[EDIT: As some commentators have suggested, I should conclude that the energy minimize feature is not intended for the purpose of Hydrogen-bonding, and primarily for refining the modelling of molecules.]

Using the Chem3D automatic Huckel charge calculator, I was able to calculate the charges of the atoms in the citrate and borate ion.

Individually, the borate ion's oxygen atoms have a small negative charge, i.e. -0.07. Individually, the citrate ion's oxygen atoms have a large negative charge, i.e. -0.56.

I use the energy minimize function to make the two hydrogen bond. I then do the charge calculation, and I found that some of the citrate's oxygens' charges increased to ~-0.67, while some of them decreased, and the borate ion's increased to ~-0.5. The hydrogen atoms do increase positive charge.

citrate ion vs borate ion

I actually noticed another particular feature, the oxygen atom of the hydroxyl involved in both hbond donating and accepting has a positive charge now. The other charges remain as I've explained above. The highlighted yellow atom was just an oxygen atom that I clicked.


For my own explanation, I would suggest that the hydrogen bonding is the cause of the charges being induced and increased. Yet, due to the size of the molecules, only two or four atoms seem to be involved in the hydrogen bonding. Then, why should the OTHER atoms still increase their charge? The atoms not involved in hydrogen bonding between the two molecules?

Would it be a feature of the calculator, or would this be the scenario in real life?

I am interested in how different ions are compatible with borate in terms of hydrogen bonding and screening, based on their charges. This will aid my experiments.

  • $\begingroup$ How are you making them hydrogen bond? Which hydrogen on which molecule are you making bond to which atom on which other molecule. You should edit the question to specify because it makes a difference in how things are set up. $\endgroup$ – R.M. Jan 29 '18 at 15:39
  • $\begingroup$ @R.M. Updated, I am making them hydrogen bond using the Energy Minimize Function. It automatically aligns the molecules to the greatest stability possible. $\endgroup$ – Peaceful Qualities Jan 29 '18 at 21:20
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    $\begingroup$ As a rule of thumb, I wouldn't trust anything from the 'energy minimise function' on Chem3D - it uses a very low level of calculation, and is prone to converging local but not global minima. You can interface GAMESS (free) to run with Chem3D, which offers more... computationally valuable calculations $\endgroup$ – NotEvans. Jan 29 '18 at 23:27
  • $\begingroup$ @NotEvans. Thank you, yet I am doing this at a high-school level. Could you please explain this further? What is the difference between local and global minima? Do you mean that it is inefficient to use the function for the simulation of more than a single molecule? $\endgroup$ – Peaceful Qualities Jan 30 '18 at 4:52
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    $\begingroup$ Dear Guna, description of "non-covalent" interactions (hydrogen bonds, van der Waals and London forces) will be rather poor unless you are using a computationally expensive method (which you aren't) or a force field, that has been specifically designed to consider them (which I doubt). This means, the energy, and the geometry will be most likely wrong - in some cases the geometry wil be significantly wrong (>0.1 A). As suggested above, you can use GAMESS, or psi4 (www.psicode.org), to get a more accurate electron density and structure. I'd suggest the BLYP-D3M(BJ) functional as a start. $\endgroup$ – tetrahydrofuran Jan 30 '18 at 9:04

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