Cambridge MedChem Consulting

Calculating Physiochemical Properties

There are a number of online websites that provide property calculations, however be careful not to post proprietary information.

pKa - Difficult to calculate accurately, there are a few sites that give experimentally determined data.

pKa Data Compiled by David Ripin and David Evans (Harvard University) Bordwell pKa Table Acidity in DMSO (Univ. of Wisconsin) Zirchrom list of over 600 acids and bases

See Also:- Dissociation constants of organic bases in aqueous solution. D.D. Perrin. Butterworths, 1965. Dissociation constants of organic acids in aqueous solution. G.Kortum, W.Vogel and K.Andrussow. Butterworth, 1961.

The Chemaxon website

A variety of calculation plugins are available for Marvin. It has a rich (and growing) list of editing features, is chemically aware and is able to call ChemAxon's structure based calculation plugins for structures on the canvas.

There are a couple of demo pages

Virtual Computational Chemistry Lab

This site provides free on-line tools, which are helpful in performing computational chemistry, ADME/T and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties and the analysis of relationships between chemical structure and properties

On-line software includes:-


Compiles published experimental data about compounds and provides a property prediction service using the ACDLabs Percepta platform, EPISuite and ChemAxon tools


As well as a vast amount of biological data ChEMBL also collates published physicochemical data.


SPARC Performs Automated Reasoning in Chemistry

Current implementations (selected references):

OSIRIS Property Explorer

Is an integral part of Actelion's inhouse substance registration system.It lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and colour coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. Whereas a green colour indicates drug-conform behaviour.


The same properties can be calculated within Datawarrior.

Many desktop applications include LogP and other property calculators including Vortex, ChemDraw, ChemDoodle, Molinspiration, ACDLabs Percepta platform, Stardrop.

Cheminformatics toolkits also provide means to access some calculated properties programmatically OpenBabel, RDKit and CDK

The critical thing to note is that they all use different algorithms so if you start using one package you can't necessarily compare the results with a different package. So if you want to change you will need to recalculate all old results. Whichever package you use it is always important to get experimental results for a couple of representative examples. This will give you a feel for the accuracy of any computed results.

Sirius Analytical website

There are a number of interesting webinars, posters and presentations available from the Sirius Analytical website (registration required) they cover the measurement and use of a variety of physicochemical properties including pKa, LogP and solubility.

Medicinal Chemistry Toolkit app

The Medicinal Chemistry Toolkit app for iOS is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, we developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app is optimised for iPad and contains calculator functions designed to ease the process of calculating values of: Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding.


Asteris can calculate a range of simple “core properties”, such as logP, molecular weight, polar surface area and numbers of hydrogen bond donors and acceptors.

Last updated 9 February 2019