Reaction Enumeration Examples

Peptide Bond Formation

Reaction

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Monomers were divided into two groups: acids and amines.

Acids:

A:

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B:

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C:

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Amines:

X:

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Y:

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Z:

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Without the specification any additional options, Legio generates six products. Legio tries to perform specified reactions for each monomer from both the first group (acids) and the second group (amines):

A

B

C

X

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Y

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Z

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You can see that all the stereochemistry configurations are preserved during the reaction.

When the “all reactions” mode is specified, products can take place in another reaction too, but only with original monomers or their products. So with such options, three additional products are generated:

B + X + X:

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B + Y + Y:

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B + Z + Z:

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When the “one tube” mode is specified, any monomers and their products can make another reaction. With this mode, it is imagined that all monomers are in one tube. Another three products are generated:

B + X + Y:

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B + X + Z:

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B + Y + Z:

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Reactants Matching

When the reaction does not have any R-group atoms, matching of reactants to monomers is done according to substructure search rules.

Reaction

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Monomers:

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Products:

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Multistep Reactions

Legio can enumerate products appearing in the multistep reactions when existing monomers or produced products can take place in the reaction.

Reaction

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Monomers:

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Products:

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Generation Modes

Legio supports two generation modes for multistep reactions. In the “grid mode”, only one monomer from each group can react. This can be represented as a matrix where the columns correspond to the first group and the rows correspond to the second group. The reaction is performed in each cell. In the “one tube” mode, all of the monomers are in the same tube.

Reaction

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Monomers:

A

B

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X

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When the “grid mode” is on, each product can react with monomers from the same cell and with other products, formed earlier in this cell. For example:

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When the “one tube” mode is active, all of the products and monomers are contained in one tube and can react together. Legio generates the following new products:

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Intramolecular Interactions

Reaction

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Monomer

Product

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Tetrahedral Stereochemistry

Reaction

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Monomers

Products

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no product

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Cis-trans stereochemistry

Reaction

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Monomers

Products

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The third example shows that stereochemistry configuration modifications are dependent.

Functional Groups with 2 Connections

Reaction

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Monomers:

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Products:

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