From toukie@zui.unizh.ch Thu Jan 30 06:19:48 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id FAA23491; Thu, 30 Jan 1997 05:24:14 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA03841; Thu, 30 Jan 1997 11:29:37 +0100 Message-Id: <1.5.4.32.19970130102547.00667b14@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Jan 1997 11:25:47 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Cosmo Player version 1.0 beta 3 Dear Colleagues; I have just examined the Cosmo Player version 1.0 beta 3 version be- ing distributed by SGI for Windows 95, and I see that it is set to expire on 1 April 1997. Does anyone know with what it will be replaced, and will that replacement be distributed gratis or on a fee-basis only? Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From toukie@zui.unizh.ch Thu Jan 30 08:19:59 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id HAA24335; Thu, 30 Jan 1997 07:38:47 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA05790; Thu, 30 Jan 1997 13:44:11 +0100 Message-Id: <1.5.4.32.19970130124021.0066cba4@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Jan 1997 13:40:21 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Hammett ortho substituent constants? Dear Colleagues; It is my understanding that Hammett sigma constants are restricted to substituents at meta and para positions because steric influences on the functionality at C-1 (e.g., COOH, OH) cannot be clearly distinguished from electronic influences, whereas steric influences on the functionality at C-1 by substituents in the meta or para positions is negligible. Has anyone ever undertaken (and pubished) a detailed analysis of the influence of ortho substituents in an effort to factor the influence of ortho substituents in to electronic and steric components? I note that in the 1982 book "pKa Prediction for Organic Acids and Bases" by D. D. Perrin, B. Bempsey, and E. P. Serjeant Appendix A.5 is a small list of apparent sigma ortho values. Does anyone know of a more recent and/or extensive lists, particularly ones containing values factored into steric and electronic components for benzoic acids and phenols? Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From ccl@www.ccl.net Thu Jan 30 09:19:51 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA24838; Thu, 30 Jan 1997 08:45:24 -0500 (EST) Received: from smaug.physics.mun.ca for uli@smaug.physics.mun.ca by bedrock.ccl.net (8.8.3/950822.1) id IAA08680; Thu, 30 Jan 1997 08:45:19 -0500 (EST) Received: by smaug.physics.mun.ca (940816.SGI.8.6.9/911001.SGI) id KAA24252; Thu, 30 Jan 1997 10:16:02 -0330 Date: Thu, 30 Jan 1997 10:16:02 -0330 (NST) From: Uli Salzner To: ccl Subject: dft/user defined methods Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 6644 Hi everybody, thanks to Doug Fox, AEleen Frisch, Joe Durant, Mikhail Gloukhovtsev, and Marta Fores, who answered my questions about how to use user defined DFT methods in G94 and how to define a half/half functional. In short there is indeed a typo in the Reference Guide (the one with the red spiral). This is corrected at the Gaussian web site (address see below). I also learned how to set the parameters. The original answers are appended. One question on the side. When I submit to the list, I simply put in the address of the ccl. My mail arrives but the ccl address appears where my address should be in the mail header. Obviously I am doing something wrong here. Can somebody explain to me, how to submit to the ccl properly? Thanks again, Ulrike Salzner Department of Chemistry Memorial University of Newfoundland St. Johns, NF A1B 2N5 Canada Tel.: (709) 737-2151 Email:uli@smaug.physics.mun.ca _____________________________________________________________________________ From: Doug Fox Dr. Salzner, The BHandH/BHandHLYP functionals as implemented in G92/DFT have been restored due to popular demand starting with G94 Rev. C.3 so you may be able to simply use the keywords. If you have an earlier version the input to duplicate the G92/DFT functionals would be, BHandH: # SLYP IOP(5/45=10000500, 5/46=00000500, 5/47=10001000) BHandHLYP: # BLYP IOP(5/45=10000500, 5/46=05000500, 5/47=10001000) > > To whom it may concern: > > using the DFT user defined methods in G94, user's reference p.61-62, > I am trying to construct something like a half/half functional but I > have problems to get the order of the coefficinets right. > >From the B3LYP description (p.61) I gather the coefficients for B3LYP > to be: > > 0.8 for Slater, 0.2 for HF, 0.72 for Becke, 0.19 for VWN, and 0.81 > for LYP. > > If I transfer this to the formula below I get: > P1=1.0, P2=0.2, P3=0.72, P4=0.8, P5=0.81, and P6=0.19 > > According to the B3LYP example on p. 62 the coefficients should be: > P1=1.0, P2=0.8, P3=0.2, P4=0.72, P5=0.19, and P6=0.81 > > My question is, have I mixed up something or is there a problem with > this example? Since it would lead to fatal errors, if I got these > coefficients mixed up, I would be very grateful for commends. > ____________________________________________________________________________ Received: by m10.lorentzian.com; Mon, 27 Jan 1997 10:03:13 -0500 From: aefrisch@lorentzian.com (AEleen Frisch) X-Status: There was a typo in the first printing of the manual on these pages (with the red spiral binding). Check our web page (www.gaussian.com/00000432.htm is the exact document you want)) or the release notes that came with the program for updates. Your values for P1 through P5 appear to be correct from my brief glance. However, be aware that in order to get the local part of LYP, you want P6 to be 1.0 (P5 is just the gradient correction part). Finally, the BHandH keyword may also provide what you want. Again, see the release notes or the web site. --------------------------------------------------------------------------------- Message-Id: <199701271601.QAA16643@mephisto.ca.sandia.gov> To: uli (Uli Salzner) Date: Mon, 27 Jan 1997 08:01:22 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] Hi Uli! It's been awhile since I dug into the Gaussian manual, so I won't try that. However, appended is my explicit route statement for running Gaussian's implementation of BHandHLYP (which is not Becke's!). I remember finding multiple errors in the comment cards describing the route options; wouldn't surprise me that they found their way into the manual. My advice is run B3LYP, and then your explicit B3LYP; if you got it right, then they should be identical. I read alot of the source code to figure out what they were actually doing; that is another option. Hope this helps. Joe -- #################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9057 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 http://mephisto.ca.sandia.gov # #################################################################### # BLYP 6-31G* scf=direct iop(5/45=10000500, 5/46=05000500, 5/47=10001000) BHANDHLYP 0,1 H H,1,HH Variables: ________________________________________________________________________________ Subject: BH&HLYP Status: RO Hi, Ulrike: You can find some info at the Gaussian Web site (www.gaussian.com; FAQ secti= on). Please note that the implementation of the BH&HLYP functional in Gaussian-94 (Rev. D and higher) is as follows: ExcBH&HLYP =3D 0.5 ExLSDA + 0.5 ExHF + 0.5=90EB88 + EcLYP + EcVWN. Note that this formulation slightly differs from that proposed by Becke. Furthermore, the answer on BH&HLYP given in the FAQ also differs >from the implementation in G-94. With best wishes, -------------------------------------------------------- Mikhail Gloukhovtsev Room 275, Brown Laboratory Department of Chemistry and Biochemistry University of Delaware 19716 DE Phone # 302 831-0887 E-mail mng@UDel.edu WWW http://udel.edu/~mng/ -------------------------------------------------------- --------------------------------------------------------------------------------- Status: RO showed that in the B3LYP example on p. 62 there was a mistake. So, in order to get some energy as the one provided by the B3LYP default keyword we had to use the following parameters: P1=1 P2=0.2 P3=0.72 P4=0.8 P5=0.81 P6=1 and not P1=1 P2=0.8 P3=0.2 P4=0.72 P5=0.19 P6=0.81 as pointed by the set G94 Users reference Manual. Hope this helps, Marta -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Marta Fores _/ _/ _/ _/_/_/_/ Institut de Quimica Computacional _/ _/ _/ _/ Universitat de Girona _/ _/ _/ _/ _/ _/ _/_/ Albereda 3-5 _/ _/ _/ _/ _/ _/ 17071 Girona, CATALONIA (Spain) _/_/_/ _/ _/ _/ _/_/_/_/ Voice +34.72.41.83.57 FAX +34.72.41.83.61 _/ _/_/_/ _/_/_/ World Wide Web: http://stark.udg.es/cat/marta.html _/ _/ _/ _/ e-mail: marta@stark.udg.es _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- From ccl@www.ccl.net Thu Jan 30 18:19:54 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA00422; Thu, 30 Jan 1997 18:06:05 -0500 (EST) Received: from ucis.vill.edu for bausch@rs6chem.chem.vill.edu by bedrock.ccl.net (8.8.3/950822.1) id SAA10964; Thu, 30 Jan 1997 18:06:04 -0500 (EST) Received: from rs6chem.chem.vill.edu [153.104.73.1] by ucis.vill.edu with SMTP-OpenVMS via TCP/IP; Thu, 30 Jan 1997 18:07 EST Received: from [153.104.73.18] by rs6chem.chem.vill.edu (AIX 3.2/UCB 5.64/4.03) id AA11974; Thu, 30 Jan 1997 18:10:54 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Jan 1997 18:05:56 -0500 To: chemistry@ccl.net From: bausch@rs6chem.chem.vill.edu (Joseph W. Bausch) Subject: question about the STABLE keyword in G94 I have read in the "Exploring Chemistry With Electronic Structure Methods" that stability of scf solutions on unknown systems should be checked with the STABLE calculation. I am wondering about what the implication is if an optimized geometry then gives an instability in the wavefunction. With the Stable=opt keyword the wavefunction is reoptimized to lower energy, but the book says this is not a geometry optimization. So, my question is, is this optimized geometry (that a vibrational analysis has indicated is a mimimum with no imaginary frequencies) still legitimate? Or after this new lower energy wavefunction has been determined with the stable=opt run does another geometry optimization beginning with this new wavefunction need to be carried out? Thanks in advance, JWB bausch@rs6chem.vill.edu ----------------------- From ccl@www.ccl.net Fri Jan 31 13:29:39 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA10191; Fri, 31 Jan 1997 12:42:17 -0500 (EST) Received: from gatekeeper.eastman.com for bewilson@eastman.com by bedrock.ccl.net (8.8.3/950822.1) id MAA28657; Fri, 31 Jan 1997 12:42:15 -0500 (EST) Received: by gatekeeper.eastman.com; id MAA26146; Fri, 31 Jan 1997 12:54:05 -0500 (EST) Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (3.2) id xma026067; Fri, 31 Jan 97 12:53:47 -0500 Received: by eastman.com id AA24162 (5.67b/IDA-1.5 for chemistry@ccl.net); Fri, 31 Jan 1997 12:38:44 -0500 Received: from ntb150.kpt.emn.com by eastman.com with SMTP id AA19551 (5.67b/SMI-4.1 for ); Fri, 31 Jan 1997 12:38:43 -0500 Received: by ntb150.kpt.emn.com with SMTP (Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5) id <01BC0F73.F812F960@ntb150.kpt.emn.com>; Fri, 31 Jan 1997 12:40:41 -0500 Message-Id: From: "Wilson, Bruce" To: "'chemistry@ccl.net'" Cc: "'bewilson@eastman.com'" Subject: Summary re term symbols Date: Fri, 31 Jan 1997 12:39:27 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Following is the information I received regarding references on term symbols. Thanks to Lutfur Khundkar, J. Grant, Ole Swang, and Richard Bone for their time in responding. I found both McQuarrie's book and Atkin's book in the library and have been reading through those. ----From lkhundkr@neu.edu (Lutfur Khundkar) Don McQuarrie's "Quantum Chemistry" has an excellent section on naming and deriving atomic term symbols. The molecular symmetry symbols I learned from Cotton's book "Chemical Application of Group Theory" as well as from Herzberg's bible on Molecular spectroscopy. Herzberg's books are comprehensive, but nowhere as eloquent as McQuarrie's. -------From hert0531@argon.chem.TU-Berlin.DE (Roland Hertwig) In principle, Atkins' books suit the purpose. Look for "Physical Chemistry" or even better "Molecular Quantum Mechanics" by P.W. Atkins (OXford University Press). Also a good book is "Quantum Chemistry" by I.R.A. Levine. (Prentice Hall International). --------From jeg10@po.cwru.edu (J. Grant) The Text "Spectrophotometric Identification of Organic Compounds" Fifth Edition, by Silverstein, Bassler and Morrill contains a through chapter (20 pages) with a bibliography (at chapter's end) that I have found useful. -----From Ole.Swang@si.sintef.no (Ole Swang) The following books all treat group theory for molecules: F. A. Cotton: "Chemical Application of Group Theory" P. W. Atkins: "Molecular Quantum Mechanics" F. L. Pilar: "Elementary Quantum Chemistry" Cotton's book is the classic. The two others are textbooks on quantum chemistry, with chapters on molecular symmetry. -----From rgab@easynet.co.uk (Richard Bone) I'm not sure if you'll have had a flood of replies about this yet but two books I found useful in the education system phase of my life were: P. W. Atkins, Molecular Quantum Mechanics (Oxford University Press) M. Gerloch, Orbitals, Terms and States. The first one has useful and accurate discussion in places though is not very expansive. The second book is a specialist work devoted to the entire subject in its minutiae ... Otherwise, failing that, I always found solid spectroscopy books, e.g., by G. Herzberg, to be valuable in these areas. I wouldn't settle for any undergraduate level spectroscopy text book though as it won't be precise enough or full enough for your aims. ================================================================= Bruce E. Wilson (bewilson@eastman.com) Chemical Information Services, B-150B, Lincoln Street Eastman Chemical Company Kingsport, TN 37662-5150 Voice: (423) 229-8886 FAX: (423) 229-6114 "Opinions are mine, but available free of charge." From mn1@helix.nih.gov Fri Jan 31 18:20:07 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id SAA13653; Fri, 31 Jan 1997 18:00:09 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id RAA20320; Fri, 31 Jan 1997 17:59:33 -0500 (EST) Date: Fri, 31 Jan 1997 17:59:33 -0500 (EST) From: "M. Nicklaus" Message-Id: <199701312259.RAA20320@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G94(Sum.+Q): Problem with PES Scan in DFT Cc: mn1@helix.nih.gov Dear CCL'ers, This is the, maybe preliminary, summary of the responses I got to my question concerning a problem with PES Scan in DFT in G94. A few follow-up questions are appended. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Question: ========= ? I seem to be having a problem with a Potential Energy Surface (PES) scan ? in G94. I am running a relaxed PES scan on a nucleoside analog, trying ? to rotate the base. I am running this job at the DFT method/basis set ? B3LYP/6-31G(d). I'm using cartesian coordinates (a newzmat-generated ? input file with a Z-matrix didn't work previously), pre-optimized at ? the same level of theory from X-ray coordinates. ? ? For the first few conformations, everything seems to have proceeded nicely; ? i.e., the energy started out some 20 kcal/mol or so above the (presumed) ? global energy minimum, and then came down, during the partial optimization, ? to a reasonable value a few kcal/mol above the global min. ? With the current conformation, however, the job seems to be stuck, since ? for nearly 20 steps now, the energy has only been oscillating in a narrow ? band. [rest omitted] @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Responses: ========== From: Jan Labanowski Try to see, if you have very closely spaced HOMO/LUMO -- usually, due to Self Interaction problem of DFT, the SCF will oscillate in this case. I do not know how to fix it in G9X, since I do not use it for DFT, but other problems have some options, like DMIX (a portion of new density to be mixed with old density for new SCF iteration), or freezing occupances, or level shifting technique, or smear approach. If some of those are available in gaussian, use them. Going on with the run will not help, it will just keep oscillating. Of course, I may be wrong as to the cause, since I did not see your MO energies. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From: Jennie.Weston@org.chemie.uni-giessen.de (Jennie Weston) The problem is probably that the optimizer routine is taking too big steps for your pot E surface. You are apparently in the region of a very flat minimum (maybe the thing is quite rotationally flexible??). The routine must step smaller in order to find the stationary point. Kill the job at once, further comp time is just wasted. Cut out the geometry corresponding to the lowest energy in the many optimization cycles. Use it to make a new input file (so you don't loose the work already done) (so you don't loose the work already been done on the optimization). Include (For Gaussian) the option opt=tight in the key word line. If this still doesn't work, use opt=verytight. This decreases the tolerances for the optimization routine and forces it to step smaller. However, it takes more comp time. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From: d3g359@fido.pnl.gov (John Nicholas) Marc, yes I have seen it often with dft in G94. I do not know the origin of the problem. I would guess the job may never converge. However, you should check the forces, if the forces are still high, then maybe something is wrong other than g94's problem with convergence. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From: Samuel_Mikes@hmc.edu Is it possible that you entered the step in degrees while the program read it as radians? Sometimes the documentation is incomplete or just plain wrong. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Follow-up questions: ==================== 1. Taking up Jennie's suggestion, I realized that this conformation may indeed be in a 'difficult' region of the energy surface It is quite possible that it is very close to a local maximum relative to the scanned torsion, i.e. close to the top of the rotation barrier. With this---and only this---torsion constrained to the presribed value in the scan, I think it is very well possible that the energy surface with respect to the remaining coordinates is very flat, or otherwise 'weird looking'. Any thoughts, or experiences on this point? 2. Can one restart a PES scan job with tighter convergence for the optimization by using Opt=(Restart,Tight,AddRedundant); or will restarting the job from the checkpoint file ignore the new keyword "Tight" and proceed with the same settings as before? 3. How do I extract a specific structure from a PES scan checkpoint file; i.e., how do I tell newzmat that I want, say, the (structure of the) 17th step in the optimization of the 3rd conformation? Thanks to all who responded, and thanks in advance to future responders. Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ From ccl@www.ccl.net Fri Jan 31 19:20:07 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA13802; Fri, 31 Jan 1997 18:39:29 -0500 (EST) Received: from copland.udel.edu for sbennett@wotan.duch.udel.edu by bedrock.ccl.net (8.8.3/950822.1) id SAA09280; Fri, 31 Jan 1997 18:39:27 -0500 (EST) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.8.5/8.7.3) with SMTP id SAA22014 for <@brahms.udel.edu:chemistry@ccl.net>; Fri, 31 Jan 1997 18:38:47 -0500 (EST) Received: by wotan.duch.udel.edu (951211.SGI.8.6.12.PATCH1502/951211.SGI) id SAA05578; Fri, 31 Jan 1997 18:22:58 -0500 Date: Fri, 31 Jan 1997 18:22:57 -0500 (EST) From: Steve Bennett To: CCL Users Subject: Bond order analysis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have recently started using DMol to calculate bond orders between transition metals and main group elements. I am interesting in finding references concerning the Mayer implementation as in DMol and how it compares to other methodologies, such as NBO and Mulliken analyses. Any results will be compiled and summarized to the list. Thanks in advance Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://udel.edu/~sbennett/steves.html "Although the answer is not unknown, I'm searchin', searchin, and how I've grown; It's not all right to say goodbye, and the world on a string doesn't mean a thing" Neil Young From AFED@ichuwr.chem.uni.wroc.pl Sat Feb 1 07:20:15 1997 Received: from indigo2 for AFED@ichuwr.chem.uni.wroc.pl by www.ccl.net (8.8.3/950822.1) id GAA17398; Sat, 1 Feb 1997 06:56:01 -0500 (EST) Received: from ichuwr.chem.uni.wroc.pl by indigo2 via SMTP (940816.SGI.8.6.9/930416.SGI) for id MAA01910; Sat, 1 Feb 1997 12:54:53 -0100 Received: from ICHUWR/SMTPQueue by ichuwr.chem.uni.wroc.pl (Mercury 1.11); Sat, 1 Feb 97 12:54:32 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Sat, 1 Feb 97 12:54:22 +0100 From: "Adam Fedorowicz" To: poul@ichuwr.chem.uni.wroc.pl Date: Sat, 1 Feb 1997 12:54:17 GMT+1 Subject: Re: CCL:Summary DFT Programs CC: CCL Computational Chemistry List X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <191A3372E8@ichuwr.chem.uni.wroc.pl> Date sent: Fri, 31 Jan 1997 14:07:06 +0100 From: Alain Kessi Organization: Paul Scherrer Institut, Zuerich, Switzerland To: Cedric Merlot Copies to: CCL Computational Chemistry List Subject: CCL:Summary DFT Programs Cedric Merlot wrote: > A week ago I asked for DFT Programs : In your list of DFT software packages, you're missing Dmol, available commercially from MSI (http://www.msi.com). The same code can do molecules/clusters or crystals. It should be among the faster codes, though I haven't recently done any comparisons. (Caveat: the writer of the present message has links to the developers of Dmol) -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: alain.kessi@psi.ch -- Original Sender From: Address: alain.kessi@psi.ch CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html Adam Fedorowicz Faculty of Chemistry, Wroclaw University 14, F. Joliot-Curie 50-383 Wroclaw phone (+48)(71)204308,204200 fax (+48)(71)222348 email AFED@ICHUWR.CHEM.UNI.WROC.PL From COMBA@akcomba.oci.uni-heidelberg.de Sat Feb 1 07:30:32 1997 Received: from modem.urz.uni-heidelberg.de for COMBA@akcomba.oci.uni-heidelberg.de by www.ccl.net (8.8.3/950822.1) id HAA17419; Sat, 1 Feb 1997 07:03:07 -0500 (EST) Received: from akcomba.oci.uni-heidelberg.de by modem.urz.uni-heidelberg.de with SMTP id AA21581 (5.67b8/IDA-1.5 for ); Sat, 1 Feb 1997 13:03:06 +0100 Received: from ACI-SV1/MAILQUEUE by akcomba.oci.uni-heidelberg.de (Mercury 1.11); Sat, 1 Feb 97 12:55:09 CET Received: from MAILQUEUE by ACI-SV1 (Mercury 1.11); Sat, 1 Feb 97 12:54:46 CET From: "Peter Comba" Organization: Anorg.-Chem. Institut HD, AK Comba To: chemistry@www.ccl.net Date: Sat, 1 Feb 1997 12:54:19 CET Subject: molecular volume Cc: iqor1@cc.uab.es, irisawa@agc.co.jp Priority: normal X-Mailer: Pegasus Mail for Windows (v2.23) Message-Id: <2BB00FC0AFD@akcomba.oci.uni-heidelberg.de> Dear CCLers Attached are the very helpful answers for my recent question on programs for the calculation of molecular volumes from (computed) coordinates. Thanks for your help. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ From: Andrew Rohl I have a mac program that calculates molecular volumes very quickly on a PowerMac. See JCS Dalton Trans, 1991, 3419 for a description. I can send you a copy if you like. It is written in C if you are interested in the source. Andrew ---------------------------------------------------------------------- From: david de corte Dear Prof. Comba, There exists a program which calculates the volume starting from the coordinates... It is a small FORTRAN-program called SPACEFILL...This program is included in the MD-package called TINKER which can be freely downloaded from http://dasher.wustl.edu/tinker/ Other ways to calculate volumes include Density Funcional programs which calculate the electron density ..thereafter programs like Cerius2.1 or Molekel make it possible to calculate the volume of your molecule. I hope this information will help you further. Kind regards, David ---------------------------------------------------------------------- From: TOPPER ROBERT Again, the Molecular Monte Carlo Home Page holds the answer! If you look at http://www.cooper.edu/engineering/chemechem/monte.html under "Software and Numerical Tools for the Discriminating Monte Carlo Practitioner" you will find a link to STERIC, a program which calulates a number of steric parameters including molecular volumes. The link takes you to ftp://hobbes.gh.wits.ac.za/pub/steric/ STERIC was contributed by Brian Craig Taverner. Best, robert ---------------------------------------------------------------------- From: MARTIN@cmdb.pprd.abbott.com SAVOL2 is what you should be using. It is available from Robert Pearlman. pearlman@vax.phr.utexas.edu Yvonne Martin, Senior Project Leader ---------------------------------------------------------------------- From: davide@stinch10.csmtbo.mi.cnr.it (Davide Proserpio) Dear Peter try tolook at this page : http://www.gh.wits.ac.za/craig/ and http://hobbes.gh.wits.ac.za/craig/steric/ you will find information about STERIC a nice program by Craig Taverner You can also contact dodd@roebling.poly.edu (Larry Dodd) about his program : "Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes" L.R. Dodd and D.N. Theodorou MOLECULAR PHYSICS, Volume 72, Number 6, 20 April 1991, 1313-1345. The program is in Fortran. A typical input file contains lines of 2.247950838 -1.236565749 3.658056690 1.931050 ^^^^^^^^^^^ ^^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^ | | | | | | | | x coord y coord z coord radius I hope this helps regards from Milano (from the same group of Angelo Sironi) Davide ---------------------------------------------------------------------- From: John Waite Dear Peter, Ask Larry dodd for a copy of his MOLVOL, fortran code: dodd@roebling.poly.edu Good luck, John ---------------------------------------------------------------------- From: "P.Bladon" Yes I have a fortran routine that will do this. You would probably need to do some work to put it into/link it another program. Mail be back for more details. Peter Bladon ********************************************************************** Prof Peter Comba Anorganisch-Chemisches Institut Universitaet Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany phone ++49 6221 54 8453 fax ++49 6221 54 6617 e-mail comba@akcomba.oci.uni-heidelberg.de From dsmith@CTCnet.Net Sat Feb 1 10:20:14 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id JAA18159; Sat, 1 Feb 1997 09:56:37 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id JAA19298; Sat, 1 Feb 1997 09:52:51 -0500 Date: Sat, 1 Feb 1997 09:52:51 -0500 Message-Id: <199702011452.JAA19298@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: crystal packing calculations and programs A very interesting (to me) paper has just appeared in J. Phys. Chem. B, 1997, 101, 798 by Sorescu, Rice and Thompson. In this paper, they dev3elop an intermolecular potential for RDX (hexahydro-1,3,5-trinitro-1,3,5-s-triazine) and perform crystal packing, MC, and MD studies. The authors parameterize their potential based on the known neutron diffraction structure of RDX. They also reference several other packages for performing crystal packing calculations. What are the options when one does not have the crystal structure available? Can one reasonably start from a high quality ab initio calculation on a single molecule (gas phase) and use that structure to pack a crystal? If one does, what is the likelihood of getting the crystal structure correct? Or does one need to perform ab initio calculations in the periodic solid (e.g., CRYSTAL 95 calculations) before performing crystal packing? What packages are out there, commercial and "public domain" (free, QCPE, etc.) that can perform crystal packing calculations? I would like to predict space group, density, lattice energy, etc. Perhaps, since there are pedagogical questions here rather than just a request for pointers to software, we could keep this discussion public on the CCL, not just a series of replies directly to me. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From tratnyek@ese.ogi.edu Sat Feb 1 12:20:18 1997 Received: from ese.ogi.edu for tratnyek@ese.ogi.edu by www.ccl.net (8.8.3/950822.1) id LAA18544; Sat, 1 Feb 1997 11:31:18 -0500 (EST) Received: from [129.95.74.47] (pgt3.ese.ogi.edu) by ese.ogi.edu (4.1/SMI-4.1_0a) id AA06276; Sat, 1 Feb 97 08:31:13 PST Message-Id: In-Reply-To: <1.5.4.32.19970130124021.0066cba4@zui.unizh.ch> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Sat, 1 Feb 1997 08:33:18 -0700 To: chemistry@www.ccl.net From: "Paul G. Tratnyek" Subject: Re: CCL:Hammett ortho substituent constants? Cc: toukie@zui.unizh.ch >Has anyone ever undertaken (and pubished) a detailed analysis of the >influence of ortho substituents in an effort to factor the influence of >ortho substituents in to electronic and steric components? As of when I did the literature search for this (where we found remarkable little "ortho effect"): Tratnyek, P. G., and J. Hoign=E9. 1994. Kinetics of reactions of chlorine dioxide (OClO) in water. II. Quantitative structure-activity relationships for phenolic compounds. Water Res. 28(1): 57-66. The best/latest refs on the "ortho effect" were this: Charton, M. 1971. The nature of the ortho effect. VII. Nuclear magnetic resonance spectra. J. Org. Chem. 36(2): 266-272. Charton, M. 1971. The quantitative treatment of the ortho effect. Progr. Phys. Org. Chem. 8: 235-317. Charton, M., and B. I. Charton. 1971. The nature of the ortho effect. VI. Polarographic half-wave potentials. J. Org. Chem. 36(2): 260-265. =46ujita, T., and T. Nishioka. 1976. The analysis of the ortho effect. Progr= =2E Phys. Org. Chem. 12: 49-89. >sigma ortho values. Does anyone know of a more recent and/or extensive >lists, particularly ones containing values factored into steric and >electronic components for benzoic acids and phenols? Try the paper by Fujita. ------------------------------------------------------------------ Paul Tratnyek, Department of Environmental Science and Engineering Oregon Graduate Institute, PO Box 91000, Portland, OR, 97291-1000 http://www.ese.ogi.edu/ese_docs/tratnyek.html Phone: 503/690-1023 ------------------------------------------------------------------