I want to calculate molecular thickness of my molecule X and compare with The interlamellar distance Δd of my X-Clay. My aim is to estimate the arrangement/orientation of X into the sheets of clay.
Can anybody tell me that any software of free version available for it?
Dear Mohamed,
I generally calculate the volume of a molecule (x, y & z dimensions) using Molden program (free down-loaded program) after I conduct an optimization of the geometry using molecular quantum (DFT, ab initio or semi-empirical) or molecular mechanics(MM2 or UFF) methods.
Therefore, to get an accurate dimensions of .the molecule you are interested in, you should follow the following steps:
1-Down load Molden program (free down-loaded program).
2-Down load ArgusLab program (free down-loaded program).
3-Draw your structure in Arguslab, minimize by UFF followed by re-minimization by semi-empirical method such as AM1, PM3 or PM6).
4-Read the output file of the minimization by Molden.
5-In Molden, click on a button with a cube drawing, select Packed + Cell 1
you get a box surrounding the molecule with x, y and z dimensions in Angstrom.
The molecule thickness will be x, y or z.
Please note, that there are experimental methods by which you can estimate the volume or the thickness of a molecule.
Hoping this will be helpful.
Rafik
Dear Mohamed,
I generally calculate the volume of a molecule (x, y & z dimensions) using Molden program (free down-loaded program) after I conduct an optimization of the geometry using molecular quantum (DFT, ab initio or semi-empirical) or molecular mechanics(MM2 or UFF) methods.
Therefore, to get an accurate dimensions of .the molecule you are interested in, you should follow the following steps:
1-Down load Molden program (free down-loaded program).
2-Down load ArgusLab program (free down-loaded program).
3-Draw your structure in Arguslab, minimize by UFF followed by re-minimization by semi-empirical method such as AM1, PM3 or PM6).
4-Read the output file of the minimization by Molden.
5-In Molden, click on a button with a cube drawing, select Packed + Cell 1
you get a box surrounding the molecule with x, y and z dimensions in Angstrom.
The molecule thickness will be x, y or z.
Please note, that there are experimental methods by which you can estimate the volume or the thickness of a molecule.
Hoping this will be helpful.
Rafik
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