Drawing and Optimizing Molecular Geometry
Step 1: In the main menu, click on the "JOYDraw" option to draw and visualize structures.
Step 2: In the 2D editor located on the left sidebar ("2D SKETCHER"), draw the molecular structure and click the update buttons ("Replace 3D View" or "Append to 3D View") to project the three-dimensional model in the central panel.
Step 3: In the "3D TOOLS & PERIODIC TABLE" section on the left panel, click the "Upload File (.xyz/.joy)" button to load a local file and view its three-dimensional structure directly on the screen.
Step 4: In the lower left panel, click on "Submit Job (xTB)" to start the structure optimization. The "Running xTB" status in the upper right corner will indicate active processing, and the progress can be monitored in the "SERVER CONSOLE - orca output.log" panel. If necessary, interrupt the process by clicking "Stop Optimization".
Geometry optimizations in JOYSpectra are performed using the GFN2-xTB method fully integrated via ORCA. For more details and advanced documentation, visit the Official ORCA Tutorials.
ORCA Program:
• Neese, F. Software update: the ORCA program system – Version 6.0 Wiley Interdiscip. Rev.: Comput. Mol. Sci., 2025, 15, 2, e70019 (DOI: 10.1002/wcms.70019).
• Neese, F. The ORCA program system Wiley Interdiscip. Rev.: Comput. Mol. Sci., 2012, 2, 1, 73–78 (DOI: 10.1002/wcms.81).
GFN-xTB Methods:
• Bannwarth, C.; Ehlert, S.; Grimme, S. GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method... J. Chem. Theory Comput., 2019, 15 (3), 1652–1671 (DOI: 10.1021/acs.jctc.8b01176).
• Grimme, S.; Bannwarth, C.; Shushkov, P. A Robust and Accurate Tight-Binding Quantum Chemical Method... J. Chem. Theory Comput., 2017, 13 (5), 1989–2009 (DOI: 10.1021/acs.jctc.7b00118).
• Pracht, P.; Caldeweyher, E.; Ehlert, S.; Grimme, S. A Robust Non-Self-Consistent Tight-Binding Quantum Chemistry Method for Large Molecules. ChemRxiv, 2019 (DOI: 10.26434/chemrxiv.8326202.v1).