Benson rules essentially define a central 'atom' and the 'atoms' it is connected to it. However, just referring to the atom in the periodic table is not sufficient. For example, whether a carbon is single, double, triple or aromatic plays a significant role in the This is where the BensonAtom meta-atom comes into play. This is reflected in the original tables of Benson rules published in Benson's book, Thermochemical Kinetics: Methods for the Estimation of Thermochemical Data and Rate Parameters.
The BensonAtom is one type of Meta-Atom which is used for the purpose of expanding the definition of atom within the Benson rules. An atom is relabeled according to its connectivity. For example, a doubly bonded carbon is recognized (through the Meta-Atom structure) as having a double bond with another carbon and is recognized and appropriately labeled with c/d within the Benson rule. Within the context of Meta-Atoms, a doubly bonded carbon meta-atom has the following components:
MetaAtomName :c/d
MetaAtomType: BensonAtom. This is used to isolate all the BensonAtom's within the entire list of meta-atoms
ElementName: This is the name of the associated structure. In this case, this refers to a generalized carbon double bond (named DoubleBondCarbon in the CMLStructure table in the database.
The defined 'original' BensonAtom's in the mySQL database are the following:
select * from metaatominfo where MetaAtomType='BensonAtom';
+----------------+--------------+--------------+----------------------+
| MetaAtomKey | MetaAtomType | MetaAtomName | ElementName |
+----------------+--------------+--------------+----------------------+
| BensonAtom.co | BensonAtom | co | AldehydeKetone |
| BensonAtom.o | BensonAtom | o | SP3Oxygen |
| BensonAtom.c/d | BensonAtom | c/d | DoubleBondCarbon |
| BensonAtom.c/t | BensonAtom | c/t | TripleBondedCarbon |
| BensonAtom.c/b | BensonAtom | c/b | AromaticCarbon |
| BensonAtom.n | BensonAtom | n | SingleBondedNitrogen |
| BensonAtom.c | BensonAtom | c | CarbonAtom |
+----------------+--------------+--------------+----------------------+
7 rows in set (0.00 sec)
The structure, for example of the DoubleBondCarbon is found in the CMLStructures database:
|select * from CMLStructures where ElementName='DoubleBondCarbon';
DoubleBondCarbon
<?xml version="1.0" encoding="ISO-8859-1"?>
<molecule id="DoubleBondCarbon" xmlns="http://www.xml-cml.org/schema">
<atomArray>
<atom id="a1" elementType="Du" formalCharge="0" hydrogenCount="2"/>
<atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
<atom id="a3" elementType="Du" formalCharge="0" hydrogenCount="0"/>
<atom id="a4" elementType="Du" formalCharge="0" hydrogenCount="0"/>
</atomArray>
<bondArray>
<bond id="b1" atomRefs2="a2 a1" order="D"/>
<bond id="b2" atomRefs2="a3 a2" order="S"/>
<bond id="b3" atomRefs2="a4 a2" order="S"/>
</bondArray>
</molecule>
| Standard |