From Jeffrey.Gosper@brunel.ac.uk Fri May 30 06:45:41 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA05018; Fri, 30 May 1997 06:12:39 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by eros.brunel.ac.uk with SMTP (PP); Fri, 30 May 1997 11:11:37 +0100 Date: Fri, 30 May 1997 11:08:22 PDT From: Jeffrey Gosper Subject: IRC calculations in G94 To: CHEMISTRY@www.ccl.net cc: g@CCMSD.chem.uga.edu Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear computational chemists, I am interested in running an IRC calculation using G94 from the transition state I have located for the conformational interconversion of the chair form of cyclohexane to the twist boat form. The TS has been fully optimised, at the HF/3-21 level, and has the required single negative frequency vibration. I would like to generate a number of structures between the TS and the chair and twist boat forms such that an animation of the minimum energy pathway can be constructed. We intend to write a program that will automatically generate a multi-sturucture XYZ file which can be animated in programs such as Re_View and XMOL. I understand that one need to first run the frequency calculation and then run a second IRC which picks up the vibrational information from the checkpoint file. However although I have got the IRC calculations to initiate I find that either the terminate very prematurely or give a floating point error. I have been unable to get the calculation to run correctly and therefore seek the help of others with an interest in the field. I was wondering whether someone with experience in running IRC in G94 would give this problem a try and let me know how they get one. The co-ordinates for the TS are: 6 -0.660342 -1.246230 0.390787 6 0.660268 -1.246262 -0.390799 6 1.523246 -0.069658 0.090007 6 0.773936 1.300076 0.128374 6 -1.523253 -0.069565 -0.089989 6 -0.773855 1.300121 -0.128379 1 -1.224971 1.962348 0.600721 1 0.955284 1.751374 1.096217 1 1.202366 -2.173622 -0.238374 1 1.865733 -0.307480 1.091827 1 -1.202496 -2.173555 0.238344 1 -2.407644 0.021190 0.530657 1 -0.955173 1.751411 -1.096232 1 1.225092 1.962259 -0.600741 1 0.450392 -1.159246 -1.453049 1 2.407662 0.021041 -0.530611 1 -0.450456 -1.159250 1.453038 1 -1.865789 -0.307361 -1.091798 Thanks again, and I look forward to hearing about your results. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper, Dept. of Chemistry, BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187, facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From jorge@cosm.sc.edu Fri May 30 07:45:49 1997 Received: from cosmos.psc.sc.edu for jorge@cosm.sc.edu by www.ccl.net (8.8.3/950822.1) id HAA05191; Fri, 30 May 1997 07:09:41 -0400 (EDT) Received: (from jorge@localhost) by cosmos.psc.sc.edu (8.6.12/8.6.12) id LAA22102; Fri, 30 May 1997 11:09:40 GMT Date: Fri, 30 May 1997 11:09:40 GMT From: Jorge Seminario Message-Id: <199705301109.LAA22102@cosmos.psc.sc.edu> To: chemistry@www.ccl.net Subject: Rotation barrier, thermal enery Cc: jorge@cosmos.psc.sc.edu Dear CCL Members: I am very indebted to all the members who sent their replies regarding my question of rotation. I would like to make a small summary of what I found out based on the information I obtained from the overwhelming responses. Let me rephrase the original question: The molecule in question is tolane (diphenylacetylene, or diphenylethyne), the interest focuses in the relative rotation of one phenyl group with respect to the other. Evidently, this rotation is around the acethylene triple bond. Experiments are able to observe if a very small group of molecules rotate, and probably are also able to quantify the number of rotating molecules by, to make it short, observing a current on a detector. This current, in principle is proportional to the number of molecules that are rotating. It is measured against changes in T from close to 0 K to 300 K. The current increases with very small slope from 0K to 30 K, at 30 K the current jumps 3 to 4 orders of magnitude, then after this "jump" (I said "sudden rotation" in my previous mail), again the current increases with small slope. As few ccl members already recalculated, the barrier for this rotation is about 0.5 to 0.7 kcal/mol and the experimental value is 0.57 kcal/mol. Therefore, there is not doubt about the calculations any more. My inquiry also touched the validity of using kT (or a factor of it) as the only energy available for the rotation (within the statistical sense, i.e. understanding that still a very small fraction of molecules are going to have enough energy to overpass a barrier 10 times bigger than kT, and tunneling, etc). Despite of several concerns against, I agree with several responses that kT is not the whole story. Actually, as it was pointed out, the kT argument makes no sense, otherwise ethane should not rotate till 1500 K. We know that it rotates rapidly at 300 K. I have been advised to use transition state theory for this process, and also to treat it as a unimolecular reaction using RRKM theory. However, what is not clear yet is why the jump at 30 K. Can it be predicted theoretically? I am tempted to suggest, as several colleagues have indicated, that the total thermal energy (which is one order of magnitude bigger than kT) plays a role on this jump. Wether is the energy of the rotational barrier alone or with the inclusion of the interactions between adjacent molecules. This barrier have to be, at least, matched by the total thermal energy so we can have the jump in rotations at the T corresponding to the total thermal energy. Your comments are more than welcome Cordially Jorge Seminario -------------------------------------------- Jorge M. Seminario Department of Chemistry and Biochemistry University of South Carolina Columbia, South Carolina 29208 Tel: 803-777-9567 Fax: 803-777-9521 email: jorge@cosm.sc.edu -------------------------------------------- From jubert@nahuel.biol.unlp.edu.ar Fri May 30 10:45:44 1997 Received: from biol.unlp.edu.ar for jubert@nahuel.biol.unlp.edu.ar by www.ccl.net (8.8.3/950822.1) id KAA06153; Fri, 30 May 1997 10:16:08 -0400 (EDT) Received: from jubert2.biol.unlp.edu.ar (jubert2.biol.unlp.edu.ar [163.10.7.17]) by biol.unlp.edu.ar (8.8.3/8.8.3) with SMTP id LAA22174 for ; Fri, 30 May 1997 11:16:15 -0300 Date: Fri, 30 May 1997 11:16:15 -0300 Message-Id: <199705301416.LAA22174@biol.unlp.edu.ar> X-Sender: jubert@nahuel.biol.unlp.edu.ar X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: jubert@nahuel.biol.unlp.edu.ar (Alicia Jubert) Subject: normal vibrationnal calculations I wonder whether somebody knows about a free program which, from the gaussian output of a normal vibrational calculations, one could get the potential energy distribution of the normal modes. Please send the reply, if there is anyone, directly to my address. Thanks, Alicia Jubert jubert@nahuel.biol.unlp.edu.ar From herrmann@hermes.informatik.uni-stuttgart.de Fri May 30 10:52:56 1997 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.8.3/950822.1) id KAA06327; Fri, 30 May 1997 10:34:08 -0400 (EDT) Date: Fri, 30 May 1997 16:33:36 +0200 Message-Id: <199705301433.QAA06501@odysseus.informatik.uni-stuttgart.de> Received: by odysseus.informatik.uni-stuttgart.de; Fri, 30 May 1997 16:33:36 +0200 From: Frank Herrmann To: zjhu@IRIS3.shmm.ac.cn CC: chemistry@www.ccl.net In-reply-to: <9412210444.AA25514@IRIS3> (zjhu@IRIS3.shmm.ac.cn) Subject: Re: software GA,NN,SA Dear Hu, You can find Genetic Algorithm software at the GA archives: http://www.aic.nrl.navy.mil/galist I have some more GA Links on my home page (see signature). There is a Neural Network Simulator (SNNS) developed at our department: http://www.informatik.uni-stuttgart.de/ipvr/bv/projekte/snns/snns.html here are some Simulated Annealing links:
  • Simulated Annealing
  • Adaptive Simulated Annealing Lester Ingber
  • Annealing & Optimization Web Tour hope this helps, --------------------------------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Institute of Parallel and Distributed High-Performance Systems (IPVR) University of Stuttgart Breitwiesenstrasse 20-22 D-70565 Stuttgart (Germany) Tel: (49) 711-7816-358, FAX: (49) 711-7816-250 email: Frank.Herrmann@informatik.uni-stuttgart.de http://www.informatik.uni-stuttgart.de/ipvr/bv/personen/herrmann.html --------------------------------------------------------------------- - Future is alterable but unknown - - Past is known but unalterable - --------------------------------------------------------------------- From kotelyan@plmsc.psu.edu Fri May 30 10:59:59 1997 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id KAA06028; Fri, 30 May 1997 10:03:52 -0400 (EDT) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id KAA22716; Fri, 30 May 1997 10:03:06 -0400 (EDT) Date: Fri, 30 May 1997 10:03:06 -0400 (EDT) From: Mike Kotelyanskii To: Jorge Seminario cc: chemistry@www.ccl.net, jorge@cosmos.psc.sc.edu Subject: Re: CCL:Rotation barrier, thermal enery In-Reply-To: <199705301109.LAA22102@cosmos.psc.sc.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII First, let me clarify what you are implying is that the energy can be "consolidated" from the other degtrees of freedom to overcome the barrier? Well it is possible, but is apparently improbable. Otherwise a stone lying on the road would be able to jump up, and pretty high. It's thermal energy is enough to overcome it's gravity. Doesn't happen though. This justifies the Arrhenius approach. It's kT that gives you a possibility to overcome the barrier. Another contribution is "entropic" and is given by the preexponent in the Transition State theory. Do I understand correctly that the experiment is done in condensed phase (probably solid as I can judge form the temperatures you mention) Then I would assume this 30K jump may come from some sort of structural or other phase transition. May be I am wrong but can it be the insulator - semiconductor transition? In both cases, current increases with the temperature (opposit to conductors), but current in semiconductor is higher than in insulator (provided, the same voltage is applied) May be this helps... Michael ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsilvania State University University Park, PA 16802, USA -------------------------------------------------------------------------------- On Fri, 30 May 1997, Jorge Seminario wrote: > Dear CCL Members: > I am very indebted to all the members who sent their replies regarding my > question of rotation. I would like to make a small summary of > what I found out based on the information I obtained from the overwhelming > responses. > > Let me rephrase the original question: > The molecule in question is tolane (diphenylacetylene, or diphenylethyne), > the interest focuses in the relative rotation of one phenyl group with > respect to the other. Evidently, this rotation is around the acethylene > triple bond. > > Experiments are able to observe if a very small group of molecules > rotate, and probably are also able to quantify the number of rotating > molecules by, to make it short, observing a current on a detector. > This current, in principle is proportional to the number of > molecules that are rotating. It is measured against changes in T from > close to 0 K to 300 K. > > The current increases with very small slope from 0K to 30 K, at 30 K the > current jumps 3 to 4 orders of magnitude, then after > this "jump" (I said "sudden rotation" in my previous mail), again the > current increases with small slope. > > As few ccl members already recalculated, the barrier for this rotation is > about 0.5 to 0.7 kcal/mol and the experimental value is 0.57 kcal/mol. > Therefore, there is not doubt about the calculations any more. > > My inquiry also touched the validity of using kT (or a factor of it) > as the only energy available for the rotation (within the statistical > sense, i.e. understanding that still a very small fraction of molecules > are going to have enough energy to overpass a barrier 10 times bigger > than kT, and tunneling, etc). > > Despite of several concerns against, I agree with several responses that > kT is not the whole story. Actually, as it was pointed out, the kT > argument makes no sense, otherwise ethane should not rotate till 1500 K. > We know that it rotates rapidly at 300 K. > > I have been advised to use transition state theory for this process, and > also to treat it as a unimolecular reaction using RRKM theory. > > However, what is not clear yet is why the jump at 30 K. Can it be > predicted theoretically? I am tempted to suggest, as several colleagues > have indicated, that the total thermal energy (which is one order of > magnitude bigger than kT) plays a role on this jump. Wether is the energy > of the rotational barrier alone or with the inclusion of the interactions > between adjacent molecules. This barrier have to be, at least, matched by > the total thermal energy so we can have the jump in rotations at the T > corresponding to the total thermal energy. > > Your comments are more than welcome > > Cordially > Jorge Seminario > -------------------------------------------- > Jorge M. Seminario > Department of Chemistry and Biochemistry > University of South Carolina > Columbia, South Carolina 29208 > Tel: 803-777-9567 > Fax: 803-777-9521 > email: jorge@cosm.sc.edu > -------------------------------------------- > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jorge@cosm.sc.edu > -- Original Sender From: Address: jorge@cosm.sc.edu > 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 > > From Y0H8797@VMS1.TAMU.EDU Fri May 30 12:45:47 1997 Received: from VMS1.TAMU.EDU for Y0H8797@VMS1.TAMU.EDU by www.ccl.net (8.8.3/950822.1) id MAA07296; Fri, 30 May 1997 12:28:00 -0400 (EDT) Date: Fri, 30 May 1997 11:28:00 -0500 From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <970530112800.20261286@ACS.TAMU.EDU> Subject: Any review of radical scavenger and triplet quencher? Howdy, does anybody know a review of radical scavengers and triplet quenchers? Thank you for your help. Yong From govindan@chet.medc.umn.edu Fri May 30 12:51:26 1997 Received: from chet.medc.umn.edu for govindan@chet.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id MAA07245; Fri, 30 May 1997 12:20:38 -0400 (EDT) Received: (from govindan@localhost) by chet.medc.umn.edu (8.8.5/8.8.5) id LAA03622 for chemistry@www.ccl.net; Fri, 30 May 1997 11:20:37 -0500 (CDT) From: Govindan Subramanian Message-Id: <199705301620.LAA03622@chet.medc.umn.edu> Subject: AMBER chlorine parameters To: chemistry@www.ccl.net Date: Fri, 30 May 1997 11:20:34 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hai CCLers, I have chlorines as part of 3,4-dichloro tolyl moiety in my molecule. Could anyone help me out in getting the appropriate chlorine parameters which are not available in the parm94.dat of AMBER4.1 (I do not want to use the 'IM' values given for Cl- there). Thanks in advance. -subramanian.g e-mail: govindan@chet.medc.umn.edu From hillisch@imb-jena.de Fri May 30 12:54:43 1997 Received: from guiness.imb-jena.de for hillisch@imb-jena.de by www.ccl.net (8.8.3/950822.1) id MAA07292; Fri, 30 May 1997 12:27:56 -0400 (EDT) Received: (from hillisch@localhost) by guiness.imb-jena.de (950413.SGI.8.6.12/950213.SGI.AUTOCF/hsk) id SAA27554 for CHEMISTRY@www.ccl.net; Fri, 30 May 1997 18:28:38 +0200 From: "Alexander Hillisch" Message-Id: <9705301828.ZM27552@guiness.imb-jena.de> Date: Fri, 30 May 1997 18:28:36 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: PLS algorithm Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Zhengjian Hu wrote: > Dear CCL users, > > I have been trying to do some QSAR but I have no proper softwares. > I wonder if you could tell me how and where I can get the source code for > the following programs: > 1. Genetic algorithm > 2. Neural network > 3. Partial least squares > 4. Non-linear partial least squares > 5. Simulated annealing algorithm >-- End of excerpt from Zhengjian Hu Hallo Hu, Concerning the PLS algorithm have a look at: http://www.galactic.com/galactic/Science/pls.htm Best regards, Alexander Hillisch -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Alexander Hillisch _/ _/ Institute of Molecular Biotechnology _/ _/ Department of Molecular Biology _/ _/ Beutenbergstrasse 11 Phone: +49-3641-65-6203 _/ _/ D-07745 Jena Fax: +49-3641-65-6210 _/ _/ GERMANY Email: hillisch@imb-jena.de _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ "And all this science I don't understand it's just my job five _/ _/ days a week..." _/ _/ Elton John - Rocket man _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From hillisch@imb-jena.de Fri May 30 12:57:51 1997 Received: from guiness.imb-jena.de for hillisch@imb-jena.de by www.ccl.net (8.8.3/950822.1) id MAA07253; Fri, 30 May 1997 12:22:32 -0400 (EDT) Received: (from hillisch@localhost) by guiness.imb-jena.de (950413.SGI.8.6.12/950213.SGI.AUTOCF/hsk) id SAA27532; Fri, 30 May 1997 18:21:59 +0200 From: "Alexander Hillisch" Message-Id: <9705301821.ZM27530@guiness.imb-jena.de> Date: Fri, 30 May 1997 18:21:57 -0600 In-Reply-To: zjhu@IRIS3.shmm.ac.cn (Zhengjian Hu) "" (Dec 20, 8:44pm) References: <9412210444.AA25514@IRIS3> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: zjhu@IRIS3.shmm.ac.cn (Zhengjian Hu), chemistry@www.ccl.net Subject: PLS algorithm Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Dec 20, 8:44pm, Zhengjian Hu wrote: > Dear CCL users, > > I have been trying to do some QSAR but I have no proper softwares. > I wonder if you could tell me how and where I can get the source code for > the following programs: > 1. Genetic algorithm > 2. Neural network > 3. Partial least squares > 4. Non-linear partial least squares > 5. Simulated annealing algorithm >-- End of excerpt from Zhengjian Hu Hallo Hu, Concerning the PLS algorithm have a look at: http://www.galactic.com/galactic/Science/pls.htm Best regards, Alexander Hillisch -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Alexander Hillisch _/ _/ Institute of Molecular Biotechnology _/ _/ Department of Molecular Biology _/ _/ Beutenbergstrasse 11 Phone: +49-3641-65-6203 _/ _/ D-07745 Jena Fax: +49-3641-65-6210 _/ _/ GERMANY Email: hillisch@imb-jena.de _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ "And all this science I don't understand it's just my job five _/ _/ days a week..." _/ _/ Elton John - Rocket man _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From qibvigap@lg.ehu.es Fri May 30 13:45:50 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id NAA07638; Fri, 30 May 1997 13:03:38 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA21246; Fri, 30 May 97 19:02:19 +0100 Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA15939; Fri, 30 May 1997 19:12:43 +0100 Date: Fri, 30 May 1997 19:12:43 +0100 (WET DST) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: Second Order Perturbation Theory Analysis in NBO in G94 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Recently I've trying to learn how to use and interpret the NBO analysis available in G94. But I cannot make the program to do a Perturbation Analysis of the Natural Bonding Orbitals. Since the use of NBO is not explained in the G94 Manual, could anyone help me with this? Thanks a lot Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From shenkin@still3.chem.columbia.edu Fri May 30 16:45:50 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id PAA09240; Fri, 30 May 1997 15:48:21 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id PAA01641 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Fri, 30 May 1997 15:48:21 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id PAA05779; Fri, 30 May 1997 15:48:20 -0400 From: "Peter Shenkin" Message-Id: <9705301548.ZM5777@still3.chem.columbia.edu> Date: Fri, 30 May 1997 15:48:20 -0400 In-Reply-To: Mike Kotelyanskii "CCL:Rotation barrier, thermal enery" (May 30, 10:03am) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Rotation barrier, thermal enery Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On May 30, 10:03am, Mike Kotelyanskii wrote: > Subject: CCL:Rotation barrier, thermal enery > Do I understand correctly that the experiment is done in condensed phase > (probably solid as I can judge form the temperatures you mention) > Then I would assume this 30K jump may come from some sort of > structural or other phase transition. Yes. In addition to everything else that's been said, it could be an order-disorder transition, and not a unimolecular activated process. In this situation, thermodynamic measurements, like the volume, or heat capacity as a function of time, should be revealing. The question is: does the temperature dependence follow Arrhenius behavior (log k vs. 1/T is a straight line). If not, then other possibilities should be considered. -P. -- **** "Deep Blue can't triumph in the game of life" (NY Times, 5/13/97) **** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From T.Somasundaram@qub.ac.uk Fri May 30 19:45:46 1997 Received: from Nzambi.qub.ac.uk for T.Somasundaram@qub.ac.uk by www.ccl.net (8.8.3/950822.1) id TAA10142; Fri, 30 May 1997 19:09:39 -0400 (EDT) Received: from titus.phy.qub.ac.uk by Nzambi.qub.ac.uk with SMTP (PP); Fri, 30 May 1997 23:11:05 +0000 Received: from hyacinth by titus.phy.qub.ac.uk via SMTP (940816.SGI.8.6.9/930416.SGI.AUTO) for id AAA02920; Sat, 31 May 1997 00:09:28 +0100 Sender: theepa@qub.ac.uk Message-ID: <338F5E27.59E2@qub.ac.uk> Date: Sat, 31 May 1997 00:09:27 +0100 From: Theepa Organization: Atomistic Simulation Group, QUB X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry Subject: Nose-Hoover Thermostat and Conservtion of Momentum Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Dear Cyber Chemists, During an MD simulation, which is thermostated with Nose-Hoover, is the total momentum of the system conserved? Also how about angular momentum in slabs? Are there special cases such as pure systems/mixture bulk/slab? Thank you for you patience. Any replies will be appreciated. Theepa. -- -------------------------------------------------------------------------- |Theepaharan Somasundaram |e-mail: T.Somasundaram@qub.ac.uk| |Rm A5, Atomistic Simulation Group, |tel: (01232) 273528 | |School of Mathematics and Physics, |fax: (01232) 241958 | |Queen's University of Belfast, BT7 1NN |http://titus.phy.qub.ac.uk/ | -------------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue May 6 23:49 EDT 1997 Date: Tue, 6 May 1997 10:53:04 -0400 (EDT) From: Ajith Perera Reply-To: Ajith Perera Subject: CCL:97.06.15 50 Years of the Correlation Problem To: chemistry@www.ccl.net Message-ID: Sender: chemistry-request@www.ccl.net "FIFTY YEARS OF THE CORRELATION PROBLEM" A WORKSHOP ON COUPLED-CLUSTER THEORY AND OTHER CORRELATED METHODS (Cedar Key, Fl., june 15-19, 1997) This is the final notice for the above, one-of-a-kind meeting on Electron Correlation. This meeting will bring together the pioneers and the current principal practitioners of correlated methods in molecular electronic structure and spectra, plus applications to polymers and crystals, and related atomic and field theory applications (schedule can be found in the postscript file at ftp://www.ccl.net/pub/chemistry/info/50yrs.ps). Cedar Key, Fl, an island on the Gulf of Mexico, 60 miles from Gainesville, is the unique, rustic location for the meeting. There is still room for several more attendees. If interested, please consult our web site at http://www.qtp.ufl.edu/cct.html, and please contact zeynep@qtp.ufl.edu as soon as possible for a reservation. Thank you. Rod Bartlett, Graduate Research Professor, Quantum Theory Project, University Florida, Gainesville, FL, 32611; bartlett@qtp.ufl.edu; phone 352-392-6974. From assfeld@host8.lctn.u-nancy.fr Tue May 13 05:23 EDT 1997 Received: from host8.lctn.u-nancy.fr for assfeld@host8.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id FAA28190; Tue, 13 May 1997 05:23:36 -0400 (EDT) Received: (from assfeld@localhost) by host8.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id LAA19404 for chemistry-request@www.ccl.net; Tue, 13 May 1997 11:24:29 +0200 (DFT) From: Date: Tue, 13 May 1997 11:24:29 +0200 (DFT) Message-Id: <199705130924.LAA19404@host8.lctn.u-nancy.fr> To: chemistry@www.ccl.net Subject: Chemical Shift Anisotropy Summary Content-Type: text Content-Length: 5646 Status: R Howdy, few weeks ago I posted a request on CCL about NMR chemical shift anisotropy. Here is my previous message : > > Hi, > > I am computing chemical shielding tensor for various molecule. > Once you diagonalyze this tensor you can expressed the > isotropic chemical shield as the average of the three eigenvalues > (Txx, Tyy, and Tzz). You can also compute the anisotropy, which > is the difference between the larger eigenvalue (generally called > Tzz) and the average of the two other. > > Iso = 1/3 (Txx + Tyy + Tzz) > Ani = Tzz - 1/2 (Txx + Tyy) > > Everything is fine with me when all three eigenvalues have the same signe. > Problem arises when one eigenvalue is negative. > For exemple, here are three eigenvalues : -76.8050 6.2091 62.8089 > If you consider that Tzz = 62.8089 you'll find an anisotropy of > 62.8089-(6.2091-76.8050)/2 = 98.1069 > However, if you consider that Tzz = -76.8050, (In absolute value 76.8050 is > larger than 62.8089.) the anisotropy = -111.3140 > > My question : which one is the good choice ? > I already know that G94 use the first definition. > > Thank you in advance for your advice. I'll summarize. I received three messages from Dr. Georg Schreckenbach Jerry C.C. Chan Ernst U. Wallenborn I thank them very much. **************************************************************************** FIRST ANSWER Dr. Georg Schreckenbach I am pretty convinced that your "first" definition is correct. There is no good rationale for using absolute values of shielding, I think. Rather, the signs are important. **************************************************************************** SECOND ANSWER Jerry C.C. Chan I think you should follow the convention suggested by the participants, the leading experts of the field, in the 1992 NATO conference. See Mason J., Solid State NMR 1993, vol 2, 285-288. **************************************************************************** THIRD ANSWER Ernst U. Wallenborn I think this is buggy in g94. For example benzene #RHF 6-311++G** NMR=ALL using the Landolt-Boernstein geometry yields Magnetic properties (CSGT method) Magnetic susceptibility (cgs-ppm): Isotropic = -56.4462 Anisotropy= 35.1962 XX= -32.9831 YX= 0.0000 ZX= 0.0000 XY= 0.0000 YY= -32.9820 ZY= 0.0000 XZ= 0.0000 YZ= 0.0000 ZZ= -103.3734 Eigenvalues: -103.3734 -32.9831 -32.9820 Here it is unambiguously clear what is meant with anisotropy, namely -103.3734+.5*(32.9831+32.9820) With this definition one obtains (in cgs-ppm) RHF 6-311++G** F&S CSGT Single gauge origin X_par -103.37 -109.9 X_ortho -32.98 -41.8 iso: -56.44 -64.5 aniso: -70.39 -68.1 where F&S is Fowler and Steiner, J. Phys. Chem. A _101_ 1409 (1997), who used the SYSMO package and hence provide completely independent results for comparison and par and ortho mean parallel and orthogonal to the principal axis of symmetry. >From this it seems to be clear that g94 produces nonsenical results. To the original question: The definition of the anisotropy should be independent of the oriantation of the coordinate system to avoid above confusion. Herzberg, Molecular Spectra and Molecular Structure, Vol II, Infrared and Raman Spectra of Polyatomic Molecules Van Nostrand, 1945 suggests (Eq. (III,20)) to define the anisotropy of the polarizability tensor as b = sqrt(1/2[(a_xx-a_yy)^2+(a_yy-a_zz)^2+ (a_zz-a_xx)^2+6(a_xy^2+a_yz^2+a_xz^2)]) which in the case of a symmetric top reduces to the definition given by you. I'd use this definition and not bother about what g94 says. **************************************************************************** I found that the two definitions I gave in my previous message are corrects, and that they depend on a third parameter, the ASYMMETRY (eta). The asymmetry of a tensor must ALWAYS be less or equal to one. The definition is : (Considering that Tzz > Tyy > Txx) Eta = 3/2 (Tyy - Txx)/Ani (1) or Eta = 3/2 (Tyy - Tzz)/Ani (2) The right equation is the one which gives a number less or equal to one. Thus the anisotropy is equal to Ani = Tzz - 1/2 (Txx + Tyy) (1') or Ani = Txx - 1/2 (Tyy + Tzz) (2') Equation (1') goes with equation (1) and equation (2') with (2). Iso = 1/3 (Txx + Tyy + Tzz) To determine the set of equations to be used, one has to calculate |Tzz - Iso| and |Txx - Iso| (|a-b| means absolute value of a-b) and one has to compare these two values. If |Tzz - Iso| >= |Txx - Iso| then use the set of equations (1) and (1') otherwise use the second set (2) and (2'). Note that if Tyy = Iso, then Eta = 1. With NMR longitudinal relaxation times T1 experiment one obtain a value equal to : Exp = Ani * Ani * (1 + (Eta * Eta)/3) which is independant of the set of equations used to determine Ani and Eta. It is noteworthy that the final equation has exactly the same mathematical form as the one given by Wallenborn (Third answer) for the anisotropy of the polarizability tensor. I hope that this summary gives some enlightment on this field. Thus one is aware that the value given in G94 output files doesn't correspond to the right answer immediatly. ...Xav Xavier Assfeld Laboratoire de Chimie Theorique Universite Henri Poincare, Nancy, France