An algebraic model of constitutional chemistry as a basis for chemical computer programs

Dugundji, J.; Ugi, I.

doi:10.1007/bfb0051317

Cited by 106 publications

(107 citation statements)

References 18 publications

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“…The representation of chemical reactions as graph rewriting rules is closely related to the Dugundji-Ugi theory [36,37], which is based on the concepts of bond and reaction matrices. This approach has proved useful in particular in the analysis of metabolic reactions [38,39].…”

mentioning

confidence: 99%

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Andersen

Flamm

et al. 2013

Entropy

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Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth.HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex mixture. Here we use a computational model based on graph grammars as a means of exploring the chemical spaces of HCN polymerization and hydrolysis. A fundamental issue is to understand the combinatorial explosion inherent in large, complex chemical systems. We demonstrate that experimental data, here obtained by mass spectrometry, and computationally predicted free energies together can be used

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confidence: 99%

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Andersen

Flamm

et al. 2013

Entropy

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“…Similar ideas were set up by Ugi and Dugundji in (1973). They developed the notion of ensembles of molecules (EM) and of families of isomeric ensembles of molecules (FIEM) to describe, in mathematical terms, chemical reactions.…”

Section: Lingua Philosophica Grammars and Beyondmentioning

confidence: 97%

Chemistry, a lingua philosophica

Restrepo

Villaveces

2011

Found Chem

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We analyze the connections of Lavoisier system of nomenclature with Leibniz's philosophy, pointing out to the resemblance between what we call Leibnizian and Lavoisian programs. We argue that Lavoisier's contribution to chemistry is something more subtle, in so doing we show that the system of nomenclature leads to an algebraic system of chemical sets. We show how Döbereiner and Mendeleev were able to develop this algebraic system and to find new interesting properties for it. We pointed out the resemblances between Leibniz program and Lavoisier legacy, particularly regarding the lingua philosophica for understanding and thinking Nature, in this particular case, chemistry. In the second part we discuss, from the linguistic viewpoint, how Lavoisian algebraic system may be taken further to build a language. We study the constituents of such a chemical language. Finally, we formalize some of the ideas here presented by using elements of network theory and discrete mathematics.

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“…This definition of m is a slightly more formal version of the Dugundji-Ugi theory [14]. Our notation emphasizes the central role of the (not necessarily unique) bijection m. Since we consider I and O as given fixed input, the atom mapping m uniquely determines R m .…”

Section: Preservation Of Bond Electrons For Each Atom)mentioning

confidence: 99%

Atom Mapping with Constraint Programming

Mann

Nahar

Ekker

et al. 2013

Lecture Notes in Computer Science

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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.

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An algebraic model of constitutional chemistry as a basis for chemical computer programs

Cited by 106 publications

References 18 publications

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Chemistry, a lingua philosophica

Atom Mapping with Constraint Programming

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