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Atom mapping with constraint programming.

Mann M, Nahar F, Schnorr N, Backofen R, Stadler PF, Flamm C - Algorithms Mol Biol (2014)

Bottom Line: Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches.We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting.The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, Freiburg, 79110 Germany.

ABSTRACT
Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms is not reported by chemical reaction databases, however, so that the "Atom Mapping Problem" of finding this bijection is left as an important computational task for many practical applications in computational chemistry and systems biology. Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches. We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting. The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.

No MeSH data available.


Related in: MedlinePlus

Ambivalent reactions. (top) The Meisenheimer rearrangement [37] transforms nitroxides to hydroxylamines. It does not admit a simple alternating cycle as ITS when molecules are represented as graphs whose vertices are atoms. An extended representation, in which the additional electron at the oxygen is treated as a “pseudo-atom” can fix this issue. (bottom) Note that such even sized cycles with a virtual vertex for the moving charge (vertex label e−) can be represented by smaller odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0). See Figure 2 for further details of such an ITS layout.
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Fig5: Ambivalent reactions. (top) The Meisenheimer rearrangement [37] transforms nitroxides to hydroxylamines. It does not admit a simple alternating cycle as ITS when molecules are represented as graphs whose vertices are atoms. An extended representation, in which the additional electron at the oxygen is treated as a “pseudo-atom” can fix this issue. (bottom) Note that such even sized cycles with a virtual vertex for the moving charge (vertex label e−) can be represented by smaller odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0). See Figure 2 for further details of such an ITS layout.

Mentions: Supported ITS layouts. (top) ITS layouts found within the elementary reaction data set from [34]. The number within the vertices corresponds to atomic oxidation state changes, broken bonds are dotted given a negative bond label while formed bonds show positive numbers. (left) Homovalent elementary reactions result in even sized cycles with no oxidation state changes at the atoms (see Figure 1). (middle) Odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0 see Figure 5). (right) Similar layout involving two equivalent oxidation state changes. Note, the inverse layout was also found and used. (bottom) Additionally supported ITS layouts for ambivalent elementary reactions involving non bonding electrons. These result in odd sized cycles and oxidation state changes of one atom. Note that this situation is equivalent to a non-elementary cycle with alternating bond labeling (middle).


Atom mapping with constraint programming.

Mann M, Nahar F, Schnorr N, Backofen R, Stadler PF, Flamm C - Algorithms Mol Biol (2014)

Ambivalent reactions. (top) The Meisenheimer rearrangement [37] transforms nitroxides to hydroxylamines. It does not admit a simple alternating cycle as ITS when molecules are represented as graphs whose vertices are atoms. An extended representation, in which the additional electron at the oxygen is treated as a “pseudo-atom” can fix this issue. (bottom) Note that such even sized cycles with a virtual vertex for the moving charge (vertex label e−) can be represented by smaller odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0). See Figure 2 for further details of such an ITS layout.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4256833&req=5

Fig5: Ambivalent reactions. (top) The Meisenheimer rearrangement [37] transforms nitroxides to hydroxylamines. It does not admit a simple alternating cycle as ITS when molecules are represented as graphs whose vertices are atoms. An extended representation, in which the additional electron at the oxygen is treated as a “pseudo-atom” can fix this issue. (bottom) Note that such even sized cycles with a virtual vertex for the moving charge (vertex label e−) can be represented by smaller odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0). See Figure 2 for further details of such an ITS layout.
Mentions: Supported ITS layouts. (top) ITS layouts found within the elementary reaction data set from [34]. The number within the vertices corresponds to atomic oxidation state changes, broken bonds are dotted given a negative bond label while formed bonds show positive numbers. (left) Homovalent elementary reactions result in even sized cycles with no oxidation state changes at the atoms (see Figure 1). (middle) Odd cycles with two oppositely charged atoms separated by a non-changing pseudo bond (dashed edge labeled 0 see Figure 5). (right) Similar layout involving two equivalent oxidation state changes. Note, the inverse layout was also found and used. (bottom) Additionally supported ITS layouts for ambivalent elementary reactions involving non bonding electrons. These result in odd sized cycles and oxidation state changes of one atom. Note that this situation is equivalent to a non-elementary cycle with alternating bond labeling (middle).

Bottom Line: Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches.We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting.The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, Freiburg, 79110 Germany.

ABSTRACT
Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms is not reported by chemical reaction databases, however, so that the "Atom Mapping Problem" of finding this bijection is left as an important computational task for many practical applications in computational chemistry and systems biology. Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches. We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting. The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.

No MeSH data available.


Related in: MedlinePlus