From owner-chemistry@ccl.net Tue Apr 3 05:34:02 2007 From: "Jens Spanget-Larsen spanget[#]ruc.dk" To: CCL Subject: CCL: semiempirical single & double excitations? Message-Id: <-33953-070403050408-342-++WUUbFq+TBCYyXTIq1BFg#%#server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 03 Apr 2007 11:03:48 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget(0)ruc.dk] Dear CCL! I just wish to emphasize that a number of UV-VIS chromophores cannot be correctly described without the inclusion of multiply excited configurations in the CI procedure. Within the framework of the classical PPP pi-electron model, Michl and his coworkers developed the SECI-1 and SECI-2 procedures, with inclusion of systematic and well-defined selections of doubly excited configurations [1]. One of the early all-valence electrons CI-procedures with inclusion of doubly excited configurations was developed by H. Baumann, and his computer program (CNDUV99) was made available through QCPE [2]. A reparameterized version of Baumann's procedure was applied by Spanget-Larsen and Gleiter [3] to the prediction of electronic transitions for a variety of conjugated hydrocarbons. The investigation included 'normal' compounds as well compounds with low-lying states depending on the inclusion of doubly-excited configurations in the CI expansion. In particular, the S2 state of pleiadene and the S3 state of azuleno{1,2,3-cd)phenalene were predicted to be of 67% and 31% doubly excited character, respectively. It is important to realize that for these and other species with low HOMO-LUMO excitation energy, a CI-model without the inclusion of doubly-excited configurations does not qualitatively explain the observed low-energy transitions. Jens >--< [1] J. W. Downing, J. Michl, P. Jorgensen, E. W. Thulstrup, Theor. Chim. Acta 32, 203 (1974) [2] H. Baumann, QCPE 10, 333 (1977) [3] J. Spanget-Larsen, R. Gleiter, Helv. Chim. Acta 61, 2999 (1978) ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget|ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ From owner-chemistry@ccl.net Tue Apr 3 06:51:01 2007 From: "Marianna Fanti marianna.fanti%x%unibo.it" To: CCL Subject: CCL: SUMMARY: semiempirical single & double excitations Message-Id: <-33954-070403061226-22147-OmW3bCUamkvS2Pm5JOKwkA{}server.ccl.net> X-Original-From: Marianna Fanti Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 03 Apr 2007 10:32:01 +0200 MIME-Version: 1.0 Sent to CCL by: Marianna Fanti [marianna.fanti%unibo.it] Hello! Few days ago I posted the following question: > I'm looking for a semiempirical package with spectroscopic parametrization (INDO/S for instance) able to handle single AND double excitations when doing the CI. > > Is there any around? It seems that all the available packages are limited to single excitations (CIS). > > I will summarize. Thanks to everybody! Here is the summary of the answers I received, but first a short comment. Yes of course, CISD has many limitations, but I agree with John McKelvey answer (of course... since I posted the question.. :D ). === Pierre Archirel pierre.archirel=lcp.u-psud.fr wrote: I think that double excitations are contradictory with the semi-empirical philosophy: 1- the basic ansatz is that the wave function is a single determinant, the hamiltonian is parametrised so as to yield exact experimental values for the ground state of a list of molecules. 2- this means that electron correlation implicitely lies in the parametrisation and that CI of the doubles would be redundant. I am sure that this CID would lower the energy, but I do not see any ground for doing it. This is also true for excited states. 3- I conclude that the only way of performing a CI of the doubles in the right way would be to reoptimise the paramaters in this frame. Maybe it is what you want to do. === John McKelvey jmmckel%a%gmail.com wrote: ORCA [free] should be able to do this. Also, since INDO/S was parameterized using CIS, including doubles will likely blue shift transitions. ==== Sent to CCL by: "Greg Pearl" [greg.pearl(a)acdlabs.com] The ZINDO code developed by Mike Zerner had that functionality. Not sure how you can get that code these days but would start by contacting The Quantum Theory project at University of Florida www.qtp.ufl.edu ==== John McKelvey jmmckel%a%gmail.com wrote: From a purist point of view I agree with Pierre. However, Zerner, the major player in the INDO/S domain, was able to explain a lot of chemistry doing things with INDO/S beyond CIS. [ZINDO has the capability to do CIS, CISD, CISDT, CISDTQ, ..etc.] In fact there are times where CISD is necessary to get the orbital description of states correct, even though the energies may be incorrect. Further, there are occasions where getting the energies correct _requires_ CISD within INDO/S, as in describing solute-solvent dispersion energies where a double excitation is composed of a single excitation in the solute coupled with a single excitation in the solvent. My $0.02. ==== Sent to CCL by: Frank Neese [neese^-^thch.uni-bonn.de] Dear Marianna, i just wanted to briefly follow up on what John McKelvey posted to the list. Indeed, you can "torture" the MRCI module of the ORCA program to do a multiroot CISD calculation. It is not really what it was made for but it is possible. Below you find an input for H2CO: # # CISD calculation with ZINDO/S # ! ZINDO/S TightSCF %mrci citype mrci tsel 0 solver diag newblock 1 * nroots 5 nrootssel 1 excitations cisd refs cas(0,0) end end end * int 0 1 C 0 0 0 0 0 0 O 1 0 0 1.2 0 0 H 1 2 0 1.1 120 0 H 1 2 3 1.1 120 180 * The details are explained in the ORCA manual (http://www.thch.uni-bonn.de/tc/orca/). If you want to do it for larger molecules you have to manually select an orbital window (~200-300 MOs will be possible depending on your computer). Concerning the physical content of such CISD calculations of excited states i personally share the views of Mike Zerner - you basically overcorrelate the ground state relative to the excited states and will make things worse; also size-consistency problems will show up in the results. Third, the parameterization is done for CIS and including the doubles would require a change since you know treat part of the dynamic correlation explicitly. Finally, it will get much more computationally expensive rather quickly. Hope that helps, all the best, Frank ==== Thank you again and best regards, Marianna -- ----------------------------------------------------------------- Marianna Fanti, PhD, Dip. di Chimica "G. Ciamician" University of Bologna, via Selmi 2, I-40126 Bologna, Italy, Fax: +39-0512099456 Phone +39-0512099521, http://www.ciam.unibo.it/models/mari e-mail: marianna.fanti]=[unibo.it ----------------------------------------------------------------- All that you take with you is what you leave behind ----------------------------------------------------------------- From owner-chemistry@ccl.net Tue Apr 3 08:43:02 2007 From: "Fredrik Blomgren fredrik.blomgren|cit.chalmers.se" To: CCL Subject: CCL: IRC calculation using GAMESS Message-Id: <-33955-070403042140-28184-IOI/R7i+6XsUv1C5c7RWSg^server.ccl.net> X-Original-From: "Fredrik Blomgren" Date: Tue, 3 Apr 2007 04:21:35 -0400 Sent to CCL by: "Fredrik Blomgren" [fredrik.blomgren:-:cit.chalmers.se] Dear All I'm trying to perform an IRC calculation with GAMESS and have two problems. First I should say that my transition state is as fas as I can tell correct, so that is most likely not the problem. Problem 1): If I set up my IRC calculation using a small number for NPOINT, the entire IRC is not found. When I try to restart it using the restart information provided by the program in the *.dat file, I get the message: RADIUS IN CIRCLE OPTIMIZATION 0.0067834 DEVIATES SIGNIFICANTLY FROM CONSTRAIN CONDITION 0.0050000 IT IS POSSIBLE THAT THE NEXT IRC POINT IS CLOSE TO A MINIMUM I find it to be extremely unlikely that the system is near a minimum at exactly the point which corresponds to my setting of NPOINT. Does anybody know the fix for this problem? I guess what I am asking is how does one resart an IRC calculation correctly in GAMESS? Problem 2) When I ran into problem 1, I increased NPOINT and let the calculation run longer. Then eventually the calculation stopped with the same message (but this time at a point smaller than my setting of NPOINT): RADIUS IN CIRCLE OPTIMIZATION 0.0067834 DEVIATES SIGNIFICANTLY FROM CONSTRAIN CONDITION 0.0050000 IT IS POSSIBLE THAT THE NEXT IRC POINT IS CLOSE TO A MINIMUM This time it may be true that the system is near a minimum, I dont know. When I use the MacMolPlt-program and look at the potential enenrgy surface for the IRC-calculation the system appears NOT to be near a minimum. The potential energy surface is not curved at all for the last points in the IRC-calculation which is in my mind what should happen near the minimum. However, I can be wrong about this. Does anybody know how I should continue to reach the true minimum? I don't think I can restart using the information provided by the program because then I will run into problem 1. Thanks in advance Fredrik Blomgren From owner-chemistry@ccl.net Tue Apr 3 10:31:01 2007 From: "Roman D. Gorbunov gorbunov*theochem.uni-frankfurt.de" To: CCL Subject: CCL:G: Units of the transition dipole moments in Gaussian output. Message-Id: <-33956-070403102516-7768-W4UIxeGd8vyG3oemz8pPTw#%#server.ccl.net> X-Original-From: "Roman D. Gorbunov" Date: Tue, 3 Apr 2007 10:25:12 -0400 Sent to CCL by: "Roman D. Gorbunov" [gorbunov . theochem.uni-frankfurt.de] Dear All, I need to calculate transition dipole moments of a molecules (with the Gaussian program). I almost succeed with that. I know that in the input file I have to put "IOP(7/33=1)" and in the out put files I will find lines like the following: Dipole derivatives wrt mode 1: 6.63698D-04 3.58316D-02 2.60498D+00 Dipole derivatives wrt mode 2: -8.98377D-03 -1.05618D-02 1.02878D+00 This is exactly what I need. The only problem is that I do not know the units in which the dipole transition dipole moments are given. Does anybody know that? Or may be somebody know where I can read that about? Thanks, Roman. From owner-chemistry@ccl.net Tue Apr 3 12:10:01 2007 From: "Per Jr. Greisen pgreisen- -gmail.com" To: CCL Subject: CCL: PM3 electronic density etc Message-Id: <-33957-070403103245-9278-WqZzB7pbKs/mARKt/9zl/A[A]server.ccl.net> X-Original-From: "Per Jr. Greisen" Content-Type: multipart/alternative; boundary="----=_Part_11569_17410168.1175610738303" Date: Tue, 3 Apr 2007 16:32:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Per Jr. Greisen" [pgreisen() gmail.com] ------=_Part_11569_17410168.1175610738303 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all I have made some qm simulation of different molecules using gamess and if I use PM3 it is not possible for me to visualize orbitals, electronic density, or electrostatic potential - if I on the other hand use DFT or RHF it is no problem - it that because of PM3 or should I active some specific out put in gamess? Any help or advice appreciated. Thanks in advance. best regards Per ------=_Part_11569_17410168.1175610738303 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all

I have made some qm simulation of different molecules using gamess and if I use PM3 it is not possible for me to visualize orbitals, electronic density, or electrostatic potential - if I on the other hand use DFT or RHF it is no problem - it that because of PM3 or should I active some specific out put in gamess?

Any help or advice appreciated. Thanks in advance.
 best regards
Per
------=_Part_11569_17410168.1175610738303-- From owner-chemistry@ccl.net Tue Apr 3 13:10:01 2007 From: "Sachin Tyagi sachintyagi1__gmail.com" To: CCL Subject: CCL: Input file Message-Id: <-33958-070403121742-16443-01b+x5BRaySQ7yp4JvqauA__server.ccl.net> X-Original-From: "Sachin Tyagi" Date: Tue, 3 Apr 2007 12:17:38 -0400 Sent to CCL by: "Sachin Tyagi" [sachintyagi1 .. gmail.com] Hi can anybody please tell me or show me example of, how to put two molecules in one input file. I want to find the transition state using QST2/QST3 keywords. Thanks Sachin From owner-chemistry@ccl.net Tue Apr 3 14:41:01 2007 From: "Shobe, David David.Shobe===sud-chemie.com" To: CCL Subject: CCL: Input file Message-Id: <-33959-070403140444-5450-BbgGIWqRr2KLrAsDdmnSfQ+*+server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 3 Apr 2007 20:04:24 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe()sud-chemie.com] Sachin, With some front-ends you have to save each geometry (initial, TS, final) as a separate file, and then use a text editor to cut and paste everything together. Construct and save the initial geometry and then !important! modify the initial geometry to form the TS and then the product. If you build each geometry from scratch you're much more likely to make a mistake. Regards, --David Shobe Süd-Chemie, Inc. Attention to detial is essentail. -----Original Message----- > From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net] Sent: Tuesday, April 03, 2007 12:18 PM To: Shobe, David Subject: CCL: Input file Sent to CCL by: "Sachin Tyagi" [sachintyagi1 .. gmail.com] Hi can anybody please tell me or show me example of, how to put two molecules in one input file. I want to find the transition state using QST2/QST3 keywords. Thanks Sachinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Tue Apr 3 18:00:00 2007 From: "Cory Pye cpye-#-crux.smu.ca" To: CCL Subject: CCL: Input file Message-Id: <-33960-070403174525-30290-fbHvn1kyfXel/BuO7rteQg++server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 3 Apr 2007 18:45:14 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye(~)crux.smu.ca] Hello CCLers (esp Sachin Tyagi), Here is an example of an input file for a QST3 calc. This was a particularly nasty TS to find, as numerous calculations with an MP2/6-31g* geometry, MO guess and Hessian guess failed. It is the fragmentation of a methyltriazenyl anion into dinitrogen and methylamide ion. -Cory %rwf=/disc34/tmp/cpye/ %NoSave %chk=HNNNMe_-_ZE_frag_LST %mem=512Mb #N mp2/6-31+g* FOpt=(CalcFC,QST3,Path=20) Freq Reactant -1 1 N1 N2 N1 N2N N3 N2 N3N N1 N3NN C1 N1 C1N N2 C1NN N3 C1NNN H3 N3 H3N N2 H3NN N1 H3NNN H1A C1 H1AC N1 H1ACN N2 H1ACNN H1B C1 H1BC N1 H1BCN N2 H1BCNN H1C C1 H1CC N1 H1CCN N2 H1CCNN N2N=1.31101371 N3N=1.33796951 C1N=1.46397532 H3N=1.02857358 H1AC=1.10399525 H1BC=1.10398579 H1CC=1.09605862 N3NN=117.59023611 C1NN=113.7780536 H3NN=102.23467989 H1ACN=111.69183183 H1BCN=111.69453409 H1CCN=107.37189862 C1NNN=-0.00019353 H3NNN=179.98234974 H1ACNN=58.98790887 H1BCNN=-58.96527311 H1CCNN=-179.99289758 Product -1 1 N1 N2 N1 N2N N3 N2 N3N N1 N3NN C1 N3 C1N N2 C1NN N1 C1NNN H3 N3 H3N N2 H3NN N1 H3NNN H1A C1 H1AC N3 H1ACN N2 H1ACNN H1B C1 H1BC N3 H1BCN N2 H1BCNN H1C C1 H1CC N3 H1CCN N2 H1CCNN N2N=1.13207902 N3N=3.04265528 C1N=1.45150012 H3N=1.03197083 H1AC=1.12375843 H1BC=1.10417449 H1CC=1.12375896 N3NN=79.28215429 C1NN=97.34347942 H3NN=153.85360832 H1ACN=116.73763699 H1BCN=108.72680796 H1CCN=116.73752364 C1NNN=91.43934317 H3NNN=247.36411848 H1ACNN=107.25877488 H1BCNN=-10.80295899 H1CCNN=231.1350411 Guess TS -1 1 N1 N2 N1 N2N N3 N2 N3N N1 N3NN C1 N1 C1N N2 C1NN N3 C1NNN H3 N3 H3N N2 H3NN N1 H3NNN H1A C1 H1AC N1 H1ACN N2 H1ACNN H1B C1 H1BC N1 H1BCN N2 H1BCNN H1C C1 H1CC N1 H1CCN N2 H1CCNN N2N=1.21224981 N3N=1.38484928 C1N=2.40729226 H3N=1.04350867 H1AC=1.0915791 H1BC=1.10057133 H1CC=1.09297596 N3NN=119.20689995 C1NN=84.3980526 H3NN=105.78763147 H1ACN=89.3916906 H1BCN=147.70058149 H1CCN=85.98798999 C1NNN=-8.19672365 H3NNN=127.38226186 H1ACNN=124.76474511 H1BCNN=-2.41252662 H1CCNN=-124.60993488 On Tue, 3 Apr 2007, Shobe, David David.Shobe===sud-chemie.com wrote: > > Sent to CCL by: "Shobe, David" [David.Shobe()sud-chemie.com] > Sachin, > > With some front-ends you have to save each geometry (initial, TS, final) as a separate file, and then use a text editor to cut and paste everything together. Construct and save the initial geometry and then !important! modify the initial geometry to form the TS and then the product. If you build each geometry from scratch you're much more likely to make a mistake. > > -----Original Message----- > > From: owner-chemistry##ccl.net [mailto:owner-chemistry##ccl.net] > Sent: Tuesday, April 03, 2007 12:18 PM > To: Shobe, David > Subject: CCL: Input file > > > Sent to CCL by: "Sachin Tyagi" [sachintyagi1 .. gmail.com] > Hi can anybody please tell me or show me example of, how to put two molecules in one input file. I want to find the transition state using QST2/QST3 keywords. > > Thanks > ************* ! 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(0)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 Tue Apr 3 21:45:01 2007 From: "Dan C Fara dfara%x%salud.unm.edu" To: CCL Subject: CCL: melting point Message-Id: <-33961-070403114646-8695-wyHnzV6jNE4KS/7no6CETA=server.ccl.net> X-Original-From: "Dan C Fara" Date: Tue, 3 Apr 2007 11:46:42 -0400 Sent to CCL by: "Dan C Fara" [dfara!A!salud.unm.edu] Dear All: Is there any free software that can be used for estimating the melting point values of organic compounds? Thanks. Dan Fara Univ. of New Mexico, Division of Biocomputing From owner-chemistry@ccl.net Tue Apr 3 23:23:01 2007 From: "Soren Eustis soren_+_jhu.edu" To: CCL Subject: CCL: melting point Message-Id: <-33962-070403232123-16884-Vv8/lDI8lg6si7vU9T00wg*_*server.ccl.net> X-Original-From: "Soren Eustis" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 3 Apr 2007 23:20:17 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren##jhu.edu] The EPA EPIWin package can do this. Go to epa.gov and search for epiwin. You ought to be able to find it. Soren Eustis -----Original Message----- > From: owner-chemistry~!~ccl.net [mailto:owner-chemistry~!~ccl.net] Sent: Tuesday, April 03, 2007 11:47 AM To: Eustis, Soren Subject: CCL: melting point Sent to CCL by: "Dan C Fara" [dfara!A!salud.unm.edu] Dear All: Is there any free software that can be used for estimating the melting point values of organic compounds? Thanks. Dan Fara Univ. of New Mexico, Division of Biocomputinghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt