Convergent Theoretical Prediction of Reactive Oxidant Structures in Diiron Arylamine Oxygenases AurF and CmlI: Peroxo or Hydroperoxo?

Diverging Reaction Pathways and Key Intermediates in Ethylene Forming Enzyme

Ethylene-forming enzyme (EFE) is a non-heme iron(II)- and 2-oxoglutarate-(Fe(II)/2OG)-dependent oxygenase with distinct catalytic reactivity. While most Fe(II)/2OG-dependent oxygenases catalyze substrate hydroxylation with the 2OG decarboxylation to succinate, EFE primarily converts 2OG into CO2 and ethylene. In this work, we employ a multifaceted approach, including molecular dynamics, quantum mechanics and molecular mechanics methods, theoretical Mössbauer spectroscopy, and the analysis of the intrinsic electric field exerted by the protein environment, to examine possible reaction pathways. Our study reveals a novel second branch point, where the ethylene formation (EF) and 3-hydroxypropionate formation pathways diverge following the Fe(III)-carbonate and C3-C5-derived propion-3-yl radical intermediates, occurring earlier than suggested in previous studies. We identified multiple subsequent EF pathways characterized by a low-energy barrier and the formation of either Fe(II)-carbonates or Fe(II)-pyrocarbonates. Based on these findings, we introduce a revised reaction mechanism for ethylene formation in EFE, which is consistent with available experimental data and highlights the importance of retaining C2-derived CO2, generated in earlier stages, within the active site for the EF pathway. We also identified intermediates that can produce the Mössbauer quadrupole doublet peak observed in recent experiments and associated with unidentified Fe(II)-containing species characteristic to the ethylene-forming reaction pathway. This work provides new insights into both the first and second branchpoints of the ethylene-forming pathway that can be useful in EFE modifications aimed at shifting the product yield in the EF reaction.

Nature of the Reactive Biferric Peroxy Intermediate P' in the Arylamine Oxygenases and Related Binuclear Fe Enzymes

Binuclear nonheme iron enzymes activate O2 to perform a wide range of chemical transformations. The process of O2 activation typically involves a biferric peroxy-level intermediate P. It has been previously found that this intermediate undergoes further activation, either protonation or rearrangement to form P' or further oxidation to form high-valent intermediates Q or X. This study defines the structure of the P' intermediate in the N-oxygenases CmlI (and AurF based on previous data) using nuclear resonance vibrational spectroscopy (NRVS) in conjugation with density functional theory (DFT) calculations. These results, combined with variable temperature variable field (VTVH) magnetic circular dichroism (MCD) spectroscopy on the 1-electron cryoreduced P', define the structure of the P' intermediate as a μ-1,2-hydroxoperoxo biferric site with a second hydroxide bridge. Reaction coordinate calculations demonstrate that single electron transfer (SET) is facilitated by protonation of the peroxo, activating its reductive cleavage, and that the additional hydroxide bridge does not impact this reaction. VTVH MCD studies further reveal that the hydroxide bridge is absent in the biferrous site, suggesting that during the O2 reaction with the biferrous site, a water molecule forms the hydroxide bridge in providing the proton that activates the peroxide in P' for reactivity.

Prediction of 57Fe Mössbauer Nuclear Quadrupole Splittings with Hybrid and Double-Hybrid Density Functionals

As a crucial parameter in Mössbauer spectroscopy, nuclear quadrupole splitting (NQS) exhibits a strong dependence on quantum chemistry methods, which makes accurate theoretical predictions challenging. Meanwhile, the continuous emergence of new density functionals presents opportunities to advance current NQS research. In this study, we evaluate the performance of eleven hybrid density functionals and twelve double-hybrid density functionals, selected from widely used functionals and newly developed functionals, in predicting the NQS values of the 57Fe nuclide for 32 iron-containing molecules within about 70 atoms. The calculations have incorporated scalar relativistic effects using the exact two-component (X2C) Hamiltonian. In general, the double-hybrid functional PBE-0DH demonstrates superior performance compared to the experimental values, achieving a mean absolute error (MAE) of 0.20 mm/s. Meanwhile, rSCAN38 is the best hybrid functional for our database with an MAE = 0.25 mm/s, and it offers a significant advantage in computational efficiency over PBE-0DH. The +/- sign of NQS has also been considered in our error statistics when it has a clear physical meaning; if neglected, the errors of many functionals decrease, but PBE-0DH and rSCAN38 remain unaffected. Notably, when calculating ferrocene [Fe(C5H5)2], which involves strong static correlations, all hybrid functionals that incorporate more than 10% exact exchange fail, while several double-hybrid functionals continue to deliver reliable results. In addition, we encountered two particularly challenging species characterized by strong static correlations: [Fe(H2O)5NO]2+ and FeO2--porphyrin. Unfortunately, none of the density functionals tested in our study yielded satisfactory results for the two cases since the density functional theory (DFT) is a single-determinant approach, and it is imperative to explore large-scale multi-configurational methods for these species. This research offers valuable guidance for selecting density functionals in Mössbauer NQS calculations and serves as a reference point for the future development of new density functionals.

Relatively reliable and rapid identification of colorant compounds in food matrices by HPLC-DAD-QTOF-MS combined with theoretical calculation

A new convenient method for identifying colorant compounds (CCs) in food matrices was developed using high-performance liquid chromatography with a diode array detector and quadrupole-time-of-flight mass spectrometer (HPLC-DAD-Q/TOF-MS) combined with theoretical calculations. A model sample containing three typical CCs was completely separated via HPLC-DAD. The obtained 3D ultraviolet-visible (UV-vis) spectra revealed the maximum absorption wavelengths (MAWs) of all CCs (yellow, 430 nm; red, 520 nm; blue, 620 nm) in the range of 400-800 nm, and their colors were determined based on their MAWs. Temporary structures of the CCs were obtained using Q/TOF-MS analysis. Theoretical calculations were then performed to obtain the theoretical MAWs and colors of the CCs according to their calculated UV-vis spectra based on temporary structures. The structures of the CCs were confirmed without the need for authoritative standards by comparing the consistency between their experimental and theoretical MAWs and colors. This method is particularly suitable for identifying CCs or compounds with UV-Vis absorption, including new compounds, compounds for which standards are difficult to obtain, and known compounds without reporting relevant molecular information.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Origin of Unprecedented Formation and Reactivity of FeIV═O Species via Oxygen Activation: Role of Noncovalent Interactions and Magnetic Coupling

Emulating the capabilities of the soluble methane monooxygenase (sMMO) enzymes, which effortlessly activate oxygen at diiron(II) centers to form a reactive diiron(IV) intermediate Q, which then performs the challenging oxidation of methane to methanol, poses a significant challenge. Very recently, one of us reported the mononuclear complex [(cyclam)FeII(CH3CN)2]2+ (1), which performed a rare bimolecular activation of the molecule of O2 to generate two molecules of FeIV═O without the requirement of external proton or electron sources, similar to sMMO. In the present study, we employed the density functional theory (DFT) calculations to investigate this unique mechanism of O2 activation. We show that secondary hydrogen-bonding interactions between ligand N-H groups and O2 play a vital role in reducing the energy barrier associated with the initial O2 binding at 1 and O-O bond cleavage to form the FeIV═O complex. Further, the unique reactivity of FeIV═O species toward simultaneous C-H and O-H bond activation process has been demonstrated. Our study unveils that the nature of the magnetic coupling between the diiron centers is also crucial. Given that the influence of magnetic coupling and noncovalent interactions in catalysis remains largely unexplored, this unexplored realm presents numerous avenues for experimental chemists to develop novel structural and functional analogues of sMMO.

DFT mechanistic study of biomimetic diiron complex catalyzed dehydrogenation: Unexpected Fe(III)Fe(III)-1,1-μ-hydroperoxy active species for hydride abstraction

The diiron active site is pivotal in catalyzing transformations in both biological and chemical systems. Recently, a range of biomimetic diiron catalysts have been synthesized, drawing inspiration from the active architecture of soluble methane monooxygenase (sMMO). These catalysts have been successfully deployed for the dehydrogenation of indolines, marking a significant advancement in the field. Using density functional theory (DFT) calculations, we have identified a novel mechanistic pathway that governs the dehydrogenation of indolines catalyzed by a biomimetic diiron complex. Specifically, this reaction is facilitated by the transfer of a hybrid atom from the C1 position of the substrate to the distal oxygen atom of the Fe(III)Fe(III)-1,1-μ-hydroperoxy active species. This transfer serves as the rate-limiting step for the heterolytic cleavage of the OO bond, ultimately generating the substrate cation. The mechanism we propose aligns well with mechanistic investigations incorporating both kinetic isotope effect (KIE) measurements and evaluations of stereochemical selectivity. This research contributes to the broader scientific understanding of catalysis involving biomimetic diiron complexes and offers valuable insights into the catalytic behaviors of non-heme diiron metalloenzymes.

Conserved Enzymatic Cascade for Bacterial Azoxy Biosynthesis

Azoxy compounds exhibit a wide array of biological activities and possess distinctive chemical properties. Although there has been considerable interest in the biosynthetic mechanisms of azoxy metabolites, the enzymatic basis responsible for azoxy bond formation has remained largely enigmatic. In this study, we unveil the enzyme cascade that constructs the azoxy bond in valanimycin biosynthesis. Our research demonstrates that a pair of metalloenzymes, comprising a membrane-bound hydrazine synthase and a nonheme diiron azoxy synthase, collaborate to convert an unstable pathway intermediate to an azoxy product through a hydrazine-azo-azoxy pathway. Additionally, by characterizing homologues of this enzyme pair from other azoxy metabolite pathways, we propose that this two-enzyme cascade could represent a conserved enzymatic strategy for azoxy bond formation in bacteria. These findings provide significant mechanistic insights into biological N-N bond formation and should facilitate the targeted isolation of bioactive azoxy compounds through genome mining.

Dioxygen Activation and Nδ,Nε-Dihydroxylation Mechanism Involved in the Formation of N-Nitrosourea Pharmacophore in Streptozotocin Catalyzed by Nonheme Diiron Enzyme SznF

SznF is a nonheme diiron-dependent enzyme that catalyzes the critical N-nitrosation involved in the formation of the N-nitrosourea moiety in the pancreatic cancer drug streptozotocin. The N-nitrosation contains two successive N-hydroxylation and N-nitrosation steps, which are carried out by two separate active sites, namely, the central domain and cupin domain. Recently, the crystal structure of SznF was obtained, and the central domain was proved to contain a diiron cofactor to catalyze the N-hydroxylation. In this work, to gain insights into the O₂ activation and the successive N-hydroxylation mechanism, on the basis of the high-resolution crystal structure, the enzyme-substrate complex models were constructed, and a series of combined QM/MM calculations were performed. Based on our calculations, the activation of O₂ starts from the diiron(II,III)-superoxo (S) to generate the diiron(IV)-oxo species (Q) via a diiron(III,III)-peroxo (P)-like transition state or unstable intermediate (P'), and species P' can be described as a hybridization of diiron(IV)-oxo species and diiron(III,III)-peroxo (P) owing to the long distances of Fe1-Fe2 (4.22 Å) and O1-O2 (1.89 Å), which is different from those of other nonheme diiron enzymes. In the following hydroxylation of N^δ and N^ε, the N^δ-hydroxylation was confirmed to occur first, agreeing with the experimental observations. Because the diiron(IV)-oxo species (Q) is responsible for hydroxylation, the reaction follows the H-abstraction/OH rebound mechanism, and the first abstraction occurs on the N^δ-H rather than N^ε-H, which may be attributed to the different orientation of Fe(IV)-oxo relative to N-H as well as the bond dissociation enthalpies of two N-H bonds. The hydroxylation of N-methyl-L-arginine does not employ the diiron(III,III)-hydroperoxo (P″) to trigger the electrophilic attack of the guanidine to directly form the N-O bond, as previously suggested. In addition, our calculations also revealed that the direct attack of the Fe(IV)═O unit to the N^δ of the substrate corresponds to a higher barrier than that in the H-abstraction/OH rebound mechanism. These results may provide useful information for understanding the formation of the di-hydroxylation intermediate involved in the biosynthesis of N-nitrosation.

Second coordination sphere effects on the mechanistic pathways for dioxygen activation by a ferritin: involvement of a Tyr radical and the identification of a cation binding site

Ferritins are ubiquitous diiron enzymes involved in iron(II) detoxification and oxidative stress responses and can act as metabolic iron stores. The overall reaction mechanisms of ferritin enzymes are still unclear, particularly concerning the role of the conserved, near catalytic center Tyr residue. Thus, we carried out a computational study of a ferritin using a large cluster model of well over 300 atoms including its first- and second-coordination sphere. The calculations reveal important insight into the structure and reactivity of ferritins. Specifically, the active site Tyr residue delivers a proton and electron in the catalytic cycle prior to iron(II) oxidation. In addition, the calculations highlight a likely cation binding site at Asp65, which through long-range electrostatic interactions, influences the electronic configuration and charge distributions of the metal center. The results are consistent with experimental observations but reveal novel detail of early mechanistic steps that lead to an unusual mixed-valent iron(III)-iron(II) center.

Generation of a μ-1,2-hydroperoxo FeIIIFeIII and a μ-1,2-peroxo FeIVFeIII Complex

μ-1,2-Peroxo-diferric intermediates (P) of non-heme diiron enzymes are proposed to convert upon protonation either to high-valent active species or to activated P′ intermediates via hydroperoxo-diferric intermediates. Protonation of synthetic μ-1,2-peroxo model complexes occurred at the μ-oxo and not at the μ-1,2-peroxo bridge. Here we report a stable μ-1,2-peroxo complex {Fe^III(μ-O)(μ-1,2-O₂)Fe^III} using a dinucleating ligand and study its reactivity. The reversible oxidation and protonation of the μ-1,2-peroxo-diferric complex provide μ-1,2-peroxo Fe^IVFe^III and μ-1,2-hydroperoxo-diferric species, respectively. Neither the oxidation nor the protonation induces a strong electrophilic reactivity. Hence, the observed intramolecular C-H hydroxylation of preorganized methyl groups of the parent μ-1,2-peroxo-diferric complex should occur via conversion to a more electrophilic high-valent species. The thorough characterization of these species provides structure-spectroscopy correlations allowing insights into the formation and reactivities of hydroperoxo intermediates in diiron enzymes and their conversion to activated P′ or high-valent intermediates.

Iron coordination complexes can be used to gain insight on biologically relevant iron-oxygen compounds generated in iron metalloenzymes. Here, the authors characterise a μ-1,2-hydroperoxo Fe^IIIFe^III and a μ-1,2-peroxo Fe^IVFe^III, and study their reactivity in C-H activation.

Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis

PtmU3 is a newly identified nonheme diiron monooxygenase, which installs a C-5 β-hydroxyl group into the C-19 CoA-ester intermediate involved in the biosynthesis of unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 possesses a noncanonical diiron active site architecture of a saturated six-coordinate iron center and lacks the μ-oxo bridge. Although the hydroxylation process is a simple reaction for nonheme mononuclear iron-dependent enzymes, how PtmU3 employs the diiron center to catalyze the H-abstraction and OH-rebound is still unknown. In particular, the electronic characteristic of diiron is also unclear. To understand the catalytic mechanism of PtmU3, we constructed two reactant models in which both the Fe1^II-Fe2^III-superoxo and Fe1^II-Fe2^IV═O are considered to trigger the H-abstraction and performed a series of quantum mechanics/molecular mechanics calculations. Our calculation results reveal that PtmU3 is a special monooxygenase, that is, both atoms of the dioxygen molecule can be incorporated into two molecules of the substrate by the successive reactions. In the first-round reaction, PtmU3 uses the Fe1^II-Fe2^III-superoxo to install a hydroxyl group into the substrate, generating the high-reactive Fe1^II-Fe2^IV═O complex. In the second-round reaction, the Fe1^II-Fe2^IV═O species is responsible for the hydroxylation of another molecule of the substrate. In the diiron center, Fe2 adopts the high spin state (S = 5/2) during the catalysis, whereas for Fe1, in addition to its structural role, it may also play an assistant role for Fe1 catalysis. In the two successive OH-installing steps, the H-abstraction is always the rate-liming step. E241 and D308 not only act as bridging ligands to connect two Fe ions but also take part in the electron reorganization. Owing to the high reactivity of Fe1^II-Fe2^IV═O compared to Fe1^II-Fe2^III-superoxo, besides the C5-hydroxylation, the C3- or C18-hydroxylation was also calculated to be feasible.

Rapid evaluation of the substrate specificity of 3-nitrobenzoic acid dioxygenase MnbAB via colorimetric detection using Saltzman reagent

Nitroaromatic compounds are essential materials for chemical industry, but they are also potentially toxic environmental pollutants. Therefore, their sensitive detection and degradation are important concerns. The microbial degradation pathways of nitroaromatic compounds have been studied in detail, but their usefulness needs to be evaluated to understand their potential applications in bioremediation. Here, we developed a rapid and relatively sensitive assay system to evaluate the activities and substrate specificities of nitroaromatic dioxygenases involved in the oxidative biodegradation of nitroaromatic compounds. In this system, nitrous acid, which was released from the nitroaromatic compounds by the dioxygenases, was detected and quantified using the Saltzman reagent. Escherichia coli producing the 3-nitrobenzoic acid dioxygenase complex MnbAB from Comamonas sp. JS46 clearly showed the apparent substrate specificity of MnbAB as follows. MnbAB accepted not only 3-nitrobenzoic acid but also several other p- and m-nitrobenzoic acid derivatives as substrates, although it much preferred 3-nitrobenzoic acid to others. Furthermore, the presence of a hydroxy or an amino group at the ortho position of the nitro group decreased the activity of MnbAB. In addition, MnbAB accepted 2-(4-nitrophenyl)acetic acid as a substrate, which has one additional methylene group between the aromatic ring and the carboxy group of 3-nitrobenzoic acid. This is the first report about the detailed substrate specificity of MnbAB. Our system can be used for other nitroaromatic dioxygenases and contribute to their characterization.

Nitrogen-Nitrogen Bond Formation Reactions Involved in Natural Product Biosynthesis

Construction of nitrogen-nitrogen bonds involves sophisticated biosynthetic mechanisms to overcome the difficulties inherent to the nucleophilic nitrogen atom of amine. Over the past decade, a multitude of reactions responsible for nitrogen-nitrogen bond formation in natural product biosynthesis have been uncovered. On the basis of the intrinsic properties of these reactions, this Review classifies these reactions into three categories: comproportionation, rearrangement, and radical recombination reactions. To expound the metallobiochemistry underlying nitrogen-nitrogen bond formation reactions, we discuss the enzymatic mechanisms in comparison to well characterized canonical heme-dependent enzymes, mononuclear nonheme iron-dependent enzymes, and nonheme di-iron enzymes. We also illuminate the intermediary properties of nitrogen oxide species NO₂^-, NO⁺, and N₂O₃ in nitrogen-nitrogen bond formation reactions with clues derived from inorganic nitrogen metabolism driven by anammox bacteria and nitrifying bacteria. These multidimentional discussions will provide further insights into the mechanistic proposals of nitrogen-nitrogen bond formation in natural product biosynthesis.

N-oxygenation of amino compounds: Early stages in its application to the biocatalyzed preparation of bioactive compounds

Among the compounds that contain unusual functional groups, nitro is perhaps one of the most interesting due to the valuable properties it confers on pharmaceuticals and explosives. Traditional chemistry has for many years used environmentally unfriendly strategies; in contrast, the biocatalyzed production of this type of products offers a promising alternative. The small family of enzymes formed by N-oxygenases allows the conversion of an amino group to a nitro through the sequential addition of oxygen. These enzymes also make it possible to obtain other less oxidized N-O functions, such as hydroxylamine or nitroso, present in intermediate or final products. The current substrates on which these enzymes are reported to work encompass a few aromatic molecules and sugars. The unique characteristics of N-oxygenases and the great economic value of the products that they could generate, place them in a position of very high scientific and industrial interest. The most important and best studied N-oxygenases will be presented here.

Deciphering the origin of million-fold reactivity observed for the open core diiron [HO-FeIII-O-FeIV[double bond, length as m-dash]O]2+ species towards C-H bond activation: role of spin-states, spin-coupling, and spin-cooperation

High-valent metal-oxo species have been characterised as key intermediates in both heme and non-heme enzymes that are found to perform efficient aliphatic hydroxylation, epoxidation, halogenation, and dehydrogenation reactions. Several biomimetic model complexes have been synthesised over the years to mimic both the structure and function of metalloenzymes. The diamond-core [Fe2(μ-O)2] is one of the celebrated models in this context as this has been proposed as the catalytically active species in soluble methane monooxygenase enzymes (sMMO), which perform the challenging chemical conversion of methane to methanol at ease. In this context, a report of open core [HO(L)FeIII-O-FeIV(O)(L)]2+ (1) gains attention as this activates C-H bonds a million-fold faster compared to the diamond-core structure and has the dual catalytic ability to perform hydroxylation as well as desaturation with organic substrates. In this study, we have employed density functional methods to probe the origin of the very high reactivity observed for this complex and also to shed light on how this complex performs efficient hydroxylation and desaturation of alkanes. By modelling fifteen possible spin-states for 1 that could potentially participate in the reaction mechanism, our calculations reveal a doublet ground state for 1 arising from antiferromagnetic coupling between the quartet FeIV centre and the sextet FeIII centre, which regulates the reactivity of this species. The unusual stabilisation of the high-spin ground state for FeIV[double bond, length as m-dash]O is due to the strong overlap of with the orbital, reducing the antibonding interactions via spin-cooperation. The electronic structure features computed for 1 are consistent with experiments offering confidence in the methodology chosen. Further, we have probed various mechanistic pathways for the C-H bond activation as well as -OH rebound/desaturation of alkanes. An extremely small barrier height computed for the first hydrogen atom abstraction by the terminal FeIV[double bond, length as m-dash]O unit was found to be responsible for the million-fold activation observed in the experiments. The barrier height computed for -OH rebound by the FeIII-OH unit is also smaller suggesting a facile hydroxylation of organic substrates by 1. A strong spin-cooperation between the two iron centres also reduces the barrier for second hydrogen atom abstraction, thus making the desaturation pathway competitive. Both the spin-state as well as spin-coupling between the two metal centres play a crucial role in dictating the reactivity for species 1. By exploring various mechanistic pathways, our study unveils the fact that the bridged μ-oxo group is a poor electrophile for both C-H activation as well for -OH rebound. As more and more evidence is gathered in recent years for the open core geometry of sMMO enzymes, the idea of enhancing the reactivity via an open-core motif has far-reaching consequences.

Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein

Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater Mn^II affinity than Fe^II affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.

Theoretical study on the catalytic mechanism of human deoxyhypusine hydroxylase

Deoxyhypusine hydroxylase is a critical enzyme for hypusination of eukaryotic translation initiation factor 5A.

Molecular mechanism of azoxy bond formation for azoxymycins biosynthesis

Azoxy bond is an important chemical bond and plays a crucial role in high energy density materials. However, the biosynthetic mechanism of azoxy bond remains enigmatic. Here we report that the azoxy bond biosynthesis of azoxymycins is an enzymatic and non-enzymatic coupling cascade reaction. In the first step, nonheme diiron N-oxygenase AzoC catalyzes the oxidization of amine to its nitroso analogue. Redox coenzyme pairs then facilitate the mutual conversion between nitroso group and hydroxylamine via the radical transient intermediates, which efficiently dimerize to azoxy bond. The deficiency of nucleophilic reactivity in AzoC is proposed to account for the enzyme's non-canonical oxidization of amine to nitroso product. Free nitrogen radicals induced by coenzyme pairs are proposed to be responsible for the efficient non-enzymatic azoxy bond formation. This mechanism study will provide molecular basis for the biosynthesis of azoxy high energy density materials and other valuable azoxy chemicals.

Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis

Nonheme diiron monooxygenases make up a rapidly growing family of oxygenases that are rarely identified in secondary metabolism. Herein, we report the in vivo, in vitro, and structural characterizations of a nonheme diiron monooxygenase, PtmU3, that installs a C-5 β-hydroxyl group in the unified biosynthesis of platensimycin and platencin, two highly functionalized diterpenoids that act as potent and selective inhibitors of bacterial and mammalian fatty acid synthases. This hydroxylation sets the stage for the subsequent A-ring cleavage step key to the unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 adopts an unprecedented triosephosphate isomerase (TIM) barrel structural fold for this class of enzymes and possesses a noncanonical diiron active site architecture with a saturated six-coordinate iron center lacking a μ-oxo bridge. This study reveals the first member of a previously unidentified superfamily of TIM-barrel-fold enzymes for metal-dependent dioxygen activation, with the majority predicted to act on CoA-linked substrates, thus expanding our knowledge of nature's repertoire of nonheme diiron monooxygenases and TIM-barrel-fold enzymes.

Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.

Diiron monooxygenases in natural product biosynthesis

Covering: up to 2017 The participation of non-heme dinuclear iron cluster-containing monooxygenases in natural product biosynthetic pathways has been recognized only recently. At present, two families have been discovered. The archetypal member of the first family, CmlA, catalyzes β-hydroxylation of l-p-aminophenylalanine (l-PAPA) covalently linked to the nonribosomal peptide synthetase (NRPS) CmlP, thereby effecting the first step in the biosynthesis of chloramphenicol by Streptomyces venezuelae. CmlA houses the diiron cluster in a metallo-β-lactamase protein fold instead of the 4-helix bundle fold of nearly every other diiron monooxygenase. CmlA couples O2 activation and substrate hydroxylation via a structural change caused by formation of the l-PAPA-loaded CmlP:CmlA complex. The other new diiron family is typified by two enzymes, AurF and CmlI, which catalyze conversion of aryl-amine substrates to aryl-nitro products with incorporation of oxygen from O2. AurF from Streptomyces thioluteus catalyzes the formation of p-nitrobenzoate from p-aminobenzoate as a precursor to the biostatic compound aureothin, whereas CmlI from S. venezuelae catalyzes the ultimate aryl-amine to aryl-nitro step in chloramphenicol biosynthesis. Both enzymes stabilize a novel type of peroxo-intermediate as the reactive species. The rare 6-electron N-oxygenation reactions of CmlI and AurF involve two progressively oxidized pathway intermediates. The enzymes optimize efficiency by utilizing one of the reaction pathway intermediates as an in situ reductant for the diiron cluster, while simultaneously generating the next pathway intermediate. For CmlI, this reduction allows mid-pathway regeneration of the peroxo intermediate required to complete the biosynthesis. CmlI ensures specificity by carrying out the multistep aryl-amine oxygenation without dissociating intermediate products.