From owner-chemistry@ccl.net Wed May 11 00:31:01 2011
From: "Arvydas.Tamulis|tfai.vu.lt" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: micelle structure (PDB) files
Message-Id: <-44613-110511002706-31052-3s7dA6s3iGvgVW68U3wihw*_*server.ccl.net>
X-Original-From: Arvydas.Tamulis,tfai.vu.lt
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Date: Wed, 11 May 2011 07:26:46 +0300
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Sent to CCL by: Arvydas.Tamulis{}tfai.vu.lt
Dear Andreas,
MD simulations give wrong results of micelle structure and even
semiempirical QM methods are not sufficient.
Please take a look to our DFT non local gradient investigations:
A. Tamulis, M. Grigalavicius, „The Emergence and Evolution of Life in
a “Fatty Acid World” Based on Quantum Mechanics”, Origins of Life and
Evolution of Biospheres, 2011) vol. 41, pages 51-71. Electronical
version of this article with moving micelles available at
http://www.springerlink.com/content/7122n16869843314/fulltext.html
Would you please to accept my proposal to cooperate in further
investigations of micelles in the case if you have large computing
possibilities.
With best regards,
Arvydas
http://www.itpa.lt/~tamulis/
"Andreas Klamt klamt|-|cosmologic.de" <owner-chemistry!A!ccl.net> rašė:
>
> Sent to CCL by: Andreas Klamt [klamt^^^cosmologic.de]
> Dear CCLers,
>
> this time I like to post a question instead of commenting on other
> peoples questions:
>
> Does anyone know a larger reservoir of micelle structure data (most
> like stored in PDB format)? We would be interested in collecting
> such structures, either based on experimental data or on MD
> simulations. Maybe we could host a library of such files or a
> library of links to such files on our web site.
>
> In the moment we are especially interested in SLES micelles.
>
> Thanks in advance
>
> Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>
From owner-chemistry@ccl.net Wed May 11 01:50:01 2011
From: "Andreas Klamt klamt**cosmologic.de" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: micelle structure (PDB) files
Message-Id: <-44614-110511014311-28733-643ytHOW4tC3a6kk8RD7ag(a)server.ccl.net>
X-Original-From: Andreas Klamt <klamt!^!cosmologic.de>
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Date: Wed, 11 May 2011 07:43:01 +0200
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Sent to CCL by: Andreas Klamt [klamt[#]cosmologic.de]
Dear Arvydas,
thank you very much for your reply, but from your paper I cannot really
see how you can conclude that MD results on micelles and bio-membranes
should be generally wrong. To our experience such simulations give a
reasonable picture of the composition, i.e. of probability to find
certain parts of surfactants and solvent molecules in the layers of the
micelle, and that is what we need to know in order to calculate the free
energy of solutes in such micelles with the COSMOmic tool. We do not see
major diferences in the COSMOmic results depending on which specific MD
results we are using as input for the micelle composition. It seems that
they are rather comverged in that regard.
Andreas
Am 11.05.2011 06:26, schrieb Arvydas.Tamulis|tfai.vu.lt:
>
> Sent to CCL by: Arvydas.Tamulis{}tfai.vu.lt
> Dear Andreas,
>
> MD simulations give wrong results of micelle structure and even
> semiempirical QM methods are not sufficient.
> Please take a look to our DFT non local gradient investigations:
> A. Tamulis, M. Grigalavicius, „The Emergence and Evolution of Life in
> a “Fatty Acid World” Based on Quantum Mechanics”, Origins of Life and
> Evolution of Biospheres, 2011) vol. 41, pages 51-71. Electronical
> version of this article with moving micelles available at
> http://www.springerlink.com/content/7122n16869843314/fulltext.html
>
> Would you please to accept my proposal to cooperate in further
> investigations of micelles in the case if you have large computing
> possibilities.
>
> With best regards,
> Arvydas
> http://www.itpa.lt/~tamulis/
>
> "Andreas Klamt klamt|-|cosmologic.de" <owner-chemistry(!)ccl.net> rašė:
>
>>
>> Sent to CCL by: Andreas Klamt [klamt^^^cosmologic.de]
>> Dear CCLers,
>>
>> this time I like to post a question instead of commenting on other
>> peoples questions:
>>
>> Does anyone know a larger reservoir of micelle structure data (most
>> like stored in PDB format)? We would be interested in collecting such
>> structures, either based on experimental data or on MD simulations.
>> Maybe we could host a library of such files or a library of links to
>> such files on our web site.
>>
>> In the moment we are especially interested in SLES micelles.
>>
>> Thanks in advance
>>
>> Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
>> http://server.ccl.net/chemistry/announcements/conferences/http://www.ccl.net/chemistry/sub_unsub.shtml>
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>
--
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH& Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt..cosmologic.de
web www.cosmologic.de
HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
From owner-chemistry@ccl.net Wed May 11 02:24:01 2011
From: "Sebastian Kozuch kozuchs-x-yahoo.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: van-der-Waals-complex vs. weak forces
Message-Id: <-44615-110511014141-27480-HhwaYd9ZzIZ7kyP2+1oKZg*_*server.ccl.net>
X-Original-From: Sebastian Kozuch <kozuchs(~)yahoo.com>
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Date: Tue, 10 May 2011 22:41:31 -0700 (PDT)
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Sent to CCL by: Sebastian Kozuch [kozuchs%a%yahoo.com]
--0-298607376-1305092491=:81580
Content-Type: text/plain; charset=us-ascii
Take a look at the NCIPlot program. It analyses the different non-covalent
interactions, and using VMD you can have nice plots of them.
I'm not sure, but I think that although b97d will give you proper geometries and
energies, it will not be appropriate for NCIPlot, since the dispersion
correction does not act into the electronic density, thus not being taken into
account into the program. I may use for single point energies a method that
intrinsically includes dispersion forces (M06-2X maybe), but that has to be
tested.
Best,
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...........
.. sebastian.kozuch!A!weizmann.ac.il ..
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
________________________________
> From: Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de
<owner-chemistry!A!ccl.net>
To: "Kozuch, Sebastian " <kozuchs!A!yahoo.com>
Sent: Tue, May 10, 2011 10:45:00 PM
Subject: CCL:G: van-der-Waals-complex vs. weak forces
Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de]
Hello together!
I want to exam some (mainly organic) crystal structures, which seem to be mainly
held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---Phenyl
hydrogen bonds or Pi-Pi-stacking.
I cut out the corresponding dimers of the crystal structure and subjected them
to geometry optimisation, using gaussian 09 with the input line
#T opt freq b97d/6-31g(d,p)/auto=all
which works quite well, resulting in minima for expected bonding, but striding
away molecules for dimers which are not supposed to interact in a "bonding" way.
Now having some optimized structures, is there anything to do to prove the
nature of the "bonding"?
How can I distinguish the "van-der-Waals complex" from a dispersion interaction
or some kind of hydrogen bonding?
Thanks a lot for suggestions on how to treat this problem,
Guntramhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-298607376-1305092491=:81580
Content-Type: text/html; charset=us-ascii
<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt">Take a look at the NCIPlot program. It analyses the different non-covalent interactions, and using VMD you can have nice plots of them.<br>I'm not sure, but I think that although b97d will give you proper geometries and energies, it will not be appropriate for NCIPlot, since the dispersion correction does not act into the electronic density, thus not being taken into account into the program. I may use for single point energies a method that intrinsically includes dispersion forces (M06-2X maybe), but that has to be tested.<br><br>Best,<br><div> </div><span style="font-family:courier, monaco, monospace, sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style="font-family:courier, monaco, monospace, sans-serif;"><span style="font-family:courier, monaco, monospace,
sans-serif;">..........Sebastian Kozuch...........</span><br style="font-family:courier, monaco, monospace, sans-serif;"><span style="font-family:courier, monaco, monospace, sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style="font-family:courier, monaco, monospace, sans-serif;"><span style="font-family:courier, monaco, monospace, sans-serif;">....Weizmann Institute of Science....</span><br style="font-family:courier, monaco, monospace, sans-serif;"><span style="font-family:courier, monaco, monospace, sans-serif;">...........</span><span style="font-family:courier, monaco, monospace, sans-serif;">Rehovot, Israel...........</span><br style="font-family:courier, monaco, monospace, sans-serif;"><span style="font-family:courier, monaco, monospace, sans-serif;">.. sebastian.kozuch!A!weizmann.ac.il ..</span><br style="font-family:courier, monaco, monospace, sans-serif;"><a rel="nofollow" target="_blank"
href="http://yfaat.ch.huji.ac.il/kozuch.htm"><span style="font-family:courier, monaco, monospace, sans-serif;">http://yfaat.ch.huji.ac.il/kozuch.htm</span></a><br style="font-family:courier, monaco, monospace, sans-serif;"><span style="font-family:courier, monaco, monospace, sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><div><br></div><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de <owner-chemistry!A!ccl.net><br><b><span style="font-weight: bold;">To:</span></b> "Kozuch, Sebastian " <kozuchs!A!yahoo.com><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, May 10, 2011 10:45:00 PM<br><b><span style="font-weight: bold;">Subject:</span></b> CCL:G: van-der-Waals-complex vs. weak
forces<br></font><br><br>Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de]<br>Hello together!<br><br>I want to exam some (mainly organic) crystal structures, which seem to be mainly held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking.<br><br>I cut out the corresponding dimers of the crystal structure and subjected them to geometry optimisation, using gaussian 09 with the input line<br><br>#T opt freq b97d/6-31g(d,p)/auto=all<br><br>which works quite well, resulting in minima for expected bonding, but striding away molecules for dimers which are not supposed to interact in a "bonding" way.<br><br>Now having some optimized structures, is there anything to do to prove the nature of the "bonding"?<br>How can I distinguish the "van-der-Waals complex" from a dispersion interaction or some kind of hydrogen bonding?<br><br><br>Thanks a lot for suggestions on how to treat
this problem,<br>Guntram<br><br><br><br<br<br<br<br><br>E-mail to subscribers: <a ymailto="mailto:CHEMISTRY!A!ccl.net" href="mailto:CHEMISTRY!A!ccl.net">CHEMISTRY!A!ccl.net</a> or use:<br> <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail to administrators: <a ymailto="mailto:CHEMISTRY-REQUEST!A!ccl.net" href="mailto:CHEMISTRY-REQUEST!A!ccl.net">CHEMISTRY-REQUEST!A!ccl.net</a> or use<br> <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br<br> <a
href="http://www.ccl.net/chemistry/sub_unsub.shtml" target="_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br><br>Before posting, check wait time at: <a href="http://www.ccl.net" target="_blank">http://www.ccl.net</a><br><br>Job: <a href="http://www.ccl.net/jobs" target="_blank">http://www.ccl.net/jobs</a> <br>Conferences: <a href="http://server.ccl.net/chemistry/announcements/conferences/" target="_blank">http://server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search Messages: <a href="http://www.ccl.net/chemistry/searchccl/index.shtml" target="_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br><br<br> <a href="http://www.ccl.net/spammers.txt" target="_blank">http://www.ccl.net/spammers.txt</a><br><br>RTFI: <a href="http://www.ccl.net/chemistry/aboutccl/instructions/"
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--0-298607376-1305092491=:81580--
From owner-chemistry@ccl.net Wed May 11 14:40:00 2011
From: "Shahar Keinan skeinan*gmail.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL:G: van-der-Waals-complex vs. weak forces
Message-Id: <-44616-110511093804-3758-uk/sOuoFkSFk7YONhBJC7w|,|server.ccl.net>
X-Original-From: Shahar Keinan <skeinan*gmail.com>
Content-Type: multipart/alternative; boundary=000e0cd3282eb5db9804a3002dec
Date: Wed, 11 May 2011 09:37:48 -0400
MIME-Version: 1.0
Sent to CCL by: Shahar Keinan [skeinan!=!gmail.com]
--000e0cd3282eb5db9804a3002dec
Content-Type: text/plain; charset=ISO-8859-1
I do think the NCIplot is an excellent option.
Let me just state here, that even if the functional that you are using don't
include dispersion corrections, the underlaying density does have the
correct dispersion, and thus NCIplot will be able to display vDW and
Hydrogen bonds. We have several such examples in the supporting information
of the manuscript:
http://pubs.acs.org/doi/suppl/10.1021/ja100936w
Here is the website for more information about the method and how to
download the code:
http://www.chem.duke.edu/~yang/Software/softwareNCI.html
I am one of the developers, and this email is part of our shameless
promotion division :)
Anyway, if you have problems/questions, don't hesitate to contact me,
Shahar
On Wed, May 11, 2011 at 1:41 AM, Sebastian Kozuch kozuchs-x-yahoo.com <
owner-chemistry ~ ccl.net> wrote:
> Take a look at the NCIPlot program. It analyses the different non-covalent
> interactions, and using VMD you can have nice plots of them.
> I'm not sure, but I think that although b97d will give you proper
> geometries and
> energies, it will not be appropriate for NCIPlot, since the dispersion
> correction does not act into the electronic density, thus not being taken
> into
> account into the program. I may use for single point energies a method that
> intrinsically includes dispersion forces (M06-2X maybe), but that has to be
> tested.
>
> Best,
>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> ..........Sebastian Kozuch...........
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> ....Weizmann Institute of Science....
> ...........Rehovot, Israel...........
> .. sebastian.kozuch^weizmann.ac.il ..
> http://yfaat.ch.huji.ac.il/kozuch.htm
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
>
>
>
> ________________________________
> > From: Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de
> <owner-chemistry^ccl.net>
> To: "Kozuch, Sebastian " <kozuchs^yahoo.com>
> Sent: Tue, May 10, 2011 10:45:00 PM
> Subject: CCL:G: van-der-Waals-complex vs. weak forces
>
>
> Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de]
> Hello together!
>
> I want to exam some (mainly organic) crystal structures, which seem to be
> mainly
> held together by weak forces like Phenyl-H---O hydrogen bonds,
> Phenly-H---Phenyl
> hydrogen bonds or Pi-Pi-stacking.
>
> I cut out the corresponding dimers of the crystal structure and subjected
> them
> to geometry optimisation, using gaussian 09 with the input line
>
> #T opt freq b97d/6-31g(d,p)/auto=all
>
> which works quite well, resulting in minima for expected bonding, but
> striding
> away molecules for dimers which are not supposed to interact in a "bonding"
> way.
>
> Now having some optimized structures, is there anything to do to prove the
> nature of the "bonding"?
> How can I distinguish the "van-der-Waals complex" from a dispersion
> interaction
> or some kind of hydrogen bonding?
>
>
> Thanks a lot for suggestions on how to treat this problem,
> Guntramhttp://
> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-298607376-1305092491=:81580
> Content-Type: text/html; charset=us-ascii
>
> <html><head><style type="text/css"><!-- DIV {margin:0px;}
> --></style></head><body><div
> style="font-family:arial,helvetica,sans-serif;font-size:10pt">Take a look at
> the NCIPlot program. It analyses the different non-covalent interactions,
> and using VMD you can have nice plots of them.<br>I'm not sure, but I think
> that although b97d will give you proper geometries and energies, it will not
> be appropriate for NCIPlot, since the dispersion correction does not act
> into the electronic density, thus not being taken into account into the
> program. I may use for single point energies a method that intrinsically
> includes dispersion forces (M06-2X maybe), but that has to be
> tested.<br><br>Best,<br><div> </div><span style="font-family:courier,
> monaco, monospace,
> sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br
> style="font-family:courier, monaco, monospace, sans-serif;"><span
> style="font-family:courier, monaco, monospace,
> sans-serif;">..........Sebastian Kozuch...........</span><br
> style="font-family:courier, monaco, monospace, sans-serif;"><span
> style="font-family:courier, monaco, monospace,
> sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br
> style="font-family:courier, monaco, monospace, sans-serif;"><span
> style="font-family:courier, monaco, monospace, sans-serif;">....Weizmann
> Institute of Science....</span><br style="font-family:courier, monaco,
> monospace, sans-serif;"><span style="font-family:courier, monaco, monospace,
> sans-serif;">...........</span><span style="font-family:courier, monaco,
> monospace, sans-serif;">Rehovot, Israel...........</span><br
> style="font-family:courier, monaco, monospace, sans-serif;"><span
> style="font-family:courier, monaco, monospace, sans-serif;">..
> sebastian.kozuch^weizmann.ac.il ..</span><br style="font-family:courier,
> monaco, monospace, sans-serif;"><a rel="nofollow" target="_blank"
> href="http://yfaat.ch.huji.ac.il/kozuch.htm"><span
> style="font-family:courier, monaco, monospace, sans-serif;">
> http://yfaat.ch.huji.ac.il/kozuch.htm</span></a><br
> style="font-family:courier, monaco, monospace, sans-serif;"><span
> style="font-family:courier, monaco, monospace,
> sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><div><br></div><div
> style="font-family:arial, helvetica, sans-serif;font-size:10pt"><br><div
> style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font
> face="Tahoma" size="2"><hr size="1"><b><span style="font-weight:
> bold;">From:</span></b> Guntram Schmidt guntram.schmidt]=[
> chemie.uni-halle.de <owner-chemistry^ccl.net><br><b><span
> style="font-weight: bold;">To:</span></b> "Kozuch, Sebastian " <kozuchs^
> yahoo.com><br><b><span style="font-weight: bold;">Sent:</span></b> Tue,
> May 10, 2011 10:45:00 PM<br><b><span style="font-weight:
> bold;">Subject:</span></b> CCL:G: van-der-Waals-complex vs. weak
> forces<br></font><br><br>Sent to CCL by: "Guntram Schmidt"
> [guntram.schmidt(-)chemie.uni-halle.de]<br>Hello together!<br><br>I want
> to exam some (mainly organic) crystal structures, which seem to be mainly
> held together by weak forces like Phenyl-H---O hydrogen bonds,
> Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking.<br><br>I cut out the
> corresponding dimers of the crystal structure and subjected them to geometry
> optimisation, using gaussian 09 with the input line<br><br>#T opt freq
> b97d/6-31g(d,p)/auto=all<br><br>which works quite well, resulting in minima
> for expected bonding, but striding away molecules for dimers which are not
> supposed to interact in a "bonding" way.<br><br>Now having some optimized
> structures, is there anything to do to prove the nature of the
> "bonding"?<br>How can I distinguish the "van-der-Waals complex" from a
> dispersion interaction or some kind of hydrogen bonding?<br><br><br>Thanks a
> lot for suggestions on how to treat
> this problem,<br>Guntram<br><br><br><br<br<br<br<br><br>E-mail to
> subscribers: <a ymailto="mailto:CHEMISTRY^ccl.net" href="mailto:CHEMISTRY^
> ccl.net">CHEMISTRY^ccl.net</a> or use:<br> <a href="" target="_blank"</a><br><br>E-mail to
> administrators: <a ymailto="mailto:CHEMISTRY-REQUEST^ccl.net"
> href="mailto:CHEMISTRY-REQUEST^ccl.net">CHEMISTRY-REQUEST^ccl.net</a> or
> use<br> <a href="" target="_blank"</a><br><br<br>
> <a
> href="http://www.ccl.net/chemistry/sub_unsub.shtml" target="_blank"</a><br><br>Before posting,
> check wait time at: <a href="http://www.ccl.net" target="_blank">
> http://www.ccl.net</a><br><br>Job: <a href="http://www.ccl.net/jobs"
> target="_blank">http://www.ccl.net/jobs</a> <br>Conferences: <a href="
> http://server.ccl.net/chemistry/announcements/conferences/"
> target="_blank">http://server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search
> Messages: <a href="http://www.ccl.net/chemistry/searchccl/index.shtml"
> target="_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br><br<br>
> <a href="http://www.ccl.net/spammers.txt" target="_blank"</a><br><br>RTFI: <a href="
> http://www.ccl.net/chemistry/aboutccl/instructions/"
> target="_blank">http://www.ccl.net/chemistry/aboutccl/instructions/
> </a><br><br><br></div></div>
>
>
>
> </div></body></html>
--
------------------------------------------------------
Shahar Keinan
(919) 357 5319
--000e0cd3282eb5db9804a3002dec
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
I do think the NCIplot is an excellent option.<div><br></div><div>Let me ju=
st state=A0here, that even if the functional that you are using don't i=
nclude=A0dispersion=A0corrections, the underlaying density does have the co=
rrect dispersion, and thus NCIplot will be able to=A0display=A0vDW and Hydr=
ogen bonds. We have several such examples in the supporting information of =
the manuscript:</div>
<div><a href=3D"http://pubs.acs.org/doi/suppl/10.1021/ja100936w">http://pub=
s.acs.org/doi/suppl/10.1021/ja100936w</a></div><div><br><div>Here is the we=
bsite for more information about the method and how to download the code:</=
div>
<div><a href=3D"http://www.chem.duke.edu/~yang/Software/softwareNCI.html">h=
ttp://www.chem.duke.edu/~yang/Software/softwareNCI.html</a></div><div><br><=
div>I am one of the developers, and this email is part of our shameless pro=
motion division :)</div>
<div><br></div><div>Anyway, if you have problems/questions, don't hesit=
ate to contact me,</div><div>Shahar</div><div><br><br><div class=3D"gmail_q=
uote">On Wed, May 11, 2011 at 1:41 AM, Sebastian Kozuch <a href=3D"http://k=
ozuchs-x-yahoo.com">kozuchs-x-yahoo.com</a> <span dir=3D"ltr"><<a href=
=3D"mailto:owner-chemistry ~ ccl.net">owner-chemistry ~ ccl.net</a>></span> =
wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">Take a look at the NCIPlot program. It anal=
yses the different non-covalent<br>
interactions, and using VMD you can have nice plots of them.<br>
I'm not sure, but I think that although b97d will give you proper geome=
tries and<br>
energies, it will not be appropriate for NCIPlot, since the dispersion<br>
correction does not act into the electronic density, thus not being taken i=
nto<br>
account into the program. I may use for single point energies a method that=
<br>
intrinsically includes dispersion forces (M06-2X maybe), but that has to be=
<br>
tested.<br>
<br>
Best,<br>
<br>
=A0xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx<br>
..........Sebastian Kozuch...........<br>
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx<br>
....Weizmann Institute of Science....<br>
...........Rehovot, Israel...........<br>
.. sebastian.kozuch^<a href=3D"http://weizmann.ac.il" target=3D"_blank">wei=
zmann.ac.il</a> ..<br>
<a href=3D"http://yfaat.ch.huji.ac.il/kozuch.htm" target=3D"_blank">http://=
yfaat.ch.huji.ac.il/kozuch.htm</a><br>
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx<br>
<br>
<br>
<br>
<br>
________________________________<br>
> From: Guntram Schmidt guntram.schmidt]=3D[<a href=3D"http://chemie.uni=
-halle.de" target=3D"_blank">chemie.uni-halle.de</a><br>
<owner-chemistry^<a href=3D"http://ccl.net" target=3D"_blank">ccl.net</a=
>><br>
To: "Kozuch, Sebastian " <kozuchs^<a href=3D"http://yahoo.com"=
target=3D"_blank">yahoo.com</a>><br>
Sent: Tue, May 10, 2011 10:45:00 PM<br>
Subject: CCL:G: van-der-Waals-complex vs. weak forces<br>
<br>
<br>
Sent to CCL by: "Guntram =A0Schmidt" [guntram.schmidt(-)<a href=
=3D"http://chemie.uni-halle.de" target=3D"_blank">chemie.uni-halle.de</a>]<=
br>
Hello together!<br>
<br>
I want to exam some (mainly organic) crystal structures, which seem to be m=
ainly<br>
held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---P=
henyl<br>
hydrogen bonds or Pi-Pi-stacking.<br>
<br>
I cut out the corresponding dimers of the crystal structure and subjected t=
hem<br>
to geometry optimisation, using gaussian 09 with the input line<br>
<br>
#T opt freq b97d/6-31g(d,p)/auto=3Dall<br>
<br>
which works quite well, resulting in minima for expected bonding, but strid=
ing<br>
away molecules for dimers which are not supposed to interact in a "bon=
ding" way.<br>
<br>
Now having some optimized structures, is there anything to do to prove the<=
br>
nature of the "bonding"?<br>
How can I distinguish the "van-der-Waals complex" from a dispersi=
on interaction<br>
or some kind of hydrogen bonding?<br>
<br>
<br>
Thanks a lot for suggestions on how to treat this problem,<br>
Guntramhttp://<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehtt=
p://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0=
-298607376-1305092491=3D:81580
Content-Type" target=3D"_blank">www.ccl.net/cgi-bin/ccl/send_ccl_messagehtt=
p://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0=
-298607376-1305092491=3D:81580<br>
Content-Type</a>: text/html; charset=3Dus-ascii<br>
<br>
<html><head><style type=3D"text/css"><!-- DI=
V {margin:0px;} --></style></head><body><div style=
=3D"font-family:arial,helvetica,sans-serif;font-size:10pt">Tak=
e a look at the NCIPlot program. It analyses the different non-covalent int=
eractions, and using VMD you can have nice plots of them.<br>I'm =
not sure, but I think that although b97d will give you proper geometries an=
d energies, it will not be appropriate for NCIPlot, since the dispersion co=
rrection does not act into the electronic density, thus not being taken int=
o account into the program. I may use for single point energies a method th=
at intrinsically includes dispersion forces (M06-2X maybe), but that has to=
be tested.<br><br>Best,<br><div>&nbsp;</div=
><span style=3D"font-family:courier, monaco, monospace, sans-ser=
if;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style=
=3D"font-family:courier, monaco, monospace, sans-serif;"><s=
pan style=3D"font-family:courier, monaco, monospace,<br>
=A0sans-serif;">..........Sebastian Kozuch...........</span>&=
lt;br style=3D"font-family:courier, monaco, monospace, sans-serif;&quo=
t;><span style=3D"font-family:courier, monaco, monospace, sans-s=
erif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br sty=
le=3D"font-family:courier, monaco, monospace, sans-serif;"><=
;span style=3D"font-family:courier, monaco, monospace, sans-serif;&quo=
t;>....Weizmann Institute of Science....</span><br style=3D&quo=
t;font-family:courier, monaco, monospace, sans-serif;"><span sty=
le=3D"font-family:courier, monaco, monospace, sans-serif;">...=
........</span><span style=3D"font-family:courier, monaco, mo=
nospace, sans-serif;">Rehovot, Israel...........</span><br=
style=3D"font-family:courier, monaco, monospace, sans-serif;">=
;<span style=3D"font-family:courier, monaco, monospace, sans-serif;=
">.. sebastian.kozuch^<a href=3D"http://weizmann.ac.il" target=3D"_=
blank">weizmann.ac.il</a> ..</span><br style=3D"font-family:c=
ourier, monaco, monospace, sans-serif;"><a rel=3D"nofollow&=
quot; target=3D"_blank"<br>
=A0href=3D"<a href=3D"http://yfaat.ch.huji.ac.il/kozuch.htm" target=3D=
"_blank">http://yfaat.ch.huji.ac.il/kozuch.htm</a>"><span style=
=3D"font-family:courier, monaco, monospace, sans-serif;"><a hr=
ef=3D"http://yfaat.ch.huji.ac.il/kozuch.htm" target=3D"_blank">http://yfaat=
.ch.huji.ac.il/kozuch.htm</a></span></a><br style=3D"fo=
nt-family:courier, monaco, monospace, sans-serif;"><span style=
=3D"font-family:courier, monaco, monospace, sans-serif;">xxxxx=
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><div><br></div&=
gt;<div style=3D"font-family:arial, helvetica, sans-serif;font-size=
:10pt"><br><div style=3D"font-family:arial, helvetica=
, sans-serif;font-size:10pt"><font face=3D"Tahoma" siz=
e=3D"2"><hr size=3D"1"><b><span style=
=3D"font-weight: bold;">From:</span></b> Guntram S=
chmidt guntram.schmidt]=3D[<a href=3D"http://chemie.uni-halle.de" target=3D=
"_blank">chemie.uni-halle.de</a> &lt;owner-chemistry^<a href=3D"http://=
ccl.net" target=3D"_blank">ccl.net</a>&gt;<br><b><span s=
tyle=3D"font-weight: bold;">To:</span></b> "K=
ozuch, Sebastian " &lt;kozuchs^<a href=3D"http://yahoo.com" target=
=3D"_blank">yahoo.com</a>&gt;<br><b><span style=3D"=
font-weight: bold;">Sent:</span></b> Tue, May 10, 2011 =
10:45:00 PM<br><b><span style=3D"font-weight: bold;&quo=
t;>Subject:</span></b> CCL:G: van-der-Waals-complex vs. weak=
<br>
=A0forces<br></font><br><br>Sent to CCL by: "G=
untram&nbsp; Schmidt" [guntram.schmidt(-)<a href=3D"http://chemie.=
uni-halle.de" target=3D"_blank">chemie.uni-halle.de</a>]<br>Hello tog=
ether!<br><br>I want to exam some (mainly organic) crystal stru=
ctures, which seem to be mainly held together by weak forces like Phenyl-H-=
--O hydrogen bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking.<=
br><br>I cut out the corresponding dimers of the crystal structure=
and subjected them to geometry optimisation, using gaussian 09 with the in=
put line<br><br>#T opt freq b97d/6-31g(d,p)/auto=3Dall<br>=
;<br>which works quite well, resulting in minima for expected bonding=
, but striding away molecules for dimers which are not supposed to interact=
in a "bonding" way.<br><br>Now having some optimized=
structures, is there anything to do to prove the nature of the "bondi=
ng"?<br>How can I distinguish the "van-der-Waals complex&qu=
ot; from a dispersion interaction or some kind of hydrogen bonding?<br&g=
t;<br><br>Thanks a lot for suggestions on how to treat<br>
=A0this problem,<br>Guntram<br><br><br><br<br=
<br<br<br><br>E-mail to subscribers: <a ymailto=3D&quo=
t;mailto:<a href=3D"mailto:CHEMISTRY">CHEMISTRY</a>^<a href=3D"http://ccl.n=
et" target=3D"_blank">ccl.net</a>" href=3D"mailto:<a href=3D"mail=
to:CHEMISTRY">CHEMISTRY</a>^<a href=3D"http://ccl.net" target=3D"_blank">cc=
l.net</a>">CHEMISTRY^<a href=3D"http://ccl.net" target=3D"_blank">c=
cl.net</a></a> or use:<br>&nbsp; &nbsp; &nbsp; <=
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QUEST^<a href=3D"http://ccl.net" target=3D"_blank">ccl.net</a></a> or=
use<br>&nbsp; &nbsp; &nbsp; <a href=3D"<a href=
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t=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a></a>&=
lt;br><br<br>&nbsp; &nbsp; &nbsp; <a<br>
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b.shtml" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a>=
</a><br><br>Before posting, check wait time at: <a hre=
f=3D"<a href=3D"http://www.ccl.net" target=3D"_blank">http://www.ccl.n=
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t;/div><br>
<br>
<br>
<br>
</div></body></html></blockquote></div><br><br clear=3D"a=
ll"><br>-- <br>------------------------------------------------------<br>Sh=
ahar Keinan<br>(919) 357 5319<br>
</div></div></div>
--000e0cd3282eb5db9804a3002dec--
From owner-chemistry@ccl.net Wed May 11 20:51:01 2011
From: "arslan ali arslanali1986{:}gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: which basis set
Message-Id: <-44617-110510100622-31165-B/UIWzXOEFksnrWAQDCWgw-x-server.ccl.net>
X-Original-From: arslan ali <arslanali1986|-|gmail.com>
Content-Type: multipart/alternative; boundary=0016e6dcd27d75d3a404a2ec757b
Date: Tue, 10 May 2011 07:06:13 -0700
MIME-Version: 1.0
Sent to CCL by: arslan ali [arslanali1986]-[gmail.com]
--0016e6dcd27d75d3a404a2ec757b
Content-Type: text/plain; charset=ISO-8859-1
hi,
can anybody please tell me, which basis set in DFT will be more appropriate
for geometry optimization of molecules of aprox 500 amu containing CHNO
elements only??
thanks in advance
Arslan
--0016e6dcd27d75d3a404a2ec757b
Content-Type: text/html; charset=ISO-8859-1
hi,<br><br>can anybody please tell me, which basis set in DFT will be more appropriate for geometry optimization of molecules of aprox 500 amu containing CHNO elements only??<br><br>thanks in advance<br><br>Arslan<br>
--0016e6dcd27d75d3a404a2ec757b--