Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study.

The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases

Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study.

The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases

QUANTUM CHEMICAL STUDY OF OXIDATION OF UNSATURATED FRAGMENTS OF BUTENE

Quantum chemical calculations by means of the MNDO method were carried out for the reaction pathways for the system composed of activated and non-activated butene interacting with molecular or atomic oxygen. The energy gradient estimated from the difference of total energies at two chosen points for relatively long distances between reactants was taken as the indication of the potential energy barrier encountered on approach from the given direction. The reaction pathways characterised by the lowest energy barriers were selected on the basis of such simple energy maps. From the results of the calculations, it can be concluded that when discussing the mechanism of the oxidation reaction the following factors should be taken into consideration: the relative electrophilic-nucleophilic character of reactants, their mutual orientation as well as other geometrical and structural properties of the studied system

Mechanism for cyclization reaction by clavaminic acid synthase. Insights from modeling studies.

The mechanism of the oxidative cyclization reaction catalyzed by clavaminic acid synthase (CAS) was studied in silico. First, a classical molecular dynamics (MD) simulation was performed to obtain a realistic structure of the CAS-Fe(IV)=O-succinate-substrate complex; then potential of mean force (PMF) was calculated to assess the feasibility of the beta-lactam ring, more specifically its C4' corner, approaching the oxo atom. Based on the MD structure, a relatively large model of the active site region was selected and used in the B3LYP investigation of the reaction mechanism. The computational results suggest that once the oxoferryl species is formed, the oxidative cyclization catalyzed by CAS most likely involves either a mechanism involving C4'(S)-H bond cleavage of the monocyclic beta-lactam ring, or a biosynthetically unprecedented mechanism comprising (1) oxidation of the hydroxyl group of PCA to an O-radical, (2) retro-aldol-like decomposition of the O-radical to an aldehyde and a C-centered radical, which is stabilized by the captodative effect, (3) abstraction of a hydrogen atom from the C4'(S) position of the C-centered radical by the Fe(III)-OH species yielding an azomethine ylide, and (4) 1,3-dipolar cycloaddition to the ylide with aldehyde acting as a dipolarophile. Precedent for the new proposed mechanism comes from the reported synthesis of oxapenams via 1,3-dipolar cycloaddition reactions of aldehydes and ketones

H-MOR: Density functional investigation for the relative strength of Bronsted acid sites and dynamics simulation of NH3 protonation-deprotonation

The adsorption energies of NH3 at different positions in acidic mordenite, viz., main channel, side pocket, and double four-membered rings, are investigated using periodic density functional theory method. Furthermore, for the first time, the dynamic behavior of NH3 interacting with Bronsted acid site in the main channel has been monitored. The results reveal that the adsorption energies of ammonia on Bronsted acid sites in the main channel (T-4, T-2, and T-1) are higher than that in the side pocket (TA Consequently, the strength of Bronsted acid sites follows the same order. Ammonia dynamics results show that the protons are in continuous transfer, where NH3 acts as a bridge for transferring protons in between ammonium ion and framework oxygen ions. (c) 200

Mechanism of Benzylic Hydroxylation by 4‑Hydroxymandelate Synthase. A Computational Study

Hydroxymandelate synthase (HMS) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) are highly related enzymes using the same substrates but catalyzing hydroxylation reactions yielding different products. The first steps of the HMS and HPPD catalytic reactions are believed to proceed in the same way and lead to an Fe­(IV)O–hydroxyphenylacetate (HPA) intermediate. Further down the catalytic cycles, HMS uses Fe­(IV)O to perform hydroxylation of the benzylic carbon, whereas in HPPD, the reactive oxoferryl intermediate attacks the aromatic ring of HPA. This study focuses on this part of the HMS catalytic cycle that starts from the oxoferryl intermediate and aims to identify interactions within the active site that are responsible for enzyme specificity. To this end, a HMS–Fe­(IV)O–HPA complex was modeled with molecular dynamics simulations. On the basis of the molecular dynamics-equilibrated structure, an active site model suitable for quantum chemical investigations was constructed and used for density functional theory (B3LYP) calculations of the mechanism of the native reaction of HMS, i.e., benzylic hydroxylation, and the alternative electrophilic attack on the ring, which is a step of the HPPD catalytic cycle. The most important result of this study is the finding that the conformation of the Ser201 side chain in the second coordination shell has a key role in directing the reaction of Fe­(IV)O into either the HMS or the HPPD channel

Role of Substrate Positioning in the Catalytic Reaction of 4-Hydroxyphenylpyruvate Dioxygenase-A QM/MM Study

Ring hydroxylation and coupled rearrangement reactions catalyzed by 4-hydroxyphenylpyruvate dioxygenase were studied with the QM/MM method ONIOM(B3LYP:AMBER). For electrophilic attack of the ferryl species on the aromatic ring, five channels were considered: attacks on the three ring atoms closest to the oxo ligand (C1, C2, C6) and insertion of oxygen across two bonds formed by them (C1-C2, C1-C6). For the subsequent migration of the carboxymethyl substituent, two possible directions were tested (C1-C2, C1-C6), and two different mechanisms were sought (stepwise radical, single-step heterolytic). In addition, formation of an epoxide (side)product and benzylic hydroxylation, as catalyzed by the closely related hydroxymandelate synthase, were investigated. From the computed reaction free energy profiles it follows that the most likely mechanism of 4-hydroxyphenylpyruvate dioxygenase involves electrophilic attack on the C1 carbon of the ring and subsequent single-step heterolytic migration of the substituent. Computed values of the kinetic isotope effect for this step are inverse, consistent with available experimental data. Electronic structure arguments for the preferred mechanism of attack on the ring are also presented