Step 1.

Make a folder where you will place the structure of your molecule in .xyz format,
and where you will run calculations and obtain the output file.

In my case, I created a folder in “e:\orca_work\Charef” while the folder containing the orca program is “e:\orca5”.

I run the calculations on one small molecule called alizarin.

Step 2.

Go to atomistica.online, either by googling atomistica, or by directly typing https://atomistica.online in address bar.

Click on the button START ATOMISTICA.ONLINE. If the browser warns you that the connection is dangerous, just ignore it and press the “Ignore” button.

Step 3.

When atomistica.online opens, choose Orca Input Generator from the left.

Step 4.

Upload the structure for which you want to simulate UV spectrum by clicking on the “Upload” button

Step 5.

Select method: Excitations. This will automatically set TD-DFT calculations with CAM-B3LYP functional and def2-TZVP basis set

Step 6.

Select 6-31+G** basis set and set the number of excitations to 30. Leave the Tamm-Dancoff approximation checked. Run first with this approximation, the calculations will be faster. If the results are fine ok, if not, try without the Tamm-Dancoff approximation by unchecking the corresponding check box. Larger and better basis sets are also preferable, 6-31+G** is a minimum.

Step 7.

If you want, use the solvent, by checking the “Use solvent” check box. For this tutorial, I run calculations without the effects of solvent.

Step 8.

Set the number of cpu cores available for this run (in my case 8) and type the name of the job (this will automatically set the name of the input file).

Step 9.

Click “Generate Orca Input button” to get the input file in the text area of the web browser, then click the “Download Input File” button to download the input file to the folder where you want to run calculations (mentioned in Step 1)

Step 10.

Run calculations by opening the command prompt and by typing the following: “e:\orca5\orca.exe orca_input_file.inp > orca_output_file.out” . You also get that line in the “Command for running ORCA input file:” text area when you click “generate orca input” button.

Keep in mind, if you use Windows, you have to run the full path to orca.exe file, as mentioned in my example, that is the “e:\orca5\orca.exe” part. If you use Linux, it is enough to type just “orca” to invoke orca program.

Step 11.

The calculation will take some time… You can track the progress of the calculation by opening the output file, it is convenient to use the monitor option of the Notepad++ program, as demonstrated in video tutorial.

Step 12.

When the calculation is finished, an output file is fully formed. Open it in Avogadro. Go to “Extensions/Spectra”. Avogadro will automatically plot the spectra. It is possible it will first plot the CD spectra instead of the Absorption spectra. In such a case, don’t worry, just select “Absorption” from the drop-down menu in the lower-left corner of the “Spectra Visualization” window.

Step 13.

Go to the “Advanced” tab to setup Appearance, Export, CD settings and Absorption Settings. In your case, go to the “Absorption Settings” and adjust the UV spectrum. First, pay attention to setting the “X Units” to “nm”. Then modify the value of the “Peak Width” to get the UV spectrum that matches the experimental spectrum.

Step 14.

To get the Figure, use the “Export Image” option, and use at least 300 dpi.