This document presents a method for automatically determining the oxidation number of atoms in chemical structures using electronegativity values encoded in an XML markup system. The method involves encoding electronic environment details of every atom, such as bonding information, in an XML structure editor called ChemEd. Oxidation numbers can then be calculated based on the electronegativity attributes of each atom and its electronic environment as described in the XML markup. The study demonstrates how oxidation numbers can be automatically determined from a semantic description of a chemical structure using this approach.
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Automatic Determination of Oxidation Number
This document presents a method for automatically determining the oxidation number of atoms in chemical structures using electronegativity values encoded in an XML markup system. The method involves encoding electronic environment details of every atom, such as bonding information, in an XML structure editor called ChemEd. Oxidation numbers can then be calculated based on the electronegativity attributes of each atom and its electronic environment as described in the XML markup. The study demonstrates how oxidation numbers can be automatically determined from a semantic description of a chemical structure using this approach.
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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.