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

Introduction

 

The Refractivity Plugin is able to calculate molar refractivity. This descriptor is strongly related to the volume of the molecules and to London dispersive forces that play crucial part in drug-receptor interactions. Our calculation is based on the atomic method proposed by Viswanadhan et al. 

The calculation results with the value of refractivity (the dimension is 106⋅[m3⋅mol-1]) can be displayed in 2D or 3D

 

Fig.1 Refractivity Plugin result window with 2D display in MarvinView

 

Fig. 2 Refractivity Plugin result window with 3D display in MarvinSpace

 

Options

 

Different calculation parameters can be set in the  Refractivity Options window:

  • Decimal places: setting the number of decimal places with which the result value is given.
  • Type: sets the type of the calculation
    • Increments: displays the increments given by atoms.
    • Refractivity: calculates the value of the molar refractivity
  • Increments of hydrogens: displays the increments given by hydrogens.
  • Display in MarvinSpaceif checked, the result window opens as a 3D MarvinSpace viewer; otherwose it is shown in 2D.

 

The numbers in brackets refer to the refractivity sum of the implicit hydrogen atoms.

 

Fig. 3 Refractivity Options window


References

 Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K.,  J. Chem. Inf. Comput. Sci. 1989 29 , 163-172;  doi