe²⁺, Co²⁺, Zn²⁺, and Cu²⁺) incorporated prefer DMSP as a monodentate ligand. The cases of Ni²⁺, Mn²⁺, Fe²⁺, Co²⁺, and Zn²⁺ with the same 3His-1Glu ligands have close reaction energy barriers, indicating that the lyase activity may be hardly affected by the divalent transition metal type with the same ligand type and number. The coordination loss of one histidine in Cu²⁺, forming a 2His-1Glu architecture, leads to a lower activity, revealing that the 3His-1Glu ligand set used by DddK appears to be a scaffold capable of more efficiently catalyzing the DMSP decomposition. Further analysis reveals that the inactivation of Fe³⁺-dependent PuDddK is derived from an electron transfer from the Tyr64 phenolate to Fe³⁺, with the implication that the PuDddK activity may be primarily affected by the redox effects induced by a strongly oxidizing transition metal ion (like Fe³⁺).

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

Urease catalyzes the hydrolysis of urea to form ammonia and carbamate, inducing an overall pH increase that affects both human health and agriculture. Inhibition, mutagenesis, and kinetic studies have provided insights into its enzymatic role, but there have been debates on the substrate binding mode as well as the reaction mechanism. In the present study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) calculations on urease that mainly investigate the binding mode of urea and the mechanism of the urease-catalyzed hydrolysis reaction. Comparison between the experimental data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that urea hydrolysis via a complex with bidentate-bound urea is much more favorable than via that with monodentate-bound urea for both nucleophilic attack and the subsequent proton transfer steps. We also indicate that the bidentate coordination of urea fits the active site with a closed conformation of the mobile flap and can facilitate the stabilization of transition states and intermediates by forming multiple hydrogen bonds with certain active site residues.

Nickel(II)-SNS Thiolate Complexes: Reactivity and Solution Dynamics

Nickel coordination chemistry with a biomimetic thiolate-imine-thioether SNS^Me ligand is accompanied by diverse reactivity and multidentate ligand dynamics. Reaction of Ni(acac)₂ with 2 equiv of 2-(methylthio)-phenyl-benzothiazolidine (MPB) affords the bis(arylimino-phenylene-thiolate) complex Ni(κ²-SNS^Me)₂ (1; acac = acetylacetonate). Thermolysis of 1 in refluxing toluene is accompanied by imine C-C bond formation, yielding [Ni(N₂S₂)] (2) with a redox-active ligand. Protonation of 1 with NHTf₂ at a low temperature released 1 equiv of MPB, yielding crystals of the dimeric dication {[Ni(μ-κ³-SNS^Me)]₂}(NTf₂)₂ (3; Tf = SO₂CF₃) in high yield. In contrast, the same reaction at room temperature gave also paramagnetic complexes {Ni[μ-Ni(κ³-SNS^Me)₂]₂}(NTf₂)₂ (4) and {Ni[μ-Ni(κ³-SNS^Me)₂]₃}(NTf₂)₂ (5) that feature coordination of two or three pseudo-octahedral, paramagnetic Ni(κ³-SNS^Me)₂ units to a central Ni(II) dication via thiolate bridges. Remarkably, dissolution of 3 in a variety of solvents, including weakly coordinating CH₂Cl₂, rapidly generates a mixture of 4 and Ni(NTf)₂. Treatment of this mixture with Lewis bases L gave high yields of dimers {[Ni(μ-κ³-SNS^Me)L]₂}(NTf₂)₂ for L = CNXylyl (6a) and {[Ni(μ-κ³-SNS^Me)]₂(μ-dmpm)}(NTf₂)₂ (6b; dmpm = bis(dimethylphosphino)methane) or monomers [Ni(κ³-SNS^Me)L](NTf₂) for L = PMe₃ (7a) and P(OMe)₃ (7b). Addition of 2 equiv of the strong donor N-heterocyclic carbene ligand, IPr, to 3, however, led to thioether demethylation, affording neutral dithiolate complex Ni(κ³-SNS)(IPr) (8). Reaction products were characterized by NMR and mass spectrometry and complexes 1-5, 6a, 6b, 7a, and 8 by single-crystal X-ray diffraction.

Handling methane: a Ni(i) F430-like cofactor derived from VB12 is active in methyl-coenzyme M reductase

An Ni(i) F₄₃₀-like cofactor derived from vitamin B₁₂ can catalyze methane formation in the active site of methyl-coenzyme M reductase.

Insights into the Chemical Reactivity in Acetyl-CoA Synthase

The biological synthesis of acetyl-coenzyme A (acetyl-CoA), catalyzed by acetyl-CoA synthase (ACS), is of biological significance and chemical interest acting as a source of energy and carbon. The catalyst contains an unusual hexa-metal cluster with two nickel ions and a [Fe₄S₄] cluster. DFT calculations have been performed to investigate the ACS reaction mechanism starting from three different oxidation states (+2, +1, and 0) of Ni_p, the nickel proximal to [Fe₄S₄]. The results indicate that the ACS reaction proceeds first through a methyl radical transfer from cobalamin (Cbl) to Ni_p randomly accompanying with the CO binding. After that, C-C bond formation occurs between the Ni_p-bound methyl and CO, forming Ni_p-acetyl. The substrate CoA-S^- then binds to Ni_p, allowing C-S bond formation between the Ni_p-bound acetyl and CoA-S^-. Methyl transfer is rate-limiting with a barrier of ∼14 kcal/mol, which does not depend on the presence or absence of CO. Both the Ni_p²⁺ and Ni_p¹⁺ states are chemically capable of catalyzing the ACS reaction independent of the state (+2 or +1) of the [Fe₄S₄] cluster. The [Fe₄S₄] cluster is not found to affect the steps of methyl transfer and C-C bond formation but may be involved in the C-S bond formation depending on the detailed mechanism chosen. An ACS active site containing a Ni_p(0) state could not be obtained. Optimizations always led to a Ni_p¹⁺ state coupled with [Fe₄S₄]¹⁺. The calculations show a comparable activity for Ni_p¹⁺/[Fe₄S₄]¹⁺, Ni_p¹⁺/[Fe₄S₄]²⁺, and Ni_p²⁺/[Fe₄S₄]²⁺. The results here give significant insights into the chemistry of the important ACS reaction.

Bioinorganic Chemistry of Nickel

Following the discovery of the first specific and essential role of nickel in biology in 1975 (the dinuclear active site of the enzyme urease) [...]