From owner-chemistry@ccl.net Thu Sep 22 11:08:00 2011 From: "Arindam Ganguly arindamganguly-x-gmail.com" To: CCL Subject: CCL: IR/Raman Spectra of Minerals Message-Id: <-45492-110922110602-23715-1czBJ5ogQFgt1YxB1h67fQ]_[server.ccl.net> X-Original-From: "Arindam Ganguly" Date: Thu, 22 Sep 2011 11:05:58 -0400 Sent to CCL by: "Arindam Ganguly" [arindamganguly|a|gmail.com] Deal CCL Users, Good morning and hope this messages reaches you all well. Is anyone aware of a computaional tool to predict the IR/Raman spectra of Minerals. I came across the following Caltech Database on Minerals http://rruff.info/ was looking for tools to predict the IR/Raman Spectra. Thank you. Sincerely, Arindam From owner-chemistry@ccl.net Thu Sep 22 11:42:00 2011 From: "Sam Abrash sabrash]_[richmond.edu" To: CCL Subject: CCL: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45493-110922112540-27673-9hPHMW+QA8/i/01J/WeMKw^_^server.ccl.net> X-Original-From: "Sam Abrash" Date: Thu, 22 Sep 2011 11:25:36 -0400 Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] Hi Folks, I have a job involving hydrogen bonding of 3 acetylenes to the benzene cation. I'm having trouble with the geometric convergence. I was able to get the system to converge with normal convergence criteria, opt=calcall, and MaxStep=5, but then I got an imaginary frequency of -1.9 wavenumbers. Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and have steadily reduced MaxStep to 1, but it still won't converge. The force constant criteria have been met, but the problem is the displacement criteria. Both this observation and looking at the structures with JMOL show that the problem is finding the minimum in a very shallow potential. Two questions. First, is the 1.9 wavenumber imaginary frequency real or an artifact? Second, any advice on how to force the system to converge? Model chemistry is M062X/6-311++G**. Thanks! Sam From owner-chemistry@ccl.net Thu Sep 22 12:56:00 2011 From: "Jim Kress ccl_nospam:kressworks.com" To: CCL Subject: CCL: IR/Raman Spectra of Minerals Message-Id: <-45494-110922113900-7590-0doRIZALcrdAlcOSKjjT9A+*+server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 22 Sep 2011 11:38:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%x%kressworks.com] I'd use ORCA http://www.thch.uni-bonn.de/tc/orca/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com^^^ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com^^^ccl.net] On Behalf > Of Arindam Ganguly arindamganguly-x-gmail.com > Sent: Thursday, September 22, 2011 11:06 AM > To: Kress, Jim > Subject: CCL: IR/Raman Spectra of Minerals > > > Sent to CCL by: "Arindam Ganguly" [arindamganguly|a|gmail.com] Deal CCL > Users, Good morning and hope this messages reaches you all well. Is anyone > aware of a computaional tool to predict the IR/Raman spectra of Minerals. > > I came across the following Caltech Database on Minerals http://rruff.info/ > was looking for tools to predict the IR/Raman Spectra. Thank you. > > Sincerely, > ArindamTo > recover the email address of the author of the message, please change the > strange characters on the top line to the ^^^ sign. You can also look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Thu Sep 22 13:34:00 2011 From: "Arne Dieckmann adieckma^googlemail.com" To: CCL Subject: CCL:G: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45495-110922132939-5520-DZy7fWpUYZqWZenO6Y27Kg^_^server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Sep 2011 10:29:28 -0700 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: Arne Dieckmann [adieckma . googlemail.com] I would not consider -1.9 wavenumbers an imaginary frequency. Have a look at the Gaussian manual and whitepapers, there is a section about this issue. Cheers, Arne On Sep 22, 2011, at 8:25 AM, Sam Abrash sabrash]_[richmond.edu wrote: > > Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] > Hi Folks, > > I have a job involving hydrogen bonding of 3 acetylenes to the benzene cation. I'm having trouble with the geometric convergence. I was able to get the system to converge with normal convergence criteria, opt=calcall, and MaxStep=5, but then I got an imaginary frequency of -1.9 wavenumbers. > > Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and have steadily reduced MaxStep to 1, but it still won't converge. The force constant criteria have been met, but the problem is the displacement criteria. Both this observation and looking at the structures with JMOL show that the problem is finding the minimum in a very shallow potential. > > Two questions. First, is the 1.9 wavenumber imaginary frequency real or an artifact? Second, any advice on how to force the system to converge? Model chemistry is M062X/6-311++G**. > > Thanks! > Sam> > From owner-chemistry@ccl.net Thu Sep 22 14:08:00 2011 From: "Patrick Bultinck Patrick.Bultinck%ugent.be" To: CCL Subject: CCL: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45496-110922134807-18589-0+JoP4+mMH46tBI8hzVvvw:server.ccl.net> X-Original-From: Patrick Bultinck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Sep 2011 19:47:46 +0200 Mime-Version: 1.0 (iPhone Mail 8L1) Sent to CCL by: Patrick Bultinck [Patrick.Bultinck#,#ugent.be] Just as a minor comment: drop that basis set. It does not render benzene planar for MP2, so I scare to think what it might be up to now. Second, I would get the Hessian from the fchk file, diagonalize that myself, see what that does and then compute the displacement eigenvector for the lowest eigenvalue and displace the geometry for minimal displacements along this vector and repeat the procedure. You could even think of some sort of grid of displacements and see if you could do some sort of line search along that. A near zero eigenvalue means that the energy does not change along that vector. Think of translation/rotation of the molecule as a whole. Check what your vector is like. And maybe it's just a zero direction: you may be looking at nice chemistry! Or some fragment may be so far out that you're seeing free movement. A minimal amount of algebra will tell. Patrick On 22 Sep 2011, at 17:25, "Sam Abrash sabrash]_[richmond.edu" wrote: > > Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] > Hi Folks, > > I have a job involving hydrogen bonding of 3 acetylenes to the benzene cation. I'm having trouble with the geometric convergence. I was able to get the system to converge with normal convergence criteria, opt=calcall, and MaxStep=5, but then I got an imaginary frequency of -1.9 wavenumbers. > > Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and have steadily reduced MaxStep to 1, but it still won't converge. The force constant criteria have been met, but the problem is the displacement criteria. Both this observation and looking at the structures with JMOL show that the problem is finding the minimum in a very shallow potential. > > Two questions. First, is the 1.9 wavenumber imaginary frequency real or an artifact? Second, any advice on how to force the system to converge? Model chemistry is M062X/6-311++G**. > > Thanks! > Sam> > From owner-chemistry@ccl.net Thu Sep 22 17:35:00 2011 From: "George Fitzgerald gfitzgerald,,accelrys.com" To: CCL Subject: CCL: IR/Raman Spectra of Minerals Message-Id: <-45497-110922160256-12163-uUTIwfHHz+mWAaeW8BGycg-#-server.ccl.net> X-Original-From: "George Fitzgerald" Date: Thu, 22 Sep 2011 16:02:53 -0400 Sent to CCL by: "George Fitzgerald" [gfitzgerald]![accelrys.com] Arindam asked about predicting IR & Raman spectra of minerals. MS CASTEP from Accelrys can do this including Raman intensities. Please contact me directly if you'd like more details. George Fitzgerald From owner-chemistry@ccl.net Thu Sep 22 18:12:00 2011 From: "Sten Nilsson Lill stenil-x-chalmers.se" To: CCL Subject: CCL:G: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45498-110922180909-32205-g9sKEnK9uqFRADQRa4d2bg++server.ccl.net> X-Original-From: Sten Nilsson Lill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 23 Sep 2011 00:08:57 +0200 MIME-Version: 1.0 Sent to CCL by: Sten Nilsson Lill [stenil||chalmers.se] Sam, in similar cases I've been able to reach convergence by using the keywords scf=novaracc and opt=(tight,newton). To those opt-keyword you could also add calcfc as you mention. Another aspect of this is the sensitivity of the M06 functionals to the choice of integration grid. It's recommended to use a large grid so if you are using Gaussian you can try Grid=ultrafine. Remember that it will be more costly and that you need to do all your calculations with the same grid settings when comparing energies. You can read more on this in Houk's JCTC paper from 2010: http://pubs.acs.org/doi/abs/10.1021/ct900639j and some references therein, for example some work by DiLabio and Johnson. Hope that helps, Sten Ph.D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg SE-412 96 Gothenburg, Sweden e-mail: stenil|-|chem.gu.se Phone: +46-31 786 9103 Fax: +46-31-772 3840 ________________________________________ > From: owner-chemistry+stenil==chem.gu.se|-|ccl.net [owner-chemistry+stenil==chem.gu.se|-|ccl.net] On Behalf Of Sam Abrash sabrash]_[richmond.edu [owner-chemistry|-|ccl.net] Sent: Thursday, September 22, 2011 5:25 PM To: Nilsson Lill, Sten Subject: CCL: G09: Convergence Issues for H-Bonded Systems Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] Hi Folks, I have a job involving hydrogen bonding of 3 acetylenes to the benzene cation. I'm having trouble with the geometric convergence. I was able to get the system to converge with normal convergence criteria, opt=calcall, and MaxStep=5, but then I got an imaginary frequency of -1.9 wavenumbers. Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and have steadily reduced MaxStep to 1, but it still won't converge. The force constant criteria have been met, but the problem is the displacement criteria. Both this observation and looking at the structures with JMOL show that the problem is finding the minimum in a very shallow potential. Two questions. First, is the 1.9 wavenumber imaginary frequency real or an artifact? Second, any advice on how to force the system to converge? Model chemistry is M062X/6-311++G**. Thanks! Samhttp://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 Sep 22 19:31:01 2011 From: "Bradley Welch bwelch5^^^slu.edu" To: CCL Subject: CCL:G: G09: Convergence Issues for H-Bonded Systems Message-Id: <-45499-110922193004-32757-2hQZ+RF71l3bthYGcDRFJA a server.ccl.net> X-Original-From: Bradley Welch Content-Type: multipart/alternative; boundary=0015176f0a88b22a5c04ad90111b Date: Thu, 22 Sep 2011 18:29:50 -0500 MIME-Version: 1.0 Sent to CCL by: Bradley Welch [bwelch5 a slu.edu] --0015176f0a88b22a5c04ad90111b Content-Type: text/plain; charset=ISO-8859-1 Have you optimized the system at a lower level of theory and have had success? Bradley Welch On Thu, Sep 22, 2011 at 5:08 PM, Sten Nilsson Lill stenil-x-chalmers.se < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: Sten Nilsson Lill [stenil||chalmers.se] > Sam, > > in similar cases I've been able to reach convergence by using the keywords > scf=novaracc and opt=(tight,newton). To those opt-keyword you could also add > calcfc as you mention. > > Another aspect of this is the sensitivity of the M06 functionals to the > choice of integration grid. It's recommended to use a large grid so if you > are using Gaussian you can try Grid=ultrafine. Remember that it will be more > costly and that you need to do all your calculations with the same grid > settings when comparing energies. > > You can read more on this in Houk's JCTC paper from 2010: > http://pubs.acs.org/doi/abs/10.1021/ct900639j and some references therein, > for example some work by DiLabio and Johnson. > > Hope that helps, > > Sten > > Ph.D. Sten Nilsson Lill > Dep. of Chemistry > University of Gothenburg > SE-412 96 Gothenburg, Sweden > e-mail: stenil^-^chem.gu.se > Phone: +46-31 786 9103 > Fax: +46-31-772 3840 > ________________________________________ > > From: owner-chemistry+stenil==chem.gu.se^-^ccl.net[owner-chemistry+stenil== > chem.gu.se^-^ccl.net] On Behalf Of Sam Abrash sabrash]_[richmond.edu[owner-chemistry^-^ > ccl.net] > Sent: Thursday, September 22, 2011 5:25 PM > To: Nilsson Lill, Sten > Subject: CCL: G09: Convergence Issues for H-Bonded Systems > > Sent to CCL by: "Sam Abrash" [sabrash_+_richmond.edu] > Hi Folks, > > I have a job involving hydrogen bonding of 3 acetylenes to the benzene > cation. I'm having trouble with the geometric convergence. I was able to > get the system to converge with normal convergence criteria, opt=calcall, > and MaxStep=5, but then I got an imaginary frequency of -1.9 wavenumbers. > > Subsequently, I changed to Opt=tight, tried both calcfc and calcall, and > have steadily reduced MaxStep to 1, but it still won't converge. The force > constant criteria have been met, but the problem is the displacement > criteria. Both this observation and looking at the structures with JMOL > show that the problem is finding the minimum in a very shallow potential. > > Two questions. First, is the 1.9 wavenumber imaginary frequency real or an > artifact? Second, any advice on how to force the system to converge? Model > chemistry is M062X/6-311++G**. > > Thanks! > Samhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > --0015176f0a88b22a5c04ad90111b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Have you optimized the system at a lower level of theory and have had succe= ss?


Bradley Welch


On Thu,= Sep 22, 2011 at 5:08 PM, Sten Nilsson Lill stenil-x-chalmers.se <owner-chemistry*ccl.net> wrote:

Sent to CCL by: Sten Nilsson Lill [stenil||chalmers.se]
Sam,

in similar cases I've been able to reach convergence by using the keywo= rds scf=3Dnovaracc and opt=3D(tight,newton). To those opt-keyword you could= also add calcfc as you mention.

Another aspect of this is the sensitivity of the M06 functionals to the cho= ice of integration grid. It's recommended to use a large grid so if you= are using Gaussian you can try Grid=3Dultrafine. Remember that it will be = more costly and that you need to do all your calculations with the same gri= d settings when comparing energies.

You can read more on this in Houk's JCTC paper from 2010: http://pubs.= acs.org/doi/abs/10.1021/ct900639j and some references therein, for exam= ple some work by DiLabio and Johnson.

Hope that helps,

Sten

Ph.D. Sten Nilsson Lill
Dep. of Chemistry
University of Gothenburg
SE-412 96 Gothenburg, Sweden
e-mail: stenil^-^chem.gu.se=
Phone: +46-31 = 786 9103
Fax: +46-31-772 = 3840
________________________________________
> From: owner-chemistry+stenil=3D=3Dchem.gu.se^-^c= cl.net [owner-chemistry+stenil=3D=3Dchem.gu.se^-^= ccl.net] On Behalf Of Sam Abrash sabrash]_[richmond.edu [owner-chemistry^-^ccl.net]
Sent: Thursday, September 22, 2011 5:25 PM
To: Nilsson Lill, Sten
Subject: CCL: G09: Convergence Issues for H-Bonded Systems

Sent to CCL by: "Sam =A0 Abrash" [sabrash_+_richmond.edu]
Hi Folks,

I have a job involving hydrogen bonding of 3 acetylenes to the benzene cati= on. =A0I'm having trouble with the geometric convergence. =A0I was able= to get the system to converge with normal convergence criteria, opt=3Dcalc= all, and MaxStep=3D5, but then I got an imaginary frequency of -1.9 wavenum= bers.

Subsequently, I changed to Opt=3Dtight, tried both calcfc and calcall, and = have steadily reduced MaxStep to 1, but it still won't converge. =A0The= force constant criteria have been met, but the problem is the displacement= criteria. =A0Both this observation and looking at the structures with JMOL= show that the problem is finding the minimum in a very shallow potential.<= br>
Two questions. =A0First, is the 1.9 wavenumber imaginary frequency real or = an artifact? =A0Second, any advice on how to force the system to converge? = =A0Model chemistry is M062X/6-311++G**.

Thanks!
Samhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

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