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Chemistry
Organic Chemistry

The Potential of a Chemical Graph Transformation System

Profile image of maneesh yadavmaneesh yadav

2004, Lecture Notes in Computer Science

https://doi.org/10.1007/978-3-540-30203-2_8
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13 pages

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Abstract

Chemical reactions can be represented as graph transformations. Fundamental concepts that relate organic chemistry to graph rewriting, and an introduction to the SMILES chemical graph specification language are presented. The utility of both deduction and unordered finite rewriting over chemical graphs and chemical graph transformations, is suggested. The authors hope that this paper will provide inspiration for researchers involved in graph transformation who might be interested in chemoinformatic applications.

Figures (7)
Fig. 2. Generalized depictions of three well known reactions a) esterfication b) acetylene-azide cycloaddition c) Diels-Alder cycloaddition. The molecules on the left hand side of the arrow are termed reactants and those on the right hand side, prod- ucts. The asterisk denotes any molecular fragment. Depictions usually omit atoms that are not part of the main carbon skeleton, such as the Ht (hydrogen cation) and Cl~ (chlorine anion) in a). Note how some reactions can give multiple products, as in c). Fig. 1. Two depictions of the same molecule. Organic chemists tend to use the depiction on the left, omitting the labels for carbon (C) atoms and implicitly assuming the presence of hydrogen (H) atoms from the bond type (note the double bond). Wedged and and dashed edges represent bonds projecting out of and into the page, respectively. These figures primarily depict molecular connectivity, real molecules are embedded into distributions of three dimensional conformations. Atoms generally do not lie in one plane, and are tied to each other in a spring-like fashion by chemical bonds.
Fig. 2. Generalized depictions of three well known reactions a) esterfication b) acetylene-azide cycloaddition c) Diels-Alder cycloaddition. The molecules on the left hand side of the arrow are termed reactants and those on the right hand side, prod- ucts. The asterisk denotes any molecular fragment. Depictions usually omit atoms that are not part of the main carbon skeleton, such as the Ht (hydrogen cation) and Cl~ (chlorine anion) in a). Note how some reactions can give multiple products, as in c). Fig. 1. Two depictions of the same molecule. Organic chemists tend to use the depiction on the left, omitting the labels for carbon (C) atoms and implicitly assuming the presence of hydrogen (H) atoms from the bond type (note the double bond). Wedged and and dashed edges represent bonds projecting out of and into the page, respectively. These figures primarily depict molecular connectivity, real molecules are embedded into distributions of three dimensional conformations. Atoms generally do not lie in one plane, and are tied to each other in a spring-like fashion by chemical bonds.
Fig. 3. The synthetic route to an antibiotic compound|[5] that goes by the commercial name Zyvoz.
Fig. 3. The synthetic route to an antibiotic compound|[5] that goes by the commercial name Zyvoz.
Fig. 8. Transformation a) in Figure 2 is applied once to two different molecules. In a) we would predict that the more abundant product (boxed) comes from the intra- molecular reaction, as the molecule will more “quickly” react internally with itself than with another molecule in solution. In b), the molecule is constrained conformationally so that only the inter-molecular product is formed (the graphs shown in reaction diagram actually depict physical multi-sets of molecules).
Fig. 8. Transformation a) in Figure 2 is applied once to two different molecules. In a) we would predict that the more abundant product (boxed) comes from the intra- molecular reaction, as the molecule will more “quickly” react internally with itself than with another molecule in solution. In b), the molecule is constrained conformationally so that only the inter-molecular product is formed (the graphs shown in reaction diagram actually depict physical multi-sets of molecules).
Fig. 9. An example[12] of a non-deterministic application of a chemical transformation. Either or both carbonyl groups (carbon double bonded to oxygen) can be transformed, but under the conditions of the reaction, only one (boxed product) is physically abun- dant. The reasons for this observed selectivity in reactivity, are due to both reaction conditions (written above the arrow) and the three dimensional conformation of the molecule.
Fig. 9. An example[12] of a non-deterministic application of a chemical transformation. Either or both carbonyl groups (carbon double bonded to oxygen) can be transformed, but under the conditions of the reaction, only one (boxed product) is physically abun- dant. The reasons for this observed selectivity in reactivity, are due to both reaction conditions (written above the arrow) and the three dimensional conformation of the molecule.
4 Utility of a Chemical Graph Trasformation System The references that are provided in this section demonstrate that there are many researchers who have implimented and applied graph rewriting over molecular
4 Utility of a Chemical Graph Trasformation System The references that are provided in this section demonstrate that there are many researchers who have implimented and applied graph rewriting over molecular
Fig. 11. A retrosynthetic transformation (denoted with the double lined arrow), using reaction b) from Figure 2. This is only a formal construction, the actual reaction happens in the forward sense[16].
Fig. 11. A retrosynthetic transformation (denoted with the double lined arrow), using reaction b) from Figure 2. This is only a formal construction, the actual reaction happens in the forward sense[16].

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Related topics

  • Computer Science
  • Organic Chemistry
  • Graph Transformation
  • Graph Rewriting
  • Specification Language
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