Reactor Training

  1. Combinatorial enumeration
  1. Generate an acylation reaction library in sequential mode using the predefined „nucleophile acylation with acid halide” generic reaction from theUSERHOME>/nucleophile_acylation_with_acid_halide.mrv file. Please use the the USERHOME>/nucleophiles.smiles and the <USERHOME>/acidhalides.smiles files as input. Save the resulting reaction library to <USERHOME>/result1.smiles file. Pay attention to the mapping of the output reactions
  1. Repeat the above process , but this time, enumerate a combinatoral molecule library. Save the resulting library to <USERHOME>/result2.smiles file. Do not generate hydrogen halides to the output!
  1. Reaction Design
  1. Design a Baeyer-Villiger oxidation reaction, which converts ketons to esters, and aldehides to carboxylic acids.
  2. Beta diketones able to enolize do not react.
  3. The examples below illustrate the reaction and its selectivity.
  4. Exclude reagents containing BH, NH, OH, SiH, PH, SH groups or aromatic N, S or sulfide, disulfide, sulfoxyde, sulfimide, thiocarbonyl, carboxyl or carboxylate groups.

Some SMARTS

The first reactant contains BH, SiH, PH or SH group / match(reactant(0), "[H][B,Si,P,S]")
The first reactant contains thiocarbonyl group / match(reactant(0), "C=S")
The first reactant contains carboxyl or carboxylate group / match(reactant(0), "[H]OC=O") || match(reactant(0), "[O-]C=O")
Reactant atom having map number 2 is a CH carbon between to carbonyl groups (beta diketon) / match(ratom(2), "[H][C:1](C=O)C=O", 1)
Reactant atom having map number 2 is NOT a CH carbon between to carbonyl groups (not beta diketon) / !match(ratom(2), "[H][C:1](C=O)C=O", 1)
Number of hydrogens on product atom with map number 2 / hcount(patom(2))
Partial charge on reactant atom with map number 2 / charge(ratom(2))
The sigma component of the partial charge on reactant atom with map number 2 / charge(ratom(2), "sigma")
The sum of partial charges in the aromatric system of reactant atom 1 is below -0.2 / charge(ratom(1), "aromaticsystem") < -0.2
Electrophilic localizaion energy on reactant atom 1 / -energyE(ratom(1))
  1. Add the examples below to your generic reaction and save it to the <USERHOME>/result3.mrv file in Marvin format.
  1. Test your reaction with the added examples both in the Reaction Editor and in the Reaction Wizard. Do you get the expected products?
  1. Take your reaction and convert the molecules from the <USERHOME>/carbonyls.sdf file and save the products in SDfile format to the <USERHOME>/result4.sdf file.