Atoms

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.

 

There are no restrictions on atom connectivity, even if for atoms with too many bonds some errors may occur in descriptor calculation.

 

The main atomic parameters used in Dragon are:

atomic mass (m);
van der Waals volume (v);
atom electronegativity (e);
atom polarizability (p);
first ionization potential (i);

 

Other atomic parameters used for calculation of specific classes of molecular descriptors are the covalent radius (r) and atomic number (Z).

 

Atomic parameters are usually scaled on the corresponding carbon atom value. View unscaled and scaled property values for all the considered atoms by clicking the item 'Weighting schemes' in the menu 'View' of the main menu bar.

 

Another atomic parameter, which is topological in nature, is the intrinsic state (s), that is a local vertex invariant derived from the molecular graph.