Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology

Punnaivanam Sankar1, Krief Alain, Gnanasekaran Aghila

  • 1Department of Chemistry, Pondicherry Engineering College, Puducherry-605 014, India. gapspec@yahoo.com

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Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.Two regions of electron density in a diatomic...
Structure of Benzene: Molecular Orbital Model01:18

Structure of Benzene: Molecular Orbital Model

According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
Structure and Nomenclature of Epoxides02:38

Structure and Nomenclature of Epoxides

Cyclic ethers are heterocyclic compounds with an oxygen atom in the ring along with carbon atoms. They are named depending on the number of carbon atoms present in their ring system. Cyclic ethers with a three-membered ring system are called “oxirane”, four-membered ring systems as “oxetane”, five-membered ring systems as “oxolane”, and six-membered ring systems as “oxane”. The cyclic structure of these rings imposes angle strain, and this strain is more in the ring having a smaller number of...
Structure of Benzene: Kekulé Model01:07

Structure of Benzene: Kekulé Model

In 1865, August Kekule suggested the structure of benzene according to the structural theory of organic chemistry based on the three assertions—formula of benzene is C6H6, all the hydrogens of benzene are equivalent, and each carbon must have four bonds due to its tetravalency.
He proposed that benzene has a cyclic structure of six carbon atoms attached to one hydrogen atom each, with three alternating pi bonds.
Aromatic Hydrocarbon Cations: Structural Overview01:18

Aromatic Hydrocarbon Cations: Structural Overview

Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
Removing one hydrogen from the intervening CH2 group with both...