Reaction Enumeration Examples

Peptide Bond Formation

Reaction
image1

Monomers were divided into two groups: acids and amines.

Acids:

A:

image2

B:

image3

C:

image4

Amines:

X:

image5

Y:

image6

Z:

image7

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

image8

image9

image10

Y

image11

image12

image13

Z

image14

image15

image16

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:

image17

B + Y + Y:

image18

B + Z + Z:

image19

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:

image20

B + X + Z:

image21

B + Y + Z:

image22

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:

image27 image28

Products:

image31 image32

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:

image37 image38

Products:

image41 image42

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
image44

Monomers:

A B
image47 image48
X
image50

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:

image55 image56
image57 image58

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:

image61 image62

Intramolecular Interactions

Reaction
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Monomer Product
image67 image68

Tetrahedral Stereochemistry

Reaction
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Monomers Products
image80 image81
image82 image83
image84 image85
image86 no product
image87 image88

Cis-trans stereochemistry

Reaction
image90
Monomers Products
image97 image98
image99 image100
image101 image102

The third example shows that stereochemistry configuration modifications are dependent.

Functional Groups with 2 Connections

Reaction
image104

Monomers:

image107 image108

Products:

image112
image113
image114