From owner-chemistry@ccl.net Tue Jul 8 00:58:01 2008 From: "Zheng Xu zjuxuzheng###hotmail.com" To: CCL Subject: CCL: Failure TS opt caused by methyl rotation Message-Id: <-37309-080707221933-24254-gHGqa4PijV0577EZP92P/A ~ server.ccl.net> X-Original-From: "Zheng Xu" Date: Mon, 7 Jul 2008 22:19:29 -0400 Sent to CCL by: "Zheng Xu" [zjuxuzheng|-|hotmail.com] Dear CCLers, I'm trying to get the TS of dimethylsilylene (Me2Si) insertion into Si-Cl bond of SiH2FCl. I have tried many times with different opt keywords(gdiis,tight or verytight ), howerver alll attempt was a failure. From the plot of "total energy" vs. "optimization step number", an unregular energy perturbation aroused by the rotation of two methyl groups was detected. Howerver, when ths substrate was changed from SiH2FCl to SiH3Cl, a right TS can be obtained. Why? What should I do, is there anyone have good suggestion? --------------------------------------------------------------------------- #p rb3lyp/6-31++g(d,p) opt(calcfc,ts,noeigen,gdiis) freq pop(regular,nbo) test --------------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 8 05:23:01 2008 From: "Tommaso Marcelli marcelli(!)theochem.kth.se" To: CCL Subject: CCL: Failure TS opt caused by methyl rotation Message-Id: <-37310-080708052118-17475-CJaga5izG+EO1pUOXvtSPQ{}server.ccl.net> X-Original-From: "Tommaso Marcelli" Date: Tue, 8 Jul 2008 05:21:14 -0400 Sent to CCL by: "Tommaso Marcelli" [marcelli]|[theochem.kth.se] what about trying with a smaller stepsize (maxstep)? sometimes that helps... > "Zheng Xu zjuxuzheng###hotmail.com" wrote: > > Sent to CCL by: "Zheng Xu" [zjuxuzheng|-|hotmail.com] > Dear CCLers, > > I'm trying to get the TS of dimethylsilylene (Me2Si) insertion into Si-Cl bond of SiH2FCl. > > I have tried many times with different opt keywords(gdiis,tight or verytight ), howerver alll attempt was a failure. From the plot of "total energy" vs. "optimization step number", an unregular energy perturbation aroused by the rotation of two methyl groups was detected. > > Howerver, when ths substrate was changed from SiH2FCl to SiH3Cl, a right TS can be obtained. > Why? What should I do, is there anyone have good suggestion? > > --------------------------------------------------------------------------- > #p rb3lyp/6-31++g(d,p) opt(calcfc,ts,noeigen,gdiis) freq pop(regular,nbo) test > --------------------------------------------------------------------------- > > From owner-chemistry@ccl.net Tue Jul 8 09:15:00 2008 From: "Thiago Correra tcorrera##iq.usp.br" To: CCL Subject: CCL: Sulfur basis set Message-Id: <-37311-080708080832-18265-fM5E82kmxzNyHkwU2PAOww a server.ccl.net> X-Original-From: "Thiago Correra" Date: Tue, 8 Jul 2008 08:08:28 -0400 Sent to CCL by: "Thiago Correra" [tcorrera(-)iq.usp.br] Dear CCL subscribers, I'm wondering if there's not some review or any other information about sulfur basis set. I want to model conformational transition states for C=S bond containing heterocyclic compounds, and I don't know if the 6-311+G(d,p) is a good choice. There are about 40 atoms in those compounds, and 5 of them are heavy, like sulfur and clorine, so please, be gentle. Thanks in advance, Thiago Correra - tcorrera*o*iq.usp.br Instituto de Qumica, Universidade de So Paulo - Brasil. From owner-chemistry@ccl.net Tue Jul 8 10:10:00 2008 From: "Raj S r.subramanian**ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: why processors are reduced?? Message-Id: <-37312-080708100546-18270-OuMcYGARiJ2Q5zBbaq6h5w#,#server.ccl.net> X-Original-From: "Raj S" Date: Tue, 8 Jul 2008 10:05:42 -0400 Sent to CCL by: "Raj S" [r.subramanian-x-ipc.uni-stuttgart.de] Dear CCL members, Whenever i try to calculate (using G03) normal/fundamental frequencies i get the following message somewhere in the middle of the output file:- Number of processors reduced to 2 by ecpmxn. But i used %nproc=4. I dont know why it is reduced....sometimes it is reduced to 1. Many of my calculation this is happening...Does any one have some idea about this...Or is it possible to avoid this processor reduction??? Or will this affect calculation time, etc... thanks for your reply raj s. From owner-chemistry@ccl.net Tue Jul 8 10:45:01 2008 From: "Alessandro Contini alessandro.contini*unimi.it" To: CCL Subject: CCL: Sulfur basis set Message-Id: <-37313-080708101636-25092-9H+ZykMBpG7DtUHWWywTuw.:.server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7bit Content-type: text/plain Date: Tue, 08 Jul 2008 16:16:23 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini\a/unimi.it] Hi Thiago, check "[2+4] and [4+2] Cycloadditions of o-Thioquinones with 1,3-dienes: a Computational Study", A. Contini, S. Leone, S. Menichetti, C. Viglianisi, P. Trimarco, J. Org. Chem. 2006, 71(15), 5507-5514. hope this help Alessandro Il giorno mar, 08/07/2008 alle 08.08 -0400, Thiago Correra tcorrera##iq.usp.br ha scritto: > Sent to CCL by: "Thiago Correra" [tcorrera(-)iq.usp.br] > Dear CCL subscribers, > > I'm wondering if there's not some review or any other information about sulfur basis set. > I want to model conformational transition states for C=S bond containing heterocyclic compounds, and I don't know if the 6-311+G(d,p) is a good choice. > There are about 40 atoms in those compounds, and 5 of them are heavy, like sulfur and clorine, so please, be gentle. > Thanks in advance, > > Thiago Correra - tcorrera#iq.usp.br > Instituto de Qumica, Universidade de So Paulo - Brasil.> > -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini!A!unimi.it skype alessandrocontini From owner-chemistry@ccl.net Tue Jul 8 11:19:00 2008 From: "Ol Ga eurisco1-.-pochta.ru" To: CCL Subject: CCL: Failure TS opt caused by methyl rotation Message-Id: <-37314-080708104454-7316-pim2JxRVHdT+yVuwgui01g[a]server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 8 Jul 2008 10:44:50 -0400 Sent to CCL by: "Ol Ga" [eurisco1 .. pochta.ru] Dear Zheng Xu ! I intend that correct route sections are Step 1. #p ub3lyp/6-31++g(d,p) pOpt(qst2,noeigen,ModRedun) # scf(xqc,vshift,tight,Maxcycle=512) and freeze some (possible all) H-atoms to forbid rotation CH3-groups. You need to find out numbers of H-atoms in Z-mat and type in the job file number_H-atom_1 F number_H-atom_2 F ................ Step 2. #p ub3lyp/6-31++g(d,p) opt(calcall,ts,noeigen,gdiis,tight) guess=always # scf(xqc,tight,Maxcycle=512) Possible a lot of trials is necessary to achieve a saddle point if it exists on the level of theory Sincerely Ol Ga ----- Original Message ----- > From: "Zheng Xu zjuxuzheng###hotmail.com" To: "Ga, Ol " Sent: Tuesday, July 08, 2008 6:19 AM Subject: CCL: Failure TS opt caused by methyl rotation > > > Sent to CCL by: "Zheng Xu" [zjuxuzheng|-|hotmail.com] > Dear CCLers, > > I'm trying to get the TS of dimethylsilylene (Me2Si) insertion into Si-Cl bond of SiH2FCl. > > I have tried many times with different opt keywords(gdiis,tight or verytight ), howerver alll attempt was a failure. From the plot of "total energy" vs. "optimization step number", an unregular energy perturbation aroused by the rotation of two methyl groups was detected. > > Howerver, when ths substrate was changed from SiH2FCl to SiH3Cl, a right TS can be obtained. > Why? What should I do, is there anyone have good suggestion? > > --------------------------------------------------------------------------- > #p rb3lyp/6-31++g(d,p) opt(calcfc,ts,noeigen,gdiis) freq pop(regular,nbo) test > --------------------------------------------------------------------------- > From owner-chemistry@ccl.net Tue Jul 8 11:55:01 2008 From: "Ol Ga eurisco1],[pochta.ru" To: CCL Subject: CCL:G: why processors are reduced?? Message-Id: <-37315-080708110921-27441-633auaaipBnBAot/a/kbMg.@.server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 8 Jul 2008 11:09:18 -0400 Sent to CCL by: "Ol Ga" [eurisco1#%#pochta.ru] Dear Raj S! I intend that You should type in the job file keyword NoSymm and set %Mem so high as it is possible. Best results in G03 parallelisation are on %Nproc=2. Sincerely Ol Ga > > Sent to CCL by: "Raj S" [r.subramanian-x-ipc.uni-stuttgart.de] > Dear CCL members, > Whenever i try to calculate (using G03) normal/fundamental frequencies i get the following message somewhere in the middle of the output file:- > > Number of processors reduced to 2 by ecpmxn. > > But i used %nproc=4. I dont know why it is reduced....sometimes it is reduced to 1. Many of my calculation this is happening...Does any one have some idea about this...Or is it possible to avoid this processor reduction??? Or will this affect calculation time, etc... > > thanks for your reply > raj s. From owner-chemistry@ccl.net Tue Jul 8 12:53:01 2008 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas{}chem.elte.hu" To: CCL Subject: CCL:G: why processors are reduced?? Message-Id: <-37316-080708120356-3618-UNx87URgxW7cVfCZQnK2iA,,server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 08 Jul 2008 18:03:14 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas~!~chem.elte.hu] Hi Raj, Give more memory to the job. Also, read the manual: http://www.gaussian.com/g_ur/m_eff.htm Best wishes, Ödön On Tue, 2008-07-08 at 10:05 -0400, Raj S r.subramanian**ipc.uni-stuttgart.de wrote: > Sent to CCL by: "Raj S" [r.subramanian-x-ipc.uni-stuttgart.de] > Dear CCL members, > Whenever i try to calculate (using G03) normal/fundamental frequencies i get the following message somewhere in the middle of the output file:- > > Number of processors reduced to 2 by ecpmxn. > > But i used %nproc=4. I dont know why it is reduced....sometimes it is reduced to 1. Many of my calculation this is happening...Does any one have some idea about this...Or is it possible to avoid this processor reduction??? Or will this affect calculation time, etc... > > thanks for your reply > raj s.> > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Tue Jul 8 15:23:00 2008 From: "ysubboti..ucalgary.ca" To: CCL Subject: CCL: Sulfur basis set Message-Id: <-37317-080708144656-18770-g1+awv9xGYHVSQVScouMSA::server.ccl.net> X-Original-From: ysubboti:-:ucalgary.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 8 Jul 2008 11:54:41 -0600 (MDT) MIME-Version: 1.0 Sent to CCL by: ysubboti|,|ucalgary.ca Hello Thiago, I have faced this problem too sometime ago. But in my case I also had to analyze the density. And I still don't know a correct answer on the question what basis set is better to calculate sulphur containing compounds. I have found one paper about sulphur basis sets with some comparison. But this paper is very old (1982), so basis sets are simple. The highest level was 6-31G*: Ab initio calculations on sulfur-containing compounds. I. Uniform quality basis sets for sulfur: Total energies and geometries of H2S R. A. Poirier , R. Daudel , P. G. Mezey , I. G. Csizmadia http://www3.interscience.wiley.com/journal/109575791/abstract International Journal of Quantum Chemistry Volume 21, Issue 5 , Pages 799 - 811 And do you mind to post the final summary with all feedbacks you receive for this topic? I will appreciate it. My best, Julia Subbotina, PhD University of Calgary > > Sent to CCL by: "Thiago Correra" [tcorrera(-)iq.usp.br] > Dear CCL subscribers, > > I'm wondering if there's not some review or any other information about > sulfur basis set. > I want to model conformational transition states for C=S bond containing > heterocyclic compounds, and I don't know if the 6-311+G(d,p) is a good > choice. > There are about 40 atoms in those compounds, and 5 of them are heavy, like > sulfur and clorine, so please, be gentle. > Thanks in advance, > > Thiago Correra - tcorrera#iq.usp.br > Instituto de Qumica, Universidade de So Paulo - Brasil.> > > > From owner-chemistry@ccl.net Tue Jul 8 16:37:00 2008 From: "Alcides Simao alsimao.],[.gmail.com" To: CCL Subject: CCL: Sulfur basis set Message-Id: <-37318-080708163346-24727-lKNveFt+aXAj3qX5meW6pA],[server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_10272_18304532.1215549213756" Date: Tue, 8 Jul 2008 21:33:33 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao.!=!.gmail.com] ------=_Part_10272_18304532.1215549213756 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello! Just my 2 cents... https://bse.pnl.gov/bse/portal This site allows you to find suitable basis set for *any* element. See if it helps! See how to use it :) It is neatly done and quite helpful! GreetZ from Lusa Athens! Alcides ------=_Part_10272_18304532.1215549213756 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello!

Just my 2 cents...
 
https://bse.pnl.gov/bse/portal

This site allows you to find suitable basis set for *any* element. See if it helps! See how to use it :) It is neatly done and quite helpful!

GreetZ from Lusa Athens!
 
Alcides
 

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