BensonAtom is a meta atom which is used to describe functional groups within the benson rules (as found, for example, in Benson's original tables in appendix A). Benson atoms needed to be defined because some of the groups in the benson rules, for example from the original tables, consisted not only of single atoms, but also had other 'atoms' that had more information other than atomic number, for example valence or even functional groups.

Within the philosophy of JThermodyanamics, this 'problem' was solved by the use of meta-atoms. These meta-atoms have a name that is used within the Benson rule specifications and an associated chemical structure.

Within JThermodynamics, the input to the benson rules database have the text form :

C-(a1)/n1-(a2)/n1-...

where C, a1, a2, ... are the 'atoms' and n1, n2, ... designate how many times these atoms are bonded to the center atom. The atoms in the benson rules are either the name of the atom, such as h, o, cl, etc., or a BensonAtom meta-atom.

A benson meta atom has a more encompassing description of the atom beyond the atomic number. For example, it could be how the atom is bonded, such as single, double or triple bonded. A BensonAtom can also be a functional group such as aldehyde/ketone, nitrate, sulfate, etc.

The definition of a benson atom consists of the following:

• The internal name of the group

• The name used within the benson rules

• The associated structure (the name of structure in the CMLStructure database)

• The meta-atom type, in this case BensonAtom.

The following is a brief outline of the 'standard' BensonAtoms that needed to be defined.

Carbon

• Single Bonded: (c)

• Double Bonded (c/d)

• Triple Bonded (c/t)

• Aromatic (c/b)

Oxygen

• Single bonded oxygen: (o)

• CO: (co) aldehyde/carbonyl group

• 
  

Nitrogen

• Single Bonded: (n)

• Imino: (c/i) basically double bonded nitrogen with one group attached =N-R. The double bond group is not specified. And the attachment to the single bond is used in the benson rules, for example n/i-(h) or n/i-(c). The double bonded group does not appear in the Benson rule

• Azo: (c/a) An R-N=N-R group

• Cyano: (cn) This group is not listed as a center atom

• NO : (no) R-N=O

• NO2 (no2): nR(//o)o The structure is inheirently plus, but this is not in the linear form

Sulfer

• SO4 : (so4) s(//o)2(/oR)2

• SO2: (so2) s(//o)2R2

• SO3 (so3) s(//o)2(oR)R

• SO3H: (so3h) s(//o)2(oh)R

• SO: (so) s(//o)R2

• Single bonded: S (s) sR2

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