Chemical space

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View of PubChem chemical space; a projection of the 42-dimensional MQN-property space of PubChem (with 5 virtually created libraries of compounds) using PCA. Color coding is according to fraction (blue 0, red 1) of ring atoms in molecules.[1]

Chemical space is the space spanned by all possible (i.e. energetically stable) molecules and chemical compounds – that is, all stoichiometric combinations of electrons and atomic nuclei, in all possible topology isomers. Chemical reactions allow us to move in chemical space. The mapping between chemical space and molecular properties is often not unique, meaning that there can be very different molecules exhibiting very similar properties. Material design and drug discovery both involve the exploration of chemical space.

As of July 2009, there were 49,037,297 organic and inorganic substances registered with the Chemical Abstracts Service, indicating that they have been reported in the scientific literature.[2] Systematic exploration of chemical space is possible by creating in silico databases of virtual molecules,[3] which can be visualized by projecting multidimentional property space of molecules in lower dimensions.[4][5]

See also[edit]


  1. ^ J.-L. Reymond and M. Awale (2012). "Exploring chemical space for drug discovery using the chemical universe database.". ACS Chem. Neurosci 3 (9): 649–657. doi:10.1021/cn3000422. PMID 23019491. 
  2. ^
  3. ^ L. Ruddigkeit, R. van Deursen, L. C. Blum and J.-L. Reymond (2012). "Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17". J. Chem. Inf. Model. 52 (11): 2864–2875. doi:10.1021/ci300415d. PMID 23088335. 
  4. ^ M. Awale, R. van Deursen and J. L. Reymond (2013). "MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13". J. Chem. Inf. Model 53 (2): 509–18. doi:10.1021/ci300513m. PMID 23297797. 
  5. ^ L. Ruddigkeit, L. C. Blum and J.-L. Reymond (2013). "Visualization and Virtual Screening of the Chemical Universe Database GDB-17". J. Chem. Inf. Model 53 (1): 56–65. doi:10.1021/ci300535x. PMID 23259841.