This manual gives you a walk-through on how to use the logP Plugin:


Introduction
 

The logP Plugin calculates the octanol/water partition coefficient, which is used in QSAR analysis and rational drug design as a measure of molecular hydrophobicity. The calculation method is based on the publication of Viswanadhan et al. The logof a molecule is composed of the increment of its atoms. However, the algorithm described in the paper was modified at several points:

  1. Many atomic types were redefined to accommodate electron delocalization and contributions of ionic forms were added. 
  2. The logof zwitterions are calculated from their logD value at their isoelectric point. 
  3. The effect of hydrogen bonds on the logP is considered if there is a chance to form a six membered ring between suitable donor and acceptor atoms. 
  4. New atom types were introduced especially for sulfur, carbon, nitrogen and metal atoms. 

To find details on logP calculation, see the following page

The result of the calculation appears in a new window, either in a MarvinView (for a 2D view) window or in a MarvinSpace (for a 3D view) window.
 

Fig. 1 LogP result window with atomic increments displayed in MarvinView

 

Fig. 2 LogP result window with atomic increments displayed in MarvinSpace

 

Options
 

General Options

 

Different general options can be set in the logP Options window:

Method
 

This option defines the method for calculating logP. These can be:

The Consensus logP method is a unique, in-house developed logP model based on the methods listed above. Comparison-wise, our Consensus logP method is similar (but not identical) to the ClogP method, while our ChemAxon logP method is similar (but not identical) to the AlogP method.

 

Other options

 

These options are for refining the logP calculation. 

Fig. 3 logP Options window with the General Options panel

 

Display Options

 

Different display options can be set in the logP Options window:

 

Fig. 4 logOptions window with the Display Options panel


References

  1. Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K., J. Chem. Inf. Comput. Sci.198929, 163-172; doi
  2. Klopman, G.; Li, Ju-Yun.; Wang, S.; Dimayuga, M.: J.Chem.Inf.Comput.Sci.199434, 752; doi
  3. PHYSPROP© database
  4. Csizmadia, F; Tsantili-Kakoulidou, A.; Pander, I.; Darvas, F., J. Pharm. Sci.199786, 865-871; doi