From owner-chemistry@ccl.net Mon Jun 11 08:37:00 2007 From: "Dr. Robert C. Mawhinney dr.robert.mawhinney^^gmail.com" To: CCL Subject: CCL:G: AIM information Message-Id: <-34455-070610213234-15794-JlIneMCaW8AOmX7tfEcuhw%server.ccl.net> X-Original-From: "Dr. Robert C. Mawhinney" Content-Type: multipart/alternative; boundary="----=_Part_29041_20029248.1181522223264" Date: Sun, 10 Jun 2007 20:37:03 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Robert C. Mawhinney" [dr.robert.mawhinney ~ gmail.com] ------=_Part_29041_20029248.1181522223264 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Guermoune, The value of the laplacian and electron density at the bond critical point (bcp) depend on several factors: the distance between the nuclei, the distance of the bcp from each of the respective nuclei, the value of the three components of the laplacian, etc. What you are probably observing has to do with the bcp being much closer to one of the two nuclei - possibly within that nucleus's valence shell. If you plot the the laplacian and locate where the bcp is, you should be able to assess whether this is the case. Sincerely, On 6/10/07, Guermoune Abdeladim lguermoune(_)hotmail.com < owner-chemistry:-:ccl.net> wrote: > > > Sent to CCL by: "Guermoune Abdeladim" [lguermoune*_*hotmail.com] > Hello, > A few days I asked by the way for help on this forum about method AIM. I > thank all those that gave me some ideas. Unfortunately the problem is not > solved even though I increased the basis set or if I add 6d 10F for metal, I > always have the density that is not coherent with the value of laplacian for > the Bond critical points (I treat the file wfn starting from Gaussian03 by > program AIM). > I recall that the part of my system to study is composed by iron as > metallic center with two borons and two hydrogens, all forming a cycle. > I > All suggestions or remark would be well the come > Best regard.> > > > ------=_Part_29041_20029248.1181522223264 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Guermoune,

The value of the laplacian and electron density at the bond critical point (bcp) depend on several factors:  the distance between the nuclei, the distance of the bcp from each of the respective nuclei, the value of the three components of the laplacian, etc. 

What you are probably observing has to do with the bcp being much closer to one of the two nuclei - possibly within that nucleus's valence shell.  If you plot the the laplacian and locate where the bcp is, you should be able to assess whether this is the case.

Sincerely,



On 6/10/07, Guermoune Abdeladim lguermoune(_)hotmail.com <owner-chemistry:-:ccl.net > wrote:

Sent to CCL by: "Guermoune  Abdeladim" [lguermoune*_* hotmail.com]
Hello,
A few days I asked by the way for help on this forum about method AIM. I thank all those that gave me some ideas. Unfortunately the problem is not solved even though I increased the basis set or if I add 6d 10F for metal, I always have the density that is not coherent with the value of laplacian for the Bond critical points (I treat the file wfn starting from Gaussian03 by program AIM).
I recall that the part of my system to study is composed by iron as metallic center with two borons and two hydrogens, all forming a cycle.
I
All suggestions or remark would be well the come
Best regard.



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------=_Part_29041_20029248.1181522223264-- From owner-chemistry@ccl.net Mon Jun 11 09:11:01 2007 From: "Roger Robinson r.robinson_+_imperial.ac.uk" To: CCL Subject: CCL:G: Rate Data Message-Id: <-34456-070611074729-11769-uBzmZ/PfiyWeJUxBjZFh3w.@.server.ccl.net> X-Original-From: "Roger Robinson" Date: Mon, 11 Jun 2007 07:47:26 -0400 Sent to CCL by: "Roger Robinson" [r.robinson]_[imperial.ac.uk] Dear CCL, I'm interested in calculating rate data from Gaussian Calculations. I've downloaded Polyrate and Gaussrate 9.5. I've installed them and got the test jobs to run. I've starting trying to get my own jobs to run but I having problems. Im finding the manuals for both these programs quite hard work too. I was wondering if anyones got any opinions on them or anywhere I could find some tutorials. Or any information on alternatives. My current problem is that I keep getting a message that my Number of Atoms is higher than NAtoms. I've changed this is param.inc and recompiled Gaussrate but I'm stilling get the same message. Also I not quite sure of what the best way to use Gaussrate would be. I've already located the structures I what Start,End and TS. Would it be best to do this first or is it best to get Gaussrate to call Gaussian then optimise. Generally any help would be appreciated. Thanks Roger From owner-chemistry@ccl.net Mon Jun 11 10:41:01 2007 From: "Gary W Breton gbreton%a%berry.edu" To: CCL Subject: CCL:G: Negative frequency problem Message-Id: <-34457-070611103934-6742-OLfRVEHICHvqUaqqvdvRCA]*[server.ccl.net> X-Original-From: "Gary W Breton" Date: Mon, 11 Jun 2007 10:39:30 -0400 Sent to CCL by: "Gary W Breton" [gbreton[-]berry.edu] I know this problem has been discussed before, but even after searching the archives, I have yet to find a satisfactory answer or solution, so please bear with me. I conducted a TS search using G03 and found an expected TS structure. However, in addition to the larger negative frequency (-196 cm-1) that is indicative (through animation) of the proper vibration, there was a second, much smaller, (-18 cm-1) frequency. I tried two things to eliminate the smaller frequency. First (and this usually fixes such a problem for me), I animated the -18 cm-1 vibration, "twisted" the structure in the direction of this vibration and re-optimized to a TS. It optimized right back to the original structure with both negative frequencies. I tried several times, each time increasing the degree of "twisting", but each time it settled back to the original TS structure with identical negative frequencies. Second, I ran the convergence using keyword OPT=Tight with the hope that the tighter convergence criteria might eliminate the negative frequency. But no, the exact same TS structure with the same two negative frequencies was obtained. My question then: i. Is there some sort of technique i should try that I haven't yet tried? ii. Should i even worry about such a small negative frequency given the limits of error (which i have read to be +/- 30 cm-1). If I should ignore it, how do I pitch this to reviewers of a paper? Thanks for any advice Gary Breton Berry College From owner-chemistry@ccl.net Mon Jun 11 12:54:01 2007 From: "Schwan Hosseiny s.s.hosseiny*_*tnw.utwente.nl" To: CCL Subject: CCL: Redox Potential Message-Id: <-34458-070611104444-8468-0lhwoh4d0K28rqYCU8OQiQ~!~server.ccl.net> X-Original-From: "Schwan Hosseiny" Date: Mon, 11 Jun 2007 10:44:41 -0400 Sent to CCL by: "Schwan Hosseiny" [s.s.hosseiny[-]tnw.utwente.nl] Dear colleagues, at present I'm working on reversible and quasi reversible transition metal redox couple complexes. I just start my work and the aim of the project is to find a good redox couple with a quite high negative redox potential. Therefore I want to calculate the redox potential at first before I start doing some experiments. But everytime I try to optimize a molecule by Gamess (Chemoffice) I get an error. My Question is now, has somebody an idea, what type of methode and basis set i have to use if i want to calculate my redox potential in an aqueous medium? At present I'm using DFT/B3LYP, 6-31G (d,p), PCM model (water). Is there an other way to calculate the redox potential? I tried already with the Lever equation but it's not that accurate for non six coordinated complexes. Thanks, and kind regards Schwan Hosseiny From owner-chemistry@ccl.net Mon Jun 11 13:39:00 2007 From: "Cory Pye cpye-.-crux.smu.ca" To: CCL Subject: CCL:G: Negative frequency problem Message-Id: <-34459-070611123308-8310-g8iCIXxTg7Rsgm+9z/6hTg###server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 11 Jun 2007 12:49:32 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye!=!crux.smu.ca] Hi Gary, I would try first to do something like (1) #N XXX FOpt=(CalcFC,TS) using your distorted geometry. I find twists of 10-20 deg sufficient to get it started. (2) If that doesn't work, you might wish to do an old-fashioned z-matrix optimization. #N XXX FOpt=(CalcFC,TS,z-matrix) Sometimes the automatic generation of internal coordinates might miss some important ones. It also helps if your molecule has symmetry, as you can generally optimize a subset of parameters (those belonging to the totally symmetric representation). Another alternative is to look at the coordinates that Gaussian generates and add by hand those that you think should be there, but aren't. (3) If your molecule has 50 or fewer optimization variables, then I find that #N FOpt=(Calc,TS,EF) can work wonders on occasion. On Mon, 11 Jun 2007, Gary W Breton gbreton%a%berry.edu wrote: > > Sent to CCL by: "Gary W Breton" [gbreton[-]berry.edu] > I know this problem has been discussed before, but even after searching the archives, I have yet to > find a satisfactory answer or solution, so please bear with me. > > I conducted a TS search using G03 and found an expected TS structure. However, in addition to the > larger negative frequency (-196 cm-1) that is indicative (through animation) of the proper > vibration, there was a second, much smaller, (-18 cm-1) frequency. I tried two things to eliminate > the smaller frequency. > > First (and this usually fixes such a problem for me), I animated the -18 cm-1 vibration, "twisted" > the structure in the direction of this vibration and re-optimized to a TS. It optimized right back to > the original structure with both negative frequencies. I tried several times, each time increasing the > degree of "twisting", but each time it settled back to the original TS structure with identical negative > frequencies. > > Second, I ran the convergence using keyword OPT=Tight with the hope that the tighter convergence > criteria might eliminate the negative frequency. But no, the exact same TS structure with the same > two negative frequencies was obtained. > > My question then: > > i. Is there some sort of technique i should try that I haven't yet tried? > ii. Should i even worry about such a small negative frequency given the limits of error (which i have > read to be +/- 30 cm-1). If I should ignore it, how do I pitch this to reviewers of a paper? > > Thanks for any advice > > Gary Breton > Berry College > > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye(-)crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Mon Jun 11 14:13:00 2007 From: "dedey#alumni.bilkent.edu.tr" To: CCL Subject: CCL:G: Negative frequency problem Message-Id: <-34460-070611134608-4551-51OREEfjObt2LmqMQY0OFA!^!server.ccl.net> X-Original-From: Date: Mon, 11 Jun 2007 19:44:14 EEST Sent to CCL by: [dedey%%alumni.bilkent.edu.tr] Hi Gary, I asked a similar question to the list a couple of months ago. The comments were about the ways of eliminating the imaginary frequencies. I hoped to find a paper, published such small frequencies, and commented on them as being insignificant. I managed to find one recent paper. Here it is. Transition Metal-Carbon Complexes. A Theoretical Study Krapp, A., Pandey, K.K., and Frenking, G. J. Am. Chem. Soc., 2007, 10.1021/ja0691324 I hope, this helps... yavuz On 11 Jun 2007 18:12 EEST you wrote: > > Sent to CCL by: "Gary W Breton" [gbreton[-]berry.edu] > I know this problem has been discussed before, but even after searching the archives, I have yet to > find a satisfactory answer or solution, so please bear with me. > > I conducted a TS search using G03 and found an expected TS structure. However, in addition to the > larger negative frequency (-196 cm-1) that is indicative (through animation) of the proper > vibration, there was a second, much smaller, (-18 cm-1) frequency. I tried two things to eliminate > the smaller frequency. > > First (and this usually fixes such a problem for me), I animated the -18 cm-1 vibration, "twisted" > the structure in the direction of this vibration and re-optimized to a TS. It optimized right back to > the original structure with both negative frequencies. I tried several times, each time increasing the > degree of "twisting", but each time it settled back to the original TS structure with identical negative > frequencies. > > Second, I ran the convergence using keyword OPT=Tight with the hope that the tighter convergence > criteria might eliminate the negative frequency. But no, the exact same TS structure with the same > two negative frequencies was obtained. > > My question then: > > i. Is there some sort of technique i should try that I haven't yet tried? > ii. Should i even worry about such a small negative frequency given the limits of error (which i have > read to be +/- 30 cm-1). If I should ignore it, how do I pitch this to reviewers of a paper? > > Thanks for any advice > > Gary Breton > Berry College> > Yavuz Dede, Ph.D. Comp. Chem. Lab. Dep. of Chem. METU 06531 Ankara TURKEY +90 312 210 3187 From owner-chemistry@ccl.net Mon Jun 11 14:53:00 2007 From: "Sergio Emanuel Galembeck segalemb^usp.br" To: CCL Subject: CCL: Redox Potential Message-Id: <-34461-070611145132-13537-OPYBOhNxxiooABKVUCTQww _ server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 11 Jun 2007 15:51:25 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb(_)usp.br] Dear Schwan, I sugest that you use an ECP for the metal, as HW or SBK, and a full-electron basis for the representative elements. B3LYP or other DFT, as BP86 is OK as a method. Best regards, Sergio Citando "Schwan Hosseiny s.s.hosseiny*_*tnw.utwente.nl" : > > Sent to CCL by: "Schwan Hosseiny" [s.s.hosseiny[-]tnw.utwente.nl] > Dear colleagues, > > at present I'm working on reversible and quasi reversible transition > metal redox couple complexes. > I just start my work and the aim of the project is to find a good > redox couple with a quite high negative redox potential. Therefore I > want to calculate the redox potential at first before I start doing > some experiments. But everytime I try to optimize a molecule by > Gamess (Chemoffice) I get an error. My Question is now, has somebody > an idea, what type of methode and basis set i have to use if i want > to calculate my redox potential in an aqueous medium? > At present I'm using DFT/B3LYP, 6-31G (d,p), PCM model (water). > > Is there an other way to calculate the redox potential? I tried > already with the Lever equation but it's not that accurate for non > six coordinated complexes. > > Thanks, and kind regards > > Schwan Hosseiny> > > > From owner-chemistry@ccl.net Mon Jun 11 15:29:00 2007 From: "errol lewars elewars%a%trentu.ca" To: CCL Subject: CCL:G: Negative frequency problem Message-Id: <-34462-070611144849-12318-W6JwP/u5Itz7S7Bx7y0iGQ*o*server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Mon, 11 Jun 2007 13:51:34 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars/a\trentu.ca] 2007 June 11 hello, if it's not too complicated, what are your reactant, product, and "failed" TS (brief description and charge, multiplicity and cartesians)? E. Lewars ==== Gary W Breton gbreton%a%berry.edu wrote: >Sent to CCL by: "Gary W Breton" [gbreton[-]berry.edu] >I know this problem has been discussed before, but even after searching the archives, I have yet to >find a satisfactory answer or solution, so please bear with me. > >I conducted a TS search using G03 and found an expected TS structure. However, in addition to the >larger negative frequency (-196 cm-1) that is indicative (through animation) of the proper >vibration, there was a second, much smaller, (-18 cm-1) frequency. I tried two things to eliminate >the smaller frequency. > >First (and this usually fixes such a problem for me), I animated the -18 cm-1 vibration, "twisted" >the structure in the direction of this vibration and re-optimized to a TS. It optimized right back to >the original structure with both negative frequencies. I tried several times, each time increasing the >degree of "twisting", but each time it settled back to the original TS structure with identical negative >frequencies. > >Second, I ran the convergence using keyword OPT=Tight with the hope that the tighter convergence >criteria might eliminate the negative frequency. But no, the exact same TS structure with the same >two negative frequencies was obtained. > >My question then: > >i. Is there some sort of technique i should try that I haven't yet tried? >ii. Should i even worry about such a small negative frequency given the limits of error (which i have >read to be +/- 30 cm-1). If I should ignore it, how do I pitch this to reviewers of a paper? > >Thanks for any advice > >Gary Breton >Berry College> > > > > From owner-chemistry@ccl.net Mon Jun 11 16:37:00 2007 From: "David Santos Carballal spectrum_dav ~~ operamail.com" To: CCL Subject: CCL:G: Gaussian/NBO/zero and first order perturbational energies Message-Id: <-34463-070611161249-1748-lzOJtoF4iRhZqf0/fNliOA\a/server.ccl.net> X-Original-From: "David Santos Carballal" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 11 Jun 2007 15:08:47 -0500 MIME-Version: 1.0 Sent to CCL by: "David Santos Carballal" [spectrum_dav-x-operamail.com] Dear CCL'rs: The Gaussian output of the NBO's (3.1) just gives the second order perturbational energies. These energies can be used to quantify conjugative effects of the molecular systems. I want to estimate steric repulsions on molecular systems using zero and first order perturbational energies. Is this idea correct? Any suggest to obtain the zero and first order contributions to the energy in Gaussian are welcome. David Santos -- _______________________________________________ Surf the Web in a faster, safer and easier way: Download Opera 9 at http://www.opera.com Powered by Outblaze