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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 2.4.0 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 OXDACE [tris(oxydiacetato-O,O',O'')-cerium(iii)], 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 oxdace.mop.
- Convert the .arc file, oxdace.arc, generated by MOPAC2012 into the optimized .mop file using your favorite text editor: open the .arc file and save it with another name with the .mop extension. Find the line which reads
FINAL GEOMETRY OBTAINED and remove everything above and including this line.
- Now, you must choose the solvent for your complex. Since we will use the COSMO model as implemented in MOPAC2012, the solvent is primarily defined by its dielectric constant (consult tables of dielectric constants of Common Solvents). Let us consider water as the solvent. Water has a dielectric constant of 78.4 at 25ºC.
- Replace the keywords GNORM=0.25 and BFGS by the keywords 1SCF and EPS=78.4. The keyword line should now read
AM1 XYZ AUX SPARKLE 1SCF XYZ AUX EPS=78.4 CHARGE=-3 Singlet.
- Save the file as a .mop file with another name. For convenience we provide oxdace_opt.mop.
- Run this new .mop file in MOPAC2012.
- If you run into any problems with the complex geometry, please review the warning in the bottom part of the tutorial Drawing Complexes.
- After completion of the calculation, the computed energies will be the energies in the presence of the solvent.
- To compute the solvation energy simply run two MOPAC2012 calculations: one with the EPS=78.4 keyword, and one without. The solvation enthalpy will be the difference between the heats of formation of the solvated and of the non-solvated complex. For example, for the OXDACE complex, the solvation energy will be:
[-8891.55379 - (-3228.62655)] kJ.mol-1 = -5662.92724 kJ.mol-1
- Let us now visualize the solvent accessible surface around the complex. After completion of the calculation, open the 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 “Orbitals” > “Read geometries and orbitals from a Mopac aux file”. Find your .aux file and click on "Open” (for convenience, we provide oxdace_opt.aux). If you prefer, close the "Orbitals" window.
- Right-click on the black screen and choose “SAS” > “Solvent Accessible Surface”. This will open a new window called “Compute Solvent Accessible Surface”.
- In the field “Number of points” add value 150 and then click OK.
- Gabedit will start computing the solvent accessible ssurface around the molecule. Be patient! The progress of the calculation can be checked on the left bottom part of the screen.
- The solvent accessible surface will drawn when the calculation ends, as in the example bellow:
