From owner-chemistry@ccl.net Sun Feb 20 04:49:01 2011 From: "adnane lina b_fethi2000{}yahoo.fr" To: CCL Subject: CCL:G: hdc method with gaussian Message-Id: <-43988-110220044645-15593-jmU2uTHbEYl/1R4AvI7X+w_._server.ccl.net> X-Original-From: "adnane lina" Date: Sun, 20 Feb 2011 04:46:43 -0500 Sent to CCL by: "adnane lina" [b_fethi2000%%yahoo.fr] dear cclers, Could you help me to generate hdc method in calculating mep with gaussian. thanks From owner-chemistry@ccl.net Sun Feb 20 09:33:00 2011 From: "Close, David M. CLOSED*o*mail.etsu.edu" To: CCL Subject: CCL:G: Gaussian03 optimisation problems Message-Id: <-43989-110220092556-11681-0mjyulirf3Zh8W4yEwMbzA[*]server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 20 Feb 2011 14:25:47 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED+*+mail.etsu.edu] Eli: If you have a viewer you should animate the frequency that has the imaginary eigenvector. This represents a vibration in the direction that will lead to the true minimum. The trick is to make a few changes in the X Y Z coordinates listed under the frequency and redo the calculation. Some trial and error may be needed, but it is not too difficult to displace the vibration off of the local minima and get it to move towards the true minima. Try this. If you don't succeed, send me the X Y Z coordinates and I will give it a try. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu * ccl.net [mailto:owner-chemistry+closed==etsu.edu * ccl.net] On Behalf Of Eli Lam elizabeth.shlam!A!gmail.com Sent: Saturday, February 19, 2011 8:27 PM To: Close, David M. Subject: CCL: Gaussian03 optimisation problems Sent to CCL by: "Eli Lam" [elizabeth.shlam() gmail.com] Hi, Recently when I do optimisation of a organometallic molecules, I've found an imaginary frequency in the optimized structure, I know it would mean that the structure is not a minima in the PES. But how should I optimise again to find the true minimum? Thanks! Elihttp://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 Sun Feb 20 16:22:00 2011 From: "David M. Close closed\a/etsu.edu" To: CCL Subject: CCL:G: Gaussian .chk files Message-Id: <-43990-110220162004-20472-hAPApsu2HjhdXL3qOsgJXA|*|server.ccl.net> X-Original-From: "David M. Close" Date: Sun, 20 Feb 2011 16:19:56 -0500 Sent to CCL by: "David M. Close" [closed++etsu.edu] Last month I wrote a question to CCL about a problem with Gaussian .chk files. I got a few replies about which keywords to use, but this I already knew. I should have been more specific. I was trying to do a frequency calculation on a previous SCRF calculation using G98. Apparently this cannot be done. The calulation begin by reading the .chk file, but then fails to open the information needed for the frequency calculation. I gave up on this and switched to G03. This program does the same SCRF calculation as G98 and gives the same answers. But there are still problems with the frequency calculation if I do the following. 1) Run a geometry optimization. 2) Run a single point SCRF calculation using geom=checkpoint on the geometry optimized xyz coordinates from part (1). 3) Do a frequency calculation on the SCRF job again using geom=checkpoint. Step three does the frequency calculation on the geometry from step (1), which may be expected since I didn't reoptimize the structure in the SCRF step. However I get a completely different answer if I elimate step (3) and run step (2) with the combined SCRF and freq keywords in a single step. This procedure produces numbers that are not in agreement with calculations in the literature. Of course I may be doing something wrong here. For example I have no idea how the command geom=checkpoint is used. Does anyone know if you use a .chk file to do several calculations, which part is read by default if you try to read it again? Regards, Dave Close. From owner-chemistry@ccl.net Sun Feb 20 16:56:00 2011 From: "Olexandr Isayev olexandr.isayev[]case.edu" To: CCL Subject: CCL:G: Gaussian03 optimisation problems Message-Id: <-43991-110220160300-4683-SPXJaZBVzN1XrLttnsi47w[]server.ccl.net> X-Original-From: Olexandr Isayev Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 20 Feb 2011 15:02:32 -0600 MIME-Version: 1.0 Sent to CCL by: Olexandr Isayev [olexandr.isayev[]case.edu] Dear Eli and Dave: Instead of manual geometry manipulation you can use Opt=Tight or Opt=Verytight on the route card to specify that you'd like to use tighter convergence criteria. For DFT, you may also need to specify Int=Ultrafine, which uses a more accurate numerical integration grid. Please see a nice case study at the G  web site: http://www.gaussian.com/g_whitepap/vib.htm ("A note about low frequencies" section) Sincerely, Olexandr ________________________________ Olexandr Isayev, Ph.D. Department of Chemistry Case Western Reserve University 10900 Euclid Avenue Cleveland, OH 44106-7078 USA Phone:   769 218-9812 Fax:       216 368-3006 http://olexandrisayev.com On Sat, Feb 19, 2011 at 19:27, Eli Lam elizabeth.shlam!A!gmail.com wrote: > > Sent to CCL by: "Eli  Lam" [elizabeth.shlam() gmail.com] > Hi, > > Recently when I do optimisation of a organometallic molecules, I've found an imaginary frequency in > the optimized structure,  I know it would mean that the structure is not a minima in the PES.  But how > should I optimise again to find the true minimum?  Thanks! > > Eli>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Sun Feb 20 18:23:00 2011 From: "Mikael Johansson mikael.johansson++iki.fi" To: CCL Subject: CCL:G: Absolute zero in orbital energies Message-Id: <-43992-110220135152-21269-myU4G5rXK4vyv5KOuFcYBA\a/server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sun, 20 Feb 2011 20:51:43 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson()iki.fi] Hello Eli, On Sat, 19 Feb 2011, Eli Lam elizabeth.shlam%%gmail.com wrote: > I would like to ask about the physical meaning of the absolute zero in > orbital energies calculated by gaussian03. I know the orbital energy is > of relative meaning, but could I compare the orbital energies of > different molecules simply by viewing their energies calculated from > gaussian03? Thank you very much! The orbital energies can be used as a measure of how strongly the corresponding electrons are bound to the system, and how difficult they are to remove. In this respect, you can compare the orbital energies between different systems. The zero-level can be taken as the divider between bound and unbound electrons. If you have positive energy occupied orbitals, you are in trouble, as it is an indication that the loosest electron are not actually bonded at all. Especially using non-hybrid DFT functionals, this can become an (artificial) problem. The electrons can also be only partly bound. Another thing you can get out from comparing orbital energies between systems is some measure of reactivity or stability. The higher the HOMO-LUMO gap, the less reactive the species, in many cases. You naturally need to be aware of the limitations and approximations of the method used to compute the orbitals and their energies, whatever interpretation and comparison you want to get out of them. A selection of somewhat random papers in chronological order you might find illuminating: Z. Zhou, R.G. Parr, "Activation hardness: new index for describing the orientation of electrophilic aromatic substitution", J. Am. Chem. Soc. 112 (1990) 5720. DOI: 10.1021/ja00171a007 D.P. Chong, O.V. Gritsenko, E.J. Baerends, "Interpretation of the Kohn-Sham orbital energies as approximate vertical ionization potentials", J. Chem. Phys. 116 (2002) 1760. DOI: 10.1063/1.1430255 F. Jensen, "Describing Anions by Density Functional Theory: Fractional Electron Affinity", J. Chem. Theory Comput. 6 (2010) 2726. DOI: 10.1021/ct1003324 Happy reading, Mikael J. http://www.iki.fi/~mpjohans/