Abstract
The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, ‘animate’ matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic ‘chemical space’. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of ‘chemical spaces’ beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems.This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Highlights
To a first-order consideration, organic structure space is composed of all molecules containing carbon which satisfy Lewis electron pairing rules [1]
While one-dimensional high-resolution mass spectrometry is able to determine exact masses and molecular formulae with a great deal of accuracy, as mentioned above there is an enormous amount of structural isomerism in organic chemistry, each detected unique formula may be representative of an as-yet-unknown number of structural isomers
It is clear that organic chemical structure space is very large, and that abiotic, and possibly prebiotic, chemistry sampled a significant but relatively small subspace of this set
Summary
To a first-order consideration, organic structure space is composed of all molecules containing carbon which satisfy Lewis electron pairing rules [1]. Organic formula space belies the complexity of organic structure space: a single molecular formula can represent many structural isomers [6,7], the number per unique formula may be highly variable (see for example [8,9]) Today, this plentitude of chemical structures offers scientists in medicinal chemistry, pharmaceutical research and biotechnology an almost endless array of possibilities to design new drugs and materials. In the 1970s and 1980s, mathematicians provided new techniques to increase the efficiency of the first approaches [12,13], and, starting in the 1990s, implementations became available as software packages for personal computers [14] These methods have been rediscovered for applications in astrobiology and origins of life research, for generating and analysing virtual chemical compound libraries of amino acids and nucleotide analogues [8,9,15], the scope of their potential application is much wider. We review here some approaches and general methods, and some results and ongoing work from our research group
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