From owner-chemistry@ccl.net Wed Mar 28 09:57:00 2007
From: "Qian Wang xie.wang-*-gmail.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Message-Id: <-33916-070328095411-30860-z4kPY5IhIpXFytLbjBojIQ/a\server.ccl.net>
X-Original-From: "Qian Wang" <xie.wang^-^gmail.com>
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Sent to CCL by: "Qian Wang" [xie.wang**gmail.com]
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Dear all,

(I have sent this problem yesterday, here I include more details about the
molecule)

I am optimizing a molecule with 10 atoms. Surprisely, the optimized geometry
> from HF/6-31G is more close to experimental X-ray structure than optimized
geometry from MP2/6-31G* is. Could anyone suggest a possible reason why
higher level of calculation does not work better in this case?

I also found the  gas phase electron diffraction experimental structure, it
has slightly longer bond lengths than X-crystal structure, but it is still
more close to HF structure than MP2 structure. The molecule does not contain
metal and hydrogen ((CN)2C=C(CN)2), I did not use periodic cell. So is there
any reason why HF is more close to the gas phase structure?

Thanks in advance!

Qian

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Dear all,<br><br>(I have sent this problem yesterday, here I include more details about the molecule)<br><br>I am optimizing a molecule with 10 atoms. Surprisely, the optimized geometry from HF/6-31G is more close to experimental X-ray structure than optimized geometry from MP2/6-31G* is. Could anyone suggest a possible reason why higher level of calculation does not work better in this case?
<br><br>I also found the&nbsp; gas phase electron diffraction experimental
structure, it has slightly longer bond lengths than X-crystal
structure, but it is still more close to HF structure than MP2
structure. The molecule does not contain metal and hydrogen
((CN)2C=C(CN)2), I did not use periodic cell. So is there any reason
why HF is more close to the gas phase structure?<br>
<br>Thanks in advance!<br><span class="sg"><br>Qian<br>
</span>

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From owner-chemistry@ccl.net Wed Mar 28 12:31:00 2007
From: "Radoslaw Kaminski rkaminski _ acid.ch.pw.edu.pl" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Message-Id: <-33917-070328033643-684-VeEqhfpE6N3TiVIPuGD67w##server.ccl.net>
X-Original-From: "Radoslaw Kaminski" <rkaminski_+_acid.ch.pw.edu.pl>
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Sent to CCL by: "Radoslaw Kaminski" [rkaminski[]acid.ch.pw.edu.pl]

Dear Qian,

Remember that quantum calculations are aimed to search for the minimum of
the energy, and in crystal you have all those thermal factors. It means
that in calculations you have ground state and in X-ray structure excited
state. In crystal you have also could have some intermolecular
interactions. In my opinion if it is not fitting to the experiment it is
good.

Of course, you should also try MP2 in larger basis set, for example
AUG-cc-pvDZ, it's because of that the basis sets like 6-31G* and so on
have been optimized for HF method and in DFT a MP2 are not good.

I hope this can help a little.

Radek Kaminski


> Dear all,
>
> I am optimizing a molecule with 10 atoms. Surprisely, the optimized
> geometry
>> from HF/6-31G is more close to experimental X-ray structure than
>> optimized
> geometry from MP2/6-31G* is. Could anyone suggest a possible reason why
> higher level of calculation does not work better in this case?
>
> Thanks in advance!
>
> Qian


From owner-chemistry@ccl.net Wed Mar 28 13:08:01 2007
From: "Damiano Portinari damiano~~chem.gla.ac.uk" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: acid-base reaction energy barrier
Message-Id: <-33918-070328110849-25947-klLzgQ8t/R86nwJL4UpC3w*server.ccl.net>
X-Original-From: "Damiano  Portinari" <damiano,+,chem.gla.ac.uk>
Date: Wed, 28 Mar 2007 11:08:46 -0400


Sent to CCL by: "Damiano  Portinari" [damiano%%chem.gla.ac.uk]
Dear CCL members,

I am studying a reaction between a heterocyclic aromatic compound and a primary amine. The amine reacts with this compound with a nucleophilic addition and then does a cyclisation with a SN2 reaction. After the nucleophilic addition the amino group became an ammonium group reacting then with a base (triethylamine) that takes off the proton before the cyclization. I found the transition states of the nucleophilic addition and of the SN2 reaction but I miss the transition state where is involved the acid-base reaction. Can I think maybe that the energy barrier of the transition state of this acid-base reaction is negligible and so doesnt change too much the potential energy surface profile? Do I maybe need to study, with some STQN method, the proton exchange between the base and the ammonium group? Can I presume that the main energy barrier of the first step of my reaction path is determined by the N-C bond formation of the nucleophilic addition or should I also think about the acid-base reaction that is involved?

Many thanks in advance for your Help!


Best Regards,

Damiano.


From owner-chemistry@ccl.net Wed Mar 28 13:56:01 2007
From: "Close, David M. CLOSED^_^mail.etsu.edu" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Message-Id: <-33919-070328114936-29150-i3LFZboyOLH6eIaq+m+68Q-,-server.ccl.net>
X-Original-From: "Close, David M." <CLOSED---mail.etsu.edu>
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Sent to CCL by: "Close, David M." [CLOSED##mail.etsu.edu]
This is a multi-part message in MIME format.

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Qian:

  The reason is that this is your lucky day.  It is only an accident
that the HF calculations agree better than the MP2 calculations. =20

  If you have x-ray crystallographic data, you are looking at a highly
ordered structure.  But you are doing gas phase calculations.  So you
are leaving out the intricate H-bonding that holds the crystal together.
By not including the influence of the neighbors on things like bond
lengths and bond angles, it is just a coincidence that the HF
calculations agree with the crystal data.

  Dave Close.

=20

________________________________

> From: owner-chemistry##ccl.net [mailto:owner-chemistry##ccl.net]=20
Sent: Wednesday, March 28, 2007 9:25 AM
To: Close, David M.
Subject: CCL: geometry optimization problem: why lower level geometry is
more close to experimental results?

=20

Dear all,

(I have sent this problem yesterday, here I include more details about
the molecule)

I am optimizing a molecule with 10 atoms. Surprisely, the optimized
geometry from HF/6-31G is more close to experimental X-ray structure
than optimized geometry from MP2/6-31G* is. Could anyone suggest a
possible reason why higher level of calculation does not work better in
this case?=20

I also found the  gas phase electron diffraction experimental structure,
it has slightly longer bond lengths than X-crystal structure, but it is
still more close to HF structure than MP2 structure. The molecule does
not contain metal and hydrogen ((CN)2C=3DC(CN)2), I did not use periodic
cell. So is there any reason why HF is more close to the gas phase
structure?

Thanks in advance!

Qian


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<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
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10.0pt;font-family:Arial;color:navy'>Qian:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>&nbsp; The reason is that this is =
your
lucky day. &nbsp;It is only an accident that the HF calculations agree =
better
than the MP2 calculations. &nbsp;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>&nbsp; If you have x-ray =
crystallographic
data, you are looking at a highly ordered structure. &nbsp;But you are =
doing
gas phase calculations.&nbsp; So you are leaving out the intricate =
H-bonding
that holds the crystal together. By not including the influence of the
neighbors on things like bond lengths and bond angles, it is just a =
coincidence
that the HF calculations agree with the crystal =
data.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>&nbsp; Dave =
Close.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

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<p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span =
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font-family:Tahoma;font-weight:bold'>From:</span></font></b><font =
size=3D2
face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'>
owner-chemistry##ccl.net [mailto:owner-chemistry##ccl.net] <br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Wednesday, March =
28, 2007
9:25 AM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> Close, David M.<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> CCL: geometry
optimization problem: why lower level geometry is more close to =
experimental
results?</span></font><o:p></o:p></p>

</div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Dear all,<br>
<br>
(I have sent this problem yesterday, here I include more details about =
the
molecule)<br>
<br>
I am optimizing a molecule with 10 atoms. Surprisely, the optimized =
geometry
> from HF/6-31G is more close to experimental X-ray structure than =
optimized
geometry from MP2/6-31G* is. Could anyone suggest a possible reason why =
higher
level of calculation does not work better in this case? <br>
<br>
I also found the&nbsp; gas phase electron diffraction experimental =
structure,
it has slightly longer bond lengths than X-crystal structure, but it is =
still
more close to HF structure than MP2 structure. The molecule does not =
contain
metal and hydrogen ((CN)2C=3DC(CN)2), I did not use periodic cell. So is =
there
any reason why HF is more close to the gas phase structure?<br>
<br>
Thanks in advance!<br>
<br>
<span class=3Dsg>Qian</span><o:p></o:p></span></font></p>

</div>

</body>

</html>

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From owner-chemistry@ccl.net Wed Mar 28 15:13:00 2007
From: "errol lewars elewars*|*trentu.ca" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Message-Id: <-33920-070328130902-18059-X61A8tlvbr9Xbd/v8YHH/Q-.-server.ccl.net>
X-Original-From: errol lewars <elewars!=!trentu.ca>
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Sent to CCL by: errol lewars [elewars:trentu.ca]
2007 March 28

Hello,

I don't know the details of your particular computation, but there is no 
reason why a "higher-level" (better treatment of electron correlation 
and/or bigger basis set) calculation  _must_ give a better geometry, or 
better relative energies, or better anything,  than a lower-level one: 
as long as there are significant errors in the calculation, the errors 
in the lower-level job could cancel out better. This is called geting 
the right answer for the wrong reason. There is a paper with "Getting 
the right answer for the right reason" in the title: R. J. Bartlett, I. 
V. Schweigert, THEOCHEM, 2006, 771(1-3), 1. A fairly notorious case of 
the phenomenon is evinced by the dipole moment of carbon monoxide:
HF/STO-3G             0.12 D
HF/6-31G*               0.26 D (bigger bases can give still worse results)
B3LYP/6-311+G**  0.07
The experimental value is said to be 0.11 D

Close to an exact solution of the Schroedinger equation, _higher-level_ 
and _better_ should match up.

E. Lewars
====

Qian Wang xie.wang,gmail.com wrote:

> Dear all,
>
> I am optimizing a molecule with 10 atoms. Surprisely, the optimized 
> geometry from HF/6-31G is more close to experimental X-ray structure 
> than optimized geometry from MP2/6-31G* is. Could anyone suggest a 
> possible reason why higher level of calculation does not work better 
> in this case?
>
> Thanks in advance!
>
> Qian


From owner-chemistry@ccl.net Wed Mar 28 18:20:00 2007
From: "Brian Salter-Duke b_duke*bigpond.net.au" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Message-Id: <-33921-070328100044-32725-ZCu3eBnH8A98O2NDtLFodA__server.ccl.net>
X-Original-From: Brian Salter-Duke <b_duke-x-bigpond.net.au>
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Date: Wed, 28 Mar 2007 21:47:24 +1000
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Sent to CCL by: Brian Salter-Duke [b_duke^_^bigpond.net.au]

On Tue, Mar 27, 2007 at 10:27:43PM -0400, Qian Wang xie.wang,gmail.com wrote:
> Dear all,
> 
> I am optimizing a molecule with 10 atoms. Surprisely, the optimized geometry
> from HF/6-31G is more close to experimental X-ray structure than optimized
> geometry from MP2/6-31G* is. Could anyone suggest a possible reason why
> higher level of calculation does not work better in this case?

HF/6-31G can give good bond lengths. If you increase the basis, the bond
lengths will decrease below the experimental values. Adding correlation
increases the bond length. Think of it as configuration interaction
between the bonding orbital and the antibonding for each bond. MP2 with
6-31G* may just not be good enough and give bond lengths that are too
long. Is that what you observe?

Regards, Brian.
 
> Thanks in advance!
> 
> Qian

-- 
       Brian Salter-Duke (Brian Duke)    b_duke**bigbond.net.au 
       Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia
 Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm
    Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.


From owner-chemistry@ccl.net Wed Mar 28 23:54:01 2007
From: "Soren Eustis soren]=[jhu.edu" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Message-Id: <-33922-070328185601-30574-pWuOQY6hNzcEJYDSBVGa7g.@.server.ccl.net>
X-Original-From: "Soren Eustis" <soren : jhu.edu>
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Date: Wed, 28 Mar 2007 18:55:00 -0400
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Sent to CCL by: "Soren Eustis" [soren[-]jhu.edu]
let's be very clear here.  The second to last respondent  had the correct answer.  You cannot compare solid state and gas phase.  Apples and oranges.

Soren Eustis

Sent via Sprint PCS PowerVision

-----Original Message-----

> From:  "Brian Salter-Duke b_duke*bigpond.net.au" <owner-chemistry]![ccl.net>
Subj:  CCL: geometry optimization problem: why lower level geometry is more close to experimental results?
Date:  Wed Mar 28, 2007 6:48 pm
Size:  2K
To:  "Eustis, Soren " <soreneustis]![gmail.com>


Sent to CCL by: Brian Salter-Duke [b_duke^_^bigpond.net.au]

On Tue, Mar 27, 2007 at 10:27:43PM -0400, Qian Wang xie.wang,gmail.com wrote:
> Dear all,
> 
> I am optimizing a molecule with 10 atoms. Surprisely, the optimized geometry
> from HF/6-31G is more close to experimental X-ray structure than optimized
> geometry from MP2/6-31G* is. Could anyone suggest a possible reason why
> higher level of calculation does not work better in this case?

HF/6-31G can give good bond lengths. If you increase the basis, the bond
lengths will decrease below the experimental values. Adding correlation
increases the bond length. Think of it as configuration interaction
between the bonding orbital and the antibonding for each bond. MP2 with
6-31G* may just not be good enough and give bond lengths that are too
long. Is that what you observe?

Regards, Brian.
 
> Thanks in advance!
> 
> Qian

-- 
       Brian Salter-Duke (Brian Duke)    b_duke .. bigbond.net.au 
       Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia
 Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm
    Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt