International Journal of Computer Applications (0975 – 8887)

Volume 150 – No.3, September 2016

Automatic Determination of Oxidation Number on in-

silico basis using Electronegativity through a Semantic
Markup system in XML
Durairaj Vijayasarathi Panneerselvam Vinoth
Department of Chemistry Department of Chemistry
Kanchi Mamunivar Pondicherry Engineering College
Centre for Post Graduate Studies Puducherry- 605 008, India
Puducherry- 605 008, India

Asok Kumar Jana Punnaivanam Sankar

Department of Chemistry Department of Chemistry
Kanchi Mamunivar Pondicherry Engineering College
Centre for Post Graduate Studies Puducherry- 605 008, India
Puducherry- 605 008, India

based method in which ON is determined by using the

ABSTRACT electrons allocated around the atoms. It is calculated as an
A methodology to determine the oxidation numbers of every
imaginary charge arising on an atom by counting the electrons
atom in a chemical structure is arrived on in-silico basis. This
around that atom according to a set of rules4. The second
method involves a structure markup system developed in
method is based on the relative electronegativity of atoms
XML, where the electron environment of every atom is
bonded to each other in the molecule. According to this
encoded explicitly. The calculation of oxidation number is
method it is possible to calculate the oxidation numbers
achieved automatically through a structure editor, ChemEd
automatically with the information about the electronegativity
utilizing the electronegativity attributes of every atom in the
of the atom and its electronic environment in the structure.
structure markup.
The basic requirement for this determination is the details of
Keywords electronic status around every atom such as unpaired electron
status, shared electron status, unshared electron status, vacant
Oxidation Number, XML, Chemical Bonding, Chemical
status etc. This kind of electronic information about every
Structure, Electronegativity.
atom in the existing structure representation systems like CT,
1. INTRODUCTION Mole file, InChI, SMILES, CML etc. are either not available
Oxidation number (ON) of an atom is a measure of the degree or not explicit. Recently it is reported that the electronic
of oxidation of an atom in a molecule1. The oxidation number environment of every atom in the structure can be encoded
of an atom in a compound is considered as a hypothetical using XML markup9-13. This markup system describes the
charge of the corresponding atomic ion2. It is arrived by chemical structures with a deeper semantics by including the
heterolytically cleaving the bonds associated with the atoms electronic details around every atom explicitly. The semantics
of different electronegativity and allocating the electrons to about the electrons are encoded with appropriate number of
the atom with higher electronegativity whereas, the bonds <electronLink> XML tags representing the valence electrons
between like atoms are cleaved homolytically2,3. of every atom. These attributes are used to arrive at the
information about the type of bonding such as ionic, covalent,
The oxidation number is normally used in naming co-ordinate covalent and polar covalent in a chemical
compounds4 like Iron (II) Sulphate, Iron (III) Sulphate etc. structure.
Since the oxidation number shows the number of electrons
lost or gained or shared as a result of chemical bonding in A methodology to determine the oxidation numbers of every
molecules, it is also used to identify the oxidation state of any atom in chemical structures using the semantic structure
atom in oxidation, reduction, and in redox reactions5. Bentley markup system11 is reported here. This study demonstrates the
et al6 reported the method of oxidation number determination determination of oxidation number of atoms in a structure
using relative electronegativity and its significance in description using the electronegativity data associate to the
metabolic redox reactions. It is useful especially in atom in the markup. The study involves the structure editor
understanding the reaction mechanisms in a complex ChemEd11 developed and reported earlier to encode the
metabolic pathway and to arrive at an inference about an chemical structures in XML along with the details of
oxidation reaction. A related study reported by Halkides7 electronic status around atoms11.
reveals the significance of the oxidation number in
biochemistry. The oxidation number also plays a key role in
2. METHOD
The structure markup system describes the semantics about
coordination chemistry and organometallic compounds8.
the electrons using <electronLink> element with appropriate
There are two different methods recommended for attributes inside <atom> element. The <atom> element is
determining the oxidation number by IUPAC4, one is a rule described with necessary attributes to signify appropriate
elements in Periodic Table.

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