Fast generation of an alkane-series dictionary ordered by side-chain complexity

Area of Science:

• Computational Chemistry
• Organic Chemistry
• Algorithm Development

Background:

• Accurate and efficient generation of alkane structures is crucial for chemical databases and computational studies.
• Existing methods for alkane isomer generation can be computationally intensive and lack efficient coding strategies.

Purpose of the Study:

• To develop a novel algorithm for generating alkane isomers based on main chain selection to minimize side chain complexity.
• To establish an efficient coding system for alkane nomenclature and isomer representation.
• To enhance the speed of alkane structure generation and name translation.

Main Methods:

• The algorithm selects the main alkane chain to minimize side chain complexity, avoiding maximum length constraints.
• Representation of the generation process using nested binary trees.
• Development of a coding system using a ranked alphabet of 33 C1-C6 alkyl groups for name translation.

Main Results:

• The largest required side chain for an N-carbon alkane is (N-1)/3.
• The algorithm can code 3.8 million C1-C22 alkanes for dictionary-ordered name translation.
• Generated isomer codes are reversible and in canonical order.
• Computation rate is inversely linear with N, significantly outperforming other generators.

Conclusions:

• The developed algorithm provides an efficient and rapid method for generating and coding alkane isomers.
• The nested binary tree representation and complexity-ranked alkyl group alphabet offer a novel approach to chemical structure representation.
• This work significantly advances the computational efficiency of handling alkane isomerism.