Calculated Physicochemical Properties
The physicochemical properties for metabolites in Metabolomics Structure Database were calculated using an external open source package named MayaChemTools. The current list of calculated phsicochemical properties is shown below.
| Name | Description |
|---|---|
| Heavy Atoms | # of non-hydrogen atoms |
| Rings | # of rings |
| Aromatic Rings | # of aromatic rings |
| Rotatable Bonds1 | # of rotatable bonds corresponds to single bonds excluding following types of single bonds: terminal bonds; attached to triple bonds; amide, thioamide and sulfonamide bonds. |
| van der Waals Molecular Volume2 (Units: Å3 molecule-1) | van der Waals molecular volume calculated from 2D structure using atomic radii with adjustments for number of bonds, aromatic and non-aromatic rings |
| Topological Polar Surface Area3 (Units: Å2 molecule-1) | Topological Polar Surface Area corresponding to nitrogen and oxygen atoms calculated from 2D structure using contributions from pre-defined structure fragments containing these atoms |
| Hydrogen Bond Donors4,5 | # of hydrogen bond donors corresponding to sum of nitrogen and oxygen atoms with at least one implicit/explicit hydrogen atom |
| Hydrogen Bond Acceptors4,5 | # of hydrogen bond acceptors corresponding to sum of nitrogen atoms without any any implicit/explicit hydrogen atom and all oxygen atoms |
| logP6 | logP partition coefficient calculated from 2D structure using contributions from pre-defined structure fragments. It corresponds to: log(Poctanol/Pwater) = log(SoluteInOctanol/SoluteInWater) |
| Molar Refractivity6 | Molar refractivity calculated from 2D structure using contributions from pre-defined structure fragments |
| Fraction sp3 Carbons7,8,9 | Fraction of sp3 carbons corresponds to number of sp3 carbons divided by total number of carbon atoms |
| sp3 Carbons7,8,9 | # of sp3 carbon atoms |
References
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[3] Ertl, P.; Rohde, B.; Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport Properties. J. Med. Chem. 43, 3714-3717 (2000).
[4] Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Scaffold-hopping by topological pharmacophore search: A contribution to virtual screening. Angew. Chem. Int. Ed. 38, 2894-2896 (1999).
[5] McGregor, M. J.; Muskal, S. M. Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J. Chem. Inf. Comput. Sci. 39, 569-574 (1999).
[6] Wildman, S. A.; Crippen, G. M.; Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 39, 868-873 (1999).
[7] Yan, A.; Gasteiger, J.; Prediction of aqueous solubility of organic compounds by topological descriptors. QSAR Comb Sci. 2003, 22, 821-829.
[8] Lovering, F.; Bikker, J.; Humblet, C. Escape from flatland: Increasing saturation as an approach to improving clinical success. J. Med. Chem. 2009, 52, 6752-6756.
[9]i Walters, W.P.; Green, J.; Weiss, J.R.; Murcko, M. A. What do medicinal chemists actually make? A 50-year retrospective. J. Med. Chem. 2011, 54, 6405-6416.
