From owner-chemistry@ccl.net Mon May 14 00:57:00 2012 From: "Adam Kubas ad.kubas[#]gmail.com" To: CCL Subject: CCL: RI-MP2 optimization Message-Id: <-46903-120514005314-22504-brHM4v3hqaY3la6FPoigMg()server.ccl.net> X-Original-From: Adam Kubas Content-Type: text/plain; charset=UTF-8 Date: Mon, 14 May 2012 06:53:08 +0200 MIME-Version: 1.0 Sent to CCL by: Adam Kubas [ad.kubas-$-gmail.com] Dear Tymofii, Turbomole has both analytical RI-MP2 energy gradients and optimization with bsse correction. However, it is not free. Best, Adam From owner-chemistry@ccl.net Mon May 14 01:53:00 2012 From: "Michael F. Peintinger mpei::thch.uni-bonn.de" To: CCL Subject: CCL: RI-MP2 optimization Message-Id: <-46904-120514015123-4626-Rvzsb2Isti43yk1KUovmsA%a%server.ccl.net> X-Original-From: "Michael F. Peintinger" Content-Type: multipart/alternative; boundary="----JZRDSQN81HDKC8TU7RVMR88K2TDKKP" Date: Mon, 14 May 2012 07:51:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Michael F. Peintinger" [mpei\a/thch.uni-bonn.de] ------JZRDSQN81HDKC8TU7RVMR88K2TDKKP Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit And it can run geometry optimization. With BSSE correction. -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. "John McKelvey jmmckel+/-gmail.com" wrote: Sent to CCL by: John McKelvey [jmmckel-x-gmail.com] Agreed, ORCA! Is very fast... and free... John McKelvey On Sun, May 13, 2012 at 12:48 PM, Michael F. Peintinger mpei{:}thch.uni-bonn.de wrote: > Am 05/13/2012 04:08 PM, schrieb Tymofii Nikolaienko tim_mail(a)ukr.net: > > Dear CCL users! > > Coulg anyone suggest the software able to perform an RI-MP2 geometry > optimization > applying analytical energy gradients? > Is that software free for academics ? > > Thank you in advance! > > Sincerely > Tymofii Nikolaienko > Taras Shevchenko National University of Kyiv > > > I recommend using ORCA from th group of Prof. Frank Neese. > It is free for academic use and can be obtained here: > > http://www.mpibac.mpg.de/bac/logins/neese/description.php > > The MP2 module is excellent and supports RI and RIJCOSX. > You can also run OO-MP2 and RI-MP2 calculations. > > Cheeers > > Michael > > -- > Dipl. Chem. Michael F. Peintinger > > Mulliken Center for Theoretical Chemistry > University of Bonn, Germany > > Beringstraße 6 > Room Number 2.003 > D-53115 Bonn > > Phone: 0228/73-3834 > E-Mail: mpei,,thch.uni-bonn.de -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel%gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------JZRDSQN81HDKC8TU7RVMR88K2TDKKP Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit And it can run geometry optimization. With BSSE correction.

--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.

"John McKelvey jmmckel+/-gmail.com" <owner-chemistry===ccl.net> wrote:

Sent to CCL by: John McKelvey [jmmckel-x-gmail.com]
Agreed,  ORCA!  Is very fast... and free...

John McKelvey

On Sun, May 13, 2012 at 12:48 PM, Michael F. Peintinger
mpei{:}thch.uni-bonn.de <owner-chemistry%ccl.net> wrote:
> Am 05/13/2012 04:08 PM, schrieb Tymofii Nikolaienko tim_mail(a)ukr.net:
>
> Dear CCL users!
>
> Coulg anyone suggest the software able to perform an RI-MP2 geometry
> optimization
> applying analytical energy gradients?
> Is that software free for academics ?
>
> Thank you in advance!
>
> Sincerely
> Tymofii Nikolaienko
> Taras Shevchenko National University of Kyiv
>
>
> I recommend using ORCA from th group of Prof. Frank Neese.
> It is free for academic use and can be obtained here:
>
> http://www.mpibac.mpg.de/bac/logins/neese/description.php
>
> The MP2 module is excellent and supports RI and RIJCOSX.
> You can also run OO-MP2 and RI-MP2 calculations.
>
> Cheeers
>
> Michael
>
> --
> Dipl. Chem. Michael F. Peintinger
>
> Mulliken Center for Theoretical Chemistry
> University of Bonn, Germany
>
> Beringstraße 6
> Room Number 2.003
> D-53115 Bonn
>
> Phone: 0228/73-3834
> E-Mail: mpei,,thch.uni-bonn.de



-- 
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel%gmail.com




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------JZRDSQN81HDKC8TU7RVMR88K2TDKKP-- From owner-chemistry@ccl.net Mon May 14 02:43:01 2012 From: "Jussi Lehtola jussi.lehtola:_:helsinki.fi" To: CCL Subject: CCL: Symmetry of NMR data Message-Id: <-46905-120514024152-29010-6KbbKG065RsW1lMxhy2UxQ-$-server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 14 May 2012 09:41:39 +0300 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola(0)helsinki.fi] On Sun, 13 May 2012 22:10:11 +0000 "Jürgen Gräfenstein jurgen]|[chem.gu.se" wrote: > Sent to CCL by: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= > [jurgen^-^chem.gu.se] Dear Emmanuel, > > A possible cause are the numerical integrations used in DFT > calculations. The grids for the angular integrations are all oriented > in the same way, and thus, the grids around different > symmetry-equivalent atoms are not symmetry-equivalent to each other. > > As a test, could you redo one of your calculations with HF instead of > B3LYP? HF gives no reliable results for NMR properties but is not > dependent on integration grids. Or, you could turn off the use of symmetry and redo the NMR calculation with B3LYP. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola : helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola : helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Mon May 14 03:18:00 2012 From: "=?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= jurgen{}chalmers.se" To: CCL Subject: CCL:G: Symmetry of NMR data Message-Id: <-46906-120514031205-28612-gK1ftkuwBwW0CU+N/IJaxg++server.ccl.net> X-Original-From: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 14 May 2012 09:11:54 +0200 MIME-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= [jurgen[]chalmers.se] Dear Jussi, That would still leave you with different shielding values for the various symmetry-equivalent nuclei. What you would need is a set of grids around those nuclei that reflect the molecular symmetry. Unfortunately, this is in general impossible to accomplish with the Lebedev grids used in Gaussian (and other packages). You would have to construct symmetry-adapted grids for that. Best, Jürgen On May 14, 2012, at 8:41 AM, Jussi Lehtola jussi.lehtola:_:helsinki.fi wrote: > > Sent to CCL by: Jussi Lehtola [jussi.lehtola(0)helsinki.fi] > On Sun, 13 May 2012 22:10:11 +0000 > "Jürgen Gräfenstein jurgen]|[chem.gu.se" > wrote: >> Sent to CCL by: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= >> [jurgen^-^chem.gu.se] Dear Emmanuel, >> >> A possible cause are the numerical integrations used in DFT >> calculations. The grids for the angular integrations are all oriented >> in the same way, and thus, the grids around different >> symmetry-equivalent atoms are not symmetry-equivalent to each other. >> >> As a test, could you redo one of your calculations with HF instead of >> B3LYP? HF gives no reliable results for NMR properties but is not >> dependent on integration grids. > > Or, you could turn off the use of symmetry and redo the NMR > calculation with B3LYP. > -- From owner-chemistry@ccl.net Mon May 14 05:53:00 2012 From: "Uwe Huniar huniar::cosmologic.de" To: CCL Subject: CCL:G: Symmetry of NMR data Message-Id: <-46907-120514054354-25052-ulm9QKr0DAmt/onxWVyslQ:-:server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 14 May 2012 11:43:44 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [huniar]=[cosmologic.de] Hello, > What you would need is a set of > grids around those nuclei that reflect the molecular symmetry. > Unfortunately, this is in general impossible to accomplish with the > Lebedev grids used in Gaussian (and other packages). unless you rotate the Lebedev grid such that it (better) matches the symmetry axes, see: 'Efficient molecular numerical integration schemes', Oliver Treutler and Reinhart Ahlrichs, J. Chem. Phys. 102, 346 (1995) http://link.aip.org/link/doi/10.1063/1.469408 and the references therein. > You would have > to construct symmetry-adapted grids for that. right. This is implemented e.g. in Turbomole as you can judge from the authors of the paper mentioned above... Regards, Uwe > > On May 14, 2012, at 8:41 AM, Jussi Lehtola > jussi.lehtola:_:helsinki.fi wrote: > >> >> Sent to CCL by: Jussi Lehtola [jussi.lehtola(0)helsinki.fi] On Sun, >> 13 May 2012 22:10:11 +0000 "Jürgen Gräfenstein >> jurgen]|[chem.gu.se" wrote: >>> Sent to CCL by: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= >>> [jurgen^-^chem.gu.se] Dear Emmanuel, >>> >>> A possible cause are the numerical integrations used in DFT >>> calculations. The grids for the angular integrations are all >>> oriented in the same way, and thus, the grids around different >>> symmetry-equivalent atoms are not symmetry-equivalent to each >>> other. >>> >>> As a test, could you redo one of your calculations with HF >>> instead of B3LYP? HF gives no reliable results for NMR properties >>> but is not dependent on integration grids. >> >> Or, you could turn off the use of symmetry and redo the NMR >> calculation with B3LYP. -- > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the _ sign. You can > alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-363665 fax +49-2171-731689 e-mail huniar _ cosmologic.de turbomole _ cosmologic.de info _ turbomole.com web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013 From owner-chemistry@ccl.net Mon May 14 07:21:00 2012 From: "=?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= jurgen,+,chalmers.se" To: CCL Subject: CCL:G: Symmetry of NMR data Message-Id: <-46908-120514071955-28203-6luLcmXK8k2VadO2OsR0oQ[-]server.ccl.net> X-Original-From: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 14 May 2012 13:19:45 +0200 MIME-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= [jurgen[#]chalmers.se] Dear Uwe, >> Unfortunately, this is in general impossible to accomplish with the >> Lebedev grids used in Gaussian (and other packages). > > unless you rotate the Lebedev grid such that it (better) matches the symmetry axes, see: > > 'Efficient molecular numerical integration schemes', Oliver Treutler and Reinhart Ahlrichs, J. Chem. Phys. 102, 346 (1995) > http://link.aip.org/link/doi/10.1063/1.469408 > > and the references therein. You are right. The Lebedev grids are O_h symmetric and can be rotated to fit the most common point groups (with the exception of fivefold and higher rotation axes). In the present case (D_3) they could thus be rotated in a proper way (not implemented in Gaussian, though, as far as I know). Regards, Jürgen From owner-chemistry@ccl.net Mon May 14 09:04:00 2012 From: "Joop van Lenthe j.h.vanlenthe**uu.nl" To: CCL Subject: CCL: IR Spectra (Frequency Calculation) Message-Id: <-46909-120514043936-31223-P3pW5FHh/kt/o+GtubpMsA%a%server.ccl.net> X-Original-From: Joop van Lenthe Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 14 May 2012 10:39:24 +0200 MIME-Version: 1.0 (Apple Message framework v1278) Sent to CCL by: Joop van Lenthe [j.h.vanlenthe^_^uu.nl] We had a paper on this . P.D. Todorov, L.W. Jenneskens, and J.H. van Lenthe, Assignment of phantom bands in the solid-state infrared and Raman spectra of coronene: The importance of a minute out-of-plane distortion. J. Chem. Phys., 132(3) 034504/1-034504/9 (2010). (PDF) ============================== Joop van Lenthe Theoretical Chemistry Group Utrecht Condensed matter and Interfaces Ornstein Laboratory, k108 tel. -31-30-2532733 joop*o*chem.uu.nl http://tc5.chem.uu.nl/joop/ =============================== On 12/05/2012, at 5:50 PM, John McKelvey jmmckel%%gmail.com wrote: > > Sent to CCL by: John McKelvey [jmmckel*gmail.com] > Thought... > > Without external constraints surely a molecule will still vibrate > freely on going from State A to State B. How, then, does one > characterize the vibrations along the path from State A to State B? I > think the original question is still worth answering if possible. > > I once had to deal with a similar type conundrum related to how > structural changes would affect the dipole moments of charged > systems... > > John McKelvey > > On Fri, May 11, 2012 at 6:05 AM, Dillen, Jan jlmda/sun.ac.za > JLMDa/sun.ac.za wrote: >> >> Sent to CCL by: "Dillen, Jan [jlmd:-:sun.ac.za]" >> Hi Joe >> >> I may read too much in your question but if you intend to calculate "frequencies" for a conformation that is not a stationary point on your energy surface, the answer is: NO. >> >> Of course you can ask the computer program to do it, but the numbers are not vibrational frequencies because the eigenvalues of a mass-weighted hessian matrix are only related to normal modes (aka frequencies) if the gradient of the energy is zero, e.g. at a energy minimum of maximum. >> >> See the classic, but still relevant book by Wilson, Decius & Cross. >> >> Jan >> >> -----Original Message----- >>> From: owner-chemistry+jlmd==sun.ac.za!=!ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za!=!ccl.net] On Behalf Of Joe Golab joseph.golab .. ineos.com >> Sent: 09 May 2012 17:52 >> To: Dillen, Jan >> Subject: CCL: IR Spectra (Frequency Calculation) >> >> >> Sent to CCL by: "Joe Golab" [joseph.golab(-)ineos.com] CCL Members: >> >> We would like to study the IR spectrum of a molecule as a function of its conformation. >> >> Obviously, a strictly theoretical treatment can only predict one conformer's spectrum, i.e. the lowest energy one. >> >> But what if the environment around a molecule prevented it from existing in its "lowest energy" (geometry optimized) configuration? >> >> We cannot take the environment into account, i.e. use the environment to "force" conformations for the frequency calculation. >> >> So, is it possible to study the IR spectrum of a molecule as a function of its conformation? >> >> Thanks for your consideration. >> >> Joe >> ___________________________ >> Joseph T. Golab, PhD >> Molecular Modeling & Simulation Scientist Senior Research Scientist INEOS Technologies, Nitriles R&D >> Phone: +1 (630) 420-5063 >> Cell: +1 (630) 336-0063 >> Email: Joseph.Golab_at_ineos.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtE-pos vrywaringsklousule >> >> Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige lêers aangeheg by hierdie e-pos nie. >> >> E-mail disclaimer >> >> This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.> >> > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel===gmail.com> > From owner-chemistry@ccl.net Mon May 14 10:22:00 2012 From: "Pedro Sivla pedros^ufp.edu.pt" To: CCL Subject: CCL: Looking for a reference Message-Id: <-46910-120514102111-14239-zCDan1xZbpqy/AMomwo+pA+/-server.ccl.net> X-Original-From: "Pedro Sivla" Date: Mon, 14 May 2012 10:21:06 -0400 Sent to CCL by: "Pedro Sivla" [pedros*o*ufp.edu.pt] Dear CCLers: Some time ago I was looking for papers on DFT studies of platinum/palladium -catalyzed organic reactions. I distinctly remember finding a study (probably in an ACS journal) with the reaction pathway studied with several different functionals, and with a comparison with the MP2 PES. One of the DFT-postulated transition states could not be located in the MP2 PES, and this is the part of the paper that I would really like to read again. Unfortunately, I have since lost track of that paper. I have unsuccessfullly tried everywhere to locate it again (pubs.acs.org, web of sciece, etc,). I just need the reference to it, and I thought I might get lucky: maybe one of the authors is a CCL-subscriber.... Thanks, Pedro From owner-chemistry@ccl.net Mon May 14 11:44:00 2012 From: "SC Chan wileyregister2-x-gmail.com" To: CCL Subject: CCL: Energy Decompostion Analysis for Periodic Boundary Condition Message-Id: <-46911-120514091506-13909-JZV3yXhhXq1GC3vJeEEKiQ_+_server.ccl.net> X-Original-From: "SC Chan" Date: Mon, 14 May 2012 09:15:02 -0400 Sent to CCL by: "SC Chan" [wileyregister2**gmail.com] Dear Colleague Does anybody know any code which can do an Energy Decomposition Analysis when performing a calculation on periodic systems? Precisely, when using GTO codes such as G09/Crystal, can the NBO or AOMIX codes do the post-analysis? Thank you for your answer. SC Chan ==== Graduate Student NTU Taiwan