From chemistry-request@server.ccl.net Thu Aug 8 02:13:46 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g786Djl19963 for ; Thu, 8 Aug 2002 02:13:45 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id IAA19459; Thu, 8 Aug 2002 08:13:25 +0200 (MEST) Message-ID: <3D520CE0.E11D6F24@fy.chalmers.se> Date: Thu, 08 Aug 2002 08:17:04 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: Pong CC: chemistry@ccl.net Subject: Re: CCL:Problem of Raman calculation by Gaussian94w References: <3D51A19D.1FCCC6F2@lrb.ap-hop-paris.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Pong Freq=Raman is what you wanna say - but beware, it takes much more time (numerical calc). regards /Patrik Pong skrev: > > Dear all, > I use Gaussian94w Revision-E.1 for window. I have the problem with > frequency caculation. I prefer to calculate both IR and Raman spectra. I > used keyword in the input file as > following; > > ********************************************* > Gaussian 94: x86-Win32-G94RevE.1 23-Nov-1996 > 07-Aug-1902 > ********************************************* > %Chk=D:\g94_outputs\GLYCEROL\water\water_B3LYP_631Gd.chk > ---------------------------- > # B3LYP/6-31G* Opt Freq Test > ---------------------------- > > But in the output file, it does not have data for Raman intensity (only > IR, as shown) > > Full mass-weighted force constant matrix: > Low frequencies --- -49.0895 -47.6951 -20.2841 -.0026 > -.0022 -.0018 > Low frequencies --- 1712.8715 3727.4009 3849.4834 > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), > Raman scattering activities (A**4/AMU), Raman depolarization ratios, > reduced masses (AMU), force constants (mDyne/A) and normal coordinates: > > 1 2 3 > A' A' A' > Frequencies -- 1712.8715 3727.4009 3849.4834 > > Red. masses -- 1.0825 1.0453 1.0810 > > Frc consts -- 1.8713 8.5567 9.4382 > > IR Inten -- 75.8354 1.6952 19.4360 > > Raman Activ -- .0000 .0000 .0000 > > Depolar -- .0000 .0000 .0000 > > Atom AN X Y Z X Y Z X > Y Z > 1 8 .00 .07 .00 .00 .05 .00 .07 > >.00 .00 > 2 1 -.43 -.56 .00 .58 -.40 .00 -.55 > >.44 .00 > 3 1 .43 -.56 .00 -.58 -.40 .00 -.55 > -.44 .00 > I tried to specify keyword ,Freq Raman to the input file. But it has > error message as following; > > Gaussian 94: x86-Win32-G94RevE.1 23-Nov-1996 > 07-Aug-1902 > ********************************************* > %Chk=D:\g94_outputs\GLYCEROL\water\water_B3LYP_631Gd_raman.chk > ---------------------------------- > # B3LYP/6-31G* Opt Freq Raman Test > ---------------------------------- > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > LYP/6-31G* OPT FREQ RAMAN TEST > ' > Last state="GCL" > TCursr= 2963 LCursr= 24 > Error termination via Lnk1e in C:\G94W\l1.exe. > Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. > File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 1 Scr= > 1 > > Any-way, I changed to other level of basis set, for example MP2. It > still be the same problem, except when I used the HF level of > calculation, the program can calculate both > IR and Raman. How can i solve this problem? Could you please give me the > advises directly to my e-mail address; > > jaturong.pratuangdejkul@lrb.ap-hop-paris.fr > > Finally, I would like to thank for all kindness to help me solving my > problem. > > Best regards, > > Pratuangdejkul J. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Patrik Johansson (patrikj@fy.chalmers.se) Scientist @ Materials Physics Group Chalmers University of Technology 412 96 Goteborg SWEDEN NEW!!! http://fy.chalmers.se/mf/Computer.html http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Thu Aug 8 03:37:08 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g787b7l22381 for ; Thu, 8 Aug 2002 03:37:07 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id JAA26920 for ; Thu, 8 Aug 2002 09:36:48 +0200 (MEST) Message-ID: <3D52206A.9D56B0AC@fy.chalmers.se> Date: Thu, 08 Aug 2002 09:40:26 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: Volume and electronic spatial extent (G98) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all If a regular Gaussian calculation is performed there is an output part: "Electronic spatial extent (au): = numerical value" Can this be related to a volume? And if so, how is it defined and what's the difference compared to calculations done with the Volume keyword (where 0.001 e/bohr**3 is used)? any help is much appreciated - and I'll of course summarize sincerely /Patrik -- Patrik Johansson (patrikj@fy.chalmers.se) Scientist @ Materials Physics Group Chalmers University of Technology 412 96 Goteborg SWEDEN NEW!!! http://fy.chalmers.se/mf/Computer.html http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Thu Aug 8 04:31:43 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g788Vhl25878 for ; Thu, 8 Aug 2002 04:31:43 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 2F0C53F8F68; Thu, 8 Aug 2002 10:31:42 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 2F6853F8F65; Thu, 8 Aug 2002 10:31:41 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 8 Aug 02 10:31:41 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 8 Aug 02 10:31:39 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: patrikj@fy.chalmers.se, jaturong.pratuangdejkul@lrb.ap-hop-paris.fr Date: Thu, 8 Aug 2002 10:31:15 +0100 Subject: CCL:Problem of Raman calculation by Gaussian94w Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <226D5D35873@virgil.ruc.dk> Patrik: > Freq=Raman is what you wanna say - but beware, it takes much more > time (numerical calc). Sure, freq=raman is what you need if you wish to compute Raman scattering activities with DFT, and it does take a considerable amount of time. But G98 has a more efficient numerical routine, it computes Raman data much faster than G94. Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Aug 8 04:42:45 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g788gil26494 for ; Thu, 8 Aug 2002 04:42:45 -0400 Received: from localhost (sundius@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id LAA11846; Thu, 8 Aug 2002 11:40:59 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: sundius owned process doing -bs Date: Thu, 8 Aug 2002 11:40:59 +0300 (EET DST) From: Tom Sundius X-Sender: To: Patrik Johansson cc: Pong , Subject: Re: CCL:Problem of Raman calculation by Gaussian94w In-Reply-To: <3D520CE0.E11D6F24@fy.chalmers.se> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 8 Aug 2002, Patrik Johansson wrote: > Dear Pong > > Freq=Raman is what you wanna say - but beware, it takes much more time > (numerical calc). This seems to be the right answer for Gaussian 98, but in Gaussian 94 you cannot compute Raman activities for DFT methods. Looking through the CCL archives, I found the following answer in a message posted on March 22, 1998: "A few days ago I posted a question concerning calculation of Raman Activities in Gaussian94. The answer on my question is that Raman scattering Activities and Raman depolarization Ratios require calculation of third derivatives which is only available at HF level in Gaussian." regards, Tom Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophecy in part +++ From chemistry-request@server.ccl.net Thu Aug 8 05:52:51 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g789qpl28975 for ; Thu, 8 Aug 2002 05:52:51 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 9A4C23F972B; Thu, 8 Aug 2002 11:52:50 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id A40883F9728; Thu, 8 Aug 2002 11:52:49 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 8 Aug 02 11:52:49 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 8 Aug 02 11:52:46 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: sundius@pcu.helsinki.fi Date: Thu, 8 Aug 2002 11:52:32 +0100 Subject: CCL:Problem of Raman calculation by Gaussian94w Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net, jaturong.pratuangdejkul@lrb.ap-hop-paris.fr, patrikj@fy.chalmers.se Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <22830017BC5@virgil.ruc.dk> Tom Sundius: >> Freq=Raman is what you wanna say - but beware, it takes much more >> time (numerical calc). > This seems to be the right answer for Gaussian 98, but in Gaussian > 94 you cannot compute Raman activities for DFT methods. .... Correction! It IS possible to compute DFT Raman data with G94, but with G94 you need to specify the option FREQ=CUBIC (in my recent message, I forgot about this crucial detail!). - FREQ=CUBIC is extremely slow; the new numerical procedure implemented in G98 and called with FREQ=RAMAN is faster by an order of magnitude. Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Aug 8 04:34:07 2002 Received: from hotmail.com ([64.4.21.154]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g788Y6l26013 for ; Thu, 8 Aug 2002 04:34:06 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 8 Aug 2002 01:34:01 -0700 Received: from 203.116.61.131 by lw14fd.law14.hotmail.msn.com with HTTP; Thu, 08 Aug 2002 08:34:01 GMT X-Originating-IP: [203.116.61.131] From: "xu xiao feng" To: chemistry@ccl.net Subject: Tinker Date: Thu, 08 Aug 2002 08:34:01 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 08 Aug 2002 08:34:01.0459 (UTC) FILETIME=[58CCEC30:01C23EB6] Hi, Anybody can tell me how to constrain two atoms to a specified distance instead of a range by using tinker? Your help is much appreciated! Charlie _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Thu Aug 8 08:55:56 2002 Received: from web12803.mail.yahoo.com ([216.136.174.38]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g78Cttl00815 for ; Thu, 8 Aug 2002 08:55:55 -0400 Message-ID: <20020808125554.64948.qmail@web12803.mail.yahoo.com> Received: from [61.9.73.249] by web12803.mail.yahoo.com via HTTP; Thu, 08 Aug 2002 05:55:54 PDT Date: Thu, 8 Aug 2002 05:55:54 -0700 (PDT) From: amor san juan Subject: Viewer docked output To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Summary of softwares replied in viewing docked output ligand+protein: 1) MidasPlus 2) VMD 3) Qmol 4) Pymol 5) SPDB 6) Viwer lite 7) Viwer Pro Added to those is ADT. Does anyone of those mentioned softwares capable of viewing simultaneously the docked ligand and protein(aside from ADT ofcourse). If there is what is the input file you used. Thanks, Amor __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From chemistry-request@server.ccl.net Thu Aug 8 03:13:37 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g787DZl21911 for ; Thu, 8 Aug 2002 03:13:36 -0400 Received: from fen.bilkent.edu.tr (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id KAA21675 for ; Thu, 8 Aug 2002 10:09:09 +0300 (EET DST) Message-ID: <3D521AA8.2080200@fen.bilkent.edu.tr> Date: Thu, 08 Aug 2002 10:15:52 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: pyramidalization of amides Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Collegues, thanks for the replies to my question about calculating geometries of amides with flat potential energy surfaces. There does not seem to be a major problem with applying standard methods, although it seems that most people prefer the empirical approach, that is comparing results with experiment rather than doing a theoretical analysis. My original letter and the anwers are summarized below. Regards, Ulrike Salzner Hello, I am reviewing a thesis which deals with pyramidalization in amides, S, Se anlogues and amids in larger ring systems. Substituent effects are analyzed and compared with AIM and NBO. All of these systems have inversion barriers smaller than ammonia, some of them are planar. Thus, like ammonia, these molecules probably violate the Born-Oppenheimer approximation. How reliable are standard calculations (B3LYP/6-31G*, MP2/6-31G*) of bond angles, i.e. degree of pyramidalization? Should trends be ok? I would appreciate opinions on this. Sincerely, Ulrike Salzner This is an interesting question. I am not sure there is a good answer. It is known that gas phase calculations lead to pyramidalization of nitrogens. This may or may not be the case in a crystal or in a hydrogen bonded network. One would like to have good crystal data, but it is very hard to locate hydrogens with x-ray crystallography. There is also a bias towards planarity in comercial programs. If you enter coordinates and do an optimization involving nitrogens, the molecule comes out planar. I have studied this problem in nucleic acids. I can send you references if you like. As for the amides, the problem would be even more difficult. X-ray structures were probably done in the 60's, so there was no hope of locating the hydrogens. One could fine tune the theoretical procedures if one knew the answer. But since the answer is not available, I'm not sure what to make of the theoretical claims about pyramidalization in the gas phase. David Close IMHO, B3LYP and MP2, with 6-31G* basis set, give good geometries for anilines: according to B3LYP/6-31G* aniline is pyramidal N-Me aniline has the Me group almost in the plane, but the H notably out NN di methyl aniline is planar. I've never encountered an amide that was not planar in a CHNOX [X=halogen]compound. John McKelvey (This is a hard question -- I'd be inclined to check geometries with MP4 or CCSD(T), and also find out how it behaves with increasing the basis set size) -- do you have a reference to molecules with small inversion barriers and the consequences of violating the Born-Oppenheimer approximation? I've run into this problem with lactam tautomers of heterocycles. Yours sincerely, Jeremy --------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 --------------------------------------------------------------------- My opinion: the calculations will be valid, if interpreted properly. I tend to think of such systems as "obeying" a modified, three-level Born-Oppenheimer approximation. In the standard two-level Born-Oppenheimer approximation, the nuclei are frozen, with the electrons treated in quantum mechanical fashion, giving the familiar potential energy surface. However, once we have that potential energy surface, we can use it to give the nuclei a quantum treatment: that is what we do when calculating zero-point and thermal energies. However, hydrogen compounds can be better treated with a three way distinction between electrons, hydrogen nuclei (especially if they are protons, i.e. 1H), and then the heavier nuclei. One calculates the potential energy surface in the usual fashion (freezing all nuclei and allowing quantum mechanical treatment of electrons). However, once that potential energy surface is calculated, the hydrogen atoms would be treated quantum mechanically while other nuclei are still frozen. A new heavy atom potential energy surface is thus generated, and wavefunctions and probability distributions are calculated for the hydrogen nuclei. There was an article in Accounts of Chemical Research a few years ago in which this was done for water clusters. Back to your question: a planar amide is still distinguished from a pyramdialized amide in having a one-minimum or two-minima potential energy surface for the amide hydrogen. These produce one-maximum or two-maxima probability distributions (respectively) for the hydrogen nuclei. Experimental geometries typically come from diffraction studies, which actually measure these probability distributions since the results are averaged among the molecules in the sample. Thus, the experimental geometries should correspond to the minima found by B3LYP/6-31G* and the like. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Hello, The NIST Computational Chemistry Comparison and Benchmark database (http://srdata.nist.gov/cccbdb) has experimental data and a bunch of calculations for a few amides: acetamide, urea, and version 7 (September 2002) will have experimental data as well for formamide and alanine. The pyramidalization can be compared at different levels of theory by looking a the HNCH dihedral, which is 180 degrees for a planar amide. The comparison can be set up in section IV.D.1 Hope this helps, Russ Johnson 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 Aug 8 14:36:15 2002 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g78IaFl09822 for ; Thu, 8 Aug 2002 14:36:15 -0400 Received: from dhcp.csuohio.edu (scifac209-53.dhcp.csuohio.edu [137.148.209.53]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H0J00IHZFOPV1@sims.csuohio.edu> for CHEMISTRY@ccl.net; Thu, 8 Aug 2002 14:36:25 -0400 (EDT) Date: Thu, 08 Aug 2002 14:36:04 -0400 From: "David W. Ball" Subject: freqchk job X-Sender: d.ball@popmail.csuohio.edu To: CHEMISTRY@ccl.net Message-id: <5.1.0.14.0.20020808143319.00a57680@popmail.csuohio.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT Yesterday I posted a comment regarding possible problems using G98's freqchk utility with molecules having negative frequencies. Several people responded that this utility should work fine even with negative frequencies present. Jim Hess at help@gaussian.com nailed down the problem; the job and corresponding checkpoint file were probably incomplete. Mea culpa. Many thanks to Jim and the several other respondents. dwb From chemistry-request@server.ccl.net Thu Aug 8 15:25:11 2002 Received: from georgetown.edu ([141.161.1.110]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g78JPBl10797 for ; Thu, 8 Aug 2002 15:25:11 -0400 Received: from mailhost.georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by georgetown.edu (8.12.2/8.12.2) with ESMTP id g78JPAZ0001299 for ; Thu, 8 Aug 2002 15:25:10 -0400 (EDT) Received: from georgetown.edu (knauer.chemistry.georgetown.edu [141.161.37.20]) (user=knauerc mech=PLAIN bits=0) by mailhost.georgetown.edu (8.12.2/8.12.2) with ESMTP id g78JPAjq017963 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 8 Aug 2002 15:25:10 -0400 (EDT) Message-ID: <3D52C65A.1728A54E@georgetown.edu> Date: Thu, 08 Aug 2002 15:28:26 -0400 From: knauerc Organization: Georgetown University X-Mailer: Mozilla 4.75 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:SUMMARY:Equilibrium Constants Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks to everyone for your help, and my apologies for being so late in posting this summary of responses. My question was: Does anyone know where I can find good data for the equilibrium constants, (as a function of temperature), for the reactions: H2 + Cl2 = 2HCl and H2 + Br2 = 2HBr The answers I received were: 1) Abhishek Jha (ajha@midway.uchicago.edu) Hi! Try www.nist.gov I have used this before so I am sure you will get what you are looking for. Best of luck! Cheers! Abhishek Jha 2) Wayne Steinmetz (WES04747@pomona.edu) Consider using the JANF Thermochemical Tables. 3) Bill Smith (bilsmith@uoguelph.ca) Apart from standard tables like the JANAF Tables (CHASE,M.,Jr.,1998, {\it NIST-JANAF Thermochemical Tables, 4th ed., J. Phys. and Chem. Reference Data Monograph No. 9,} (Am. Chem. Society, Am. Inst. Physics).Data, you can get a lot of this data from the free Lite version of the reaction equilibrium software package EQS4WIN, available at http://www.mathtrek.com 4) Chuck McFarland (cwm001@apk.net) Given that enthalpy and entropy easily lead to free energies, which in turn lead to equilibrium constants, and that Shomate equation coefficients give temperature dependence, most, if not all, of what you need is at http://webbook.nist.gov/chemistry/ 5) David Shobe (dshobe@sud-chemieinc.com) The NIST WebBook (http://webbook.nist.gov/chemistry/) has thermochemical data as a function of temperature, and you can calculate equilibrium constants in the usual way. (Also note that the answers and necessary data sets will differ considerably for gas-phase and aqueous-phase equilibrium constants). 6) Viswanathan Balakrishnan (bviswan@chem1.chem.dal.ca) The equilibrium constants can be calculated from the thermodynamic data available at http://webbook.nist.gov/chemistry/ 7) Michael J. Zehe (Michael.J.Zehe@grc.nasa.gov) A convenient source of up-to-date thermodynamic data in an easily-used form is the program PFC, at http://cea.grc.nasa.gov/. PFC allows the user to get accurate data for over 2000 species contained in the NASA Glenn, (formerly NASA Lewis),database documented in NASA TP-2002-211556 and at http://www>.grc.nasa.gov/www/ceaweb>. This database has been maintained and documented for almost 50 years by Ms. Bonnie Mcbride et al at NASA Glenn in support of the NASA chemical equilibrium program CEA. From chemistry-request@server.ccl.net Thu Aug 8 12:14:30 2002 Received: from web20203.mail.yahoo.com ([216.136.226.58]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g78GEUl06567 for ; Thu, 8 Aug 2002 12:14:30 -0400 Message-ID: <20020808161429.28553.qmail@web20203.mail.yahoo.com> Received: from [130.83.244.130] by web20203.mail.yahoo.com via HTTP; Thu, 08 Aug 2002 09:14:29 PDT Date: Thu, 8 Aug 2002 09:14:29 -0700 (PDT) From: Hatice Can To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear All, If I try to do potental energy surface scan with gaussian by using SCAN keyword, do I have use z-matrix for the molecule specification.If the answer is not, please could you sent to me an iput file sample which can work. I used cartesian coordinates, but it gave the error. my input file: #T HF/STO-3G Scan testtext 0 1 Cartesian coordinates of molecule Variables: 2 1 4 111 s 3 20 7 6 1.0964 s 3 0.01 Thank you in advance, Hatice __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From chemistry-request@server.ccl.net Thu Aug 8 12:48:50 2002 Received: from gatekeeper.tripos.com (firewall-user@[192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g78Gmol07343 for ; Thu, 8 Aug 2002 12:48:50 -0400 Received: (from uucp@localhost) by tripos.com (8.8.8+Sun) id LAA12168 for ; Thu, 8 Aug 2002 11:48:49 -0500 (CDT) Received: from celaeno.tripos.com(172.20.5.232) by gatekeeper.tripos.com via smap (V5.5) id xma012108; Thu, 8 Aug 02 11:48:03 -0500 Received: from oculus.tripos.com ([172.20.5.253]) by celaeno.tripos.com with esmtp (Exim 3.33 #4) id 17cqSB-0006cq-00 for chemistry@ccl.net; Thu, 08 Aug 2002 11:48:03 -0500 Received: from Unknown [172.20.5.232] by oculus.tripos.com - SuperScout Email Filter (4.0); Thursday, 08 August 2002, 11:48:02 Received: from stlvpn1.tripos.com ([172.20.5.182] helo=algenib) by celaeno.tripos.com with esmtp (Exim 3.33 #4) id 17cqS8-0006cZ-00 for chemistry@ccl.net; Thu, 08 Aug 2002 11:48:01 -0500 Message-ID: From: "Ramesh Durvasula" To: Date: Thu, 8 Aug 2002 12:47:44 -0400 Subject: Viewer docked output MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal Hello, I just wanted to add one more tool to the list of software that can be used in viewing the results of docking. Lithium is a Windows-based molecular visualization and analysis tool. In collaboration with Pfizer, Tripos has developed a Lithium module called the Docking Surveyor, which allows scientists to browse and evaluate the ligand-protein complexes generated > from docking runs. You can find more info on Lithium at www.tripos.com. Thanks, Ramesh --------------------------------------- Ramesh V. Durvasula, PhD Senior Director, Applied Science Tripos, Inc. > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of amor san juan > Sent: Thursday, August 08, 2002 8:56 AM > To: chemistry@ccl.net > Subject: CCL:Viewer docked output > > Summary of softwares replied in viewing docked output > ligand+protein: > > 1) MidasPlus > 2) VMD > 3) Qmol > 4) Pymol > 5) SPDB > 6) Viwer lite > 7) Viwer Pro > > Added to those is ADT. > > Does anyone of those mentioned softwares capable of > viewing simultaneously the docked ligand and > protein(aside from ADT ofcourse). If there is what is > the input file you used. > > Thanks, > Amor From chemistry-request@server.ccl.net Thu Aug 8 18:49:34 2002 Received: from TheWorld.com ([199.172.62.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g78MnYl18412 for ; Thu, 8 Aug 2002 18:49:34 -0400 Received: from vaio.theworld.com (1Cust94.tnt4.bos10.da.uu.net [63.10.168.94]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id SAA23008 for ; Thu, 8 Aug 2002 18:49:25 -0400 Message-Id: <5.1.0.14.1.20020808185120.00a32850@pop.theworld.com> X-Sender: jle@pop.theworld.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 08 Aug 2002 18:52:15 -0400 To: chemistry@ccl.net From: Joe Leonard Subject: Does anybody have a converter, Smiles/SLN? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Folks, does anybody have a converter which changes one type of line notation into another? Daylight Smiles and Tripos SLN seem to be two commonly-used line-notations (at least ones I'm familiar with), and it would be nice if I can intercovert the two w/o drawing the structure and translating it by hand... Any ideas? (thanks in advance!) Joe Leonard jle@theworld.com