As you can see in the screenshot, there is no dimension in the Steric hindrance display. I suppose it is in kcal/mol, but I could not find any definition in the documentation of the software. What is the steric hindrance in the methane example ?
as I already suggested in two other topics
there should be more documentation about the methods Marvin is using.
There should be a link "More Information" to a more detailed description.
As for the "steric hindrance" I got the paper and studied it. And I find the sentences:
"Neil Isaacs ( Physical Organic Chemistry 2nd ed.; 1996; p 424) pointed out 'There are three important sources of steric strain. (a) Prelog strain: intramolecular van der Waals repulsive forces resulting from crowding together of large atoms or groups. This can result in permanent deformations. (b) Baeyer strain: bond-angle distortion. (c) Pitzer strain.' The TSEI (Topological Steric Effect Index) does not express any one of the above three kinds of steric strains, and it represents the decrement of probality for an attacking atom (or group) approaching to the reaction center Rrc. That is, the larger the TSEI of the substituent connected with Rrc is, the less the probality of the attacking atom approaching Rrc will be.
The three definitions (abc) are of course basic organic chemistry. And now it is clear that the index
has no dimension. And it is also clear, that in methane (see screenshot above) the indices are not zero.
But I suggest to name the window not "steric hindrance" but to use the original denomination " TSEI (Topological Steric Effect Index)
And to put the sentences above "Neil Isaacs ... will be" in the documentation. And also to cite the original paper.
Your comments about the missing references and documentation are right, we will add them asap.
Please note, that the TopologyAnalyser plugin provides a Steric Effect Index function according to the article, and its name fits your proposal. The steric hindrance function is similar, the only difference is, that it uses geometrical distances not topological ones. So, it is not a TSEI but rather a GSEI.
As you pointed out well, the steric hindrance is just a relative value and not a precise measurement of the steric strains. Most of the calculation functions were developed for batch calculations, and they are used in filtering or combichem library generation. The current steric hindrance can be used for the rapid comparison of reaction sites to improve regioselectivity of virtual reactions. However, the topological steric effect index has a major advantage, as it does not require 3D coordinates.
The disadvantage of the TSEI is that the hindrance effect of ortho substituents like isopropyl or isobutyl are diminished.
Do you have any proposals, references for new topological steric hindrance like functions to be implemented?