Tutorial – Module 1

Module 1 – Geometry Optimization

Geometry optimization is the first step in studying the luminescence of a system containing a lanthanide ion. The geometry is crucial for the theoretical prediction of the Judd-Ofelt parameters, as these parameters depend on the chemical environment surrounding the lanthanide ion (first coordination sphere). To this end, LUMPAC features a module that serves as a graphical interface for the semiempirical package MOPAC (Figure 1). This module further simplifies the application of semiempirical models developed by our research group, [1–6] which are implemented in MOPAC.

Figure 1. Module responsible for the geometry optimization using the semiempirical models included in the MOPAC package.

All features implemented in LUMPAC 2.0 will be demonstrated using the [Eu(btfa)₃(bpy)] complex (Figure 2) as a case study, where btfa ligand is β-diketone 4,4,4-trifluoro-1-phenyl-1,3-butanedione, while bpy stands for bipyridine.[7]

Figure 2. Two-dimensional representation of the [Eu(btfa)₃(bpy)] complex.

A file with a .mol2 extension containing the geometry of the compound is required for the geometry optimization. The .mol2 file (“Tripos Mol2 file”) is a file format that contains atomic positions in Cartesian coordinates and information about the bonds connecting the atoms. (Figure 3) shows the .mol2 file of the [Eu(btfa)₃(bpy)] complex, created using the Mercury program from the corresponding crystallographic structure.

Figure 3. .mol2 file of the [Eu(btfa)₃(bpy)] system created using the Mercury program.

An input file for MOPAC with a .mop extension is created based on the atomic connectivities present in the .mol2 file. The structure is organized to enable LUMPAC to easily identify the coordination polyhedron. The .mol2 file can be generated using graphical programs such as HyperChem,[8] Gabedit,[9] Avogadro,[10] Mercury,[11] and others. Additionally, programs like HyperChem, Gabedit, and Avogadro enable the interactive drawing of three-dimensional chemical structures. A detailed tutorial on how to build chemical structures using Gabedit and HyperChem can be accessed at the following link: http://www.sparkle.pro.br/tutorial/drawing-complexes.

Attention: It is crucial to ensure that, if the structure is manually constructed, all bonds involving the lanthanide ion and the donor atoms are explicitly represented, as shown in Figure 4.

Figure 4. Structure of the [Eu(btfa)₃(bpy)] complex constructed using the Avogadro program, explicitly showing all bonds between the lanthanide ion and the donor atoms of the ligands.

Procedure for Geometry Optimization using LUMPAC

1. Ensure that the “Open .mol2 File” option is selected. Then, click on button (Figure 5) to open the .mol2 file.

Figure 5 provides a detailed overview of the functionalities of each graphical element in Module 1 of LUMPAC, emphasizing the different types of files that can be used as input files for LUMPAC.

Figure 5. Different types of files can be used as input files for the geometry optimization using LUMPAC.

2. Click on button (Figure 6) to define the directory of the external MOPAC program.

Since 2022, the latest source code of MOPAC [12] has been freely distributed through the following GitHub repository: https://github.com/openmopac/mopac. The executable version of MOPAC is installed without requiring an activation key. MOPAC includes all semiempirical models parameterized for the lanthanide ions, namely: RM1, Sparkle/AM1, Sparkle/PM3, Sparkle/PM6, Sparkle/PM7, and Sparkle/RM1. Integrating MOPAC into LUMPAC is straightforward, requiring only the provision of the directory where MOPAC is located (Figure 6).

Figure 6. Procedure for integrating a MOPAC executable into LUMPAC.

3. The keywords (Figure 7) must be appropriately specified before performing the geometry optimization. Once the .mol2 file is opened, the button (Figure 5) will be enabled.

The LUMPAC interface (Figure 7) allows for the editing of keywords. The semiempirical model and the total charge of the system are the most important parameters to define. As users type, the edit line autocompletes the keywords. In this way, the edit line ensures that the user enters the keywords with the correct syntax.

Figure 7. MOPAC keyword editor in the geometric optimization module.

4. Select the Compare Models group box (Figure 8) to compare the geometry of the input file with the geometries calculated by the semiempirical models.

The Compare Models group box allows for the estimation of the differences between the input geometry and the geometries calculated using different semiempirical models. This estimation is performed by superimposing the calculated structures onto the initial structure and using RMSD (root mean square deviation of atomic positions) to quantify errors in bond distances and angles. The resulting error values are saved in a text file named rmsd.txt (Figure 9), located in a folder called compare_geoms along with other calculation output files.

Figure 8. Selection of models for comparison and configuring the number of logical cores for parallel computation using the Compare Models feature.

Figure 9. The rmsd.txt file contains the estimated errors between the input structure and the structures calculated using the selected semiempirical models.

5. Click on button to execute the geometry optimization using the MOPAC program.

Attention: The output file generated by MOPAC will have a .out extension and retains the same name as the input file. This output file will be saved in the same directory as the input file. As soon as the .out file is modified during the background execution of MOPAC, the LUMPAC file viewer updates its content to show the progress of the geometry optimization.

6. After the calculation completes, the user can view either the initial or optimized structure (Figure 10).

Figure 10 displays the LUMPAC file and molecule viewers within the geometry optimization module. The molecule viewer can be highlighted to visualize the molecular structure in detail, modify visual parameters, and save the image as a .png file (Figure 11). Double-clicking the molecule viewer window returns it to its original position.

Figure 10. LUMPAC file and molecule viewers contained in the geometry optimization module.

Figure 11. Visualization of the [Eu(btfa)₃(bpy)] complex and options for editing the image.

Table 1 lists the mouse cursor commands for translation, rotation, and zoom functions, which control visualization settings.

Table 1. Translation, rotation, and zoom commands for the molecule viewer.

Command	Function
Press the left mouse button and move the mouse.	The view is moved freely.
While holding SHIFT, press the left mouse button and move the mouse.	A translation is performed.
Press the right mouse button and move the mouse.	Moving the mouse forward increases the zoom; moving it backward decreases the zoom.
Scroll the mouse wheel up or down.	The zoom is increased or decreased.
While holding CTRL, press the left mouse button and move the mouse.	A rotation transformation is applied.

LUMPAC can perform geometry optimization with a .mop file (MOPAC input file), but MOPAC keywords editing is disabled within the LUMPAC interface. Therefore, users must edit the .mop file using a text editor.

References

[1] M. A. M. Filho, J. D. L. Dutra, H. L. B. Cavalcanti, G. B. Rocha, A. M. Simas, R. O. Freire, J. Chem. Theory Comput., 2014, 10, 3031–3037.

[2] M. A. M. Filho, J. D. L. Dutra, G. B. Rocha, R. O. Freire, A. M. Simas, RSC Adv., 2013, 3, 16747–16755.

[3] N. B. Da Costa, R. O. Freire, G. B. Rocha, A. M. Simas, Inorg. Chem. Commun., 2005, 8, 831–835.

[4] R. O. Freire, G. B. Rocha, A. M. Simas, J. Braz. Chem. Soc., 2009, 20, 1638–1645.

[5] R. O. Freire, A. M. Simas, J. Chem. Theory Comput., 2010, 6, 2019–2023.

[6] J. D. L. Dutra, M. A. M. Filho, G. B. Rocha, R. O. Freire, A. M. Simas, J. J. P. Stewart, J. Chem. Theory Comput., 2013, 9, 3333–3341.

[7] I. J. Al-Busaidi, R. Ilmi, D. Zhang, J. D. L. Dutra, W. F. Oliveira, N. K. Al Rasbi, L. Zhou, W. Y. Wong, P. R. Raithby, M. S. Khan, Dye. Pigment., 2022, 197.

[8] O. Ivanciuc, J. Chem. Inf. Comput. Sci., 1996, 36, 612–614.

[9] A. Allouche, J. Comput. Chem., 2012, 32, 174–182.

[10] M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeerschd, E. Zurek, G. R. Hutchison, J. Cheminform., 2012, 4.

[11] C. F. MacRae, I. Sovago, S. J. Cottrell, P. T. A. Galek, P. McCabe, E. Pidcock, M. Platings, G. P. Shields, J. S. Stevens, M. Towler, P. A. Wood, J. Appl. Crystallogr., 2020, 53, 226–235.

[12] J. E. Moussa, J. J. P. Stewart, MOPAC. 2024.

LUMPAC: Lanthanide Luminescence Software Package

Module 1: Geometry Optimization

Module 1 – Geometry Optimization

Figure 1. Module responsible for the geometry optimization using the semiempirical models included in the MOPAC package.

All features implemented in LUMPAC 2.0 will be demonstrated using the [Eu(btfa)₃(bpy)] complex (Figure 2) as a case study, where btfa ligand is β-diketone 4,4,4-trifluoro-1-phenyl-1,3-butanedione, while bpy stands for bipyridine.[7]

Figure 2. Two-dimensional representation of the [Eu(btfa)₃(bpy)] complex.

Figure 3. .mol2 file of the [Eu(btfa)₃(bpy)] system created using the Mercury program.

Attention: It is crucial to ensure that, if the structure is manually constructed, all bonds involving the lanthanide ion and the donor atoms are explicitly represented, as shown in Figure 4.

Figure 4. Structure of the [Eu(btfa)₃(bpy)] complex constructed using the Avogadro program, explicitly showing all bonds between the lanthanide ion and the donor atoms of the ligands.

Procedure for Geometry Optimization using LUMPAC

1. Ensure that the “Open .mol2 File” option is selected. Then, click on button (Figure 5) to open the .mol2 file.

Figure 5 provides a detailed overview of the functionalities of each graphical element in Module 1 of LUMPAC, emphasizing the different types of files that can be used as input files for LUMPAC.

Figure 5. Different types of files can be used as input files for the geometry optimization using LUMPAC.

2. Click on button (Figure 6) to define the directory of the external MOPAC program.

Figure 6. Procedure for integrating a MOPAC executable into LUMPAC.

3. The keywords (Figure 7) must be appropriately specified before performing the geometry optimization. Once the .mol2 file is opened, the button (Figure 5) will be enabled.

Figure 7. MOPAC keyword editor in the geometric optimization module.

4. Select the Compare Models group box (Figure 8) to compare the geometry of the input file with the geometries calculated by the semiempirical models.

Figure 8. Selection of models for comparison and configuring the number of logical cores for parallel computation using the Compare Models feature.

Figure 9. The rmsd.txt file contains the estimated errors between the input structure and the structures calculated using the selected semiempirical models.

5. Click on button to execute the geometry optimization using the MOPAC program.

6. After the calculation completes, the user can view either the initial or optimized structure (Figure 10).

Figure 10. LUMPAC file and molecule viewers contained in the geometry optimization module.

Figure 11. Visualization of the [Eu(btfa)₃(bpy)] complex and options for editing the image.

Table 1 lists the mouse cursor commands for translation, rotation, and zoom functions, which control visualization settings.

Table 1. Translation, rotation, and zoom commands for the molecule viewer.

LUMPAC can perform geometry optimization with a .mop file (MOPAC input file), but MOPAC keywords editing is disabled within the LUMPAC interface. Therefore, users must edit the .mop file using a text editor.

References

[1] M. A. M. Filho, J. D. L. Dutra, H. L. B. Cavalcanti, G. B. Rocha, A. M. Simas, R. O. Freire, J. Chem. Theory Comput., 2014, 10, 3031–3037.

[2] M. A. M. Filho, J. D. L. Dutra, G. B. Rocha, R. O. Freire, A. M. Simas, RSC Adv., 2013, 3, 16747–16755.

[3] N. B. Da Costa, R. O. Freire, G. B. Rocha, A. M. Simas, Inorg. Chem. Commun., 2005, 8, 831–835.

[4] R. O. Freire, G. B. Rocha, A. M. Simas, J. Braz. Chem. Soc., 2009, 20, 1638–1645.

[5] R. O. Freire, A. M. Simas, J. Chem. Theory Comput., 2010, 6, 2019–2023.

[6] J. D. L. Dutra, M. A. M. Filho, G. B. Rocha, R. O. Freire, A. M. Simas, J. J. P. Stewart, J. Chem. Theory Comput., 2013, 9, 3333–3341.

[7] I. J. Al-Busaidi, R. Ilmi, D. Zhang, J. D. L. Dutra, W. F. Oliveira, N. K. Al Rasbi, L. Zhou, W. Y. Wong, P. R. Raithby, M. S. Khan, Dye. Pigment., 2022, 197.

[8] O. Ivanciuc, J. Chem. Inf. Comput. Sci., 1996, 36, 612–614.

[9] A. Allouche, J. Comput. Chem., 2012, 32, 174–182.

[10] M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeerschd, E. Zurek, G. R. Hutchison, J. Cheminform., 2012, 4.

[11] C. F. MacRae, I. Sovago, S. J. Cottrell, P. T. A. Galek, P. McCabe, E. Pidcock, M. Platings, G. P. Shields, J. S. Stevens, M. Towler, P. A. Wood, J. Appl. Crystallogr., 2020, 53, 226–235.

[12] J. E. Moussa, J. J. P. Stewart, MOPAC. 2024.

LUMPAC: Lanthanide Luminescence Software Package

Module 1: Geometry Optimization

Module 1 – Geometry Optimization

Figure 1. Module responsible for the geometry optimization using the semiempirical models included in the MOPAC package.

All features implemented in LUMPAC 2.0 will be demonstrated using the [Eu(btfa)3(bpy)] complex (Figure 2) as a case study, where btfa ligand is β-diketone 4,4,4-trifluoro-1-phenyl-1,3-butanedione, while bpy stands for bipyridine.[7]

Figure 2. Two-dimensional representation of the [Eu(btfa)3(bpy)] complex.

Figure 3. .mol2 file of the [Eu(btfa)3(bpy)] system created using the Mercury program.

Attention: It is crucial to ensure that, if the structure is manually constructed, all bonds involving the lanthanide ion and the donor atoms are explicitly represented, as shown in Figure 4.

Figure 4. Structure of the [Eu(btfa)3(bpy)] complex constructed using the Avogadro program, explicitly showing all bonds between the lanthanide ion and the donor atoms of the ligands.

Procedure for Geometry Optimization using LUMPAC

1. Ensure that the “Open .mol2 File” option is selected. Then, click on button (Figure 5) to open the .mol2 file.

Figure 5 provides a detailed overview of the functionalities of each graphical element in Module 1 of LUMPAC, emphasizing the different types of files that can be used as input files for LUMPAC.

Figure 5. Different types of files can be used as input files for the geometry optimization using LUMPAC.

2. Click on button (Figure 6) to define the directory of the external MOPAC program.

Figure 6. Procedure for integrating a MOPAC executable into LUMPAC.

3. The keywords (Figure 7) must be appropriately specified before performing the geometry optimization. Once the .mol2 file is opened, the button (Figure 5) will be enabled.

Figure 7. MOPAC keyword editor in the geometric optimization module.

4. Select the Compare Models group box (Figure 8) to compare the geometry of the input file with the geometries calculated by the semiempirical models.

Figure 8. Selection of models for comparison and configuring the number of logical cores for parallel computation using the Compare Models feature.

Figure 9. The rmsd.txt file contains the estimated errors between the input structure and the structures calculated using the selected semiempirical models.

5. Click on button to execute the geometry optimization using the MOPAC program.

6. After the calculation completes, the user can view either the initial or optimized structure (Figure 10).

Figure 10. LUMPAC file and molecule viewers contained in the geometry optimization module.

Figure 11. Visualization of the [Eu(btfa)3(bpy)] complex and options for editing the image.

Table 1 lists the mouse cursor commands for translation, rotation, and zoom functions, which control visualization settings.

Table 1. Translation, rotation, and zoom commands for the molecule viewer.

LUMPAC can perform geometry optimization with a .mop file (MOPAC input file), but MOPAC keywords editing is disabled within the LUMPAC interface. Therefore, users must edit the .mop file using a text editor.

References

[1] M. A. M. Filho, J. D. L. Dutra, H. L. B. Cavalcanti, G. B. Rocha, A. M. Simas, R. O. Freire, J. Chem. Theory Comput., 2014, 10, 3031–3037.

[2] M. A. M. Filho, J. D. L. Dutra, G. B. Rocha, R. O. Freire, A. M. Simas, RSC Adv., 2013, 3, 16747–16755.

[3] N. B. Da Costa, R. O. Freire, G. B. Rocha, A. M. Simas, Inorg. Chem. Commun., 2005, 8, 831–835.

[4] R. O. Freire, G. B. Rocha, A. M. Simas, J. Braz. Chem. Soc., 2009, 20, 1638–1645.

[5] R. O. Freire, A. M. Simas, J. Chem. Theory Comput., 2010, 6, 2019–2023.

[6] J. D. L. Dutra, M. A. M. Filho, G. B. Rocha, R. O. Freire, A. M. Simas, J. J. P. Stewart, J. Chem. Theory Comput., 2013, 9, 3333–3341.

[7] I. J. Al-Busaidi, R. Ilmi, D. Zhang, J. D. L. Dutra, W. F. Oliveira, N. K. Al Rasbi, L. Zhou, W. Y. Wong, P. R. Raithby, M. S. Khan, Dye. Pigment., 2022, 197.

[8] O. Ivanciuc, J. Chem. Inf. Comput. Sci., 1996, 36, 612–614.

[9] A. Allouche, J. Comput. Chem., 2012, 32, 174–182.

[10] M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeerschd, E. Zurek, G. R. Hutchison, J. Cheminform., 2012, 4.

[11] C. F. MacRae, I. Sovago, S. J. Cottrell, P. T. A. Galek, P. McCabe, E. Pidcock, M. Platings, G. P. Shields, J. S. Stevens, M. Towler, P. A. Wood, J. Appl. Crystallogr., 2020, 53, 226–235.

[12] J. E. Moussa, J. J. P. Stewart, MOPAC. 2024.

All features implemented in LUMPAC 2.0 will be demonstrated using the [Eu(btfa)₃(bpy)] complex (Figure 2) as a case study, where btfa ligand is β-diketone 4,4,4-trifluoro-1-phenyl-1,3-butanedione, while bpy stands for bipyridine.[7]

Figure 2. Two-dimensional representation of the [Eu(btfa)₃(bpy)] complex.

Figure 3. .mol2 file of the [Eu(btfa)₃(bpy)] system created using the Mercury program.

Figure 4. Structure of the [Eu(btfa)₃(bpy)] complex constructed using the Avogadro program, explicitly showing all bonds between the lanthanide ion and the donor atoms of the ligands.

Figure 11. Visualization of the [Eu(btfa)₃(bpy)] complex and options for editing the image.