From owner-chemistry@ccl.net Fri Sep 7 11:57:00 2012 From: "Zahrabatoul Mosapour kota.jaya88[#]gmail.com" To: CCL Subject: CCL: Error Message-Id: <-47545-120907085130-6920-UI6tqm9BNCzcdESD3ZqyzQ/./server.ccl.net> X-Original-From: "Zahrabatoul Mosapour" Date: Fri, 7 Sep 2012 08:51:28 -0400 Sent to CCL by: "Zahrabatoul Mosapour" [kota.jaya88|-|gmail.com] Hello everyone/everybody, I got error for my project from go9 . The method and basis set is: B3LYP/6-31G fopt scrf=(pcm, solvent=water) Could anyone please help me understand the meaning of this error message and give pointers as to how to fix it? Berny optimization. NTrRot= -1 NTRed= 1438 NAtoms= 194 NSkip= 862 IsLin=F Error in internal coordinate system. Error termination via Lnk1e in /root/g09/l103.exe at Fri Sep 7 15:34:33 2012. Job cpu time: 0 days 11 hours 30 minutes 4.2 seconds. File lengths (MBytes): RWF= 3075 Int= 0 D2E= 0 Chk= 25 Scr= 1 Thank you very much, Best regards Zahra From owner-chemistry@ccl.net Fri Sep 7 13:38:00 2012 From: "Luke Crawford luke.crawford.437]![gmail.com" To: CCL Subject: CCL: Error Message-Id: <-47546-120907133507-1388-UNz+KR17sMLIntVQnihedw+/-server.ccl.net> X-Original-From: Luke Crawford Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 7 Sep 2012 18:34:21 +0100 MIME-Version: 1.0 Sent to CCL by: Luke Crawford [luke.crawford.437 ~~ gmail.com] Hello Zahra, The error is associated with something going awry with the redundant internal coordinates used for your system. I often find that such an issue can arise with the use of a continuum solvation model (such as PCM). To rectify this you can manually perturb the geometry of your input structure by a small amount. Alternatively, optimizing in cartesian coordinates is worth looking into should your computational resources allow for increased calculation times. If the first route does not help, try opt=cartesian in your input line. These are typically the methods that I try first when geometry optimization proves to be unsuccessful. Here is a previous CCL thread which deals with your error: http://server.ccl.net/chemistry/resources/messages/2010/05/23.001-dir/index.html Hope that is of some use, Luke Crawford School of Chemistry, University of St. Andrews, Fife, Scotland On Fri, Sep 7, 2012 at 1:51 PM, Zahrabatoul Mosapour kota.jaya88[#]gmail.com wrote: > > Sent to CCL by: "Zahrabatoul Mosapour" [kota.jaya88|-|gmail.com] > Hello everyone/everybody, > > I got error for my project from go9 . The method and basis set is: B3LYP/6-31G fopt scrf=(pcm, solvent=water) > Could anyone please help me understand the meaning of this error message and give pointers as to how to fix it? > > Berny optimization. > NTrRot= -1 NTRed= 1438 NAtoms= 194 NSkip= 862 IsLin=F > Error in internal coordinate system. > Error termination via Lnk1e in /root/g09/l103.exe at Fri Sep 7 15:34:33 2012. > Job cpu time: 0 days 11 hours 30 minutes 4.2 seconds. > File lengths (MBytes): RWF= 3075 Int= 0 D2E= 0 Chk= 25 Scr= 1 > > Thank you very much, > > Best regards > Zahra> > From owner-chemistry@ccl.net Fri Sep 7 15:34:00 2012 From: "Roby Kurian Roby_Kurian a umit.maine.edu" To: CCL Subject: CCL: Error Message-Id: <-47547-120907153105-5558-CglknIgecFvzZMTVLsr37w(-)server.ccl.net> X-Original-From: "Roby Kurian" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 07 Sep 2012 15:30:59 -0400 MIME-Version: 1.0 Sent to CCL by: "Roby Kurian" [Roby_Kurian=-=umit.maine.edu] "CCL Subscribers" writes: > >Sent to CCL by: "Zahrabatoul Mosapour" [kota.jaya88|-|gmail.com] >Hello everyone/everybody, > >I got error for my project from go9 . The method and basis set is: B3LYP/6-31G fopt scrf=(pcm, solvent=water) >Could anyone please help me understand the meaning of this error message and give pointers as to how to fix it? > >Berny optimization. > NTrRot= -1 NTRed= 1438 NAtoms= 194 NSkip= 862 IsLin=F > Error in internal coordinate system. > Error termination via Lnk1e in /root/g09/l103.exe at Fri Sep 7 15:34:33 2012. > Job cpu time: 0 days 11 hours 30 minutes 4.2 seconds. > File lengths (MBytes): RWF= 3075 Int= 0 D2E= 0 Chk= 25 Scr= 1 I have encountered this error for some of my QST3 calculations. Check the last geometry of your optimization cycle and most probably you will find at least one angle approaching 180 degree. If so, that's the problem. You can figure out that particular angle by looking at the out put file. From the last geometry, look for this part. Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 2.88708 -0.00097 0.00000 -0.00030 0.00022 2.88729 R2 2.91330 -0.00139 0.00000 -0.00693 -0.00750 2.90580 R3 2.07212 -0.00003 0.00000 -0.00001 -0.00001 2.07211 . . . . A223 1.45482 0.00061 0.00000 0.00009 -0.00828 1.44654 A224 1.68661 -0.00035 0.00000 0.00989 0.00844 1.69505 A225 3.14106 0.00088 0.00000 0.03355 0.00052 3.14159 You can see that, the 'New X' for angle A225 is close to the value of pi, meaning angle is approaching 180 degree. If its not a TS job, try freezing that angle in the input file. Best, Roby Kurian Graduate student Dept of Chemistry University of Maine Orono, ME 04469 From owner-chemistry@ccl.net Fri Sep 7 16:35:00 2012 From: "Serdar Badoglu sbadoglu#%#gazi.edu.tr" To: CCL Subject: CCL: Tautomer ratios and NMR Message-Id: <-47548-120907163314-3187-PtGqq847BwM8mvu7ADtchQ|,|server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Fri, 7 Sep 2012 16:33:13 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu(!)gazi.edu.tr] Hi CCLers, I have question on NMR experiments. I have experimental H-NMR data of my sample. Depending on my DFT calculations I claim that the sample contains two tautomers. In the experimental spectrum I could identified which signal is due to the which tautomers proton. By considering the Beer-Lambert Law, I thought that if I basically get ratio of peak intensities this gives me the tautomeric ratio. Is it right? Should I take peak integrals instead of intensities? Or are there any other methods to obtain the abundance from experimental NMR data? Regards. ------------------------ Serdar Badoglu Gazi University Deptartment of Physics From owner-chemistry@ccl.net Fri Sep 7 18:08:00 2012 From: "Bruce Palfey brupalf,umich.edu" To: CCL Subject: CCL: Tautomer ratios and NMR Message-Id: <-47549-120907180605-23204-PDFeIg+A/R0l5puyy2AnmA_._server.ccl.net> X-Original-From: Bruce Palfey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 7 Sep 2012 18:05:09 -0400 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Bruce Palfey [brupalf * umich.edu] You should use the integrals. ciao, Bruce On Sep 7, 2012, at 4:33 PM, Serdar Badoglu sbadoglu#%#gazi.edu.tr wrote: > > Sent to CCL by: "Serdar Badoglu" [sbadoglu(!)gazi.edu.tr] > Hi CCLers, > > I have question on NMR experiments. I have experimental H-NMR data of my > sample. Depending on my DFT calculations I claim that the sample contains two > tautomers. In the experimental spectrum I could identified which signal is due > to the which tautomers proton. By considering the Beer-Lambert Law, I thought > that if I basically get ratio of peak intensities this gives me the tautomeric > ratio. Is it right? Should I take peak integrals instead of intensities? Or are > there any other methods to obtain the abundance from experimental NMR data? > > Regards. > > ------------------------ > Serdar Badoglu > Gazi University > Deptartment of Physics> > > > From owner-chemistry@ccl.net Fri Sep 7 20:17:00 2012 From: "David Eisenberg david.eisen2{:}gmail.com" To: CCL Subject: CCL: Tautomer ratios and NMR Message-Id: <-47550-120907192519-22459-Hi1Otpig7SC3u2MpzY/L3Q~!~server.ccl.net> X-Original-From: David Eisenberg Content-Type: multipart/alternative; boundary=14dae93409af7dcb5b04c924eb2c Date: Fri, 7 Sep 2012 18:24:43 -0500 MIME-Version: 1.0 Sent to CCL by: David Eisenberg [david.eisen2 : gmail.com] --14dae93409af7dcb5b04c924eb2c Content-Type: text/plain; charset=ISO-8859-1 Dear Serdar, You should use integrals, but you must make sure that you run a quantitative NMR experiment. That is, that the collection time is at least 5 times the decay time (T1). The latter you can measure in a separate simple experiment (see various NMR guides), but if the signal is a regular (non-exchanging) proton and you don't expect anything out of the ordinary, you may skip it and just use some very large collection time after each pulse (e.g. 10 seconds). Then you will be sure that all of the decay signal was collected, and the integrals truly represent relative populations. In fact, there is much more you can do with such a system, especially in a combination of experiment/DFT calculation. You can run EXSY (quantitative NOESY, basically) and obtain the rate of exchange between the tautomers - and then compare it to the calculated energy barriers for isomerization, to try and see any special effects in solution. Sorry for the self-promotion, but you can look at our paper on it: - David Eisenberg, Alexander S. Filatov, Edward A. Jackson, Mordecai Rabinovitz, Marina A. Petrukhina, Lawrence T. Scott, and Roy Shenhar - Bicorannulenyl: Stereochemistry of a C40H18 Biaryl Composed of Two Chiral Bowls - J. Org. Chem. 2008, 73, 6073-6078. Good luck! David On Fri, Sep 7, 2012 at 3:33 PM, Serdar Badoglu sbadoglu#%#gazi.edu.tr < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "Serdar Badoglu" [sbadoglu(!)gazi.edu.tr] > Hi CCLers, > > I have question on NMR experiments. I have experimental H-NMR data of my > sample. Depending on my DFT calculations I claim that the sample contains > two > tautomers. In the experimental spectrum I could identified which signal is > due > to the which tautomers proton. By considering the Beer-Lambert Law, I > thought > that if I basically get ratio of peak intensities this gives me the > tautomeric > ratio. Is it right? Should I take peak integrals instead of intensities? > Or are > there any other methods to obtain the abundance from experimental NMR data? > > Regards. > > ------------------------ > Serdar Badoglu > Gazi University > Deptartment of Physics> > > --14dae93409af7dcb5b04c924eb2c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Serdar,

You should use integrals, but you must make= sure that you run a quantitative NMR experiment. That is, that the collect= ion time is at least 5 times the decay time (T1). The latter you can measur= e in a separate simple experiment (see various NMR guides), but if the sign= al is a regular (non-exchanging) proton and you don't expect anything o= ut of the ordinary, you may skip it and just use some very large collection= time after each pulse (e.g. 10 seconds). Then you will be sure that all of= the decay signal was collected, and the integrals truly represent relative= populations.

In fact, there is much more you can do with such a syst= em, especially in a combination of experiment/DFT calculation. You can run = EXSY (quantitative NOESY, basically) and obtain the rate of exchange betwee= n the tautomers - and then compare it to the calculated energy barriers for= isomerization, to try and see any special effects in solution.

Sorry for the self-promotion, but you can look at our p= aper on it:=A0
  • David Eisenberg, Alexander S. Filatov, Edward A. Jackson, Mordecai Rabi= novitz, Marina A. Petrukhina, Lawrence T. Scott, and Roy Shenhar
  • Bicorannulenyl: Stereochemist= ry of a C40H18=A0Biaryl Composed of Two Chiral Bowls<= /li>
  • J. Org. Chem. 2008, 73, 6073-6078.
Good l= uck!
David


On = Fri, Sep 7, 2012 at 3:33 PM, Serdar Badoglu sbadoglu#%#gazi.edu.tr <owner-chemistry**ccl.net> w= rote:

Sent to CCL by: "Serdar =A0Badoglu" [sbadoglu(!)gazi.edu.tr]
Hi CCLers,

I have question on NMR experiments. I have experimental H-NMR data of my sample. Depending on my DFT calculations I claim that the sample contains t= wo
tautomers. In the experimental spectrum I could identified which signal is = due
to the which tautomers proton. By considering the Beer-Lambert Law, I thoug= ht
that if I basically get ratio of peak intensities this gives me the tautome= ric
ratio. Is it right? Should I take peak integrals instead of intensities? Or= are
there any other methods to obtain the abundance from experimental NMR data?=

Regards.

------------------------
Serdar Badoglu
Gazi University
Deptartment of Physics



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--14dae93409af7dcb5b04c924eb2c-- From owner-chemistry@ccl.net Fri Sep 7 20:51:01 2012 From: "Jean Jules FIFEN julesfifen|gmail.com" To: CCL Subject: CCL:G: Total partition functions Message-Id: <-47551-120907203733-675-DgO5EvwhqLcQx0gI6Pa8xw]*[server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 8 Sep 2012 01:37:26 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen^^gmail.com] The total partition function depends on the energy reference. If the energy reference is taken at the bottom of the well, the total partition function of that molecule is computed to be Qtot=0.101811D-15. However, if the energy reference is taken at the first vibrational level (V=0), the total partition function of that molecule is computed to be Qtot=0.125827D+19. Note that the rate constant does not depend on such references. Hope this would help. On 05/09/2012, Arup Kumar Chakrabartty chakrabarttyarup.-*-.gmail.com wrote: > > Sent to CCL by: "Arup Kumar Chakrabartty" [chakrabarttyarup.:.gmail.com] > Dear all, > I am trying to calculate rate constant using transition state theory from > thermochemical output obtained by Gaussian09. The thermochemical output is > given below > Q Log10(Q) Ln(Q) > Total Bot 0.101811D-15 -15.992205 -36.823412 > Total V=0 0.125827D+19 18.099774 41.676269 > Vib (Bot) 0.658774D-30 -30.181264 -69.494928 > Vib (Bot) 1 0.627580D+01 0.797669 1.836701 > Vib (Bot) 2 0.437441D+01 0.640919 1.475771 > Vib (Bot) 3 0.381061D+01 0.580994 1.337789 > Vib (Bot) 4 0.242888D+01 0.385406 0.887431 > Vib (Bot) 5 0.138901D+01 0.142705 0.328591 > Vib (Bot) 6 0.983124D+00 -0.007392 -0.017020 > Vib (Bot) 7 0.798275D+00 -0.097848 -0.225303 > Vib (Bot) 8 0.681738D+00 -0.166383 -0.383110 > Vib (Bot) 9 0.571170D+00 -0.243235 -0.560068 > Vib (Bot) 10 0.501433D+00 -0.299787 -0.690286 > Vib (Bot) 11 0.431845D+00 -0.364672 -0.839689 > Vib (Bot) 12 0.373929D+00 -0.427210 -0.983688 > Vib (Bot) 13 0.304842D+00 -0.515925 -1.187961 > Vib (Bot) 14 0.295855D+00 -0.528921 -1.217887 > Vib (Bot) 15 0.280599D+00 -0.551913 -1.270828 > Vib (Bot) 16 0.244908D+00 -0.610998 -1.406874 > Vib (V=0) 0.814169D+04 3.910715 9.004753 > Vib (V=0) 1 0.679569D+01 0.832233 1.916288 > Vib (V=0) 2 0.490289D+01 0.690452 1.589825 > Vib (V=0) 3 0.434327D+01 0.637817 1.468628 > Vib (V=0) 4 0.297981D+01 0.474189 1.091860 > Vib (V=0) 5 0.197626D+01 0.295844 0.681207 > Vib (V=0) 6 0.160297D+01 0.204924 0.471855 > Vib (V=0) 7 0.144194D+01 0.158946 0.365986 > Vib (V=0) 8 0.134544D+01 0.128864 0.296720 > Vib (V=0) 9 0.125910D+01 0.100061 0.230398 > Vib (V=0) 10 0.120812D+01 0.082110 0.189066 > Vib (V=0) 11 0.116067D+01 0.064710 0.149001 > Vib (V=0) 12 0.112436D+01 0.050905 0.117212 > Vib (V=0) 13 0.108560D+01 0.035670 0.082134 > Vib (V=0) 14 0.108097D+01 0.033815 0.077862 > Vib (V=0) 15 0.107336D+01 0.030743 0.070789 > Vib (V=0) 16 0.105676D+01 0.023976 0.055206 > Electronic 0.100000D+01 0.000000 0.000000 > Translational 0.107851D+09 8.032826 18.496265 > Rotational 0.143296D+07 6.156233 14.175251 > > I want to know the value of total partition functions for this molecule. > Any help or suggestion is highly appreciated. > > With regards > Arup Kumar Chakrabartty > Research Scholar> > > -- Jules.