Iridium-promoted deoxyglycoside synthesis: stereoselectivity and mechanistic insight.
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ABSTRACT:
SUBMITTER: Pal KB
PROVIDER: S-EPMC8179265 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Herein the reaction mechanism and the origin of stereoselectivity of asymmetric hydrogenation of oximes to hydroxylamines catalyzed by the cyclometalated iridium (III) complexes with chiral substituted single cyclopentadienyl ligands (Ir catalysts A1 and B1) under acidic condition were unveiled using DFT calculations. The catalytic cycle for this reaction consists of the dihydrogen activation step and the hydride transfer step. The calculated results indicate that the hydride transfer step is the chirality-determining step and the involvement of methanesulfonate anion (MsO-) in this reaction is of importance in the asymmetric hydrogenation of oximes catalyzed by A1 and B1. The calculated energy barriers for the hydride transfer steps without an MsO- anion are higher than those with an MsO- anion. The differences in Gibbs free energies between TSA5-1fR/TSA5-1fS and TSB5-1fR/TSB5-1fS are 13.8/13.2 (ΔΔG‡ = 0.6 kcal/mol) and 7.5/5.6 (ΔΔG‡ = 1.9 kcal/mol) kcal/mol for the hydride transfer step of substrate protonated oximes with E configuration (E-2a-H+) with MsO- anion to chiral hydroxylamines product R-3a/S-3a catalyzed by A1 and B1, respectively. According to the Curtin-Hammet principle, the major products are hydroxylamines S-3a for the reaction catalyzed by A1 and B1, which agrees well with the experimental results. This is due to the non-covalent interactions among the protonated substrate, MsO- anion and catalytic species. The hydrogen bond could not only stabilize the catalytic species, but also change the preference of stereoselectivity of this reaction.
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Project description:We report the formation of a series of novel [Ir(H)2(IMes)(α-13C2-carboxyimine)L] complexes in which the identity of the coligand L is varied. When examined with para-hydrogen, complexes in which L is benzylamine or phenethylamine show significant 1H hydride and 13C2 imine enhancements and may exist in 13C2 singlet spin order. Isotopic labeling techniques are used to double 13C2 enhancements (up to 750-fold) and singlet state lifetimes (up to 20 seconds) compared to those previously reported. Exchange spectroscopy and Density Functional Theory are used to investigate the stability and mechanism of rapid hydrogen exchange in these complexes, a process driven by dissociative coligand loss to form a key five coordinate intermediate. When L is pyridine or imidazole, competitive binding to such intermediates leads to novel complexes whose formation, kinetics, behaviour, structure, and hyperpolarization is investigated. The ratio of the observed PHIP enhancements were found to be affected not only by the hydrogen exchange rates but the identity of the coligands. This ligand reactivity is accompanied by decoherence of any 13C2 singlet order which can be preserved by isotopic labeling. Addition of a thiol coligand proved to yield a thiol oxidative addition product which is characterized by NMR and MS techniques. Significant 870-fold 13C enhancements of pyridine can be achieved using the Signal Amplification By Reversible Exchange (SABRE) process when α-carboxyimines are used to block active coordination sites. [Ir(H)2(IMes)(α-13C2-carboxyimine)L] therefore acts as unique sensors whose 1H hydride chemical shifts and corresponding hyperpolarization levels are indicative of the identity of a coligand and its binding strength.
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Project description:Free fatty acid receptor 1 (FFAR1) is a potential therapeutic target for the treatment of type 2 diabetes (T2D). It has been validated that agonists targeting FFAR1 can achieve the initial therapeutic endpoints of T2D, and the epimer agonists (R,S) AM-8596 can activate FFAR1 differently, with one acting as a partial agonist and the other as a full agonist. Up to now, the origin of the stereoselectivity of FFAR1 agonists remains elusive. In this work, we used molecular simulation methods to elucidate the mechanism of the stereoselectivity of the FFAR1 agonists (R)-AM-8596 and (S)-AM-8596. We found that the full agonist (R)-AM-8596 disrupts the residue interaction network around the receptor binding pocket and promotes the opening of the binding site for the G-protein, thereby resulting in the full activation of FFAR1. In contrast, the partial agonist (S)-AM-8596 forms stable electrostatic interactions with FFAR1, which stabilizes the residue network and hinders the conformational transition of the receptor. Our work thus clarifies the selectivity and underlying molecular activation mechanism of FFAR1 agonists.
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Project description:G-protein-coupled receptors (GPCRs) are involved in a wide range of physiological processes, and they have attracted considerable attention as important targets for developing new medicines. A central and largely unresolved question in drug discovery, which is especially relevant to GPCRs, concerns ligand selectivity: Why do certain molecules act as activators (agonists) whereas others, with nearly identical structures, act as blockers (antagonists) of GPCRs? To address this question, we employed all-atom, long-timescale molecular dynamics simulations to investigate how two diastereomers (epimers) of dihydrofuroaporphine bind to the serotonin 5-HT1A receptor and exert opposite effects. By using molecular interaction fingerprints, we discovered that the agonist could mobilize nearby amino acid residues to act as molecular switches for the formation of a continuous water channel. In contrast, the antagonist epimer remained firmly stabilized in the binding pocket.
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Project description:Thiosugars, sugars that have their endocyclic oxygen substituted for a sulfur atom, have been used as stable bioisosteres of naturally occurring glycans because the thiosugar glycosydic linkage is supposed to be stabilized toward chemical and enzymatic hydrolysis. We have performed an in-depth investigation into the stability and reactivity of furanosyl thiacarbenium ions, by assessing all four diastereoisomeric thiofuranosides experimentally and computationally. We show that all furanosyl thiacarbenium ions react in a 1,2- cis-selective manner with triethylsilane, reminiscent of their oxo counterparts. The computed conformational space occupied by the thiacarbenium ions is strikingly similar to that of the corresponding furanosyl oxycarbenium ions, indicating that the stereoelectronic substituent effects governing the stability of furanosyl oxocarbenium ions and thiacarbenium ions are very similar. While the thio- ribo-furanose appears to be less reactive than its oxo counterpart, the thio- ara-, lyxo-, and xylo-furanosides appear to be more reactive than their oxygen equivalents. These differences are accounted for using the conformational preference of the donors and the carbocation intermediates. The lower reactivity of the thio- ribo furanosides in (Lewis) acid-mediated reactions and the similarity of the thia- and oxocarbenium ions make thio- ribo-furanosides excellent stabilized analogues of the naturally occurring ribo-furanose sugars.
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Project description:The current existing methods for the amide bond synthesis via acceptorless dehydrogenative coupling of amines and alcohols all require high reaction temperatures for effective catalysis, typically involving reflux in toluene, limiting their potential practical applications. Herein, we report a system for this reaction that proceeds under mild conditions (reflux in diethyl ether, boiling point 34.6 °C) using ruthenium PNNH complexes. The low-temperature activity stems from the ability of Ru-PNNH complexes to activate alcohol and hemiaminals at near-ambient temperatures through the assistance of the terminal N-H proton. Mechanistic studies reveal the presence of an unexpected aldehyde-bound ruthenium species during the reaction, which is also the catalytic resting state. We further utilize the low-temperature activity to synthesize several simple amide bond-containing commercially available pharmaceutical drugs from the corresponding amines and alcohols via the dehydrogenative coupling method.
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Project description:Solid-state synthesis has historically focused on reactants and end products; however, knowledge of reaction pathways, intermediate phases and their formation may provide mechanistic insight of solid-state reactions. With an increased understanding of reaction progressions, design principles can be deduced, affording more predictive power in materials synthesis. In pursuit of this goal, in situ powder X-ray diffraction is employed to observe crystalline phase evolution over the course of the reaction, thereby constructing a "panoramic" view of the reaction from beginning to end. We conducted in situ diffraction studies in the K-Bi-Q (Q = S, Se) system to understand the formation of phases occurring in this system in the course of their reactions. Powder mixtures of K2Q to Bi2Q3 in 1 : 1 and 1.5 : 1 ratios were heated to 800 °C or 650 °C, while simultaneously collecting diffraction data. Three new phases, K3BiS3, β-KBiS2, and β-KBiSe2, were discovered. Panoramic synthesis showed that K3BiQ3 serves an important mechanistic role as a structural intermediate in both chalcogen systems (Q = S, Se) in the path to form the KBiQ2 structure. Thermal analysis and calculations at the density functional theory (DFT) level show that the cation-ordered β-KBiQ2 polymorphs are the thermodynamically stable phase in this compositional space, while Pair Distribution Function (PDF) analysis shows that all α-KBiQ2 structures have local disorder due to stereochemically active lone pair expression of the bismuth atoms. The formation of the β-KBiQ2 structures, both of which crystallize in the α-NaFeO2 structure type, show a boundary where the structure can be disordered or ordered with regards to the alkali metal and bismuth. A cation radius tolerance for six-coordinate cation site sharing of ∼ 1.3 is proposed. The mechanistic insight the panoramic synthesis technique provides in the K-Bi-Q system is progress towards the overarching goal of synthesis-by-design.
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Project description:In view of the serious health problems concerning infectious diseases in heavily populated areas, we followed the strategy of lead compound diversification to evaluate the near-by chemical space for new organic compounds. To this end, twenty derivatives of nitazoxanide (NTZ) were synthesized and tested for activity against Entamoeba histolytica parasites. To ensure drug-likeliness and activity relatedness of the new compounds, the synthetic work was assisted by a quantitative structure-activity relationships study (QSAR). Many of the inherent downsides - well-known to QSAR practitioners - we circumvented thanks to workarounds which we proposed in prior QSAR publication. To gain further mechanistic insight on a molecular level, ligand-enzyme docking simulations were carried out since NTZ is known to inhibit the protozoal pyruvate ferredoxin oxidoreductase (PFOR) enzyme as its biomolecular target.
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Project description:Lipoteichoic acid (LTA) is an important cell wall component required for proper cell growth in many Gram-positive bacteria. In Listeria monocytogenes, two enzymes are required for the synthesis of this polyglycerolphosphate polymer. The LTA primase LtaP(Lm) initiates LTA synthesis by transferring the first glycerolphosphate (GroP) subunit onto the glycolipid anchor and the LTA synthase LtaS(Lm) extends the polymer by the repeated addition of GroP subunits to the tip of the growing chain. Here, we present the crystal structures of the enzymatic domains of LtaP(Lm) and LtaS(Lm). Although the enzymes share the same fold, substantial differences in the cavity of the catalytic site and surface charge distribution contribute to enzyme specialization. The eLtaS(Lm) structure was also determined in complex with GroP revealing a second GroP binding site. Mutational analysis confirmed an essential function for this binding site and allowed us to propose a model for the binding of the growing chain.
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Project description:A ligand capable of adopting two pseudo-enantiomeric helically chiral states when bound to copper has been applied as an asymmetric catalyst in the Michael addition of malonate substrates to nitrostyrenes. The absolute configuration of the helically chiral ligand is inverted upon oxidation/reduction of the copper center. In this way, the handedness of the Michael addition product (R/S) can be selected based on the handedness of the catalyst (?/?). Exciton coupled circular dichroism (ECCD) was used to identify which of the two pseudo-enantiomeric forms the catalyst adopted after reduction/oxidation, with additional support from X-ray crystallographic data. The synthesis of the ligand was achieved in five steps with an overall 61% yield. Enantiomeric excesses of the Michael addition products of up to 72% (S) and 70% (R) were obtained in acetonitrile. The ability to choose the handedness of the product based on the chiral state of the catalyst has been demonstrated with several different solvents, bases, nitrostyrene/malonate substrates, and prochiral malonate substrates. A combination of molecular modelling, crystal structure and kinetic data suggest that one urea moiety of the catalyst ligand likely binds the nitrostyrene substrate while blocking the Re face of the nitrostyrene in the transition state.
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