From ccl@probe.ac1.uni-duesseldorf.de Thu Sep 1 06:42:47 1994 Received: from probe.ac1.uni-duesseldorf.de for ccl@probe.ac1.uni-duesseldorf.de by www.ccl.net (8.6.9/930601.1506) id GAA06142; Thu, 1 Sep 1994 06:21:38 -0400 Received: by probe.ac1.uni-duesseldorf.de (5.61/1.34) id AA10063; Thu, 1 Sep 94 12:19:15 +0200 From: ccl@probe.ac1.uni-duesseldorf.de (Computational Chemistry List) Message-Id: <9409011019.AA10063@probe.ac1.uni-duesseldorf.de> Subject: QSAR software To: chemistry@ccl.net (Theochem-Liste) Date: Thu, 1 Sep 1994 11:19:14 +0100 (MET) X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 544 Hi netters! I am searching for a program (PD preferred, but not absolutely necessary) for QSAR analysis (PC or SGI INDY with IRIX 5.2). I also need a little help in exploring the method, that means information about books and articles for beginners. I hope, I am not boring you with a question discussed often before. I looked for 'QSAR software' in the osc index files of 91-93 and didn't find much, so I think, I can run the risk of asking this question 8-) Naturally I will post a summary if desired. Thanks in advance Kay Kreidler From smb@smb.chem.niu.edu Thu Sep 1 10:42:50 1994 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.9/930601.1506) id KAA10132; Thu, 1 Sep 1994 10:06:55 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA26794 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net>); Thu, 1 Sep 1994 09:06:54 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net) id AA12891; Thu, 1 Sep 94 08:31:49 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:chemistry@ccl.net) id AA21324; Thu, 1 Sep 94 08:31:48 -0500 Date: Thu, 1 Sep 94 08:31:48 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9409011331.AA21324@smb.chem.niu.edu> To: chemistry@ccl.net Subject: Electronic Computational Chemistry Conference - 2nd Announcement ********* SECOND ANNOUNCEMENT ************** ELECTRONIC COMPUTATIONAL CHEMISTRY CONFERENCE The First Electronic Computational Chemistry Conference (ECCC) will be held November 7-18, 1994. This conference will cover any and all areas of computational chemistry, including electronic structure, molecular mechanics, molecular dynamics, statistical mechanics, drug design, and QSAR. The conference will be held entirely on the Internet. Papers will be prepared in HTML (HyperText Markup Language) and participants will view the papers via the World-Wide Web. Discussions will take place using e-mail through a bulletin board established exclusively for the conference. Detailed information on the conference, including dates of interest, how to prepare a paper, how to coonnect to the World-Wide Web, and how to register, is available by three means: 1) gopher to hackberry.chem.niu.edu port 70 2) world-wide web URL: http://hackberry.chem.niu.edu:70/0/ECCCinformation.html 3) anonymous ftp to hackberry.chem.niu.edu and obtain the file /pub/ECCCinformation.txt As a reminder, abstracts are due by SEPTEMBER 23, 1994. The deadline for registration is NOVEMBER 4, 1994. (As an aside, there is no registration fee for this conference.) The ECCC is sponsored by the Henry and Camille Dreyfus Foundation and the Chemistry Department of Northern Illinois University. Any questions or comments can be sent to smb@smb.chem.niu.edu Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From grzesb@asp.biogeo.uw.edu.pl Thu Sep 1 10:47:31 1994 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id KAA10360; Thu, 1 Sep 1994 10:22:26 -0400 Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA22741; Thu, 1 Sep 94 16:19:08 +0200 Date: Thu, 1 Sep 94 16:19:08 +0200 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9409011419.AA22741@asp.biogeo.uw.edu.pl> To: chemistry@ccl.net Subject: summ:DMOL v.2.35 for CRAY Dear CCL A week ago I asked a question about DMol v.2.35 for Cray computers. Thanks to all who has replied, especially to Dr. Michael Wrinn from Biosym who has provided us full answer for a question. This is summary of relevant answers. Grzegorz Original question: > Dear CCL, > > > I'd like to ask if anyone of you has ever used (or seen) DMol version 2.35 > on CRAY computer system. (DMOL is a DFT program from Biosym, San Diego). We have > version 2.3 which has some serious bugs ( e.g. LYP functional). This version > was "new" in the end of 1992 (we got it then running on workstation). > Lately, for some period I have used v. 2.35 running on SGI and I have got several > good results using LYP and new minimizer (quite good). But I need it running on > big machine, because I plan to investigate big molecular systems ( about 50 atoms). > So, please send me any information about new (!) version of DMOL for CRAY (if exist > - how is its performance; if not exist - when will it be available (if ever). > Thanks in advance. Best wishes, > Grzegorz *********************************************** Replies ************************************************* >From wrinn@iris104.biosym.com Thu Aug 25 19:23 DST 1994 Hello Grzegorz, This message was forwarded to me from CCL. It happens that we are working on the Cray version of DMol right now, but version 2.36. We had found some additional bugs in 2.35, and decided to fix those before releasing a version on the Cray. This week and next, the SGI versions of 2.36 are shipping; we expect to have the Cray image to ship in September. regards, Michael Wrinn (Manager, Quantum Chemistry) ******************************************************* From: gene@jersey.cray.com (Eugene Fleischmann) Grzegorz, As an alternative, you may wish to consider DGauss from Cray Research, Inc. It is a very, user-friendly gaussian function based DFT code with many state-of-the-art features, including high performance on Cray systems, of course. A brief comparison of the speeds of DMol versus DGauss follows. (stuff deleted) For more information about DGauss and/or UniChem please send mail to any of the following individuals at Cray Research, Inc: Dr. George Fitzgerald george@gravity.cray.com Dr. Thomas Raeuchle raeuchle@gravity.cray.com Dr. Eugene Fleischmann gene@jersey.cray.com Best Wishes, Gene ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Computational Chemist Cray Research, Inc. (609) 252-1250 121 Commons Way gene@jersey.cray.com Princeton, NJ 08540 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ______________________________________________________________________ DGauss versus DMol ______________________________________________________________________ Dgauss DMol molecule MaxMem #fcn CPU Perf. MaxMem #fcn CPU Perf. -------- -------------------------- -------------------------- C6H6 4.9 102 19 253 ? 114 40 413 Fe2(CO)9 5.1 322 603 442 ? 300 433 677 C18H14 5.4 298 198 372 ? 322 467 576 ______________________________________________________________________ NOTE: MaxMem in MegaWords (64-bit), CPU in sec., Perf. in MegaFlops. *************************************************** >From mberger@strider.esd.sgi.com Fri Aug 26 22:17 DST 1994 Grzegorz, Hello, I'm the chemistry market manager at SGI and I work with the software partners. You might be interested to know that we have 3 Ph.D.s working full time to parallelize chemistry codes on the Challenge and Power Challenge (R8000 chip). They have parallelized Dmol on the Challenge and will be working to parallelize it on the Power Challenge. We've seen results with Discover that have 4 R8000 CPUs beating a Cray C90. You might want to take a look at Power Challenge to rum Dmol on. Mark *************************************************** end of replies From help15@cas.org Thu Sep 1 10:49:10 1994 Received: from srv01s4.cas.org for help15@cas.org by www.ccl.net (8.6.9/930601.1506) id JAA09414; Thu, 1 Sep 1994 09:43:06 -0400 Date: Thu, 1 Sep 94 09:41:57 EDT From: help15@cas.org (CAS Customer Support, help@cas.org) Message-Id: <9409010941.AA8474@cas.org> Subject: Ref: Douglas Smith's "CCL:morphology of zinc phospate on steel" To: chemistry@ccl.net Cc: theochem@ctc.com Ref: Your Internet message "CCL:morphology of zinc phospate on steel" Dear Mr. Smith: As you probably already know, Chemical Abstracts (CA) covers literature on Ferrous Metals and Alloys in CA Section 55 and should contain abstracts related to your question. I noticed that you have tried searching the CAS files on STN and were unsuccessful so I posed your question to one of our Material Science specialist. He developed two search strategies for you to try on STN. The first strategy uses the CAS Registry and CAS CA files while the second strategy relies just on the CAS CA file. The first strategy has the advantage of being more extensive and precise while the second strategy would be less expensive. His comments about the various steps are noted by this symbol ">>". For those of you not familiar with STN, STN is an online search service offered by CAS. It has over 180 scientific and technical databases that account holders can use to search for various types of information. If any of you are interested, I have an STN Information Package (contains a database catalog, price list, and registration forms) that I can mail to you. Please forward your postal mailing address to: CAS 2540 Olentangy River Rd PO Box 3012 Columbus, OH 43210 Internet E-mail: help@cas.org Customer Service Telephone: 800-753-4227 or 614-447-3600 Customer Service Telefax: 614-447-3751 Sincerely, Glen R. Davis CAS Customer Service Representative ============================================================================= ***** SEARCH STRATEGY 1 ***** => fil reg >>Zn phosphate coatings on steel may contain Fe, the principal component of >>the substrate, hence the search begins with searching both salts in REG/CN. >>Names are truncated to allow for various hydrates. => s zinc phosphate?/cn or iron zinc phosphate?/cn 18 ZINC PHOSPHATE?/CN 6 IRON ZINC PHOSPHATE?/CN L2 24 ZINC PHOSPHATE?/CN OR IRON ZINC PHOSPHATE?/CN >>Display mol. formula field to see false drops (compounds with organic >>component) => d mf 1-24 L2 ANSWER 1 OF 24 REGISTRY COPYRIGHT 1994 ACS MF C6 H7 O3 P . x H2 O . x H O4 P . x H O3 P . x Zn L2 ANSWER 2 OF 24 REGISTRY COPYRIGHT 1994 ACS MF C7 H9 N . x H2 O . x H O4 P . x H O3 P . x Zn L2 ANSWER 3 OF 24 REGISTRY COPYRIGHT 1994 ACS MF C7 H5 N O4 . x H2 O . x H O4 P . x H O3 P . x Zn L2 ANSWER 4 OF 24 REGISTRY COPYRIGHT 1994 ACS MF C9 H9 N O3 . x H2 O . x H O4 P . x H O3 P . x Zn L2 ANSWER 5 OF 24 REGISTRY COPYRIGHT 1994 ACS MF C7 H8 O . x H2 O . x H O4 P . x H O3 P . x Zn L2 ANSWER 6 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H O4 P . H O3 P . Zn L2 ANSWER 7 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Fe . O4 P . Zn L2 ANSWER 8 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Fe . O4 P . Zn L2 ANSWER 9 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Fe . O4 P . Zn L2 ANSWER 10 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . 5/4 Zn L2 ANSWER 11 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . x H2 O . Zn L2 ANSWER 12 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Fe . x H3 O4 P . x Zn L2 ANSWER 13 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Fe . 2 H3 O4 P . 2 Zn L2 ANSWER 14 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Fe . 2 H3 O4 P . 4 H2 O . 2 Zn L2 ANSWER 15 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . H2 O . 3/2 Zn L2 ANSWER 16 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . Zn L2 ANSWER 17 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . H2 O . 1/2 Zn L2 ANSWER 18 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . H2 O . Zn L2 ANSWER 19 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . 1/2 Zn L2 ANSWER 20 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H O3 P . 1/2 Zn L2 ANSWER 21 OF 24 REGISTRY COPYRIGHT 1994 ACS MF Unspecified L2 ANSWER 22 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . 3/2 Zn L2 ANSWER 23 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H3 O4 P . 2 H2 O . 3/2 Zn L2 ANSWER 24 OF 24 REGISTRY COPYRIGHT 1994 ACS MF H4 O7 P2 . 2 Zn >>select MF and continue search to get the minerals (they do not have chem. >>names like "zinc phosphate" but have the same mol. formulas) that may be >>used (incorrectly) to index phosphate coatings => select mf l2 6-20,22-24 E1 THROUGH E16 ASSIGNED => s e1-e16 3 FE.O4P.ZN/MF 3 FE.XH3O4P.XZN/MF 1 FE.2H3O4P.2ZN/MF 2 FE.2H3O4P.4H2O.2ZN/MF 1 "HO3P.1/2ZN"/MF 1 HO4P.HO3P.ZN/MF 1 H3O4P.H2O.ZN/MF 1 "H3O4P.H2O.1/2ZN"/MF 1 "H3O4P.H2O.3/2ZN"/MF 1 H3O4P.XH2O.ZN/MF 1 H3O4P.ZN/MF 1 "H3O4P.1/2ZN"/MF 3 "H3O4P.2H2O.3/2ZN"/MF 1 "H3O4P.3/2ZN"/MF 1 "H3O4P.5/4ZN"/MF 1 H4O7P2.2ZN/MF L3 23 (FE.O4P.ZN/MF OR FE.XH3O4P.XZN/MF OR FE.2H3O4P.2ZN/MF OR F E.2H3O4P.4H2O.2ZN/MF OR "HO3P.1/2ZN"/MF OR HO4P.HO3P.ZN/MF OR H3O4P.H2O.ZN/MF OR "H3O4P.H2O.1/2ZN"/MF OR "H3O4P.H2O. 3/2ZN"/MF OR H3O4P.XH2O.ZN/MF OR H3O4P.ZN/MF OR "H3O4P.1/2 ZN"/MF OR "H3O4P.2H2O.3/2ZN"/MF OR "H3O4P.3/2ZN"/MF OR "H3 O4P.5/4ZN"/MF OR H4O7P2.2ZN/MF) >>get the reg. number for a single phosphate with unspecified structure (see >>displayed answer set above) => select rn l2 21 E17 THROUGH E17 ASSIGNED >>do the same for the rest of compounds (l3 set) and go to the file CA => select rn l3 1-23 E18 THROUGH E40 ASSIGNED => fil ca => s e17-e40 5 12741-07-0/BI 1 100356-35-2/BI 0 101764-37-8/BI 1 117314-57-5/BI 1 117314-58-6/BI 1 117314-59-7/BI 138 13566-15-9/BI 120 13598-37-3/BI 0 136938-52-8/BI 16 13814-03-4/BI 30 13986-21-5/BI 77 14332-60-6/BI 15 14485-28-0/BI 100 15491-18-6/BI 15 15551-65-2/BI 21 15662-48-3/BI 16 16842-47-0/BI 38 35743-71-6/BI 1 63692-76-2/BI 0 67183-34-0/BI 11 70629-49-1/BI 134 7446-26-6/BI 107 7543-51-3/BI 1162 7779-90-0/BI L4 1799 (12741-07-0/BI OR 100356-35-2/BI OR 101764-37-8/BI OR 1173 14-57-5/BI OR 117314-58-6/BI OR 117314-59-7/BI OR 13566-15 -9/BI OR 13598-37-3/BI OR 136938-52-8/BI OR 13814-03-4/BI OR 13986-21-5/BI OR 14332-60-6/BI OR 14485-28-0/BI OR 1549 1-18-6/BI OR 15551-65-2/BI OR 15662-48-3/BI OR 16842-47-0/ BI OR 35743-71-6/BI OR 63692-76-2/BI OR 67183-34-0/BI OR 7 0629-49-1/BI OR 7446-26-6/BI OR 7543-51-3/BI OR 7779-90-0/ BI) >>search in section 55 restricts the substrate to steel; coating should be >>searched as a controlled vocabulary term in the basic index to eliminate >>false drops => s l4 and coat? and (morph? or struc?) and 55/sc,sx 489112 COAT? 191512 MORPH? 1422542 STRUC? 271162 55/SC 72890 55/SX L5 45 L4 AND COAT? AND (MORPH? OR STRUC?) AND 55/SC,SX => d all L5 ANSWER 1 OF 45 CA COPYRIGHT 1994 ACS AN 119:273469 CA TI Characterization of poly(acrylic acid)-modified zinc phosphate crystal conversion ***coatings*** AU Wragg, J. L.; Chamberlain, J. E.; Chann, L.; White, H. W.; Sugama, T.; Manalis, S. CS Dep. Phys. Astron., Univ. Missouri, Columbia, MO, 65211, USA SO J. Appl. Polym. Sci. (1993), 50(5), 917-28 CODEN: JAPNAB; ISSN: 0021-8995 DT Journal LA English CC 42-10 (Coatings, Inks, and Related Products) Section cross-reference(s): ***55*** OS CJWILEY AB Raman spectroscopy and at. force microscopy were used to investigate the compn. and surface ***structure*** of poly(acrylic acid)(I)-modified zinc phosphate crystal conversion ***coatings*** on steel. Addn. of high-mol. wt. I to the phosphating bath can significantly improve both resistance to corrosion and topcoat adherence. Raman spectra show the compns. of both unmodified and I-modified films to be zinc phosphate dihydrate, Zn3(PO4)2.cntdot.2H2O. At. force microscopy (AFM) was used to measure the ***morphologies*** of single cryst. surfaces. ***Morphologies*** of the unmodified and modified films obtained by AFM were quite similar, but subtle differences were apparent. ST polyacrylic acid zinc phosphate ***coating*** ; conversion ***coating*** steel polyacrylic acid IT ***Coating*** materials (conversion, poly(acrylic acid)-modified zinc phosphate, on steel) IT ***7779-90-0*** (conversion ***coatings*** , poly(acrylic acid)-modified, on steel) IT 9003-01-4, Poly(acrylic acid) (zinc phosphate conversion ***coatings*** modified by, on steel) => d 45 all L5 ANSWER 45 OF 45 CA COPYRIGHT 1994 ACS AN 74:56562 CA TI Phosphate- and zinc- ***coated*** steel sheets IN Bijl, Cornelis L.; Vrijburg, Hans H. PA Koninklijke Nederlandsche Hoogevens en Staalfabrieken N. V. SO Ger. Offen., 17 pp. CODEN: GWXXBX PI DE 2029660 710107 PRAI NL 690618 DT Patent LA German IC C23F CC ***55*** (Ferrous Metals and Alloys) AB Phosphate layers, with a uniform cryst. ***structure*** distribution on Zn- ***coated*** steel sheets, were obtained by passing the sheets through pairs of rolls of 60-80.degree. Shore hardness acting at 20 kg/cm roll length and immersing the sheets .apprx.3 sec at .apprx.70.degree. in a phosphate soln. ST phosphatizing zinc ***coated*** steel; zinc ***coated*** steel phosphatizing; steel zinc ***coated*** phosphatizing; galvanized steel phosphatizing IT Galvanized iron ( ***coating*** of, with phosphates) IT ***Coating*** process (of galvanized steel, with phosphates) IT ***7543-51-3*** (in phosphate ***coatings*** , on galvanized steel) ============================================================================ ***** SEARCH STRATEGY 2 ***** => s coat?/ct(l)phosph? and coat?/ct(l)(morph? or struct?) and (zn or zinc) and 55/sc,sx not review/dt 195479 COAT?/CT 813569 PHOSPH? 7186 COAT?/CT(L)PHOSPH? 195479 COAT?/CT 191512 MORPH? 1421775 STRUCT? 2739 COAT?/CT(L)(MORPH? OR STRUCT?) 222979 ZN 240332 ZINC 271162 55/SC 72890 55/SX 978353 REVIEW/DT L16 22 COAT?/CT(L)PHOSPH? AND COAT?/CT(L)(MORPH? OR STRUCT?) AND (ZN OR ZINC) AND 55/SC,SX NOT REVIEW/DT => d all L16 ANSWER 1 OF 22 CA COPYRIGHT 1994 ACS AN 119:76969 CA TI Study of the structure and composition of phosphate coatings on mild steel surfaces as a function of process parameters and design of the phosphating chemicals AU Roy, P. K.; Debnath, N. C. CS Appl. Res. Dev. Dep. (Paints), ICI (India) Ltd., West Bengal, India SO Surf. Coat. Int. (1993), 76(5), 214-16, 218-20 CODEN: SCOIE6 DT Journal LA English CC ***55-6*** (Ferrous Metals and Alloys) Section cross-reference(s): 42 AB For ***Zn*** phosphating chems. based on nitrate/nitrite type accelerators, both chem. concn. and nitrite concn. play an important role in controlling the stability of processing bath. Optimum coating morphol. is obsd. for both studied baths (A - TA15-40 at pH 2.6-2.8 and B - TA15-40 at pH 2.25-2.55) around toner levels of 2.5 mL. Coating wt. variation for bath A is almost insignificant, while for bath B only slight redn. is obsd. with the increase of toner level. ST mild steel phosphating bath compn IT ***Coating materials*** ( ***zinc*** ***phosphate*** , on mild steel surfaces, effect of chems. on ***structure*** and compn. of) IT ***Coating process*** ( ***phosphating*** , of mild steel) IT 11121-90-7, miscellaneous (phosphating of) ******************************************************************************* From prasad@chem.psu.edu Thu Sep 1 12:43:05 1994 Received: from PSUVM.PSU.EDU for prasad@chem.psu.edu by www.ccl.net (8.6.9/930601.1506) id MAA12959; Thu, 1 Sep 1994 12:15:27 -0400 Received: from portal.chem.psu.edu by PSUVM.PSU.EDU (IBM VM SMTP V2R2) with TCP; Thu, 01 Sep 94 12:10:42 EDT Received: from galilei.chem.psu.edu by portal.chem.psu.edu (AIX 3.2/UCB 5.64/RS6000-Server-1.0) id AA15534; Thu, 1 Sep 1994 12:12:26 -0400 Received: by galilei.chem.psu.edu (AIX 3.2/UCB 5.64/Client-1.0) id AA47690; Thu, 1 Sep 1994 12:11:09 -0400 Date: Thu, 1 Sep 1994 12:11:09 -0400 From: "Prasad B.S Kodali" Message-Id: <9409011611.AA47690@galilei.chem.psu.edu> To: chemistry@ccl.net Subject: MD with MM3 Dear netters, I am planning to do MD simulations using MM3 force field for Naphthalene crystal. I am having a problem with the VDW interactions. According to reference: Norman L. Allinger and Jenn-Huei Lii J. of Computational Chemistry, Vol. 8, 1146-1153 (1987) The van der waals potential for two atoms interacting with each other and not bound together nor to a common atom is given by E(vdw) = sqrt(e1*e2)(1.85*(10**5)exp -(12/p) - 2.25(p**6)) p = (r1(vdw) + r2(vdw)) / (r) The parameters for r(vdw) for C(sp2) 1.96 Angstroms r(vdw) for H 1.62 Angstroms e1(vdw) for C(sp2) 0.056 e2(vdw) for H 0.020 NAPHTHALENE : 12 15 | | | | 11 | | \ / 2\ /7\ /16 \ / \ / \ / \/ \ / \/ |1 3| 8| | | | | | | |6 4| 9| /\ / \ /\ / \ / \10 / \ 14/ \5 / \ / \ | | 17 | | | | 13 18 If we consider the interaction between C(2) - H(15) it satisfies the above mentioned criteria, the distance is roughly 2.7 Angstroms which is on the repulsive wall of the potential with an energy of approx. 0.5 kcal/mole. For these atoms to get to equilibrium positions in the minimum energy confirmations, the angles have to change away from the equilibrium values. There are three other such interactions, namely C(5) - H(18), C(7) - H(12) and C(10) - H(13) and also the same problem with H(12) - H(15) and H(13) - H(18). I am sure that I am missing something here. I think this will be a problem even when getting the minimum energy confirmation in a single molecule using MM3 with the above set of parameters. Any help in this regard will be very useful. Thank you for your time Prasad prasad@chem.psu.edu From CHMORA@LSUVAX.SNCC.LSU.EDU Thu Sep 1 13:43:15 1994 Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by www.ccl.net (8.6.9/930601.1506) id NAA14621; Thu, 1 Sep 1994 13:03:51 -0400 Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426) id <01HGLIJII2SG8WZ1B3@LSUVAX.SNCC.LSU.EDU>; Thu, 1 Sep 1994 12:06:00 CST Date: Thu, 01 Sep 1994 12:06:00 -0600 (CST) From: CHMORA@LSUVAX.SNCC.LSU.EDU Subject: Need help on using MOPAC. To: chemistry@ccl.net Message-id: <01HGLIJIIM2Q8WZ1B3@LSUVAX.SNCC.LSU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters: I'm getting my feet wet in semiempirical calculations using MOPAC 6 and I would like to know if there is any book (or handbook) about semiempirical calculations using MOPAC. I want to take a look at the input and output files so I can get a better understanding of the use of MOPAC's keywords, how one can determine transition sates and reaction's mechanism, how one can tell the program that you are dealing with an aromatic system (such as benzene) not just with an unsaturated cyclic system, etc. All your answers will be appreciated. Thanks a lot in advance. Sincerely, Guillermo A. Morales Department of Chemistry Louisiana State University Baton Rouge, LA. 70803-1804 PHONE: (voice) (504) 388-2706 (fax) (504) 388-3458 e-mail address: chmora@sn01.sncc.lsu.edu From sigfrido@unamvm1.dgsca.unam.mx Thu Sep 1 16:42:55 1994 Received: from unamvm1.dgsca.unam.mx for sigfrido@unamvm1.dgsca.unam.mx by www.ccl.net (8.6.9/930601.1506) id QAA20024; Thu, 1 Sep 1994 16:03:39 -0400 Received: by unamvm1.dgsca.unam.mx (5.57/Ultrix3.0-C) id AA05056; Thu, 1 Sep 94 14:03:07 -0500 Date: Thu, 1 Sep 1994 13:49:19 -0500 (CDT) From: Escalante Tovar Sigfrido-FQ Subject: Pb parameters To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleages: I have been looking for Lead (Pb) parameters to be used in a)force fields in molecular mechanics b)semi-empirical molecular orbital calculations I will really appreciate any useful information, which I will share with all the netters. Sigfrido Escalante Tovar Departamento de Quimica Inorganica Facultad de Quimica, UNAM, MEXICO e-mail: sigfrido@unamvm1.dgsca.unam.mx From MARYJO@neu.edu Thu Sep 1 17:42:55 1994 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by www.ccl.net (8.6.9/930601.1506) id RAA20931; Thu, 1 Sep 1994 17:00:50 -0400 From: Received: from neu.edu by neu.edu (PMDF V4.2-13 #4985) id <01HGLST73E9C8X18JD@neu.edu>; Thu, 1 Sep 1994 17:01:35 EST Date: Thu, 01 Sep 1994 17:01:35 -0500 (EST) Subject: XPS versus theoretical IP's To: chemistry@ccl.net Message-id: <01HGLST74GUA8X18JD@neu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello everybody. I have a question about comparing experimental XPS energies with ab initio computed molecular electronic I.P.'s Since XPS is a solid state measurement, its electron energies are not the same as the gas-phase I.P.'s one obtains from, say, Koopman's theorem. What I am wondering is, how well do these two sets of numbers compare to each other? (i.e. How well do the theoretical computed values compare with experiment?) Are the relative values the same for sets of valence and core orbitals within the same molecule? Will the computed I.P. spectrum for the gas phase look anything like the experimental spectrum? How important is the potential field for the solid? Will computed I.P.'s for a set of compounds correctly predict the relative I.P.'s measured for the same set of molecules in the solid state? For a molecular crystal, how well does the solid state band structure relate to the free molecule's electronic structure? I would appreciate advice from anybody who has experience with these things. Thanks very much, Mary Jo Ondrechen From nauss@ucmod2.che.uc.EDU Thu Sep 1 19:42:56 1994 Received: from ROLL.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.9/930601.1506) id SAA22881; Thu, 1 Sep 1994 18:48:18 -0400 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-8 #4918) id <01HGLWHQU4B48X481U@UCBEH.SAN.UC.EDU>; Thu, 01 Sep 1994 18:44:45 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA22144; Thu, 1 Sep 94 18:46:47 -0400 Date: Thu, 01 Sep 1994 18:46:47 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Crystal structure for alginic acid To: CHEMISTRY@ccl.net Message-id: <9409012246.AA22144@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT Would anyone have, or know where to obtain, a set of coordinates for alginic acid, poly-beta-D-mannuronic acid, and/or poly-alpha-L-guluronic acid? These structures were reported by Atkins et al. in Biopolymers, vol 12, pages 1865 and 1879 (1973). However, the coordinates do not appear to be in either the Brookhaven or Cambridge data banks. Thank you. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC * **************************************************************************** From GERARD@XRAY.BMC.UU.SE Thu Sep 1 20:42:58 1994 Received: from XRAY.BMC.UU.SE for GERARD@XRAY.BMC.UU.SE by www.ccl.net (8.6.9/930601.1506) id UAA23275; Thu, 1 Sep 1994 20:04:20 -0400 Date: Fri, 2 Sep 1994 2:03:13 +0300 (MET-DST) From: GERARD@XRAY.BMC.UU.SE (Gerard Kleijwegt a.k.a. gerard@xray.bmc.uu.se) Message-Id: <940902020313.21604e1f@XRAY.BMC.UU.SE> Subject: RE: CCL:Crystal structure for alginic acid To: CHEMISTRY@ccl.net X-Vmsmail-To: SMTP%"CHEMISTRY@ccl.net" From: XRAY::GERARD "Gerard Kleijwegt a.k.a. gerard@xray.bmc.uu.se" 2-SEP-1994 01:47:49.86 To: SMTP%"chemistry-request@ccl.net" CC: GERARD Subj: RE: CCL:Crystal structure for alginic acid my pdb says: 1C4S CHONDROITIN-4-SULFATE (AN ALTERNATING COPOLYMER OF BETA-D-GLUCURONIC ACID AND ... 4HYA HYALURONIC ACID (POLY D-GLUCURONIC ACID-N-ACETYL-D-GLUCOSAMINE) HIGH HUMIDITY ... --gerard kleywegt bmc, uppsala From jeremy@med.su.oz.au Thu Sep 1 21:43:00 1994 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.6.9/930601.1506) id VAA23737; Thu, 1 Sep 1994 21:19:01 -0400 Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.8.1/8.6.4) id LAA14889 for chemistry@ccl.net Fri, 2 Sep 1994 11:18:55 +1000 From: Jeremy R Greenwood Message-Id: <199409020118.LAA14889@blackburn.med.su.oz.au> Subject: Modelling Pyridazindiones To: chemistry@ccl.net Date: Fri, 2 Sep 1994 11:18:54 +1000 (EST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1708 As a newcomer to the field and to this list, please forgive any naivety. I am currently attempting to model structures containing the unusual heterocycle pyridazine-3,6-dione, which displays multiple lactam-lactim tautomerism. Experimental evidence suggests that the oxo-hydroxy tautomer is most stable. I've been using MOPAC, however I don't know if I can trust the results (based on W.Fabian, J. Molecular Structure (Theochem), 200 (1990), 295). Which semi-empirical technique is most likely to give me reasonably accurate structures and energies for this ring system? If I have to resort to ab initio calculations, what is the minimum level of theory necessary to handle this ring? Secondly, the structures I am modelling are most likely zwitterionic in physiological solution, as they contain an amino group in addition to the acidic pyridazindione. Is there any point in modelling zwitterions on MOPAC or Gaussian 92 in the gas phase and trying to extrapolate to solution behaviour? Is there an appropriate (not too computationally expensive) technique for simulating solution behaviour, reliable for predicting zwitterionic and tautomeric structure, or does one have to resort to coordinating water molecules etc.? Thirdly, the atomic charges returned by various semi-empirical methods vary widely for these structures. I would like to be able to predict qualitatively if not quantitatively, which proton(s) are the most acidic. I realise that this may once again depend on aqueous behaviour rather than gas-phase, and hence be rather a tall order. Any suggestions? Thanks in advance, Jeremy Greenwood Department of Pharmacology, University of Sydney NSW 2006, Australia