There have been many requests with regards to what equations are used to calculate the physchem properties in ScienceCloud Project Data during a registration. They are as follows:

Solubility:

The method used to calculate the solubility is the published multiple linear regression model: "Estimation of Aqueous Solubility of Chemical Compounds Using E-State Indices" by Tetko et al., J Chem Inf. Comput. Sci, 2001, 41, 1488-1493.

Polar Surface Area:

• Molecular_PolarSurfaceArea: Polar surface area for each molecule is calculated using a 2D approximation.
• The Molecular_SurfaceArea and Molecular_PolarSurfaceArea descriptors are calculated using a method based on the published method: "Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties", Ertl, P., Rohde, B., Selzer, P., J. Med. Chem. 2000, 43, 3714-3717.

logD:

• The PP component logD calculates the value of logD, the octanol-water partition coefficient calculated taking into account the ionization states of the molecule.

ALogP:

• The Ghose and Crippen octanol-water partition coefficient
• The ALogP PP component uses the atom-based method published by Ghose and Crippen to calculate the octanol-water partition coefficient (LogP), and the molar refractivity (MR) for the incoming molecules. LogP provides a measure of the hydrophobicity of the molecule, while MR contains information about molecular volume and polarizability.

pKa:

• pKa pipeline component identifies pKa sites in the molecule and calculate the corresponding pKa values. The calculated pKa values are output as atom properties (named pKa), not as properties of the whole molecule. They can be visualized by displaying the molecules in the HTML Molecular Table Viewer, where the pKa values will appear in the Atom Properties table for each molecule.