From owner-chemistry@ccl.net Thu Dec 19 10:00:00 2013 From: "Kai Leonhard kai.leonhard~!~ltt.rwth-aachen.de" To: CCL Subject: CCL: AW: BSSE in transition states Message-Id: <-49460-131219053810-24727-yrRxjbvJtcRwTJeHponNoQ,,server.ccl.net> X-Original-From: Kai Leonhard Content-Language: de-DE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 19 Dec 2013 10:37:58 +0000 MIME-Version: 1.0 Sent to CCL by: Kai Leonhard [kai.leonhard-,-ltt.rwth-aachen.de] Dear all, The application of CPC to TSs seems to be quite controversial to me. There are other Papers that claim that applying the CPC to TSs is better than not doing so (or even the only acceptable way). E.g. Kobko and Dannenberg claim that 'Clearly, CP-corrected surfaces lead to noticeable improvements in the geometrically optimized TSs obtained with relatively small basis sets. The geometries and associated activation energies become closer to those obtained with larger basis sets. The CP corrections to these parameters tend to diminish as the basis sets are improved. These observations may be contrasted with the earlier suggestion by Lendvay and Mayer that CP correction is inappropriate for the optimizations of TSs.[18] They quite correctly noted that certain choices for the fragments used in the CP correction calculation would be inappropriate. In particular, they criticized two applications of CP to TSs.[21] For example, had we used two fragments (CH4 and CH3*) for the methane/methyl H-transfer reaction, we would have obtained an inappropriate, unsymmetrical TS. However, a flexible choice of the fragments will usually allow reasonable CP calculations of the TS, at least for cases where all fragments are neutral. Nevertheless, the seemingly arbitrary nature of the fragment choices bear some detailed discussion.' My impression is that maybe Lendvay and Mayer wrote their paper mainly to motivate their CHA method because they state that CPC is not perfect and that a better method is desirable. This is true, but applying CPC seems better to me than completely ignoring BSSE. More recently, it was discussed by Richard et al. that intramolecular BSSE is even relevant for stable molecules. They suggest a 3:1 weighted average of CPC and non-cpc results as best energy estimates (for cluster interactions, though). My question is now whether the debate can be considered resolved now or it is still an ongoing discussion. Any thoughts or experiences on CPC for TSs are highly appreciated. Best regards, Kai Prof. Dr. Kai Leonhard Juniorprofessor for Model-Based Fuel Design Room 215 Schinkelstraße 8 D-52056 Aachen Phone: +49 (0)241 80 - 98174 Fax: +49 (0)241 80 - 92255 E-Mail: kai.leonhard|-|ltt.rwth-aachen.de Kobko, N. & Dannenberg, J. J. Effect of basis set superposition error (BSSE) upon ab initio calculations of organic transition states J. Phys. Chem. A, {2001}, {105}, {1944-1950} Richard, R. M.; Lao, K. U. & Herbert, J. M. Approaching the Complete-Basis Limit with a Truncated Many-Body Expansion J. Chem. Phys., 2013, 139, 224102 -----Ursprüngliche Nachricht----- Von: owner-chemistry+leonhard==ltt.rwth-aachen.de|-|ccl.net [mailto:owner-chemistry+leonhard==ltt.rwth-aachen.de|-|ccl.net] Im Auftrag von Florent LOUIS florent.louis(-)univ-lille1.fr Gesendet: Mittwoch, 11. Dezember 2013 18:11 An: Kai Leonhard Betreff: CCL: BSSE in transition states Sent to CCL by: "Florent LOUIS" [florent.louis~~univ-lille1.fr] Dear John, The BSSE correction with the counterpoise method is applicable to weakly interacting molecular complexes but not to TS, where it can lead to discontinuous potential surfaces (see paper from Lendvay and Mayer, Some Difficulties in Computing BSSE Corrected Potential Surfaces of Chemical Reactions. Chem. Phys. Lett.1998, 297 (56), 365373) Therefore, the CP correction can be just viewed as an estimate of the error bars for reaction barriers. Best regards, Florent > "John Simmie john.simmie]_[nuigalway.ie" wrote: > > Sent to CCL by: "John Simmie" [john.simmie .. nuigalway.ie] I have > recently seen quite large BSSE corrections of ca 20 kJ/mol claimed for > a TS (C, H, O only) for coupled cluster calculations with basis set > aug-cc-pVDZ for zero-point corrected electronic energy barriers of ca > 90 kJ/mol The correction decreases to ca 10 kJ/mol with aug-cc-pVTZ > > is this well-known and/or documented somewhere please? > > John M. Simmie//NUI Galway//Irelandhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Dec 19 10:35:00 2013 From: "Manali Joshi manalijoshi###unipune.ac.in" To: CCL Subject: CCL: Purchasing chemicals Message-Id: <-49461-131219045725-22908-1fx+URo898bPntoSSJugRA]=[server.ccl.net> X-Original-From: "Manali Joshi" Date: Thu, 19 Dec 2013 04:57:24 -0500 Sent to CCL by: "Manali Joshi" [manalijoshi _ unipune.ac.in] Dear all, I am interested in purchasing a set of chemicals and came across Molport which seemed to be an excellent resource for the same. Are there any other parallel resources that work in the same way ? Thanks in advance for your answers! -Manali Joshi From owner-chemistry@ccl.net Thu Dec 19 12:53:00 2013 From: "benchouk wafaa wafaab2/a\yahoo.fr" To: CCL Subject: CCL: NBO and AIM analysis Message-Id: <-49462-131219125047-17113-qaeKozl9AY4FkotT/B5GBQ[]server.ccl.net> X-Original-From: "benchouk wafaa" Date: Thu, 19 Dec 2013 12:50:46 -0500 Sent to CCL by: "benchouk wafaa" [wafaab2:_:yahoo.fr] Dear CCLers, For each point along the IRC path, the wave function was obtained, can we follow this function by the NBO and AIM analysis. Therefore any help or your suggestions would be appreciated. Dr. W Benchouk ****************************************************************************** Dr. Wafaa BENCHOUK Laboratoire de Thermodynamique Applique et Modlisation Molculaire Universit Abou Bekr Belkaid de Tlemcen, Algrie e-mail: benchouk_wafaa-.-mail.univ-tlemcen.dz ****************************************************************************** From owner-chemistry@ccl.net Thu Dec 19 14:50:00 2013 From: "Thomas Manz thomasamanz:gmail.com" To: CCL Subject: CCL: AW: BSSE in transition states Message-Id: <-49463-131219142348-17699-aigKsOlUX70gWkZ+dkELAQ---server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=bcaec548a6276f523404ede81954 Date: Thu, 19 Dec 2013 12:23:41 -0700 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz{:}gmail.com] --bcaec548a6276f523404ede81954 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable In my experience, the counterpoise correction can sometimes worsen the results. For example, in Figure 2 of Organometallics 27 (2008) 5504-5520, I compared ion pair separation energies of olefin polymerization catalysts at the OLYP/LANL2DZ and OLYP/6-311++G** levels of theory. The 6-311++G** values were 1 (average) +/- 1 (standard deviation) kcal/mol higher than the LANL2DZ values. The counterpoise correction was ~2 kcal/mol for the 6-311++G** basis set and ~5 to 10 kcal/mol for the LANL2DZ basis set. Consequently, including the counterpoise correction would have worsened the results. Tom Manz On Thu, Dec 19, 2013 at 3:37 AM, Kai Leonhard kai.leonhard~!~ ltt.rwth-aachen.de wrote: > > Sent to CCL by: Kai Leonhard [kai.leonhard-,-ltt.rwth-aachen.de] > Dear all, > > The application of CPC to TSs seems to be quite controversial to me. Ther= e > are other Papers that claim > that applying the CPC to TSs is better than not doing so (or even the onl= y > acceptable way). > > E.g. Kobko and Dannenberg claim that > 'Clearly, CP-corrected surfaces lead to noticeable improvements > in the geometrically optimized TSs obtained with > relatively small basis sets. The geometries and associated > activation energies become closer to those obtained with larger > basis sets. The CP corrections to these parameters tend to > diminish as the basis sets are improved. These observations may > be contrasted with the earlier suggestion by Lendvay and Mayer > that CP correction is inappropriate for the optimizations of TSs.[18] > They quite correctly noted that certain choices for the fragments > used in the CP correction calculation would be inappropriate. > In particular, they criticized two applications of CP to TSs.[21] > For example, had we used two fragments (CH4 and CH3*) for > the methane/methyl H-transfer reaction, we would have obtained > an inappropriate, unsymmetrical TS. However, a flexible choice > of the fragments will usually allow reasonable CP calculations > of the TS, at least for cases where all fragments are neutral. > Nevertheless, the seemingly arbitrary nature of the fragment > choices bear some detailed discussion.' > > My impression is that maybe Lendvay and Mayer wrote their paper mainly to > motivate their CHA method because they state that CPC is not perfect and > that > a better method is desirable. This is true, but applying CPC seems better > to me than > completely ignoring BSSE. > > More recently, it was discussed by Richard et al. that intramolecular BSS= E > is even relevant for stable molecules. They suggest a 3:1 weighted averag= e > of > CPC and non-cpc results as best energy estimates (for cluster > interactions, though). > > My question is now whether the debate can be considered resolved now or i= t > is > still an ongoing discussion. Any thoughts or experiences on CPC for TSs > are highly appreciated. > > > Best regards, > > Kai > > > Prof. Dr. Kai Leonhard > > Juniorprofessor for Model-Based Fuel Design > Room 215 > Schinkelstra=DFe 8 > D-52056 Aachen > Phone: +49 (0)241 80 - 98174 > Fax: +49 (0)241 80 - 92255 > E-Mail: kai.leonhard ~ ltt.rwth-aachen.de > > > > > Kobko, N. & Dannenberg, J. J. > Effect of basis set superposition error (BSSE) upon ab initio calculation= s > of organic transition states > J. Phys. Chem. A, {2001}, {105}, {1944-1950} > > Richard, R. M.; Lao, K. U. & Herbert, J. M. > Approaching the Complete-Basis Limit with a Truncated Many-Body Expansion > J. Chem. Phys., 2013, 139, 224102 > > > > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry+leonhard=3D=3Dltt.rwth-aachen.de ~ ccl.net [mailto: > owner-chemistry+leonhard=3D=3Dltt.rwth-aachen.de ~ ccl.net] Im Auftrag vo= n > Florent LOUIS florent.louis(-)univ-lille1.fr > Gesendet: Mittwoch, 11. Dezember 2013 18:11 > An: Kai Leonhard > Betreff: CCL: BSSE in transition states > > > Sent to CCL by: "Florent LOUIS" [florent.louis~~univ-lille1.fr] Dear > John, > > The BSSE correction with the counterpoise method is applicable to weakly > interacting molecular complexes but not to TS, where it can lead to > discontinuous potential surfaces (see paper from Lendvay and Mayer, Some > Difficulties in Computing BSSE Corrected Potential Surfaces of Chemical > Reactions. Chem. Phys. Lett.1998, 297 (56), 365373) Therefore, the CP > correction can be just viewed as an estimate of the error bars for reacti= on > barriers. > > Best regards, > > Florent > > > "John Simmie john.simmie]_[nuigalway.ie" wrote: > > > > Sent to CCL by: "John Simmie" [john.simmie .. nuigalway.ie] I have > > recently seen quite large BSSE corrections of ca 20 kJ/mol claimed for > > a TS (C, H, O only) for coupled cluster calculations with basis set > > aug-cc-pVDZ for zero-point corrected electronic energy barriers of ca > > 90 kJ/mol The correction decreases to ca 10 kJ/mol with aug-cc-pVTZ > > > > is this well-known and/or documented somewhere please? > > > > John M. Simmie//NUI Galway//Irelandhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_= unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --bcaec548a6276f523404ede81954 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
In my experience, the counterpoise correction can sometime= s worsen the results.
For example, in Figure 2 of Organometallics 27 (2= 008) 5504-5520, I compared ion pair separation energies of olefin polymeriz= ation catalysts at the OLYP/LANL2DZ and OLYP/6-311++G** levels of theory. T= he 6-311++G** values were 1 (average) +/- 1 (standard deviation) kcal/mol h= igher than the LANL2DZ values. The counterpoise correction was ~2 kcal/mol = for the 6-311++G** basis set and ~5 to 10 kcal/mol for the LANL2DZ basis se= t. Consequently, including the counterpoise correction would have worsened = the results.

Tom Manz


=
On Thu, Dec 19, 2013 at 3:37 AM, Kai Leonhard ka= i.leonhard~!~ltt.rwth-aachen.de <= span dir=3D"ltr"><owner-chemistry#,#ccl.net> wrote:

Sent to CCL by: Kai Leonhard [kai.leonhard-,-ltt.rwth-aachen.de]
Dear all,

The application of CPC to TSs seems to be quite controversial to me. There = are other Papers that claim
that applying the CPC to TSs is better than not doing so (or even the only = acceptable way).

E.g. Kobko and Dannenberg claim that
'Clearly, CP-corrected surfaces lead to noticeable improvements
in the geometrically optimized TSs obtained with
relatively small basis sets. The geometries and associated
activation energies become closer to those obtained with larger
basis sets. The CP corrections to these parameters tend to
diminish as the basis sets are improved. These observations may
be contrasted with the earlier suggestion by Lendvay and Mayer
that CP correction is inappropriate for the optimizations of TSs.[18]
They quite correctly noted that certain choices for the fragments
used in the CP correction calculation would be inappropriate.
In particular, they criticized two applications of CP to TSs.[21]
For example, had we used two fragments (CH4 and CH3*) for
the methane/methyl H-transfer reaction, we would have obtained
an inappropriate, unsymmetrical TS. However, a flexible choice
of the fragments will usually allow reasonable CP calculations
of the TS, at least for cases where all fragments are neutral.
Nevertheless, the seemingly arbitrary nature of the fragment
choices bear some detailed discussion.'

My impression is that maybe Lendvay and Mayer wrote their paper mainly to motivate their CHA method because they state that CPC is not perfect and th= at
a better method is desirable. This is true, but applying CPC seems better t= o me than
completely ignoring BSSE.

More recently, it was discussed by Richard et al. that intramolecular BSSE<= br> is even relevant for stable molecules. They suggest a 3:1 weighted average = of
CPC and non-cpc results as best energy estimates (for cluster interactions,= though).

My question is now whether the debate can be considered resolved now or it = is
still an ongoing discussion. Any thoughts or experiences on CPC for TSs are= highly appreciated.


Best regards,

Kai


Prof. Dr. Kai Leonhard

Juniorprofessor for Model-Based Fuel Design
Room 215
Schinkelstra=DFe 8
D-52056 Aachen
Phone: =A0+49 (0)241 80 - 98174
Fax: =A0 =A0 =A0 =A0+49 (0)241 80 - 92255
E-Mail: kai.leonhard ~ ltt.rwth-aachen.de




Kobko, N. & Dannenberg, J. J.
Effect of basis set superposition error (BSSE) upon ab initio calculations = of organic transition states
J. Phys. Chem. A, {2001}, {105}, {1944-1950}

Richard, R. M.; Lao, K. U. & Herbert, J. M.
Approaching the Complete-Basis Limit with a Truncated Many-Body Expansion J. Chem. Phys., 2013, 139, 224102



-----Urspr=FCngliche Nachricht-----
Von: owner-chemistry+leonhard=3D=3Dltt.rwth-aachen.de ~ ccl.net [mailto:owner-chemistry+leonhard=3D=3Dltt.rwth-aachen.de ~ ccl.net] Im Auftrag von Florent LOUIS florent.louis(-)univ-lille1.fr
Gesendet: Mittwoch, 11. Dezember 2013 18:11
An: Kai Leonhard
Betreff: CCL: BSSE in transition states


Sent to CCL by: "Florent =A0LOUIS" [florent.louis~~univ-lille1.fr] Dear John,

The BSSE correction with the counterpoise method is applicable to weakly in= teracting molecular complexes but not to TS, where it can lead to discontin= uous potential surfaces (see paper from Lendvay and Mayer, Some Difficultie= s in Computing BSSE Corrected Potential Surfaces of Chemical Reactions. Che= m. Phys. Lett.1998, 297 (56), 365373) Therefore, the CP correction can be j= ust viewed as an estimate of the error bars for reaction barriers.

Best regards,

Florent

> "John Simmie john.simmie]_[nuigalway.ie" =A0wrote:
>
> Sent to CCL by: "John =A0Simmie" [john.simmie .. nuigalway.ie] I have
> recently seen quite large BSSE corrections of ca 20 kJ/mol claimed for=
> a TS (C, H, O only) for coupled cluster calculations with basis set > aug-cc-pVDZ for zero-point corrected electronic energy barriers of ca<= br> > 90 kJ/mol The correction decreases to ca 10 kJ/mol with aug-cc-pVTZ >
> is this well-known and/or documented somewhere please?
>
> John M. Simmie//NUI Galway//Irelandhttp://www.ccl.net/cgi-bin/ccl/s= end_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.n= et/spammers.txt


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--bcaec548a6276f523404ede81954-- From owner-chemistry@ccl.net Thu Dec 19 23:11:00 2013 From: "Elvis Martis elvis_bcp .. elvismartis.in" To: CCL Subject: CCL: Purchasing chemicals Message-Id: <-49464-131219221004-11948-V3CkL/1HyMQaUzGFjmGeMQ::server.ccl.net> X-Original-From: Elvis Martis Content-Type: multipart/alternative; boundary=089e013a1d90f5815d04edee9c87 Date: Fri, 20 Dec 2013 08:39:58 +0530 MIME-Version: 1.0 Sent to CCL by: Elvis Martis [elvis_bcp..::..elvismartis.in] --089e013a1d90f5815d04edee9c87 Content-Type: text/plain; charset=ISO-8859-1 Hello You may try Enamine too. I have purchased from them. For More such suppliers you may visit the website of Zinc database and there is list of suppliers. *Regards* *Elvis A. F. Martis* *Research Fellow* *Prof. Coutinho's Molecular Modeling Group* *Department of Pharmaceutical Chemistry* *Bombay College of Pharmacy* *[University of Mumbai]* *Kalina, Santacruz [E]* *Mumbai 400098* *Personal website: www.elvismartis.in * *Group website: www.profeccoutinho.net.in * Information is not knowledge. -*Albert Einstein* On Thu, Dec 19, 2013 at 3:27 PM, Manali Joshi manalijoshi###unipune.ac.in < owner-chemistry.::.ccl.net> wrote: > > Sent to CCL by: "Manali Joshi" [manalijoshi _ unipune.ac.in] > Dear all, > > I am interested in purchasing a set of chemicals and came across Molport > which > seemed to be an excellent resource for the same. > Are there any other parallel resources that work in the same way ? > > Thanks in advance for your answers! > > -Manali Joshi> > > --089e013a1d90f5815d04edee9c87 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello=A0
You may try Enamine too. I have purchased from them. F= or More such suppliers you may visit the website of Zinc database and there= is list of suppliers.

<= /div>

Regards
Research Fellow
= <= b>Prof. Coutinho's Molecular Modeling Group
Department of Pharmaceutical Chemistry
= Bombay College of Pharmacy
[University of Mumbai]
Kalina, Santacruz [E]
Mumbai 400098
<= font face=3D"georgia, serif">Personal website:=A0www.elvismart= is.in

Information is not knowledge.
-Albert Einstein=



On Thu, Dec 19, 2013 at 3:27 PM, Manali = Joshi manalijoshi###unipune.ac.in <owner-chemistry.::.ccl.net> wrote:

Sent to CCL by: "Manali =A0Joshi" [manalijoshi _ unipune.ac.in]
Dear all,

I am interested in purchasing a set of chemicals and came across Molport wh= ich
seemed to be an excellent resource for the same.
Are there any other parallel resources that work in the same way ?

Thanks in advance for your answers!

-Manali Joshi



-=3D This is automatically added to each message by the mailing script =3D-=
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--089e013a1d90f5815d04edee9c87--