From P8946019@csdvax.csd.unsw.EDU.AU Wed May 3 00:02:52 1995 Received: from csdvax.csd.unsw.EDU.AU for P8946019@csdvax.csd.unsw.EDU.AU by www.ccl.net (8.6.10/930601.1506) id XAA00706; Tue, 2 May 1995 23:47:30 -0400 From: Received: from csdvax.csd.unsw.EDU.AU by csdvax.csd.unsw.EDU.AU (PMDF V4.3-13 #6323) id <01HQ2GXMRXD08X32U4@csdvax.csd.unsw.EDU.AU>; Wed, 03 May 1995 13:46:36 +1000 Date: Wed, 03 May 1995 13:46:36 +1000 Subject: WANTED- computational success stories- a survey To: chemistry@ccl.net Message-id: <01HQ2GXMRXD28X32U4@csdvax.csd.unsw.EDU.AU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Computational Chemist I am preparing a PhD thesis on the implementation and interpretation of the Hartee Fock method. If you have used a semi-empirical or ab initio program to successfully predict a property or characteristic of a molecule or solid, BEFOREit was measured, could you please send me an enote and tell me all about it. Thanks Heaps, Hugh Kennedy p8946019@csdvax.csd.unsw.edu.au From Patrick.Bultinck@rug.ac.be Wed May 3 04:02:55 1995 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.10/930601.1506) id DAA02947; Wed, 3 May 1995 03:48:22 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA23719 (5.67b/IDA-1.5 for ); Wed, 3 May 1995 09:47:04 +0200 Received: by allserv.rug.ac.be (5.x/SMI-SVR4) id AA18435; Wed, 3 May 1995 09:48:01 +0200 Date: Wed, 3 May 1995 09:48:00 +0200 (MET DST) From: Patrick Bultinck To: chemistry@ccl.net Subject: NBO on Gamess Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am looking for NBO (Weinhold) for GAMESS (US). The Gamess manual provides some info on the possibility to use NBO with GAMESS. I have tried to contact Dr. Weinhold by E-mail, but it seems he changed address or something. I have found NBO on the qcpe telnet site, but want to be sure that is the right version for GAMESS too. Thanks, Patrick Bultinck, University of Ghent, Belgium From savary@sc2a.unige.ch Wed May 3 10:48:01 1995 Received: from UNI2B.UNIGE.CH for savary@sc2a.unige.ch by www.ccl.net (8.6.10/930601.1506) id KAA08571; Wed, 3 May 1995 10:47:25 -0400 Received: from uni2b.unige.ch (129.194.16.78) by uni2b.unige.ch (PMDF V4.3-8 #2502) id <01HQ2NGIMKG000CJHS@uni2b.unige.ch>; Wed, 3 May 1995 16:46:42 WET-DST Date: Wed, 03 May 1995 16:46:12 +0000 From: savary@sc2a.unige.ch (Francois Savary) Subject: Public defense available thru WWW X-Sender: savary@sc2a.unige.ch To: CHEMISTRY@ccl.net Message-id: <01HQ2NGNCFEU00CJHS@uni2b.unige.ch> X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.3 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hi there CCLers, I am annoucing a new document at our WWW server. this document is the public defense of my Ph.D thesis I made the 28th April, 1995 in Geneva. Come and take a look at the URL : http://scsg9.unige.ch/eng/pubdef.html See you Francois PS: it is in french, sorry about that. ----------------------------------------------------------------- Francois Savary 13, rue Caroline CH-1227 Acacias voice : +4122 301 36 42 fax : +4122 301 36 42 (on request) email : savary@sc2a.unige.ch WWW : http://scsg9.unige.ch/tabmat.html en francais http://scsg9.unige.ch/eng/toc.html in English http://scsg9.unige.ch/eng/pubdef.html (public defence of my Ph.D.) resume : http://scsg9.unige.ch/eng/cv.html ---------------------------------------------------------------- From states@ibc.wustl.edu Wed May 3 11:18:02 1995 Received: from medicine for states@ibc.wustl.edu by www.ccl.net (8.6.10/930601.1506) id LAA09039; Wed, 3 May 1995 11:08:06 -0400 Received: from ibc.WUStL.EDU (ibc.wustl.edu [128.252.122.174]) by medicine (8.6.11/8.6.5) with SMTP id KAA14700; Wed, 3 May 1995 10:03:23 -0500 Received: by ibc.WUStL.EDU (5.x/SMI-SVR4) id AA02868; Wed, 3 May 1995 10:08:02 -0500 Date: Wed, 3 May 1995 10:08:02 -0500 From: states@ibc.wustl.edu (David J. States) Message-Id: <9505031508.AA02868@ibc.WUStL.EDU> To: rbw@msc.edu, chemistry@ccl.net Subject: Re: CCL:Computational Chemistry on SUN Sparc Systems ... X-Sun-Charset: US-ASCII |> From chemistry-request@ccl.net Tue May 2 19:36 CDT 1995 |> Date: Tue, 2 May 1995 16:43:37 -0500 |> To: CHEMISTRY@ccl.net |> Subject: CCL:Computational Chemistry on SUN Sparc Systems ... |> Sender: Computational Chemistry List |> |> |> To the CCL oracle: |> |> While SUN dominates the workstation market in overall number |> of units sold, its impact in the computational chemistry |> submarket is, to the best of my knowlegde, very limited. What |> is its real presence here (magnitude)? In what direction is |> it moving? Limited applications supported and the connection |> of chemistry applications often to GL graphics are must be |> among the rate limiting factors. How severe are these? What are |> the other factors? |> |> Your reflections would be of interest ... |> |> |> Sincerely, |> |> |> Richard Walsh |> Minnesota Supercomputer Center, Inc./CRAY Research, Inc. Suns have traditionally been behind the curve on floating point price performance. They may be catching up with the newer processors, but then SGI and DEC are also raising the mark. With the R8000 SGI chips being so heavily optimized for FP, the performance of integer codes suffers significantly. We use Suns extensively in molecular biology computing applications because these codes require more integer and pointer manipulation where the Suns do well. The development tools are also better on Suns, for example Purify is only now announcing support for SGIs. Much better public domain software is available for Suns in areas like GUI development (Tcl/Tk) and database support (exodus, etc.). Is computational chemistry still driven by high end graphics? My impression is that Hollywood has moved well beyond what is needed to support scientific data display, including molecular graphics. OpenGL is going to open up competition for the scientific desktop, particularly from Windows NT/Pentium/Alpha machines. David States Institute for Biomedical Computing / Washington University in St. Louis From jle@toyota.wavefun.com Wed May 3 11:33:02 1995 Received: from volvo.wavefun.com for jle@toyota.wavefun.com by www.ccl.net (8.6.10/930601.1506) id LAA09649; Wed, 3 May 1995 11:28:01 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA19741; Wed, 3 May 95 08:28:13 -0700 Received: from toyota.wavefun.com(198.147.95.4) by volvo via smap (V1.3) id sma019739; Wed May 3 08:28:07 1995 Received: by toyota.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA06770; Wed, 3 May 95 08:27:56 -0700 From: "Joe Leonard" Message-Id: <9505030827.ZM6768@toyota.wavefun.com> Date: Wed, 3 May 1995 08:27:53 -0700 Reply-To: jle@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Followup of sorts on 3rd row TM basis sets Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Earlier, I posted a request for valence-shell STO-ng basis sets for 3rd row transition metals... Jimmy Stewart emailed me the information for scaled 6S and 6P basis sets, but I am still missing any information on 5D functions for these atoms. I have tried the two net repositories (OSC and PNL) but they do not have basis sets that go far enough. Anybody have any ideas for where I can get 5D functions? Thanks in advance, Joe P.S. I can send what I have so far if anybody else is interested... -- ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com From wdi@ccl.net Wed May 3 13:03:01 1995 Received: from schiele for wdi@ccl.net by www.ccl.net (8.6.10/930601.1506) id MAA11469; Wed, 3 May 1995 12:50:40 -0400 Received: by schiele (950215.SGI.8.6.10/940406.SGI.AUTO) for chemistry@ccl.net id SAA10078; Wed, 3 May 1995 18:46:17 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9505031846.ZM10076@schiele> Date: Wed, 3 May 1995 18:46:14 -0600 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Computational Chemistry on SUN Sparc Systems ... Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii David States Institute for Biomedical Computing / Washington University in St. Louis writes: > Purify is only now announcing support for SGIs. Much better public > domain software is available for Suns in areas like GUI development > (Tcl/Tk) and database support (exodus, etc.). Tcl/Tk can be compiled without problems un SGI computers (not surprising, it runs on about every Unix which runs X11R4 upwards). We'll be releasing some chemistry tools written in Tcl/Tk in connection with a new network chemistry service real soon now. They wil run on SunOS4.1, Solaris 2.4 IRIX5.3 and maybe HPUX. Tcl/Tk configuration is nearly automatic on all these systems. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From lohrenz@zinc.chem.ucalgary.ca Wed May 3 13:09:04 1995 Received: from zinc.chem.ucalgary.ca for lohrenz@zinc.chem.ucalgary.ca by www.ccl.net (8.6.10/930601.1506) id NAA11729; Wed, 3 May 1995 13:02:42 -0400 Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA16724; Wed, 3 May 1995 11:05:35 -0600 From: lohrenz@zinc.chem.ucalgary.ca (John Lohrenz) Message-Id: <9505031705.AA16724@zinc.chem.ucalgary.ca> Subject: Summary: DFT functionals To: CHEMISTRY@ccl.net (Everyone CCL) Date: Wed, 3 May 1995 11:05:33 -0600 (MDT) Cc: ziegler@zinc.chem.ucalgary.ca (), tkwoo@zinc.chem.ucalgary.ca (Tom Woo), lohrenz@zinc.chem.ucalgary.ca (John Lohrenz) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 17966 A week ago or so I posted a query about the reliability of functionals in DFT. Thanks for all who responded. Although I didn't answer every comment personally I appreciate the information. My personal feeling is, that there still is a lot of work left for the evaluation of the different functionals. Second there is no! standard functional although some seem to do better than other in general. I am looking forward to see how the "mixed" or "hybrid" methods will do... Furtheron it would be nice to see, what is a good choice for TM complexes and properties. Once again thanks to every single one. John =========================================================================== The original question: Hi everone, while browsing through the most recent summaries I noticed that someone stated that BLYP (in his eyes) is the best combination of functionals. I heard a lot of this kind of information. Other people favour the mixed HF-methods... There seems to be some confusion. I would like to hear, what experiences are there, concerning the quality of results calculated with different combinations of functionals. Has somebody systematically studied this? What about transition metal complexes? Quality of geometries? Relative energies? Transition states? Bond energies? I would like to summerize the responses. I think it should be of general interest to a least have an idea of the quality of the applied functional. I get the strange feeling that BLYP is becoming something like a standard just because it is stated so in the G92/DFT manual. John And here the answers: ============================================================================= Gabor I. Csonka (csonka@iris.inc.bme.hu) wrote: Hello John, We recently published a paper on the First ECCC (ECCC1). It is the Paper 50. As far as I know it was accepted for the final CD release. The details: Title: The performance of Gradient Generalized Approximation DFT Methods with Gaussian Basis Sets: Sulfur-containing Molecule Gábor I. Csonka, N. Anh and J. Réffy

Department of Inorganic Chemistry, Technical University of Budapest

H-1521 Budapest, Hungary

E-mail: csonka@iris.inc.bme.hu

The abstract: The performance of Gradient Generalized Approximation Density Functional Theory (GGA-DFT) methods with Gaussian basis sets are examined by studying 5 small molecules. Their geometries are optimized by HF, MP2 and DFT methods to which we have applied four different DFT functionals. The gradual improvements of basis sets gradually decrease the bond lengths and increase the bond angles. Accidentally the HF/6-311G(d) results are close to the experimental results while the improvement of the basis sets to 6-311G(2d,f) decreased the agreement with experimental observations. The inclusion of the electron correlation effect increases the bond lengths considerably. The various GGA-DFT results agree qualitatively with each other and with the MP2 results. Some functionals provide exaggerated effects and poor agreement with experimental results while others yield reasonable correlation. Conclusion: The results show that various GGA-DFT methods introduce different strength of electron correlation. It was found that the correlation strengths increase in the following order: B3-P86, B3-LYP, B-P86 and B-LYP. In general the basis set dependence of the GGA-DFT methods is not larger than that of the HF method for the present cases. --------------------------------------- Comment: One can fine tune the approximate functionals by increasing or decreasing the correlation effects. If correlation effects are weak mixed functionals from the above list will perform well. Otherwise you should apply methods wich can reproduce the stronger correlation. The paper contanis lot of figures. You can find the paper on my web home page or on the ECCC1 hompage -- Gabor I. Csonka Budapest University of Technology Tel/FAX: (361) 463.18.35 Inorganic Chemistry Dept. Ch. Bldg csonka@iris.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 http://www.fsz.bme.hu/bme/chemical/csonka.html ============================================================================= Jan Hrusak (hrusak@jh-inst.cas.cz) wrote: Hi John, we are using DFT methods now for a good while comparing the results quite often to those obtained by sophisticated ab initio calculations like CCSD(T) (larger polarized basis sets). In the beginning I got the same impression You mentioned." B-LYP is a standard". Now after spending few CPU years on comparing the different DFT and approximate DFT methods for neutral, cationic, anionic, organic and metalorganic systems I would be more carefull. There is nothing like a general standard method. For many cases I saw the B3LYP working in a excelent agreement with experiment and highly correlated ab initio methods for both structures and energies. Using ECP's we got also quite a lot very nice results even for heavy transition metal containing systems. However, in other case this parametrized method fails and pure DFT proceed better. An (in my opinion) still unsolved problem are the open shell systems (often found with TM). Here DFT/HF methods give often unphysical results like wrong ground states, while pure DFT offer the qualiattive agreement with the experiment. I would be interested to get the summary on Your request Jan ---------------------------------------------------------------------------- Dr. Jan Hrusak ############################### J. Heyrovsky Institute of Physical Chemistry ## MEMOR ESTO CONGREGATIONIS ## Academy of Sciences of the Czech Republic ## TVAE QVAM POSSEDISTI ## Dolejskova 3, CZ-182 23 Prague 8 ## AB INITIO ## Czech Republic ############################### ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Phone: (0042 2) 66 05 3436 FAX: (0042 2) 858 2307 E-Mail: hrusak@jh-inst.cas.cz ---------------------------------------------------------------------------- ============================================================================= Jack A. Smith (jas@medinah.atc.ucarb.com) wrote John: Warren Hehre's new book on "Practical Strategies for Electronic Structure Calculations" (from Wavefunction, Inc) gives a presents a very good comparison of the differents methods (AM1, HF, SVWN, BLYP, B3LYP, MP2) and basis sets (STO-3G, 3-21G(*), 6-31G*, 6-311+G((2d,p)) for equilibrium geometries, transition state structures, conformational energies, reaction (thermodynamic) energies , activation (kinetic) barriers, dipole moments, charges, etc. He discusses when correlation (MP2 or DFT) is important, when geometries from lower-level theories are adequate, when basis set choice is critical, the importance of posing problems as an anlogous series of isodesmic reactions where possible, etc. I found the book very informative. The book doesn't discuss any other energy functionals besides the 3 mentioned (nor any form of CI, CC theory, or MP beyond 2nd order). It doesn't cover any transition metal complexes. It doesn't discuss any "strategies" like G2 or CBS-4, but maybe "S5" (Spartan-5) is in the works? ;-) - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH || Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ============================================================================= Andrew T. Pudzianowski (pudzianowski@bms.com) wrote: John - I have made a fairly thorough comparison of the B-LYP combin- ation with the Becke3-LYP (B3-LYP) combo, where the B3 exchange functional has a Hartree-Fock component. This was done with the 6-311++G(d,p) basis and compared with MP2/6-311++G(d,p) results for the same systems, which were 10 ionic H-bonded binary systems, i.e., 10 ion/molecule systems of which 5 were cationic and 5 were anionic. Two examples are CH3NH3+/NH3 and HCOO-(formate)/H2O. The B3-LYP results are tangibly closer than B-LYP to the MP2 values. To make things simpler I'll quote you root mean square dev- iations from MP2 for complexation energies at 0 K (delta E0), comp- lexation enthalpies at 298.15 K (delta H), acceptor-hydrogen distances (A--H) and acceptor-donor center distances (A--D) for the fully optim- ized H-bonded complexes. For delta H I also have rms deviations from experimental gas-phase values. Energies are in kcal/mol, distances in Angstroms. (delta E0)rms (delta H)rms(MP2) (delta H)rms(exp) B-LYP 0.92 1.06 1.92 B3-LYP 0.69 0.73 1.65 MP2 ---- ---- 1.21 (A--H)rms (A--D)rms B-LYP 0.034 0.026 B3-LYP 0.019 0.014 Remember, these are rms deviations of the specified results from the the corresponding MP2 values for all ten systems except in the compar- ison with experimental enthalpies, where the deviations are with res- pect to the experimental quantities. I think you'll agree that B3-LYP does a better job on ionic H-bonded systems. I'm busy writing all this stuff up and with luck it will appear in print towards the end of the year. Best wishes, Andy Pudzianowski *********************************************************************** Andrew T. Pudzianowski,Ph.D. Bristol-Myers Squibb PRI Box 4000 * "There are two ways to do things. Princeton NJ 08543-4000 * There's the scientific way, and (609) 252-4248 * there's the disgusting way." (609) 252-5747: fax * pudzianowski@bms.com * "Beakman's World", 1994 *********************************************************************** ============================================================================= Benny Johnson (JOHNSONB@B.PSC.EDU) wrote: Dear Dr. Lohrenz, For a systematic study of DFT geometries, vibrational frequencies, dipole moments and atomization energies by different combinations of functionals see B.G. Johnson, P.M.W. Gill and J.A. Pople, J. Chem. Phys. 98, 5612 (1994). Qualitatively, it was found that Becke gradient-corrected exchange + a correlation functional (either local or gradient corrected) gave the best results, with B-LYP giving the best performance out of the set of 6 functionals studied. A later paper examined open-shell H abstraction barrier heights with even more combinations of functionals, including GGA's: B.G. Johnson, C.A. Gonzalez, P.M.W. Gill and J.A. Pople, Chem. Phys. Lett. 221, 100 (1994). Here it was found that none of the functionals gave acceptable results. However, the performance of the various gradient-corrected functional pairs on this particular problem was similar, e.g. the GGA91-GGA91 results were not too different from the B-LYP results. Other studies have found similar results as to the quality of functionals. There are definitely some functionals that are much better than others -- generally these involve gradient corrections. However, there currently does not seem to be a single combination of functionals which is demonstrably superior to all others on a wide range of chemical problems. B-LYP is one of the leaders, but by no means does it always perform well. This, plus the fact that there is no real way to systematically improve the quality of a density functional (as contrasted with usual ab initio theories, where one can e.g. keep going to larger and larger CI expansions) makes systematic validation studies of DFT methods critically important. Cheers, Benny Johnson Q-Chem, Inc. 317 Whipple St. Pittsburgh, PA 15218 ============================================================================= Scott E. Boesch (SBOESCH@aardvark.ucs.uoknor.edu) wrote: Dr. Lohrenz, I noticed your message on CCL and I would refer you to a paper that is currently in press for the Journal of Physical Chemistry. S.E. Boesch and R.A. Wheeler ; Jouranl of Physical Chemistry; 1995. I will send you a preprint as soon as I receive them. It is supposed to be published in May. The title of the paper is 'Pi-Donor Substituent Effects on Calculated Structures and Vibrational Frequencies of p-Benzoquinone, p-Fluoranil, and p-Chloranil' We did geometry optimizations and frequency calculations on the three molecules mentioned above. For, p-benzoquinone we did optimizations using every possible combination of exchange and correlation functionals available in G92/DFT . (Of course, we did not include all of that in the paper.) For p-benzoquinone, we found that the hybrid Hartree-Fock/Density Functional methods ( B3P86 and B3LYP) gave the best geometries, almost within experimental error of electron diffraction structures. The pure density functional method that gave the best structures was the local density functional method, SVWN, which uses Slater's exchange functional and the correlation functional of Vosko, Wilk, and Nusair. I would be happy to send you a preprint as soon as they are available. Also, if you want information regarding the different combinations of functionals that we did not put in the paper, I could provide that. If you have any questions, feel free to email me at SBOESCH@aardvark.ucs.uoknor.edu Scott E. Boesch Department of Chemistry @ Biochemistry University of Oklahoma Norman, OK 73019 ============================================================================= Joe Durant (jdurant@ca.sandia.gov) wrote: Hi John! First off, I am interested in a summary of the responses you get. On to the meat of the matter. I have been focussing on calculation of transition states, and have been comparing various DFT functionals to a set of transition states which I believe have been well characterized by more traditional methods (see J. Chem. Phys. 98, 8031o 1993 for the full list). The transition states include things like H + H2 -> H2 + H, F + H2 -> HF + H, O + HCl -> OH + Cl; I feel fairly comfortable that the energies, frequencies and geometries are not too far off reality. I have looked at these transition states using G92/DFT with the BLYP, B3LYP, B3P86 and BHandHLYP functionals. First off, BLYP fails miserably. O + HCl -> OH + Cl has a 8.5 kcal/mole barrier. BLYP predicts that the surface is completely attractive, although there is an inflection point at about the right geometry for the transition state. It also fails to find the barrier in the F + H2 -> HF + H system. I gave up on it at that point. The B3xx functionals fared somewhat better, but they both systematically underpredicted the barriers for reactions (average underprediction of 5+ kcal/mole for B3P86, and 4+ kcal/mole for B3LYP, with average deviations of about 2 kcal/mole in each case). B3LYP failed to find the F + H2 -> HF + H transition state. BHandHLYP wins my vote for the best functional. It underpredicted barriers by less than 1 kcal/mole, with an average deviation of about 2 kcal/mole. (I suspect that this performance is comparable to that for the G2 data set). Geometries are generally good to < 0.05 A and < 4 degrees. Frequencies aren't as good, with errors of the order of 300 cm-1 being common. I have quoted performances using "about" and "order of" because I have done calculations using 6-31G*, 6-311G**, 6-311++G** and 6-311G(3df,2p) basis sets. I don't find any systematic trends... bigger basis sets don't seem to offer better performance (although I am settling on 6-311G** as a "standard"). One other note: Gaussian noted that BHandHLYP as implemented in G92/DFT is a different functional than that proposed by Becke. But it works. Joe -- #################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9055 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 http://mephisto.ca.sandia.gov # #################################################################### ============================================================================= John M. McKelvey (mckelvey@Kodak.COM) wrote: I prefer Beck3LYP....It gives very good geometries, which seem more accurate than from BLYP, at least for my applications. In general Gaussian, Inc., prefers Becke3LYP, overall. Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- ============================================================================= Max Muir (mxm@biosym.com) wrote: Dear Dr. Lohrenz, you may care to look at "A study of some organic reactions using density functional theory" Jon Baker, Max Muir, and Jan Andzelm, J. Chem. Phys. 102(5), 1995. We studied twelve reactions (6 radical and 6 closed shell) with BIOSYM's TurboDFT at the 6-31G* level. Regards, Max Muir ============================================================================= end -- ========================================================================= Dr. John Lohrenz Dept. of Chemistry Phone: (403) 220 3232 University of Calgary FAX: (403) 289 9488 2500 University Drive, N.W. Calgary, Alberta, T2N 1N4 email: lohrenz@zinc.chem.ucalgary.ca Canada ========================================================================= From dimitris@3dp.com Wed May 3 13:48:03 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/930601.1506) id NAA12863; Wed, 3 May 1995 13:38:00 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA19598; Wed, 3 May 95 13:41:08 -0400 Received: by europa.3dp.com (931110.SGI) id AA27987; Wed, 3 May 95 13:39:55 -0400 From: "Dimitris Agrafiotis" Message-Id: <9505031339.ZM27985@europa.3dp.com> Date: Wed, 3 May 1995 13:39:54 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Tcl/Tk (was Computational Chemistry on SUN Sparc Systems) Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 David States writes: > Purify is only now announcing support for SGIs. Much better public > domain software is available for Suns in areas like GUI development > (Tcl/Tk) and database support (exodus, etc.). Tcl/Tk and many of its extensions run on almost any Unix machine that supports X. The fact that John Ousterhout is now working for Sun makes very little difference; Tcl/Tk is rapidly becoming a de-facto standard for cross-platform GUI development. Which raises the following question: would it be worth setting up a repository for chemistry-oriented Tcl-based tools, or should we rely exclusively on alcatel? Actually, has anyone compiled such a list (of chemistry-oriented tcl tools, that is)? Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From longshot@chem.duke.edu Wed May 3 15:33:07 1995 Received: from duke.cs.duke.edu for longshot@chem.duke.edu by www.ccl.net (8.6.10/930601.1506) id PAA15619; Wed, 3 May 1995 15:30:43 -0400 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.10G/4.1.3) id AA05554; Wed, 3 May 95 15:30:31 -0400 Received: from canada.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA13418; Wed, 3 May 95 15:30:30 -0400 Received: by canada.chem.duke.edu (5.64/2.12L/4.1) id AA23280; Wed, 3 May 95 15:30:29 -0400 Date: Wed, 3 May 95 15:30:29 -0400 From: longshot@chem.duke.edu (Brad Isbister) Message-Id: <9505031930.AA23280@canada.chem.duke.edu> To: amber@cgl.ucsf.edu, water@gibbs.oit.unc.edu, chemistry@ccl.net Subject: WANTED: Radial Distribution of water World at large: I am running simulations of solvated small molecules (analgesics & carbohydrates) with AMBER 4.0. With the help of a great plug-in courtesy of Chris Chipot, I am calculating the RDF around various solute atoms. This is all well and good, but I need to compare the results with the radial distribution for pure water. I've seen plots in many different places, but I need the actual data to run through GNUPlot, superimpose with my own results, etc. Does anyone have g(r), r in electronic form? Any references to a paper with the data that I can type in by hand :( ? Thanks for your help and suggestions, -Brad Isbister ---------------------------------------------------------------------------- Brad Isbister Duke University E.J. Toone group Department of Chemistry longshot@chem.duke.edu DukeChem Home Page http://www.chem.duke.edu/~longshot http://www.chem.duke.edu/ From stuart@wucmd.wustl.edu Wed May 3 17:03:07 1995 Received: from wugate.wustl.edu for stuart@wucmd.wustl.edu by www.ccl.net (8.6.10/930601.1506) id QAA17883; Wed, 3 May 1995 16:55:43 -0400 Received: from wucmd (wucmd.wustl.edu [128.252.137.1]) by wugate.wustl.edu (8.6.11/8.6.11) with SMTP id PAA28003; Wed, 3 May 1995 15:55:36 -0500 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA21556; Wed, 3 May 95 13:47:05 -0500 Date: Wed, 3 May 1995 13:41:33 -0500 (CDT) From: Stuart Green Sender: Stuart Green Reply-To: Stuart Green Subject: Journal of Computer-Aided Molecular Design To: CHEMISTRY@ccl.net, molmodel@net.bio.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Volume 9 Number 2 (April) 1995 of the Journal of Computer-Aided Molecular Design is now available on WWW (http://wucmd.wustl.edu/jcamd/jcamd.html). We still seek your comments and thoughts on the Web-based production of this journal (email: jcamd@wucmd.wustl.edu) The respective authors are requested to donate the electronic originals of the figures to improve the quality of those scanned. We also ask for example molecules as used in their calculations so we may take full advantage of the interactive capabilities of WWW. Enjoy, Stuart --- Stuart M. Green stuart@wucmd.wustl.edu Center for Molecular Design Campus Box 1099 Washington University Tel 314-935-4671 St. Louis, MO 63130-4899 Fax 314-935-4979 From wong@chem.chemistry.uq.oz.au Wed May 3 20:48:05 1995 Received: from bunyip.cc.uq.oz.au for wong@chem.chemistry.uq.oz.au by www.ccl.net (8.6.10/930601.1506) id UAA20579; Wed, 3 May 1995 20:46:40 -0400 Received: from chem.chemistry.uq.oz.au by bunyip.cc.uq.oz.au with SMTP (PP); Thu, 4 May 1995 10:46:25 +1000 Received: by chem.chemistry.uq.oz.au (5.65/DEC-Ultrix/4.3) id AA12073; Thu, 4 May 1995 10:45:42 +1000 Message-Id: <9505040045.AA12073@chem.chemistry.uq.oz.au> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 3 May 1998 23:03:19 +0900 To: chemistry@ccl.net From: wong@chem.chemistry.uq.oz.au (Richard Wong) Subject: summary (II): teaching material for computational chemistry summary continue ..... -------------------------------------------------------------------- >From James Foresman (foresman@lorentzian.com) As regards your question about Computational Chem. in the undergraduate curricullum, I would like to inform you of the existence of two resources: 1. The MoleCVUE Consortium (Molecular Computation and Visualization in Undergraduate Education Consortium) This is a group of a dozen of so active undergraduate educators who are working together to build various experiences of comput. chem. into undergraduate curriculla (freshman-senior years). You may contact the organizer at: ranck@vax.etown.edu This is the email address of John Ranck of Elizabethtown College. If you desire, he can put you on the email list for distribution and information regarding the activities of the consortium. We welcome people who are interested in reviewing and/or adding to the things which we develop. 2. The book, "Exploring Chemistry Through Computational Methods: A Guide to using Gaussian," J.B. Foresman and AE. Frisch, 1993. Is available from Gaussian Inc. A copy comes free with the purchase of Gaussian or it may be obtained for $35 by contacting Gaussian Inc 4415 Fifth Ave Pittsburgh, PA 15213 voice: 412-621-2050 fax: 412-621-3563 This is a work which I co-authored with AEleen Frisch Which was intending to be used as a special topics course or as a part of a physical chemistry course. Let me know if I can comment further on either of these resources. --------------------------------------------------------------- >From Bill DeSimone: You might want to call Warren Hehre of Wavefunction, Inc. (SPARTAN). He is interested in this market and has done some prelimary work. Warren doesn't use e-mail, but you may get through to him through Joe Leonard. Anyway, his phone number is 714-955-2120. [I talked with Warren Hehre and he graciously sent me a lab manual of projects that he has developed. His approach is a practical one that seeks to develop judgment about the capabilities of various kinds of software.] --------------------------------------------------------------- >From Ken Fountain (sc18@NEMOMUS): He has put together such a course in a pair of lab manuals he wrote around the old AEON coprocessor boards running MOPAC. The course is being totally revised this summer around HYPERCHEM and some more standard computer engines. -------------------------------------------------------------- >From Dan Thomas (CHMTHOM@vm.uoguelph.ca ) Last fall I attempted such a course. Briefly, it was very difficult but quite rewarding. I hope to give it another try or two and see if it is possible. The reasoning behind this attempt was rather obvious. In looking in the offices of my various colleagues in the department, it became clear that the individuals who were most regularly using "quantum mechanics" were not the physical chemists but rather the organic and inorganic chemists, who with their commerical molecular modeling programs were daily looking at structures and assessing stabilities of molecules. The theoretician in the department was naturally the power user, but the people, some of whom admitted to never having had a course in quantum mechanics, who really "used" quantum mechanics were from this other group. With the advent of more and more software, it is only to be expected that our students will be utilizing these tools upon graduation. It is requisite upon us to make sure that we generate students with sufficient knowledge to be able to critically evaluate the results from these commercial programs, for we all know the multiplicity of dangers which lurk behind the blind acceptance of the results from these programs (we used Hyperchem from AutoDesk). Hence I approached this course from the idea that this might be the last P. Chem. course the students would take and that it would prepare them to intelligently use the upcoming software tools. I hoped to get the students to the point where they could appreciate the significance of the various semi-empirical techniques, starting with Extended Huckel and going through CNDO, MINDO/3, NNDO, to AM1. They also need to understand the various molecular modeling procedures like MM2 or MM3. As well, a number of programs employ routines for biochemically important species with different forcefields such as AMBER or CHARMM. Most chemists only employ these kinds of calculations, leaving ab initio techniques to the real quantum chemists, but an appreciation of what is involved in running a progam such as GAUSSIAN 92 would not be inappropriate for these people. Such were the objectives of the course. So, what happened. The course had previously been given as a third year, one semester course in quantum mechanics. The students had previously only had about 5 weeks of quantum based physical chemistry in second year. I determined that it would be important to start from the beginning, review vector and matrix algebra and then briefly demonstrate the correlation between functional analysis and vector analysis. This, of course, justifies the mixed usage of the terms "wavevector" or "wavefunction". We also discussed eigenvalue problems. We spent some time with simple models (free particle, tunneling through a barrier, particle in a box, particle on a ring, particle on a sphere, particle in a sphere), showing how to apply these ideas rigorously. We quickly got into Dirac notation, emphasizing that we will let others solve these problems from first principles, but that we will simply use the known results. From there, we needed to touch on spin and atomic spectroscopy. This lead to the theory of bonding and molecular orbital theory. At this point one can start to discuss the various semiempirical techniques. As you can see, this is an horrific amount of material and it was my downfall. There were 14 students in the course. 1 had not had any quantum before, 3 were physics students who had 2 full courses of quantum before, 1 was a mathematics student with lots of math but no chemistry, and the rest were mainstream chemistry students with the background I was expecting. The spectrum of preparation was too broad. We spent about 5 hours a week in classes and it was grueling. At the end, we were all glad we did it. The physics students regularly expressed appreciation for the physical descriptions given for the equations employed - they had been taught how to use the mathematics but had never received an explanation for what they meant. The other students were pushed far beyond what they thought they could do. (Near the end, they reported incidents of where they were able to assist friends with problems in the physics quantum courses). We are learned a lot, but it was not a pedagogically sound course. It should take at least a full year to cover this material. We used the text "Elementary Quantum Chemistry" by Pilar (McGraw-Hill). I chose it because it was the only one I found which had extensive sections on the semiempirical and ab initio techniques (about half the book). It did start from the beginning and it was a good development, but it was more appropriate for a grad course or at least to be covered in a full year. I am worried that the answer needs to be something like: We can either teach non-physical chemists how to use these programs and to give them an appreciation of the procedures so that they can start to critically evaluate the results OR we can teach quantum chemistry to physical chemists. I would like to think we could do both, but I'm afraid that the two may be mutually exclusive if one or two semesters is all that is available. I want to try it again and I would appreciate any feedback you may have from your own experiences. I have a colleague who may be trying to start this kind of program at a small college (Goucher in Baltimore) this coming year. He is currently at IBM Almaden but would equally be interested in any comments or suggestions. If you have information or more questions you might try communicating with him at johnson@ibm.almaden.com (his name is Kevin Johnson). ------------------------------------------------------------ >From Pat Hogue(hogue@canada.den.mmc.com) As a graduate student using a MOPAC-type program (GEOMOS QCPE #584) I think undergraduates would benefit especially if a graphical output is used. I learened a lot just by modelling molecules like HF an O2 etc. The little graphical demo from CaCHE can teach a lot about the quantum mechanical basis for thermodynamics.God bless your efforts. =---------------------------------------------------------------- From: ranck@albert.etown.edu (John P. Ranck) Welcome to the MoleCVUE Consortium e-mail list. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PURPOSE ======= The MoleCVUE [Molecular Computation and Visualization in Undergraduate Education] consortium was formed by faculty in undergraduate chemistry departments (principally members of MAALACT): to focus and stimulate cooperative development, testing, sharing, and promulgation of ideas, systems, and pedagogical materials for teaching and using computationally-aided molecular structure and reactivity tools in the undergraduate curriculum; to develop and distribute instructional materials freely; to influence commercial developments supportive of these activities; to serve as a model for cooperative curricular development among faculty at geographically dispersed institutions working via the Internet and to stimulate the formation of other such groups in other fields of chemistry. MEMBERSHIP & COMMUNICATIONS =========================== We are currently fifteen active members from Pennsylvania, Maryland, Virginia, North Carolina, New York, Missouri, and South Dakota and approximately thirty "listeners" from a much wider geographic region. We are trying to make this an open consortium. All interested parties are invited to listen to and/or join in the electronic discussions and to become "active" members by attending our workshops or otherwise participating in the work. E-MAIL: ------- Messages posted to: MOLECVUE@VAX.ETOWN.EDU will be forwarded to all known participants -- by email if you have email, otherwise by U.S. Mail periodically until things get out of hand. Members may of course communicate directly among themselves as it serves their purposes. FTP: ---- I will maintain an ftp site Host: VAX.ETOWN.EDU (I.P.Address: 192.146.186.2) Username: MOLECVUE Password: MOLECVUE I will maintain several files and directories in this "library" MEMBERS : A current list of names, addresses, phone numbers, etc. A member will be identified as "active" if he/she has participated in one or more of the activities of the consortium until is is apparent that he/she is no longer active. Others on the distribution list will be identified as "listeners" until they choose to participate. Commercial "listeners" will be identified separately. INTERESTS : A directory containing a text file submitted by each member who cares to contribute -- stating his/her interests and/or (ESPECIALLY) current projects. Please post an entry for yourself to MOLECVUE@VAX.ETOWN.EDU This posting will be automatically distributed to all and I will update your entry in the ftp library. New members will be able to find out who is doing what by reading this library. You are free to "roam" the library and "get" anything of interest or to create directories in which you may "put" files others may be interested in. Please use descriptive names for your directories and files, include some obvious .DOC or README file to describe what is there, and announce your contribution to all by posting a message to everybody (via the MOLECVUE@VAX.ETOWN.EDU address). PLEASE BE CAREFUL AND TRY NOT TO CREATE HEADACHES FOR ME OR FOR THE SYSTEM ADMINISTRATORS. Contact me if you need any assistance getting anything in or out of the ftp library. CURRENT ACTIVITIES ================== The consortium meets two or three times yearly for several days to examine and learn new software and techniques and to plan cooperative projects. The next such workshop is planned for early summer 1993, probably at Elizabethtown College. Currently, each member is exploring a variety of instructional tools and techniques by developing one or more instructional units from his/her own pedagogical perspective. These units are to be completed by May 1, 1993 and shared with other participants for criticism (via Internet). At the Summer 1993 meeting, we expect to select the best tools and methods, select appropriate curricular writing projects, assign teams, and begin work in earnest with definite deadlines. A substantial amount of our current activities and development are related to the molecular modeling program HyperChem by Autodesk, Inc. COMPUTERS ========= An essential requirement in our efforts is that the hardware and software be affordable by any undergraduate chemistry department. Currently, we are examining computational systems and tools running on Intel 386 based systems under Microsoft Windows 3.1. There is some interest in low-end unix systems. We have had little discussion and made no decisions regarding MacIntoshes. FINANCIAL ========= We are pledged to distributing all materials as freely as possible and have no expectation of individual financial rewards. (We are also actively attempting to influence commercial software developers and vendors to provide software for undergraduate instruction at affordable prices.) CONTACT ======= John P. Ranck Internet: RANCK@VAX.ETOWN.EDU Department of Chemistry Voice: 717-361-1315 Elizabethtown College FAX: 717-361-1207 Elizabethtown, PA 17022-2298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: C.S.Raman(raman@bioc01.uthscsa.edu): The package that meets most of your requirements is HYPERCHEM, marketed by Autodesk Inc. I believe that the cost of the package with educational discount is $595; but, there are programs tailored towards educational and research institutions in mind and involve obtaining Hyperchem at no cost to the researcher. In return, the user must provide a detailed account of what he/she wants to do with the package. So, contact Autodesk for additional details about how the latter can be achieved. The program is quite easy to use and runs under a windows environment on a 486DX. The more memory you have the faster it runs. So, with about 8MB of RAM, one should be able to model and energy minimize small compounds with ease. ------------------------------------------------------------------- from: Fred Brouwer Laboratory of Organic Chemistry , University of Amsterdam Nieuwe Achtergracht 129 , 1018 WS AMSTERDAM , The Netherlands phone 31 20 5255491, fax 20 31 5255670 I am running an undergraduate course on Molecular Modeling (molecular mechanics, dynamics, quantum chemistry) for third year chemistry students. We use Sybyl and Spartan on SGI and IBM workstations and PCModel on an IBM PC and a Macintosh. The approach is mainly to give hands-on experience. It turns out that these young people have very little computer experience, and dealing with the programs is a major effort. The theoretical part of the course is rather superficial. Most students are oriented towards organic chemistry (unfortunately primarily identified with synthesis in this lab, as in many other places) or inorganic chemistry (which in our department happens to be organometallic chemistry), and most of them hate everything that looks like an equation. In any case I hope they learn that they can use MM as a practical tool in their research, if only to help to look more closely to their molecules. After the course (3 credit points = 3 weeks of full-time work) they have some idea of Molecular Mechanics, are deeply aware of the multiple conformation problem, and know which systems they can and cannot submit to quantum chemical calculation. The course material is still in a primitive state, I don't dare to show it to anyone outside. ----------------------------------------------------------------------- I received from Lee Wilson (LWILSON@polaris.lasierra.edu) a copy of the syllabus used at LaSierra University in the mail. There is too much for me to retype here. Please contact Dr. Wilson directly if you would like a copy of the syllabus. ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ || __ |\ Dr. Ming Wah (Richard) Wong || || / |_| \ ----------------------------------------------|| || .' \ Department of Chemistry || || / *\ The University of Queensland || || \ __ / Brisbane, Qld 4072, Australia || || \_.-' \_ / Fax: +61 7 365 4299 | Phone: +61 7 365 3829 || || v email address: wong@chem.chemistry.uq.oz.au || ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ From wong@chem.chemistry.uq.oz.au Wed May 3 20:52:44 1995 Received: from bunyip.cc.uq.oz.au for wong@chem.chemistry.uq.oz.au by www.ccl.net (8.6.10/930601.1506) id UAA20510; Wed, 3 May 1995 20:42:12 -0400 Received: from chem.chemistry.uq.oz.au by bunyip.cc.uq.oz.au with SMTP (PP); Thu, 4 May 1995 10:41:51 +1000 Received: by chem.chemistry.uq.oz.au (5.65/DEC-Ultrix/4.3) id AA12031; Thu, 4 May 1995 10:41:09 +1000 Message-Id: <9505040041.AA12031@chem.chemistry.uq.oz.au> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 3 May 1998 22:58:47 +0900 To: chemistry@ccl.net From: wong@chem.chemistry.uq.oz.au (Richard Wong) Subject: summary (I): teaching material for computational chemistry Dear netters, Last week I posted a question on the availability of teaching material in internet suitable for undergraduate courses in computational chemistry and molecular modeling. Many thanks to people who replied to my request. Appended below is the summary. Cheers! Richard From: savary@sc2a.unige.ch (Francois Savary) ____________________________________________ You can take a look at my WWW Document, it might interest you. It deals with Molecular Graphics and Rendering techniques. http://scsg9.unige.ch/eng/toc.html in English http://scsg9.unige.ch/tabmat.html in French hope it helps Francois From: b_duke@lacebark.ntu.edu.au (Brian Duke) _____________________________________________ We have a CAUT grant for doing exactly what you are asking. It is early days however. Point your browser to http://www.chem.swin.edu.au/CAUT.htnl and you will see where we are at. If you want any more information, mail me. I would be interested to hear what you you are planning. I have done a lot of Gaussian work with final level students here. Cheers, Brian. From: borkent@camms1.caos.kun.nl (Hens Borkent) _______________________________________________ In reply to your question I would like to point to our www page at www.caos.kun.nl which contains links to html courses 'under development'. There is one on computational chemistry, albeit confined to the programs we offer. See under 'tutorials' on the home page, and 'watch the progress' of the compchem course. Comments are very welcome! Hens Borkent CAOS/CAMM Center From: jim@volvo.wavefun.com (jim Parisi) ________________________________________ Have you tried "Experiments in Computational Organic Chemistry" by Hehre, Burke, Shusterman, and Pietro? If you are interested in a copy, please let me know. Thanks! Jim Parisi Marketing/Sales Coordinator From: "Jeffry D. Madura" _______________________________________________________ I am teaching such a course right now. I will be placing the lecture notes, course outline and homework assignments on Mosaic in the next few weeks. I will send a follow-up e0mail to you and the CCL list when I have this done. You may wish to look at Chapter 4 in vol 4 of Rev. Comp. Chem. where we discuss this topic. Best Regards, Jeffry D. Madura From: "Wayne Huang" _____________________________________________ Regarding your quest for teaching materials or media, we have developed some undergraduate computational chemistry materials over the time which might be related what you asked (1) Textbook: Warren Hehre, Lonnie Burke, Alan Shusterman & William Pietro, Experiments in Computational Organic Chemistry, wavefunction, 1993. (2) CD-Rom: Tom Hehre, Lonnie Burke, Wayne Huang & Warren Hehre, Chemistry Disk I, Wavefunction, 1995 (3) Warren Hehre, Wayne Huang, Chemistry with Computation, wavefunction, 1995. Currently we are working on a book "Computational Experiments in General Chemistry". We also offer three-day intensive workshops in Computational Chemistry which has been helpful for people interested in undergraduate education. For workshop info: workshop@wavefun.com For book info: sales@wavefun.com From: P8946019@csdvax.csd.unsw.EDU.AU _____________________________________ I have written and put together a teaching package which can be used to illustrate the basic priciples of computational chemistry and quantum mechanics.If you are interested, send me an enote and I'll give you some further info. Try science@uniserve.edu.au for other educational science progs. Hugh From: kcousins@wiley.csusb.edu (Kimberley Cousins) __________________________________________________ I posted this a while back. Hope it helps. Kimberley Cousins Date: Tue, 8 Jun 93 14:52:18 -0500 From: tony@wucmd.wustl.edu (Tony Dueben) Subject: undergrad computational chem Sender: chemistry-request@ccl.net Netters: As promised, better late than never, summary of responses to my query about teaching computational chemistry at the undergraduate level. Thanks to all who responded by e-mail, phone, or letter. Anthony J. Duben (tony@wucmd.wustl.edu) Center for Molecular Design Washington University Campus Box 1099 One Brookings Drive St. Louis MO 63130-4899 314-935-4672 ------------------------------------------------------------- Henry Rzepa has been using Cache on a Mac and has developed a lot of material. He can be contacted -- Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3, Tel:+44 71 225 8339, Fax:+44 71 589 3869. --------------------------------------------------------------- Volume 4 of REVIEWS IN COMPUTATIONAL CHEMISTRY has been published in the Spring of 1993. Not every library has a copy of it yet so you may not be aware of its contents. It contains a long article on the topic of teaching computational chemistry at the undergraduate level. "Computational Chemistry in the Undergraduate Curriculum" by Roger L. DeKock (Calvin College), Jeffry D. Madura (University of South Alabama), Frank Rioux (St. John's University), and Joseph Casanova (California State University at Los Angeles). REVIEWS IN COMPUTATIONAL CHEMISTRY is edited by K. B. Lipkowitz (IUPUI) and Donald B. Boyd (Lilly Research Laboratories). Information about Volume 4 (280 pp, ISBN 1-56081-620-1, 1993) can be obtained from VCH Publishers, Inc., 303 NW 12th Avenue, Deerfield Beach, Florida 33442. In the U.S., call 800-367-8249, FAX: 1-800-367-8247; in Europe, 49-6201-6060, FAX: 49-6201-606328. Price $79. With a standing order for the book series, the price is $65. ------------------------------------------------------------------ Greg Landrum at Cornell has used CaChe software and believes that it would be suitable in an instructional setting. -greg Landrum landrum@chemres.tn.cornell.edu ------------------------------------------------------------------ Ganesan Ravishanker (ravishan@swan.wesleyan.edu) will be teaching a modeling course here at Wesleyan in the Fall and will use Hyperchem on a 486PC running MS Windows. HyperChem is marketed by Autodesk. ------------------------------------------------------------------------ For the sake of reminding everyone of a complete set of notes at the graduate level, recall C. Cramer's earlier e-mail: Colleagues, Given the increased interest in computational chemistry courses taught at the undergraduate and graduate levels, I have provided the computational chemistry archive at the Ohio State Supercomputer Center with an ASCII ftp file containing the majority of the materials used in the teaching of Chemistry 8003 here at the University of Minnesota. All chemistry graduate students are required to take at least two of three core courses during their first two years, and Chemistry 8003 is one of these. This core program is new. Thus, this was the first time 8003 was taught. In this posting, I include only the general description (2nd below). The ftp file is roughly twenty pages long (Microsoft Word single spaced text only file). Jan has kindly provided me the foolproof instructions for getting this by either ftp or e-mail (1st below). If you access these materials, we would be VERY grateful to receive your comments. Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 cramer@staff.tc.umn.edu (612) 624-0859 ---------------------------------------------------------------- [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] You can obtain the materials (over 40kBytes file) via ftp or by e-mail: How to get it using FTP: ======================== ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: Your_email_address ftp> cd pub/chemistry/comp-chem-courseware ftp> ascii ftp> get chem8003.txt ftp> quit How to get it using e-mail: =========================== Send the following message (exactly as written): send comp-chem-courseware/chem8003.txt from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET and the message containig the materials will be forwarded automatically to your electronic mailbox. ---------------------------------------------------------------- [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Chemistry 8003 was a one quarter, four credit course. It met 30 times in ten weeks for one hour each class. The classroom included a Mac IIsi on the ethernet hooked to a large-screen projector for demos. The course was taught for the first time in the Winter Quarter of 1992. Attached are the course syllabus, outline, problem sets, handouts, and the final exam and final assigned paper. Literature articles were used heavily for discussion; the references are included in the course outline. The attached materials are not copyrighted, and we encourage their use by any organization or individual so inclined. Certain handouts did not lend themselves to ASCII reproduction, and are not included. The 39 students (and roughly 15 auditors) had access 12 hours per day to a microcomputer lab. The software used in the course included PCModel, running on IBM 386 clones and Macintosh IIci's (we preferred the latter), AMSOL v.3.0.1 and Gaussian92. The latter two program suites were run on an IBM RS/6000 model 560. Communication with the workstation used NCSA Telnet v.2.5 for Macintosh. Students also had access to Microsoft Word 5.0, ChemDraw 3.0 and Chem3D 3.1 all running on Macs. All software was obtained under the appropriate license agreements except AMSOL and NCSA Telnet, which are currently public domain. Problem sets were completed by groups of two, the final exam and critical analysis paper were individual projects. Some overall impressions were: 1) our syllabus was a bit ambitious given the time constraints -- we cut a few things down, although we still tried to cover all topics. 2) We converted about 5-10% of the class to computational chemistry, inspired another 25-30% to start using some modeling software in their experimental research, left another 50% with a demonstrably larger (and perhaps even appreciated) understanding of computational chemistry, and the remainder left with the same prejudices against theory with which they came in. 3) As a rule, physical chemists thought there wasn't enough theory, organic chemists thought there was far, far too much theory, inorganic chemists felt slighted that so few techniques existed to treat metals effectively , and biological chemists wondered who cared about small molecules anyway. 4) More workstation power would have been nice. 5) As far as the course text(s), Clark is very out of date at this point with regard to ab initio HF theory, fairly out of date with regard to semiempirical MO theory, but still quite reasonable for molecular mechanics and technical issues like Z-matrices, etc. Hehre, Radom, Pople and Schleyer was placed on reserve for the class, but deemed a bit too expensive and technical to be a required textbook. The same was true for the Reviews in Computational Chemistry series edited by Boyd and Lipkowitz. -- With the exception of the conversion to comp. chem. rate (which we never expected to be so high!), all of these things were about what we expected, and we were pleased with the initial offering of the course. Obviously, we hope to improve on this in future years. Christopher J. Cramer Steven R. Kass ------------------------------------------------------------- Rozeanne Stecker (steckler@sdsc.edu) has been teaching such a course for the past four years. ------------------------------------------------------------ Tom Cundari at Memphis State (cundarit@memstvx1.memst.edu0 has begun teaching such a course at the upper division undergrad/. lower division grad level. He has taken what may be an unorthodox approach in that he has used no texts, no handouts, tests or anything. He subdivides the students into groups and has them work on projects where the chemistry is of interest to them. As most of undergrads do research with the profs here at MSU, they have some feel for what they find interesting and what they would like to calculate (some feasible; some not). Th e only requirement is to write a paper in JACS format abut their project: successes, failures, what new chemistry the learned, what could be done (or avoided) for the future, etc. By taking the "learn by doing" approach it is more work (for students and prof), but he believes that the approach is more realistic than giving canned projects or just lecturing on the laws of quantum mechanics. The benefits are 1) the students are forced to work together as a team, crucial in modern research. 2) the students are given ample opportunity to screw up (no amount of lecturing can reinforce what one simple deletion of a full days work can!) and discover (e.g., why does MOPAC work for this and not that; what can be calcd. and what can't and why?), 3) being in the lab is just plain more fun than sitting in lecture! The main deficit in addition to the extra work is that the class will fail for students who are not self motivated. They have been fortunate in that this has not been a problem. Some of the projects have turned out to be quite neat. Perhaps the best thing from his point of view is that nearly all of the projects correlate with experimental research going on in the Chemistry Department at Memphis State (either that of the students taking the courses or their fellow students). Examples: "A Semi-empirical Study of Homoaromaticity in Nitrogen-Substituted Carbocycles;" "A Semi-empirical Study of the Synthesis of Potential Drugs and a Comparison of the Stabilities of Ene-amine and Imine Tautomers;" "Designing New Cyclopentadienyl Ligands with Chelating Substituents;" "A Computational Study of Spin-Density Patterns in Substituted Dihydropyrazine Cation Radicals;" "An Ab-initio Investigation of Transition and Lanthanide Metal Catalyzed Hydrogen Exchange in the Presence of an Electric Field;" "An Ab-initio Investigation of Metal-Sulfido Bonding;" Future modifications: First, introduce more cutting edge technology, in particular parallel computing access. Second, induce/force/coerce more of the computational students into taking the class, even though they know most of this already! This gives the exptl. folks an anchor for the first few weeks while learning the mechanics of the programs; it also forces the comp. chem. people to talk to exptlsts. (and vice versa) and gives everyone a better comprehension for the problems of each other and what it takes to solve these problems and get the job done. Hardware Resources: 3 RS-6000 550's; 2 VAX mainframes; a DECstation 3100, and attendant PCs and Macs to serve as front end GUIs and back end data analysis stations. Student Prerequisites: The students must have at least taken up to the first semester of P. Chem. All I really want is for them to have an open mind to the potential of comp. chem. to act as an aid to traditional experimental research. The class is taught in a fashion which resembles the running of a research group. The students stop by usually with a day or so notice and work for 3-5 hours at a clip. It is very informal and we have been lucky to have independent students who can handle this set up and who when they run into problem call me or get a book out and learn how to assign a point group, the diff. between ROHF and UHF, why MOPAC doesn't work for TMs, etc. and related discoveries. Since we have some very good comp chem grad students between Henry Kurtzand myself it has been like having full time TA's to get the exptl. folks up to speed as quickly as possible. I will be very interested to see how others have tackled the problems of teaching a comp chem class. [We have limited ourselves to the programs MOPAC (because of its relative ease of use and applicability to large organic systems) and GAMESS (because I am familiar with it and it forces the students to know how to assign point groups!).] ----------------------------------------------------------------- Brian Duke (B_DUKE@DARWIN.NTU.EDU.AU) and Brian O'Leary carried out a survey last year of what is going on in this area and there is quite a lot. Unfortunately both have massive teaching loads at present and analysing the results keeps getting postponed. They hope to write it up for J Chem Ed. Brian Duke teachs a final level course (or unit as we call them in Australia) here that includes comp chem, but mainly comp quantum chem - use of ab initio (GAUSSIAN), Huckel, EHM,etc. This goes down quite well. I would like to broaden the Comp Chem material, but it is also the only final year Phys Chem and it includes Stat Mech, Spectroscopy, general Quant Chem etc. --------------------------------------------------------------- >From Jeffry Madura(madura@moe.chem.usouthal.edu): Attached below is a copy of my syllabus for the course I teach here at the Univ. of South Alabama. %% This document created by Scientific Word (R) \documentstyle[12pt,qqaalart]{article} \author{Jeffry D. Madura} \title{Computational Chemistry } \input tcilatex \begin{document} \maketitle The application of computational chemistry methods to solve problems in chemistry and biology will be discussed. Topics to be covered in the course include {\it ab initio}, density functional, semiempirical, and empirical methods, molecular modeling, and molecular and protein dynamics. Each of the above topics will be reinforced through the use of the latest software available on the ASN supercomputer and the IBM workstations located in the Chemistry Department. \medskip\ \TeXButton{Text} {\begin{tabular}{p{5.5in}} \centerline{{\bf Text}} \\ "A Computational Approach to Chemistry" David M. Hirst, Blackwell Scientific Publications, Oxford, 1990. \\ "A Handbook of Computational Chemistry: A Practical Guide to Chemical Structure and Energy Calculations" Tim Clark, Wiley-Interscience, 1985. \\ "Dynamics of Proteins and Nucleic Acids" J. A. McCammon and S. C. Harvey, Cambridge University Press, Cambridge, 1987. \\ "Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics" C. L. Brooks III, M. Karplus, and B. M. Pettitt, Wiley Interscience, 1988. \\ "Molecular Mechanics" U. Burkert and N. L. Allinger, American Chemical Society, 1982. \\ "Learning the UNIX Operating System" O'Reilly and Associates, Inc., 1987. \\ "Computational Chemistry Using the P.C." Donald W. Rogers, VCH, 1990. \\ "Computer Modeling of Chemical Reactions in Enzymes and Solutions", Arieh Warshel, Wiley, 1991. \\ "Molecular Dynamics Simulation: Elementary Methods" J. M. Haile, Wiley, 1992. \end{tabular} } \medskip\ \TeXButton{Programs} {\begin{tabular}{lp{3.25in}} \multicolumn{2}{c}{{\bf Software}} \\ HyperChem & Molecular modeling program that runs on the PC. \\ QUANTA/CHARMm & Molecular modeling program that runs on the IBM. \\ Gaussian 92 & {\it ab initio} program that runs on the ASN Cray. \\ SPARTAN 2.0 & {\it ab initio} program that runs on the IBM. \\ DMol 2.2 & Density Functrional program that runs on the IBM. \\ UHBD & Electrostatics and Brownian Dynamics program that runs on the IBM and ASN Cray. \\ MS Word & Word processing program that runs on a PC. \\ MS Excel 4.0 & Spreadsheet program that runs on a PC. \\ MS FORTRAN 5.1 & Programming language that runs on a PC. \\ \end{tabular} } \medskip\ \TeXButton{Syllabus} {\begin{tabular}{ll} \multicolumn{2}{c}{{\bf Material to be Covered}} \\ Topic & Laboratory Topic \\ \\ {\it ab initio} methods & {\it ab initio} experiment \\ & Gaussian 92 calculation or SPARTAN \\ \\ Density Functional methods & DFT experiment \\ & using DMol 2.2 \\ \\ Semiempirical methods & Semiempirical experiment \\ & MNDO and AM1 calculation \\ & using HyperChem or SPARTAN \\ \\ Empirical methods & Empirical application \\ & Extended H\"uckel calculation\\ & using HyperChem \\ \\ Molecular Mechanics & Energy minimization application \\ & using HyperChem or SPARTAN \\ \\ Molecular Dynamics & Molecular dynamics application \\ & using HyperChem or QUANTA \\ \\ Protein Dynamics & Protein dynamics application \\ & using HyperChem or QUANTA \\ \\ Electrostatics & Electrostatic calculation \\ & using in house program (UHBD) \\ \\ Brownian Dynamics & Calculate diffusion-controlled \\ & rate constant by writing a simple \\ & FORTRAN program \\ \end{tabular} } \bigskip\ \begin{center} {\bf Guidelines} \end{center} \medskip\ Since this is a ``Directed Studies'' type of course the following guidelines will be enforced. \begin{itemize} \item Eleven (11) laboratory units covering the topics outlined above must be completed within the quarter. It is suggestted that two units be completed each week and handed in within one week of finishing the laboratory. \item The laboratory report will have the following sections \begin{itemize} \item abstract \item introduction \item computatioanl method \item results \item discussion and conclusions \item references \item answer to questions \end{itemize} \item Each experiment should take 2-3 hours to execute on the computers. \item It is anticipated that each laboratory should take approximately 2 hours to write. \item Preparation time, i.e. becoming knowledgable about the topic, should take about 6-8 hours. \item Arrange a time in which I can sit down with you for about 1 hour to discuss any problems or explain what is going on. \end{itemize} \end{document} ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ || __ |\ Dr. Ming Wah (Richard) Wong || || / |_| \ ----------------------------------------------|| || .' \ Department of Chemistry || || / *\ The University of Queensland || || \ __ / Brisbane, Qld 4072, Australia || || \_.-' \_ / Fax: +61 7 365 4299 | Phone: +61 7 365 3829 || || v email address: wong@chem.chemistry.uq.oz.au || ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ From michaels@jake.chem.unsw.EDU.AU Wed May 3 21:03:06 1995 Received: from jake.chem.unsw.EDU.AU for michaels@jake.chem.unsw.EDU.AU by www.ccl.net (8.6.10/930601.1506) id VAA20733; Wed, 3 May 1995 21:02:43 -0400 Received: by jake.chem.unsw.EDU.AU (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA10184; Thu, 4 May 95 13:04:02 -0700 From: michaels@jake.chem.unsw.EDU.AU (Michael Shephard) Message-Id: <9505042004.AA10184@jake.chem.unsw.EDU.AU> Subject: G92 - order of atoms in the input To: CHEMISTRY@ccl.net Date: Thu, 4 May 95 13:04:01 PDT X-Mailer: ELM [version 2.3 PL11] -- I thought I would draw this to the attention of the CCL subscribers and invite any explanation of this problem encountered (and solved) with G92/DFT A HF/3-21G single point calc on a large system (132 atoms, 93 heavies) The calculation was done in cartesian coordinates. Route card: #P HF/3-21G GEOM=COORD SCF=(DIRECT, TIGHT) Now, running this calculation with my initial input file, where the Hydrogens and Heavies were listed in no particular order resulted in a failure of the calculation: > Leave Link 303 at Fri Apr 21 00:47:53 1995, MaxMem=7000000 cpu:157.6 > (Enter /usr/local/g92/l401.exe) > PROJECTED INDO GUESS. > Unable to orthonormalize alpha MO coefficients. > Error termination in Lnk1e. > Segmentation fault I then reordered the atoms in the input file so as to place all heavy atoms first. The calculation now proceeded without trouble, (as did a repeat of this calculation with all heavy atoms reordered to place them at the end of the input). Oddly enough, a similar calculations, involving a different conformers of this system, was successful using an "unordered" input file. These successful input files only had a very slightly different order of heavies and hydrogens compared to the failed input. Any ideas as to why this happened? _________________________________________________________________________ | Michael Shephard. | M.Shephard@unsw.EDU.AU | | University of New South Wales. | michaels@jake.chem.unsw.EDU.AU | | Australia | |