Skeletal Formula Notations

This section provides a quick introduction on what is atomic bond that ties atoms together to form molecules.

There are a number of notations are used Skeletal Formula to simiplify molecule diagrams.

1. Carbon Element Symbols Removed - Since carbon elements are so common in molecules, carbon element symbols are removed from Skeletal Formula diagrams. When you see a bond end point without element symbol, you can assume that it is a carbon element.

Skeletal Diagram with Carbon Symbol Removed
Skeletal Diagram with Carbon Symbol Removed

2. Hydrogen Elements and Bonds Removed - Since bonds between hydrogen elements and carbon Elements are so common in molecules, all hydrogen-carbon bonds are removed from Skeletal Formula diagrams. When you see a carbon element missing bonds, you can assume that it has additional bonds with hydrogen elements.

Skeletal Diagram with Hydrogen Element Removed
Skeletal Diagram with Hydrogen Element Removed

3. Wedge and Dash Projections - If 3 dimensional information needs to be maintained in Skeletal Formula diagrams, you can use Wedge and Dash projections. A wedge projection indicates a bond that pointing forward towards the viewer. A dash projection indicates a bond that pointing away from the viewer.

Skeletal Diagram with Wedge and Dash Projections
Skeletal Diagram with Wedge and Dash Projections

4. Condensed Branches - Some simple branches can be written as condensed Formulas like OH, NH2.

Skeletal Diagram with Condensed Branches
Skeletal Diagram with Condensed Branches

Table of Contents

 About This Book

Introduction of Molecules

 What Is Molecule

 What Is Molecular Formula

 What Is Atomic Bond

 What Is Molecule Structure

Skeletal Formula Notations

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB