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α-Substituted ketones or aldehydes can be synthesized from enamines by the Stork enamine reaction, named after its pioneer Gilbert Stork. Enamines are useful synthetic intermediates where the lone pair on nitrogen is in conjugation with the C=C bond. They resemble enolate ions, as the resonance forms of both species have a nucleophilic α carbon.
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In an SN2 reaction, the nucleophilic attack on the substrate and departure of the leaving group occurs simultaneously through a transition state. As the nucleophile approaches the substrate from the back-side, the configuration of the substrate carbon changes from tetrahedral to trigonal bipyramidal and then back to tetrahedral, leading to an inversion in the configuration of the product.
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Acetoacetic ester synthesis is a method to obtain ketones from alkyl halides and β-keto esters. The reaction occurs in the presence of an alkoxide base that abstracts the acidic proton of the β-keto esters. The step results in an enolate ion which is doubly stabilized. The enolate then reacts with an alkyl halide via the SN2 process to produce an alkylated ester intermediate with a new C–C bond. The hydrolysis of the intermediate, followed by acidification, results in an...
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Alkenes are converted to 1,2-diols or glycols through a process called dihydroxylation. It involves the addition of two hydroxyl groups across the double bond with two different stereochemical approaches, namely anti and syn. Dihydroxylation using osmium tetroxide progresses with syn stereochemistry.
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Catalytic hydrogenation of alkenes is a transition-metal catalyzed reduction of the double bond using molecular hydrogen to give alkanes. The mode of hydrogen addition follows syn stereochemistry.
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Updated: Sep 20, 2025

Rapid One-step Enzymatic Synthesis and All-aqueous Purification of Trehalose Analogues
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Similarity based enzymatic retrosynthesis.

Karthik Sankaranarayanan1, Esther Heid1,2, Connor W Coley1

  • 1Department of Chemical Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA kfjensen@mit.edu.

Chemical Science
|June 10, 2022
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Summary
This summary is machine-generated.

A new algorithm facilitates enzymatic synthesis of natural product analogs by predicting retrosynthetic steps. This tool, RDEnzyme, uses molecular similarity to propose reactions and evaluates enzyme evolution success for planning synthesis routes.

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Area of Science:

  • Biocatalysis and Synthetic Chemistry
  • Computational Chemistry and Cheminformatics
  • Enzyme Engineering and Evolution

Background:

  • Enzymes enable efficient, selective synthesis of complex natural products.
  • Biocatalysis offers sustainable alternatives to conventional organic synthesis, reducing waste and harsh conditions.
  • Developing computational tools for enzymatic synthesis planning is crucial for advancing green chemistry.

Purpose of the Study:

  • To develop a single-step retrosynthesis search algorithm for planning enzymatic synthesis of natural product analogs.
  • To create a tool (RDEnzyme) for extracting and applying stereochemically consistent enzymatic reaction templates.
  • To evaluate the effectiveness of molecular similarity for proposing retrosynthetic disconnections and predict enzyme evolution success.

Main Methods:

  • Developed RDEnzyme to extract enzymatic reaction templates from molecular structures.
  • Utilized molecular similarity to propose retrosynthetic disconnections based on precedent enzymatic reactions in UniProt/RHEA.
  • Trained a statistical model on SwissProt reaction pairs to discriminate homologous and evolutionarily distant enzymes and predict evolution success.
  • Recursively applied the workflow to plan synthesis routes for pharmaceuticals and commodity chemicals.

Main Results:

  • RDEnzyme successfully proposed known reactants within the top 10 suggestions for 71% of test reactions using RHEA as a knowledge base.
  • The statistical model accurately identified patterns in enzyme promiscuity, aiding in the evaluation of experimental evolution.
  • The workflow successfully planned retrospective enzymatic synthesis routes for active pharmaceutical ingredients and commodity chemicals.
  • Demonstrated the feasibility of a computer-aided synthesis planning workflow integrating enzymatic and organic chemistry.

Conclusions:

  • Molecular similarity is an effective metric for predicting enzymatic retrosynthetic disconnections.
  • The developed algorithm and statistical model facilitate the planning of enzymatic synthesis routes.
  • This approach represents a significant step towards integrating biocatalysis into computer-aided synthesis planning.
  • The methodology supports the sustainable production of valuable chemicals and pharmaceuticals.