AMBER Archive (2009)

Subject: Re: [AMBER] Ki and G

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Sep 14 2009 - 15:24:05 CDT

On Mon, Sep 14, 2009, Marek Maly wrote:

> http://en.wikipedia.org/wiki/Thermodynamic_free_energy

This page confirms what I said earlier: the term "free energy" might mean
either Gibbs free energy (G) or Helmholtz free energy (A), depending on
context.

>
> I think that much more important and
> little surprising is the fact, that binding constant,
> (which is the experimental measure of the strength of the inter-molecular
> interaction) is related only to enthalpic part (dH)
> of the free energy of binding and do not reflect whole free energy of
> binding (dH-TdS).

The above is not correct -- equilibrium (binding) constants are related to free
energies, not just to enthalpies.

But this whole subject is not really well-suited to discussion on a
mailing list. For example, what Thomas wrote looks perfectly correct to
me, but used a somewhat unfamiliar term ("free enthalpy") that may have
caused confusion. Your assertion above, that a binding constant "is the
experimental measure of the strength of inter-molecular interaction", is
itself subject to mis-interpretation. It is better to refer to textbooks,
where both words and mathematics can be carefully constructed, and the
thread of the discussion is not fragmented into a bunch of separate
emails from a variety of authors and viewpoints.

...dac

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