Infrared Lanthanide Spectroscopy Software

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lanthanide complexes A Comprehensive Strategy to Boost the Quantum Yield of Luminescence of Europium Complexes

                                       Nathalia B. D. Lima, Simone M. C. Gonçalves, Severino A. Júnior, and Alfredo M. Simas
                                                               Scientific Reports 3, Article number: 2395, 2013

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  • To perform this task you will need the following softwares: MOPAC2012, Gabedit and a text editor of your preference (Notepad, Textpad, etc.).
     
  • This tutorial uses version 2.2.8 of GABEDIT. If you installed a different version of GABEDIT, the commands you will have to use may differ from the ones appearing below.

  • As an example, let us consider the complex HANBIH [Triaqua-(pentaethyleneglycol)-europium], below:


     
  • First draw and optimize the geometry of your complex following the instructions in Drawing Complexes. You should now have the corresponding .out and .arc files. As an example, we provide the hanbih.mop.
     
  • Convert the .arc file, hanbih.arc, generated by MOPAC2012 which should then be modified into the optimized .mop file using your favorite text editor as such: open the .arc file and save it with another name with the .mop extension. Find the line which reads FINAL GEOMETRY OBTAINEDand remove everything above and including this line.
     
  • Replace the keywords GNORM=0.25 and BFGS by the keywords AUX and FORCE.
     
  • Warning: please, do not forget to use the keyword FORCE as indicated above. Without it, the IR spectrum will not be calculated.
     
  • Save the file as a .mop file with another name. For convenience we provide hanbih_opt.mop.
     
  • Run this new .mop file in MOPAC2012.
     
  • If you run into any problems, please review the warning in the bottom part of the tutorial Drawing Complexes.
     
  • After completion of the calculation, you should now have a corresponding .aux file. For convenience, we provide hanbih_opt.aux.
     
  • Theoretical calculations of vibrational frequencies tend to deviate from experimental ones in a systematic way, which can be easily corrected by means of scaling factors.
  • Accordingly, we now need to generate a new .aux file, with the scale factors properly applied.
    Please, send your .aux file in the field below to be processed.


     

     
  • You should now have a new .aux file, named old_name-IR_scaled.aux.
    For convenience, we provide hanbih_opt-IR_scaled.aux.
     
  • Open Gabedit and click on “Display Geometry/Orbitals/Density/Vibration” button: . This will open a new window called “Gabedit: Orbitals/Density/Vibration”.
     
  • Right click on the black screen and choose the option “Animation” in the menu that appears. Select the option “Vibration” in the sub-menu.
     
  • In the window called “Vibration” go to the “File” menu, and then go to the option “Read”. Select the option “Read a MOPAC aux file”. Find your IR_scaled.aux file and click on “Open”.
     
  • In the window called “Vibration”, go to the “Tools” menu and select the option “Draw IR Spectrum”.
     
  • A new window will open with the infrared spectrum of your lanthanide complex, as shown below:

    sparkle gabedit infrared spectrum
     
  • To adjust the intensity scale so that the spectrum does not appear chopped, choose the option “Set ymax=1”.

     
  • To save the infrared spectrum right click on it, choose the option “Screen Capture” and save it in the PNG format. Your .png file should now look like this one:


     

  • For comparison purposes, below we present the infrared spectrum computed without applying the frequency scale factors, from the original .aux file.

    sparkle infrared spectrum gadolinium