Quantum mechanics/molecular mechanics study of oxygen binding in hemocyanin

The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase

Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

Computational Evaluation of Potential Molecular Catalysts for Nitrous Oxide Decomposition

Nitrous oxide (N₂O) is a potent greenhouse gas (GHG) with limited use as a mild anesthetic and underdeveloped reactivity. Nitrous oxide splitting (decomposition) is critical to its mitigation as a GHG. Although heterogeneous catalysts for N₂O decomposition have been developed, highly efficient, long-lived solid catalysts are still needed, and the details of the catalytic pathways are not well understood. Reported herein is a computational evaluation of three potential molecular (homogeneous) catalysts for N₂O splitting, which could aid in the development of more active and robust catalysts and provide deeper mechanistic insights: one Cu(I)-based, [(CF₃O)₄Al]Cu (A-1), and two Ru(III)-based, Cl(POR)Ru (B-1) and (NTA)Ru (C-1) (POR = porphyrin, NTA = nitrilotriacetate). The structures and energetic viability of potential intermediates and key transition states are evaluated according to a two-stage reaction pathway: (A) deoxygenation (DO), during which a metal-N₂O complex undergoes N-O bond cleavage to produce N₂ and a metal-oxo species and (B) (di)oxygen evolution (OER), in which the metal-oxo species dimerizes to a dimetal-peroxo complex, followed by conversion to a metal-dioxygen species from which dioxygen dissociates. For the (F-L)Cu(I) activator (A-1), deoxygenation of N₂O is facilitated by an O-bound (F-L)Cu-O-N₂ or better by a bimetallic N,O-bonded, (F-L)Cu-NNO-Cu(F-L) complex; the resulting copper-oxyl (F-L)Cu-O is converted exergonically to (F-L)Cu-(η²,η²-O₂)-Cu(F-L), which leads to dioxygen species (F-L)Cu(η²-O₂), that favorably dissociates O₂. Key features of the DO/OER process for (POR)ClRu (B-1) include endergonic N₂O coordination, facile N₂ evolution from LR'u-N₂O-RuL to Cl(POR)RuO, moderate barrier coupling of Cl(POR)RuO to peroxo Cl(POR)Ru(O₂)Ru(POR)Cl, and eventual O₂ dissociation from Cl(POR)Ru(η¹-O₂), which is nearly thermoneutral. N₂O decomposition promoted by (NTA)Ru(III) (C-1) can proceed with exergonic N₂O coordination, facile N₂ dissociation from (NTA)Ru-ON₂ or (NTA)Ru-N₂O-Ru(NTA) to form (NTA)Ru-O; dimerization of the (NTA)Ru-oxo species is facile to produce (NTA)Ru-O-O-Ru(NTA), and subsequent OE from the peroxo species is moderately endergonic. Considering the overall energetics, (F-L)Cu and Cl(POR)Ru derivatives are deemed the best candidates for promoting facile N₂O decomposition.

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

Spin-projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B-DNA by Singlet Oxygen

Guanine is the most susceptible base to oxidation damage induced by reactive oxygen species including singlet oxygen (1 O2 , 1 Δg ). We clarify whether the first step of guanine oxidation in B-DNA proceeds via either a zwitterionic or a diradical intermediate. The free energy profiles are calculated by means of a combined quantum mechanical and molecular mechanical (QM/MM) method coupled with the adaptive biasing force (ABF) method. To describe the open-shell electronic structure of 1 O2 correctly, the broken-symmetry spin-unrestricted density functional theory (BS-UDFT) with an approximate spin projection (AP) correction is applied to the QM region. We find that the effect of spin contamination on the activation and reaction free energies is up to ∼8 kcal mol-1 , which is too large to be neglected. The QM(AP-ULC-BLYP)/MM-based free energy calculations also reveal that the reaction proceeds through a diradical transition state, followed by a conversion to a zwitterionic intermediate. Our computed activation energy of 5.2 kcal mol-1 matches experimentally observed range (0∼6 kcal mol-1 ).

Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions. I. A Shared-Orbital Implementation

In the modeling of spin-crossing reactions, it has become popular to directly explore the spin-adiabatic surfaces. Specifically, through constructing spin-adiabatic states from a two-state Hamiltonian (with spin-orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a "transition state" structure, where the spin crossing occurs. In this work, we report the implementation of a fully-variational spin-adiabatic approach based on Kohn-Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit-Pauli one-electron spin-orbit operator. For three model spin-crossing reactions [predissociation of N₂O, singlet-triplet conversion in CH₂, and CO addition to Fe(CO)₄], the spin-crossing points were obtained. Our results also indicated the Breit-Pauli one-electron spin-orbit coupling can vary significantly along the reaction pathway on the spin-adiabatic energy surface. On the other hand, due to the restriction that low-spin and high-spin states share the same set of molecular orbitals, the acquired spin-adiabatic energy surface shows a cusp (i.e. a first-order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin-adiabatic surfaces.

The oxidative dehydrogenation of a coumarinyl scaffold with copper ion and metal ion detection in human liver cancer cells (HepG2)

An unsymmetrical o-phenylenediamine derivative, L (7-hydroxy-4-methyl-8-(1-(phenyl- (pyridin-2-yl)methyl)-1H-benzo[d]imidazol-2-yl)-2H-chromen-2-one), has been synthesized from (E)-N¹-(phenyl(pyridine-2-yl)methylene)benzene-1,2-diamine with 7-hydroxy-4-methyl-2-oxo-2H-chromene-8-carbaldehyde and characterized by X-ray, IR, ¹H NMR and ESI-MS spectral analyses. The X-ray structure shows L as a cyclic benzimidazole derivative, but it undergoes ring-opening upon reaction with transition metal ions. L is non-emissive in 9 : 1 (v/v) EtOH/H₂O (HEPES buffer, pH 7.4) but becomes highly fluorescent upon Zn²⁺ coordination, and the emissive Zn(ii) complex undergoes transmetallation in the presence of Cu²⁺ ions specifically, followed by amine to imine oxidation, i.e. an oxidative dehydrogenation (OD) reaction -(2e + 2H⁺) occurs. The transmetallation of Zn²⁺ from the complex by Cu²⁺ (CuCl₂) separated the non-emissive X-ray diffractable crystal of [Cu(L'')Cl] (L'' = amine oxidized form of L). A square pyramidal [Cu(L'')][ClO₄] complex was also isolated from the reaction of L with Cu(CH₃CN)₄(ClO₄) in the presence of air, and in this complex the amine is also oxidized to the imine. Here, copper ions in the presence of air play an important role in the OD reaction of L as determined by EPR and cyclic voltammetry studies. The ligand, L, is used for Zn²⁺ ion recovery from a municipally supplied water sample. A paper strip detection kit for Zn²⁺ and Cu²⁺ is designed using L. The ligand is also used for intracellular Zn²⁺ detection in a human liver cancer cell line (HepG2).

Hydration facilitates oxygenation of hemocyanin: perspectives from molecular dynamics simulations

Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein. The oxygenation effect on the overall structure of the protein or polypeptide subunit was further explored via gyration radii evaluated for the metal-binding domain and for the whole subunit. The evaluation of hydration dynamics was carried out to understand the water mediated role of amino acid residues of the solvent tunnel facilitating the entry of oxygen molecule to the dicopper site of hemocyanin.

Surface hopping dynamics including intersystem crossing using the algebraic diagrammatic construction method

We report an implementation for employing the algebraic diagrammatic construction to second order [ADC(2)] ab initio electronic structure level of theory in nonadiabatic dynamics simulations in the framework of the SHARC (surface hopping including arbitrary couplings) dynamics method. The implementation is intended to enable computationally efficient, reliable, and easy-to-use nonadiabatic dynamics simulations of intersystem crossing in organic molecules. The methodology is evaluated for the 2-thiouracil molecule. It is shown that ADC(2) yields reliable excited-state energies, wave functions, and spin-orbit coupling terms for this molecule. Dynamics simulations are compared to previously reported results using high-level multi-state complete active space perturbation theory, showing favorable agreement.

Computational Study of Catalytic Reaction of Quercetin 2,4-Dioxygenase

We present a quantum mechanics/molecular mechanics (QM/MM) and QM-only study on the oxidative ring-cleaving reaction of quercetin catalyzed by quercetin 2,4-dioxygenase (2,4-QD). 2,4-QD has a mononuclear type 2 copper center and incorporates two oxygen atoms at C2 and C4 positions of the substrate. It has not been clear whether dioxygen reacts with a copper ion or a substrate radical as the first step. We have found that dioxygen is more likely to bind to a Cu(2+) ion, involving the dissociation of the substrate from the copper ion. Then a Cu(2+)-alkylperoxo complex can be generated. Comparison of geometry and stability between QM-only and QM/MM results strongly indicates that steric effects of the protein environment contribute to maintain the orientation of the substrate dissociated from the copper center. The present QM/MM results also highlight that a prior rearrangement of the Cu(2+)-alkylperoxo complex and a subsequent hydrogen bond switching assisted by the movement of Glu73 can facilitate formation of an endoperoxide intermediate selectively.

Tris(2,2'-azobispyridine) complexes of copper(II): X-ray structures, reactivities, and the radical nonradical bis(ligand) analogues

Tris(abpy) complexes of types mer-[Cu(II)(abpy)3][PF6]2 (mer-1(2+)[PF6(–)]2) and ctc-[Cu(II)(abpy)2(bpy)][PF6]2 (ctc-2(2+)[PF6(–)]2) were successfully isolated and characterized by spectra and single-crystal X-ray structure determinations (abpy = 2,2′-azobispyridine; bpy = 2,2′-bipyridine). Reactions of mer-1(2+) and ctc-2(2+) ions with catechol, o-aminophenol, p-phenylenediamine, and diphenylamine (Ph–NH–Ph) in 2:1 molar ratio afford [CuI(abpy)2](+) (3(+)) and corresponding quinone derivatives. The similar reactions of [Cu(II)(bpy)3](2+) and [Cu(II)(phen)3](2+) with these substrates yielding [Cu(I)(bpy)2](+) and [Cu(I)(phen)2](+) imply that these complexes undergo reduction-induced ligand dissociation reactions (phen = 1,10-phenanthroline). The average −N═N– lengths in mer-1(2+)[PF6(–)]2 and ctc-2(2+)[PF6(–)]2 are 1.248(4), while that in 3(+)[PF6(–)]·2CH2Cl2 is relatively longer, 1.275(2) Å, due to dCu → πazo* back bonding. In cyclic voltammetry, mer-1(2+) exhibits one quasi-reversible wave at −0.42 V due to Cu(II)/Cu(I) and abpy/abpy(•–) couples and two reversible waves at −0.90 and −1.28 V due to abpy/abpy(•–) couple, while those of ctc-2(2+) ion appear at −0.44, −0.86, and −1.10 V versus Fc(+)/Fc couple. The anodic 3(2+)/3(+) and the cathodic 3(+)/3 redox waves at +0.33 and −0.40 V are reversible. The electron paramagnetic resonance spectra and density functional theory (DFT) calculations authenticated the existence of abpy anion radical (abpy(•–)) in 3, which is defined as a hybrid state of [Cu(I)(abpy(0.5•–))(abpy(0.5•–))] and [Cu(II)(abpy(•–))(abpy(•–))] states. 3(2+) ion is a neutral abpy complex of copper(II) of type [Cu(II)(abpy)2](2+). 3 exhibits a near-IR absorption band at 2400–3000 nm because of the intervalence ligand-to-ligand charge transfer, elucidated by time-dependent DFT calculations in CH2Cl2.

On the reaction mechanism of the complete intermolecular O2 transfer between mononuclear nickel and manganese complexes with macrocyclic ligands

The recently described intermolecular O2 transfer between the side-on Ni-O2 complex [(12-TMC)Ni-O2](+) and the manganese complex [(14-TMC)Mn](2+), where 12-TMC and 14-TMC are 12- and 14-membered macrocyclic ligands, 12-TMC=1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane and 14-TMC=1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane, is studied by means of DFT methods. B3LYP calculations including long-range corrections and solvent effects are performed to elucidate the mechanism. The potential energy surfaces (PESs) compatible with different electronic states of the reactants have been analyzed. The calculations confirm a two-step reaction, with a first rate-determining bimolecular step and predict the exothermic character of the global process. The relative stability of the products and the reverse barrier are in line with the fact that no reverse reaction is experimentally observed. An intermediate with a μ-η(1):η(1)-O2 coordination and two transition states are identified on the triplet PES, slightly below the corresponding stationary points of the quintet PES, suggesting an intersystem crossing before the first transition state. The calculated activation parameters and the relative energies of the two transition sates and the products are in very good agreement with the experimental data. The calculations suggest that a superoxide anion is transferred during the reaction.