Molecular descriptors can be calculated only for molecules containing the following 38 atoms:

 

H, B, C, N, O, F, Al, Si, P, S, Cl, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Mo, Ag, Cd, In, Sb, Sn, Te, I, Gd, Pt, Au, Hg, Tl, Pb, Bi

 

Atoms are characterized by their atomic number, connectivity (i.e. the number of bonded atoms), valence (i.e. the sum of conventional bond orders of the incident bonds), charge (if specified in the input file), and some atomic properties encoding chemical information and used as the atomic weightings for molecular descriptor calculation. While atomic number, connectivity, valence and charge are properties taken from the input file and thus specified by the user, the other atomic properties are taken from a DRAGON internal database.

 

The maximum allowed atom connectivity is 10, while the minimum connectivity depends on the atom type.

 

The main atomic parameters used in DRAGON are:

 

• atomic mass (m); 
• van der Waals volume (v); 
• atom electronegativity (e) 
• atom polarizability (p). 

 

Their values are always scaled on the corresponding carbon atom values. View unscaled and scaled property values for all the considered atoms by clicking the ‘Weightings’ icon.

 

For some molecular descriptors such as the WHIMs, another atomic weighting is derived from the electrotopological state indices of Kier and Hall (Kier, L.B., Hall, L.H. (1990), Pharm.Res., 7, 801-807). These are atomic indices calculated as:

 

 

where Ii is the intrinsic state of the ith atom and DIi is the field effect on the ith atom calculated as perturbation of the intrinsic state of ith atom by all other atoms in the molecule; dij is the topological distance between the ith and the jth atoms; A is the number of non-hydrogen atoms in the molecule. The exponent k is a parameter to modify the influence of distant or nearby atoms for particular studies. In Dragon it is taken as k = 2. The intrinsic state of the ith atom is calculated by:

 

where L is the principal quantum number, dv is the number of valence electrons (valence vertex degree) and d is the number of sigma electrons (vertex degree) of the ith atom in the H-depleted molecular structure.

As all the weightings must be positive, the electrotopological indices are scaled as the following: