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


Introduction

 

Compounds having ionizable groups exist in solution as a mixture of different ionic forms. The ionization of those groups, thus the ratio of the ionic forms depends on the pH. Since loP describes the hydrophobicity of one form only, the apparent logP value can be different. The logD represents the octanol-water coefficient of compounds at a given pH value.

Learn more about how the logD Plugin works.

The result window shows the pH:logD curves for each molecule drawn in the sketcher. The molecule images are shown in the legend. When clicking on an image, the corresponding molecule is displayed in the upper-left part of the panel.

The reference logD values originally shown can be reached by either clicking on the chart outside of the legend image areas or by selecting logD at reference pHs from the View menu.

 


Fig. 1 logresult window showing the logD-pH curves for three molecules


Options


General Options

 

Different calculation (prediction) options can be set in the General Options tab of the logD Options window:

logP method

 

This option is for selecting the applied method for logP prediction. These can be:

 

Other options

 

These options are for refining the logprediction. 

 

 Fig. 2 General Options tab of the logD Options window


Display Options

 

Different display options can be set in the Display Options tab of the logD Options panel:

 

Fig. 3 Display Options tab of the logD Options window


logD Predictor demo page 


You can try the logD predictor for free on this demo page


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