Hydrogens and valence

Molecular structures with unusual valences are allowed although some restrictions are applied. Missing hydrogens can be automatically added during the calculation. If dProperties find unusual valences it asks to the user if 2D hydrogens have to be added. dProperties implements an automatic H-add procedure based on the usual valences of atoms. Note that when  dProperteis adds 2D hydrogens unusual valences of atoms will be corrected by hydrogen addition to make up the rest of common valence and this may affect the final descriptor values.


The lowest normal valences of common atoms are:

H (1), B (3), C (4), N-P-As (3, 5), O (2), aliphatic S-Se (2, 4, 6), halogens-Li (1).


Aromatic S donating a lone pair is assigned a formal valence of 3 or 5. A three-connected N (or P) with a valence of 4, i.e. pyridyl N, must be specified by a formal positive charge N+.