Hückel Molecular Orbital Calculator

This Python script calculates the Hückel molecular orbitals for a given molecule, based on its SMILES representation. It uses the RDKit library for cheminformatics and NumPy for numerical calculations. Matplotlib is used for plotting the energy levels.

Features

• Hückel Matrix Construction: Builds the Hückel matrix for a molecule based on its SMILES input.
• Energy Level Calculation: Solves the Hückel equations to compute molecular orbital energy levels and coefficients.
• Charge and Bond Order Calculation: Calculates atomic charges, bond orders, and electron density.
• Visualization:
  • Displays the molecular structure.
  • Plots molecular orbital energy levels in an Aufbau-like diagram.
• Results Export: Saves the computed results (charges, bond orders, energy levels, etc.) to a text file.
• Solves the Hückel equation to obtain eigenvalues (energy levels) and eigenvectors (molecular orbital coefficients).
• Visualizes the energy levels using a Matplotlib plot, highlighting degenerate orbitals.
• Handles molecules containing C, N, and O atoms (can be extended to other atom types).

Requirements

• Python 3.x
• NumPy
• RDKit
• Matplotlib
• PubChemPy
• Colorama

You can install the required packages using pip:

pip install -r requirements.txt

Start

To use the program open a terminal in the folder of the python file and type

python Huckel.py

How to Use

1. Run the Program: Execute the script in your Python environment.

2. Input the SMILES Code: When prompted, enter the SMILES representation of the molecule you want to analyze.

3. View Results:

   • The program will display molecular properties such as charges, bond orders, and energy levels in the terminal.
   • Use the interactive menu to:
     • Visualize the molecular structure. (1)
     • Plot the molecular orbital energy levels. (2)
     • Save the results to a text file. (3)

4. Exit: Select the q option in the menu to close the program.

Example Workflow

1. Run the program.
2. Input the SMILES code when prompted, e.g., C1=CC=CC=C1 for benzene.
3. View the calculated properties in the terminal.
4. Use the menu options to visualize the molecule or save the results.

Output

The program saves results in a text file located in the output directory. The filename includes the date and time of the analysis, e.g., risultati_huckel_2025-03-25_12-30-45.txt.