From nobes@fujitsu.co.uk Wed Aug 7 03:15:57 1996 Received: from fujitsu.co.uk for nobes@fujitsu.co.uk by www.ccl.net (8.7.5/950822.1) id DAA10254; Wed, 7 Aug 1996 03:08:35 -0400 (EDT) Received: by fujitsu.co.uk (4.1/SMI-4.1) id AA13302; Wed, 7 Aug 96 08:08:34 BST Received: from kinsei.fujitsu.co.uk(194.33.32.53) by phoenix.fujitsu.co.uk via smap (V1.3) id sma013298; Wed Aug 7 08:07:30 1996 Received: by kinsei.fujitsu.co.uk (SMI-8.6/SMI-SVR4) id IAA27393; Wed, 7 Aug 1996 08:03:27 +0100 From: nobes@fujitsu.co.uk (Ross Nobes) Message-Id: <199608070703.IAA27393@kinsei.fujitsu.co.uk> Subject: Re: CCL:M:Serious errors in MOPAC93 (2) To: tp@elptrs7.rug.ac.be (Park Tae-Yun) Date: Wed, 7 Aug 1996 08:03:27 +0100 (BST) Cc: chemistry@www.ccl.net In-Reply-To: from "Park, Tae-Yun" at Aug 6, 96 06:42:33 pm X-Mailer: ELM [version 2.4 PL25] Content-Type: text Park, Tae-Yun writes: > > I found that according to MOPAC93, the following two > alkanes have the Delta_Hf values (by AM1 parameter), > > > > C-C-C-C-C-C-C-C HEAT OF FORMATION = -58.62036 KCAL > > > C C > C-C-C-C-C HEAT OF FORMATION = -46.93710 KCAL > C > > > which means that normal alkane is more stable than branched > alkane; nonsense! > Dear Tae-Yun, It might pay to use PM3 in preference to AM1 in these studies. For example, according to J.J.P. Stewart (Journal of Computer- Aided Molecular Design, 4 (1990) 1), AM1 makes n-pentane 2.9 kcal/mol too stable but makes neopentane 7.5 kcal/mol too UNstable. In comparison, PM3 makes both n-pentane and neopentane too unstable, by 0.6 and 4.5 kcal/mol respectively. So the error in the relative energies is reduced from 10.4 to 3.9 kcal/mol on going from AM1 to PM3. Best wishes, Ross Nobes -- +---------------------------------------------------------------------+ | Ross Nobes | | Research Fellow | | Fujitsu European Centre for Information Technology | | 2 Longwalk Road Phone: +44 181 606 4417 | | Stockley Park Fax: +44 181 606 4422 | | Uxbridge UB11 1AB, UK E-mail: nobes@fujitsu.co.uk | +---------------------------------------------------------------------+ From P.E.Young@dl.ac.uk Wed Aug 7 07:15:59 1996 Received: from mserv1.dl.ac.uk for P.E.Young@dl.ac.uk by www.ccl.net (8.7.5/950822.1) id GAA10956; Wed, 7 Aug 1996 06:54:39 -0400 (EDT) Received: from tcxs1.dl_sun_server by mserv1.dl.ac.uk with SMTP id LAA28792 (8.6.13/5.3[ref postmaster@dl.ac.uk] for dl.ac.uk from P.E.Young@dl.ac.uk); Wed, 7 Aug 1996 11:54:35 +0100 Precedence: first-class Received: by tcxs1.dl_sun_server (4.1/SMI-4.1) id AA09452; Wed, 7 Aug 96 11:53:03 BST Date: Wed, 7 Aug 96 11:53:03 BST From: P.E.Young@dl.ac.uk (P. Young) Message-Id: <9608071053.AA09452@tcxs1.dl_sun_server> To: chemistry@www.ccl.net Subject: CCP1 Study Weekend - Final Call CCP1 Study Weekend Topic Quantum Theory of Large Systems Date: Dinner Fri. 20 Sept. to Lunch Sun. 22 Sept. 1996 Application and Registration: Deadline 1 Sept 1996 Venue: Daresbury Laboratory, Daresbury, Warrington UK Scope of Meeting: Approximately every two years, the UK CCP1 (Collaborative Computational Project 1: Electronic Structure Methods) organises a "Study Weekend". These are very informal meetings (maximum 40 participants) that are organised around topics that may form the basis of future collaborative work in CCP1. The previous meeting was organized on Hybrid methods. The meeting this year at Daresbury is focussed on methods (mainly ab initio) for studying large molecules. Thus the scope of the meeting includes DFT theory, the coulomb problem, fast multipole methods, distributed multipole methods and related techniques. Speaker Topic P. Gill Circumventing the Coulomb Problem (Cambridge and Massey University NZ) G. Scuseria Linear Scaling Electronic Structure Methods (Rice Univ. Houston) for Large Molecules T. Ziegler Beating the Heavy Metal Blues with DFT (Calgary) N. Burton Molecular Electronic Structure Calculations (Manchester) Employing a Plane-Wave Basis: A Comparison With Gaussian Basis Calculation I. Gould Modelling Chlorophyll in solution: Experiment (Imperial College) and Theory in Unison M. Guest The Treatment of Large Molecular Systems; (Daresbury) NWchem and Fully Distributed Parallel Applications C. Reynolds Theoretical and Experimental Studies on (Essex) Cobalt-Based Bioreductive Anti-Cancer Agents V. Saunders Hartree-Fock Theory for Crystals of Large (Daresbury) Unit Cell. A. Stone Intermolecular Forces between Large Molecules (Cambridge) There will also be an "informal" poster session. Please send a title with your registration if you wish your poster title to appear in the programme. Accomdation will be in the Park Royal International Hotel in Stretton near Warrington. The hotel is located 12 minutes from Manchester Airport, 1 minute from Junction 10 of the M56, 5 minutes from Junction 20 of the M6 and midway between the cities of Chester, Liverpool and Manchester. The attendance fee is 110 pounds which includes accomodation, meals and transport to and from Daresbury Laboratory to the hotel. For those who do not require accomodation, the attendance fee is 15 pounds or 30 pounds if you wish to attend the evening meal on the Saturday. Registration enquiries and application forms to be sent to Dr. Phill Young, Daresbury Laboratory, Daresbury, Warrington, WA4 4AD e-mail p.e.young@dl.ac.uk phone +44-(0)1925-603657 fax +44-(0)1925-603634 Informal enquiries to Professor M. A. Robb, Chemistry Department,King's College London, Strand, London WC2R 2LS e-mail m.a.robb@kcl.ac.uk phone +44-(0)171-873-2098 fax +44-(0)172-873-2810 ------------------------------------------------------------------------------- R E G I S T R A T I O N F O R M Name: _____________________________________________________________________ Address: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Email: _________________________________ I will require accomodation at the hotel. (110 pounds) (Yes/No)* I will attend the workshop during the day only (15 pounds) (Yes/No)* I will attend the workshop during the day and wish to attend the evening meal on Saturday (30 pounds) (Yes/No)* Total amount enclosed:________________________ (Please make cheques payable to DARESBURY LABORATORY) Please indicate any dietery requirements below. _____________________________________________________________________ _____________________________________________________________________ From 94970459@tolka.dcu.ie Wed Aug 7 08:15:58 1996 Received: from tolka.dcu.ie for 94970459@tolka.dcu.ie by www.ccl.net (8.7.5/950822.1) id IAA11202; Wed, 7 Aug 1996 08:14:36 -0400 (EDT) Received: by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA32034; Wed, 7 Aug 1996 13:15:15 +0100 Date: Wed, 7 Aug 1996 13:15:15 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: HChem User , HChem Supp , CCL Every Subject: HyperChem and Schakal Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would be much obliged if anyone tell me if there is a file format which is compatible with both HyperChem and Schakal. Thank you in anticipation for your help. Regards, Paddy. Paddy Kane Dublin City University 94970459@tolka.dcu.ie --------------------------------------------- --------------------------------------------- From katrien@uia.ua.ac.be Wed Aug 7 11:15:59 1996 Received: from inch.uia.ac.be for katrien@uia.ua.ac.be by www.ccl.net (8.7.5/950822.1) id KAA12239; Wed, 7 Aug 1996 10:59:03 -0400 (EDT) Received: by inch.uia.ac.be; (8.7.1/1.1.8.2/22Feb95-0943AM) id QAA07970; Wed, 7 Aug 1996 16:57:18 +0200 (MET DST) Date: Wed, 7 Aug 1996 16:57:17 +0200 (MET DST) From: "Katrien.Franckaerts" X-Sender: katrien@inch.uia.ac.be To: CHEMISTRY@www.ccl.net Subject: electron density in MP2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am searching for the explicit formula representing the Moller Plesset second order electron density correction (for closed shell systems)??? Where can I find good information about this subject??? Katrien Email: katrien@uia.ua.ac.be Adress: Franckaerts Katrien University of Antwerp (UIA) Universiteitsplein 1 2610 Wilrijk Belgium From Matthew.Harbowy@unilever.com Wed Aug 7 12:16:04 1996 Received: from gatekeeper.homecare.com for Matthew.Harbowy@unilever.com by www.ccl.net (8.7.5/950822.1) id LAA12703; Wed, 7 Aug 1996 11:55:37 -0400 (EDT) Received: from x500mhub.lo.u1388.unilever.com by gatekeeper.homecare.com (5.65v3.2/1.1.8.2/24Jan95-0439PM) id AA02681; Wed, 7 Aug 1996 16:55:06 +0100 X400-Received: by /c=GB/admd=telemail/prmd=Unilever/; Relayed; 07 Aug 1996 16:54:45 +0100 X400-Received: by mta MTAandromeda in /c=GB/admd=telemail/prmd=Unilever/; Relayed; 07 Aug 1996 16:54:45 +0100 X400-Mts-Identifier: [/c=GB/admd=telemail/prmd=Unilever/; 030103208BC45234-MTAandromeda] Content-Identifier: 030103208BC45234 Content-Return: Allowed X400-Content-Type: P2-1988 ( 22 ) Conversion: Allowed Original-Encoded-Information-Types: IA5-Text Priority: normal Disclose-Recipients: Prohibited Alternate-Recipient: Allowed X400-Originator: Matthew.Harbowy@unilever.com X400-Recipients: non-disclosure; Message-Id: <030103208BC45234*/c=gb/admd=telemail/prmd=unilever/o=unilever/ou=andromeda/ou=ccmail/s=Harbowy/g=Matthew/@MHS> Date: 07 Aug 1996 16:54:45 +0100 From: "Matthew Harbowy" To: "chemistry@www.ccl.net" (Return requested) (Receipt notification requested) Cc: "hyperchem@hyper.com" (Return requested) Return-Receipt-To: "Matthew Harbowy" Subject: Branched vs straight chain alkanes Mime-Version: 1.0 In the Handbook of Chem and Physics, it reports octane: -49.82 2,2,3,3,TMB: -53.99 My results for AM1 and MM+ show (Hyperchem 3.0 calculations) am1 mm+ exp octane -58.628 (6.448 s.e.) -49.82 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 ------------- ---------- -------------- ------------ oct - tmb -18.473 -5.912 4.17 So, yes, it would seem that both semi-empirical systems *and* molecular mechanics (which should work great) fail to reproduce the experimental figures. Or, I've made a mistake. -matt From owner-chemistry@ccl.net Wed Aug 7 13:16:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id NAA13218; Wed, 7 Aug 1996 13:03:57 -0400 (EDT) Received: from europe.std.com for jle@world.std.com by bedrock.ccl.net (8.7.5/950822.1) id NAA22718; Wed, 7 Aug 1996 13:03:10 -0400 (EDT) Received: from world.std.com by europe.std.com (8.7.5/BZS-8-1.0) id NAA16477; Wed, 7 Aug 1996 13:03:08 -0400 (EDT) Received: by world.std.com (5.65c/Spike-2.0) id AA06987; Wed, 7 Aug 1996 13:01:39 -0400 Date: Wed, 7 Aug 1996 13:01:39 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199608071701.AA06987@world.std.com> To: chemistry@ccl.net Subject: Looking for pointers for analytical derivs in torsional space Folks, Does anybody have information/pointers, etc. on work involving analytical expressions for molecular mechanics functions in terms of torsional space? Things like VdW and Charge derivatives/gradients vs. rotation about the torsional angle... I'll summarize if there's sufficient interest! THanks in advance, Joe Leonard jle@world.std.com From takeuchi@ibc.wustl.edu Wed Aug 7 13:24:56 1996 Received: from wugate.wustl.edu for takeuchi@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id MAA13095; Wed, 7 Aug 1996 12:45:29 -0400 (EDT) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id LAA15360; Wed, 7 Aug 1996 11:45:19 -0500 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id LAA29075; Wed, 7 Aug 1996 11:45:11 -0500 Date: Wed, 7 Aug 1996 11:45:11 -0500 (CDT) From: Yasuo Takeuchi To: CCL cc: Felice Chu , Franca FRATERNALI Subject: Summary of Fe(III) parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I posted the following question: > Dear CCL'ers: > > I would like to calculate the compound which have Fe(III) by MM3 or > AMBER. Does anybody know Fe(III) parameters or literatures? The > compound is; > > O---------- > | Ar > ---O----------O--- > Ar | Fe(III) | > ---O----------O--- > | Ar > O---------- > > Any suggestions are welcomed. Thanks in advance. Hereby, I summerized the answers from many CCLers, which gave me a great help. I got three following literatures about Fe(III) parameters: 1. Lin, W. et al. Inorg. Chem. 1994, 33, 884. 2. Bernhardt, P. V. et al. Inorg. Chem. 1992, 31, 2638. 3. Bouraoui, A. et al. J. Chem. Soc., Perkin Trans. 1990, 2, 1211. Thanks a lot to every one. Sincerely, Yasuo Takeuchi ---------------------------------------------------------------- Yasuo Takeuchi, Ph.D. Institute for Biomedical Computing takeuchi@ibc.wustl.edu Washington University, Box 8036 FAX 314-362-0234 700 South Euclid Avenue PHONE 314-362-2273 St. Louis, MO 63110-1012 U.S.A. ****************************************************************** Date: Thu, 01 Aug 1996 16:42:13 -0700 (PDT) From: Wayne Steinmetz To: takeuchi@ibc.wustl.edu Subject: calculations on your iron(III) complex You suggested molecular mechanics as your method of choice. Have you considered semi empirical molecular orbital methods? Warren Hehre of Wavefunction, Inc. has done an excellent job of parameterizing transition metal elements. His flagship product Spartan is easy to use. ******************* Date: Fri, 2 Aug 1996 09:52:01 GMT+1 From: "Dr. Uwe Schmitz" To: Yasuo Takeuchi Subject: Re: CCL:Fe(III) parameters Dear Yasuo Takeuchi: This is probably of interest for you. What is MOMEC? MOMEC is a molecular mechanics system that has been developed for strain energy minimisation of metal complexes and operates in a Microsoft Windows environment. It has a number of features that facilitate its application to a wide variety of problems and features that are not available in most molecular mechanics programs. It is designed to be used in conjugation with HyperChem. MOMEC 1.0 offers: - Graphical input and output through HyperChem. - A choice of either conjugate gradients or full matrix Newton Raphson refinement or a combination of the two methods. - True constraints of internal coordinates. Raphson refinement or a combination of the two methods. - True constraints of internal coordinates. - Selective inclusion of 1,3-interactions. - Modeling of coordination geometries by either intraligand repulsion, electrostatic interactions, ligand field based electronic functions or a combination of various methods. - An existing extensive force field for metal complexes. - An editor for force field parameters and data files. - Ready extension to new systems. - Run of batch jobs. - Additional modules are available for applications in conjunction with MOMEC and/or HyperChem include Jahn-Teller, Energy and Conversion. - Implemented parameter sets: Ti, Cr, Fe, Co, Ni, Cu, Zn, Rh, Pt Additional parameters are under development. What is Provided? MOMEC is an Microsoft Windows program. It is designed to accept input >from HyperChem and produce output readable by HyperChem. MOMEC has a Windows surface that can be used to set up and modify the MOMEC control file, to modify force field parameters, coo r dinates and atom types, to run MOMEC either interactively or as a batch job, to look at a summary of any MOMEC run and examine errors that occurred during the strain energy minimisation, to run various other modules that are available for the use in conj u nction with MOMEC, and to launch HyperChem with or without the most recently minimised structure in the workspace. Additional modules available for applications in conjunction with MOMEC and/or HyperChem include Jahn-Teller (structural optimisation of Jahn-Teller distorted hexacoordinate compounds), Energy (computation of energy as a function of constrained internal c oordinates) and Conversion (input and output of structure files in various formats such as cartesian coordinates SCHAKAL, SHELX, CSD, ORTEP, MacroModel etc.). Additional modules are under development. See also: Peter Comba, Trevor W. Hambley; Molecular Modeling of Inorganic Compounds (1995), VCH Publishers (Weinheim); ISBN 3-527-29076-1 ------------------------------------------------------- | academic users | profit users | ------------------------------------------------------- | intern. | Germany | intern. | Germany | |Product US $ | DM | US $ | DM | |Product US $ | DM | US $ | DM | -----------------------|--------------------|---------- |MOMEC 1.0 1L 615.- | 800.- | 1230.- | 1600.- | |MOMEC 1.0 2L 1154.- | 1500.- | 2307.- | 3000.- | |MOMEC 1.0 3L 1615.- | 2100.- | 3231.- | 4200.- | |MOMEC 1.0 4L 2000.- | 2600.- | 4000.- | 5200.- | |MOMEC 1.0 5L 2307.- | 3000.- | 4615.- | 6000.- | |MOMEC 1.0 10L 3846.- | 5000.- | 8462.- | 11000.- | ------------------------------------------------------- !!! prices exclusive taxes and shipping !!! We will be establishing a dealer channel around the world. In the moment you are kindly asked to purchase the products from Germany. If you require more information send us an email with your questions and address. Regards Uwe Schmitz ------------------------------------------------------------------ Dr. Uwe Schmitz Email: schmitz@docadchem.com Mobile: +49 (171) 3116631 ALTENHOFF+SCHMITZ Westfalendamm 35 Tel: +49 (231) 421575 D-44141 Dortmund FAX: +49 (231) 414963 Germany WWW: http://www.docadchem.com/ http://www.asw.topnet.de/ ------------------------------------------------------------------ Have a look at our restyled WEB pages URL http://www.docadchem.com 1. August 1996 *********************** Date: Fri, 02 Aug 1996 10:16:50 -0500 From: Lipkowitz To: Yasuo Takeuchi Subject: RE: CCL:Fe(III) parameters I compiled a list of published MM parameters. Maybe what you're looking for is in that list. See Reviews in Computational Chemistry, Volume 6, 1995, VCH Publishing Co. *********************** From sichelj@Umoncton.CA Wed Aug 7 14:16:01 1996 Received: from bosoleil.ci.umoncton.ca for sichelj@Umoncton.CA by www.ccl.net (8.7.5/950822.1) id NAA13423; Wed, 7 Aug 1996 13:33:15 -0400 (EDT) Received: by bosoleil.ci.umoncton.ca (1.37.109.16/16.2) id AA153009285; Wed, 7 Aug 1996 14:34:45 -0300 Date: Wed, 7 Aug 1996 14:34:45 -0300 (ADT) From: "John-M. Sichel" Subject: Re: CCL:electron density in MP2 To: "Katrien.Franckaerts" Cc: CHEMISTRY@www.ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII See I.N.Levine, Quantum Chemistry, 4th edn (1991), p.511-5 (2) (0) 2 The formula is: E = Sum || 0 s not 0 s 0 -------------------- (0) (0) E - E 0 s with symbols as defined in Levine. On Wed, 7 Aug 1996, Katrien.Franckaerts wrote: > Hi, > > I am searching for the explicit formula representing the Moller Plesset > second order electron density correction (for closed shell systems)??? > Where can I find good information about this subject??? > > Katrien > > Email: katrien@uia.ua.ac.be > Adress: Franckaerts Katrien > University of Antwerp (UIA) > Universiteitsplein 1 > 2610 Wilrijk > Belgium > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: katrien@uia.ua.ac.be > -- Original Sender From: Address: katrien@uia.ua.ac.be > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada E1A 3E9 Tel: (506-)858-4313 E-mail: SICHELJ@UMONCTON.CA I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. (Gaussian92) From peon@medchem.dfh.dk Wed Aug 7 14:22:08 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.7.5/950822.1) id NAA13330; Wed, 7 Aug 1996 13:21:02 -0400 (EDT) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.4/8.6) with SMTP id NAA19263 for <@danpost.uni-c.dk:chemistry@www.ccl.net>; Wed, 7 Aug 1996 13:23:00 -0400 (EDT) Received: from [130.225.177.59] by medchem.dfh.dk via SMTP (940816.SGI.8.6.9/940406.SGI) for id TAA27598; Wed, 7 Aug 1996 19:28:36 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 7 Aug 1996 19:21:02 +0200 To: chemistry@www.ccl.net From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:Branched vs straight chain alkanes Matthew Harbowy wrote: > My results for AM1 and MM+ show (Hyperchem 3.0 calculations) > > am1 mm+ exp > > octane -58.628 (6.448 s.e.) -49.82 > > 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 > > ------------- ---------- -------------- ------------ > > oct - tmb -18.473 -5.912 4.17 > > > So, yes, it would seem that both semi-empirical systems *and* > molecular mechanics (which should work great) fail to reproduce the > experimental figures. The semi-empirical results are one thing, the molecular mechanics something completely different. You *CANNOT* use molecular mechanics steric energies as heats of formation. In fact, you can only compare molecular mechanics steric energies when you have identical connectivities. Naturally the steric energy of tmb is higher than oct, it is much more congested. Of the molecular mechanics programs I'm aware of, only the true MM2 and MM3 from Allinger are able to estimate heats of formation. (I don't think any of the various MM2-copies out there includes this feature). Even in the Allinger programs, this feature is limited to a small number of structural features for which corrections have been included. However, the alkanes are there. The MM2(91) values for octane and tmb are given below (in kcal/mol) steric energy heat of formation octane (all trans) 4.7433 -53.59 tmb 11.7932 -54.00 As you can see, the trend is right. I believe the value for octane will get closer to the experimental value if you include the contributions >from other conformations. As for the AM1 values, energy errors average 1-2 kcal/mol even when you compare conformations (Gundertofte et al, J.Comp.Chem. 12, 200, 1991), so isomeric energies should have larger errors. I'm a bit surprised by an error of over 20 kcal/mol though, I had expected better. Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From Alan.Shusterman@directory.Reed.EDU Wed Aug 7 14:27:21 1996 Received: from reed.edu for Alan.Shusterman@directory.Reed.EDU by www.ccl.net (8.7.5/950822.1) id OAA13736; Wed, 7 Aug 1996 14:10:52 -0400 (EDT) Received: from isis.Reed.EDU [134.10.2.1 no identification] by reed.edu (/\oo/\ Smail3.1.29.1 #29.5) id ; Wed, 7 Aug 96 11:10 PDT Message-id: <1539076@isis.Reed.EDU> Date: 07 Aug 96 11:10:52 PDT From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: CCL: Branched vs straight chain alkanes To: chemistry@www.ccl.net --- Matthew Harbowy wrote: So, yes, it would seem that both semi-empirical systems *and* molecular mechanics (which should work great) fail to reproduce the experimental figures. Or, I've made a mistake. --- end of quote --- A number of comments (such as the one above) regarding AM1 and MM+, and their apparent inability to reproduce the effect of branching on experimental heats of formation are misplaced. First, molecular mechanics strain energies (MM+) should never, by themselves, be used to compare heats of formation of geometric isomers, such as octane and 2,2,3,3-tetramethylbutane. Different parameters are used to calculate the strain energies of geometric isomers. Therefore, even if both isomers were calculated to have identical energies they might still have different heats of formation. Strain energy comparisons are only useful for stereoisomers, conformational isomers, and other molecules whose energies are calculated using identical parameters. Second, as has already been remarked by others, AM1 (and PM3) heats of formation do not reproduce experimental heats of formation with arbitrary precision. This was never claimed by the inventors of these methods, and thousands of calculations have borne this out. "Typical" errors for these methods are in the range of 5-10 kcal/mol, but much larger errors are frequently encountered. Third, it is important before complaining about poor computational results to analyze the results correctly. This means taking a good look at the structure of the calculated molecule. Many of the molecular formulas that have recently been attributed to various hydrocarbons and carbocations have been incorrect (note: it is much easier to identify the correct formula when a graphical model is used than when a Z matrix is used, but one must still be careful). Fourth, 2,2,3,3-tetramethylbutane is hardly a typical "branched" hydrocarbon. Although it is highly branched and should, therefore, have a "low" heat of formation, it is also very crowded, and this should raise its heat of formation, i.e., its heat of formation results from compensating factors. This is borne out by the following series of C8 experimental heats of formation: octane (-49.8), 4-methylheptane (-50.7), 2,2-dimethylhexane (-53.7), 2,5-dimethylhexane (-53.2), 2,2,3,3-tetramethylbutane (-54.0). By the way, AM1 provides reasonable estimates of these heats of formation for all but two molecules: octane (-58.5), 4-methylheptane (-54.9), 2,2-dimethylhexane (-51.2), 2,5-dimethylhexane (-53.3), 2,2,3,3-tetramethylbutane (-40.0). Three of the errors are less than 5 kcal/mol, and only one is greater than 10 kcal/mol. Not bad, but not useful for comparing the effects of branching. Unfortunately, while one might have guessed that the most crowded molecule, 2,2,3,3-tetramethylbutane, would be the most difficult to model correctly, one would not have guessed that the most "normal" molecule, octane, would be the next worse in this series. Modeling is not for the careless. Alan Shusterman Department of Chemistry Reed College Portland, OR 97202 From gabriel@jg1.bchem.temple.edu Wed Aug 7 15:16:02 1996 Received: from jg1.bchem.temple.edu for gabriel@jg1.bchem.temple.edu by www.ccl.net (8.7.5/950822.1) id OAA13856; Wed, 7 Aug 1996 14:27:25 -0400 (EDT) Received: by jg1.bchem.temple.edu (931110.SGI/911001.SGI) for CHEMISTRY@www.ccl.net id AA11820; Wed, 7 Aug 96 02:03:46 -0700 Date: Wed, 7 Aug 96 02:03:46 -0700 From: gabriel@jg1.bchem.temple.edu (Dr. Jerome L. Gabriel) Message-Id: <9608070903.AA11820@jg1.bchem.temple.edu> To: CHEMISTRY@www.ccl.net Subject: New Web Site The Department of Biochemistry at Temple University School of Medicine is proud to announce a new web site containing easy access to chemistry and molecular biology related resources. Our new site, entitled "Protein and Nucleic acid Resource Manager" or PNaRM is located at http://www.temple.edu/medbiochem/pnarm.html. We hope that you find this site useful for your work. Jerome L. Gabriel Department of Biochemistry Temple University School of Medicine gabriel@jg1.bchem.temple.edu From topper@cooper.edu Wed Aug 7 15:20:27 1996 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.7.5/950822.1) id PAA14095; Wed, 7 Aug 1996 15:12:12 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA05115 (5.65c/IDA-1.4.4 for ); Wed, 7 Aug 1996 15:13:44 -0400 Received: by zeus.cooper.edu id AA17608 (5.67b/IDA-1.5 for chemistry@www.ccl.net); Wed, 7 Aug 1996 15:10:10 -0400 From: TOPPER ROBERT Message-Id: <199608071910.AA17608@zeus.cooper.edu> Subject: CCL:Branched vs straight chain alkanes To: chemistry@www.ccl.net Date: Wed, 7 Aug 1996 15:10:10 -0400 (EDT) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit On this topic, several articles by DeTar are enlightening, in which he discusses how one can estimate heats of formation from steric energies. See D.F. DeTar, J.Org.Chem.56, p.1463 (1991) and articles thereafter in that volume. Other useful/relevant references are: K.B. Wiberg and J.J. Wendoloski, JACS 104, p.5679 (1982); Wiberg, J.Comput. Chem. 5, p.197 (1984); ibid., J.Org. Chem. 50, p.5285 (1985). and N.L. Allinger,L.R. Schmitz, I. Motoc, C. Bender and J.K. Labanowski, J. Phys. Org. Chem. 3, p.732 (1990). Hope this helps rqt ************************************************************************ Robert Q. Topper email: topper@cooper.edu Asst. Prof. of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ Check out the Molecular Monte Carlo home page! http://www.cooper.edu/engineering/chemechem/monte.html ************************************************************************ From kotelyan@che.udel.edu Wed Aug 7 15:24:01 1996 Received: from che.udel.edu for kotelyan@che.udel.edu by www.ccl.net (8.7.5/950822.1) id OAA14005; Wed, 7 Aug 1996 14:53:44 -0400 (EDT) Received: by che.udel.edu (AIX 3.2/UCB 5.64/4.03) id AA50287; Wed, 7 Aug 1996 14:52:21 -0400 Date: Wed, 7 Aug 1996 14:51:28 +22305133 (EDT) From: Michael Kotelyanskii Subject: Re: CCL:Branched vs straight chain alkanes To: Matthew Harbowy Cc: "chemistry@www.ccl.net" , "hyperchem@hyper.com" In-Reply-To: <030103208BC45234*/c=gb/admd=telemail/prmd=unilever/o=unilever/ou=andromeda/ou=ccmail/s=Harbowy/g=Ma Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Just a silly comment: Are you sure, that the energy is calculated in the LOWEST conformation? I mean global, vs. just a local minimum? Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 On 7 Aug 1996, Matthew Harbowy wrote: > > In the Handbook of Chem and Physics, it reports > > octane: -49.82 > 2,2,3,3,TMB: -53.99 > > > My results for AM1 and MM+ show (Hyperchem 3.0 calculations) > > am1 mm+ exp > > octane -58.628 (6.448 s.e.) -49.82 > > 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 > > ------------- ---------- -------------- ------------ > > oct - tmb -18.473 -5.912 4.17 > > > So, yes, it would seem that both semi-empirical systems *and* > molecular mechanics (which should work great) fail to reproduce the > experimental figures. > > Or, I've made a mistake. > > > -matt > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Matthew.Harbowy@unilever.com > -- Original Sender From: Address: Matthew.Harbowy@unilever.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From rpgrasso@ssnet.com Wed Aug 7 17:16:03 1996 Received: from marlin.ssnet.com for rpgrasso@ssnet.com by www.ccl.net (8.7.5/950822.1) id QAA14789; Wed, 7 Aug 1996 16:33:43 -0400 (EDT) Received: from ss10.ssnet.com (ss10.ssnet.com [205.216.96.60]) by marlin.ssnet.com (8.6.12/8.6.12) with SMTP id QAA03059 for ; Wed, 7 Aug 1996 16:33:04 -0400 Date: Wed, 7 Aug 1996 16:33:04 -0400 Message-Id: <199608072033.QAA03059@marlin.ssnet.com> X-Sender: rpgrasso@ssnet.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: rpgrasso@ssnet.com (Bob Grasso) Subject: beta cyclodextrin coords X-Mailer: Greetings all, I'm looking for the coordinates for beta cyclodextrin. Can anyone help? Thanks, Bob ---------------------------------------------------------------------- Bob Grasso rpgrasso@ssnet.com Hercules Research Center Voice: 302/995-4380 500 Hercules Rd. FAX: 302/995-4117 Wilmington DE 19808-1599 http://ssnet.com/~rpgrasso/homepage.html ---------------------------------------------------------------------- From Matthew.Harbowy@unilever.com Wed Aug 7 17:26:26 1996 Received: from gatekeeper.homecare.com for Matthew.Harbowy@unilever.com by www.ccl.net (8.7.5/950822.1) id QAA14774; Wed, 7 Aug 1996 16:32:05 -0400 (EDT) Received: from x500mhub.lo.u1388.unilever.com by gatekeeper.homecare.com (5.65v3.2/1.1.8.2/24Jan95-0439PM) id AA08007; Wed, 7 Aug 1996 21:31:35 +0100 Received: by x500mhub.lo.u1388.unilever.com; Wed, 7 Aug 96 21:19:08 Z X400-Received: by /c=GB/admd=telemail/prmd=Unilever/; Relayed; 07 Aug 96 21:18:51 Z X400-Received: by mta MTAunilever in /c=GB/admd=telemail/prmd=Unilever/; Relayed; 07 Aug 96 21:18:51 Z X400-Mts-Identifier: [/c=GB/admd=telemail/prmd=Unilever/; 00FF33208FA2B012-MTAunilever] Content-Identifier: 00FF33208FA2B012 Content-Return: Allowed X400-Content-Type: P2-1988 ( 22 ) Conversion: Allowed Priority: normal Disclose-Recipients: Prohibited Alternate-Recipient: Allowed X400-Originator: Matthew.Harbowy@unilever.com X400-Recipients: non-disclosure; Message-Id: <00FF33208FA2B012*/c=gb/admd=telemail/prmd=unilever/o=unilever/ou=ccmail/s=Harbowy/g=Matthew/@MHS> Date: 07 Aug 96 21:18:51 Z From: "Matthew Harbowy" Cc: "chemistry@www.ccl.net" (Return requested) Subject: Re: CCL:Branched vs straight chain alkanes Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART.BOUNDARY.x500mhub.0ff4.3208fa3c.0001" --PART.BOUNDARY.x500mhub.0ff4.3208fa3c.0001 Content-Type: text/plain; charset=us-ascii RFC-822-Headers: Errors-To: ccl@www.ccl.net Precedence: bulk --PART.BOUNDARY.x500mhub.0ff4.3208fa3c.0001 Content-Type: text/plain; charset=us-ascii The modelling results, although they were minima indeed, were intended as a 'careless once-off' in continuations of Tae-Yung Park's ongoing discussion. I wasn't attempting to publish hard numbers, just to back his observation that AM1 did not reproduce reality. I expected better results, to be honest, and so I decided to post them after I calculated them. I fully *expected* my am1 results to mirror the experimental results. As people have suggested, I should not have mentioned the strain energy results in the same breath, and probably should have taken my own advice when I was composing the post and left it out. Indeed, as most have suggested, modelling is not for the careless. Neither is thermodynamics, I might add, since one can couch any variation plus or minus as a combination of conjugation, strain, hyperconjugation, etc., ad-nauseam. To make an argument that I would expect Dewar himself to resound, it isn't the numbers, or how you get them, but what they tell you about the experiments. There's been a lot of noise about the 'accuracy' of the numbers, and getting gradients below 0.01 etc, but not a lot of talk about what the point of doing something like that is. I'm not really sure, other than perhaps eating up computer time, why someone would *want* a gradient to drop from 0.1 to 0.01 or less. What could be so accurate that the inherent error of modelling doesn't swamp? matt ______________________________ Reply Separator _________________________________ Subject: CCL:Branched vs straight chain alkanes Author: chemistry-request@www.ccl.net at INTERNET Date: 8/7/96 3:32 PM Just a silly comment: Are you sure, that the energy is calculated in the LOWEST conformation? I mean global, vs. just a local minimum? Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 On 7 Aug 1996, Matthew Harbowy wrote: > > In the Handbook of Chem and Physics, it reports > > octane: -49.82 > 2,2,3,3,TMB: -53.99 > > > My results for AM1 and MM+ show (Hyperchem 3.0 calculations) > > am1 mm+ exp > > octane -58.628 (6.448 s.e.) -49.82 > > 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 > > ------------- ---------- -------------- ------------ > > oct - tmb -18.473 -5.912 4.17 > > > So, yes, it would seem that both semi-empirical systems *and* > molecular mechanics (which should work great) fail to reproduce the > experimental figures. > > Or, I've made a mistake. > > > -matt > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Matthew.Harbowy@unilever.com > -- Original Sender From: Address: Matthew.Harbowy@unilever.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: kotelyan@che.udel.edu -- Original Sender From: Address: kotelyan@che.udel.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --PART.BOUNDARY.x500mhub.0ff4.3208fa3c.0001-- From chpajt@bath.ac.uk Wed Aug 7 19:16:04 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id SAA15272; Wed, 7 Aug 1996 18:19:18 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Wed, 7 Aug 1996 23:19:14 +0100 Date: Wed, 7 Aug 1996 23:19:10 +0100 (BST) From: A J Turner To: Matthew Harbowy cc: "chemistry@www.ccl.net" Subject: Re: CCL:Branched vs straight chain alkanes In-Reply-To: <00FF33208FA2B012*/c=gb/admd=telemail/prmd=unilever/o=unilever/ou=ccmail/s=Harbowy/g=Matthew/@MHS> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! To answer the point on gradient. You need the gradient at least as low as 0.01 to properly acquire vibrational frequencies. A gradient of 0.1Kcal/angs.mol will give a hessian asymetery of around 0.1% and a gradient of 0.01 will give a asymetry of about 0.01% (easy to remeber) for central finit difference (like that in MOPAC). A gradient of 1.0 will often give incorrect low frequencies - or spurious negative frequencies. My point my be that accuracy and self consistency are not the same thing. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From usdcc2p5@ibmmail.com Wed Aug 7 19:56:31 1996 Received: from ibmmail.COM for usdcc2p5@ibmmail.com by www.ccl.net (8.7.5/950822.1) id TAA15479; Wed, 7 Aug 1996 19:10:11 -0400 (EDT) Received: from JPCANNAD.mp.dowcornusa.com by ibmmail.COM (IBM VM SMTP V2R3) with TCP; Wed, 07 Aug 96 14:48:49 EDT Message-ID: <32090FBA.2E33@ibmmail.com> Date: Wed, 07 Aug 1996 14:50:50 -0700 From: "J. Pat Cannady, Ph.D." Organization: Dow Corning Corporation X-Mailer: Mozilla 2.0 (Win16; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Branched vs. straight chain alkanes X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Matthew Harbowy wrote: > My results for AM1 and MM+ show (Hyperchem 3.0 calculations) > > am1 mm+ exp > > octane -58.628 (6.448 s.e.) -49.82 > > 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 > > ------------- ---------- -------------- ------------ > > oct - tmb -18.473 -5.912 4.17 > To this I should like to add the pm3 results (as suggested earlier) (MOPAC 6): octane: -50.75 2,2,3,3, TMB: -49.96 ------------- oct - tmb: -.79 Thus the better (but still not quite good enough) accuracy of pm3 for this type of system over that of am1 is easily demonstrated. The error relative to experimental for octane is less than 1 kcal, that for TMB just 4 kcal, much better in each case than the am1 values. It has been said elsewhere (check the CCL archive) that when one has a system with "lots of protons", pm3 should be used over am1. I think this is a good example. -- J. Patrick Cannady Dow Corning Corporation jpcannady@dcrn.e-mail.com All opinions expressed are those of the author and not necessarily those of Dow Corning Corporation. From dzirl@nyknicks.asd.sgi.com Wed Aug 7 20:16:07 1996 Received: from sgi.sgi.com for dzirl@nyknicks.asd.sgi.com by www.ccl.net (8.7.5/950822.1) id TAA15704; Wed, 7 Aug 1996 19:53:51 -0400 (EDT) Received: from odin.corp.sgi.com (odin.corp.sgi.com [192.26.51.194]) by sgi.sgi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA07952 for <@external-mail-relay.sgi.com:chemistry@www.ccl.net>; Wed, 7 Aug 1996 16:53:26 -0700 Received: from giraffe.asd.sgi.com by odin.corp.sgi.com via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI) for <@fddi-odin.corp.sgi.com:chemistry@www.ccl.net> id QAA11945; Wed, 7 Aug 1996 16:53:25 -0700 Received: from nyknicks.asd.sgi.com by giraffe.asd.sgi.com via SMTP (931110.SGI/930416.SGI) for @fddi-odin.corp.sgi.com:chemistry@www.ccl.net id AA27604; Wed, 7 Aug 96 16:53:13 -0700 Received: (from dzirl@localhost) by nyknicks.asd.sgi.com (950413.SGI.8.6.12/960327.SGI.AUTOCF) id QAA08751; Wed, 7 Aug 1996 16:53:11 -0700 Date: Wed, 7 Aug 1996 16:53:11 -0700 From: dzirl@nyknicks.asd.sgi.com (David Zirl) Message-Id: <9608071653.ZM8749@nyknicks.asd.sgi.com> X-Mailer: Z-Mail-SGI (3.2S.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Molecular Inventor Workshop at ACS Exposition Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Mark Benzel, the author of Molecular Inventor at Silicon Graphics, will be presenting a workshop at the American Chemical Society Exposition entitled "Programming and Using Molecular Inventor" on Wednesday, August 28, 1996 at 9am in room 221E. If you are attending the exposition, you are encouraged to register and attend. To pre-register please send e-mail with your name, address, e-mail, phone, fax and the name and number of the workshop (#14) to K_poole@acs.org For more information on Molecular Inventor see: http://www.sgi.com/ChemBio/MolecularInventor or send e-mail to chembio@sgi.comm ----------------------------------------------------------------------------- Workshop # 14: Programming and Using Molecular Inventor(TM). Sponsor: Silicon Graphics, booths 300-302. Instructor: Mark Benzel. August 28, 9am-noon. Room 221E in the Orange County Convention Center, Orlando, Florida. Molecular Inventor is a set of extensions to Open Inventor which simplifies the development of molecular graphics applications. In addition, it specifies extentions to the Open Inventor file format which allow the transfer of chemical data between applications and the display of the data even in applications which have no knowledge of chemical systems. The features of Molecular Inventor include optimized rendering of molecular structures, advanced selection and highlighting mechanisms and generation of isosurfaces and 3D contours. This session will discuss the basic architecture of Molecular Inventor and how to use it to create applications. Use of Molecular Inventor with Silicon Graphics collaborative tools will also be presented.