An ESR analysis of the mechanism of pericyclic reactions of bicyclobutane.
Ontology highlight
ABSTRACT:
SUBMITTER: Walczak MA
PROVIDER: S-EPMC2737485 | biostudies-literature | 2009 Jun
REPOSITORIES: biostudies-literature
Publications
An ESR analysis of the mechanism of pericyclic reactions of bicyclobutane.
Walczak Maciej A A MA Shin Byong-Kyu BK Wipf Peter P Saxena Sunil S
Organic & biomolecular chemistry 20090406 11
Experimental and simulated ESR data are in good agreement with a biradical mechanism for the intramolecular pericyclic reactions of bicyclo[1.1.0]butanes. ...[more]
Similar Datasets
Project description:One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure--function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions. Specifically, salicylate synthesis by the two-enzyme pathway in Pseudomonas aeruginosa is examined. The isochorismate-pyruvate lyase is discussed in the context of its homologues, the chorismate mutases, and the isochorismate synthase is compared to its homologues in the MST family (menaquinone, siderophore, or tryptophan biosynthesis) of enzymes. The tentative conclusion is that the activities observed cannot be reconciled by inspection of the active site participants alone. Instead, individual activities must arise from unique dynamic properties of each enzyme that are tuned to promote specific chemistries.
| S-EPMC3164438 | biostudies-literature
Project description:Pericyclic reactions-which proceed in a concerted fashion through a cyclic transition state-are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon-carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels-Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-l-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels-Alder and hetero-Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme 'toolboxes'. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.
| S-EPMC5679075 | biostudies-literature
Project description:The rules for allowable pericyclic reactions indicate that the photoisomerizations of retinals in rhodopsins can be formally analogous to thermally promoted Diels-Alder condensations of monoenes with retinols. With little change in the seven-transmembrane helical environment these latter reactions could mimic the retinal isomerization while providing highly sensitive chemical reception. In this way archaic progenitors of G-protein-coupled chemical quantal receptors such as those for pheromones might have been evolutionarily plagiarized from the photon quantal receptor, rhodopsin, or vice versa. We investigated whether the known structure of bacteriorhodopsin exhibited any similarity in its active site with those of the two known antibody catalysts of Diels-Alder reactions and that of the photoactive yellow protein. A remarkable three-dimensional motif of aromatic side chains emerged in all four proteins despite the drastic differences in backbone structure. Molecular orbital calculations supported the possibility of transient pericyclic reactions as part of the isomerization-signal transduction mechanisms in both bacteriorhodopsin and the photoactive yellow protein. It appears that reactions in all four of the proteins investigated may be biological analogs of the organic chemists' chiral auxiliary-aided Diels-Alder reactions. Thus the light receptor and the chemical receptor subfamilies of the heptahelical receptor family may have been unified at one time by underlying pericyclic chemistry.
| S-EPMC1300565 | biostudies-other
Project description:The enzyme 3-methylglutaconyl coenzyme A (CoA) decarboxylase (called AibA/AibB) catalyzes the decarboxylation of 3-methylglutaconyl CoA to generate 3,3-dimethylacrylyl-CoA, representing an important step in the biosynthesis of isovaleryl-coenzyme A in Myxococcus xanthus when the regular pathway is blocked. A novel mechanism involving a pericyclic transition state has previously been proposed for this enzyme, making AibA/AibB unique among decarboxylases. Herein, density functional calculations are used to examine the energetic feasibility of this mechanism. It is shown that the intramolecular pericyclic reaction is associated with a very high energy barrier that is similar to the barrier of the same reaction in the absence of the enzyme. Instead, the calculations show that a direct decarboxylation mechanism has feasible energy barriers that are in line with the experimental observations.
| S-EPMC7756340 | biostudies-literature
Project description:Hierarchical, convergent ab initio benchmark computations were performed followed by a systematic analysis of DFT performance for five pericyclic reactions comprising Diels-Alder, 1,3-dipolar cycloaddition, electrocyclic rearrangement, sigmatropic rearrangement, and double group transfer prototypes. Focal point analyses (FPA) extrapolating to the ab initio limit were executed via explicit quantum chemical computations with electron correlation treatments through CCSDT(Q) and correlation-consistent Gaussian basis sets up to aug'-cc-pV5Z. Optimized geometric structures and vibrational frequencies of all stationary points were obtained at the CCSD(T)/cc-pVTZ level of theory. The FPA reaction barriers and energies exhibit convergence to within a few tenths of a kcal mol-1. The FPA benchmarks were used to evaluate the performance of 60 density functionals (eight dispersion-corrected), covering the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. The meta-hybrid M06-2X functional provided the best overall performance [mean absolute error (MAE) of 1.1 kcal mol-1] followed closely by the double-hybrids B2K-PLYP, mPW2K-PLYP, and revDSD-PBEP86 [MAE of 1.4-1.5 kcal mol-1]. The regularly used GGA functional BP86 gave a higher MAE of 5.8 kcal mol-1, but it qualitatively described the trends in reaction barriers and energies. Importantly, we established that accurate yet efficient meta-hybrid or double-hybrid DFT potential energy surfaces can be acquired based on geometries from the computationally efficient and robust BP86/DZP level.
| S-EPMC9348522 | biostudies-literature
Project description:This research study will examine how often hypersensitivity, or allergic reactions, occur in patients receiving the chemotherapy medication oxaliplatin. Hypersensitivity reactions can vary from a transient skin rash and fever to more severe symptoms such as shortness of breath, chest tightness, and a more severe allergic reaction that can affect blood pressure called anaphylaxis. We will be examining how often hypersensitivity reactions occur and how severe the reactions are when they occur. We will also examine whether there are factors that place people at risk for developing hypersensitivity reactions to oxaliplatin. In an optional portion to this study, we will examine whether allergy skin testing can predict whether someone will develop a hypersensitivity reaction.
Participants who develop a moderate to severe allergic reaction to oxaliplatin will be invited to participate in an additional portion of the study examining a desensitization process. This part of the study will examine whether a desensitization process can prevent future hypersensitivity reactions to oxaliplatin in patients who previously developed moderate to severe hypersensitivity reactions and allow therapy with oxaliplatin to continue.
| 2067027 | ecrin-mdr-crc
Project description:We report here reactions of alkyl sulfides with benzynes thermally generated by the hexadehydro-Diels-Alder (HDDA) cycloisomerization. The initially produced 1,3-betaine (o-sulfonium/aryl carbanion) undergoes intramolecular proton transfer to generate a more stable S-aryl sulfur ylide. This can react in various manners, including engaging weak acids (HA) in the reaction medium. This can produce transient ion pairs ArSR2(+)A(-) that proceed to the products ArSR + RA. When cyclic sulfides are used, A(-) opens the ring and is incorporated into the product, an outcome that constitutes a versatile, three-component coupling process.
| S-EPMC5136460 | biostudies-literature
Project description:Photocatalytic redox reactions are important for synthesizing fine chemicals from olefins, but the limited lifetime of radical cation intermediates severely restricts semiconductor photocatalysis efficiency. Here, we report that Ag3PO4 can efficiently catalyze intramolecular and intermolecular [2 + 2] and Diels-Alder cycloadditions under visible-light irradiation. The approach is additive-free, catalyst-recyclable. Mechanistic studies indicate that visible-light irradiation on Ag3PO4 generates holes with high oxidation power, which oxidize aromatic alkene adsorbates into radical cations. In photoreduced Ag3PO4, the conduction band electron (eCB-) has low reduction power due to the delocalization among the Ag+-lattices, while the particle surfaces have a strong electrostatic interaction with the radical cations, which considerably stabilize the radical cations against recombination with eCB-. The radical cation on the particle's surfaces has a lifetime of more than 2 ms, 75 times longer than homogeneous systems. Our findings highlight the effectiveness of inorganic semiconductors for challenging radical cation-mediated synthesis driven by sunlight.
| S-EPMC10834519 | biostudies-literature
Project description:Phosphoryl-transfer reactions are central to biology. These reactions also have some of the slowest nonenzymatic rates and thus require enormous rate accelerations from biological catalysts. Despite the central importance of phosphoryl transfer and the fascinating catalytic challenges it presents, substantial confusion persists about the properties of these reactions. This confusion exists despite decades of research on the chemical mechanisms underlying these reactions. Here we review phosphoryl-transfer reactions with the goal of providing the reader with the conceptual and experimental background to understand this body of work, to evaluate new results and proposals, and to apply this understanding to enzymes. We describe likely resolutions to some controversies, while emphasizing the limits of our current approaches and understanding. We apply this understanding to enzyme-catalyzed phosphoryl transfer and provide illustrative examples of how this mechanistic background can guide and deepen our understanding of enzymes and their mechanisms of action. Finally, we present important future challenges for this field.
| S-EPMC3418923 | biostudies-literature
Project description:Herein, the power of multicenter electron delocalization analysis to elucidate the intricacies of concerted reaction mechanisms is brought to light by tracking the transition of [1,3] sigmatropic rearrangements from the high-barrier pericyclic mechanism in 1-butene to the barrierless pseudopericyclic mechanism in 1,2-diamino-1-nitrosooxyethane. This transition has been progressively achieved by substituting the migrating group, changing the donor and acceptor atoms, and functionalizing the alkene unit with weak and strong electron-donating and electron-withdrawing groups. Fourteen [1,3] sigmatropic reactions with electronic energy barriers ranging from 1 to 89 kcal/mol have been investigated. A very good correlation has been found between the barrier and the four-center electron delocalization at the transition state, the latter calculated for the atoms involved in the four-centered ring adduct formed along the reaction path. Surprisingly, the barrier has been found to be independent of the bond strength between the migrating group and the donor atom so that only the changes induced in the multicenter bonding control the kinetics of the reaction. Additional insights into the effect of atom substitution and group functionalization have also been extracted from the analysis of the multicenter electron delocalization profiles along the reaction path and qualitatively supported by the topological analysis of the electron density.
| S-EPMC8693182 | biostudies-literature