Configure Analysis Parameters

You can configure your search by pressing the ‘Analysis Configuration’ icon next to the ‘Start Analysis’ button.

Options

Options are useful “synthetic tricks” that can help tailor your analysis.

• Allow multiple identical retrosynthetic disconnections in one step
  Look for multiple retrosynthetic disconnections that can be made in a single step. This filter is useful when the target molecule contains symmetry or multiple equivalent groups. For example, bis-alkylation of piperazine using ethyl iodide can be performed in one step, instead of sequentially.
  Use: for symmetric molecules and molecules with two or more identical motifs.
  
  
• Start from smaller precursors
  Eliminates precursors with higher molecular weights than the target compound.
  Use: to avoid ring contraction. Use carefully as some halide or boronic acid precursors could be heavier than the target compound.
  
  
• Exclude diastereoselective-only reactions
  Only show reactions that are enantioselective and eliminate any proposed reactions that are only diastereoselective.
  For example: Catalytic hydrogenations of double bonds, Diels-Alder reactions, cyclopropanations.
  Use: when only one enantiomer is exclusively wanted.

Tip: The ‘Allow multiple identical retrosynthetic disconnections in one step’ option can be used for global deprotection of a molecule if multiple protecting groups are required, for example in sugar chemistry.

Advanced Path Ranking – Rules Databases

SYNTHIA™ is built on our expert-coded rules database, which consists of over 100,000 reaction rules. These rules are based on transformations you would find in organic chemistry textbooks or in the literature and are written in a general way, so that they can be applied to any molecules, including novel ones. They consider full stereo- and regio-chemistry, and include protection information, reactivity conflicts, literature sources, and reaction conditions. By applying these rules to potential retrosynthetic disconnections, SYNTHIA™ will suggest reactions that are possible based on the chemistry that we know, and compatible with the rest of the molecule structure.

Moreover, you can find four additional rules databases. They consist of machine-extracted rules, which cover specialized chemistries. They may be used to supplement the expert-coded rules database, particularly if your structure contains stereochemistry, complex aromatic systems, or unusual heterocycles. These rules were automatically extracted from the literature and may not contain all possible reaction condition incompatibilities, reactivity conflicts or protection requirements.

• Uncommon chemistry: Reaction rules for uncommon transformations that have a minimum of 10 examples
• Rare chemistry: Reaction rules for rare transformations that have a minimum of 3 examples
• Stereoselective chemistry: Reaction rules for stereoselective transformations
• Heterocyclic chemistry: Reaction rules for the synthesis of aromatic heterocycles

In addition to reaction rules databases, SYNTHIA™ also includes several databases of reactions that have been published in the literature.

• SPRESI by DeepMatter covers organic synthesis literature from 1974 to 2014, and contains 4.6 million chemical reactions abstracted from 700,000 references
• USPTO includes reactions from United States patents published between 1976 and 2016
• Enzyme-Catalyzed Reactions is a collection of expert-curated enzymatic reactions from the literature
• Rhea is an expert-curated database of biochemical reactions, that includes enzymatic reactions and transport reactions as well as reactions that occur spontaneously in biological systems, such as metabolic reactions.
  Rhea-db

By default, only the Expert-Coded Rules, SPRESI, USPTO and the Enzyme-Catalyzed Reactions databases are enabled.