On Wed, Jun 8, 2016 at 3:29 PM, Nisler, Collin R. <
nisler.1.buckeyemail.osu.edu> wrote:
> Hi Adrian, thanks for the reply. You actually brought up another question
> I had. The atoms that I was thinking would be negative are the oxygens in
> aspartate or glutamate residues. I wasn't sure if this is correct, because
> even though they would have a negative charge physiologically, it still
> wouldn't be a full negative charge since they are all paired electrons.
> Would they all be 0 charge then? Thanks.
>
You're overthinking it. Charge is just the total number of protons in the
region minus the total number of electrons. The QM Hamiltonian will figure
out where to put those electrons and, by extension, the general charge
distribution ;).
For a deprotonated carboxylate, there will be one more electron than proton
(since the side-chain was "deprotonated", but kept the electron), so the
charge on a single aspartate or glutamate is -1. But as Adrian pointed
out, anionic species tend to require more care when computing with QM, as
the wavefunctions tend to be far more diffuse.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Jun 08 2016 - 13:30:02 PDT
