Dear E. Varathan,
At the first look, it sounds that the question is too easy, however, when thinking deeply you find it to be difficult.
The intermolecular distance between two molecules is defined as the distance between their centers. However, the big question is how to define the center of a molecule. In most publications the intermolecular distance in dimers for example is referred to the hydrogen bond distance formed between the two monomers (http://link.springer.com/article/10.1007%2Fs11224-005-4454-9). In bis porphyrins, the intermolecular distance is the distance between the two porphyrins cores (Karaman et al, ResearchGate). In metal complexes, the intermolecular distance is the distance between the two metals contained in the two molecules.
An estimation of intermolecular distance between two molecules can be done using different computational methods such as ab initio, DFT, semi-empirical or molecular mechanics. Experimentally the distance can be estimated from x-ray structure of the molecules.
There are several programs that can be used to view or read intermolecular distances of molecules after being optimized by appropriate methods. These programs include, ArgusLab, Molden, Gaussview and many others.
Hoping this will be helpful,
Rafik
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