[adf-list] fwd:绑定自由能量和粘合能量(通过eda)_它们不同的方式???

Biswajit Sadhu. biswajit.chem001在gmail.com
星期四2014年5月8日13:47:31

Dear Dr Alexei and Dr Swart,
                                        Thanks for your answers and
important attachment. In one of my systems where I used Metal hydrate
system(let us take M(H2O)4) as one fragment and protein(L) as another
fragments, I got a huge bonding energy of -1800 kcal mol-1 (by adding all
possible terms). While binding free energy was only -26 kcal mol-1. Can we
explain the difference by using your same argument?

Thanks again,
Biswajit


On Thu, May 8, 2014 at 4:01 PM, Marcel Swart <marcel.swart at udg.edu> wrote:

> Note that EDA gives the electronic energy (∆E), not Gibbs (which can be
> obtained from vibrational frequencies);
> did you include Pauli repulsion in the interaction? (you don’t mention it)
>
> The binding of a metal to protein is similar to binding to a ligand,
> where for transition-metals the spin-state should be taken into account.
> See e.g.
>
> A.C. Castro, M.P. Johansson, G. Merino and M. Swart
> "Chemical bonding in supermolecular flowers"
> Phys. Chem. Chem. Phys. 2012, 14, 14905-14910
> http://dx.doi.org/10.1039/c2cp42045g
>
> M. Swart
> "Accurate spin-state energies for iron complexes"
> J. Chem. Theory Comput. 2008, 4, 2057-2066
> http://dx.doi.org/10.1021/ct800277a
>
> M. Swart
> "Metal-ligand bonding in metallocenes: differentiation between spin state,
> electrostatic and covalent bonding"
> Inorg. Chim. Acta 2007, 360, 179-189
> http://dx.doi.org/10.1016/j.ica.2006.07.073
>
> On 2014-05-08, at 12:14, adflist-request at scm.com wrote:
>
> Message: 7
> Date: Thu, 08 May 2014 12:14:19 +0200
> From: Alexei Yakovlev <yakovlev at scm.com>
> To: ADF user list <adflist at scm.com>
> Subject: Re: [ADF-LIST] Fwd: Binding free energy and Bonding energy
> (by EDA)_which way they are different???
> Message-ID: <536B58FB.4090806 at scm.com>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
>
> Hi Biswajit,
>
> An important point to remember when comparing ADF bonding energies is
> that they are calculated with respect to the fragments in their
> respective electronic state and that fragments used in the EDA may not
> be spin-polarized. So here's the caveat: a metal atom usually has an
> open shell in the ground state but it has to be calculated closed-shell
> for EDA. Thus to get the energy right you need to calculate your metal
> atom in its ground state and subtract its "bonding" energy from the -170
> kcal/mol you obtained for the metal-protein complex.
>
> Kind regards,
> Alexei
>
> On 08/05/2014 08:54, Biswajit Sadhu wrote:
>
>
>
> Hi,
>
>
>  Can anyone please explain the basic difference between the binding
>  free energy and bonding energy of a complex A-B formed by the
>  reaction of A and B?
>
> I want illustrate my question a bit. In my case, I wanted to know
> binding free energy (gibbs free energy) for a metal inside a protein
> cavity. So, I used following equations for free energy:
> Metal + Protein = Metal-Protein
> The entropic contribution is indeed an important factor. I found delta
> G : -20 kcal/mol (where delta H= -30 kcal/mol).
> But in case of ADF i took protein and metal as a fragment and tried to
> calculate bonding energy (morokuma type) for Metal-Protein (which is
> sum of electrostatic, orbital contributions and dispersion factor).
> The resulted bonding energy are -170 kcal/mol.
> As in the fragments, it took the coordinates (geometries) from the
> complex structures thus the calculated bonding energy certainly do not
> corrleate to the free energy term.
> why such a huge difference is coming between binding free energy and
> total bonding energy?
>
> Thanks in advance,
> Biswajit
>
> --
> *Biswajit Sadhu*
> *Scientific Officer*
> *Bhabha Atomic Research Centre*
> *Mumbai-400094
>
>
>
> ===================================
> Prof. Dr. Marcel Swart
>
> ICREA Research Professor at
> Institut de Química Computacional i Catàlisi
> Universitat de Girona
>
> Facultat de Ciències
> Campus Montilivi
> 17071 Girona
> Catalunya (Spain)
>
> tel
> +34-972-418861
> fax
> +34-972-418356
> e-mail
> marcel.swart at icrea.cat
> marcel.swart at udg.edu
> web
> http://www.marcelswart.eu
> vCard
> addressbook://www.marcelswart.eu/MSwart.vcf
> ===================================
>
>
>
>
>
>
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-- 
*Biswajit Sadhu*
*Scientific Officer*
*Bhabha Atomic Research Centre*


*Mumbai-400094*

*Contact information: 022-25593207 (O) 7303060845 (M)*

*"But I have promises to keep*
*  and miles to go before I sleep"*
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