From owner-chemistry@ccl.net Fri Apr  8 08:29:00 2011
From: "Marcel Swart marcel.swart~!~icrea.cat" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: preparation energy of EDA
Message-Id: <-44319-110408082105-17293-p4e7ts1SMOJ0mQ/IclkCJw ~~ server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart::icrea.cat>
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Date: Fri, 8 Apr 2011 14:20:53 +0200
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Sent to CCL by: Marcel Swart [marcel.swart(_)icrea.cat]

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Much depends on the electronic state of your system and the fragments;
for instance, for a hydrogen-bond the preparation energy contains only
deformation energy:

M. Swart, C. Fonseca Guerra and F.M. Bickelhaupt=20
"Hydrogen Bonds of RNA Are Stronger than Those of DNA, But NMR Monitors =
Only Presence of Methyl Substituent in Uracil/Thymine"
J. Am. Chem. Soc. 2004, 126, 16718-16719
http://dx.doi.org/10.1021/ja045276b

For systems containing transition-metals, it also contains other terms
(valence excitation, ligand-ligand):

M. Swart
"Accurate spin-state energies for iron complexes"
J. Chem. Theory Comput. 2008, 4, 2057-2066
http://dx.doi.org/10.1021/ct800277a

And for other fragments, you may need to include pairing as well:

F. M. Bickelhaupt, E. J. Baerends=20
The Case for Steric Repulsion Causing the Staggered Conformation of =
Ethane=20
Angew. Chem. 2003, 115, 4315-4320
http://www3.interscience.wiley.com/cgi-bin/abstract/105557159/ABSTRACT

All that is explained in detail in:

F. M. Bickelhaupt, E. J. Baerends
Kohn-Sham Density Functional Theory: Predicting and Understanding =
Chemistry
In: Rev. Comput. Chem.; K. B. Lipkowitz and D. B. Boyd, Eds.; Wiley-VCH: =
New York, 2000, Vol. 15, pp. 1-86

and in the above mentioned papers.

For any specific ADF questions (technical ones), it is better to have a =
look
at ADF forums and ask the question there:
http://www.scm.com/forums/

Marcel

On Apr 8, 2011, at 12:55 PM, Ajitha. John aji.john07|a|gmail.com wrote:

> Dear abdelghani,
>=20
> EDA analysis is done by the following equation,
> DEAB =3D DEint + DEprep            -->   eqn. 1
>=20
> where DEAB  is the dissociation energy or the binding energy.
> DEint is the energy difference between the transition state and its =
frozen fragments in the transition state.=20
> DEprep is the energy required to promote the fragments from their most =
stable electronic ground state to the electronic ground state which they =
possess in the transition state.
>=20
> DEprep is obtained from the following procedures (1 or 2),
>=20
> 1) Do single point energy calculation on each frozen fragments.
> Then subtract the ground state energy of each fragment from the single =
point energy of frozen fragment. Add each preparation energies to get =
total DEprep.
>=20
>=20
> DEprep =3D (E[frozen-F1]-E[optimized-F1]) + (E[frozen-F2]- =
E[optimized-F2]) +....
> i.e DEprep =3D DEprep1 +  DEprep2 +  ...    where DEprep1=3D =
E[frozen-F1]-E[optimized-F1] in the above equation
>=20
>  2) calculate DEAB and then subtract DEint. (see eqn. 1)
>=20
> DEAB=3DE(optimized complex) -(E[optimized F1]-E[optimized F2]- .....)
>=20
> where DEint =3D DEele + DEPauli +  DEorb  (which is directly obtained =
> from EDA analysis).
>=20
>=20
> Two procedures should give same DEprep.
>=20
> On Fri, Apr 8, 2011 at 2:09 PM, may abdelghani may01dz:+:yahoo.fr =
<owner-chemistry . ccl.net> wrote:
>=20
>=20
> Hello,
> How to calculate the value of preparation energy "deltEpre" > from =
energy decomposition analysis of ADF.
>=20
> Thank you very much
>=20

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
dr. Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica Computacional
Universitat de Girona

Facultat de Ci=E8ncies
Campus Montilivi
17071 Girona
Catalunya (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mail
marcel.swart]![icrea.cat
marcel.swart]![udg.edu
web
http://www.marcelswart.eu
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


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<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; =
"><div><br></div>Much depends on the electronic state of your system and =
the fragments;<div>for instance, for a hydrogen-bond the preparation =
energy contains only</div><div>deformation =
energy:</div><div><br></div><div>M. Swart, C. Fonseca Guerra and F.M. =
Bickelhaupt&nbsp;<br>"Hydrogen Bonds of RNA Are Stronger than Those of =
DNA, But NMR Monitors Only Presence of Methyl Substituent in =
Uracil/Thymine"<br>J. Am. Chem. Soc.&nbsp;2004,&nbsp;126, =
16718-16719</div><div><a =
href=3D"http://dx.doi.org/10.1021/ja045276b">http://dx.doi.org/10.1021/ja0=
45276b</a></div><div><br></div><div>For systems containing =
transition-metals, it also contains other terms</div><div>(valence =
excitation, ligand-ligand):</div><div><br></div><div>M. =
Swart<br>"Accurate spin-state energies for iron complexes"<br>J. Chem. =
Theory Comput.&nbsp;2008,&nbsp;4, 2057-2066</div><div><a =
href=3D"http://dx.doi.org/10.1021/ct800277a">http://dx.doi.org/10.1021/ct8=
00277a</a></div><div><br></div><div>And for other fragments, you may =
need to include pairing as well:</div><div><br></div><div>F. M. =
Bickelhaupt, E. J. Baerends&nbsp;<br>The Case for Steric Repulsion =
Causing the Staggered Conformation of Ethane&nbsp;<br>Angew. =
Chem.&nbsp;2003,&nbsp;115, 4315-4320</div><div><a =
href=3D"http://www3.interscience.wiley.com/cgi-bin/abstract/105557159/ABST=
RACT">http://www3.interscience.wiley.com/cgi-bin/abstract/105557159/ABSTRA=
CT</a></div><div><br></div><div>All that is explained in detail =
in:</div><div><br></div><div>F. M. Bickelhaupt, E. J. =
Baerends<br>Kohn-Sham Density Functional Theory: Predicting and =
Understanding Chemistry<br>In:&nbsp;Rev. Comput. Chem.; K. B. Lipkowitz =
and D. B. Boyd, Eds.; Wiley-VCH: New York,&nbsp;2000,&nbsp;Vol. 15, pp. =
1-86</div><div><br></div><div>and in the above mentioned =
papers.</div><div><br></div><div>For any specific ADF questions =
(technical ones), it is better to have a look</div><div>at ADF forums =
and ask the question there:</div><div><a =
href=3D"http://www.scm.com/forums/">http://www.scm.com/forums/</a></div><d=
iv><br></div><div>Marcel</div><div><br><div><div>On Apr 8, 2011, at =
12:55 PM, Ajitha. John aji.john07|a|gmail.com wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><p =
class=3D"MsoNormal"><span style=3D"">Dear
abdelghani,<br>
<br>
EDA analysis is done by the following equation,<br>
DE<sub>AB</sub> =3D DE<sub>int</sub> + =
DE<sub>prep</sub>&nbsp;&nbsp;</span><span style=3D"font-family: =
Wingdings;"><span style=3D""></span></span><span =
style=3D"">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
--&gt;&nbsp;&nbsp; eqn. 1<br>
<br>
where DE<sub>AB</sub>&nbsp; is the dissociation energy or the binding =
energy.<br>
DE<sub>int</sub> is the energy difference between the transition state =
and its
frozen fragments in the transition state. <br>
DE<sub>prep</sub> is the energy required to promote the fragments from =
their
most stable electronic ground state to the electronic ground state which =
they
possess in the transition state.<br>
<br>
DE<sub>prep</sub>&nbsp;is obtained from the following procedures (1 or =
2),<br>
<br>
1) Do single point energy calculation on each frozen fragments.<br>
Then subtract the ground state energy of each fragment from the single =
point
energy of frozen fragment. Add each preparation energies to get total =
DE<sub>prep.</sub></span></p><p class=3D"MsoNormal"><sub><span =
style=3D""><br>
</span></sub><span style=3D"">DE<sub>prep
=3D </sub>(E[frozen-F<sub>1</sub>]-E[optimized-F<sub>1</sub>]) + =
(E[frozen-F<sub>2</sub>]-
E[optimized-F<sub>2</sub>]) +....<br>
i.e DE<sub>prep =3D </sub>DE<sub>prep1 </sub>+ <sub><span =
style=3D"">&nbsp;</span></sub>DE<sub>prep2 </sub>+<sub> <span =
style=3D"">&nbsp;</span>...&nbsp;&nbsp;&nbsp; </sub>where =
DE<sub>prep1=3D</sub>
E[frozen-F1]-E[optimized-F1] in the above equation<br>
<sub><br>
</sub>&nbsp;2) calculate DE<sub>AB </sub>and then subtract DE<sub>int. =
</sub>(see
eqn. 1)<br>
<br>
DE<sub>AB</sub>=3DE(optimized complex) -(E[optimized =
F<sub>1</sub>]-E[optimized F<sub>2</sub>]-
.....)</span></p><p class=3D"MsoNormal"><span style=3D"">where
DE<sub>int</sub> =3D DE<sub>ele </sub>+ DE<sub>Pauli</sub> +&nbsp; =
DE<sub>orb</sub>&nbsp;
(which is directly obtained from EDA analysis).</span></p><p =
class=3D"MsoNormal"><span style=3D""><br>
Two procedures should give same DE<sub>prep.</sub></span></p><p =
class=3D"MsoNormal">On Fri, Apr 8, 2011 at 2:09 PM, may abdelghani =
may01dz:+:<a href=3D"http://yahoo.fr/">yahoo.fr</a> <span =
dir=3D"ltr">&lt;<a =
href=3D"mailto:owner-chemistry%20.%20ccl.net">owner-chemistry . =
ccl.net</a>&gt;</span> wrote:</p><div class=3D"gmail_quote">
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid =
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: =
1ex;"><table border=3D"0" cellpadding=3D"0" =
cellspacing=3D"0"><tbody><tr><td style=3D"font-family: inherit; =
font-style: inherit; font-variant: inherit; font-weight: inherit; =
font-size: inherit; line-height: inherit; font-size-adjust: inherit; =
font-stretch: inherit;" valign=3D"top">
<br>Hello,<br><p class=3D"MsoNormal" style=3D"text-align: =
justify;"><span><span lang=3D"EN">How to</span></span><span><span =
lang=3D"EN"> <span title=3D"Cliquer ici pour voir d'autres =
traductions"></span></span><span><span =
lang=3D"EN">calculate</span></span><span><span lang=3D"EN"> <span =
title=3D"Cliquer ici pour voir d'autres =
traductions"></span></span><span><span lang=3D"EN">the value =
of</span></span></span><span><span lang=3D"EN"> <span title=3D"Cliquer =
ici pour voir d'autres traductions"></span></span><span><span =
lang=3D"EN">preparation energy "deltEpre"
&gt; from energy decomposition analysis of =
ADF.</span></span></span></span></p><p class=3D"MsoNormal" =
style=3D"text-align: justify;">Thank you very =
much<br><span><span><span><span lang=3D"EN"> </span></span><span =
style=3D"font-size: 12pt; line-height: 115%; font-family: &quot;Times =
New Roman&quot;,&quot;serif&quot;;"></span></span></span></p>
=
</td></tr></tbody></table></blockquote></div></blockquote></div><br><div>
<div style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; "><div style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; "><div style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; =
">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br>dr. Marcel Swart<br><br>ICREA =
Research Professor at<br>Institut de Qu=EDmica =
Computacional<br>Universitat de Girona<br><br>Facultat de =
Ci=E8ncies<br>Campus Montilivi</div><div style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">17071 =
Girona</div><div style=3D"word-wrap: break-word; -webkit-nbsp-mode: =
space; -webkit-line-break: after-white-space; ">Catalunya =
(Spain)<br><br>tel<br>+34-972-418861<br>fax<br>+34-972-418356<br>e-mail<br=
><a =
href=3D"mailto:marcel.swart]![icrea.cat">marcel.swart]![icrea.cat</a><br>marce=
l.swart]![udg.edu<br>web<br>http://www.marcelswart.eu<br>=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D<br></div></div></div></div>
</div>
<br></div></body></html>=

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