Dear prof. Case,
regarding to terminology I have never saw label dA for
free energy of binding, I saw always dG and the letter G is here connected
probably with the specification GIBBS free energy - please see:
http://en.wikipedia.org/wiki/Thermodynamic_free_energy
Label A is rather used for Helmholtz free energy.
Also in Amber MM-PBSA tutorial
http://ambermd.org/tutorials/advanced/tutorial3/
is used dG for free energy of binding.
But OK this is not so important, 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).
I don't know how much is water compressibility important regarding to TdS
part of
free energy of binding between two molecules. If I am not wrong TdS is
connected
with change in degrees of freedom (usually reduction) caused by
complexation.
So I assume that important role here have for example flexibility of
molecular structure, strength of the interaction etc.
but OK I am not an expert on this field ...
But anyway my last, logic and principal question now is:
Is there any experimental (common if possible) quantity which could be
connected
(by some mathematical formula) with whole FREE ENERGY OF BINDING (dH-TdS)
and so
could be used to check the accuracy of the whole binding energy
calculation ? or
the only one possible check is through direct experimentally measured
values of the
free energy of binding (for example using calorimetry approach), which is
unfortunately
not so common/available like for example binding constant ?
Thanks in advance for this final answer !
Best regards,
Marek
Dne Mon, 14 Sep 2009 19:23:49 +0200 case <case.biomaps.rutgers.edu>
napsal/-a:
> On Mon, Sep 14, 2009, Marek Maly wrote:
>
>> Thomas is explicitly speaking about free ENTHALPY of binding, although
>> Bill is asking about relationship of the total free ENERGY of binding
>
> Strictly speaking (which is what Thomas was doing), G is "free enthalpy"
> and A is "free energy".
>
> However, widely in the literature, the term "free energy" is used to
> mean either G or A (where the context is used to make the distinction),
> and
> the term "free enthalpy" is much less commonly used. Note that in nearly
> incompressible liquids like water, G and A are almost the same, which is
> why
> "free energy" can often be used to refer to either one of these.
>
> Don't confuse, however free enthalphy (G) with enthalpy (H).
>
> ...hope this helps...dac
>
>
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Received on Mon Sep 14 2009 - 13:47:05 PDT
