From chemistry-request@server.ccl.net Tue Nov 14 14:42:31 2000 Received: from localhost (ccl@localhost) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08959 for ; Tue, 14 Nov 2000 14:42:31 -0500 Date: Tue, 14 Nov 2000 14:42:31 -0500 (EST) From: Computational Chemistry List To: chemistry@ccl.net Subject: CHRAMm help (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I'm doing free energy calculations with CHARMm using the PERT module. I want to mutate a SER residue into an ASN in a given protein. Are there any topology and parameter files available for such a mutation ? Thank you in advance, Meir Glick glick@bellatrix.pcl.ox.ac.uk From chemistry-request@server.ccl.net Tue Nov 14 18:54:00 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA10759 for ; Tue, 14 Nov 2000 18:53:58 -0500 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id WAA23424; Tue, 14 Nov 2000 22:32:16 +0100 Date: Tue, 14 Nov 2000 22:32:15 +0100 (MET) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net cc: help@gaussian.com Subject: spectroscopic terms in Gaussian98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I wonder if it is possible, in the calculation of an isolated atom with Gaussian, to select the spectroscopic term or symmetry group of the final state. In the case this is not possible, how can the corresponding spectroscopic term (or L**2 value) be assigned to a given output ? Regards -- Damian Scherlis Department of Physical Chemistry Faculty of Sciences University of Buenos Aires From chemistry-request@server.ccl.net Wed Nov 15 04:51:08 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA13163 for ; Wed, 15 Nov 2000 04:51:08 -0500 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id EAA16172 for ; Wed, 15 Nov 2000 04:50:57 -0500 (EST) Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id BAA28943 for ; Wed, 15 Nov 2000 01:52:55 -0800 (PST) Received: from dial8.msi.com(146.202.9.108) by mailhost.msi.com via smap (V2.0) id xma028940; Wed, 15 Nov 00 01:52:39 -0800 Message-Id: <5.0.0.25.2.20001115104534.00ac6970@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 15 Nov 2000 10:50:07 +0100 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:Another CHARMM question.; larger water box In-Reply-To: <3A11B2B5.1CADE1E6@cornell.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Richard, I have written a CHARMm script that will make any box; the only consideration will be the maxatom limit on the CHARMm version you are using. You can get the script, and the origin-centered 15A box of water it uses, through MSI's anon. ftp server ftp to ftp.msi.com cd pub/dist get mk_solv_box.tar Try this script (changing some env.variables etc.) and let me know if it helps. I am interested in putting scripts like this one, and any others that users may have created and would think others would find useful, into a 'script library' on MSI's support web-site. If you can think of any other useful scipts, or come across any, please let me know. Thanks! Don Gregory At 04:46 PM 11/14/00 -0500, Richard Wood wrote: >I have a new CHARMM question/problem. I finally figured out the last >one. > >This one goes like this. I have an image file and the coordinates for >512 TIP3P water molecules. I cn generate a box of 3456 TIP3P water >molecules with the box being 24.8616 A on a side. > >My question is this: how can I generate a bigger box that has more water >molecules in it? The box needs to be about 80 A or so (I'm trying to >solvate a protein) > >Thanks to all of you for your suggestions and Thanks to Rick Venable and >Michael Brunsteiner for their help with my last problem. > >Richard > >-- >Richard L. Wood, Ph. D. >Physical/Computational Chemist >Post-doctoral Associate >Cornell University, Ithaca, NY 14853 > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Dr. Don Gregory (dgregory@msi.com) CHARMm Product Marketing Manager Molecular Simulations Inc. (http://www.msi.com) 9685 Scranton Rd. San Diego, CA 92121 Office Phone: (858) 799-5331 Mobile Phone: (619) 200-3613 From chemistry-request@server.ccl.net Wed Nov 15 09:53:01 2000 Received: from server.ttpharma.com (ttpharma.com [206.74.77.186]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15468 for ; Wed, 15 Nov 2000 09:53:01 -0500 Received: from jerome ([192.168.4.24]) by server.ttpharma.com (8.9.3/8.8.7) with SMTP id IAA14422; Wed, 15 Nov 2000 08:44:13 -0600 From: "Jerome Baudry" To: "'K. Watanabe.'" , Subject: RE: About Retinal Date: Wed, 15 Nov 2000 09:44:12 -0500 Message-ID: <000001c04f12$85c72380$1804a8c0@ttpharma.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: <3A1091A5.DB707537@hitachi-ul.co.jp> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hi Katsuhiro The following papers are about parametrization of the CHARMM force field for retinal (all-trans and (13,15)di-cis) from ab-initio calculations. These papers also include calculations on retinal in bacteriorhodopsin and comparison with experimental results that validate the parameters (papers listed by chronological order): Nina, M.; Roux, B. and J.C. Smith. . Ab initio quantum chemical analysis of retinal schiff base hydration in bacteriorhodopsin. 1993 J. Mol. Struct. (Theochem) 286:231-245 Baudry, J.; Crouzy, S.; Roux, B and J.C. Smith Quantum chemical and free energy simulation analysis of retinal conformational energetics. 1997 J. Chem. Inf. Comput. Sci. 37:1018-1024 Baudry, J.; Crouzy, S.; Roux, B and J.C. Smith Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin 1999 Biophys. J. 76:1909-1917 The following paper adresses some of the differences in various parametrizations: Tajkhorshid, E.; Baudry, J.; Schulten, K and S. Suhai, Molecular Dynamics study of the nature and origin of retinal's twisted struture in bacteriorhodopsin 2000 Biophys. J. 78:683-693 The following paper does not describe the details of the parametrization per se, but is another interesting study of the influence of parametrization: Humphrey, W.; D, Xu; M. Sheves and K. Schulten Molecular Dynamics study of the early intermediates in the bacteriorhodpsin photocycle 1995 J. Phys. Chem. 99:14549-14560 Hope it helps, Please contact me if you need additional information ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On Behalf Of K. Watanabe. > Sent: Monday, November 13, 2000 8:13 PM > To: CHEMISTRY@ccl.net > Subject: CCL:About Retinal > > > Hi, > > We want to do MD simulation for a protein that include > Retinal molecule. > Does anyone know some information about Retinal Parameters for MD? > > Katsuhiro Watanabe > Hitachi ULSI Systems Co.,Ltd. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Wed Nov 15 11:22:47 2000 Received: from uucphost.mcs.net (Kitten2.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16022 for ; Wed, 15 Nov 2000 11:22:47 -0500 Received: from becky (P62-Chi-Dial-2.pool.mcs.net [205.253.224.126]) by uucphost.mcs.net (8.9.3/8.9.3) with SMTP id KAA06645; Wed, 15 Nov 2000 10:22:22 -0600 (CST) (envelope-from rone@mcs.net) Message-ID: <000001c04f20$1c3161c0$7ee0fdcd@becky> From: "Rebecca Rone" To: "Robert Jorissen" , References: <3A10D1C2.3EACDBF5@ludwig.edu.au> Subject: Re: CCL:help with MMFF94 in CHARMM Date: Tue, 14 Nov 2000 11:19:16 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Dear Robert, You may have slightly altered conformations of the molecule. It goes without saying that different conformations will have the same bonded energies and only the non-bonded energies will be different. Were you using distance dependent dielectric (RDIE) or constant dielectric (CDIE)? The electrostatic energy is very sensitive to this. Also, EES and VdW are both highly sensitive to the coordinates of the system. Even just a change from double precision to single precision on an already minimized structure can produce changes to these two energy terms which shows up more heavily in the EES term. Are you using a standard set of coordinates for all systems or did you re-minimize something? Another thing that can happen is if there is a random number generation in the minimization scheme and one of the standard test structures (with its conformation)was sitting at an undiscovered saddle point. In this case different brands of computers can reach very different minimized structures. If this could be the source of the problem try using the option in CHARMM which let's you set the number. I think it is RANDOM SEED, or some such. Most computers do not truly use a random number in their random number generators so successive runs on the same computer may generate the same structure even if it is a saddle point. Alternately, two miniumized conformations from different computers may have found two different minima which are on different sides of a conformational divide, although in this case the non-bonded energies should be more different than what you are seeing. Ages ago SGI had a problem with some non-standard chips (which has long since been resolved), but one of the first signals to this problem was that computers with defective chips first failed on the standard test cases in the fashion you described. If it is a similar chip problem, watch for the calculations to become progessively more disturbed over time. To check this run and re-run several dynamics calculations in bursts of 50 or so steps at a batch and re-minimize after each. Totally bad chips may fail in the manner we saw before where the structure ultimately becomes completely entangled in a spiderweb construction. SGI has long since created quality control measures to monitor chips for this problem but other manufacturers may not have. Regards, Becky Dr. Rebecca Rone Rone Biotechnology Consulting Boston, MA. Chicago, IL. Phone: 773-646-2585 Mobile: 630-638-2585 ----- Original Message ----- From: "Robert Jorissen" To: Sent: Monday, November 13, 2000 11:46 PM Subject: CCL:help with MMFF94 in CHARMM > Hello > > I wish to perform some calculations using the MMFF94 forcefield in > CHARMM. > (I am using the acedemic version 25b1). I calculated the energies of a > small > number of small molecules from the MMFF94 validation set. Although the > energy > components from the bonded parameters (bond stretch, angle bending etc) > seem to > agree with those listed in the Batchmin and Optimol log files provided > as part > of the validation set files, I seem to have slight discrepencies with > the > van der Waals energies in some (but not all) of the systems and with the > electrostatic energies in all of the small number of systems I have > looked at > so far. > > The results for one molecule are shown below. (Easy to compare the > numbers if > Courier font is used to view them.) The results from each energy term > are from > my CHARMM calculation, the calculation using Optimol and the > calculations using > Batchmin in double precision and single precision respectively. > > I would appreciate hearing from anyone who has used the MMFF94 > forcefield in > CHARMM and whether they encountered this problem. I doubt that this can > be > explained by numerical imprecision in calculation since calculations "by > hand" > using a spreadsheet yield values for the electrostatic energy far closer > to > the Optimol and Batchmin values than the values I calculated using > CHARMM. > Also, the partial charges produced by CHARMM agreed with those in the > input > coordinate files. > > Any assistance would be appreciated. > > Rob > > > BEWCUB - 18-ACETATO-ASPARENOMYCIN A P-NITROBENZYL ESTER > > "?BOND" to "4.74997" > Optimol: 4.74997 > BMin DP: 4.74997559238 > BMin SP: 4.749975 > > "?ANGL" to "20.6828" > Optimol: 20.68285 > BMin DP: 20.6828388838 > BMin SP: 20.68284 > > "?DIHE" to "24.6512" > Optimol: 24.65119 > BMin DP: 24.6511913190 > BMin SP: 24.65120 > > "?OOPL" to "-4.39081" > Optimol: -4.39082 > BMin DP: -4.39081620274 > BMin SP: -4.390817 > > "?STRB" to "0.136841" > Optimol: 0.13684 > BMin DP: 0.136842257168 > BMin SP: 0.1368436 > > "?ELEC" to "-41.184" > Optimol: -41.40216 > BMin DP: -41.4021642936 > BMin SP: -41.40216 > > "?VDW" to "48.2924" > Optimol: 48.18183 > BMin DP: 48.1818461796 > BMin SP: 48.18185 > > "?ENER" to "52.9385" > Optimol: 52.60970 > BMin DP: 52.6097137356 > BMin SP: 52.60972 > > > -- > ----------------------------------------------------- > Robert Jorissen > > Ludwig Institute for Cancer Research > P.O. BOX 2008, Royal Melbourne Hospital > Parkville, Victoria 3050, Australia > > phone: ++61-3-9341-3155 > fax: ++61-3-9341-3104 > > e-mail: Robert.Jorissen@ludwig.edu.au > WWW: http://modelling.ludwig.edu.au/~jorissen/ > > ----------------------------------------------------- > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Nov 15 11:31:17 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16096 for ; Wed, 15 Nov 2000 11:31:16 -0500 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JWKFYSW2UI009JT4@trentu.ca> for chemistry@ccl.net; Wed, 15 Nov 2000 11:30:52 EST Date: Wed, 15 Nov 2000 11:35:56 -0500 From: elewars Subject: Re: CCL:Excited State Reviews To: chemistry@ccl.net Message-id: <3A12BB6C.BDFFD7C5@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <00111411241301.01255@borussia> W. Sudholt asked for the calc of electronic excited states: Hello, Good results for electronically excited states are often obtained from ZINDO/S, a semiempirical method (fast), and from time-dependent DFT (DDFT) (much slower). Another standard method is RCIS. I think ZINDO/S and TDDFT are best. All three are available in Gaussian 98. I could send you some typical input files. ZINDO/S is a version of INDO/S (M. Kotzian, N. Rosch, and M. C. Zerner, Theor Chim Acta, 1992, 81, 201) developed by the group of the late Michael Zerner (hence Z). TDDFT: M. E. Casida in "Recent developments and applications of modern density functional theory", J. M. Seminario, Ed., Elsevier, Amsterdam, 1996 and refs therein. R. E. Stratmen et al, J Chem Phys, 1998, 109, 8218. K. B. Wiberg e al, Chem Phys Lett, 1998, 297, 60 RCIS J. B. Foresman and A. Frisch, "Exploring Chemistry..." Gaussian Inc, Pittsburgh, PA, 1996, p. 218. E. Lewars ==== Wibke Sudholt wrote: > Dear CCLers, > > I'm looking for review papers and/or key articles and/or web pages about the > quantum chemical calculation of electronically excited states (especially > singlet excited states). I'm interested in organic molecules with about 10 > heavy atoms (about 20 atoms in total). > > The question I would like to answer is: Which semiempirical/ab initio/density > functional methods are known for this purpose? How expensive and accurate are > they? > > I'm aware of the CASSCF/CASPT2 articles of Roos et al. and also of some papers > about CIS, TDDFT, DFT/SCI and DFT/MRCI. > > Thank you very much in advance! > > Best regards > > Wibke Sudholt > Institute of Theoretical Chemistry > Heinrich-Heine-University > Duesseldorf, Germany > wibke@theochem.uni-duesseldorf.de > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Nov 15 12:25:42 2000 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA16358 for ; Wed, 15 Nov 2000 12:25:42 -0500 Received: from cornell.edu (phobos.mbg.cornell.edu [128.84.203.151]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA06852 for ; Wed, 15 Nov 2000 12:25:27 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3A12C79F.6869AA94@cornell.edu> Date: Wed, 15 Nov 2000 12:27:59 -0500 From: Richard Gillilan Reply-To: reg8@cornell.edu X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-3 i686) X-Accept-Language: en MIME-Version: 1.0 CC: CHEMISTRY@ccl.net Subject: new OPLS/MMFF ? References: <000001c04f12$85c72380$1804a8c0@ttpharma.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I recall seeing an abstract by Thomas Halgren (I think it was a recent ACS meeting) about an new hybrid OPLS/MMFF forcefield. Did anyone here attend that talk? If so, would you care to comment? Will the FF be available to the public? Is there a paper out on it yet? Thanks Richard From chemistry-request@server.ccl.net Wed Nov 15 13:29:51 2000 Received: from mailserv.wright.edu (mailserv.wright.edu [130.108.128.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA16830 for ; Wed, 15 Nov 2000 13:29:51 -0500 Received: from CONVERSION-DAEMON by mailserv.wright.edu (PMDF V5.2-33 #39224) id <0G4200301WPC8A@mailserv.wright.edu> for CHEMISTRY@ccl.net; Wed, 15 Nov 2000 13:29:36 -0500 (EST) Received: from unconfigured (o137142.wright.edu [130.108.137.142]) by mailserv.wright.edu (PMDF V5.2-33 #39224) with SMTP id <0G4200KPTWPCZD@mailserv.wright.edu> for CHEMISTRY@ccl.net; Wed, 15 Nov 2000 13:29:36 -0500 (EST) Date: Wed, 15 Nov 2000 13:28:02 -0500 From: Kevin Gross Subject: Getting charges from AIM2000 To: CCL Message-id: <000f01c04f31$ca209a60$8e896c82@wright.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Content-type: text/plain; charset="Windows-1252" Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-priority: Normal Hi all, I recently got Bader's AIMPAC code working thanks to the help of others on this list. However, I've been short on time and haven't yet learned the input syntax to set up calculations. To quickly get some results, I decided to try AIM2000 for the PC. It seems user-friendly; however, I'm not sure where in the output the atomic charge is. As I understand it, one must first compute the critical points of the charge distribution. Then one can distinguish the atoms in the molecule. It seems after integration of the charge density over an atomic basin, the atom's charge is determined. When I integrate over an atomic basin in AIM2000, I get a lot of results, none of which appear to be an atomic charge. What am I (obviously) missing? Thanks, Kevin From chemistry-request@server.ccl.net Wed Nov 15 10:01:44 2000 Received: from server.ttpharma.com (ttpharma.com [206.74.77.186]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA15529 for ; Wed, 15 Nov 2000 10:01:44 -0500 Received: from jerome ([192.168.4.24]) by server.ttpharma.com (8.9.3/8.8.7) with SMTP id IAA14499; Wed, 15 Nov 2000 08:53:00 -0600 From: "Jerome Baudry" To: "'Wibke Sudholt'" , Subject: RE: Excited State Reviews Date: Wed, 15 Nov 2000 09:52:58 -0500 Message-ID: <000101c04f13$bf589380$1804a8c0@ttpharma.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: <00111411241301.01255@borussia> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear Wibke You can have a look at: Characterization of a Conical Intersection between the Ground and First Excited State for a Retinal Analog. Ferenc Molnar, Michal Ben-Nun, Todd J. Martínez, and Klaus Schulten. Journal of Molecular Structure (THEOCHEM), WATOC special issue, 506:169--178, 2000. abstract visible at: http://www.ks.uiuc.edu/Publications/Papers/abstract.cgi?tbcode=MOLN2000A Hope it helps, Cheers ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On > Behalf Of Wibke Sudholt > Sent: Tuesday, November 14, 2000 4:58 AM > To: CHEMISTRY@ccl.net > Cc: wibke@theochem.uni-duesseldorf.de > Subject: CCL:Excited State Reviews > > > Dear CCLers, > > I'm looking for review papers and/or key articles and/or web > pages about the > quantum chemical calculation of electronically excited states > (especially > singlet excited states). I'm interested in organic molecules > with about 10 > heavy atoms (about 20 atoms in total). > > The question I would like to answer is: Which > semiempirical/ab initio/density > functional methods are known for this purpose? How expensive > and accurate are > they? > > I'm aware of the CASSCF/CASPT2 articles of Roos et al. and > also of some papers > about CIS, TDDFT, DFT/SCI and DFT/MRCI. > > Thank you very much in advance! > > Best regards > > Wibke Sudholt > Institute of Theoretical Chemistry > Heinrich-Heine-University > Duesseldorf, Germany > wibke@theochem.uni-duesseldorf.de > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Wed Nov 15 11:00:27 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15886 for ; Wed, 15 Nov 2000 11:00:26 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id LAA12187; Wed, 15 Nov 2000 11:00:13 -0500 (EST) Message-ID: Date: 15 Nov 2000 11:18:32 -0500 From: "Boyd" Subject: Re: free energy of formation To: "Kalathingal, Giju T." , "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear Giju, >Hi Everybody, >Could you please give me some references or suggestions on how >to estimate classical free energy of formation of a molecule? >Thanks in advance, >Giju You will find some useful material in the chapter: L. A. Curtiss, P. C. Redfern, and D. J. Frurip, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol. 15, pp. 147-211. Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Wed Nov 15 13:52:04 2000 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA17079 for ; Wed, 15 Nov 2000 13:52:03 -0500 Received: from [128.97.45.51] ([128.97.45.51]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id KAA14290 for ; Wed, 15 Nov 2000 10:51:48 -0800 (PST) Mime-Version: 1.0 Message-Id: Date: Wed, 15 Nov 2000 10:51:46 -0800 To: CHEMISTRY@ccl.net From: Eric Scerri Subject: call for papers/chemical education Content-Type: multipart/alternative; boundary="============_-1237808188==_ma============" --============_-1237808188==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" CALL FOR PAPERS: SPECIAL ISSUE OF FOUNDATIONS OF CHEMISTRY ON "CHEMICAL EDUCATION" Articles are invited on the general theme of Chemical Education and in particular topics under the following general categories; Models and Analogies in Teaching Chemistry, Ethics & Chemistry, Chemistry & Philosophy, Computational Chemistry and Chemical Education, The role of Philosophy of Science in Chemical Education, The use and development of conceptual thinking in Chemical Education, Biology and Chemical Education, Recent trends in Chemical Education Research, The role of Comprehension & Literacy in Chemical Education. Visualization and Chemistry, Chemistry, Chemical Education and the Internet, The particular nature and style of Chemical Explanations, Constructivism in Chemical Education, The use of History in Chemical Education, The historical development of Chemical Education Research, New themes in Chemical Education, What is special about Chemical Education within Science Education. Literature reviews of specific areas in Chemical Education scholarship. The role of mathematics and abstraction in Chemical Education. etc. All articles should be submitted directly to the publisher (Kluwer Academic Press) see journal web page address below. Deadline: End of April 2001. Papers received later than this date will be considered for regular Varia issues. Inquiries regarding suitability of submissions etc should be sent to the editor, Eric Scerri, preferably by E-mail. Please consult the web pages below if you have not already done so for instructions to authors, tables of contents, references to work in philosophy of chemistry/chemical education etc. -- Eric Scerri , Visiting Professor, UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/journalhome.htm/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html --============_-1237808188==_ma============ Content-Type: text/html; charset="us-ascii" call for papers/chemical education


CALL FOR PAPERS:     SPECIAL ISSUE OF FOUNDATIONS OF CHEMISTRY

                                                ON

                                "CHEMICAL EDUCATION"


Articles are invited on the general theme of Chemical Education and in particular topics under the following general categories;


Models and Analogies in Teaching Chemistry,
Ethics & Chemistry,
Chemistry & Philosophy,
Computational Chemistry and Chemical Education,
The role of Philosophy of Science in Chemical Education,
The use and development of conceptual thinking in Chemical Education,
Biology and Chemical Education,
Recent trends in Chemical Education Research,
The role of Comprehension & Literacy in Chemical Education.
Visualization and Chemistry,
Chemistry, Chemical Education and the Internet,
The particular nature and style of Chemical Explanations,
Constructivism in Chemical Education,
The use of History in Chemical Education,
The historical development of Chemical Education Research,
New themes in Chemical Education,
What is special about Chemical Education within Science Education.
Literature reviews of specific areas in Chemical Education scholarship.
The role of mathematics and abstraction in Chemical Education.
etc.


All articles should be submitted directly to the publisher (Kluwer Academic Press) see journal web page address below.  Deadline:  End of April 2001.  Papers received later than this date will be considered for regular Varia issues.

Inquiries regarding suitability of submissions etc should be sent to the editor, Eric Scerri, preferably by E-mail.

Please consult the web pages below if you have not already done so for instructions to authors, tables of contents, references to work in philosophy of chemistry/chemical education etc.

--
Eric Scerri ,
Visiting Professor,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.wkap.nl/journalhome.htm/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html
--============_-1237808188==_ma============-- From chemistry-request@server.ccl.net Wed Nov 15 14:00:52 2000 Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA17108 for ; Wed, 15 Nov 2000 14:00:51 -0500 Received: from ccc.uni-erlangen.de (temeraire.chemie.uni-erlangen.de [131.188.128.73]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id UAA21091 for ; Wed, 15 Nov 2000 20:00:33 +0100 (MET) Sender: Anselm.Horn@Organik.Uni-Erlangen.DE Message-ID: <3A12DB39.DC7EDB55@ccc.uni-erlangen.de> Date: Wed, 15 Nov 2000 19:51:37 +0100 From: Anselm Horn Organization: CCC X-Mailer: Mozilla 4.74 [en] (X11; U; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Sybyl atom types Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I am looking for a (free) tool to assign the "native" Sybyl atom types to a 3D-structure. Of course, there is babel, but I learned that it sometimes fails. A descripiton of the Sybyl algorithm for assigning the atom types would also be sufficient. I would greatly appreciate, if anybody could send me such a tool or point me to some references (literature/web). Thank you in advance ! Regards, Anselm -- _______________________________________________________________________ Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de ___ / __| ___ Computer Chemie Centrum | / ___ / __| | | / __|| / Naegelsbachstrasse 25 \ \__ | / | | D-91025 Erlangen \___|| | \ \__ Deutschland / Germany \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html _______________________________________________________________________ From chemistry-request@server.ccl.net Wed Nov 15 14:08:28 2000 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA17164 for ; Wed, 15 Nov 2000 14:08:27 -0500 Received: from [128.97.45.51] ([128.97.45.51]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id LAA14953 for ; Wed, 15 Nov 2000 11:08:12 -0800 (PST) Mime-Version: 1.0 Message-Id: Date: Wed, 15 Nov 2000 11:08:11 -0800 To: CHEMISTRY@ccl.net From: Eric Scerri Subject: thanks for responses on Hund etc Content-Type: text/plain; charset="us-ascii" ; format="flowed" Thanks to all who responded to my request for whether or not Hund's rule of maximum spin multiplicity. I think the variety of responses in itself says something about these kinds of questions, namely that issues of this kind are rather unclear and it really depends on what one means by a theoretical justification/derivation. I hope to collate responses and post them soon. So far we have three types of responses which I characterize as, (1) weak plausibility explanations whereby unpaired electrons in different degenerate orbitals are justified on the basis of the Pauli type repulsion etc. (2) Somewhat stronger plausibility explanations based on the Hartree-Fock treatment of helium as found in several textbooks. Too bad that that the ground state of the helium atom does not require us to invoke Hund's rule although it is obviously of some value to see that the triplet state is more stable that the singlet according to the formalism. How about a general argument for any atom or is this asking for too much? (3) Stronger arguments yet which appeal to published articles which I have not yet had time to dig up. I hope I am not being too negative in my broad assessment? I also recall an interesting article by Jorgensen and Katriel of several years ago which I need to find. regards, eric scerri -- Eric Scerri , Visiting Professor, UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/journalhome.htm/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html