one of our hydrogen bonded complex doesn't have proper isosurface region around the hydrogen bond site. The perti. complex have a strong hydrogen bonding interaction which is observed in values of interaction energy and the distance of hydrogen bond (1.55 A). And the QTAIM analysis also shows a larger value of electron density on bcp of the hydrogen bond. But still the NCI analysis doesnt gives a proper isosurface around the hydrogen bonding site.
Dear Thabassum A Nattikallungal
The only thing I could suggest you without knowing your system is to try with a different Software. We developed IGMPlot, freely available and compilable on various sytems :
http://igmplot.univ-reims.fr/
We put an algorithm for defining "fragments" of your molecules and so, only, extract the interesting interaction between the two fragments.
I hope this could help you !
I'd say something is wrong in the calculation of NCI. My guess is the following: typically, when calculating NCI isosurfaces, you give an electron density cutoff to show only non-covalent interactions and cut out covalent ones that have a much higher electron density at the critical point. Perhaps that hydrogen bond is so strong that its electron density is beyond the cutoff.
So, in short: try increasing the electron density cutoff.
This is because in most codes for calculating NCI such as Multiwfn (http://sobereva.com/multiwfn), the RDG is screened in the region having relatively large electron density. For example, in Multiwfn there is a parameter "RDG_maxrho" in settings.ini file, which is default to 0.05 a.u., namely if a point has an electron density > 0.05, the RDG at this point will be automatically set to 100 to avoid showing its isosurface in NCI map. This design is used to avoid occurrence of RDG isosurfaces irrelevant to weak interactions.
In your case, you should set "RDG_maxrho" to a slightly larger value to avoid the screening of the strong H-bond. It is also highly suggested to consider another way of visualizing the interaction, namely using the Interaction Region Indicator (IRI) proposed by me recently. This function is able to very clearly exhibit all kinds of interactions in a chemical system. The paper describing IRI and comparing it with NCI and AIM has been available in ChemRxiv recently, see DOI: 10.26434/chemrxiv.13591142, you will find IRI extremely useful for you system. IRI has been supported in Multiwfn, the supplemental information of this ChemRxiv paper contains a detailed tutorial showing how to perform various kinds of IRI analyses in Multiwfn, plotting an IRI map via Multiwfn+VMD is as easy as NCI.
Another choice is using the independent gradient model based on Hirshfeld (IGMH) I recently proposed and implemented in Multiwfn. IGMH is able to nicely exhibit interactions between two specific fragments, see Section 4.20.11 of Multiwfn manual. The paper fully describing IGMH will be prepared and submitted soon.
I know it is any related question. Sorry for it, I wonder can we calculate the non-covalent interactions (NCI), more precisely the amount of hydrogen bonding, van-der waals interactions and steric repulsions? I know I can plot it but can we see their amount in output?
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