From owner-chemistry@ccl.net Tue Jan 2 01:20:00 2018
From: "Andreas Klamt klamt##cosmologic.de" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: Reference for structural details not amenable to forcefield analysis?
Message-Id: <-53126-180102010746-24296-9uyTKHvY3WMOF07rWY6eDg**server.ccl.net>
X-Original-From: Andreas Klamt <klamt_-_cosmologic.de>
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Sent to CCL by: Andreas Klamt [klamt-#-cosmologic.de]
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Joe,
what forcefields can describe ornot depends on the forcefield you
choose. Some people fit forcefields to quantum chemical interaction
energies of the molecules, they want to simulate. By that you will be
able to catch most effects. But most likely your question is where
typical forcefields fail.
My standard example is bromoform: Standard forcefields will describe the
electrostatics by point charges, i.e. typically a negative point charge
on halogens. Thus the most negative points on the the surface of
bromoform are the tops of the bromine atoms. But if you look quantum
chemically on bromoform, e.g. for the polarization charge density sigma
on a COSMO surface, or the electrostatic potential on an
iso-electrondensity surface, you will find that bromoform has even
positive polarity at the top. And indeed, halogens are known to form
interations with negative atoms, e.g. the lonepairs of oxygens, in
crystal structures. This is the so-called halogen bonding effect,
resulting from the so called sigma-hole, the electron depletion at the
opposite side of sigma bonds.
Forcefields based on point charge electrostatics are unable to describe
this.
Best regards
Andreas
Am 01.01.2018 um 20:32 schrieb Joe Leonard jleonard42-#-gmail.com:
> Folks, does anybody have a (recent) reference to a study discussing
> forcefield difficulties reproducing things like 1-5 interactions -
> things that are well-modeled by QM but not by forcefields…
>
> Thanks in advance! And happy new year!
>
> Joe Leonard
> jleonard42~~gmail.com <mailto:jleonard42%7E%7Egmail.com>
> —
> What's the difference between hardware and software? If you
> use hardware long enough, it breaks. If you use software long enough,
> it works.
>
>
>
--
Join us at the 5th-COSMO-RS-Symposium March 2018
Details at www.cosmologic.de/symposium_2018.html
--------------------------------------------------
Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt()cosmologic.de
web www.cosmologic.de
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
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<div class="moz-cite-prefix">Joe,<br>
<br>
what forcefields can describe ornot depends on the forcefield you
choose. Some people fit forcefields to quantum chemical
interaction energies of the molecules, they want to simulate. By
that you will be able to catch most effects. But most likely your
question is where typical forcefields fail.<br>
<br>
My standard example is bromoform: Standard forcefields will
describe the electrostatics by point charges, i.e. typically a
negative point charge on halogens. Thus the most negative points
on the the surface of bromoform are the tops of the bromine atoms.
But if you look quantum chemically on bromoform, e.g. for the
polarization charge density sigma on a COSMO surface, or the
electrostatic potential on an iso-electrondensity surface, you
will find that bromoform has even positive polarity at the top.
And indeed, halogens are known to form interations with negative
atoms, e.g. the lonepairs of oxygens, in crystal structures. This
is the so-called halogen bonding effect, resulting from the so
called sigma-hole, the electron depletion at the opposite side of
sigma bonds. <br>
Forcefields based on point charge electrostatics are unable to
describe this.<br>
<br>
Best regards<br>
<br>
Andreas<br>
<br>
<br>
<br>
<br>
Am 01.01.2018 um 20:32 schrieb Joe Leonard jleonard42-#-gmail.com:<br>
</div>
<blockquote type="cite"
cite="mid:-id%234nd-53125-180101143244-28935-kC3jADUAzy4UQ8MwUVg%2FHA()server.ccl.net">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Folks, does anybody have a (recent) reference to a study
discussing forcefield difficulties reproducing things like 1-5
interactions - things that are well-modeled by QM but not by
forcefields…
<div class=""><br class="">
</div>
<div class="">Thanks in advance! And happy new year!</div>
<div class=""><br class="">
</div>
<div class="">Joe Leonard</div>
<div class=""><a href="mailto:jleonard42%7E%7Egmail.com" class=""
moz-do-not-send="true">jleonard42~~gmail.com</a><br class="">
<div class="">
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style="text-align:
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<div
style="text-align:
start;
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0px;
word-wrap:
break-word;
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space;
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after-white-space;" class="">
<div
style="color:
rgb(0, 0, 0);
letter-spacing: normal; text-transform: none; white-space: normal;
word-spacing:
0px;
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0px;
text-align:
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after-white-space;" class="">—</div>
<div
style="text-align:
start;
text-indent:
0px;
word-wrap:
break-word;
-webkit-nbsp-mode:
space;
-webkit-line-break:
after-white-space;" class="">What's the difference between hardware and
software? If
you
use hardware
long enough,
it breaks. If
you use
software long
enough,
it works.<br
class="">
<br class="">
<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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</div>
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</div>
</div>
</div>
</div>
<br class="">
</div>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
Join us at the 5th-COSMO-RS-Symposium March 2018
Details at <a class="moz-txt-link-abbreviated" href="http://www.cosmologic.de/symposium_2018.html">www.cosmologic.de/symposium_2018.html</a>
--------------------------------------------------
Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail <a class="moz-txt-link-abbreviated" href="mailto:klamt()cosmologic.de">klamt()cosmologic.de</a>
web <a class="moz-txt-link-abbreviated" href="http://www.cosmologic.de">www.cosmologic.de</a>
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
</pre>
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From owner-chemistry@ccl.net Tue Jan 2 06:58:00 2018
From: "Mohamed E. A. Safy m.safy-x-compchem.net" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Reference for structural details not amenable to forcefield analysis?
Message-Id: <-53127-180102065339-10263-j8kt1egSn+HN11jh5UgsEw#,#server.ccl.net>
X-Original-From: "Mohamed E. A. Safy" <m.safy ~~ compchem.net>
Date: Tue, 2 Jan 2018 06:53:35 -0500
Sent to CCL by: "Mohamed E. A. Safy" [m.safy],[compchem.net]
Dear CCl users
Merry Christmas and happy new year for all of you,
Halogen bonding in terms of Molecular Mechanics can be described using a new
approach called positive extra point (PEP) approach. Inside PEP approach
sigma-hole of halogen atom was represented by an extra-point (EP) of charge.
More details about PEP approach can be found at the following links:
https://link.springer.com/article/10.1007/s00894-012-1454-8
http://onlinelibrary.wiley.com/doi/10.1002/jcc.21836/full
http://pubs.acs.org/doi/abs/10.1021/jp3003905
M.Safy
From owner-chemistry@ccl.net Tue Jan 2 10:38:00 2018
From: "Andreas Klamt klamt%x%cosmologic.de" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: Reference for structural details not amenable to forcefield analysis?
Message-Id: <-53128-180102090742-18823-KjN3zK6c90QbFuofj0PwUw-$-server.ccl.net>
X-Original-From: Andreas Klamt <klamt%a%cosmologic.de>
Content-Language: de-DE
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=utf-8
Date: Tue, 2 Jan 2018 15:07:30 +0100
MIME-Version: 1.0
Sent to CCL by: Andreas Klamt [klamt- -cosmologic.de]
... no question, as I already wrote, by special fitting and addition of
special correction terms forcefields are able to reproduce every effect.
But that is like predicting the weather of yesterday. As long as the
electrostatics in forcefields is mainly described by the crude concept
of atom centered point charges, they will in geral fail regarding the
directionality of the electrostatics. The papers you mention describe
local fits of corrections, which surely will correct nicely the
deficiency they are made for, but in many other cases the deficiencies
remain, because it is practically impossible to use these corrections
for all atom types.
Best regards
Andreas
Am 02.01.2018 um 12:53 schrieb Mohamed E. A. Safy m.safy-x-compchem.net:
> Sent to CCL by: "Mohamed E. A. Safy" [m.safy],[compchem.net]
> Dear CCl users
> Merry Christmas and happy new year for all of you,
> Halogen bonding in terms of Molecular Mechanics can be described using a new
> approach called positive extra point (PEP) approach. Inside PEP approach
> sigma-hole of halogen atom was represented by an extra-point (EP) of charge.
> More details about PEP approach can be found at the following links:
> https://link.springer.com/article/10.1007/s00894-012-1454-8
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.21836/full
> http://pubs.acs.org/doi/abs/10.1021/jp3003905
> M.Safy>
>
>
--
Join us at the 5th-COSMO-RS-Symposium March 2018
Details at www.cosmologic.de/symposium_2018.html
--------------------------------------------------
Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt(~)cosmologic.de
web www.cosmologic.de
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
From owner-chemistry@ccl.net Tue Jan 2 15:01:00 2018
From: "Hans-Ullrich SIEHL ullrich.siehl..uni-ulm.de" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: electrostatics in force-fields Re: CCL: Reference for structural details not amenable to forcefield analysis?
Message-Id: <-53129-180102141213-9119-1W9+lCLSjd1b8fIfja2BJg++server.ccl.net>
X-Original-From: Hans-Ullrich SIEHL <ullrich.siehl-*-uni-ulm.de>
Content-Language: en-US
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=utf-8; format=flowed
Date: Tue, 2 Jan 2018 20:12:08 +0100
MIME-Version: 1.0
Sent to CCL by: Hans-Ullrich SIEHL [ullrich.siehl|uni-ulm.de]
To get rid of the limitation of fixed charges im MM calculations, the
consistent charge equilibration method (CQEq) has been introduced.
We have applied this concept to a special group of ionic liquids.
"An application of the consistent charge equilibration (CQEq) method to
guanidinium ionic liquid systems
Chemical Physics Letters, Volume 457, Issue 1, p. 263-266.
DOI:10.1016/j.cplett.2008.03.087
best regards Ulli
--
send from: <ullrich.siehl~~uni-ulm.de>
On 02.01.2018 15:07, Andreas Klamt klamt%x%cosmologic.de wrote:
>
> Sent to CCL by: Andreas Klamt [klamt- -cosmologic.de]
> ... no question, as I already wrote, by special fitting and addition of
> special correction terms forcefields are able to reproduce every effect.
> But that is like predicting the weather of yesterday. As long as the
> electrostatics in forcefields is mainly described by the crude concept
> of atom centered point charges, they will in geral fail regarding the
> directionality of the electrostatics. The papers you mention describe
> local fits of corrections, which surely will correct nicely the
> deficiency they are made for, but in many other cases the deficiencies
> remain, because it is practically impossible to use these corrections
> for all atom types.
>
> Best regards
>
> Andreas
>
> Am 02.01.2018 um 12:53 schrieb Mohamed E. A. Safy m.safy-x-compchem.net:
>> Sent to CCL by: "Mohamed E. A. Safy" [m.safy],[compchem.net]
>> Dear CCl users
>> Merry Christmas and happy new year for all of you,
>> Halogen bonding in terms of Molecular Mechanics can be described using a new
>> approach called positive extra point (PEP) approach. Inside PEP approach
>> sigma-hole of halogen atom was represented by an extra-point (EP) of charge.
>> More details about PEP approach can be found at the following links:
>> https://link.springer.com/article/10.1007/s00894-012-1454-8
>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.21836/full
>> http://pubs.acs.org/doi/abs/10.1021/jp3003905
>> M.Safy>
>>
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