From javito@netcom.com Tue Apr 26 01:31:33 1994 Received: from netcom.com for javito@netcom.com by www.ccl.net (8.6.4/930601.1506) id AAA03596; Tue, 26 Apr 1994 00:52:30 -0400 Received: by netcom.com (8.6.8.1/SMI-4.1/Netcom) id VAA28177; Mon, 25 Apr 1994 21:47:08 -0700 From: javito@netcom.com (James Vito) Message-Id: <199404260447.VAA28177@netcom.com> Subject: PDB Format ? To: chemistry@ccl.net Date: Mon, 25 Apr 1994 21:47:07 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 114 I was wondering if anyone knew where a detailed description of the PDB format could be found. Thanks. Jim Vito From P84031@VM.BIU.AC.IL Tue Apr 26 03:31:38 1994 Received: from phem3 for P84031@VM.BIU.AC.IL by www.ccl.net (8.6.4/930601.1506) id DAA04415; Tue, 26 Apr 1994 03:01:20 -0400 Received: from VM.BIU.AC.IL (MAILER@BARILVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HBM68KYOXC99F1KO@phem3.acs.ohio-state.edu>; Tue, 26 Apr 1994 03:01:06 EDT Received: from VM.BIU.AC.IL (NJE origin P84031@BARILVM) by VM.BIU.AC.IL (LMail V1.2a/1.8a) with BSMTP id 2269; Tue, 26 Apr 1994 09:38:40 +0300 Date: Tue, 26 Apr 94 09:37:36 IDT From: "Dr. Pinchas Aped" Subject: ab initio matrix elements calc. To: CHEMISTRY@ccl.net Message-id: <01HBM68KYOXE99F1KO@phem3.acs.ohio-state.edu> MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Dear Netters: Does anybody have or know of any ab initio codes that can calculate first and second derivative matrix elements between orthogonal wave functions - the kind that appear in Born-Oppenheimer couplings? Any help will be greatly appreciated. Pinchas Aped ------------------------------------------------------------------------ Dr. Pinchas Aped Tel.: (+972-3) 531-8634 Department of Chemistry FAX : (+972-3) 535-1250 Bar-Ilan University E-Mail: P84031@BARILVM (bitnet) 52900 Ramat-Gan, ISRAEL aped@gefen.cc.biu.ac.il ------------------------------------------------------------------------ From Patrick.Bultinck@rug.ac.be Tue Apr 26 03:33:50 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id DAA04567; Tue, 26 Apr 1994 03:28:01 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA10634 (5.67b/IDA-1.5 for ); Tue, 26 Apr 1994 09:27:32 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA02111; Tue, 26 Apr 94 09:24:42 +0200 Date: Tue, 26 Apr 1994 09:24:41 +0200 (MET DST) From: Patrick Bultinck Subject: Re:Ethylen calculation with GAMESS To: chemistry@ccl.net In-Reply-To: <01HBLL24R0YA8WWL50@MPS.OHIO-STATE.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1759 If I recall correctly... When you input a Z-matrix, you would normally have to state COORD=ZMT in your $CONTRL group. Looking at the GAMESS (US,1993) manual I believe that the only occassion on which you can use symmetry as well as giving only the symmetry unique atoms at the same time is when you choose COORD=UNIQUE. This however requires you to use cartesian coordinates. When you really wish to use a Z-matrix (which I do) you have to input all atoms. Specifying a symmetry point group is useful because symmetry may be exploited in your integral evaluations e.g. Also the result of an optimisation will never yield a lower symmetry that the one given at the beginning. Bear in mind that your Z-matrix has to respect the symmetry point group you gave... Best regards, |-----------------------------------------------------------------------| | C-C Patrick Bultinck | | / \ Dept. Physical & Inorganic Chemistry | | C-O O-C Section Quantum Chemistry | | | | University of Ghent | | C-O O-C Krijgslaan 281 (S-3) | | \ / 9000 Gent | | C-C Belgium | | Tel. Int'l code/32/9/264.44.44 | | Macrocycles Fax. Int'l code/32/9/264.49.83 | | Quantum Chemical E-mail : Patrick.Bultinck@rug.ac.be | | Calculations | |-----------------------------------------------------------------------| From J0LIU001@ULKYVX.LOUISVILLE.EDU Tue Apr 26 04:31:35 1994 Received: from ulkyvx.louisville.edu for J0LIU001@ULKYVX.LOUISVILLE.EDU by www.ccl.net (8.6.4/930601.1506) id DAA04927; Tue, 26 Apr 1994 03:58:14 -0400 Received: from ULKYVX.LOUISVILLE.EDU by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #6403) id <01HBM3VN4RNK9QVAGK@ULKYVX.LOUISVILLE.EDU>; Tue, 26 Apr 1994 02:07:44 EST Date: Tue, 26 Apr 1994 02:07:44 -0500 (EST) From: "jianling liu-->DERBY HORSE" Subject: mosaic To: chemistry@ccl.net Message-id: <01HBM3VN5KLE9QVAGK@ULKYVX.LOUISVILLE.EDU> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: J0LIU001 MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT hello netters: can some computer guru teach me how to install mosaic on PC (which does has TCP access to the internet) ? I know I do need winsock 1.1-compliant, but where? I got the Trumpet Winsock , which is a shareware. But I can not figure out how...? Will it require me to uninstall my original networking package(which is PCTCP ,from FTP INC.) enjoy the beautiful spring ! From Patrick.Bultinck@rug.ac.be Tue Apr 26 04:34:07 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id DAA04812; Tue, 26 Apr 1994 03:37:41 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA10740 (5.67b/IDA-1.5 for ); Tue, 26 Apr 1994 09:37:12 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA02416; Tue, 26 Apr 94 09:34:22 +0200 Date: Tue, 26 Apr 1994 09:34:22 +0200 (MET DST) From: Patrick Bultinck Subject: Use of symmetry in optimisations To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2092 Netters, I have just sent a reply to a question concerning the use of a Z-matrix for a calculation on ethylene, using GAMESS (US). As a direct consequence I rembered something that I am not very comfortable with... In section 4 of the GAMESS manual, I find under a title : ***The role of symmetry*** that it is best to use symmetry during an optimisation. However GAMESS never lowers the symmetry during an optimisation. It is a well known fact that sometimes a minimal energy structure differs (a lot) from the symmetry you might expect. Isn't it then safer to always do unconstrained optimisations, and if you think that the result differs so little from a certain symmetry point group, you can always do a symmetry-optimisation starting from the geometry with that symmetry, and compare energies... The most important disadvantage is off course that it often takes a lot of time to reach a certain symmetry point group, when you start from zero-symmery. Any thoughts on this... Those interested in a summary of some sort should send me a note, if enough interest exists, I send one to CCL. Thanks, |-----------------------------------------------------------------------| | C-C Patrick Bultinck | | / \ Dept. Physical & Inorganic Chemistry | | C-O O-C Section Quantum Chemistry | | | | University of Ghent | | C-O O-C Krijgslaan 281 (S-3) | | \ / 9000 Gent | | C-C Belgium | | Tel. Int'l code/32/9/264.44.44 | | Macrocycles Fax. Int'l code/32/9/264.49.83 | | Quantum Chemical E-mail : Patrick.Bultinck@rug.ac.be | | Calculations | |-----------------------------------------------------------------------| From cosgrove@zeneca-ph.co.uk Tue Apr 26 05:31:43 1994 Received: from eros.britain.eu.net for cosgrove@zeneca-ph.co.uk by www.ccl.net (8.6.4/930601.1506) id EAA05470; Tue, 26 Apr 1994 04:59:20 -0400 Received: from zeneca-ph.co.uk by eros.britain.eu.net with UUCP id ; Tue, 26 Apr 1994 09:58:33 +0100 From: Dave Cosgrove Date: Tue, 26 Apr 94 09:50:46 GMT Message-Id: <19412.9404260950@iciukph.zeneca-ph.co.uk> Received: from zeneca by iciukph.zeneca-ph.co.uk; Tue, 26 Apr 94 09:50:46 GMT To: chemistry@ccl.net Subject: PDB formats Presumably the definitive work on PDB formats is supplied by Brookhaven. A copy is in /pub/format.desc.ps at pdb.pdb.bnl.gov. *** --- __o __o __o *** *** ------ \<, \<, \<, *** *** ----- ( )/ ( ) ( )/ ( ) ( )/ ( ) *** +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dave Cosgrove Zeneca Pharmaceuticals ---------------------------------- 26T8, Mereside | Tel (0)625 515521 | Alderley Park | Fax (0)625 586900 | Macclesfield | | Cheshire | email cosgrove@zeneca-ph.co.uk | SK10 4TG ---------------------------------- Great Britain +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From dvsg23424@ggr.co.uk Tue Apr 26 06:31:41 1994 Received: from gate.ggr.co.uk for dvsg23424@ggr.co.uk by www.ccl.net (8.6.4/930601.1506) id FAA05961; Tue, 26 Apr 1994 05:39:59 -0400 From: Received: from mailhub.ggr.co.uk by gate.ggr.co.uk; Tue, 26 Apr 1994 10:38:12 +0100 Message-Id: <12820.199404260934@mailhub.ggr.co.uk> Received: from UKSYSA.ggr.co.uk by mailhub.ggr.co.uk; Tue, 26 Apr 1994 10:34:44 +0100 Date: 26 Apr 94 10:12:00 BST Subject: CD spectra To: chemistry@ccl.net Dear All, I am hoping to contact anyone working in the area of circular dichroism (CD), especially any groups working on the interpretation, quantification or prediction of the spectra by quantum mechanical methods. I will summarise for the net if appropriate. Darren. Dr D Green Glaxo R&D Ware Herts. UK From moshe_o@VNET.IBM.COM Tue Apr 26 09:31:41 1994 Received: from VNET.IBM.COM for moshe_o@VNET.IBM.COM by www.ccl.net (8.6.4/930601.1506) id IAA07064; Tue, 26 Apr 1994 08:51:50 -0400 Message-Id: <199404261251.IAA07064@www.ccl.net> Received: from HAIFASC3 by VNET.IBM.COM (IBM VM SMTP V2R2) with BSMTP id 1652; Tue, 26 Apr 94 08:50:53 EDT Date: Tue, 26 Apr 94 15:28:27 IDT From: "Moshe Olshansky" To: chemistry@ccl.net Subject: Hartree Fock on PC Dear netters! We are trying to speed up the computation of 4 centers 2 electron repulsion integrals by using a new formula. To test our algorithm (in the future) and to get started beyond just formulae (in the present) we need a package doing HF computations. We would like to replace their routines computing the above ERIs by ours (both to compare speeds and to verify the correctness of our routines). To be able to do so we will obviously need the source code of the original package. Since only 1.5 to 2 people are working on this subject at our institution, it would be very difficult to get even RS/6000 just for ourselves, and it is always a problem to get enough disk space for our purposes (even though we are at IBM). Moreover, since this project is aside from the mainstream of things being done here, we won't like to invest too much funds in it (at least at this stage). So we are thinking of buying a Pentium-based PC (or PS) with a relatively large disk to be used almost solely for our project. My question is: could anybody recommend a decent package doing HF on PC (as stated earlier, getting the source code is absolutely a MUST for us)? As you may guess, we do not need (and to be honest, a bit afraid of) too advanced graphics. Both public domain and (reasonably priced) commercial packages are O.K. Thank you very much in advance Moshe Olshansky IBM Science & Technology Haifa, Israel From DURRAN@chem.surrey.ac.uk Tue Apr 26 11:32:27 1994 Received: from mail-server.surrey.ac.uk for DURRAN@chem.surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id LAA09246; Tue, 26 Apr 1994 11:22:39 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <20569-0@mail-server.surrey.ac.uk>; Tue, 26 Apr 1994 16:22:01 +0100 Received: from chemcharon.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (1.37.109.8/16.2) id AA25281; Tue, 26 Apr 1994 16:21:57 +0100 Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.940426162152.480; 26 Apr 94 16:28:22 +500 Message-Id: To: chemistry@ccl.net From: Michael Organization: Chemistry Department, Uni of Surrey Date: Tue, 26 Apr 1994 16:21:50 GMT Subject: PSI88/Graphics libraries Priority: normal X-Mailer: WinPMail v1.0 (R1) Dear All, I am trying to compile PSI88 on an SG. But I don't think I have the required libraries to plot (GKS? PHIGS?). I wonder if anybody knows of an FTP site where I can obtain them ? Thankyou in advance. Mike. (DURRAN@CHEM.SURREY.AC.UK) From jxh@ibm12.biosym.com Tue Apr 26 12:31:47 1994 Received: from ibm12.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.4/930601.1506) id MAA10301; Tue, 26 Apr 1994 12:28:52 -0400 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA14526; Tue, 26 Apr 1994 09:28:25 -0700 Date: Tue, 26 Apr 1994 09:28:25 -0700 From: jxh@ibm12.biosym.com (Joerg Hill) Message-Id: <9404261628.AA14526@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: Re: CCL:Atom-Atom partitioning of El. Energy Look at "Theory of multicenter partioning of molecular energies", C.S. Ewig, J. Chem. Phys. 92 (1990), 6620. This paper contains some examples with standard Pople basis sets. Joerg-R. Hill From shepard@dirac.tcg.anl.gov Tue Apr 26 12:33:01 1994 Received: from dirac.tcg.anl.gov for shepard@dirac.tcg.anl.gov by www.ccl.net (8.6.4/930601.1506) id MAA10242; Tue, 26 Apr 1994 12:21:40 -0400 Received: by dirac.tcg.anl.gov (4.1/SMI-4.1) id AA16245; Tue, 26 Apr 94 11:21:40 CDT Date: Tue, 26 Apr 94 11:21:40 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9404261621.AA16245@dirac.tcg.anl.gov> To: CHEMISTRY@ccl.net Subject: CCL:helix dipole Cc: shepard@tcg.anl.gov Gregory King (GKING@arserrc.gov) wrote: >>On Fri, 22 Apr 1994, Srinivasan S. Iyengar wrote: [...] >>> (a) Find the center of mass of all the positive charges. ^^^^^^^^^^^^^^ >>> (b) Find the center of mass of all the negative charges. ^^^^^^^^^^^^^^ >>> (c) Find the dipole moment between these two points. [...] >As was noted by a previous poster, the definition of the dipole moment vector >is: > > mu_x = SUM_i q_i * (x_i - x0) > mu_y = SUM_i q_i * (y_i - y0) > mu_z = SUM_i q_i * (z_i - z0) > >where mu_x, mu_y, mu_z are the components of the dipole moment vector mu along >the x, y, z axes (respectively); q_i is the charge of entity i; x_i, y_i, z_i >are the cartesian coordinates of entity i; and x0, y0, z0 are the cartesian >coordinates of a reference point. For electrically neutral molecules mu is >independent of the reference point. Otherwise the molecule's >center of mass ^^^^^^^^^^^^^^ >is conventionally used as (x0,y0,z0). [...] Basically I think what Gregory King said is correct. I just wanted to point out that it is "center of charge" and not "center of mass" that should be used in Iyengar's approach. I don't know about the conventional choice of origin for charged molecules; is it center of charge or center of mass? $.02 -Ron Shepard From windus@mercury.chem.nwu.edu Tue Apr 26 12:34:05 1994 Received: from mercury.chem.nwu.edu for windus@mercury.chem.nwu.edu by www.ccl.net (8.6.4/930601.1506) id MAA10027; Tue, 26 Apr 1994 12:00:26 -0400 Received: by mercury.chem.nwu.edu (AIX 3.2/UCB 5.64/4.03.02) id AA35877; Tue, 26 Apr 1994 10:58:49 -0500 From: windus@mercury.chem.nwu.edu (Theresa Windus) Message-Id: <9404261558.AA35877@mercury.chem.nwu.edu> Subject: Re: CCL:Use of symmetry in optimisations To: Patrick.Bultinck@rug.ac.be (Patrick Bultinck) Date: Tue, 26 Apr 1994 10:58:48 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: from "Patrick Bultinck" at Apr 26, 94 09:34:22 am X-Mailer: ELM [version 2.4 PL23alpha2] Content-Type: text Content-Length: 2607 In reply to Patrick Bultinck's question about symmetry: > > In section 4 of the GAMESS manual, I find under a title : ***The role of > symmetry*** that it is best to use symmetry during an optimisation. > However GAMESS never lowers the symmetry during an optimisation. It is a > well known fact that sometimes a minimal energy structure differs (a lot) > from the symmetry you might expect. Isn't it then safer to always do > unconstrained optimisations, and if you think that the result differs so > little from a certain symmetry point group, you can always do a > symmetry-optimisation starting from the geometry with that symmetry, and > compare energies... > > The most important disadvantage is off course that it often takes a lot > of time to reach a certain symmetry point group, when you start from > zero-symmery. > Several quantum chemistry codes do not lower symmetry during an optimization. As a matter of fact, if the gradient does not reflect the full symmetry of the point group used, there is a symmetrization problem. Concerning using point group symmetry or not: If a molecule has a possibility of a higher point group symmetry than C1, it is a good idea to exploit it. Integrals, optimizations, etc. can run faster if the program is able to use symmetry information. While the molecule with symmetry may not be the global minimum on the surface it is certainly some sort of stationary point on the surface. (Note that it might be a transition state or "higher order transition state". If the stationary point is a transition state, it is possible to follow the imaginary frequency leading to a minimum. You would also have found an important point on the reaction surface!) Even if you find a non-symmetric minimum that is lower than the symmetric molecule, you are not guaranteed that it is the global minimum. Only in fairly small molecules is it "easy" to verify that the global minimum has been found. As was pointed out, it can take time to "find" symmetry if you don't start out with it. On the other hand, if you have a symmetric molecule, it is possible to distort it into lower symmetry and search for a lower symmetry molecule. My point is that even if it is not necessarily the lowest energy isomer on the surface, a molecule with symmetry may tell you something about the surface and it is a good starting point. Of course, "forcing" a molecule into higher symmetry than is practical is not necessarily a good idea either. Hope this helps, Theresa Windus Department of Chemistry e-mail: windus@chem.nwu.edu Northwestern University From stevens@jordan.uchicago.edu Tue Apr 26 13:31:43 1994 Received: from jordan.uchicago.edu for stevens@jordan.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id MAA10862; Tue, 26 Apr 1994 12:42:19 -0400 Received: by jordan.uchicago.edu (AIX 3.2/UCB 5.64/4.03) id AA17057; Tue, 26 Apr 1994 11:39:23 -0500 Date: Tue, 26 Apr 1994 11:39:23 -0500 From: stevens@jordan.uchicago.edu (Jonathan Stevens) Message-Id: <9404261639.AA17057@jordan.uchicago.edu> To: CHEMISTRY@ccl.net Subject: Ab initio calculation of nuclear derivative couplings Recently, Dr. Pinchas Aped posted an inquiry concerning the existence of ab initio codes capable of calculating first and second (nuclear) derivative matrix elements between orthogonal Born-Oppenheimer wave functions. I, also, would be interested to learn of the existence of any such codes. At the University of Chicago, Professor Karl Freed, in colaboration with the experimental research group of Laurie Butler, has been using ab initio techniques to facilitate the interpretation of experiments probing non-adiabatic reaction dynamics (see, for example, Jensen et al. J. Chem. Phys. 98(4) 2882 (1993)). Professor Freed's research group has discussed plans for the development of techniques for evaluating nuclear radial derivative couplings using the effective valence shell Hamiltonian (Hv). As a researcher with Professors Butler and Freed I would be interested in hearing form anyone involved in projects concerned with the evaluation of such couplings. With thanks, Jonathan Stevens From jkl@ccl.net Tue Apr 26 13:33:01 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id MAA10933; Tue, 26 Apr 1994 12:46:01 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id MAA02420; Tue, 26 Apr 1994 12:46:01 -0400 Date: Tue, 26 Apr 1994 12:46:01 -0400 Message-Id: <199404261646.MAA02420@krakow.ccl.net> To: chemistry@ccl.net Subject: Doc on finding e-mail addresses of people Cc: jkl@ccl.net Dear Netters As you know, address enquires are strongly discouraged on the list. To lower the noise/information ratio, I offered my body to help in finding the email addresses/phones. However, the question on "How do I find the e-mail address of person XYZ" is the one I get frequently. I wrote a one-pager on it. Since I am no guru on this, I would appreciate your additions, comments and experiences, so I can make this doc better. Of course, when you look for somebody, you can always ask me, when you lost hope, but remember that I am only human and have essentially the same resources as most of you have. Also, at some point, I will try to make a database of "computational chemists" (whatever it means), but not this or next month, probably after summer. The "How to..." doc is available via: 1) e-mail send a message: select chemistry get info/finding-e-mail-address quit to MAILSERV@ccl.net 2) ftp: ftp www.ccl.net Login: anonymous Name: Your_email_address ftp> cd /pub/chemistry/info ftp> get finding-e-mail-address ftp> quit 3) gopher: gopher www.ccl.net 73 info finding-e-mail-address 4) WWW http://ccl.net/~ccl/info.html or gopher://www.ccl.net:73/00/info/finding-e-mail-address Jan -------- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From CULMER@uoft02.utoledo.edu Tue Apr 26 13:39:36 1994 Received: from uoft02.utoledo.edu for CULMER@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id MAA10476; Tue, 26 Apr 1994 12:33:08 -0400 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #5345) id <01HBMQ2PTW3K000PJW@UOFT02.UTOLEDO.EDU>; Tue, 26 Apr 1994 12:32:25 EST Date: Tue, 26 Apr 1994 12:32:25 -0500 (EST) From: "Chuck Ulmer, D.A.Smith Group" Subject: Re: Symmetry To: chemistry@ccl.net Cc: Patrick.Bultinck@rug.ac.be Message-id: <01HBMQ2PU5QQ000PJW@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: IN%"Patrick.Bultinck@rug.ac.be" MIME-version: 1.0 Content-transfer-encoding: 7BIT Patrick Bultinck writes..... >Netters, > >I have just sent a reply to a question concerning the use of a Z-matrix >for a calculation on ethylene, using GAMESS (US). > >As a direct consequence I rembered something that I am not very >comfortable with... > >In section 4 of the GAMESS manual, I find under a title : ***The role of >symmetry*** that it is best to use symmetry during an optimisation. >However GAMESS never lowers the symmetry during an optimisation. It is a >well known fact that sometimes a minimal energy structure differs (a lot) >from the symmetry you might expect. Isn't it then safer to always do >unconstrained optimisations, and if you think that the result differs so >little from a certain symmetry point group, you can always do a >symmetry-optimisation starting from the geometry with that symmetry, and >compare energies... > >The most important disadvantage is off course that it often takes a lot >of time to reach a certain symmetry point group, when you start from >zero-symmery. > >Any thoughts on this... Yes, I would like to see a discussion on this subject opened up. I would especially be interested in comments from some of the more experienced computation chemists. Also, those persons who did calculations long enough ago when the lack of computer power necessitated the use of symmetry could, I am sure, have some interesting input on this subject. Up to this point, I thought that the use of symmetry in calculations was a big NO-NO because you are arbitrarily constraining the system and "garbage in is garbage out". But I just ran across a time when we had to use symmetry: We are investigating a complexation between a small organic molecule and a fragment containing several metal centers. The whole point is to match the metal orbitals with those calculated for the organic fragment and determine why one fragment reacts one way and other fragments react anther way. The only way that we can make sense out of the orbitals in the organic fragment is to constrain the system to some point group - must get orbital symmetries. So, the questions is: If this works, is it by some stroke of luck or does this reaction ONLY occure if the organic fragment (considering free rotation) reaches d3h symmetry while in the proximity of the metal centers? (I am being facetious to some degree). Don't we, as scientists, have to keep all constraints and limitations of our model in mind when looking at systems and use our chemical intuition as a guide? Isn't the use of symmetry just one more constraint to keep in mind or does the use of symmetry *invalidate* any scientific findings? Of course, the symmetry argument (to use or not to use) probably goes along with the "bigger is better" argument and I will probably still stay away from symmetry as much as possible and run with the largest basis set and highest level of theory that disk allows, provided OSC permits. Chuck -- Charles W. Ulmer, II Graduate Student Senior Scientist D.A.Smith Group DASGroup, Inc. University of Toledo 3807 Elmhurst Road Toledo, OH, 43606 Toledo, OH 43613 phone: (419)537-4028 culmer@uoft02.utoledo.edu fax: (419)537-4033 WE ARE PERHAPS NOT FAR REMOVED FROM THE TIME WHEN WE SHALL BE ABLE TO SUBMIT THE BULK OF CHEMICAL PHENOMENA TO CALCULATION. -- JOSEPH LOUIS GAY-LUSSAC MEMOIRES DE LA SOCIETE D'ARCUEIL, 2, 207 (1808) From billg@SCGROUP.BARRNET.NET Tue Apr 26 14:31:55 1994 Received: from mail.barrnet.net for billg@SCGROUP.BARRNET.NET by www.ccl.net (8.6.4/930601.1506) id NAA12005; Tue, 26 Apr 1994 13:55:48 -0400 Received: from fujitsu1.fai.com by mail.barrnet.net (5.67/1.37) id AA02621; Tue, 26 Apr 94 10:55:47 -0700 Received: from scg.scg.fai.com by fujitsu.fai.com (4.1/SMI-4.1) id AA10765; Mon, 25 Apr 94 15:20:04 PDT Received: by scg.scg.fai.com (4.1/SMI-4.1) id AA00730; Mon, 25 Apr 94 15:21:14 PDT Date: Mon, 25 Apr 94 15:21:14 PDT From: billg@scg.fai.com (Marketing) Message-Id: <9404252221.AA00730@scg.scg.fai.com> To: chemistry@ccl.net Subject: molecular pseudopotentials Netters, We are looking at an excess electron interacting with a large closed-shell system (e.g., an electron tunneling through a protein). This becomes a one-electron problem if the closed-shell system is represented by a pseudopotential. This is very much like effective core potentials for heavy-atom calculations, except here we are interested in molecular systems and do not use basis sets. Atom-centered potentials where the pseudopotential is local (given simply as a function of R) are available. However, pi systems are not well represented as a sum of atom-centered functions ... so how would one go about it? Perhaps something simple akin to a particle in a box over the region where the pi cloud resides might do? Any insight, facts, or opinions will be most appreciated. I will summarize the responses if there is interest. -Bill ********************************************************************* * William A. Glauser, Ph.D. | Internet: billg@scg.fai.com * * Computational Chemist | Voice: (610) 436-8125 * * SuperComputer Group | FAX: (610) 430-1526 * * Fujitsu America, Inc. | * ********************************************************************* From psubram@Texaco.COM Tue Apr 26 15:31:56 1994 Received: from Texaco.COM for psubram@Texaco.COM by www.ccl.net (8.6.4/930601.1506) id OAA12883; Tue, 26 Apr 1994 14:51:05 -0400 Received: by Texaco.COM (4.1/SMI-4.1) id AA09624; Tue, 26 Apr 94 13:50:49 CDT Date: Tue, 26 Apr 94 13:50:49 CDT From: psubram@Texaco.COM (Palavo Subramanian) Message-Id: <9404261850.AA09624@Texaco.COM> To: chemistry@ccl.net Subject: Hydrate Inhibitor Hi, I am looking at modeling hydrate inhibitors. If any of you has experience in this could you please contact me via email. These are gas hydrates, I just want some input as to how to go about modeling hydrate inhibitors. Thanks P.S. Subramanian psubram@texaco.com From rgab@purisima.molres.org Tue Apr 26 15:48:25 1994 Received: from purisima.molres.org for rgab@purisima.molres.org by www.ccl.net (8.6.4/930601.1506) id OAA12833; Tue, 26 Apr 1994 14:47:20 -0400 Message-Id: <199404261847.OAA12833@www.ccl.net> Received: by purisima.molres.org (1.37.109.4/16.2) id AA02649; Tue, 26 Apr 94 11:27:44 -0700 Date: Tue, 26 Apr 94 11:27:44 -0700 From: "R.G.A. Bone" To: chemistry@ccl.net Subject: symmetry in electronic structure computations To add a few remarks to Theresa Windus's comments, which are basically all correct. It is true that symmetry is handled differently by different programs. "Gaussian" finds symmetry present in the input nuclear coordinates and applies it unless you explicitly switch it off. But geometry optimizations will typically, irritatingly, quit as soon as a change in point group occurs. It is actually easier to deal with symmetry in programs like "cadpac" where you just input the symmetry-unique atoms and/or specify internal coordinates which are constrained to be related to one another by symmetry. The gradient of the energy w.r.t. nuclear displacements should transform as the totally symmetric 'irrep' in whatever point group you happen to be in. For 'closed-shell' systems (no electronic degeneracies) this means in practice that 'symmetric' structures are usually stationary points. The only distortions to which the energy gradient could be non-zero are totally symmetric. Thus one should be cautious with, say, van der Waals clusters, in which a totally- symmetric distortion which corresponds to dissociation might be favourable if the high-symmetry structure contains repulsions. The matter in 'open-shell' systems is more complicated. Imposing high symmetry on a Jahn-Teller system, for example, will obviously lead to problems. In other systems in which the electronic state does not transform as the totally symmetric irrep, one should be careful. Finally, also in open-shell systems, the use of symmetry in UHF-type calculations contains many 'hidden' pitfalls, most of which are documented. It is critical to examine the wavefunction of whatever state you converge to. One can carry out the calculation in a symmetric nuclear configuration both with and without the constraining the symmetry of the wavefunction. This can lead to massive energetic differences, and totally different behaviour w.r.t. spin-contamination, etc. All results are sensitive to starting guess, etc., and the "solution" can change during the course of an optimization. Advice: examine your *whole* computer output very thoroughly! The belief that 'transition states' are high-symmetry species is all-but totally dispelled at this time. Basically, for minima, anything goes, but there is no guarantee that "nature" favours symmetric structures over their lower-symmetry counterparts. (One only has to look at van der Waals molecules to see evidence of that.) For transition states, all that the supposedly-useful symmetry theorems tell you is an upper-limit on the point group symmetry but even that is almost always a lower symmetry than either of the pertinant minima. In general, surfaces are sufficiently complicated that transition states end up having little symmetry at all. If you somehow converged to one during a _minimization_ then you either made a shrewd guess or were very lucky. Finally, there is an unfortunate tendency, which is widespread, to refer to stationary points at which more than one Hessian eigenvalue is negative as "higher _order_ saddles". This nomenclature is incorrect. The 'order' of a stationary point specifies the lowest non-vanishing term in a locally- expanded Taylor series. Thus almost all stationary points that we, as "chemists" meet, are second-order points, because they have non-vanishing second derivatives. Third order points have zero-second derivatives, and are characterised by cubic terms in the potential, e.g., "monkey-saddles". As has been discussed many times, these points are extremely rare and, to my knowledge, a 'real' one has yet to be conclusively identified on a molecular PES. The characterisation of second-order stationary points is achieved by stating the Hessian "index" - the number of negative eigenvalues. Thus a transition state has a Hessian index of 1. Structures with indexes>1 are 'maxima' in a subspace. The term "rank" also has a distinct meaning - it is the number of non-zero Hessian eigenvalues - and rarely finds application in chemistry. All these terms are described more fully in P.G.Mezey's book, "Potential Energy Hypersurfaces", Elsevier. This point might seem to be pedantic, but there are a number of terms to be used, and each has a specific and DISTINCT meaning: 'order', 'index', 'rank' and also 'signature'. (For the meaning of the last of these, see R.F.W. Bader, "The Theory of Atoms in Molecules", OUP.) Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org From bewilson@emn.com Tue Apr 26 16:31:57 1994 Received: from emngw1.emn.com for bewilson@emn.com by www.ccl.net (8.6.4/930601.1506) id QAA14784; Tue, 26 Apr 1994 16:13:52 -0400 Received: by emngw1.emn.com (AIX 3.2/UCB 5.64/4.03) id AA21701; Tue, 26 Apr 1994 15:20:06 -0400 Date: Tue, 26 Apr 1994 15:20:06 -0400 From: bewilson@emn.com (Wilson_Bruce) Message-Id: <9404261920.AA21701@emngw1.emn.com> To: chemistry@ccl.net Subject: Re: Symmetry Regarding the use of symmetry in quantum calculations. Most of the stuff I've looked at never was more than C1 to start with so it's not been a problem. By tinkering with the Z-matrix and enforcing certain types of symmetry (like requiring selected C-H bonds to have the same length), I've seen between 10 and 300% differences in speed for test systems I've worked with. For example, in dimethyl terephthalate, I can require all of the aromatic C-H bonds to be of the same length, and I can require certain other bonds (e.g. both carbonyls) to be the same length. Any time I'm really interested in the most accurate, quantitative results, I'll do a symmetry disallowed optimization, or at least a symmetry disallowed frequency calculation, to see how far from a true minimum I happen to be. My opinion (worth what you paid for it ;-) ): Symmetry can be used to advantage, particularly less restrictive symmetry than full point group symmetry, but you take a risk of getting a misleading answer when you do that. The classic one (and one that a student of mine got tripped up on this fall) was keeping the symmetry and getting a planar biphenyl. If I'm really concerned, I've been known to run the starting geometry through a few femtoseconds of dynamics to completely ruin any symmetry/stationary points I've happened to introduce in constructing the molecule. Bruce Wilson (bewilson@emn.com) From dan@omega.chem.yale.edu Tue Apr 26 16:35:51 1994 Received: from omega.chem.yale.edu for dan@omega.chem.yale.edu by www.ccl.net (8.6.4/930601.1506) id QAA15137; Tue, 26 Apr 1994 16:29:07 -0400 Received: by omega.chem.yale.edu; Tue, 26 Apr 94 16:28:26 -0400 From: Dan Severance Message-Id: <9404262028.AA26826@omega.chem.yale.edu> Subject: Re: CCL:symmetry in electronic structure computations To: CHEMISTRY@ccl.net Date: Tue, 26 Apr 94 16:28:25 EDT In-Reply-To: <199404261847.OAA12833@www.ccl.net>; from "R.G.A. Bone" at Apr 26, 94 11:27 am Organization: Laboratory for Computational Chemistry X-Mailer: ELM [version 2.3 PL11] Hi, Just a few more remarks regarding Richard Bone's comments: > "Gaussian" finds symmetry present in the input nuclear coordinates and > applies it unless you explicitly switch it off. But geometry optimizations > will typically, irritatingly, quit as soon as a change in point group occurs. If you wish to force the symmetry, this can be averted by using the same variable name for the symmetric lengths and angles, thus there is no possibility of a change in point group. > The gradient of the energy w.r.t. nuclear displacements should transform as > the totally symmetric 'irrep' in whatever point group you happen to be in. >For 'closed-shell' systems (no electronic degeneracies) this means in practice > that 'symmetric' structures are usually stationary points. The only There are actually a number of cases where this is indeed not the case. Amides, for instance, tend not to be planar but are slightly puckered at the N. It often doesn't take much energy to force it to be planar, but non-planar is the minimum at any levels of theory that I've seen. Also, quite bulky molecules often avoid a symmetric form in favor of spreading out the steric interactions. The only way to be sure anything is really a minimum or a transition state is to perform a frequency calculation at the end, whether or not one uses symmetry in the calculation. I had started the methyl groups in DMA in one orientation and they stayed put, even though I did not invoke symmetry. The frequency calculation showed it to be a transition state, and further optimizations using those forces lead to the minimum structure. The use of symmetry is still quite useful in speeding computations, and the freq. calc. will tell you whether you were correct or incorrect in assuming the particular level of symmetry. (Use individual variables for each bond and angle if you want to optimize further, though!) Dan Severance (APLS - Association for Prevention of Long Sigs) dan@omega.chem.yale.edu From burkhart@goodyear.com Tue Apr 26 16:39:19 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id QAA15163; Tue, 26 Apr 1994 16:31:01 -0400 Received: from rdsrv2 by goodyear.com (4.1/SMI-4.1) id AA15639; Tue, 26 Apr 94 16:31:01 EDT Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA07010; Tue, 26 Apr 94 16:31:00 EDT Received: by rds325 (940406.SGI/931108.SGI.AUTO.ANONFTP) for chemistry@ccl.net id AA01705; Tue, 26 Apr 94 16:30:59 -0400 Date: Tue, 26 Apr 94 16:30:59 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9404262030.AA01705@rds325> To: chemistry@ccl.net Subject: NEOMIG/PAIMG Joint Meeting Agenda ********** GENERAL NOTICE ************* MEETING AGENDA The First Joint Meeting of Northeastern Ohio Modeling Interest Group and Pittsburgh Academic and Industrial Modeling Group FRIDAY MAY 3, 1994 The Wick-Pollock Inn Youngstown, Ohio 9:00 Meeting Registration/Arrival 9:25 Welcoming Remarks Dr. Peter J. Kasvinsky, Dean of Graduate Studies Youngstown State University MORNING SESSION Richard Ross, PPG Industries, Presiding 9:30 M. Rush & David Ewing John Carroll University "An Ab Initio Quantum Chemical Model of the Active Site of Hemocyanin" 10:00 Tom Fabish Aluminum Corporation of America "Initial Molecular Modeling Tests for a Relationship between Molecular Compliance and Invoked Biological Response for Polychlorinated Biphenyls (PCBs)" 10:30 Charles W. Ulmer, II and Douglas A. Smith University of Toledo "Theoretical Studies of Substituent Effects on the Pentadienyl Cation Electocyclization" 11:00 Morning Break 11:30 Janet Del Bene Youngstown State University "An Ab Initio Study of Complexes of HF with the Chloromethanes, and Comparison with HCl Chloromethane Complexes" 12:00 Anne Chaka Lubrizol Corporation "A Quantum Mechanical Study of the Mechanisms for the Alkylation of Arylamines" 12:30 - 2:00 LUNCHEON AND POSTER SESSION POSTER PRESENTATIONS 1. Genzo Tanaka University of Akron "Thermal and Mechanical Properties of PVC by Molecular Modeling Techniques" 2. Sergei Chvalun, Muhammad Ishaq and John Blackwell Case Western Reserve University "Structure of Thermotropic Polyesters with Phenyl and Thio-Phenyl Side Chains" 3. Samir Kudchadkar and J.M. Wiest Purdue University "Molecular Dynamics of the Glass-Former ortho-Terphenyl" 4. L. Rendek and David Ewing John Carroll University "Semi-Empirical Quantum Chemical Studies of Hydrogen Transfer Reactions of Hydrocarbons" 5. C.E. Wozny, Bobby Sumpter and Donald Noid Oak Ridge National Laboratory "Novel Methods for Spectral Analysis of Polymers" AFTERNOON SESSION. Craig Burkhart, Goodyear Research, Presiding 2:00 Bobby Sumpter, Donald Noid and Andrei Gakh Oak Ridge National Laboratory "A Computational Paradigm for Predicting Materials Properties" 2:30 Beverly Bendiksen Calgon Corporation "Calcium Carbonate Inhibitor Design - Approach and Methods" 3:00 Donald H. Napper University of Sydney "Modelling Free Radical Entry into Latex Particles in Emulsion Polymerization" 3:30 Donald Noid & Bobby Sumpter Oak Ridge National Laboratory, "Computational Simulations of Polymeric Materials" 4:00 Afternoon Break 4:30 Wayne L. Mattice University of Akron "Local Dynamics in Amorphous Polybutadienes" 5:00 Lynn Brower MasterBuilders "Molecular Modeling for Industrial Materials Product Development - Starting Up" 5:30 Rick Ross PPG Industries "Molecular Mechanics and Dynamics Studies in Research at PPG Industries" ************* -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From U13145@UICVM.CC.UIC.EDU Tue Apr 26 20:31:46 1994 Received: from phem3 for U13145@UICVM.CC.UIC.EDU by www.ccl.net (8.6.4/930601.1506) id UAA19562; Tue, 26 Apr 1994 20:27:04 -0400 Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HBN6R9W5YO99F7SY@phem3.acs.ohio-state.edu>; Tue, 26 Apr 1994 20:26:58 EDT Received: from UICVM (NJE origin U13145@UICVM) by UICVM.CC.UIC.EDU (LMail V1.2a/1.8a) with BSMTP id 8109; Tue, 26 Apr 1994 18:01:49 -0500 Date: Tue, 26 Apr 1994 17:54:18 -0500 (CDT) From: U13145%UICVM.BITNET@phem3.acs.ohio-state.edu Subject: Csp3-NH-Csp3 crystal bond angle value To: CHEMISTRY@ccl.net Message-id: <01HBN6R9W5YQ99F7SY@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I am looking for any references that contain crystal structural information of small compounds containing a Csp3-NH-Csp3 bond angle. I have already calculated a theoretical value for this angle using dimethylamine and employing both MOPAC and AM1 but would like to compare this with an X-ray crystal structure value. Any help would be appreciated. Thank You John S. Tokarski u13145@uicvm.uic.edu From dlim@minerva.cis.yale.edu Tue Apr 26 22:31:48 1994 Received: from minerva.cis.yale.edu for dlim@minerva.cis.yale.edu by www.ccl.net (8.6.4/930601.1506) id VAA20087; Tue, 26 Apr 1994 21:55:38 -0400 Received: from capstan.secf.cis.yale.edu by minerva.cis.yale.edu (5.0/SMI-SVR4) id AA11655; Tue, 26 Apr 1994 21:55:28 +0500 From: dlim@minerva.cis.yale.edu (Dongchul Lim) Message-Id: <9404270155.AA11655@minerva.cis.yale.edu> Subject: calculation of atomic charges To: chemistry@ccl.net Date: Tue, 26 Apr 1994 21:54:51 -0400 (EDT) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 167 Are there Q&D (=quick and dirty) methods to estimate atomic charges for given molecular coordinates? -D. Lim, Chemistry Dept., Yale Univ. (dlim@minerva.cis.yale.edu)