Introduction to Chemoinformatics
2. Representation of chemical reactions
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
Reactions in Chemoinformatics
Typical problems/tasks:
Storing information on chemical reactions (databases). Retrieving information on chemical reactions. Comparing and analyzing sets of reactions. Defining the scope and limitations of a reaction type. Developing models of chemical reactivity. Predicting the course of chemical reactions. Analyzing reaction networks (e.g. organic syntheses, metabolic pathways, pathways of chemical degradation in the atmosphere). Developing methods for the design of syntheses.
Joo Aires de Sousa www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions
OUTLINE
Reactions in the SMILES notation. Reactions in the MDL RDF format (derivative of Molfile). Specification of reaction centers.
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions with SMILES
SMILES_1.SMILES_2 >> SMILES_3.SMILES_4
Reactant 1 Reactant 2 Represents the reaction arrow Represents the + symbol Product 1 Product 2
Example:
Joo Aires de Sousa
CC=O.CCCN>>CCC\N=C\C.O
www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions with SMILES
Example: CC=O.CCCN>>CCC\N=C\C.O
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions with SMILES
Non-reacting compounds in between the two > (e.g. solvents or catalysts) CCC(=O)O.OCC>[H+].[Cl-].OCC>CCC(=O)OCC.O
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions in the RXN format
nr of reactants nr of products
Molfile of 1st reactant
Molfile of 2nd reactant
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions in the RXN format
Molfile of 1st product
Molfile of 2nd product
Joo Aires de Sousa www.dq.fct.unl.pt/staff/jas/qc
Representation of reactions in the RDF format
Several reactions in the RXN format in one file.
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
Specification of the reaction center
Bonds broken
Bonds made If bonds involved in the reaction are identified, it is easier to e.g. find in a database two cases of the same reaction with different reactants.
Joo Aires de Sousa www.dq.fct.unl.pt/staff/jas/qc
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Specification of the reaction center in the RDF format
(bonds made and broken)
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
11
Specification of the reaction center in the RDF format
( http://www.mdli.com/downloads/public/ctfile/ctfile.jsp )
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
12
Atom-to-atom mapping
Which atoms of the reactants correspond to which atoms of the products.
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
13
Atom-to-atom mapping in the RDF format
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
14
Specification of the reaction center with ChemAxon MarvinSketch
Right-click on a bond
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
15
Atom-to-atom mapping with ChemAxon MarvinSketch
Joo Aires de Sousa
www.dq.fct.unl.pt/staff/jas/qc
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