Hi,
I do molecular dynamics simulations and new in quantum calculations. Recently i studied the interaction of amino acid with ZnS nanotube by DMOL3 and i wanted to know that does any bond formed or not(i want to use as an input in MD ). i couldn't see any binding visually but, how should i analyze hybridization or anything that prove binding happened or these 2 structures can interact more efficiently Under certain circumstances? ( by DMOL3 or any other packages or analysis )
Best
The most straightforward way to prove formation of chemical bonds is calculating Mayer bond order. If the value is evidently larger than zero, then chemical bond should have formed. Mayer bond order can be easily calculated via Multiwfn (http://sobereva.com/multiwfn), example is given in Section 4.9.1 of Multiwfn manual. Multiwfn doesn't support Dmol3 because Multiwfn only supports Gauss type basis function, however you can use such as the freely available ORCA program to carry out a single point for the optimized geometry to yield .molden file, which could be used as input file of Multiwfn. More discussion about bond order can be found in my paper Phys. Chem. A, 117, 3100−3108 (2013), introduction of all kinds of bond orders supported by Multiwfn can be found in Section 3.11 of Multiwfn manual.
Other kinds of analyses, such as AIM analysis, ELF or LOL analysis, deformation map of electron density, are also quite useful for studying chemical bonding, all of them are fully supported by Multiwfn.
I have written a blog article devoted to discuss how to determine whether a chemical bond has formed, see http://sobereva.com/414 or http://bbs.keinsci.com/thread-9840-1-1.html, it should be very useful for you, but it was written in Chinese (however you could use Google translator to try to understand article content)
Mrs/Miss Rahmani,
By means of CASSCS MDs, for instance you can try BOMD or ADMP. The active space should be representative as much as possible according to the capability of your cluster.
Bojidarka B. Ivanova Thank you so much. maybe i couldn't explain my problem well. please forget about MD. I optimized the ZnS nanotube and amino acid structure by DFT calculations(by DMOL3). i want to know how should i analyze that any bond formed between these 2 structures or not.
Hi
There are several ways to analyse whether you have a bonding interaction in your system.
First, you can do a visual analysis. For instance, you can look at the distance between the two atoms that you think might be bonded, and compare this distance with the sum of covalent radii (J. Am. Chem. Soc., 1947, 69, 542–553; Dalton Trans., 2008, 2832-2838). If the distance is smaller, it is likely there will be a bonding interaction. Also, looking for small deformations in the molecule might be helpful. For example, you might observe slight bond lengthenings or angle distortions in the bonds nearby those two atoms, compared with the two separate molecules.
After that, you can also perform a deeper (and more quantitative) analysis by performing some additional calculations. NBO and QTAIM analysis are usually particularly useful. From the NBO you can analyse the orbital interactions (that may indicate a bonding interaction) and bond orders, and the QTAIM will give you the distribution of electron density. Logically, if there is electron density between the two atoms (visualised as a bond path) you will have a bonding interaction. QTAIM also provides more advanced analysis tools, but probably you don't need more to prove the existence of a bond.
Concerning the software to do this, I typically use NBO6 (in conjuction with Gaussian) and AIMAll (for QTAIM analysis). Unfortunately, these programs are not free, but there are other free programs that will allow you to do practically the same analysis. I would suggest Multiwfn as a free software capable of doing both QTAIM and bonding analysis.
Hope this helps. Best regards,
Martí
Dear Martí Garçon , thank you so much for your detailed and helpful answer.
Best regards,
Roja
The most straightforward way to prove formation of chemical bonds is calculating Mayer bond order. If the value is evidently larger than zero, then chemical bond should have formed. Mayer bond order can be easily calculated via Multiwfn (http://sobereva.com/multiwfn), example is given in Section 4.9.1 of Multiwfn manual. Multiwfn doesn't support Dmol3 because Multiwfn only supports Gauss type basis function, however you can use such as the freely available ORCA program to carry out a single point for the optimized geometry to yield .molden file, which could be used as input file of Multiwfn. More discussion about bond order can be found in my paper Phys. Chem. A, 117, 3100−3108 (2013), introduction of all kinds of bond orders supported by Multiwfn can be found in Section 3.11 of Multiwfn manual.
Other kinds of analyses, such as AIM analysis, ELF or LOL analysis, deformation map of electron density, are also quite useful for studying chemical bonding, all of them are fully supported by Multiwfn.
I have written a blog article devoted to discuss how to determine whether a chemical bond has formed, see http://sobereva.com/414 or http://bbs.keinsci.com/thread-9840-1-1.html, it should be very useful for you, but it was written in Chinese (however you could use Google translator to try to understand article content)
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