Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450cam: Theory Supports a Two-State Rebound Mechanism

Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments

Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to the biodegradation of xenobiotics, but recent work has shown that fungi utilize P450s for the activation of lignin fragments, such as monomer and dimer units. These fragments often are the building blocks of valuable materials, including drug molecules and fragrances, hence a highly selective biocatalyst that can produce these compounds in good yield with high selectivity would be an important step in biotechnology. In this work a detailed computational study is reported on two reaction channels of two P450 isozymes, namely the O-deethylation of guaethol by CYP255A and the O-demethylation versus aromatic hydroxylation of p-anisic acid by CYP199A4. The studies show that the second-coordination sphere plays a major role in substrate binding and positioning, heme access, and in the selectivity patterns. Moreover, the local environment affects the kinetics of the reaction through lowering or raising barrier heights. Furthermore, we predict a site-selective mutation for highly specific reaction channels for CYP199A4.

A density functional study of the photocatalytic degradation of polycaprolactone by the decatungstate anion in acetonitrile solution

A recent experimental study has reported that decatungstate [W10O32]4- can degrade various polyesters in the presence of light and molecular oxygen [Li et al., Nanoscale, 2023, 15, 15038]. We apply density functional theory to the photocatalyst-polycaprolactone model complex in acetonitrile solution and elucidate the degradation mechanisms and catalytic cycle. We consider hydrogen atom transfer (HAT) and single electron transfer (SET) mechanisms. The potential energy profiles show that the former proceeds exergonically in a single step but that the latter involves a subsequent proton transfer and finally yields HAT products as well. Oxygenated polymer species can regain the transferred hydrogen and regenerate the reduced photocatalyst. We propose a photocatalytic cycle that realizes both the photocatalyst regeneration and the polymer degradation.

Reaction engineering blocks ether cleavage for synthesizing chiral cyclic hemiacetals catalyzed by unspecific peroxygenase

Hemiacetal compounds are valuable building blocks in synthetic chemistry, but their enzymatic synthesis is limited and often hindered by the instability of hemiacetals in aqueous environments. Here, we show that this challenge can be addressed through reaction engineering by using immobilized peroxygenase from Agrocybe aegerita (AaeUPO) under neat reaction conditions, which allows for the selective C-H bond oxyfunctionalization of environmentally significant cyclic ethers to cyclic hemiacetals. A wide range of chiral cyclic hemiacetal products are prepared in >99% enantiomeric excess and 95170 turnover numbers of AaeUPO. Furthermore, by changing the reaction medium from pure organic solvent to alkaline aqueous conditions, cyclic hemiacetals are in situ transformed into lactones. Lactams are obtained under the applied conditions, albeit with low enzyme activity. These findings showcase the synthetic potential of AaeUPO and offer a practical enzymatic approach to produce chiral cyclic hemiacetals through C-H oxyfunctionalization under mild conditions.

Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases

Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.

New insight into biodegradation mechanism of phenylurea herbicides by cytochrome P450 enzymes: Successive N-demethylation mechanism

Phenylurea herbicides (PUHs) present one of the most important herbicides, which have cause serious effects on ecological environment and humans. Nowadays enzyme strategy shows great advantages in degradation of PUHs. Here density functional theory (DFT), quantitative structure - activity relationship (QSAR) and quantum mechanics/molecular mechanics (QM/MM) approaches are used to investigate the degradation mechanism of PUHs catalyzed by P450 enzymes. Two successive N-demethylation pathways are identified and two hydrogen abstraction (H-abstraction) reaction pathways are identified as the rate-determining step through high-throughput DFT calculations. The Boltzmann-weighted average energy barrier of the second H-abstraction pathway (19.95 kcal/mol) is higher than that of the first H-abstraction pathway (16.80 kcal/mol). Two QSAR models are established to predict the energy barriers of the two H-abstraction pathways based on the quantum chemical descriptors and mordred molecular descriptors. The determination coefficient (R2) values of QSAR models are > 0.9, which reveal that the established QSAR models have great predictive capability. QM/MM calculations indicate that human P450 enzymes are more efficient in degradation of PUHs than crop and weed P450 enzymes. Correlations between energy barriers and key structural/charge parameters are revealed and key parameters that have influence on degradation efficiency of PUHs are identified. This study provides lateral insights into the biodegradation strategy and removal method of PUHs and valuable information for designing or engineering of highly efficient degradation enzymes and genetically modified crops.

Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations

Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen dilemma faced by cytochrome P450s and exhibit greater stability than the latter. As such, they hold great potential for industrial applications. A thorough understanding of their catalysis is needed to improve their catalytic performance. However, it remains elusive how UPOs effectively convert peroxide to Compound I (CpdI), the principal oxidizing intermediate in the catalytic cycle. Previous computational studies of this process primarily focused on heme peroxidases and P450s, which have significant differences in the active site from UPOs. Additionally, the roles of peroxide unbinding in the kinetics of CpdI formation, which is essential for interpreting existing experiments, have been understudied. Moreover, there has been a lack of free energy characterizations with explicit sampling of protein and hydration dynamics, which is critical for understanding the thermodynamics of the proton transport (PT) events involved in CpdI formation. To bridge these gaps, we employed multiscale simulations to comprehensively characterize the CpdI formation in wild-type UPO from Agrocybe aegerita (AaeUPO). Extensive free energy and potential energy calculations were performed in a quantum mechanics/molecular mechanics setting. Our results indicate that substrate-binding dehydrates the active site, impeding the PT from H2O2 to a nearby catalytic base (Glu196). Furthermore, the PT is coupled with considerable hydrogen bond network rearrangements near the active site, facilitating subsequent O-O bond cleavage. Finally, large unbinding free energy barriers kinetically stabilize H2O2 at the active site. These findings reveal a delicate balance among PT, hydration dynamics, hydrogen bond rearrangement, and cosubstrate unbinding, which collectively enable efficient CpdI formation. Our simulation results are consistent with kinetic measurements and offer new insights into the CpdI formation mechanism at atomic-level details, which can potentially aid the design of next-generation biocatalysts for sustainable chemical transformations of feedstocks.

Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides

Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.

Biotransformation of Bisphenol by Human Cytochrome P450 2C9 Enzymes: A Density Functional Theory Study

Bisphenol A (BPA, 2,2-bis-(4-hydroxyphenyl)propane) is used as a precursor in the synthesis of polycarbonate and epoxy plastics; however, its availability in the environment is causing toxicity as an endocrine-disrupting chemical. Metabolism of BPA and their analogues (substitutes) is generally performed by liver cytochrome P450 enzymes and often leads to a mixture of products, and some of those are toxic. To understand the product distributions of P450 activation of BPA, we have performed a computational study into the mechanisms and reactivities using large model structures of a human P450 isozyme (P450 2C9) with BPA bound. Density functional theory (DFT) calculations on mechanisms of BPA activation by a P450 compound I model were investigated, leading to a number of possible products. The substrate-binding pocket is tight, and as a consequence, aliphatic hydroxylation is not feasible as the methyl substituents of BPA cannot reach compound I well due to constraints of the substrate-binding pocket. Instead, we find low-energy pathways that are initiated with phenol hydrogen atom abstraction followed by OH rebound to the phenolic ortho- or para-position. The barriers of para-rebound are well lower in energy than those for ortho-rebound, and consequently, our P450 2C9 model predicts dominant hydroxycumyl alcohol products. The reactions proceed through two-state reactivity on competing doublet and quartet spin state surfaces. The calculations show fast and efficient substrate activation on a doublet spin state surface with a rate-determining electrophilic addition step, while the quartet spin state surface has multiple high-energy barriers that can also lead to various side products including C⁴-aromatic hydroxylation. This work shows that product formation is more feasible on the low spin state, while the physicochemical properties of the substrate govern barrier heights of the rate-determining step of the reaction. Finally, the importance of the second-coordination sphere is highlighted that determines the product distributions and guides the bifurcation pathways.

Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation?

Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C⁶-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C⁶-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.

The role of the intermediate triplet state in iron-catalyzed multi-state C-H activation

Efficient activation and functionalization of the C-H bond under mild conditions are of a great interest in chemical synthesis. We investigate the previously proposed spin-accelerated activation of the C(sp²)-H bond by a Fe(II)-based catalyst to clarify the role of the intermediate triplet state in the reaction mechanism. High-level electronic structure calculations on a small model of a catalytic system utilizing the coupled cluster with the single, double, and perturbative triple excitations [CCSD(T)] are used to select the density functional for the full-size model. Our analysis indicates that the previously proposed two-state quintet-singlet reaction pathway is unlikely to be efficient due to a very weak spin-orbit coupling between these two spin states. We propose a more favorable multi-state quintet-triplet-singlet reaction pathway and discuss the importance of the intermediate triplet state. This triplet state facilitates a spin-accelerated reaction mechanism by strongly coupling to both quintet and singlet states. Our calculations show that the C-H bond activation through the proposed quintet-triplet-singlet reaction pathway is more thermodynamically favorable than the single-state quintet and two-state singlet-quintet mechanisms.

Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC

The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por^•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por^•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ^• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.

QM-Cluster Model Study of the Guaiacol Hydrogen Atom Transfer and Oxygen Rebound with Cytochrome P450 Enzyme GcoA

The key step of the O-demethylation of guaiacol by GcoA of the cytochrome P450-reductase pair was studied with DFT using two 10-residue and three 15-residue QM-cluster models. For each model, two reaction pathways were examined, beginning with a different guaiacol orientation. Based on this study, His354, Phe349, Glu249, and Pro250 residues were found to be important for keeping the heme in a planar geometry throughout the reaction. Val241 and Gly245 residues were needed in the QM-cluster models to provide the hydrophobic pocket for an appropriate guaiacol pose in the reaction. The aromatic triad Phe75, Phe169, and Phe395 may be necessary to facilitate guaiacol migrating into the enzyme active site, but it does not qualitatively affect kinetics and thermodynamics of the proposed mechanism. All QM-cluster models created by RINRUS agree very well with previous experimental work. This study provides details for better understanding enzymatic O-demethylation of lignins to form catechol derivatives by GcoA.

Insight into the Selective Methylene Oxidation Catalyzed by Mn(CF3-PDP)(SbF6)2/H2O2/CH2ClCO2H) System: A DFT Mechanistic Study

DFT study was employed to gain insight into methylene oxidation catalyzed by Mn(CF₃-PDP)(NCMe)₂ (SbF₆)₂/H₂O₂/HOAc^Cl(OAC^Cl ═OC(O)CH₂Cl). The active catalyst was characterized to be [Mn](O)OAc^Cl ([Mn]═Mn(CF₃-PDP)²⁺) which is generated via a sequence from [Mn] to [Mn]OH to [Mn]OAc^Cl to [Mn]OOH. With the active catalyst, the methylene group is sequentially oxidized to an alcohol and then to a carbonyl group via rebound mechanism. The mechanism explains the observed site selectivity.

How external perturbations affect the chemoselectivity of substrate activation by cytochrome P450 OleTJE

Cytochrome P450 enzymes are versatile biocatalysts found in most forms of life. Generally, the cytochrome P450s react with dioxygen and hence are haem-based mono-oxygenases; however, in specific isozymes, H2O2 rather than O2 is used and these P450s act as peroxygenases. The P450 OleTJE is a peroxygenase that binds long to medium chain fatty acids and converts them to a range of products originating from Cα-hydroxylation, Cβ-hydroxylation, Cα-Cβ desaturation and decarboxylation of the substrate. There is still controversy regarding the details of the reaction mechanism of P450 OleTJE; how the products are formed and whether the product distributions can be influenced by external perturbations. To gain further insights into the structure and reactivity of P450 OleTJE, we set up a range of large active site model complexes as well as full enzymatic structures and did a combination of density functional theory studies and quantum mechanics/molecular mechanics calculations. In particular, the work focused on the mechanisms leading to these products under various reaction conditions. Thus, for a small cluster model, we find a highly selective Cα-hydroxylation pathway that is preferred over Cβ-H hydrogen atom abstraction by at least 10 kcal mol-1. Introduction of polar residues to the model, such as an active site protonated histidine residue or through external electric field effects, lowers the Cβ-H hydrogen atom abstraction barriers are lowered, while a full QM/MM model brings the Cα-H and Cβ-H hydrogen atom abstraction barriers within 1 kcal mol-1. Our studies; therefore, implicate that environmental effects in the second-coordination sphere can direct and guide selectivities in enzymatic reaction mechanisms.

Catalytic Mechanism of Aromatic Nitration by Cytochrome P450 TxtE: Involvement of a Ferric-Peroxynitrite Intermediate

The cytochromes P450 are heme-dependent enzymes that catalyze many vital reaction processes in the human body related to biodegradation and biosynthesis. They typically act as mono-oxygenases; however, the recently discovered P450 subfamily TxtE utilizes O₂ and NO to nitrate aromatic substrates such as L-tryptophan. A direct and selective aromatic nitration reaction may be useful in biotechnology for the synthesis of drugs or small molecules. Details of the catalytic mechanism are unknown, and it has been suggested that the reaction should proceed through either an iron(III)-superoxo or an iron(II)-nitrosyl intermediate. To resolve this controversy, we used stopped-flow kinetics to provide evidence for a catalytic cycle where dioxygen binds prior to NO to generate an active iron(III)-peroxynitrite species that is able to nitrate l-Trp efficiently. We show that the rate of binding of O₂ is faster than that of NO and also leads to l-Trp nitration, while little evidence of product formation is observed from the iron(II)-nitrosyl complex. To support the experimental studies, we performed density functional theory studies on large active site cluster models. The studies suggest a mechanism involving an iron(III)-peroxynitrite that splits homolytically to form an iron(IV)-oxo heme (Compound II) and a free NO₂ radical via a small free energy of activation. The latter activates the substrate on the aromatic ring, while compound II picks up the ipso-hydrogen to form the product. The calculations give small reaction barriers for most steps in the catalytic cycle and, therefore, predict fast product formation from the iron(III)-peroxynitrite complex. These findings provide the first detailed insight into the mechanism of nitration by a member of the TxtE subfamily and highlight how the enzyme facilitates this novel reaction chemistry.

Theoretical Identification of the Factors Governing the Reactivity of C-H Bond Activation by Non-Heme Iron(IV)-Oxo Complexes

Selective functionalization of C-H bonds provides a straightforward approach to a large variety of well-defined derivatives. High-valent mononuclear iron(IV)-oxo complexes are proposed to carry out these C-H activation reactions in enzymes or in biomimetic syntheses. In this Minireview, we aim to highlight the features that delineate the distinct reactivity of non-heme oxo-iron(IV) motifs to cleave strong C-H bonds in hydrocarbons, primarily focusing on the hydrogen atom transfer (HAT) process. We describe how the structural and electronic properties of supporting ligands modulate the oxidative property of the iron(IV)-oxo complexes. Furthermore, we highlight the decisive role played by spin-state in these biomimetic reactions. We also discuss how tunneling and external perturbations like electric field influence the transfer of hydrogen atoms. Lastly, we emphasize how computations could work as a practical guide to sketch and develop synthetic models with greater efficacy.

Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions

The cytochrome P450 metalloenzyme (CYP) CYP199A4 from Rhodopseudomonas palustris HaA2 catalyzes the highly efficient oxidation of para-substituted benzoic acids. Here we determined crystal structures of CYP199A4, and the binding and turnover parameters, with different meta-substituted benzoic acids in order to establish which criteria are important for efficient catalysis. When compared to the para isomers, the meta-substituted benzoic acids were less efficiently oxidized. For example, 3-formylbenzoic acid was oxidized with lower activity than the equivalent para isomer and 3-methoxybenzoic acid did not undergo O-demethylation by CYP199A4. The structural data highlighted that the meta-substituted benzoic acids bound in the enzyme active site in a modified position with incomplete loss of the distal water ligand of the heme moiety. However, for both sets of isomers the meta- or para-substituent pointed towards, and was in close proximity, to the heme iron. The absence of oxidation activity with 3-methoxybenzoic acid was assigned to the observation that the CH bonds of this molecule point away from the heme iron. In contrast, in the para isomer they are in an ideal location for abstraction. These findings were confirmed by using the bulkier 3-ethoxybenzoic acid as a substrate which removed the water ligand and reoriented the meta-substituent so that the methylene hydrogens pointed towards the heme, enabling more efficient oxidation. Overall we show relatively small changes in substrate structure and position in the active site can have a dramatic effect on the activity.

Proton relay network in P450cam formed upon docking of putidaredoxin

Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O─O cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular mechanics computations, both on the well-studied FeOO state and on Cpd(0) (compound 0). Our simulations include (all camphor-bound): (a) WT (wild type), FeOO state. (b) WT, Cpd(0). (c) Pdx (Putidaredoxin, redox partner of P450)-docked-WT, FeOO state. (d) Pdx-docked WT, Cpd(0). (e) Pdx-docked T252A mutant, Cpd(0). Among our key findings: (a) Effect of Pdx docking appears to go far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (b) Specific proton relay networks we identify are: FeOO(H)⋯T252⋯nH ₂ O⋯D251 in WT; FeOO(H)⋯nH ₂ O⋯D251 in T252A mutant; both occur with Pdx docking. (c) Direct interaction of D251 with -FeOOH is, respectively, rare/frequent in WT/T252A mutant. (d) In WT, T252 is in the proton relay network. (e) Positioning of camphor appears significant: when camphor is part of H-bonding network, second protonation appears to be facilitated.

Reduction Potentials of P450 Compounds I and II: Insight into the Thermodynamics of C-H Bond Activation

We present a mixed experimental/theoretical determination of the bond strengths and redox potentials that define the ground-state thermodynamics for C-H bond activation in cytochrome P450 catalysis. Using redox titrations with [Ir(IV)Cl₆]^2-, we have determined the compound II/ferric (or Fe(IV)OH/Fe(III)OH₂) couple and its associated D(O-H)_Ferric bond strength in CYP158. Knowledge of this potential as well as the compound II/ferric (or Fe(IV)O/Fe(III)OH) reduction potential in horseradish peroxidase and the two-electron compound I/ferric (or Fe(IV)O(Por^•)/Fe(III)OH₂(Por)) reduction potential in aromatic peroxidase has allowed us to gauge the accuracy of theoretically determined bond strengths. Using the restricted open shell (ROS) method as proposed by Wright and co-workers, we have obtained O-H bond strengths and associated redox potentials for charge-neutral H-atom reductions of these iron(IV)-hydroxo and -oxo porphyrin species that are within 1 kcal/mol of experimentally determined values, suggesting that the ROS method may provide accurate values for the P450-II O-H bond strength and P450-I reduction potential. The efforts detailed here indicate that the ground-state thermodynamics of C-H bond activation in P450 are best described as follows: E^0'_Comp-I = 1.22 V (at pH 7, vs NHE) with D(O-H)_Comp-II = 95 kcal/mol and E^0'_Comp-II = 0.99 V (at pH 7, vs NHE) with D(O-H)_Ferric = 90 kcal/mol.

Stereo-preference of camphor for H-bonding with phenol, methanol and chloroform: A combined matrix isolation IR spectroscopic and quantum chemical investigation

Camphor is known to be held in the substrate pocket of cytochrome P450cam enzyme via H-bond with a tyrosine residue of the enzyme in a unique orientation. This structural exclusivity results in regio- and stereo-specific hydroxylation of camphor by the enzyme. We have carried out a combined IR spectroscopic and quantum chemical investigation to shed light on the factors influencing the conformational exclusivity of 1R-(+)-camphor in the substrate pocket of Cytochrome P450cam, and to determine whether the selectivity is an inherent property of the substrate itself, or is imposed by the enzyme. For this purpose, complexes of camphor have been studied with three H-bond donors namely phenol, methanol and chloroform. Each of the three donors was found to form stable complexes with two distinct conformers; the one mimicking the conformation in enzyme substrate pocket was found to be more stable of the two, for all three donors. Experimentally, both conformers of the H-bonded complexes were identified separately for phenol and methanol in an argon matrix at 8 K, but not for chloroform due to very small energy barrier for interconversion of the two conformers. In room temperature solution phase spectra of camphor with all three donors, the differences in spectral attributes between the two isomeric H-bonded complexes were lost due to thermal motions.

Design, synthesis, and insecticidal activity evaluation of novel 4-(N, N-diarylmethylamines)furan-2(5H)-one derivatives as potential acetylcholine receptor insecticides

BACKGROUND

Flupyradifurone is a member of a novel class of insecticides that possess excellent insecticidal activities. Halogen-containing phenyl groups are important and indispensable structural components of many pesticides. However, replacement of the difluoromethyl group of flupyradifurone with halogen-containing phenyl groups has not been reported. Hence, a series of novel butenolide derivatives containing phenyl groups were synthesized and bioassayed to discover novel compounds with excellent insecticidal activities.

RESULTS

Some target molecules exhibited good insecticidal activities against Aphis craccivora. Among the title compounds, 4cc showed the best insecticidal activities with an 50% lethal concentration (LC₅₀ ) value of 1.72 μg mL^-1 , which is superior to that of pymetrozine (LC₅₀  = 6.86 μg mL^-1 ). Molecular docking indicated that 4cc lacks oxidative metabolism by CYP6CM1 and metabolic resistance with imidacloprid. Furthermore, label-free quantitative proteomic analysis indicated that 4cc may be a potential acetylcholine receptor insecticide that acts on the nicotinic acetylcholine receptor. Compound 4cc also decreased the capability for oxidative metabolism, which further supported the molecular docking results.

CONCLUSION

This work can be used to further investigate the mechanism underlying the insecticidal activity of butenolide derivatives and develop potential novel butenolide insecticides. © 2018 Society of Chemical Industry.

Electronic Structure Contributions of Non-Heme Oxo-Iron(V) Complexes to the Reactivity

Oxo-iron(V) species have been implicated in the catalytic cycle of the Rieske dioxygenase. Their synthetic analog, [Fe^V(O)(OC(O)CH₃)(PyNMe₃)]²⁺ (1, PyNMe₃ = 3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene-3,6,9-trimethyl), derived from the O-O bond cleavage of its acetylperoxo iron(III) precursor, has been shown experimentally to perform regio- and stereoselective C-H and C═C bond functionalization. However, its structure-activity relation is poorly understood. Herein we present a detailed electronic-structure and spectroscopic analysis of complex 1 along with well-characterized oxo-iron(V) complexes, [Fe^V(O)(TAML)]^- (2, TAML = tetraamido macrocyclic ligand), [Fe^V(O)(TMC)(NC(O)CH₃)]⁺ (4, TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), and [Fe^V(O)(TMC)(NC(OH)CH₃)]²⁺ (4-H⁺), using wave function-based multireference complete active-space self-consistent field calculations. Our results reveal that the x/ y anisotropy of the ⁵⁷Fe A-matrix is not a reliable spectroscopic marker to identify oxo-iron(V) species and that the drastically different A _x and A _y values determined for complexes 1, 4, and 4-H⁺ have distinctive origins compared to complex 2, a genuine oxo-iron(V) species. Complex 1, in fact, has a dominant character of [Fe^IV(O···OC(O)CH₃)^2-•]²⁺, i.e., an S_Fe = 1 iron(IV) center antiferromagnetically coupled to an O-O σ* radical, where the O-O bond has not been completely broken. Complex 4 is best described as a triplet ferryl unit that strongly interacts with the trans acetylimidyl radical in an antiferromagnetic fashion, [Fe^IV(O)(^•N═C(O^-)CH₃)]⁺. Complex 4-H⁺ features a similar electronic structure, [Fe^IV(O)(^•N═C(OH)CH₃)]²⁺. Owing to the remaining approximate half σ-bond in the O-O moiety, complex 1 can arrange two electron-accepting orbitals (α σ*_O-O and β Fe-d _xz) in such a way that both orbitals can simultaneously interact with the doubly occupied electron-donating orbitals (σ_C-H or π_C-C). Hence, complex 1 can promote a concerted yet asynchronous two-electron oxidation of the C-H and C═C bonds, which nicely explains the stereospecificity observed for complex 1 and the related species.

What drives the H-abstraction reaction in bio-mimetic oxoiron-bTAML complexes? A computational investigation

Monomeric iron-oxo units have been confirmed as intermediates involved in the C-H bond activation in various metallo-enzymes. Biomimetic oxoiron complexes of the biuret modified tetra-amido macrocyclic ligand (bTAML) have been demonstrated to oxidize a wide variety of unactivated C-H bonds. In the current work, density functional theory (DFT) has been employed to investigate the hydrogen abstraction (HAT) reactivity differences across a series of bTAML complexes. The cause for the differences in the HAT energy barriers has been found to be the relative changes in the energy of the frontier molecular orbitals (FMOs) induced by electronic perturbation.

Stereoselective Metabolism of Omeprazole by Cytochrome P450 2C19 and 3A4: Mechanistic Insights from DFT Study

The efficacy of S-omeprazole as a proton pump inhibitor compared with that of its enantiomer R-omeprazole is studied using density functional theoretical calculations. The pharmacokinetic studies suggest that the efficacy of S-omeprazole presumably depends on metabolic pathway and excretion from the human body. The density functional theory calculations at SMD_water-B3LYP-D3/6-311+G(d,p)/LANL2DZ//B3LYP/6-31G(d)/LANL2DZ with triradicaloid model active species, [Por^•+Fe^IV(SH)O], of CYP2C19 enzyme with high-spin quartet and low-spin doublet states demonstrate C-H bond activation mechanism through a two-state rebound process for the hydroxylation of R-omeprazole and S-omeprazole. The calculated activation free energy barriers for the hydrogen abstraction are 15.7 and 17.5 kcal/mol for R-omeprazole and S-omeprazole, respectively. The hydroxylation of R-omeprazole and S-omeprazole is thermodynamically favored; however, the hydroxylated intermediate of S-omeprazole further disintegrates to metabolite 5- O-desmethylomeprazole with a higher kinetic barrier. We have examined the sulfoxidation of S-omeprazole to omeprazole sulfone metabolite by CYP3A4, and the observed activation free energy barrier is 9.9 kcal/mol. The computational results reveal that CYP2C19 exclusively metabolizes R-omeprazole to hydroxyomeprazole, which is hydrophilic and can easily excrete, whereas CYP3A4 metabolizes S-omeprazole to lipophilic sulfone; hence, the excretion of this metabolite would be relatively slower from the body. The spin density analysis and molecular orbital analysis performed using biorthogonalization calculations indicate that R-omeprazole favors high-spin pathway for metabolism process whereas S-omeprazole prefers the low-spin pathway.

Theoretical studies of the second step of the nitric oxide synthase reaction: Electron tunneling prevents uncoupling

Nitric oxide (NO·) is a messenger molecule with diverse physiological roles including host defense, neurotransmission and vascular function. The synthesis of NO· from l-arginine is catalyzed by NO-synthases and occurs in two steps through the intermediary Nω-hydroxy-l-arginine (NHA). In both steps the P450-like reaction cycle is coupled with the redox cycle of the cofactor tetrahydrobiopterin (H4B). The mechanism of the second step is studied by Density Functional Theory calculations to ascertain the canonical sequence of proton and electron transfer (PT and ET) events. The proposed mechanism is controlled by the interplay of two electron donors, H4B and NHA. Consistent with experimental data, the catalytic cycle proceeds through the ferric-hydroperoxide complex (Cpd 0) and the following aqua-ferriheme resting state, and involves interim partial oxidation of H4B. The mechanism starts with formation of Cpd 0 from the ferrous-dioxy reactant complex by PT from the C-ring heme propionate coupled with hole transfer to H4B through the highest occupied π-orbital of NHA as a bridge. This enables PT from NHA+· to the proximal oxygen leading to the shallow ferriheme-H2O2 oxidant. Subsequent Fenton-like peroxide bond cleavage triggered by ET from the NHA-derived iminoxy-radical leads to the protonated Cpd II diradicaloid singlet stabilized by spin delocalization in H4B, and the closed-shell coordination complex of HO- with iminoxy-cation. The complex is converted to the transient C-adduct, which releases intended products upon PT to the ferriheme-HO- complex coupled with ET to the H4B+·. Deferred ET from the substrate or undue ET from/to the cofactor leads to side products.

A competing, dual mechanism for catalytic direct benzene hydroxylation from combined experimental-DFT studies

A dual mechanism for direct benzene catalytic hydroxylation is described. Experimental studies and DFT calculations have provided a mechanistic explanation for the acid-free, Tp ^x Cu-catalyzed hydroxylation of benzene with hydrogen peroxide (Tp ^x = hydrotrispyrazolylborate ligand). In contrast with other catalytic systems that promote this transformation through Fenton-like pathways, this system operates through a copper-oxyl intermediate that may interact with the arene ring following two different, competitive routes: (a) electrophilic aromatic substitution, with the copper-oxyl species acting as the formal electrophile, and (b) the so-called rebound mechanism, in which the hydrogen is abstracted by the Cu-O moiety prior to the C-O bond formation. Both pathways contribute to the global transformation albeit to different extents, the electrophilic substitution route seeming to be largely favoured.

meso-Tetraphenylporphyrin Iron Chloride Catalyzed Selective Oxidative Cross-Coupling of Phenols

A novel catalytic system for oxidative cross-coupling of readily oxidized phenols with poor nucleophilic phenolic partners based on an iron meso-tetraphenylporphyrin chloride (Fe[TPP]Cl) complex in 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) was developed. The unique chemoselectivity of this reaction is attributed to the coupling between a liberated phenoxyl radical with an iron-ligated phenolic coupling partner. The conditions are scalable for preparing a long list of unsymmetrical biphenols assembled from a less reactive phenolic unit substituted with alkyl or halide groups.

Hydrogen Abstraction of Camphor Catalyzed by Cytochrome P450cam: A QM/MM Study

A combined quantum mechanics and molecular mechanics (QM/MM, QM = UB3LYP-D3, MM = AMBER) method is used to study the hydrogen abstraction reaction in P450_cam catalyzed hydroxylation of camphor in the quartet state. Compared to QM/MM calculations in the literature, this study uses larger basis sets for the most important atoms at the active site and QM/MM Hessian harmonic frequency calculations to determine the standard Gibbs free energy of activation and kinetic isotope effect. The QM/MM covalent boundary is treated with a capping hydrogen atom method, which is simple and robust. An energy barrier of 21.3 kcal/mol and a standard free energy of activation of 16.8 kcal/mol are obtained for this hydrogen abstraction reaction. These values are similar to those reported in the literature, suggesting that when a general protocol is followed, QM/MM results are reproducible. It is found that using a sufficiently large basis set is important to minimize basis set errors.

Molecular determinants for selective C25-hydroxylation of vitamins D2and D3by fungal peroxygenases

Regioselective hydroxylation of vitamin D byAgrocybe aegeritaandCoprinopsis cinereaperoxygenases was investigated in an experimental and computational study.

Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450

The activation barrier for the hydroxylation of camphor by cytochrome P450 was computed using a mixed quantum mechanics/molecular mechanics (QM/MM) model of the full protein-ligand system and a fully QM calculation using a cluster model of the active site at the B3LYP/LACVP*/LACV3P** level of theory, which consisted of B3LYP/LACV3P** single point energies computed at B3LYP/LACVP* optimized geometries. From the QM/MM calculation, a barrier height of 17.5 kcal/mol was obtained, while the experimental value was known to be less than or equal to 10 kcal/mol. This process was repeated using the D3 correction for hybrid DFT in order to investigate whether the inadequate treatment of dispersion interaction was responsible for the overestimation of the barrier. While the D3 correction does reduce the computed barrier to 13.3 kcal/mol, it was still in disagreement with experiment. After application of a series of transition metal optimized localized orbital corrections (DBLOC) and without any refitting of parameters, the barrier was further reduced to 10.0 kcal/mol, which was consistent with the experimental results. The DBLOC method to CH bond activation in methane monooxygenase (MMO) was also applied, as a second, independent test. The barrier in MMO was known, by experiment, to be 15.4 kcal/mol. After application of the DBLOC corrections to the MMO barrier compute by B3LYP, in a previous study, and accounting for dispersion with Grimme's D3 method, the unsigned deviation from experiment was improved from 3.2 to 2.3 kcal/mol. These results suggested that the combination of dispersion plus localized orbital corrections could yield significant quantitative improvements in modeling the catalytic chemistry of transition-metal containing enzymes, within the limitations of the statistical errors of the model, which appear to be on the order of approximately 2 kcal/mole.

QM/MM Models of the O2-Evolving Complex of Photosystem II

This paper introduces structural models of the oxygen-evolving complex of photosystem II (PSII) in the dark-stable S1 state, as well as in the reduced S0 and oxidized S2 states, with complete ligation of the metal-oxo cluster by amino acid residues, water, hydroxide, and chloride. The models are developed according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, applied in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus, recently reported at 3.5 Å resolution. Manganese and calcium ions are ligated consistently with standard coordination chemistry assumptions, supported by biochemical and spectroscopic data. Furthermore, the calcium-bound chloride ligand is found to be bound in a position consistent with pulsed electron paramagnetic resonance data obtained from acetate-substituted PSII. The ligation of protein ligands includes monodentate coordination of D1-D342, CP43-E354, and D1-D170 to Mn(1), Mn(3), and Mn(4), respectively; η(2) coordination of D1-E333 to both Mn(3) and Mn(2); and ligation of D1-E189 and D1-H332 to Mn(2). The resulting QM/MM structural models are consistent with available mechanistic data and also are compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements of PSII. It is, therefore, conjectured that the proposed QM/MM models are particularly relevant to the development and validation of catalytic water-oxidation intermediates.

Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X-ray Spectroscopy: A Simulation Study

Cytochrome P450 enzymes are an important family of biocatalysts that oxidize chemically inert CH bonds. There are many unresolved questions regarding the catalytic reaction intermediates, in particular P450 Compound I (Cpd-I) and II (Cpd-II). By using simple molecular models, we simulate various X-ray spectroscopy signals, including X-ray absorption near-edge structure (XANES), resonant inelastic X-ray scattering (RIXS), and stimulated X-ray Raman spectroscopy (SXRS) of the low- and high-spin states of Cpd-I and II. Characteristic peak patterns are presented and connected to the corresponding electronic structures. These X-ray spectroscopy techniques are complementary to more conventional infrared and optical spectroscopy and they help to elucidate the evolving electronic structures of transient species along the reaction path.

Flupyradifurone (Sivanto™) and its novel butenolide pharmacophore: Structural considerations

Flupyradifurone (4-[(2,2-difluoroethyl)amino]-2(5H)-furanone), a member of the new class of butenolide insecticides, contains a novel bioactive scaffold as pharmacophore. It is very versatile in terms of application methods to a variety of crops, exhibits excellent and fast action against a broad spectrum of sucking pest insects including selected neonicotinoid resistant pest populations such as whiteflies and aphids expressing metabolic resistance mechanisms. As a partial agonist flupyradifurone reversibly binds to insect nicotinic acetylcholine receptors (nAChRs) and lacks metabolization by CYP6CM1, a cytochrome P450 over-expressed in cotton whiteflies resistant to imidacloprid and pymetrozine. The butenolide insecticides exhibit structure-activity relationships (SAR) that are different from other nAChR agonists such as the classes of neonicotinoids and sulfoximines. The paper briefly reviews the discovery of the butenolide insecticide flupyradifurone, its SAR differentiating it from established nAChR agonists and a molecular docking approach using the binding site model of CYP6CM1vQ of Bemisia tabaci known to confer metabolic resistance to neonicotinoid insecticides.