The Core and Most Useful Molecules in Organic Chemistry

Bishop, Kyle J. M.; Klajn, Rafał; Grzybowski, Bartosz A.

doi:10.1002/anie.200600881

Cited by 88 publications

(56 citation statements)

References 13 publications

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“…For example, recently the Beilstein database [47] of all known organic compounds and reactions was studied [48,49], showing that there is a core set (a strongly connected component) that contains only 4% of the compounds, but which together give rise to 78% of all known organic molecules in just a few reactions (three steps on average). These studies, however, did not take catalysis into account.…”

Section: Autocatalytic Sets and The Origin Of Lifementioning

confidence: 99%

Autocatalytic Sets and the Origin of Life

Hordijk

Hein

Steel

2010

Entropy

162

159

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The origin of life is one of the most fundamental, but also one of the most difficult problems in science. Despite differences between various proposed scenarios, one common element seems to be the emergence of an autocatalytic set or cycle at some stage. However, there is still disagreement as to how likely it is that such self-sustaining sets could arise "spontaneously". This disagreement is largely caused by the lack of formal models. Here, we briefly review some of the criticism against and evidence in favor of autocatalytic sets, and then make a case for their plausibility based on a formal framework that was introduced and studied in our previous work.Keywords: origin of life; autocatalytic sets; RAF sets The Origin of LifeThe origin of life (OoL) remains an elusive problem, although much progress has been made in recent years. Having gone from a problem considered 'beyond science' to 'solvable in principle but maybe not in practice', many researchers now believe it will be solved in the next few decades. In fact, there are currently several OoL scenarios, but all still have some difficulties and lacunae. Although often quite different in their details, one common element which most of these scenarios have is the appearance of an autocatalytic set or cycle at some stage.Entropy 2010, 12 1734 1.1. An RNA world All life as we know it depends on a delicate interplay between DNA and proteins. However, this DNA-protein machinery seems too complex to have arisen all at once. So there appears to be a "chicken-and-egg" problem: which came first, the chicken (protein, phenotype), or the egg (DNA, genotype)?The most widely accepted resolution of this problem is that of an RNA world [1-3] preceding DNA and proteins, i.e., a collection of (self-)replicating RNA molecules, using template complementarity plus the ability to perform and catalyze their own (or each others) synthesis as a way of achieving reproduction and self-sustainability. The possibility of an RNA world has some experimental support, and is now generally considered to have been an important step in the origin of life [4,5]. However, an RNA world "spontaneously" generating proteins and DNA is not straightforward, and is certainly not (yet) proven beyond any doubt. Moreover, and perhaps more importantly, the initial appearance of an RNA world itself is still mostly an open question [2,3,6,7]. Prebiotic metabolismThe idea of a "primordial soup" [8] spontaneously generating the basic building blocks for life sounded attractive after some initial experiments along these lines [9,10], but has been much debated since then and criticized as not being capable of creating these building blocks in sufficiently large concentrations. So, there must have been something more sustainable to get anything like an RNA world started.A basic element underlying all metabolism (and therefore believed to be of very ancient origins) is the citric acid (or Krebs) cycle. This is a chemical reaction network involving a cyclic sequence of 11 substrates and reactions. It ...

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Section: Autocatalytic Sets and The Origin Of Lifementioning

confidence: 99%

Autocatalytic Sets and the Origin of Life

Hordijk

Hein

Steel

2010

Entropy

162

159

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“…Traveling in such space from one active molecule to another one, one can discover along the trajectory a certain number of novel structures which can be further analyzed in the context of lead optimization. A similar approach has been reported by Bishop et al [77] who suggested the use of chemical reactions as structural mutations connecting in the chemical space known organic compounds taken from the Beilstein database. The supergraph created in such a way enabled the authors to select a set of the "most useful compounds" from which the majority of chemical compounds can be synthesized.…”

Section: Navigation In Graph-based Chemical Spacementioning

confidence: 78%

Chemoinformatics as a Theoretical Chemistry Discipline

Varnek

Baskin

2011

Molecular Informatics

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Here, chemoinformatics is considered as a theoretical chemistry discipline complementary to quantum chemistry and force-field molecular modeling. These three fields are compared with respect to molecular representation, inference mechanisms, basic concepts and application areas. A chemical space, a fundamental concept of chemoinformatics, is considered with respect to complex relations between chemical objects (graphs or descriptor vectors). Statistical Learning Theory, one of the main mathematical approaches in structure-property modeling, is briefly reviewed. Links between chemoinformatics and its "sister" fields - machine learning, chemometrics and bioinformatics are discussed.

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“…In 1990 (Lawson and Kallies, 1990) observed that the Beilstein database forms an implicit network resulting in “a map of practically all known synthetic pathways from almost any starting material to almost any product.” In 2005 this idea was further developed by Fialkowski et al (2005) who first converted the Beilstein database into a network, called the NOC, and further investigated various properties of the NOC in a series of publications (Fialkowski et al, 2005; Bishop et al, 2006; Grzybowski et al, 2009; Gothard et al, 2012; Kowalik et al, 2012; Soh et al, 2012). The important feature of this network is that a computer with an effective network search algorithm is able to optimize a synthesis route very quickly.…”

Section: Methodsmentioning

confidence: 99%

Alternative methods of processing bio-feedstocks in formulated consumer product design

2014

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In this work new methods of processing bio-feedstocks in the formulated consumer products industry are discussed. Our current approach to formulated products design is based on heuristic knowledge of formulators that allows selecting individual compounds from a library of available materials with known properties. We speculate that most of the compounds (or functions) that make up the product to be designed can potentially be obtained from a few bio-sources. In this case, it may be possible to design a sequence of transformations required to convert feedstocks into products with desired properties, analogous to a metabolic pathway of a complex organism. We conceptualize some novel approaches to processing bio-feedstocks with the aim of bypassing the step of a fixed library of ingredients. Two approaches are brought forward: one making use of knowledge-based expert systems and the other making use of applications of metabolic engineering and dynamic combinatorial chemistry.

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The Core and Most Useful Molecules in Organic Chemistry

Cited by 88 publications

References 13 publications

Autocatalytic Sets and the Origin of Life

Autocatalytic Sets and the Origin of Life

Chemoinformatics as a Theoretical Chemistry Discipline

Alternative methods of processing bio-feedstocks in formulated consumer product design

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