Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid

Metal-ligand dual-site single-atom nanozyme mimicking urate oxidase with high substrates specificity

In nature, coenzyme-independent oxidases have evolved in selective catalysis using isolated substrate-binding pockets. Single-atom nanozymes (SAzymes), an emerging type of non-protein artificial enzymes, are promising to simulate enzyme active centers, but owing to the lack of recognition sites, realizing substrate specificity is a formidable task. Here we report a metal-ligand dual-site SAzyme (Ni-DAB) that exhibited selectivity in uric acid (UA) oxidation. Ni-DAB mimics the dual-site catalytic mechanism of urate oxidase, in which the Ni metal center and the C atom in the ligand serve as the specific UA and O2 binding sites, respectively, characterized by synchrotron soft X-ray absorption spectroscopy, in situ near ambient pressure X-ray photoelectron spectroscopy, and isotope labeling. The theoretical calculations reveal the high catalytic specificity is derived from not only the delicate interaction between UA and the Ni center but also the complementary oxygen reduction at the beta C site in the ligand. As a potential application, a Ni-DAB-based biofuel cell using human urine is constructed. This work unlocks an approach of enzyme-like isolated dual sites in boosting the selectivity of non-protein artificial enzymes.

Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions

By performing molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and QM cluster calculations, the origin of chemoselectivity of halohydrin dehalogenase (HHDH)-catalyzed ring-opening reactions of epoxide with the nucleophilic reagent NO2- has been explored. Four possible chemoselective pathways were considered, and the computed results indicate that the pathway associated with the nucleophilic attack on the Cα position of epoxide by NO2- is most energetically favorable and has an energy barrier of 12.9 kcal/mol, which is close to 14.1 kcal/mol derived from experimental kinetic data. A hydrogen bonding network formed by residues Ser140, Tyr153, and Arg157 can strengthen the electrophilicity of the active site of the epoxide substrate to affect chemoselectivity. To predict the energy barrier trends of the chemoselective transition states, multiple analyses including distortion analysis and electrophilic Parr function (Pk+) analysis were carried out with or without an enzyme environment. The obtained insights should be valuable for the rational design of enzyme-catalyzed and biomimetic organocatalytic epoxide ring-opening reactions with special chemoselectivity.

Cofactor-independent C-C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

Biosynthesis of atypical angucyclines involves unique oxidative B-ring cleavage and rearrangement reactions, which are catalyzed by AlpJ-family oxygenases, including AlpJ, JadG, and GilOII. Prior investigations established the essential requirement for FADH2/FMNH2 as cofactors when utilizing the quinone intermediate dehydrorabelomycin as a substrate. In this study, we unveil a previously unrecognized facet of these enzymes as cofactor-independent oxygenases when employing the hydroquinone intermediate CR1 as a substrate. The enzymes autonomously drive oxidative ring cleavage and rearrangement reactions of CR1, yielding products identical to those observed in cofactor-dependent reactions of AlpJ-family oxygenases. Furthermore, the AlpJ- and JadG-catalyzed reactions of CR1 could be quenched by superoxide dismutase, supporting a catalytic mechanism wherein the substrate CR1 reductively activates molecular oxygen, generating a substrate radical and the superoxide anion O2 •-. Our findings illuminate a substrate-controlled catalytic mechanism of AlpJ-family oxygenases, expanding the realm of cofactor-independent oxygenases. Notably, AlpJ-family oxygenases stand as a pioneering example of enzymes capable of catalyzing oxidative reactions in either an FADH2/FMNH2-dependent or cofactor-independent manner.

Polyvinylpyrrolidone-Coated Cubic Hollow Nanocages of PdPt3 and PdIr3 as Highly Efficient Self-Cascade Uricase/Peroxidase Mimics

Uricase-catalyzed uric acid (UA) degradation has been applied for hyperuricemia therapy, but this medication is limited by H2O2 accumulation, which can cause oxidative stress of cells, resulting in many other health issues. Herein, we report a robust cubic hollow nanocage (HNC) system based on polyvinylpyrrolidone-coated PdPt3 and PdIr3 to serve as highly efficient self-cascade uricase/peroxidase mimics to achieve the desired dual catalysis for both UA degradation and H2O2 elimination. These HNCs have hollow cubic shape with average wall thickness of 1.5 nm, providing desired synergy to enhance catalyst's activity and stability. Density functional theory calculations suggest the PdIr3 HNC surface tend to promote OH*/O* desorption for better peroxidase-like catalysis, while the PdPt3 HNC surface accelerates the UA oxidation by facilitating O2-to-H2O2 conversion. The dual catalysis power demonstrated by these HNCs in cell studies suggests their great potential as a new type of nanozyme for treating hyperuricemia.

A Wearable Electrochemical Biosensor Utilizing Functionalized Ti3C2Tx MXene for the Real-Time Monitoring of Uric Acid Metabolite

Wearable, noninvasive sensors enable the continuous monitoring of metabolites in sweat and provide clinical information related to an individual's health and disease states. Uric acid (UA) is a key indicator highly associated with gout, hyperuricaemia, hypertension, kidney disease, and Lesch-Nyhan syndrome. However, the detection of UA levels typically relies on invasive blood tests. Therefore, developing a wearable device for noninvasive monitoring of UA concentrations in sweat could facilitate real-time personalized disease prevention. Here, we introduce 1,3,6,8-pyrene tetrasulfonic acid sodium salt (PyTS) as a bifunctional molecule functionalized with Ti3C2Tx via π-π conjugation to design nonenzymatic wearable sensors for sensitive and selective detection of UA concentration in human sweat. PyTS@Ti3C2Tx provides many oxidation-reduction active groups to enhance the electrocatalytic ability of the UA oxidation reaction. The PyTS@Ti3C2Tx-based electrochemical sensor demonstrates highly sensitive detection of UA in the concentration range of 5 μM-100 μM, exhibiting a lower detection limit of 0.48 μM compared to the uricase-based sensor (0.84 μM). In volunteers, the PyTS@Ti3C2Tx-based wearable sensor is integrated with flexible microfluidic sweat sampling and wireless electronics to enable real-time monitoring of UA levels during aerobic exercise. Simultaneously, it allows for comparison of blood UA levels via a commercial UA analyzer. Herein, this study provides a promising electrocatalyst strategy for nonenzymatic electrochemical UA sensor, enabling noninvasive real-time monitoring of UA levels in human sweat and personalized disease prevention.

Neutron crystallographic refinement with REFMAC5 from the CCP4 suite

Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.

Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates-Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O2 to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O2 to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O2 picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling.

Cofactor-Free Dioxygenases-Catalyzed Reaction Pathway via Proton-Coupled Electron Transfer

Understanding the general mechanism of the metal-free and cofactor-free oxidases and oxygenases catalyzed activation of triplet O₂ is one of the most challenging questions in the field of enzymatic catalysis. Herein, we have performed Quantum Mechanics/Molecular Mechanics (QM/MM) multiscale simulations to reveal the detailed mechanism of the HOD catalyzed (i.e., 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase from Arthrobacter nitroguajacolicus Rü61a) decomposition of N-heteroaromatic compounds. The complete catalytic mechanism includes four steps: (1) proton transfer from 1-H-3-hydroxy-4-oxoquinaldine (QND) substrate to His251 residue coupled with an electron transfer from QND to triplet O₂ (i.e., PCET), (2) formation of C-O bond via an open-shell singlet diradical recombination pathway, (3) ring-closure to form a bicyclic ring, and (4) dissociation of CO. The dissociation of CO is determined as the rate-limiting step, and its calculated energy barrier of 14.9 kcal/mol is consistent with the 15.5 kcal/mol barrier derived from experimental kinetic data. The mechanistic profile is not only valuable for understanding the fundamental pathway of cofactor-free oxidases and oxygenases-catalyzed reactions involving the triplet O₂ activation but also discloses a new pathway that undergoes the processes of PCET and open-shell singlet transition state.

Characterization of a novel marine microbial uricase from Priestia flexa and evaluation of the effects of CMCS conjugation on its enzymatic properties

A novel uricase producing marine bacterium Priestia flexa alkaAU was isolated and identified. The 16S rDNA and the uricase coding gene were sequenced, analyzed and submitted to GenBank. The uricase from Priestia flexa alkaAU (PFU) was purified, determined to be 58.87 kDa, and conjugated with carboxymethyl chitosan (CMCS) by ionic gelation. CMCS conjugation had no effect on the optimum pH of PFU but decreased the optimum temperature by 10 °C. CMCS conjugation increased the specific activity of PFU by 53% at the human body temperature (37 °C) and small intestine's pH (pH 6.8). Uricase thermostabilizing ability of CMCS was significant in the range of 37-80 °C but not at lower temperatures. For improvement of the pH stability of PFU, CMCS was more effective at pHs 3-5 than pHs 6-11. CMCS increased the half-life of PFU against artificial intestinal fluid by 1.5 folds, which demonstrated the potential capability of CMCS-PFU for oral administration.

Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization

The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.

Cofactor-free ActVA-Orf6 monooxygenase catalysis via proton-coupled electron transfer: A QM/MM study

Uncovering the comprehensive catalytic mechanism for the activation of triplet O2 through metal-free and cofactor-free oxidases and oxygenases remains one of the most challenging questions in the area of enzymatic...

The chiral pyridoxal-catalyzed biomimetic Mannich reaction: the mechanism and origin of stereoselectivity

A biomimetic organocatalyst with a pyridoxal-like structure is one of the most successful examples of catalyzing organic reactions under mild conditions in an asymmetric synthesis field.

Organocatalytic insertion into C–B bonds by in situ generated carbene: mechanism, role of the catalyst, and origin of stereoselectivity

The calculated results showed that C–H⋯X (X = I, Br) hydrogen bond interactions should be the determining factors of stereoselectivity, and FMO overlap mode and ELF analyses along IRC results were performed to explore the nature of carbene insertion.

N-Heterocyclic Carbene-Catalyzed Asymmetric C-O Bond Construction Between Benzoic Acid and o-Phthalaldehyde: Mechanism and Origin of Stereoselectivity

A computational study was contributed to explore the origin of stereoselectivity of NHC-mediated cyclization reaction between benzoic acid and o-phthalaldehyde for asymmetric construction of phthalidyl ester. The most energetically favorable pathway mainly includes the following steps: (1) nucleophilic attack on carbonyl carbon of o-phthalaldehyde by catalyst NHC, (2) formation of Breslow intermediate, (3) oxidation by DQ, (4) asymmetric formation of dual C-O bonds, and (5) dissociation of catalyst with the product. The C-O bond formation was testified as the stereoselectivity-determining step, the R-configurational pathway is more energetically favorable than the S-configurational one. The non-covalent interaction (NCI) and atom-in-molecule (AIM) analyses were performed to reveal that the O-H ⋅⋅⋅ O and C-H ⋅⋅⋅ O hydrogen-bond interactions are the key factors for controlling the stereoselectivity. The detailed mechanism and origin of stereoselectivity give useful insights for understanding organocatalytic reactions for asymmetric construction of C-O bond.

Multi- and single-reference methods for the analysis of multi-state peroxidation of enolates

In spite of being spin-forbidden, some enzymes are capable of catalyzing the incorporation of O₂(Σg-3) to organic substrates without needing any cofactor. It has been established that the process followed by these enzymes starts with the deprotonation of the substrate forming an enolate. In a second stage, the peroxidation of the enolate formation occurs, a process in which the system changes its spin multiplicity from a triplet state to a singlet state. In this article, we study the addition of O₂ to enolates using state-of-the-art multi-reference and single-reference methods. Our results confirm that intersystem crossing is promoted by stabilization of the singlet state along the reaction path. When multi-reference methods are used, large active spaces are required, and in this situation, semistochastic heat-bath configuration interaction emerges as a powerful method to study these multi-configurational systems and is in good agreement with PNO-LCCSD(T) when the system is well-represented by a single-configuration.

Unraveling the Way Acetaldehyde is Formed from Acetylene: A Study Based on DFT

Acetylene hydratase (AH) of Pelobacter acetylenicus is a tungsten (W)-containing iron-sulfur enzyme that catalyzes the transformation of acetylene to acetaldehyde, the exact/true reaction mechanism of which is still in question. Scientists utilized different computational approaches to understand the reaction mechanism of acetylene hydration. Some identified it as a multistep (4-16) process that starts with the displacement of a water molecule present at the active site of AH with acetylene. However, some said that there is no need to displace water with acetylene at the active site of AH. As the reaction mechanism for the conversion of acetylene to acetaldehyde is still controversial and needs to be investigated further, DFT studies were performed on the model complexes derived from the native protein X-ray crystal structure of AH. Based on the computational results, here we are proposing the nucleophilic reaction mechanism where the water (Wat1424) molecule is coordinated to the W center and Asp13 is assumed to be in an anionic form. The Wat1424 molecule is activated by W and then donates one of its protons to the anionic Asp13, forming the W-bound hydroxide and protonated Asp13. The W-bound hydroxide then attacks the C1 atom of acetylene together with the transfer of a proton from Asp13 to its C2 atom, resulting in the formation of a vinyl alcohol intermediate complex. The energy barrier associated with this step is 14.4 kcal/mol. The final, rate-limiting, step corresponds to the tautomerization of the vinyl alcohol intermediate to acetaldehyde via intermolecular assistance of two water molecules, associated with an energy barrier of 18.9 kcal/mol. Also, the influence of the metal on the hydration of acetylene is studied when W is replaced with Mo.

Cofactor-free oxidase-mimetic nanomaterials from self-assembled histidine-rich peptides

Natural oxidases mainly rely on cofactors and well-arranged amino acid residues for catalysing electron-transfer reactions but suffer from non-recovery of their activity upon externally induced protein unfolding. However, it remains unknown whether residues at the active site can catalyse similar reactions in the absence of the cofactor. Here, we describe a series of self-assembling, histidine-rich peptides, as short as a dipeptide, with catalytic function similar to that of haem-dependent peroxidases. The histidine residues of the peptide chains form periodic arrays that are able to catalyse H₂O₂ reduction reactions efficiently through the formation of reactive ternary complex intermediates. The supramolecular catalyst exhibiting the highest activity could be switched between inactive and active states without loss of activity for ten cycles of heating/cooling or acidification/neutralization treatments, demonstrating the reversible assembly/disassembly of the active residues. These findings may aid the design of advanced biomimetic catalytic materials and provide a model for primitive cofactor-free enzymes.

Three-dimensional nitrogen-doped graphene-based metal-free electrochemical sensors for simultaneous determination of ascorbic acid, dopamine, uric acid, and acetaminophen

Three-dimensional nitrogen-doped graphene (3D-NG) networks, yielded by hydrothermal reaction and freeze-drying treatment, were used as building blocks to construct a metal-free quadruplet electrochemical sensor for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA), and acetaminophen (AP). The introduced 3D-NG materials with a 3D porous structure and a nitrogen doping effect were beneficial for the generation of multidimensional electron transfer pathways and the improvement of electrocatalytic activities by modulating their electronic properties, which could contribute to the effective differentiation of the four analytes in their quaternary mixture. Well-resolved oxidation peaks and enhanced response currents of AA, DA, UA, and AP were obtained from the 3D-NG-based electrodes. For the individual determination of one analyte, the linear concentration ranges of AA, DA, UA, and AP were 20-10 000, 1-1000, 0.5-1000, and 0.1-600 μM with detection limits of 3.91, 0.26, 0.12, and 0.02 μM (S/N = 3), respectively. After the synchronous change of the concentrations of AA, DA, UA, and AP, desirable linear relationships were observed in the ranges of 100-7000, 2-600, 1-800, and 10-550 μM with detection limits of 24.33, 0.37, 0.21, and 1.87 μM (S/N = 3), respectively. This sensitive sensing platform was successfully used to monitor AA, DA, UA, and AP in human urine samples, which indicated that 3D-NG could become a promising electrode material for the simultaneous monitoring of multiple electroactive species.

Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis

Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to de-hydro-isourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hy-droxy-isourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the 'peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H2O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O-H⋯π interaction with 8AZA. The active site Lys10-Thr57 dyad features a charged Lys10-NH3 + side chain engaged in a strong hydrogen bond with Thr57OG1, while the Thr57OG1-HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHUC5 with Thr57HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O2 exchange during catalysis.

DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*

Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O₂ at room temperature because O₂ is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.

Terpyridine-based Pd(ii)/Ni(ii) organometallic framework nano-sheets supported on graphene oxide-investigating the fabrication, tuning of catalytic properties and synergetic effects

Tailoring the structures of catalysts and the arrangement of organic bimetallic catalysts are essential in both fundamental research and applications. However, they still impose enormous challenges such as size and active species distribution, ordered uniformity, and controllable composition, which are critical in determining their specific activities and efficiency. Herein, a novel terpyridine-based hetero-bimetallic Ni/Pd nanosheet supported on graphene oxide (denoted as GO@Tpy-Ni/Pd) was fabricated, which exhibited higher catalytic activity, substrate applicability and recyclability for the Suzuki coupling reaction under mild conditions. The catalytic mechanism was heterogeneous catalysis at the interface and the synergetic effect between Pd and Ni resulted in a little Ni(0)/Pd(0) cluster including Pd(ii)/Ni(ii) as a whole being formed through electron transfer on the catalytic surface. This phenomenon could be interpreted as the nanoscale clusters of Ni/Pd being the real active centre stabilized by the ligand and GO and the synergetic effect. The absorption and desorption of different substrates and products on Ni/Pd clusters, as calculated by DFT, was proved to be another key factor.

The synergistic effect between Ni and Pd atom was the crucial factor for enhancing catalytic activity.

Copper(i)/Ganphos catalysis: enantioselective synthesis of diverse spirooxindoles using iminoesters and alkyl substituted methyleneindolinones

A copper-catalyzed asymmetric 1,3-dipolar cycloaddition of glycine iminoesters with alkyl substituted 3-methylene-2-oxindoles is described. By using de novo design of P-stereogenic phosphines as ligands, spiro[pyrrolidin-3,3'-oxindole]s are generated in good to excellent yields with high asymmetric induction. A further reduced catalyst loading of 0.1 mol% is sufficient to achieve a satisfactory enantioselectivity of 90% ee. The DFT calculations suggest the second Michael addition of the 1,3-dipole to be the rate- and enantio-determining step. A key feature of this 1,3-dipolar cycloaddition is the wide substrate applicability, even with alkyl aldehyde-derived azomethine ylide; thus it has streamlined a highly enantioselective access to a new class of antiproliferative agents, MDM2-p53.

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details of the proton transfers coupled to the phosphate cleavage is one of the key challenges in QM/MM calculations of these and other enzyme catalyzed reactions. The lack of experimental information offers both an opportunity for computations as well as often unresolved controversies. We discuss the example of small GTPases including the important human Ras protein. The high dimensionality and chemical complexity of these reactions demand carefully chosen computational techniques both in terms of the underlying quantum chemical theory and the sampling of the conformational ensemble. We also point out the important role of Mg²⁺ ions, and recent advances in their transient involvement in the catalytic mechanisms.

A systematic investigation of structural transformation in a copper pyrazolato system: a case study

Dissolution-recrystallization structural transformation (DRST) is a powerful tool to unravel unequivocally the mechanism of dynamic conversion processes, based on the structures of the initial reactants, final products and sometimes intermediates isolated from the reaction mixture. Herein, we illustrate the details of the conversion processes of (CuIpz)3 into [CuII(OH)pz]6 (pzH = 4-chloro-3,5-diphenylpyrazole) through DRSTs. Based on crystal structure determination and spectroscopic methods, the most encountered species, (CuIpz)3, is in equilibrium with (CuIpz)4 in solution with the tetramer becoming dominant at low temperature, indicating an entropy-controlled conversion between these two structural isomers. The CuI trimer/tetramer in solution further experiences an oxidation if exposed to the open air, resulting in the formation of a pentanuclear mixed-valence intermediate CuI3CuII2(OMe)2pz5 which can be isolated as single crystals at -20 °C and has been structurally characterized for the first time. The final product isolated from the solution is the fully oxidized hexanuclear [CuII(OMe)pz]6, which is easily transformed into [CuII(OH)pz]6 in the presence of humidity.

Origin of stereoselectivity in an isothiourea catalyzed Michael addition reaction of aryl ester with vinyl disulfone

The origin of stereoselectivity in an isothiourea-catalyzed addition reaction of aryl ester with vinyl disulfone was explored for the first time.

Insights into Lewis base-catalyzed chemoselective [3 + 2] and [3 + 4] annulation reactions of MBH carbonates

The chemoselectivity of Lewis base-catalyzed [3 + 2] and [3 + 4] annulation reactions of MBH carbonates can be predicted using FMO overlap analysis.

Origin and stabilization of axial chirality in the construction of naphthyl-C2-indoles: a DFT study

A novel method for predicting the stabilization of axial chirality in the construction of naphthyl-C2-indoles has been suggested for the first time.

Insights into isothiourea-catalyzed asymmetric [3 + 3] annulation of α,β-unsaturated aryl esters with 2-acylbenzazoles: mechanism, origin of stereoselectivity and switchable chemoselectivity

The switchable chemoselectivity of isothiourea-catalyzed asymmetric [3 + 3] annulation of α,β-unsaturated aryl esters with 2-acylbenzazoles has been predicted successfully.

Insights into N-heterocyclic carbene and Lewis acid cooperatively catalyzed oxidative [3 + 3] annulation reactions of α,β-unsaturated aldehyde with 1,3-dicarbonyl compounds

N-Heterocyclic carbene and Lewis acid cooperatively catalyzed oxidative [3 + 3] annulation reactions of 1,3-dicarbonyl compounds have been systematically studied in theory.

Ion exchange collaborating coordination substitution: More efficient Cr(VI) removal performance of a water-stable CuII-MOF material

An unusual water-stable cationic metal-organic framework {[Cu(L)_0.5(bpe)(H₂O)](NO₃)•(H₂O)_0.5}_n (1) (H₄L = bis(3,5-dicarboxypyridinium)-p-xylylene) was synthesized, which was developed into an effective capture material for removal chromate from water. The results show that this material efficiently traps HCrO₄^- pollutant ions via single-crystal to single-crystal (SCSC) coordination substitution process. The HCrO₄^- uptake capacity of 1 is high to 190 mg/g. Meaningfully, the structure of 1-HCrO₄ ({[Cu(L)_0.5(bpe)(HCrO₄)]}_n) can be accurately obtained by single-crystal X-ray diffraction, where the chromate enter the framework to form stable coordination with central metal ions Cu²⁺. This is the first example of a stable coordination between chromate and the framework during the capture process. The captured HCrO₄^- are not dissociated easily into the solution due to the coordination bond. This interaction makes the enrichment of HCrO₄^- more stable and the capture capacity excellent. Furthermore, the HCrO₄^- releasing process displays good regeneration in a single crystal state, which further elaborates the reversible SCSC transformation. The mechanism of Cr(VI) removal was also confirmed by DFT calculation studies. This work provides a new way to design and develop efficient MOF capture materials.

Human Acetyl-CoA Carboxylase 1 Is an Isomerase: Carboxyl Transfer Is Activated by Catalytic Effect of Isomerization

Obesity and its related diseases such as cancer and diabetes are leading life-threatening issues in the modern world. Thus, new drugs toward obesity and obesity-caused diseases are highly desired. Human acetyl-CoA carboxylase 1 (hACC1) in charge of the rate-limiting step of the human fatty acid synthesis was recognized as an attractive target for rational drug design. The fundamental reaction mechanism and nature of the transition state of hACC1 remain unclear. In this study, combined quantum mechanics and molecular mechanics (QM/MM), molecular dynamics (MD), and free-energy simulations were performed to investigate the catalytic mechanism of the hACC1-catalyzed carboxyl-transfer reaction. Our computational results show a three-step mechanism for carboxyl transferase (CT)-catalyzed reaction, including isomerization of carboxybiotin, proton-transfer from acetyl-CoA to carboxybiotin, and carboxylation of acetyl-CoA enolate. Interestingly, isomerization of carboxybiotin is the rate-limiting step of the entire reaction pathway, indicating hACC1 has the catalytic effect of isomerization and thus might be an isomerase also. The activation free-energy barrier of carboxyl-transfer catalyzed by hACC1 was calculated to be 16.4 kcal/mol, in excellent agreement with the experimental result (16.7 kcal/mol). The obtained reaction mechanism together with the nature of the transition state provides helpful knowledge not only for future investigation of other ACCs but also for rational design of hACC1 inhibitors, such as TS analogue. The catalytic effect of hACC1 isomerization is discussed.

Insights into N-Heterocyclic Carbene-Catalyzed Oxidative α-C(sp3)-H Activation of Aliphatic Aldehydes and Cascade [2 + 2] Cycloaddition with Ketimines

Predicting the chemoselectivity of [2 + 2] cyclizations is an important challenge in organic chemistry. Herein, we provided a valuable case for this issue. Density functional theory calculations were performed to systematically study the possible mechanisms and origin of selectivities for the N-heterocyclic carbene (NHC)-catalyzed oxidative α-C(sp³)-H activation of aliphatic aldehydes and the cascade [2 + 2] cycloaddition with ketimines. The [2 + 2] cycloaddition of azolium enolate intermediates to the C═N bond, rather than the C═O bond of ketimine, is revealed to be determined by chemo- and stereoselectivity. By comparing the energy gap between the frontier molecular orbitals (FMOs) of the two reacting parts involved in the [2 + 2] cycloaddition transition states, we propose a new strategy to determine the origin of the reaction chemoselectivity. Moreover, the local nucleophilic index can efficiently predict the active site of ketimines. Further analyses illustrate that NHC can increase the nucleophilicity of aldehydes and the acidity of the α-C(sp³)-H bond, and 3,3',5,5'-tetra- tert-butyl diphenoquinone (DQ) acts as an oxidant and promotes α-C(sp³)-H bond deprotonation. This work is useful not only for understanding the NHC-catalyzed oxidative [2 + 2] annulation but also for developing new applications of the FMO theory in organocatalytic cyclizations.

Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn-Sham Density Functional Calculations

Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is the primary carbon-fixing enzyme in photosynthesis, fixing CO₂ to a 5-carbon sugar, RuBP, in a series of five reactions. However, it also catalyzes an oxygenase reaction by O₂ addition to the same enolized RuBP substrate in an analogous reaction series in the same active site, producing a waste product and loss of photosynthetic efficiency. Starting from RuBP, the reactions are enolization to the enediolate form, addition of CO₂ or O₂ to form the carboxy or peroxo adduct, hydration to form a gemdiolate, scission of the C2-C3 bond of the original RuBP, and stereospecific or nonstereospecific protonation to form two molecules of the 3-carbon PGA product, or one molecule of PGA, one of 2-carbon PG (waste product), and one water molecule. Reducing the loss of efficiency from the oxygenase reaction is an attractive means to increase crop productivity. However, lack of understanding of key aspects of the catalytic mechanisms for both the carboxylase and oxygenase reactions, particularly those involving proton exchanges and roles of water molecules, has stymied efforts at re-engineering Rubisco to reduce losses from the oxygenation reaction. As the stable form of molecular oxygen is the triplet biradical state (³O₂), its reaction with near-universal singlet-state molecules is formally spin forbidden. Although in oxygenase enzymes, ³O₂ activation is usually achieved by one-electron transfers using transition-metal ions or organic cofactors, recently, cofactor-less oxygenases in which the substrate itself is the source of the electron for ³O₂ activation have been identified, but in all such cases an aromatic ring stabilizes the substrate's negative charge. Here we present the first large-scale Kohn-Sham density functional theory study of the reaction mechanism of the Rubisco oxygenase pathway. First, we show that the enediolate substrate complexed to Mg²⁺ and its ligands extends the region for charge delocalization and stabilization of its negative charge to allow formation of a caged biradical enediolate-O₂ complex. Thus, Rubisco is a unique type of oxygenase without precedent in the literature. Second, for the O₂ addition to proceed to the singlet peroxo-adduct intermediate, the system must undergo an intersystem crossing. We found that the presence of protonated LYS334 is required to stabilize this intermediate and that both factors (strongly stabilized anion and protonated LYS334) facilitate a barrier-less activation of ³O₂. This finding supports our recent proposal that deoxygenation, that is, reversal of gas binding, is possible. Third, as neither CO₂ nor O₂ binds to the enzyme, our findings support the proposal from our recent carboxylase study that the observed K_C or K_O (Michaelis-Menten constants) in the steady-state kinetics reflect the respective adducts, carboxy or peroxo. Fourth, after computing hydration pathways with water addition both syn and anti to C3, we found, in contrast to the results of our carboxylation study indicating anti addition, that in the oxygenation reaction only syn-hydration is capable of producing a stable gemdiolate that facilitates the rate-limiting C2-C3 bond scission to final products. Fifth, we propose that an excess proton we previously found was required in the carboxylation reaction for activating the C2-C3 bond scission is utilized in the oxygenation reaction for the required elimination of a water molecule. In summary, despite its oxygenase handicap, Rubisco's success in directing 75% of its substrate through the carboxylation pathway can be considered impressively effective. Although native C3 Rubiscos are in a fix with unwanted activity of ³O₂ hampering its primary carboxylase function, mechanistic differences presented here with findings in our recent carboxylase study for both the gas-addition and subsequent reactions provide some clues as to how creative Rubisco re-engineering may offer a solution to reducing the oxygenase activity.

The catalytic mechanism of S-acyltransferases: acylation is triggered on by a loose transition state and deacylation is turned off by a tight transition state

The reaction of S-acyltransferase is characterized by a loose transition state.

Insights into highly selective ring expansion of oxaziridines under Lewis base catalysis: a DFT study

The possible mechanism and stereoselectivity of the NHC-catalyzed ring expansion reaction of oxaziridines have been theoretically studied for the first time.

Mechanistic studies on the N-heterocyclic carbene-catalyzed reaction of isatin-derived enals with hydrazones

The detailed mechanism and origin of stereoselectivity of the NHC-catalyzed annulation reaction were investigated.

Mechanistic insights and origin of chemoselectivity for S–O bond cleavage in dinitrobenzenesulfonic carbamates

A computational study on the NHC-catalyzed chemoselective S–O bond cleavage in dinitrobenzenesulfonic carbamates.

Prediction on the origin of chemoselectivity in Lewis base-mediated competition cyclizations between allenoates and chalcones: a computational study

The HOMO_TSs and p-orbital contributions of the center atoms were used to predict the origin of chemoselectivity in this work.

Insights into NHC-catalyzed oxidative α-C(sp3)–H activation of aliphatic aldehydes and cascade [2 + 3] cycloaddition with azomethine imines

The NHC catalyst is identified to promote [2 + 3] cycloaddition by avoiding the poor FMO overlap mode in theory.