Models, concepts, theories, and formal languages in chemistry and their use as a basis for computer assistance in chemistry

Ugi, I.; Bauer, Johannes; Blomberger, Carola; Brandt, Josef; Dietz, Andreas; Fontain, Eric; Gruber, Bernhard; Scholley-Pfab, Annette v.; Senff, Antje; Stein, Natalie

doi:10.1021/ci00017a001

Cited by 38 publications

(24 citation statements)

References 15 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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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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“…The graph-theoretical reaction rules can be understood as an alternative formulation of the Ugi and Dugundji matrix model of reactions, introduced in 1970s, which has emerged as classical methodology for the representation and generation of chemical mechanisms [3][4][5]. It is based on the encoding of the bond order changes during a transformation with the use of the reaction matrix (R-matrix).…”

Section: Ugi and Dugundji Formal Theory For Reactions And Reaction Mementioning

confidence: 99%

Generation of Chemical Transformations: Reaction Pathways Prediction and Synthesis Design

Nowak¹,

Fic²

2012

Statistical Modelling of Molecular Descriptors in QSAR/QSPR

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“…Different approaches have been used in the development of programs for reaction prediction [20][21][22][23][24][25][26][27]. These programs, which have chemical knowledge based on a library of known chemical reactions or on a mathematical theory, usually achieve their results by making use of heuristics based on empirical or formal rules, and experimental or estimated physical data.…”

Section: Computational Strategymentioning

confidence: 99%

Computational assessment of synthetic procedures

Goodman

Socorro

2007

J Comput Aided Mol Des

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Synthetic chemistry is hard because some reasonable looking molecules cannot be made, because there are errors in the chemical literature, because it is easy to miss reaction possibilities and because even the shape of molecules is very difficult to determine. We propose an approach to the computational analysis of reactions that tries to circumvent these difficulties, by restricting the analysis to simple rules for reactivity that can generate a large number of competing pathways. This huge ensemble is filtered using computational methods to pick out the most likely pathways, and to suggest possible products.

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Models, concepts, theories, and formal languages in chemistry and their use as a basis for computer assistance in chemistry

Cited by 38 publications

References 15 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

Generation of Chemical Transformations: Reaction Pathways Prediction and Synthesis Design

Computational assessment of synthetic procedures

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