understanding problem of NCI analysis

zako

Hello everybody,
I performed the NCI analysis of a transition state, and there is things that i don't understand, so i have two questions:
1-Why there is a hole in the isosurface ? (see image)
2-The isosurface color inside the aromatic ring should be red (steric effect), but i get the green color. (see image)

量化小菜鸡

Hi,

Did you read and follow the instructions correctly based on this (http://sobereva.com/68) and relevant ones (e.g. http://sobereva.com/291). A small detail like color range setting can affect overall results. Google translation may help you to understand this in Chinese.

I think as long as you read these thoroughly, then there should be no issue for your final results.

Best

sobereva

1 The reason is that electron density between the two carbon atoms is much larger than the case of common weak interactions (because the interaction already has covalent nature to some extent). By default, the "RDG_maxrho" parameter in Multiwfn is 0.05, therefore, the RDG isosurface will be screened if electron density in this region is higher than 0.05 a.u. You can change this threshold by adjusting "RDG_maxrho" in settings.ini. If you only focus on weak interaction, you can simply ignore this observation.

2 The color is sensitive to the color scale you used in VMD. Commonly I prefer to use -0.035~0.02, in this case the steric region in benzene ring is always red.

zako

Dear Professor,
Thank you very much for the clarifications, my problem is gone.