Re: Dioxygen atom type with CHARMM36

From: Kenno Vanommeslaeghe (
Date: Tue Nov 11 2014 - 14:19:40 CST

On 11/11/2014 02:34 PM, Francesco Pietra wrote:
> QM at which level? In my experience, triplet O2 is such a definitely
> multireference species that ab initio calculations become a problem,
> while DFT has no room.

Good point. Since there's only one bond length and one vibrational mode,
it's probably better anyhow to scratch the QM and go uniquely with
experimental data.

> As to the chance of finding problems with proteins involving triplet O2, I
> would not say it is an uncommon event. Since O2 begun to populate the
> atmosphere some billion years ago, most organisms, at all taxonomic
> levels, adapted to it and can't survive without it.

Be that as it may, people ask us for free oxygen parameters approximately
once every 2 years, and there's a seemingly infinite list of force field
improvements that are in higher demand (In this context, I deliberately
wrote "biological MD systems" rather than "biological systems".) Note that
heme-bound oxygen is a different story, which is why that species is in

Or to put it in "philosophical" (i.e. biological) terms, significant
levels of free oxygen in the cyptoplasm will cause oxidative damage and
limit the life span of aerobic organisms; oxygen is mostly bound to
transporters, and rendering these transporters inoperative at the genetic
level compromises viability. It's somewhat related to the reason why
eukaryotes have mitochondria; this way, the oxidative violence is
contained in a sub-organism with a shorter life cycle than the host cell.

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