Bimolecular nucleophilic substitution (S2) mechanisms occupy a central place in the historical development and teaching of the field of organic chemistry. Despite the importance of S2 pathways in synthesis, catalytic control of ionic S2 pathways is rare and notably uncommon even in biocatalysis, reflecting the fact that any electrostatic interaction between a catalyst and the reacting ion pair necessarily stabilizes its charge and, by extension, reduces polar reactivity. Nucleophilic halogenase enzymes navigate this tradeoff by desolvating and positioning the halide nucleophile precisely on the S2 trajectory, using geometric preorganization to compensate for the attenuation of nucleophilicity. Here we show that a small-molecule (646 Da) hydrogen-bond-donor catalyst accelerates the S2 step of an enantioselective Michaelis-Arbuzov reaction by recapitulating the geometric preorganization principle used by enzymes. Mechanistic and computational investigations show that the hydrogen-bond donor diminishes the reactivity of the chloride nucleophile yet accelerates the rate-determining dealkylation step by reorganizing both the phosphonium cation and the chloride anion into a geometry that is primed to enter the S2 transition state. This new enantioselective Arbuzov reaction affords highly enantioselective access to an array of H-phosphinates, which are in turn versatile P-stereogenic building blocks amenable to myriad derivatizations. This work constitutes, to our knowledge, the first demonstration of catalytic enantiocontrol of the phosphonium dealkylation step, establishing a new platform for the synthesis of P-stereogenic compounds.
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http://dx.doi.org/10.1038/s41586-024-07811-4 | DOI Listing |
ACS Phys Chem Au
November 2024
Rosalind Franklin Institute, Harwell OX11 0QX, Oxfordshire, United Kingdom.
Efficient photoredox chemical transformations are essential to the development of novel, cost-effective, and environmentally friendly synthetic methodologies. The concept of the entatic state in bioinorganic catalysis proposes that a preorganized structural configuration can reduce the energy barriers associated with chemical reactions. This concept provides one of the guiding principles to enhance catalytic efficiency by maintaining high-energy conformations close to the reaction's transition state.
View Article and Find Full Text PDFbioRxiv
August 2024
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Enzymes that proceed through multistep reaction mechanisms often utilize complex, polar active sites positioned with sub-angstrom precision to mediate distinct chemical steps, which makes their de novo construction extremely challenging. We sought to overcome this challenge using the classic catalytic triad and oxyanion hole of serine hydrolases as a model system. We used RFdiffusion to generate proteins housing catalytic sites of increasing complexity and varying geometry, and a newly developed ensemble generation method called ChemNet to assess active site geometry and preorganization at each step of the reaction.
View Article and Find Full Text PDFNature
August 2024
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Bimolecular nucleophilic substitution (S2) mechanisms occupy a central place in the historical development and teaching of the field of organic chemistry. Despite the importance of S2 pathways in synthesis, catalytic control of ionic S2 pathways is rare and notably uncommon even in biocatalysis, reflecting the fact that any electrostatic interaction between a catalyst and the reacting ion pair necessarily stabilizes its charge and, by extension, reduces polar reactivity. Nucleophilic halogenase enzymes navigate this tradeoff by desolvating and positioning the halide nucleophile precisely on the S2 trajectory, using geometric preorganization to compensate for the attenuation of nucleophilicity.
View Article and Find Full Text PDFInorg Chem
June 2024
College of Chemistry, Nanchang University, Nanchang 330031, China.
The performance of covalent-organic frameworks (COFs) for the photocatalytic extraction of uranium is greatly limited by the number of adsorption sites. Herein, inspired by electronegative redox reactions, we designed a nitrogen-oxygen rich pyrazine connected COF (TQY-COF) with multiple redox sites as a platform for extracting uranium via combining superaffinity and enhanced photoinduction. The preorganized bisnitrogen-bisoxygen donor configuration on TQY-COF is entirely matched with the typical geometric coordination of hexavalent uranyl ions, which demonstrates high affinity (tetra-coordination).
View Article and Find Full Text PDFJ Org Chem
February 2023
Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 La Laguna, Tenerife, Spain.
For molecular architectures based on dynamic covalent chemistry (DCvC), strict preorganization is a paradigmatic concept and the generally accepted strategy for their rational design. This results in the creation of highly rigid building blocks which are expected to fulfill the ideal geometry of the assembly, coming at a price that small geometric mismatches result in unpredicted and/or unproductive reaction outcomes. In this study, we show that feet of a tripodal platform have a great influence on the assembly of tetrahedral organic cages based on boronate ester formation.
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