how is it possible to determine whether there is a hydrogen in a molecule or not? can it be done with gaussian?
Hi,
You can analyze the orbitals with gaussian and check the HOMO-LUMO interaction. It helps to see which atom is donor and which one is accepotor. So, it gives you some idea regarding whether you have hydrogen bond or not.
There are some other programs that may help more such as GENNBO.
If you are able to run a short MD simulations for your system in AMBER or other MD progtrams), then you can use their analysis module to find the hydrogen bonds.
Hope it helps.
Best,
Hedieh
Yes you can determine whether there is a hydrogen bond or not in a molecule wit the gaussian 09 program. The choice of the functioned and basis set are essential criteria.
For hydrogen bond prediction it's probable best to use simple geometric criteria (like e.g. https://academic.oup.com/peds/article/15/5/359/1508259) and couple them with NBO analysis from gussian/other QM software (like in e.g. Article Topological and NBO analysis of hydrogen bonding interaction...
)
of course yes. Analyzing the geometry of the molecule that you want it is possibily know if hydrogen bridges are formed or not. If you use DFT, do not forget to use a functional that includes terms for long-distance interactions. Although, if you do an natural bond orbital analysis (NBO), without a doubt you could check the existence of hydrogen bond.
All the above. I have had success putting the two molecules in a classical hydrogen bond definition and included solvent dielectric effects (PCM) to get the trends of hydrogen-bond strength for a series of compounds. Of course, you can add spectroscopic evidence as well as the thermodynamic evidence. Hopefully, among the answers above and my experience you will get on to a track that you find helpful. ---Shannon
Yes, the best way to identify intermolecular hydrogen bonding, the best way is to calculate the electrostatic potential (ESP) at nuclear positions with the DFT optimized and to evaluate the interaction strength between the atoms which are expected to undergo intermolecular hydrogen bonding. The energy for such bonding can be calculated from the obtained potential energy density.
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