From chemistry-request@www.ccl.net Tue Dec 1 09:03:49 1998 Received: from camd1.kkpcr.re.kr (camd1.kkpcr.re.kr [134.75.174.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA01238 Tue, 1 Dec 1998 09:03:48 -0500 (EST) Received: (from jeonghy@localhost) by camd1.kkpcr.re.kr (8.8.6H1/8.8.6) id XAA08815 for chemistry@www.ccl.net; Tue, 1 Dec 1998 23:04:26 -0900 (PST) From: Ho Young Jeong Message-Id: <199812020804.XAA08815@camd1.kkpcr.re.kr> Subject: cohesive energy density from MD To: chemistry@www.ccl.net Date: Tue, 1 Dec 1998 23:04:26 -0900 (PST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL user: I'm looking for the references to calculate cohesive energy density (CED) from MD. CED value computed by my own code is so far from the experimental one. There are several problem in the code, but I suspect the equation to obtain it from the radial distribution function of MD trajectory. Please let me know the introductory books, reviews or papers in this field. Thank you in advance, Ho Young Jeong Kumho Chemical Lab., Korea. From chemistry-request@www.ccl.net Tue Dec 1 12:07:16 1998 Received: from hercules.telenet-ops.be (hercules.telenet-ops.be [195.130.132.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA03267 Tue, 1 Dec 1998 12:07:13 -0500 (EST) Received: from a.pandora.be ([195.130.139.203]) by hercules.telenet-ops.be (Netscape Messaging Server 3.6) with SMTP id AAA1B45 for ; Tue, 1 Dec 1998 18:07:08 +0100 Message-ID: <36642343.480E@pandora.be> Date: Tue, 01 Dec 1998 18:11:31 +0100 From: Violon Daniel Reply-To: comed@pandora.be X-Mailer: Mozilla 3.01 [nl]C-PAN1 (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: mopac7/cosmo Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit From Daniel VIOLON Belgium comed@pandora.be Subject: COSMO in MOPAC7 (DOS) Hello! I would like to use COSMO on molecules containing approximatively 65 atoms ("heavy" and "light" together). Apparently, the COSMO routine (available in the free downloadable MOPAC7 for DOS) does not work for molecules containing more than 50 atoms (producing an error message and returning to the C prompt), although AM1 and MNDO work normally for my larger molecules, without the COSMO keywords. This COSMO properly handles smaller molecules (Klamt's glycine testrun is OK). Am I missing something important? Is there any place where a MOPAC7 version could be found with a COSMO module able to work with the required number of atoms (approximatively maximum 65) for DOS or even WIN95, without having to recompile the code, not being a native programmer? Thank you very much for helping! Daniel comed@pandora.be From chemistry-request@www.ccl.net Tue Dec 1 12:33:39 1998 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA03742 Tue, 1 Dec 1998 12:33:38 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with ESMTP id SAA14979 for ; Tue, 1 Dec 1998 18:33:49 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with SMTP id SAA26714; Tue, 1 Dec 1998 18:31:03 +0100 (MET) Received: by styx.bruyeres.cea.fr (CEANET-1.1+) id AA24856; Tue, 1 Dec 1998 18:33:20 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by styx via smap id sma024824; Tue Dec 1 18:32:50 1998 Received: from ripault.cea.fr (manse.ripault.cea.fr [132.165.32.9]) by ripault.cea.fr. (8.8.7/8.7.3) with ESMTP id SAA02242; Tue, 1 Dec 1998 18:32:44 +0100 Received: from manse.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id SAA05522; Tue, 1 Dec 1998 18:33:06 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <36642852.19691851@ripault.cea.fr> Date: Tue, 01 Dec 1998 17:33:06 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: Elmar Gerwalin Cc: chemistry@www.ccl.net Subject: Re: CCL:G:Calculate Heat of formation ? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Elmar Gerwalin wrote: > > Hi > I want to use Gaussian94 to calculate the heat of > formation for organic compounds. > > Do I have to perform a frequency calculation to get the > Zero point vinbration energy to get correct results ? Concerning calculation of Heats of formation and other thermochemical quantities, there is a very useful (to me) recent book, in which a wide variety of methods, from purely empirical to very high level ab initio, are discussed: Computational Thermochemistry ACS Symposium Series No 677 K. Irikura and D.J. Frurip (eds). This book is available from the Amazon bookshop: http://www.amazon.com > Or is there a better way to get the values ? It depends on a number of factors such as the target accuracy, the size of the molecules considered... If you can afford high-level ab initio techniques of course calculation of zero-point energy is recommended, and also others less significant contributions (thermal vib+rot+trans and delta(PV)...) easy to obtain. My version of Gaussian is G92 but I think in Gaussian94 calculation of formation enthalpies is implemented in an automated way (G2 or CBS models). If more efficient techniques are required, you need "atom equivalents": see S.J. Mole et al. J. Phys. Chem. 100, 14665 (1996) and ref. therein. A set of atom equivalents for C,H,N,O,F,Cl compounds has been derived by Habibollahzadeh et al. J. Comp. Chem. 16, 654 (1995). To come back to the original question, I believe than explicit calculation of frequencies is useful only at the highest levels, because using HF or popular DFT functional the errors stem mostly from the equilibrium energies (even after correction through atom equivalents) rather than from the neglect of ZPE and thermal contributions. Maybe with B3LYP and large basis set (Mole et al.) introducing explicit calculation of the frequencies might be useful, but it is doubtful to me. For instance, in JCC 16, 654 (1995) all contributions are calculated explicitly. However, it yields no improvement over the more usual method were everything is dumped into atom equivalents exepted the DFT energy. We tried both schemes and obtained very similar results. To save CPU time, you can simply perform single point energy calculations on geometries optimized with accurate molecular mechanics force field such as MMFF. We developed a set of atom equivalents suitable for BP/DN**//MMFF calculations. There were obtained from a calibration set of 84 molecules and tested on the panel of JCC 16, 654 (1995): we obtained the same accuracy of the original method at a much reduced cost. I can send the group equivalents. However, one must be careful with the environments of the atoms. For instance we found out that the atom equivalents for F bonded to C CANNOT be used for F bonded to N, at least at the BP/DN**//MMFF level. Moreover, MMFF wrongly predicts nitro groups to be perpendicular to the ring plane for nitroaromatics! In JCC 16, 654 (1996) it is obvious that uncorrected theoretical enthalpies are very poor. For fast calculations we use the PIMM model available from the university of Darmstadt: http://tutor.oc.chemie.th-darmstadt.de/TZ/AKLindner/pimm_e.html To my experience, the PIMM method is faster and more reliable than both AM1 (significantly) and PM3 for energetic materials, although it was not designed for this specific application. Here is a comparaison of performance for ~100 molecules, most of them staken from JCC 16, 654 (1995): values reported = average absolute deviation and max. abs. dev. (kJ/mol): PIMM method 19.5 13.3 BP/DN**//MMFF (*) 12.5 59.6 BP/DN**//MMFF (**) 12.3 64.8 BP/6-31G(d,p) 13.3 43.8 (*) freq. calculated explicitly, hence VIB+ROT+TRANS+D(PV) (**) no explicit calculation of the above contributions Regards Didier -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From chemistry-request@www.ccl.net Tue Dec 1 10:15:44 1998 Received: from reddeer.fisica.ufpr.br (reddeer.fisica.ufpr.br [200.17.214.184]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA02033 Tue, 1 Dec 1998 10:15:36 -0500 (EST) Received: from localhost (edulsa@localhost) by reddeer.fisica.ufpr.br (8.8.8/8.8.8) with SMTP id NAA19997 for ; Tue, 1 Dec 1998 13:15:25 -0200 (EDT) (envelope-from edulsa@reddeer.fisica.ufpr.br) Date: Tue, 1 Dec 1998 13:15:25 -0200 (EDT) From: Eduardo To: "ccl.osc" Subject: sources to ampac2.1 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by www.ccl.net id KAA02036 Dear netters Does somebody know where I can find a ampac2.1 (or higher) sources to compiling at UNIX (FreeBSD or Linux) enviroment? I've tried to use these from ccl.osc, but I can't to solve the problem from SIZES/NOLIST file (isn't have any file with this name in the package) thanks a lot Eduardo edulsa@quimica.ufpr.br Univ. Feder. Paraná - Curitiba - Brazil From chemistry-request@www.ccl.net Tue Dec 1 15:08:25 1998 Received: from ns01.sbphrd.com (firewall-user@ns01.sbphrd.com [208.198.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA19728 Tue, 1 Dec 1998 15:08:25 -0500 (EST) Received: by ns01.sbphrd.com; id PAA09481; Tue, 1 Dec 1998 15:08:26 -0500 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma009405; Tue, 1 Dec 98 15:08:17 -0500 Received: from phufs2.um.us.sbphrd.com by phinet.sbphrd.com; (/) id AA06065; Tue, 1 Dec 1998 15:08:17 -0500 Received: from phu198.um.us.sbphrd.com (phu198.um.us.sbphrd.com [139.136.98.47]) by phufs2.um.us.sbphrd.com (8.8.8/8.8.8/sbphrd/mh/19971204) with ESMTP id PAA26803 for ; Tue, 1 Dec 1998 15:08:17 -0500 (EST) From: M Dominic Ryan Received: (from ryanmd@localhost) by phu198.um.us.sbphrd.com (8.8.8/8.8.8) id PAA96044 for chemistry@www.ccl.net; Tue, 1 Dec 1998 15:10:37 -0500 (EST) Date: Tue, 1 Dec 1998 15:10:37 -0500 (EST) Message-Id: <199812012010.PAA96044@phu198.um.us.sbphrd.com> To: chemistry@www.ccl.net Subject: Travel Grants Available, addendum As posted last week, the Computers in Chemistry Division is making available a limited number of grants of up to $500. Two addenda should be added: The deadline for submission is January 28, 1999. This will permit sufficient time to process the submissions and make the awards for the candidate to still adjust travel plans. Only authors presenting a paper in the Division of Computers in Chemistry are eligible. The original notice is included below: --------------- The Computers in Chemistry Division of American Chemical Society invites students presenting a paper at the spring meeting in Anaheim to apply for a travel grant. A limited number of grants of up to $500 will be awarded to selected students. 1. Candidates must be graduate students OR undergraduate students in good standing as confirmed by their department. 2. Students must have a supporting letter from their (primary) thesis advisor or the department chair if the latter is not possible (with an explanatory note). 3. No more than one award will be given to a research group. 4. Funds must be used to attend the Spring 1999 National meeting of the American Chemical Society. 5. Candidates must be presenting either an oral paper or a poster. 6. To apply, send letter of request, C.V. and supporting documents to the address below. Supporting Letters must be sent by mail (i.e. hard-copy). M. Dominic Ryan, UW2412 SmithKline Beecham Pharmaceuticals 709 Swedeland Rd King of Prussia, PA 19406 USA There is still limited time to submit a paper to either the General oral section or to the Posters. If you have already been accepted, forward your application for consideration. If you would like to present a paper, please forward both the grant application and the abstract form. ---------------- Dominic Ryan Program Chair Division of Computers in Chemistry American Chemical Society. __ M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals Internet: ryanmd@mms.sbphrd.com King of Prussia, PA From chemistry-request@www.ccl.net Tue Dec 1 15:57:55 1998 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA23484 Tue, 1 Dec 1998 15:57:54 -0500 (EST) Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id MAA15380; Tue, 1 Dec 1998 12:51:06 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma015378; Tue, 1 Dec 98 12:51:04 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id MAA18817; Tue, 1 Dec 1998 12:57:13 -0800 (PST) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2232.9) id ; Tue, 1 Dec 1998 12:57:54 -0800 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE55A7806@shepherd.mdli.com> From: Guenter Grethe To: CHMINF-L , Computational Chemistry List , Diversity LIst , isisforum , Medicinal Chemistry List Cc: "'Guenter Grethe'" , "'Wendy Warr'" Subject: Fifth International Conference on Chemical Structures - Call for Papers Date: Tue, 1 Dec 1998 12:57:51 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain You will find information about the conference and for submitting abstracts at the following URL. http://ChemWeb.com/conference/5iccs/5iccs.html The site will be updated continously as new information becomes available. Hardcopy announcements will not be mailed out. If you plan to present a paper it is recommended to send in your abstracts as soon as possible as this conference fills up early. Guenter Grethe Conference Chairman From chemistry-request@www.ccl.net Tue Dec 1 20:50:40 1998 Received: from teapot06.domain1.bigpond.com (teapot06.bigpond.com [139.134.5.237]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA27176 Tue, 1 Dec 1998 20:50:38 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by teapot06.domain1.bigpond.com (NTMail 3.02.13) with ESMTP id ra820343 for ; Wed, 2 Dec 1998 11:45:30 +1000 Received: from BDIP-T-009-p-235-34.tmns.net.au ([139.134.235.34]) by mail1.bigpond.com (Claudes-Predictive-MailRouter V2.1); 02 Dec 1998 11:45:30 Message-ID: <003e01be1d96$1f1d8200$09007a81@hnlsyd8> Reply-To: "Dr Huang" From: "Dr Huang" To: Cc: Subject: I uploaded my software polar31p.zip to ftp.ccl.net/incoming Date: Wed, 2 Dec 1998 12:50:20 +1100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Polar 3.1 for Windows: electrochemical simulation and data analysis Dr Weiguang HUANG 124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia Phone: 61 2 96620516, 0413 008 019 mailto:polarography@bigfoot.com, showing@bigfoot.com http://www.bigfoot.com/~polarography/ http://showing.home.ml.org It analytically and digitally simulates voltammograms and stripping voltammograms with charge current, resistance and noise on about 20 mechanisms at 8 electrode geometries (planar, spherical, semi-spherical, cylindrical, semi-cylindrical, microdisc, thin film, and rotating electrodes) in 5 techniques (linear sweep and CV, DC, normal pulse, differential pulse, and squre wave voltammetries), and outputs current, resitance, conductivity and surface concentration. Its data analysis include detecting peak area, current and potential, semi-derivative, derivative, intergral, semi-intergral, curve fitting, and separating overlapped peaks. It shows tip when the user put mouse cursor over a lable. The progrom can separate overlapped voltammograms into individuals, and extract real peak from voltammogram with noise and baseline. It outputs the theoretical peak values, the peak current and potential, and current-potential data, which can be imported into other program (e.g. MS Excel). User can copy-and-paste the voltammogram into his document. It has been successfully applied to fit experimental polarograms (voltammograms) of In(III), Cd(II), Pb(II), Tl(I), Cr(III). Zn(II), and binuclear copper complex in aqueous and non-aqueous media at mercury, solid metal and non-metal electrodes (specifically the dropping mercury, hanging mercury drop, gold, platinum and glassy carbon electrodes) by various electrochemical techniques (differential pulse, sqware wave, and pseudo-derivative normal pulse polargraphies) [1]. It runs on IBM PC under Windows 95/98/NT, available from the author or download from my Web site. REFERENCES [1] W. Huang, T. Henderson, A.M. Bond and K.B. Oldham, Curve fitting to resolve overlapping voltammetric peaks: model and examples, Anal. Chim. Acta, 1995, 304, 1-15.