ZINDO | Lanthanide Complexes Computational Chemistry

UV Visible Spectra of lanthanide complexes can be calculated from Sparkle Model optimized geometries, followed by ORCA calculations, in which the lanthanide ion is replaced by a +3e point charge.

The required citation, where this procedure has been first described, is:

Theoretical model for the prediction of electronic spectra of lanthanide complexes

Antonio V. M. de Andrade, Ricardo L. Longo, Alfredo M. Simas and Gilberto F. de Sá
J. Chem. Soc., Faraday Trans., 1996, 92, 1835 - 1839.

Tutorial

To perform this task you will need the following softwares: Gabedit, MOPAC2012, ORCA, and a text editor of your preference (Notepad, Textpad, etc.).
As an example, let us consider the complex CCSD: BAFWUB [(Diglyme)-tris(hexafluoroacetylacetonato)-terbium(iii)], below:
First draw the geometry of your complex following the instructions in Drawing Complexes.
Please, do not forget to optimize the geometry of the complex using MOPAC, as described in Drawing Complexes. As an example, we provide bafwub.out.
Please, right click on the black screen of the "Gabedit: Draw Geometry" window, go to "Read" > "Mopac" > "Last geometry from a Mopac output file" and open the ".out" MOPAC output file.
Ignore what appears on the screen and close the "Gabedit: Draw Geometry" window.
From the main menu of Gabedit, click on the "New Orca input file" icon . A new window, called "Orca input", appears.
If you chose the correct charge and if your complex is properly drawn, the "Spin Multiplicity" field will be automatically set to 1 (singlet). If it is not 1, then this is an evidence that there is something wrong either with your charge, with the drawn complex, or both; in which case you should recheck your complex. Please, read the Drawing Complexes tutorial.
In the "Orca input" window, go to "Type of method" option, and select "Semiempirical Methods". Then, go to the "Excited states" option and select "CIS". Click OK.
The ORCA input will appear in the main window of Gabedit.
Now you must replace the lanthanide ion by a +3e point charge. That is done by creating a new file with the point charge information only. Firts, find and cut the line containing the lanthanide atom coordinates in the ORCA input editor. To create the new file, now paste that line in the text editor of your preference. Replace the lanthanide symbol by 3.0. Add one line above this line in the text editor with the number of point charges. For example, if your complex has only one lanthanide atom, then set this number to 1 (example below). Save the file, with a name of your preference, in a specific folder of your choice (you may even create a new folder for this purpose) and close the file. Please, write down the name of this folder, you will need this information in item 20, below.
This is how the new file should look like. As an example, for convenience, we provide bafwub.txt.
```
1
 3.0 -0.133700 -0.192700 0.014300
```
Go to Gabedit again, add the line:

%pointcharges "bafwub.txt"

below the line "! PrintBasis", where "bafwub.txt" is the file containing the point charge information. Of course, change "bafwub.txt" to whatever file name you assigned to the file in item 10, above.
IMPORTANT: Replace the total charge of the lanthanide complexes by the charge of the ligands.
Why?
Because, we eliminated the lanthanide ions and replaced them by points of charge +3.
Therefore, ORCA will compute the ligands only, in the presence of these point charges. And, consequently, we have to tell ORCA the charge of the ligands.
Thus, the sum of the charge of the ligands plus the sum of the point charges, must be equal to the charge of the complex.
For example, the total charge of the BAFWUB complex is 0. Since we replaced only one lanthanide by a charge of +3, the ligands must now have a total charge of -3. Therefore, we have to set, as the charge of the species being calculated charge -3.
In the Gabedit editor, the charge of the system is indicated in the figure below:

Figure detail:
Now, you must choose nroots, the number of excited states to be calculated for the ligands in the presence of the point charges. The predicted absorption spectrum is highly dependent on this parameter. As it increases, the number of peaks in the spectrum will also increase, due to the inclusion of new possibilities of excitations being considered. For this complex, we chose nroots to be 28.
Please, make sure that maxdim set to a value to at least equal to five times the value of nroots. For this complex, we chose maxdim to be 140.
Finally, you must choose the excitation window which is controlled by parameter EWin, the orbital energy window in Hartrees. The larger this window, the lower will be the excitation energies, and the spectrum will tend to be displaced towards smaller frequencies. For this complex, we chose the GABEDIT default value of -3,100. If you prefer to modify its values, remove the # sign in front of it (uncomment)and set your chosen values.
IMPORTANT: Make sure that Gabedit is properly configured to run ORCA:
On UNIX like systems (Linux, MacOS X, ...): Make sure that your PATH variable contains a reference to the directory of ORCA binary files.
On Windows: Run Gabedit. From the drop-down menu "Settings", select "Preferences". A periodic table will appear. Now, choose the "Others" tab. Make sure that in the line which says "Orca directory", appears the correct path where the orca.exe file, and the other necessary .exe files are.
Now run ORCA. Click on the "Run a program" icon. A new window, called "Run", appears.
In the "Run" window, go to "Folder" option, and select the same folder you used in item 11 above . Then, go to the "Save data in file " option and choose a name for the file, which will automatically have extension .inp. As example, we provide orca_bafwub.inp. Click OK.
OBS: If Gabedit returns an error message, please follow the instructions in item 18 above.
You can follow the progress of the ORCA calculation. There are two tabs in the Gabedit editor. Click on the output tab, which, in this example, is called "orca_bafwub.out". You will visualize the output of the ORCA calculation for the lanthanide complex. In order to keep following the progress of the calculation, keep clicking on "Update/end" button on the right side of the Gabedit window, as shown bellow:

An ORCA calculation may take some time, anything from a few minutes to even a few hours. You can also follow the execution of the ORCA calculation by examining the .out file located in the folder you used in item 11 above. You may open this corresponding .out file with any text editor, as a text file.
A successful calculation will be completed only when the phrase ****ORCA TERMINATED NORMALLY**** appears, as in the figure below.

		Timings for individual modules:

Sum of individual times         ...      127.343 sec (=   2.122 min)
STO integral calculation        ...        0.072 sec (=   0.001 min)   0.1 %
SCF iterations                  ...        0.757 sec (=   0.013 min)   0.6 %
CIS module                      ...      126.514 sec (=   2.109 min)  99.3 %
                             ****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 2 minutes 8 seconds 250 msec

For visualizing the spectrum, go to "Tools" > "UV spectrum" > "Read energies and intensities from a Orca output file", navigate to the same folder you used in items 11 and 20, and find the .out file produced by ORCA. It should have the same name of the .inp file saved in item 19 above. As example, we provide orca_bafwub.out. Click in "Open". The spectrum will be shown, as below.
For better visualization, please choose the Set Data options as indicated above.

Acknowledgments
We are grateful to Sebastiaan Akerboom from Leiden University, Netherlands, for the suggestion of this tutorial.