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Isomerism

Isomerism

Isomers are molecules with the same molecular formula but different structural arrangements. Isomers can be further classified into constitutional isomers and stereoisomers. Constitutional isomers differ in the connectivity of their constituent atoms. For example, 2-butanol and diethyl ether are constitutional isomers, as they have the same chemical formula, C4H10O, but differ in the connectivity of the carbon and oxygen atoms. Constitutional isomers have different physical and chemical...

Structural Isomerism

Structural Isomerism

Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can...

Stereoisomerism of Cyclic Compounds

Stereoisomerism of Cyclic Compounds

In this lesson, we delve into the role of ring conformation and its stability, which determines the spatial arrangement and, consequently, the molecular symmetry and stereoisomerism of cyclic compounds. 1,2-Dimethylcyclohexane is used as a case study to evaluate the possible number of stereoisomers. Here, given the multiple (n = 2) chiral centers, there are 2n = 4 possible configurations that lack a plane of symmetry, as the ring skeleton exists in a non-planar chair conformation. In addition,...

Development of Analytical Methods

Development of Analytical Methods

An analytical methodology can be divided into four sequential steps: technique, method, procedure, and protocol. A technique is a scientific principle that rationalizes a specific phenomenon through chemical measurements. Adapting a technique for analyzing a sample of interest is termed a method. The procedure outlines the directions for performing the analysis via an analytical method. The protocol is the detailed guidelines on the procedure, which should be strictly followed to obtain the...

Isomerism in Alkenes

Isomerism in Alkenes

Alkenes like 1-butene and 2-butene exhibit constitutional isomerism, as they differ in the position of the double bond. Further, 2-butene exhibits stereoisomerism and exists as two distinct compounds differing in spatial arrangement.
An isomer is called cis-2-butene when the methyl groups are on the same side of the double bond, and the other stereoisomer, in which methyl groups are on the opposite side of the double bond, is called trans-2-butene. The cis and trans stereoisomers are not...

Stereoisomerism

Stereoisomerism

Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula.
Transition metal complexes often exist as geometric isomers, in which the same atoms are connected through the same types of bonds but with differences in their orientation in space. Coordination complexes with two different ligands in the cis and trans positions from a ligand of interest form isomers. For example, the octahedral [Co(NH3)4Cl2]+ ion has two isomers (Figure 1) In the cis...

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Related Experiment Video

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Hierarchical and Programmable One-Pot Oligosaccharide Synthesis

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Development of an open-source software for isomer enumeration.

Salomé R Rieder¹, Marina P Oliveira¹, Sereina Riniker¹

¹Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.

Journal of Cheminformatics

|January 22, 2023

Summary

This summary is machine-generated.

enu is an open-source program that enumerates constitutional and stereoisomers from molecular formulas using graph theory. It generates isomer lists as canonical SMILES strings for computational efficiency.

Keywords:

Graph isomorphism Isomer enumeration Stereoisomerism

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Area of Science:

Computational Chemistry
Cheminformatics
Graph Theory

Background:

Enumerating molecular isomers is crucial for understanding chemical space.
Existing methods may lack efficiency or flexibility for diverse molecular families.

Purpose of the Study:

To introduce enu, a novel, open-source software for comprehensive isomer enumeration.
To provide a computationally efficient tool for constitutional and stereoisomer generation.

Main Methods:

Utilizes graph theory and canonical adjacency matrices to identify constitutional isomers.
Employs automorphism groups of matrices for stereoisomer enumeration.
Outputs results as canonical SMILES strings in XML format.

Main Results:

Successfully enumerates constitutional and stereoisomers for given molecular formulas.
Demonstrates computational efficiency and flexibility in handling various molecule families.
Provides a freely available, stand-alone C++ program.

Conclusions:

enu offers a robust and efficient solution for molecular isomer enumeration.
The program's open-source nature facilitates wider adoption in computational chemistry.
Facilitates detailed analysis of chemical structures and their variations.