The orbital visualization module in JLmol is designed for computational chemists and educators who need to analyze quantum chemistry results. It supports advanced features for exploring molecular orbitals, energy levels, and electronic structure, with a focus on usability and clarity.
Capabilities:
- HOMO/LUMO Identification: Instantly highlight the Highest Occupied and Lowest Unoccupied Molecular Orbitals.
- Orbital Navigation: Use arrow keys or a clickable list to browse all computed orbitals.
- Energy Level Display: View a sorted list of orbitals by energy, with clear distinction between occupied and virtual orbitals.
- Quick Switching: Jump directly between HOMO and LUMO for rapid analysis.
- Visual Distinction: Color coding and style differences for HOMO, LUMO, and other orbitals.
- Interactive List: Click to select and display any orbital, with real-time updates in the 3D viewer.
Technical Details:
- Supports visualization of orbitals from MOLDEN and compatible quantum chemistry output files.
- Energy levels are parsed and displayed alongside the orbital list.
- Handles large basis sets and complex molecules efficiently.
- Integrates with the calculation runner for seamless workflow from computation to analysis.
Best Practices & Troubleshooting:
- Use keyboard navigation for fast orbital browsing.
- If orbitals do not display, check that your calculation output is in a supported format (MOLDEN recommended).
- For large molecules, use simplified display styles for better performance.
References: