Dear Renjith,
As other researchers have mentioned, direct visualization of hydrogen bonding using GaussView is impossible. There are some electronic and geometrical parameters which can easily be used to detect the formation of hydrogen bonding and its strength. When a hydrogen atom involves in a hydrogen bonding, its stretching and bending vibrational frequencies will change. In addition, its chemical shift changes as well. NBO or AIM can provide an estimation of hydrogen bonding strength. For detailed explanations you can see the following reference:
"Journal of Chemical Sciences 05/2013; 125(4):939-948"
As you know, in order to form a hydrogen bonding, two orbitals should participate. One, the lone pair of hydrogen bonding donor and, other, sigma anti-bonding of hydrogen bonding acceptor (see the attached pdf). If visualization of such interaction is particularly your target, the NBOView can be helpful by which you can nicely visualize the mentioned interaction in either 2D and 3D views.
Best,
Saeed
Gaussian is not a visualising program, and it does not have graphic interface, but you can use Gaussview, that is visualising program in which you can visualise any molecular property.
Can you tell me how we can visualize intermolecular hydrogen bonding using Gaussview
There is no exact option in the program that it can recognize the intermolecular hydrogen bonding, but if you have optimized geometry or single point calculated structure you can describe hydrogen bonding mapping the electrostatic potential, or visuallising molecular orbitals. If you want a visualising program that can tell where intermolecular hydrogen bonding could potentially be found I recommend Maestro.
It is impossible to visualize hydrogen bonding using Gaussview. you can use AIM and NBO methods to estimate the hydrogen bond strength.
Dear Renjith,
As other researchers have mentioned, direct visualization of hydrogen bonding using GaussView is impossible. There are some electronic and geometrical parameters which can easily be used to detect the formation of hydrogen bonding and its strength. When a hydrogen atom involves in a hydrogen bonding, its stretching and bending vibrational frequencies will change. In addition, its chemical shift changes as well. NBO or AIM can provide an estimation of hydrogen bonding strength. For detailed explanations you can see the following reference:
"Journal of Chemical Sciences 05/2013; 125(4):939-948"
As you know, in order to form a hydrogen bonding, two orbitals should participate. One, the lone pair of hydrogen bonding donor and, other, sigma anti-bonding of hydrogen bonding acceptor (see the attached pdf). If visualization of such interaction is particularly your target, the NBOView can be helpful by which you can nicely visualize the mentioned interaction in either 2D and 3D views.
Best,
Saeed
Dear Renjith,
You can generate a wave function with GAUSIAN09 by optimizing your molecular system, and then use programs such as MORPHY98 and AIMAll to obtain the chemical topology. You should encounter a hydrogen bond critical point, which is a pretty strong evidence of the hydrogen bond. There are more ways to identify the hydrogen bond within the AIM theory, you should read into it. I would also take a look at the following references: MORPHY98, a program written by P. L. A. Popelier with a contribution from R. G. A. Bone, UMIST, Manchester, England, EU 1998. AIMAll (Version 14.06.21), Todd A. Keith, TK Gristmill Software, Overland Park KS, USA, 2014 (aim.tkgristmill.com) and 1. R. F. W. Bader. Atoms in Molecules: A Quantum Theory. Clarendon Press, (1990) Oxford.
Best regards
Arnaldo Filho
Dear colleagues!
And if hydrogen bonding is exchange by proton, how can you visualize it?
If you just want to visualize H-bond, you may use other visualizers. Avogadro software can read G09 output files. And it shows H-bonding.
Use VMD software and it is free. First save your coordinates either in xyz format or pdb format , then load the molecule in vmd. Then select graphics----> Representation--->Drawing method------>HBonds. It is really easy to handle.
A graphical tool that, analogously to Avogadro, is capable of evidencing hydrogen bonds (based only on geometrical parameters) is Molden, which is freely available and runs on a variety of platforms (Win, OS X, linux, for example).
There are several programs to visualize the Hydrogen Bond. Atoms in molecules (AIM) is one of the options. [Niu et al, J. Chem. Sci. Vol. 125, No. 4, July 2013, pp. 949–958].
Yes, you can view the hydrogen bond in gaussian, better option you should again optimized your geomentry using NBO analysis for example , KEYWORD LIKE "B3LYP/631G* POP=NBO".
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