From chemistry-request@server.ccl.net Wed Dec 5 19:30:21 2001 Received: from mercury.chem.nwu.edu (gwuxi@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB60ULi31964 for ; Wed, 5 Dec 2001 19:30:21 -0500 Received: from localhost (gwuxi@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id fB60Tt705517; Wed, 5 Dec 2001 18:29:55 -0600 (CST) Date: Wed, 5 Dec 2001 18:29:55 -0600 (CST) From: Guosheng Wu X-X-Sender: To: "Shobe, Dave" cc: "'laidig.wd@pg.com'" , ccl , Guosheng Wu Subject: on "Prediction of chemical reactivity" In-Reply-To: <157A51F55AAAD3119CD70008C7B1629D01C15770@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id fB60ULi31965 Hi everyone: It seems there are lots of people getting interested in predicting chemical reactivity. However, half of my thesis work may challenge any current program or method which declaims the ability to predict chemical reactivity. Maybe most of you are talking about different level of quality about "prediction" from mine, but here are some of my comments about this topic: Vibrational excitation (for suitable mode coupling to the reaction channel) will push a reaction from activated behavior(Arrhenius like: an activation energy needed) to activationless behavior (no any barrier, like H+H, O+H2, or many reactions between an ion and a molecule). And the enhancement of reactivity is really huge, thinking of the exponential term! Such an effect can be accomplished by continuous vibrational excitation: the potential between reactants will switch from repulsive to totally attractive (like K+ + Cl- ---> form an ionic bond). How much excitation is needed? Usually the energy of the system (vib-excited) higher than the barrier (ground state reaction) is a crucial condition, but it's dependent on the vib-mode, and some steric effect. Our research on H+H2O(OH local mode excited)--> H2+OH is the first example, and results for more systems are going to come out soon... This has seldomly been realized because it's really tough to get an accurate potential energy surface(fit from ab initio results) for 4-atomic reaction, and previous surfaces are not accurate enough to describe vib-excited reactions. If there is more interest, check (1)Faraday Discussion, 1999, 113,181 and (2)J. Chem. Phys. 2000, 113, 3150... To keep an eye on the progress of this direction, check my advisor(G. C. Schatz)'s publications in the future... What all of these tell us? Previous theoretical results on vib-excitation reaction dynamics, or high temperature rate constants(contribution from the channel of vib-excited state is very big) may need to be corrected. And we need to work harder to get the "predicting the reactivity"... It's very hard for H+H2O, then it's obviously harder for most reactions you are interested in. One easy solution is to decrease the level of "prediction", and be careful of vib-excited effect or results at high temperature. Hope my message may give you another kind of taste on this topic. Any comments, please send to me one week later since my defence is coming very soon, otherwise I can not reply to you in time. Thanks. Guosheng --------------------------------------------- Guosheng Wu gwuxi@chem.nwu.edu Ph: (847)491-7189 fax: (847)491-7713 Department of Chemistry, Northwestern Univ. 2145 Sheridan Road, Evanston, IL, 60208-3113 --------------------------------------------- On Wed, 5 Dec 2001, Shobe, Dave wrote: > I remember a program called Cameo (WL Jorgensen et al) that predicted the > products of a reaction mixture. I think it used rho-and-sigma-type > substituent effects for calculation of reaction rates and equilibria rather > than any quantum calculations. There is still a home page for Cameo at > http://zarbi.chem.yale.edu/products/cameo/ if you're interested. > > I don't know what's been written since then (and probably I only know about > Cameo because I used to know some of the people that worked on the project). > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Don't bother flaming me: I'm behind a firewall. > > > > -----Original Message----- > From: laidig.wd@pg.com [mailto:laidig.wd@pg.com] > Sent: Monday, December 03, 2001 3:39 PM > To: chemistry@ccl.net > Subject: CCL:Predictionj of chemical reactivity > > > All, > > I have a colleague who needs software forpredicting the probability of a > aqueous > chemical reaction occurring between a variety of reactive chemicals at > around > pH7. Specificly, > 1)nucleophilic substitiution of halogenated compounds > 2) Schiff base formaiton > 3) addition-elimination of acids, esters, amides > 4) nucleophilic adition of aldehydes and ketones > 5) Michael addition of alpha,beta unsaturated compounds > 6) addition by ring cleavage of epoxides > 7) electrophilic substitiution of diazonium salts > I am not up on current synthetic prediction program and would appreciate am > pointers to current software, recommendations, etc. I will summarize > responsews > to the list > > Thanks, Bill > > William D. Laidig > CADMol Group > Corporate Analytical CR-TD > 513-627-2857 > 513-627-1233 (FAX) > laidig.wd@pg.com > > > > > > > > > > -= 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 Thu Dec 6 01:10:37 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB66Abi10779 for ; Thu, 6 Dec 2001 01:10:37 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id fB66AMa16254; Thu, 6 Dec 2001 00:10:22 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id AAA26447; Thu, 6 Dec 2001 00:10:22 -0600 (CST) Date: Thu, 6 Dec 2001 00:10:22 -0600 From: John Stone To: chemistry@ccl.net Cc: vmd@ks.uiuc.edu Subject: Announce: VMD 1.7.1b1 test version is available... Message-ID: <20011206001019.B26410@geneseo.ks.uiuc.edu> Mail-Followup-To: John Stone , chemistry@ccl.net, vmd@ks.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i Dear CCL, We have just built a test version, VMD 1.7.1b1, that we'd like to get user feedback on. This new version includes several new features that required changes to our graphics code, so that's one of the major items I'd like feedback on. If people have any trouble running this version on their graphics boards, please let us know. This is the first version of VMD to use the texture mapping hardware on the graphics accelerators, specifically it now makes use of 3-D texturing in support of new volumetric data display for potential maps, isosurfaces, EDM files, etc. Those people wishing to try out these new features with some of the early scripts we've got for reading volumetric data files should feel free to email us. You can download VMD 1.7.1b1 from: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD The full list of features and improvements in this test version is included below. Thanks, John Stone vmd@ks.uiuc.edu What's new in VMD 1.7.1? ------------------------ New Features o New volume rendering features including isosurface display, volume slicing with support for hardware accelerated 3-D texture mapping, and a Tcl volume data loader interface. o Support for scanline-interleaved stereoscopic rendering for hardware such as the Eye3D stereo glasses and decoders. General Improvements and Bug Fixes o Multi-level OpenGL stipple-based "screen door" transparency. Now implements varying levels of transparency. o Improved support for WireGL cluster-based rendering and tiled display walls. o The IMD code now closes down active socket connections more carefully, allowing the kernel to complete any in-progress write operations before closing the socket. o Tachyon scene export improved with new camera parameters for matched perspective views with VMD. o POV-Ray scene export improved with new camera parameters and support for orthographic views, shadow control, and matched perspective camera views. o Replaced DNA example molecule with a better one. o H-bond shown in the H-bond rep are now pickable. o Added code to read the unit cell data from Charmm trajectory files. o Improved robustness and error handling when reading Raster3D scene files. Fixed Raster3D file reading crash. o Eliminated atom selection and Tcl related memory leaks Fixed PRs: 168, 170, 171, 172 User Interface Changes o Users can select either FLTK or Tk file browsers according to their personal preference. Some people prefer the Windows-like function of the Tk browsers, while others like the filename completion of the FLTK file browser. This is configured by setting the VMDFILECHOOSER environment variable. o Reverted behavior of the edit form old "-1" index use. User Documentation Updates o Updated the betacolor example script included in the docs for new versions of VMD. o Updated the animation scripts in the script library for new versions of VMD. o Improved index entries pertaining to lighting and shading. -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Thu Dec 6 05:54:25 2001 Received: from tlr-es01.eu.unilever.com ([194.60.106.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6AsOi19144 for ; Thu, 6 Dec 2001 05:54:24 -0500 Received: from pts-001.ps.u1889.unilever.com by tlr-es01.eu.unilever.com with ESMTP for chemistry@ccl.net; Thu, 6 Dec 2001 10:47:13 Z Received: from dhcp-68-28.ps.u1889.unilever.com by pts-001.ps.u1889.unilever.com with ESMTP for chemistry@ccl.net; Thu, 6 Dec 2001 10:47:11 Z Date: Thu, 6 Dec 2001 10:47:16 +0000 (GMT Standard Time) From: "Edward Griffiths" Subject: Effect of pH To: "chemistry@ccl.net" Message-Id: MIME-Version: 1.0 Content-Type: MULTIPART/ALTERNATIVE; DIFFERENCES=Content-Language; BOUNDARY="8342385-17012-1007635636=:252" Content-Language: en-GBR --8342385-17012-1007635636=:252 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Language: en-GBR Dear CCLs, Does anyone know how I could include the effects of pH into a quantum chemistry calculation? Are there any models to include it? Thank you in advance for any replies. Regards, Edward Dr Edward Griffiths, Research Scientist, Molecular Modelling and Statistics Unit, Unilever Research Port Sunlight Laboratories, Quarry Road East, Bebington, CH63 3JW e-mail: Edward.Griffiths@Unilever.com Tel: +44 (0)151 641 1416 Fax: +44 (0)151 641 1826 --8342385-17012-1007635636=:252 Content-Type: TEXT/x-cdsi-msrtf; CHARSET=US-ASCII Content-ID: 0 Content-Language: en-GBR {\rtf1\ansi\ansicpg1252\deff0\deflang2057{\fonttbl{\f0\fswiss\fcharset0 Arial;}{\f1\fnil\fcharset0 Tahoma;}} \viewkind4\uc1\pard\f0\fs20 Dear CCLs,\par \par Does anyone know how I could include the effects of pH into a quantum chemistry calculation?\par Are there any models to include it?\par \par Thank you in advance for any replies.\par \par Regards,\par \par Edward\par \par \par \pard\tx720\fs16 Dr Edward Griffiths, Research Scientist,\par Molecular Modelling and Statistics Unit,\par Unilever Research Port Sunlight Laboratories,\par Quarry Road East, Bebington, CH63 3JW\par e-mail: Edward.Griffiths@Unilever.com\par Tel: +44 (0)151 641 1416\par Fax: +44 (0)151 641 1826\par \pard\f1\fs17\par \f0\fs20\par } --8342385-17012-1007635636=:252-- From chemistry-request@server.ccl.net Thu Dec 6 05:04:20 2001 Received: from oxygen.chem.nthu.edu.tw ([140.114.45.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6A4Ji18318 for ; Thu, 6 Dec 2001 05:04:19 -0500 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id B942E154CE; Thu, 6 Dec 2001 18:04:06 +0800 (CST) Date: Thu, 6 Dec 2001 18:04:06 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Subject: Re: CCL:Gaussian 98 benchmark for PC systems Message-ID: <20011206180406.A733@OXYGEN.chem.nthu.edu.tw> References: <20011206011124.A19953@OXYGEN.chem.nthu.edu.tw> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: ; from mn1@helix.nih.gov on Wed, Dec 05, 2001 at 03:51:42PM -0500 On Wed, Dec 05, 2001 at 03:51:42PM -0500, M. Nicklaus wrote: > Very interesting results! Can you tell which ones were the "about a dozen > of test jobs" that you used for these benchmarks, and if you ran them > right out of the box or if you modified the input (.com) files? We'll prepare a detail list of the test files that we have done the benchmark. We just used those original test files; no modifications were made to them in order to compare the outcomes to the logfiles provided by Gaussian. > Not that it should matter too much, but what distribution(s) of Linux did > you use? The Linux distributions that are used include Slackware 8.0 (with gcc 2.95.3); http://www.slackware.org Debian 3.0 "Woody" pre-release (with gcc 2.95.4); http://www.debian.org My first choice will be Slackware, and Debian is the second. The reasons are the simplicity, stability and the compact size. Both distributions are very flexible during installation, and take less than 800 MB in size for full installation (exclude X and TeX). Kenny -- Yu, Jen-Shiang Kenny // jsyu@Platinum.chem.nthu.edu.tw http://oxygen.chem.nthu.edu.tw/~jsyu Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN From chemistry-request@server.ccl.net Thu Dec 6 08:11:43 2001 Received: from bbhm.na.pg.com ([192.44.184.159]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6DBhi21274 for ; Thu, 6 Dec 2001 08:11:43 -0500 X-ExtMailInfo: pandora.na.pg.com [155.118.176.101] Received: from pandora.na.pg.com (pandora.na.pg.com [155.118.176.101]) by bbhm.na.pg.com (8.8.8/8.11.1/v1r32) with ESMTP id fB6CxkS17900; Thu, 6 Dec 2001 07:59:46 -0500 (EST) Received: from morpheus.na.pg.com (morpheus.na.pg.com [143.5.24.124]) by pandora.na.pg.com (SGI-8.9.3/8.9.3) with ESMTP id IAA53897; Thu, 6 Dec 2001 08:11:59 -0500 (EST) Received: from pg.com (localhost [127.0.0.1]) by morpheus.na.pg.com (SGI-8.9.3/8.9.3) with ESMTP id IAA50149; Thu, 6 Dec 2001 08:06:12 -0500 (EST) Sender: laidig@pg.com Message-ID: <3C0F6D43.B0136CE5@pg.com> Date: Thu, 06 Dec 2001 08:06:12 -0500 From: Bill Laidig X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, laidig@pg.com Subject: Summary on Prediction of Chemical Reactions Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit All, I sent the following message to the list a few days ago: : I have a colleague who needs software for predicting the probability of a aqueous : chemical reaction occurring between a variety of reactive chemicals at around : pH7. Specificly, : 1)nucleophilic substitiution of halogenated compounds : 2) Schiff base formaiton : 3) addition-elimination of acids, esters, amides : 4) nucleophilic adition of aldehydes and ketones : 5) Michael addition of alpha,beta unsaturated compounds : 6) addition by ring cleavage of epoxides : 7) electrophilic substitiution of diazonium salts :I am not up on current synthetic prediction program and would appreciate am :pointers to current software, recommendations, etc. I will summarize responsews :to the list and have received a number of helpful responses. First, I must apologize for not being entirely clear in my question. I more or less resent the message my non-computational chemist colleague wrote. What he is actually looking for is a fast method, probably expert-system basedthat can estimate the likelyhood of whether any of reaction(s) of the type above can occur. The program need not be quantitative and he is exploring using non-QM approaches (simple QM approaches have been tried in the past). To summarize the responses so far, they have fallen into a couple categories: 1. Recommended expert system programs: Several responses suggested CAMEO developed by Prof. Jorgenson's group at Yale. There is also a new Windows version under development at CambrideSoft. (Anyone know of other programs that use a similar approach?) 2. Several responses pointed out the difficulty in accurately predicting chemical reactions and their rates, etc. and stressed the need for rigorous quantum modeling. The fact that this is an active research frontier and not a solved problem was stressed as well. (thanks for your responses here - this may give my experimental collegue some perspective into the dificulty of accurately doing what he proposes.) Here are the specific responses: *********************************************************************** Whoa! Predicting reactivity is one hell of a problem especially if you want to cover such a wide range of systems. There are many programs that can help you to find reasonable structures for transition states, and more or less plausible activation energies. But to quantitatively predict relative rates simply from the identities of reactant pairs is not trivial! I don't think anyone can do it in a meaningful way. We are working on a "simple" problem related to case 1 below - nucleophilic substitution of primary alkyl chlorides. Believe me, it is consuming large amounts of high powered computer time, and we still haven't convinced referees that we are right in our explanation of the relative reactivities (although I am sure that we are ;-) )! You are not going to find this sort of thing "off the shelf". Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ *********************************************************************** > From mdb@chem.ucla.edu: You may wish to check the current status of the "CAMEO" program system, as developed by the Jorgensen group at Yale. Perhaps this might be helpful to you. Best regards, -Mike *********************************************************************** I remember a program called Cameo (WL Jorgensen et al) that predicted the products of a reaction mixture. I think it used rho-and-sigma-type substituent effects for calculation of reaction rates and equilibria rather than any quantum calculations. There is still a home page for Cameo at http://zarbi.chem.yale.edu/products/cameo/ if you're interested. I don't know what's been written since then (and probably I only know about Cameo because I used to know some of the people that worked on the project). --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. *********************************************************************** Also from David Shode: Just by coincincidence I got this notice from CambridgeSoft today: ------------------------ 3. Cameo Comes to Windows ------------------------ One of the most useful applications of artificial intelligence to organic chemistry is to design syntheses of big and hairy molecules. Perhaps the next most useful is to identify and rectify the weak steps in a proposed scheme before any reagents are committed to flasks. To this end, the CAMEO program is used by a variety of chemical and pharmaceutical companies to shed light on their syntheses. Given starting materials and reaction conditions, CAMEO predicts the various reaction products, accompanied by comments explaining factors affecting their yield. Hitherto it has been available on VAX/VMS, Unix (Sun, SGI and AIX), and the Macintosh. CambridgeSoft is now porting the application to Windows using Excel as part of the front (i.e. display) end. Read more about this exciting product development at: http://chemnews.cambridgesoft.com/art.cfm?S=160 or email software@cambridgesoft.com for more information *********************************************************************** Michael Bartberger and others have suggested CAMEO as a viable way of predicting reactivity. I have not seen CAMEO recently, and I certainly do not intend to "diss" it or its creators. As I understand it, CAMEO is a sort of "expert system" based on empirical rules. This may well be the sort of prediction that William Laidig was seeking, and there is nothing wrong with that. Perhaps I understood the question about "predicting reactivity" in a different context than was meant. An "expert system" is only as good as its rules when it comes to addressing chemical systems outside the range of structures that went into its parameterization. Unfortunately, many of the "rules and rationalizations" that we learned as undergraduates and that are still widely used by research chemists are simply incorrect at a fundamental level, particularly as they apply to reactions in solution. While they are in many cases qualitatively successful, the fundamental flaws in their logic mean that they will fail for some (unknown) set of situations. If you don't agree with this assertion about "rules and rationalizations", you should consider the usual explanation organic chemists use for the differing acidities of organic acids. If it was true that acidities could be correctly understood in terms of delocalization of charge in the conjugate base (by inductive withdrawal or by resonance), then a) gas-phase acidities and solution phase acidities would show parallel trends (they do not in general) and b)the trend would be reflected in the enthalpies of ionization in solution (it is not, in general). The data on this have been available for decades and can be found in standard (older) physical organic textbooks as well as compendia of physical data. So, to return to my argument about reactivity, if we base our analysis of an unknown reaction on rationalizations that are based on questionable (or false) premises, are we actually able to predict its behavior? Or are we simply lucky? Speaking as an experimental organic chemist who has turned recently to computational chemistry to find answers to nagging questions that conventional wisdom (at least among organic chemists!) has not adequately addressed, I still maintain that accurate prediction of reactivity remains a highly challenging problem that is not really dealt with by off-the-shelf solutions. Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ *********************************************************************** Hi everyone: It seems there are lots of people getting interested in predicting chemical reactivity. However, half of my thesis work may challenge any current program or method which declaims the ability to predict chemical reactivity. Maybe most of you are talking about different level of quality about "prediction" from mine, but here are some of my comments about this topic: Vibrational excitation (for suitable mode coupling to the reaction channel) will push a reaction from activated behavior(Arrhenius like: an activation energy needed) to activationless behavior (no any barrier, like H+H, O+H2, or many reactions between an ion and a molecule). And the enhancement of reactivity is really huge, thinking of the exponential term! Such an effect can be accomplished by continuous vibrational excitation: the potential between reactants will switch from repulsive to totally attractive (like K+ + Cl- ---> form an ionic bond). How much excitation is needed? Usually the energy of the system (vib-excited) higher than the barrier (ground state reaction) is a crucial condition, but it's dependent on the vib-mode, and some steric effect. Our research on H+H2O(OH local mode excited)--> H2+OH is the first example, and results for more systems are going to come out soon... This has seldomly been realized because it's really tough to get an accurate potential energy surface(fit from ab initio results) for 4-atomic reaction, and previous surfaces are not accurate enough to describe vib-excited reactions. If there is more interest, check (1)Faraday Discussion, 1999, 113,181 and (2)J. Chem. Phys. 2000, 113, 3150... To keep an eye on the progress of this direction, check my advisor(G. C. Schatz)'s publications in the future... What all of these tell us? Previous theoretical results on vib-excitation reaction dynamics, or high temperature rate constants(contribution from the channel of vib-excited state is very big) may need to be corrected. And we need to work harder to get the "predicting the reactivity"... It's very hard for H+H2O, then it's obviously harder for most reactions you are interested in. One easy solution is to decrease the level of "prediction", and be careful of vib-excited effect or results at high temperature. Hope my message may give you another kind of taste on this topic. Any comments, please send to me one week later since my defence is coming very soon, otherwise I can not reply to you in time. Thanks. Guosheng --------------------------------------------- Guosheng Wu gwuxi@chem.nwu.edu Ph: (847)491-7189 fax: (847)491-7713 Department of Chemistry, Northwestern Univ. 2145 Sheridan Road, Evanston, IL, 60208-3113 --------------------------------------------- -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@server.ccl.net Thu Dec 6 06:19:07 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6BI6i19527 for ; Thu, 6 Dec 2001 06:19:06 -0500 Received: by MAIL with Internet Mail Service (5.5.2650.21) id ; Thu, 6 Dec 2001 11:17:42 -0000 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A667E91@GABRIELLE> From: "Robinson, James" To: "'Edward Griffiths'" Cc: "'CCL'" Subject: RE: Effect of pH Date: Thu, 6 Dec 2001 11:17:25 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Umm good, errr.. crumbs, I usually add protons or remove them for the appropriate species. AS for a general pH affect, crumbs.. How about adding H3O+ or OH- in the environment? Or adjust the dielectric constant for acid or basic media. Cant really think of anything else. Mr James Robinson -----Original Message----- From: Edward Griffiths [mailto:Edward.Griffiths@unilever.com] Sent: Thursday, December 06, 2001 10:47 AM To: chemistry@ccl.net Subject: CCL:Effect of pH Dear CCLs, Does anyone know how I could include the effects of pH into a quantum chemistry calculation? Are there any models to include it? Thank you in advance for any replies. Regards, Edward Dr Edward Griffiths, Research Scientist, Molecular Modelling and Statistics Unit, Unilever Research Port Sunlight Laboratories, Quarry Road East, Bebington, CH63 3JW e-mail: Edward.Griffiths@Unilever.com Tel: +44 (0)151 641 1416 Fax: +44 (0)151 641 1826 From chemistry-request@server.ccl.net Thu Dec 6 10:08:33 2001 Received: from moutvdom01.kundenserver.de ([195.20.224.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6F8Wi23791 for ; Thu, 6 Dec 2001 10:08:32 -0500 Received: from [195.20.224.209] (helo=mrvdom02.schlund.de) by moutvdom01.kundenserver.de with esmtp (Exim 2.12 #2) id 16C07l-0000Kk-00; Thu, 6 Dec 2001 16:07:45 +0100 Received: from [212.65.26.58] (helo=anterio.internal.anterio.com) by mrvdom02.schlund.de with esmtp (Exim 2.12 #2) id 16C02g-0007nP-00; Thu, 6 Dec 2001 16:02:31 +0100 Received: (from gerd@localhost) by anterio.internal.anterio.com (8.11.0/8.11.0) id fB6F2SJ03274; Thu, 6 Dec 2001 16:02:28 +0100 Date: Thu, 6 Dec 2001 16:02:28 +0100 Message-Id: <200112061502.fB6F2SJ03274@anterio.internal.anterio.com> X-Authentication-Warning: anterio.internal.anterio.com: gerd set sender to gerd@anterio.com using -f From: Gerd Raether To: Edward.Griffiths@unilever.com CC: james.robinson@evotecoai.com, chemistry@ccl.net, schrodinger@anterio.com In-reply-to: <5FD8C12EECBBD4119DD10002B3027B9A667E91@GABRIELLE> (james.robinson@evotecoai.com) Subject: Re: CCL:Effect of pH References: <5FD8C12EECBBD4119DD10002B3027B9A667E91@GABRIELLE> Dear Dr. Griffiths, Dear Dr. Robinson, Schrödinger offers a pKa module together with his fastest ab initio programm Jaguar. Here the user just have to specify the protonation site. Please find more information at http://www.schrodinger.com/docs/jaguar4.1/html/manual/Jaguar41_Manual.html in 12. The pKa Prediction Module or as a jaguar developer I would also be pleased to answer more detailed questions. Best Regards Gerd Räther . * www.anterio.com Gerd Räther - developer anteri o Augustaanlage 26 gerd@anterio.com * * D-68165 Mannheim +49 621 40041 -[t]33 -[f]40 From: "Robinson, James" Cc: "'CCL'" Date: Thu, 6 Dec 2001 11:17:25 -0000 Umm good, errr.. crumbs, I usually add protons or remove them for the appropriate species. AS for a general pH affect, crumbs.. How about adding H3O+ or OH- in the environment? Or adjust the dielectric constant for acid or basic media. Cant really think of anything else. Mr James Robinson -----Original Message----- From: Edward Griffiths [mailto:Edward.Griffiths@unilever.com] Sent: Thursday, December 06, 2001 10:47 AM To: chemistry@ccl.net Subject: CCL:Effect of pH Dear CCLs, Does anyone know how I could include the effects of pH into a quantum chemistry calculation? Are there any models to include it? Thank you in advance for any replies. Regards, Edward Dr Edward Griffiths, Research Scientist, Molecular Modelling and Statistics Unit, Unilever Research Port Sunlight Laboratories, Quarry Road East, Bebington, CH63 3JW e-mail: Edward.Griffiths@Unilever.com Tel: +44 (0)151 641 1416 Fax: +44 (0)151 641 1826 -= 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 Thu Dec 6 11:49:07 2001 Received: from email.nist.gov ([129.6.2.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6Gn6i25882 for ; Thu, 6 Dec 2001 11:49:07 -0500 Received: from silyl.nist.gov (silyl.nist.gov [129.6.194.163]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id LAA10698 for ; Thu, 6 Dec 2001 11:48:54 -0500 (EST) Message-Id: <5.0.0.25.2.20011206113523.023ea620@mailserver.nist.gov> X-Sender: rdj3@mailserver.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Thu, 06 Dec 2001 11:48:50 -0500 To: chemistry@ccl.net From: Russ Johnson Subject: Re: CCL:Scaling Factor In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed At 12:01 PM 12/3/01 +0530, you wrote: >Dear Sir/Madam: >Could anyone please tell me the scaling factor for the frequencies >calculated using G-94, at MP2/6-311++G(2d,2p) level. >Thanks in advance. >ANANT The NIST Computational Chemistry Comparison and Benchmark Database (CCCBDB) (http://srdata.nist.gov/cccbdb/) has some information on scaling factors for vibrational frequencies. While it does not have results from the 6-311++G(2d,2p) basis set, an estimate of an appropriate scaling factor can be made looking at other basis sets. For example the web site has a page (section III.C.2) to calculate a least-squares best scaling factor given a selection of molecules. Using five (arbitrary) hydrocarbons with double bonds: Ethylene, allene, Propene, (E)2-Butene, and (Z)2-Butene, the website returns the following scaling factors: MP2/6-31G* 0.9383 +- 0.0011 MP2/6-31G** 0.9326 +- 0.0014 MP2/6-31+G** 0.9366 +- 0.0016 MP2/6-311G* 0.9484 +- 0.0013 cc-pVDZ 0.9490 +- 0.0019 aug-cc-pVDZ 0.9550 +- 0.0019 cc-pVTZ 0.9503 +- 0.0016 As the scaling factors vary slightly with the type of molecules, you could try molecules more similar to your interests. The web page on scaling also returns a fit of the inverse frequencies, which may be more appropriate to use if you are using the frequencies to calculate an entropy. Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice 301+975-2513 fax 301+869-4020 email: russell.johnson@nist.gov From chemistry-request@server.ccl.net Thu Dec 6 12:13:05 2001 Received: from aquila.cscs.ch ([148.187.130.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6HD5i26318 for ; Thu, 6 Dec 2001 12:13:05 -0500 Received: from cscs.ch (bogno [148.187.130.109]) by aquila.cscs.ch (Mail) with ESMTP id 3D03B1A812 for ; Thu, 6 Dec 2001 18:12:57 +0100 (MET) Sender: redaelli@cscs.ch Message-ID: <3C0FA714.BC9CBCE2@cscs.ch> Date: Thu, 06 Dec 2001 18:12:52 +0100 From: "Claudio Redaelli (CSCS)" Organization: Swiss Center for Scientific Computing - Via Cantonale, CH-6928 Manno (CH) X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en, el MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: G98 HP-UX Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all could anybody tell me if the G98 Revision A.10/A.11 should be able to write >16 BGyte scratch file?? Thanks in advance. -- Claudio Redaelli From chemistry-request@server.ccl.net Thu Dec 6 12:20:19 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6HKJi26519 for ; Thu, 6 Dec 2001 12:20:19 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id fB6HK7a27274; Thu, 6 Dec 2001 11:20:07 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id LAA27644; Thu, 6 Dec 2001 11:20:07 -0600 (CST) Date: Thu, 6 Dec 2001 11:20:07 -0600 From: John Stone To: chemistry@ccl.net Cc: biosoftdb@ks.uiuc.edu Subject: Announce: Struc. Bio. Software DB updates Message-ID: <20011206112004.M27195@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i Dear CCL, We have added many software packages and a few categories to the structural biology software database in the past few months. We would like to invite you to try it out and provide feedback if you have suggestions for new content, or general improvements. The software that implements the DB is also freely available for those that wish to create their own similar databases. http://www.ks.uiuc.edu/Development/biosoftdb/ Thanks, John Stone biosoftdb@ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Thu Dec 6 13:12:49 2001 Received: from wrzx07.rz.uni-wuerzburg.de ([132.187.1.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6ICni28520 for ; Thu, 6 Dec 2001 13:12:49 -0500 Received: from wocx51.chemie.uni-wuerzburg.de (wocx51.chemie.uni-wuerzburg.de [132.187.64.51]) by wrzx07.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.03) with ESMTP id TAA15685; Thu, 6 Dec 2001 19:12:37 +0100 (MET) Received: from chemie.uni-wuerzburg.de (bernd@wocd70.chemie.uni-wuerzburg.de [132.187.64.170]) by wocx51.chemie.uni-wuerzburg.de (SGI-8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id TAA94979; Thu, 6 Dec 2001 19:12:37 +0100 (CET) Sender: bernd@chemie.uni-wuerzburg.de Message-ID: <3C0FB6B3.BF4700BD@chemie.uni-wuerzburg.de> Date: Thu, 06 Dec 2001 19:19:31 +0100 From: Bernd Engels Organization: Institut =?iso-8859-1?Q?f=FCr?= Organische Chemie X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.10 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, petra.meurer@mail.uni-wuerzburg.de Subject: Near-infrared spectra Content-Type: multipart/mixed; boundary="------------5E4A61E979D5BC29E6A63A74" This is a multi-part message in MIME format. --------------5E4A61E979D5BC29E6A63A74 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, somebody I know would like to predict / calculate the near-infrared spectra (vibrational overtone absorption) of some molecules (glucose, lactic acid, urea and ascorbic acid) in aqueous solution, preferable in relation to the temperature and the concentration. So far she only found a paper on this topic (C.E. Wozny, et al. J. Near Infrared Spectrosc. 8, 133-150 (2000). Has anybody experience with this kind of calculations or can give information about useful papers or even better programs? We will review Bernd Engels -- Prof. Dr. Bernd Engels Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany Phone : (0049) (0)931-888-5394 Fax : (0049) (0)931-888-4606 e-mail: bernd@chemie.uni-wuerzburg.de --------------5E4A61E979D5BC29E6A63A74 Content-Type: text/x-vcard; charset=us-ascii; name="bernd.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Bernd Engels Content-Disposition: attachment; filename="bernd.vcf" begin:vcard n:Engels;Bernd tel;fax:0049-(0)931-888-4606 tel;work:0049-(0)931-888-5394 x-mozilla-html:FALSE org:Institut für Organische Chemie;der Universität Würzburg adr:;;;97074 Würzburg;Am Hubland;; version:2.1 email;internet:bernd@chemie.uni-wuerzburg.de x-mozilla-cpt:;9056 fn:Prof. Dr. Bernd Engels end:vcard --------------5E4A61E979D5BC29E6A63A74-- From chemistry-request@server.ccl.net Thu Dec 6 13:39:57 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6Idti29763 for ; Thu, 6 Dec 2001 13:39:56 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id fB6Id2F43555; Thu, 6 Dec 2001 20:39:02 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Thu, 6 Dec 2001 20:39:02 +0200 (EET) From: Arvydas Tamulis To: Janusz Rak cc: , Subject: Re: Fwd: Re: RHO-CI density In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Janusz and other CCL Colleagues, Actually I am looking for literature for the definitions of charges on atoms in ground and certain excited states in DFT-TD calculating by G98. We are investigating charge transfer in photoactive supermolecules taking difference between charges on atoms in ground and excited states (see our WEBsite: www.itpa.lt/~tamulis/). Referees in my previous articles wrote that charges on atoms in Gaussian 98 DFT-TD are not correctly defined. Zilvinas Rinkevicius remember that saw in "Exploring Chemistry" that charges in ground and certain excited states are defined by different formulae. I am receiving reasonable qualitative results investigating charge transfer in different excited states and wish to publish these my results but it is neccessary as much as possible give theoretical background why I am receiving reasonable results despite that seems charges on atoms using density=all in G98 are differently defined and therefore difference between ground and excited state values is not correct. Please say your opinion. Best regards, Arvydas ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Vilnius University, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +370-9919397 ******************************************************************* From chemistry-request@server.ccl.net Thu Dec 6 18:01:50 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB6N1oi09441 for ; Thu, 6 Dec 2001 18:01:50 -0500 Received: from [165.91.177.236] (account fan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5b3) with ESMTP id 764036 for chemistry@ccl.net; Thu, 06 Dec 2001 16:55:23 -0600 Sender: fan@ccl.net Message-ID: <3C0FF8DC.3BA5E1F2@mail.chem.tamu.edu> Date: Thu, 06 Dec 2001 17:01:48 -0600 From: Hua-Jun Fan Organization: Texas A&M University X-Mailer: Mozilla 4.77C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: CISD error References: <5.0.0.25.2.20011206113523.023ea620@mailserver.nist.gov> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, CCLer, I encountered a problem running CISD job. I have a closed shell, (-1) charge system with 24 atoms and 366 basis functions. It finished SCF calculation and it failed before starting CISD calculations. By increasing memory and/or disk space have no good to the problem and still result in the same error. I attached the error below and wish someone on the list could give me a hand. Thanks a lot for your time and wish you all a happy holidays! Huajun ---error--- SCF Done: E(RHF) = -717.766122435 A.U. after 27 cycles Convg = 0.8123D-08 -V/T = 2.1063 S**2 = 0.0000 KE= 6.488167847207D+02 PE=-3.048890174757D+03 EE= 9.813469100708D+02 Leave Link 502 at Thu Dec 6 19:52:21 2001, MaxMem= 117964800 cpu: 18175.4 (Enter /usr/local/g98.a7/g98/l801.exe) Windowed orbitals will be sorted by symmetry type. Range of M.O.s used for correlation: 13 366 NBasis= 366 NAE= 44 NBE= 44 NFC= 12 NFV= 0 NROrb= 354 NOA= 32 NOB= 32 NVA= 322 NVB= 322 **** Warning!!: The largest alpha MO coefficient is 0.68292341D+02 Leave Link 801 at Thu Dec 6 19:52:22 2001, MaxMem= 117964800 cpu: 0.0 (Enter /usr/local/g98.a7/g98/l804.exe) Closed-shell transformation, MDV= 117964800 ITran=6 ISComp=1. Estimate disk for full transformation 15573422962 words. Semi-Direct transformation. Would use 2389457459 words of disk, but MaxDisk= 2359296000. ModeAB= 4 MOrb= 18 LenV= 114370507 LASXX= 137040232 LTotXX= 137040232 LenRXX= 276389528 LTotAB= 139349296 MaxLAS= 854878848 LenRXY= 0 NonZer= 413429760 LenScr= 734515147 LnRSAI= 480869352 LnScr1= 836152435 MaxDsk= 2359296000 Total= 2327926462 SrtSym= F ITran= 3 JobTyp=0 Pass 1: I= 1 to 16. PickT4: no shell combinations can fit! NKLS2p= 257 NKLS2= 257 MaxCom= 254 Error termination via Lnk1e in /usr/local/g98.a7/g98/l804.exe. ---end of error---