Bonds

Bonds between atoms are characterized by a conventional bond order which accounts for different bond lenghts.

 

Conventional bond order takes the following values:

1 for single bonds
2 for double bonds
3 for triple bonds
1.5 for aromatic bonds

 

Several molecular descriptors encode information on bond multiplicity by using the conventional bond order. They are thus affected by the conventional bond order assignment to molecules bonds.

 

When dProperties reads a molecule input file, initial bond order values are assigned to molecule bonds according to the specific information contained in the input file. Single, double and triple bonds are specified in all the input files, excluding SMILES notations where single bonds are usually omitted. Aromatic bonds may be specified by specific symbols, e.g. "a" in HyperChem files, "Ar" in MDL and Sybyl files, ":" in SMILES notations. In SMILES notations, aromatic bonds are usually omitted, nonetheless dProperties assigns bond order of 1.5 to bonds between two atoms entered by lower case atomic symbols. In Sybyl files, bonds represented by the symbols "am" and "du" are always assigned a bond order of 1.

 

The dProperties algorithm for conventional bond order rearrangement has been developed with the main goal of assigning value of 1.5 only to bonds belonging to effective aromatic structures (see rules for aromaticity detection). Examples are:

bonds2

bonds1

 

Delocalized bonds, such as in nitro groups, are represented as covalent bonds to both uncharged oxygens (N = O); they are always assigned a conventional bond order of 2. Examples are:

bonds3

bonds4

bonds5

 

Moreover, if bond orders of 1.5 have been improperly assigned to non-aromatic structures, they are changed in such a way to obtain alternating single and double bonds. This correction is mainly concerned with HyperChem files and SMILES notations where the user has more liberty to explicitely define aromatic bonds. Examples are:

bonds6

bonds7

 

Some structures erroneously entered as aromatic by the user may be rejected if they are formally incorrect. This happens when alternating single and double bond assignments cannot be made. Example is:

bonds8

 

In the example above, there is no way to assign alternating single and double bonds without leaving one carbon atom with valence lower than 4.

 

If a non-aromatic structure is entered as aromatic, it may also happen that different interpretations are possible. This is much more likely when the structure includes nitrogen atoms, which, having common valences of 3 and 5, but also valence of 4 in the case of a positively charged type (N+), can cause some ambiguities. An example is:

 

first solution:

bonds9

 

second solution:

bonds10

 

The dProperties algorithm would give the first solution.

 

In reading SMILES notations dProperties may initially assign several wrong bond orders of 1.5 if the user has entered atoms by lower case atomic symbols. Therefore, to avoid an erroneous molecule representation, the SMILES user is suggested to use lower case atomic symbols only for atoms effectively belonging to aromatic structures or to allow dProperties to rearrange the conventional bond orders according to the internal algorithm for aromaticity detection.