From chemistry-request@www.ccl.net Fri Mar 26 01:14:59 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA01838 Fri, 26 Mar 1999 01:14:59 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id BAA18009; Fri, 26 Mar 1999 01:14:56 -0500 (EST) Date: Fri, 26 Mar 1999 01:14:55 -0500 (EST) From: Jan Labanowski To: chemistry@www.ccl.net cc: Jan Labanowski , team@ccl.net Subject: From the Arministrator: Problems with distributing CCL... Message-ID: Dear CCL Subscribers... While some of you may have enjoyed the silence in the ether, I had many inquires about "What is happening? I am not getting CCL...". For many of us the CCL became the daily annoyance, but the one which is quite addictive. Some popular proverbs about children, wifes/husbands, etc., come to mind. In short... The machine which sends the CCL out to the world had a disk problem (the /var partition which has a /var/spool/mqueue for those who know better) was ailing. The UNIX kernel, rather than sending mail, was frantically trying to read the bad spots on the disk surface. The average load on this machine (Spark 10) went up to 3 or more on occasions. Our sendmail.cf switches off the sendmail queue sweep at load 2, and sendmail refuses connections at 3. We upped it to 3 and 4, respectively, and hoped that load will go down at night and at least the sendmail queue will clear, at which time we take the machine down, put a new disk, and start again, before the ailing drive dies a gruesome death and makes the noise of a sanding machine (sounds familiar {;-)}). But you bet, you loose... The drive's health was more frail, and the life support also failed (this is a spring break time, and the gurus are hard to find). And I have a dilemma... I can resend all the messages (I have them archived on several machines). But at the same time, some of them were sent, some of them were partially sent, and some of them may not have been sent at all. When www.ccl.net vel www.ccl.net died, it had 70,000 or so, pieces of mail to deliver in its queue. And since by definition, you do not backup sendmail queues, since they change by minute, it is hard to tell whose message was delivered, to whom, etc. The suggestions are: Authors: Send your messages again, if you posted them between March 20 and 25, and you did not get any responses. If you do not have your own copy, you can look at gopher://www.ccl.net:70/11/archived-messages/99/03 or if it does not work: http://www.ccl.net/cca/archived-messages/99/03 or ftp://www.ccl.net/pub/chemistry/archived-messages/99/03/ and get them from there. If there are not there, your message was not even received and must have been refused at the moment of spurious high load by www.ccl.net machine. note here, EVERYBODY PLEASE READ... =================================== There are many files there with *.rej in the name. These are messages which had been rejected by the CCL distribution scripts for some reason (yes, computers are stupid, and my perl scripts in particular...), and are usually reviewed by my student assistants, and resent. They should end up in the next day (or so), files with no *rej*, i.e., were successfully resent. If message is in the *rej* file, it does not mean that you are on black list, etc... The message scanning is much more involved, some trivial problems with e-mail header may direct messages for human review. However, if they do not appear there, but appear in rej.pro (processed) and they SHOULD in your opinion, be distributed, please BUG ME (jkl@ccl.net) directly. The students who review the messages are not chemists. Moreover, I sometimes personally have a problem if the message is appropriate for distribution. Hard cases make bad law, and some cases are hard. On the other hand, you do not see some of the most offensive messages even in *rej* files, and if we had not had these scripts, you would have learned more about freedom of the Internet, hot sites, fantastic new products, how to be rich in a week, etc., which you may not want to, I presume... Silent Majority: Do not get upset when you see messages being posted again. Thank you for your cooperation, and sorry... I am really sorry for the mess... Now, more bad news {:-)}. Very soon, we will be moving the whole operation to other machines and try to add more redundancy, make the Web site a pleasure to access, etc. And there will be hiccups... But since you love CCL and you are even tempered, and you want to end up in heavens, you will not put a contract on my grey hairy head... But if you want to express your frustration, please send mail directly to me and be direct (I have a skin of a rhino, so get it off...). This will help to keep CCL focused. Yours, Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | From chemistry-request@www.ccl.net Tue Mar 23 05:33:44 1999 Received: from asterix.uni-muenster.de (cml@ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA07763 Tue, 23 Mar 1999 05:33:04 -0500 (EST) Received: (from cml@localhost) by asterix.uni-muenster.de (8.8.8/8.7.5) id KAA193360 for "chemistry@www.ccl.net"; Tue, 23 Mar 1999 10:32:47 GMT From: Christian Mück-Lichtenfeld Message-Id: <199903231032.KAA193360@asterix.uni-muenster.de> Subject: NBO analysis of acetamide To: chemistry@www.ccl.net Date: Tue, 23 Mar 1999 11:32:47 +0100 (MEZ) Dear colleagues, for reference purposes I would like to know whether there is any published NBO analysis of acetamide in the literature. I have searched the QCLDB and other sources. I have found some papers from K.B.Wiberg et al. concerning similar structures, esp. formamide, but I have not come to see an explicit NBO treatment of acetamide. If someone of you knows a reference for that special case, please let me know. Greetings, Christian Mueck-Lichtenfeld ---------------------------------------------- Dr. Christian Mueck-Lichtenfeld Westfaelische Wilhelms-Universitaet Organisch-Chemisches Institut Corrensstrasse 40 D-48149 Muenster, Germany cml@uni-muenster.de | +49 251 83 33239 ---------------------------------------------- From chemistry-request@www.ccl.net Wed Mar 24 06:53:11 1999 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA01435 Wed, 24 Mar 1999 06:53:09 -0500 (EST) From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id NAA01854 for ; Wed, 24 Mar 1999 13:00:50 +0100 (MET) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id MAA08983 for CHEMISTRY@www.ccl.net;Wed, 24 Mar 1999 12:50:45 +0100 (MET) Date: Wed, 24 Mar 1999 12:52:54 +0100 Message-Id: <"36F8D10F.10DD.1498.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: PC-modelling TO: CHEMISTRY@www.ccl.net Hi, I'm looking for an overview of all available molecular modelling packages on PC(Pentium)-platforms (windows or linux). I'm especially interested in ab initio, forcefield, dynamics packages. Any suggestion is helpful. Thank you, Steven From chemistry-request@www.ccl.net Wed Mar 24 11:46:44 1999 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA03587 Wed, 24 Mar 1999 11:46:38 -0500 (EST) Received: from localhost.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA18106; Wed, 24 Mar 1999 10:36:16 -0600 Sender: xiaomei@ne059.cm.utexas.edu Message-Id: <36F9147E.41C6@usa.net> Date: Wed, 24 Mar 1999 10:36:14 -0600 From: Xiaomei Yang Organization: Dept of Chem & Biochem To: chemistry@www.ccl.net Subject: Summary: convert PDB to CHARMm] Hi, CCLers, My original question on how to convert PDB file to CHARMm format seemed ridiculous, but I was in a situation without QUANTA/CHARMm in hand. Anyway, many thanks to all the people who answered my question and gave me helpful information. Now the summary. How to convert PDB files to CHARMm format ========================================= 1. CHARMm 2. QUANTA 3. RasMol 4. Babel 5. your own code 1. CHARMm itself can read PDB files and convert to CRD/PSF format. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< as suggested by G. Matthias Ullmann Ryszard Czerminski dmacks@sas.upenn.edu (Daniel E. Macks) Shobana Sundaram ) ------------------------------------------------ open read unit 12 card name "1rie.protein.pdb" read sequ pdb unit 12 generate 1rie setup rewind unit 12 read coor pdb unit 12 close unit 12 But you should read only one straint at once. If you have more than one straint, repeat the command like this: open read unit 12 card name "1rie.hetero.pdb" read sequ pdb unit 12 generate fes setup rewind unit 12 read coor pdb unit 12 appe close unit 12 You have to edit the PDB file a little bit, so that it look like ATOM 1 N THR 53 15.450 0.804 17.223 1.00 15.05 1rfs ATOM 2 CA THR 53 14.080 0.730 16.642 1.00 15.16 1rfs ATOM 3 C THR 53 14.002 1.723 15.471 1.00 14.32 1rfs ATOM 4 O THR 53 14.581 2.805 15.549 1.00 14.38 1rfs ATOM 5 CB THR 53 13.011 1.058 17.715 1.00 16.16 1rfs ATOM 6 OG1 THR 53 13.161 2.411 18.160 1.00 18.16 1rfs ATOM 7 CG2 THR 53 13.171 0.139 18.916 1.00 16.08 1rfs ATOM 8 1H THR 53 15.677 1.830 17.297 1.00 0.00 1rfs ATOM 9 2H THR 53 15.484 0.373 18.153 1.00 0.00 1rfs ATOM 10 3H THR 53 16.137 0.366 16.590 1.00 0.00 1rfs ATOM 11 HG1 THR 53 13.847 2.552 18.821 1.00 0.00 1rfs The string in the last column has to be the segid. Otherwise you can not read the coordinates properly. ----- End of Example 1. Example 2: ========== (by Shobana Sundaram ) ----------------------------------------------------- open read card unit 10 name a.pdb ('your filename') read coor pdb unit 10 close unit 10 if you want only the coordinates to be written open write unit 11 card name a.crd write coor unit 11 card * title * and if you want to write in psf format which included connectivities etc.. write psf card name a.psf * title * ----- End of Example 2 2. QUANTA - the Graphical User Interface for CHARMm can of course do this. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< as suggested by dmacks@sas.upenn.edu (Daniel E. Macks) Istvan Enyedy" Shobana Sundaram 3. RasMol can read both PDB and CHARMm formats <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< as suggested by Rick Venable RasMol can export the current image to various graphical formats, such as gif, bmp, ps; but it is not clear if it can re-write the structure into any formats other than the input one. (Xiaomei) 4. Babel reads both PDB and CHARMm formats but doesn't write to CHARMm format. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 5. Write you own code <<<<<<<<<<<<<<<<<<<<< as suggestd by Themis Lazaridis (aldo jongejan) Themis gave me his little code that helped me to accomplish my job in time. Thanks. Example 3: ========== (by Themis Lazaridis ) ----------------------------------------------- Themis Lazaridis Department of Chemistry phone (212) 650-8364 City College of New York fax (212) 650-6107 Convent Avenue & 138th St. email: themis@sci.ccny.cuny.edu New York, NY 10031 http://www.sci.ccny.cuny.edu/~themis ---------------------- c Reads PDB file, writes out charmm file c Uses a temp file c PDB format c text IATOM TYPE RES IRES X Y Z W c A6 I5 2X A4 A4 I5 4X 3F8.3 6X F6.2 c charmm format c ATOMNO RESNO RES TYPE X Y Z SEGID RESID Weighting c I5 I5 1X A4 1X A4 F10.5 F10.5 F10.5 1X A4 1X A4 F10.5 c c character*80 infile,outfile,line character*4 str1,type,res,code,segid,resid,residold,resold character*1 chain logical loxt(1000) write (6,*) 'Give input PDB files, output will be .crd' 1 read (5,'(a)') infile i=1 2 i=i+1 if (infile(i:i).eq.' ') then outfile=infile(1:i-1)//'.crd' else goto 2 endif open (unit=11, file=infile, status='old') open (unit=12, file='temppdb', status='unknown') open (unit=13, file=outfile, status='new') write (13,'(a80)') '* converted from '//infile write (13,'(a)') '*' do 4 i=1,1000 4 loxt(i)=.false. nss=0 ires=0 iat=0 residold=' ' resold=' ' do 100 i=1,100000 read (11,'(a80)',end=1000) line read (unit=line,fmt=500) str1 if (str1.eq.'SSBO') then nss=nss+1 goto 100 else if (str1.eq.'ATOM') then iat= iat+1 read (unit=line,fmt=500) str1,iatom,type,res,chain,resid, & x,y,z,a,w,code 500 format (a4,2x,i5,2x,a4,a4,a1,a4,4x,3f8.3,2f6.2,6x,a4) if ((resid.ne.residold).or.(res.ne.resold)) ires=ires+1 residold=resid resold= res if (chain.ne.' ') then segid=chain//code elseif (code.ne.' ') then segid=code else segid='MAIN' endif if (type.eq.'CD1 ') then if (res.eq.'ILE ') type='CD ' elseif (type.eq.'OCT1') then type='OT1 ' elseif (type.eq.'OCT2') then type='OT2 ' elseif (type.eq.'OXT ') then type='OT2 ' loxt(ires)=.true. endif c fluch resid left 5 if (resid(1:1).eq.' ') then resid=resid(2:4)//' ' goto 5 endif write (12,600) iat,ires,res,type,x,y,z,segid,resid,w 600 format (I5,I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,a4,F10.5) else goto 100 endif 100 continue 1000 write (6,*) 'Disulfide bonds', nss nres=ires write (13,'(i5)') iat close (unit=12) open (unit=12,file='temppdb',status='old') do 200 i=1,100000 read (12,'(a80)',end=2000) line read (unit=line,fmt=600) iatom,ires,res,type,x,y,z,segid,resid,w if (loxt(ires).and.(type.eq.'O ')) type='OT1 ' write (13,600) iatom,ires,res,type,x,y,z,segid,resid,w 200 continue 2000 close (unit=11) close (unit=12) close (unit=13) goto 1 end ----- End of Example 3 -----End of Summary ////////////////////// Xiaomei Yang, Postdoc Dept of Chem & Biochem Univ of Texas at Austin Austin, 78712 TX, USA Tel: +1-512-471-4671 (O) xiaomei@ne059.cm.utexas.edu ///////////////////////////// From chemistry-request@www.ccl.net Wed Mar 24 20:48:42 1999 Received: from quartz.super.arizona.edu (quartz.Super.Arizona.EDU [128.196.131.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA00371 Wed, 24 Mar 1999 20:48:40 -0500 (EST) Received: from localhost (fan@localhost) by quartz.super.arizona.edu (8.8.7/8.8.7) with SMTP id MAA09224; Wed, 24 Mar 1999 12:25:13 -0700 (MST) X-Authentication-Warning: quartz.super.arizona.edu: fan owned process doing -bs Date: Wed, 24 Mar 1999 12:25:13 -0700 (MST) From: Hua-Jun Fan X-Sender: fan@quartz.super.arizona.edu To: Christian Stadler cc: chemistry@www.ccl.net Subject: Re: CCL:technical problem with gaussian98 job In-Reply-To: <13C55135102@alf2.ngate.uni-regensburg.de> Message-ID: Dear Christian, According to the error message, I would think you had requested too much memory than the machine could allocate. It worked before could be because no one else was running and you had all the computer memory. > ****************************** > Insufficient memory for a single shell combination in PrsMar called > from PRISM: LenV= 483650 MaxCom= -1 Error termination > ****************************** > %mem=55000000 Here you requested 440MB memory alone > Default route: MAXDISK=4GB > -------------------------------------------------------- > #P ub3lyp/lanl2dz pop=nboread scf=(restart,maxcycle=199) Best regards. Huajun Fan From chemistry-request@www.ccl.net Wed Mar 24 21:01:53 1999 Received: from web609.yahoomail.com (web609.mail.yahoo.com [128.11.68.173]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA00613 Wed, 24 Mar 1999 21:01:52 -0500 (EST) Message-ID: <19990325000855.1208.rocketmail@web609.yahoomail.com> Received: from [148.234.75.80] by web609.mail.yahoo.com; Wed, 24 Mar 1999 16:08:55 PST Date: Wed, 24 Mar 1999 16:08:55 -0800 (PST) From: Victor Manuel "Rosas-García" Subject: Imaginary freqs in Spartan To: CCL mailing list Hello everybody, Does anyone know how to get rid of imaginary freqs in Spartan 5.1? I can't find in the manuals how to go downhill along a particular vibrational mode. I know how to do that in MOPAC, but I can't find the equivalent commands in Spartan. Any help will be appreciated. Victor == Victor M. Rosas García Computational Chemistry Apprentice e-mail: quimico69@yahoo.com _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From chemistry-request@www.ccl.net Thu Mar 25 03:32:03 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@[134.99.152.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA02445; Thu, 25 Mar 1999 03:31:31 -0500 (EST) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA27093; Thu, 25 Mar 1999 09:29:25 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universitaet To: Iraj Daizadeh , chemistry@www.ccl.net, chemistry-request@www.ccl.net Subject: OFFTOPIC (was: Re: CCL:xmgr-linux) Date: Sun, 1 May 2135 15:55:51 +0100 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain References: On Mit, 24 Mär 1999 Iraj Daizadeh wrote: >sorry about the lack of chemistry--anyone compile xmgr on alpha >linux--cannot seem to find includes... These are Motif header files you need :-( LessTif works fine, though - check out www.lesstif.org. Btw. Yes, it compiles+runs on Linux/AXP using LessTif :-) Greetings, Jochen ----------------------------------------------------------------------- Jochen Küpper Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I Universitätsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 Düsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Mar 25 06:49:54 1999 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA03167 Thu, 25 Mar 1999 06:49:35 -0500 (EST) Received: from [193.144.74.154] (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id MAA01319 for ; Thu, 25 Mar 1999 12:47:26 +0100 (MET) Message-Id: <199903251147.MAA01319@uscmail.usc.es> Subject: BSSE and solvent effects Date: Thu, 25 Mar 99 12:53:57 +0100 x-mailer: Claris Emailer 1.1 From: cronos To: I am trying to correct the BSSE error on a dimerization that occurs in the solvent THF. To take into account solvent effects we choose the Tomasi PCM model. This methodology consider the solvent as a continuum and the cavity of the solute is taken as superposition of spheres centred at the heavy atoms. To correct BSSE we use the counterpoise method (with Boys and Bernardi method) by the keyword MASSAGE of the gaussian program. My question is: When we remove a molecule of the dimer but leave their basis functions (with massage) the cavity of the solute must include: a) only spheres centred at the atoms of the molecule that was not removed ? b) or spheres centred at the atoms of all the dimer ? Thanks in advance From chemistry-request@www.ccl.net Thu Mar 25 12:25:55 1999 Received: from probity.mcc.ac.uk (probity.mcc.ac.uk [130.88.200.94]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA05112 Thu, 25 Mar 1999 12:25:51 -0500 (EST) Received: from nessie.mcc.ac.uk ([130.88.200.20] ident=ymumjc) by probity.mcc.ac.uk with esmtp (Exim 1.92 #3) for chemistry@www.ccl.net id 10QDt7-0009WD-00; Thu, 25 Mar 1999 17:25:49 +0000 Received: (from ymumjc@localhost) by nessie.mcc.ac.uk (8.8.8/8.8.8) id RAA02805 for chemistry@www.ccl.net; Thu, 25 Mar 1999 17:25:48 GMT (envelope-from ymumjc) From: Jonathan Connor Message-Id: <199903251725.RAA02805@nessie.mcc.ac.uk> Subject: chemical reaction theory To: chemistry@www.ccl.net Date: Thu, 25 Mar 1999 17:25:48 +0000 (GMT) Dear All, The papers in the PCCP Special Issue on Chemical Reaction Theory (54 papers) can now be downloaded in pdf format from http://www.rsc.org/pccp (provided your library subscribes to PCCP) Best wishes, Jonathan Connor ---------------------------------------------------------------------------- ---------------------------------------------------------------------- Physical Chemistry Chemical Physics Issue 6 Contents Research Papers 929 A very high accuracy potential energy surface for H3 Y.-S. Mark Wu, Aron Kuppermann and James B. Anderson 939 Potential energy surface for the reactions BeH2 + H ? BeH + H2 Michael A. Collins and Ryan P. A. Bettens 947 An analytical potential energy surface of the HClF (2A') system based on ab initio calculations. Variational transition state theory study of the H + ClF * F + HCl, Cl + HF and F + HCl * Cl + HF reactions and their deuterium isotope variants R.Say^ss, J. Hernando, J. Hijazo and Miguel Gonz^alez 957 Coupled ab initio potential energy surfaces for the reaction Cl(2P) + HCl * ClH + Cl(2P) Abigail J. Dobbyn, J. N. L. Connor, Nicholas A. Besley, Peter J. Knowles and George C. Schatz 967 A study of FeCO+ with correlated wavefunctions Kurt R. Glaesemann, Mark S. Gordon and Haruyuki Nakano 977 Photofragmentation spectra and potential energy surfaces of Sr+ Ar2 G. S. Fanourgakis, S. C. Farantos, Ch. L^|der, M. Velegrakis and S. S. Xantheas 983 Theoretical investigation of the potential energy surface for the reaction of NO3 with H Luminita C. Jitariu and David M. Hirst 989 A theoretical study of the kinetics of C2H3 + H Stephen J. Klippenstein and Lawrence B. Harding 999 An ab initio quasi-classical direct dynamics investigation of the F + C2H4 * C2H3F + H product energy distributions Kim Bolton, H. Bernhard Schlegel, William L. Hase and Kihyung Song 1013 Potential energy surface for unimolecular dissociations and rearrangements of the ground state of [C2H3FO] systems Lam Thanh Nguyen, Raman Sumathi and Minh Tho Nguyen 1025 A quantum chemical approach to the water assisted neutral hydrolysis of ethyl acetate and its derivatives Georg Schmeer and Peter Sturm 1031 A theoretical ab initio and Monte Carlo simulation study of the pyridine + CCl2 reaction kinetics in the gas phase and in carbon tetrachloride solution using canonical flexible transition state theory Josefredo R. Pliego, Jr. and Wagner B. De Almeida 1037 A coupling between the equilibrium state variables of open molecular and reactive systems Roman F. Nalewajski 1051 Group functions, L^vwdin partition, and hybrid QC/MM methods for large molecular systems A. L. Tchougr^ieff 1061 A reaction class approach for modeling gas phase reaction rates Thanh N. Truong, Wendell T. Duncan and Max Tirtowidjojo 1067 Quantum dynamics from ab initio points D. Y. Wang, T. Peng, J. Z. H. Zhang, W. C. Chen, and C. H. Yu 1071 Classical canonical transformation theory as a tool to describe multidimensional tunnelling in reactive scattering. Hopping method revisited and collinear H + H2 exchange reaction near the classical threshold Gennady V. Mil'nikov and Ant^snio J. C. Varandas 1081 Semiclassical calculation of cumulative reaction probabilities Sophya Garashchuk and David J. Tannor 1091 Probabilities for the F + H2 * HF + H reaction by the hyperquantization algorithm: alternative sequential diagonalization schemes Vincenzo Aquilanti, Simonetta Cavalli, Dario De Fazio, Alessandro Volpi, Antonio Aguilar, Xavier Gim^inez and Jos^i Mar^ma Lucas 1099 A theoretical study of the prereaction process of the H^w^w^wHF van der Waals molecule Toshiyuki Takayanagi and Yuzuru Kurosaki 1105 Exploring molecular motions in collinear HeH2+ and its isotopic variants using periodic orbits Pankaj Bhatia, Biswajit Maiti, Narayanasami Sathyamurthy, Stamalis Stamatiadis and Stavros C. Farantos 1115 Nearside-farside analysis of state-selected differential cross sections for reactive molecular collisions Abigail J. Dobbyn, P. McCabe, J. N. L. Connor and Jes^zs F. Castillo 1125 Exact quantum 3D cross sections for the Ne + H2+ * NeH+ + H reaction by the hyperspherical method. Comparison with approximate quantum mechanical and classical results Ferm^mn Huarte-Larra^qaga, Xavier Gim^inez, Josep M. Lucas, Antonio Aguilar and Jean-Michel Launay 1133 The influence of initial energy on product vibrational distributions and isotopic mass effects in endoergic reactions: the Mg + FH case Ferm^mn Huarte-Larra^qaga, Xavier Gim^inez, Margarita Albert^m, Antonio Aguilar, Antonio Lagan^` and Jos^i M. Alvari^qo 1141 Helicity decoupled quantum dynamics and capture model cross sections and rate constants for O(1D) + H2 * OH + H Stephen K. Gray, Evelyn M. Goldfield, George C. Schatz and Gabriel G. Balint-Kurti 1149 Quantum mechanical and quasi-classical rate constant calculations for the O(3P) + HCl * OH + Cl reaction F. J. Aoiz, L. Ba^qares, J. F. Castillo, M. Men^indez and J. E. Verdasco 1159 Quantum reaction dynamics of an asymmetric exoergic heavy-light-heavy system: Cl + HBr * HCl + Br Gennady V. Mil'nikov, Oleg I. Tolstikhin, Katsuyuki Nobusada and Hiroki Nakamura 1165 State-to-state three-atom reactive scattering using adiabatic rotation approximations Dario De Fazio and Jes^zs F. Castillo 1173 Quantum dynamics of the O(3P) + CH4 * CH3 + OH reaction David C. Clary 1181 Three-dimensional quantum scattering calculations on the Cl + CH4 ? HCl + CH3 reaction Hua-Gen Yu and Gunnar Nyman 1191 Quantum studies of H2O + Cl * HO + HCl and H2O + Br * HO + HBr reactions. A comparison of two reduced dimensionality approaches N. Rougeau, G. Nyman and C. Kubach 1197 Quantum-mechanical study of the resonances of the SN2 reaction Cl- + CH3Cl * ClCH3 + Cl- Marta I. Hern^andez, Jos^i Campos-Mart^mnez, Pablo Villarreal, Stefan Schmatz and David C. Clary 1205 Reactive and nonreactive charge transfer by the FMS method: low energy H+ + D2 and H + H2+ collisions M. Chajia and R. D. Levine 1213 A classical-path surface-hopping study of Mu, H and T hot-atom collisions with F2 Werner Jakubetz, J. N. L. Connor and Philip J. Kuntz 1227 Time-dependent studies of reaction dynamics: a test of mixed quantum/classical time-dependent self-consistent field approximations Lichang Wang and Anne B. McCoy 1237 Exciplex funnel resonances in chemical reaction dynamics: The nonadiabatic tunneling case associated with an avoided crossing at a saddle point Ronald S. Friedman, Thomas C. Allison and Donald G. Truhlar 1249 Ultrafast photoinduced dissipative hydrogen switching dynamics in thioacetylacetone N. Doslic, K. Sundermann, L. Gonz^alez, O. M^s, J. Giraud-Girard and O. K^|hn 1259 Quantum dynamics of kinematic invariants in tetra- and polyatomic systems Robert G. Littlejohn, Kevin A. Mitchell and Vincenzo Aquilanti 1265 Quantum mechanical study of photodissociation of oriented ClNO(S1) Hua Guo and Tamar Seideman 1273 Semiclassical dissociation dynamics in coplanar atom-diatom collisions Kazuhiro Sakimoto 1279 Calculation of resonance states of non-rotating HOCl using an accurate ab initio potential Sergei Skokov, Joel M. Bowman and Vladimir A. Mandelshtam 1283 Unimolecular phase space theory rates by inversion of angular momentum-conserved partition function Wendell Forst 1293 Energy-diffusion-limited unimolecular reactions in condensed phases Yin Guo and Donald L. Thompson 1299 Oscillator phase and the reaction dynamics of HN3: A model for correlated motion Karin R. Wright and John S. Hutchinson 1311 Optimal spectral filtering in a finite subspace: a Lanczos-based implementation Sean C. Smith, Hua-Gen Yu, Claude Leforestier and Jean-Claude Rayez 1317 Chemical dynamics of the protonated water trimer analyzed by transition path sampling Philip L. Geissler, Christoph Dellago and David Chandler 1323 Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase Alexander J. Turner, Vicente Moliner and Ian H. Williams 1333 Partitioning dynamic and thermal factors in quantum rate calculations: a coherent state approach Joachim Ankerhold, Frank Grossmann and David J. Tannor 1343 Local propagating Gaussians: flexible vs. frozen widths Sybil M. Anderson, Tae Jun Park and Daniel Neuhauser 1351 Eley-Rideal and hot-atom reactions between hydrogen atoms on metals: quantum mechanical studies Chakrapani Kalyanaraman, Didier Lemoine and Bret Jackson 1359 A classical study of rotational effects in dissociation of H2 on Cu(100) Drew A. McCormack and Geert-Jan Kroes 1375 Computational studies on surface reaction mechanisms: ethylene hydrogenation on platinum catalysts Dario Duca, Gianfranco La Manna and Maria Rosa Russo 1383 A quantum chemical investigation of imide adsorption at model Cu(110) surfaces Philip R. Davies and James M. Keel 1387 Regularity in chaotic reaction paths II: Ar6. Energy dependence and visualization of the reaction bottleneck Tamiki Komatsuzaki and R. Stephen Berry ---------------------------------------------------------------------------- ---------------------------------------------------------------------- -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 0161-275-4693 (national) Department of Chemistry, :+44-161-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 0161-275-4686 or 4600 England. Fax: 0161-275-4734 or 4598 ****************************************************************************** From chemistry-request@www.ccl.net Thu Mar 25 12:38:48 1999 Received: from probity.mcc.ac.uk (probity.mcc.ac.uk [130.88.200.94]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA05267 Thu, 25 Mar 1999 12:38:47 -0500 (EST) Received: from nessie.mcc.ac.uk ([130.88.200.20] ident=ymumjc) by probity.mcc.ac.uk with esmtp (Exim 1.92 #3) for chemistry@www.ccl.net id 10QE5O-0009a1-00; Thu, 25 Mar 1999 17:38:30 +0000 Received: (from ymumjc@localhost) by nessie.mcc.ac.uk (8.8.8/8.8.8) id RAA03453 for chemistry@www.ccl.net; Thu, 25 Mar 1999 17:38:30 GMT (envelope-from ymumjc) From: Jonathan Connor Message-Id: <199903251738.RAA03453@nessie.mcc.ac.uk> Subject: Roger Grice To: chemistry@www.ccl.net Date: Thu, 25 Mar 1999 17:38:30 +0000 (GMT) The Royal Society of Chemistry, Faraday Division Invitation to submit a paper A special issue of Physical Chemistry Chemical Physics (a merger of the Journal of the Chemical Society Faraday Transactions and Berichte der Bunsen-Geselr Physikalische Chemie from Jan. 1999) on Molecular Reaction Dynamics: EXPERIMENT AND THEORY will be published in 2000 to commemorate the scientific achievements of the late Roger Grice (1941-1998) Contributions in the form of regular papers are invited by 30 Sept. 1999 Further information from: Professor J N L Connor, Department of Chemistry, University of Manchester, Manchester M13 9PL, England. e-mail: J.N.L.Connor@Manchester.ac.uk -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 0161-275-4693 (national) Department of Chemistry, :+44-161-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 0161-275-4686 or 4600 England. Fax: 0161-275-4734 or 4598 ****************************************************************************** From chemistry-request@www.ccl.net Thu Mar 25 13:09:04 1999 Received: from smaug.wrq.com (smaug.wrq.com [150.215.17.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05779 Thu, 25 Mar 1999 13:09:03 -0500 (EST) Received: from ursula.wrq.com (root@ursula.wrq.com [150.215.11.58]) by smaug.wrq.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id KAA26961 for ; Thu, 25 Mar 1999 10:09:04 -0800 (PST) Received: from BIGGEEK ([150.215.141.174] (may be forged)) by ursula.wrq.com with SMTP (8.8.6 (PHNE_14041)/8.7.3) id KAA19340 for ; Thu, 25 Mar 1999 10:09:54 -0800 (PST) Received: by BIGGEEK with Microsoft Mail id <01BE76A7.827452B0@BIGGEEK>; Thu, 25 Mar 1999 10:09:03 -0800 Message-ID: <01BE76A7.827452B0@BIGGEEK> From: Mark Alan Thompson To: "'chemistry@www.ccl.net'" Subject: UFF force field Date: Thu, 25 Mar 1999 10:09:02 -0800 Dear CCL subscribers, I have spent a couple of weeks examining the literature for a complete description of the UFF method as described by Rappe and Goddard. It appears that the description of the method is incomplete due to their lack of publishing the exchanged-corrected generalized Mulliken Pauling electronegativies (GMP) for the entire periodic table. They allude to two papers that were submitted (to J. Phys. Chem) and even give the titles. However these papers appear to never have been published. Were they withdrawn? I have read the recently published Molecular Mechanics book by Rappe. I cannot find information in that book on these parameters. I've searched the CCL archives and come up with dozens of messages over the years that deal with this issue, sadly with no successful conclusions other than to buy some commercial implementation. My question to the CCL: has anyone obtained a set of these GMP values that can be legally used? Does anyone have a definitive statement as to the proprietary nature of this force field? In the end, I can always come up with my own set of GMPs, but I would probably then have to rename the method: suggestions for a name? PUFF ? or UFFDA ? Mark ************************************************* Mark Thompson WRQ Inc. 1500 Dexter Ave. N. Seattle, WA. 98109 web: www.wrq.com email: markt@wrq.com ************************************************* From chemistry-request@www.ccl.net Thu Mar 25 16:43:17 1999 Received: from qlink.queensu.ca (Qlink.QueensU.CA [130.15.129.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA06950 Thu, 25 Mar 1999 16:43:13 -0500 (EST) Received: from localhost (3tksk@localhost) by qlink.queensu.ca (8.9.0/8.9.0) with ESMTP id QAA16132 for ; Thu, 25 Mar 1999 16:43:04 -0500 (EST) Date: Thu, 25 Mar 1999 16:43:04 -0500 (EST) From: STK <3tksk@qlink.queensu.ca> To: chemistry@www.ccl.net Subject: CCL: Computational Chemist vs Theoretical Chemist Message-ID: Hello, I would like to know what the distinction is between a computational chemist and a theoretical chemist or are they the same? Many theoretical chemists who do vigorous computational calculations are adament that they are "theoretical chemists" and not "computional chemists". Whereas people in fields like QSAR, bioinformatics, and 3D modeling clearly call themselves computational chemists and not theoretical. Does computional chemistry encompass theoretical chemistry? Has there been any authoritative definition on this? Please enlighten us. Thanks, ============================================================================== Stephen T. Kim Phone: 613-533-2647 Fax: 613-533-6669 From chemistry-request@www.ccl.net Thu Mar 25 18:06:05 1999 Received: from bluemchen.dki.tu-darmstadt.de (bluemchen.dki.tu-darmstadt.de [130.83.61.64]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA00616; Thu, 25 Mar 1999 18:06:00 -0500 (EST) Received: from alannah.dki.tu-darmstadt.de (ppp187.stud.tu-darmstadt.de [130.83.177.187]) by bluemchen.dki.tu-darmstadt.de (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id AAA19796; Fri, 26 Mar 1999 00:05:58 +0100 (CET) Sender: n@alannah.dki.tu-darmstadt.de Message-ID: <36FAC340.E71D9C4B@alannah.dki.tu-darmstadt.de> Date: Fri, 26 Mar 1999 00:14:08 +0100 From: Michael Soliman X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.0.35 i586) To: CHEMISTRY@www.ccl.net Subject: Extracting Homo-Lumo Energies Moin Moin. I just wanted to ask, whether somebody of You knows how to read out the homo- and lumo-enegies for a set of molecule conformations ( enumerated by a reaction-coordinate ) from a mopac6 .out file. Of course I tried to find something in the Manual and examined the .homo.out file, discovered the list of Eigenvalues but no partitioning information. So I just wanted to ask, whether You know how to accomplish this readout or know a tool for doing this. Tschuess, Michael. -- _____________________________________________________________________________ Michael Soliman. Email: michel@soliman.de michel@alannah.dki.tu-darmstadt.de michel@sunny.dki.tu-darmstadt.de Adresse: Hauptstrasse 11a 64401 Rodau GERMANY Telephon: +(49)616660178 Fax: +(49)6166920683 ------------------------------------------------------------------------ From chemistry-request@www.ccl.net Fri Mar 26 07:44:01 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA05750 Fri, 26 Mar 1999 07:43:56 -0500 (EST) Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id OAA03731 for ; Fri, 26 Mar 1999 14:39:24 +0200 (EET) Date: Fri, 26 Mar 1999 14:39:24 +0200 (EET) From: "I. Kerkines" To: chemistry@www.ccl.net Subject: eisai monos ?diabase to (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear listmembers, a)I am interested in finding a program (in C or better in Fortran), that from classical trajectory calculations via Molecular Dynamics, is able to calculate the Raman or/and Rayleigh spectra of a mixture not necessary composed of monoatomics. b)In MD we use the term "Potential Energy".Which experi- mental quantity is very close to it and so we can compare with it when we work in the GAS phase with pure substances or mixtures of diatomics molecules. c)When we have to work a mixture we usually apply the well-known Lorentz-Berthelot rules.But it is not too accurate.Is there any general procedure when we have excess properties(enthalpy,volume) to calculate a more accurate interaction L-J potential between the dissimilar species of a mixture? Thanks in advance, Ioannis Kerkines University of Athens From chemistry-request@www.ccl.net Fri Mar 26 08:54:54 1999 Received: from mail1.uct.ac.za (exim@mail1.uct.ac.za [137.158.128.73]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA06267 Fri, 26 Mar 1999 08:54:43 -0500 (EST) Received: from mort by mail1.uct.ac.za with local (Exim 2.01 #3) for chemistry@www.ccl.net id 10QX4C-000287-00; Fri, 26 Mar 1999 15:54:32 +0200 Received: by mail1.uct.ac.za (Mort 2.23alpha) id 564 from ACHIM@PSIPSY; Fri Mar 26 15:54:32 1999 From: "Achim Lienke" Organization: University of Cape Town To: chemistry@www.ccl.net Date: Fri, 26 Mar 1999 15:57:33 SAST-2 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Cis-/Trans-Influence in transition metal complexes Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-Id: Hi there, I wonder if somebody is aware of some recent lit/review about the cis-/trans-influence in transition metal complexes and how it affects the thermodynamic stability? Is something about donor-donor bonds known stabilizing the cis-isomer? Achim From chemistry-request@www.ccl.net Fri Mar 26 13:05:02 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA08082 Fri, 26 Mar 1999 13:05:01 -0500 (EST) Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP); Fri, 26 Mar 1999 18:04:45 +0000 From: uccatvm Message-Id: <15478.199903261804@socrates-a.ucl.ac.uk> Subject: exptl. dipole moment for indole? To: chemistry@www.ccl.net (CCL) Date: Fri, 26 Mar 1999 18:04:44 +0000 (GMT) Cc: T.vanMourik@UCL.ac.uk (Tanja van Mourik) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers, My apologies if you have received this message before, but due to the recent problems with ccl I am not sure if my question ever reached the list. My original message is below: Would anyone know a value for the experimental dipole moment of indole, preferably with error bars? A recent paper on indole lists a value of 2.13 Debye, which comes >from the Tables of Experimental Dipole Moments, A.L. McClellan (1963). The original reference of this number dates back to 1944, and since our library does not have such old journals, I have no idea about the accuracy of this result. The newer version of the Tables of Experimental Dipole Moments (1974) apparently got lost in our library... I assume that there are some newer experiments available. I would be very grateful for any response. Best regards, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ====================================================================