Molecular Analysis

The Molecular Analysis module in ChemXploreML provides comprehensive tools for analyzing and visualizing molecular properties. By inputting a SMILES string, you can generate a detailed report covering various aspects of the molecule's structure and physicochemical properties.

Overview

The analysis is organized into several categories, allowing you to focus on specific areas of interest. The following sections detail the properties calculated in each category.

Key Features

Basic Properties

• Number of Atoms: Total count of atoms in the molecule.
• Number of Bonds: Total count of bonds in the molecule.
• Molecular Weight: The molecular weight of the molecule.

Ring Information

• Number of Rings: Total count of rings.
• Ring Sizes: A list of the sizes of each ring.

Chain Information

• Longest Alkane Chain: Length of the longest single-bonded carbon chain.
• Longest Alkene Chain: Length of the longest double-bonded carbon chain.
• Longest Alkyne Chain: Length of the longest triple-bonded carbon chain.
• Number of Alkane Chains: Total count of single-bonded carbon chains.
• Number of Alkene Chains: Total count of double-bonded carbon chains.
• Number of Alkyne Chains: Total count of triple-bonded carbon chains.

Aromaticity

• Number of Aromatic Rings: Total count of aromatic rings.
• Number of Aromatic Atoms: Total count of atoms participating in aromatic rings.

Functional Groups

This section provides counts for various functional groups, including but not limited to:

• Alcohols, Aldehydes, Ketones
• Carboxylic Acids, Esters, Ethers
• Amines, Amides, Nitro compounds
• Nitriles, Sulfides, Sulfoxides, Sulfones, Thiols
• Alkenes, Alkynes, Halides (Alkyl and Aryl), Phenols

Physicochemical Properties

• LogP: The logarithm of the partition coefficient, a measure of lipophilicity.
• TPSA (Topological Polar Surface Area): A measure of the polar surface area of the molecule.
• Number of Hydrogen Bond Donors (HBD)
• Number of Hydrogen Bond Acceptors (HBA)
• Number of Rotatable Bonds

Heterocyclicity

• Number of Heterocycles: The number of rings containing at least one non-carbon atom.
• Percent of Heteroatoms in Heterocycles: The percentage of non-carbon atoms within the heterocyclic rings.

Usage Guidelines

1. Input SMILES: Enter the SMILES string of the molecule you wish to analyze in the input field.
2. Run Analysis: Click the "Analyse" button to perform the calculations.
3. View Results: The calculated properties will be displayed, categorized as listed above. You can use the checkboxes to show or hide different property categories.

Next Steps

After analyzing a molecule, you can use this information for various purposes, such as:

• Comparing different molecules.
• Preparing data for machine learning models.
• Understanding structure-property relationships.