Re: [AMBER] Non-standard Hydrogen Bonding

From: David A Case <>
Date: Tue, 30 Jul 2019 16:11:34 -0400

On Tue, Jul 30, 2019, Loris Moretti wrote:
>I would like to simulate a ligand-protein complex, so I calculated the
>charges RESP (from QM HF/6-31G* calculations) and I realized that one of
>the Carbon atom of a pyrimidine group in the ligand has a separation of
>charges at the C-H bond (in attachment a picture of a simplified system
>with the calculated charges). The C-H in position meta with respect
>of the 2 Nitrogen atoms of the pyrimidine ring has a polarized bond,
>C(-0.86)-H(0.24), in the same order of an O-H group of serine (taken from
>all_amino03.lib) , O(-0.64)-H(0.45). So, if I understand correct, this
>formed dipole could give, in principle, an Hydrogen bond interaction with
>a close by second dipole (at the proper distance and angle). Would the
>force field be able to describe it?

You could try some experiments, bringing your C--H group close to a
hydrogen bond acceptor to see what happens. You'd probably need some
decent quantum chemical calculations to get an idea of what the answer
"should" be.

But I'm guessing you won't see much H-bonding: aside from electrostatic
interactions, ordinary hydrogen bonds (N--H or O--H) are favored in
force fields by having unusually small (even zero) Lennard-Jones terms
on the donor hydrogen. This allow those hydrogens to be well inside the
sum of the (ordinary) van der Waals radii to an acceptor: such a
distance is one hallmark of hydrogen bonds. Hydogens bonded to carbon
generally don't have such small radii (in, say the gaff2 force field),
so hydrogen bonds are not so stable.

But the above is just a guess: as I said, you would need to see what
happens in a model dimer with your ligand to get a better idea of what
might happen in complex with a protein.

...good luck....dac

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Received on Tue Jul 30 2019 - 13:30:02 PDT
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