From ahocquet@tamarugo.cec.uchile.cl Wed Mar 26 00:31:50 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id XAA09858; Tue, 25 Mar 1997 23:34:21 -0500 (EST) Received: from 146.83.10.50 ([146.83.10.50]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA18240; Wed, 26 Mar 1997 01:32:00 +0400 Message-Id: <33387CFF.3FD2@cec.uchile.cl> Date: Wed, 26 Mar 1997 01:33:54 +0000 From: Alexandre Hocquet Reply-To: ahocquet@tamarugo.cec.uchile.cl Organization: Universidad de Chile X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: the MM2 family summary Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Estimados CCLers, here is a summary of answers to my MM2 census. Thank you to all that answered, especially Jay Ponder and Per Ola Norrby. The original question is quoted first. -------------------------- I am currently attempting to make a census of the MM2 versions, those natural sons that are based upon, but not identical to (they are no clones) one of the official Allinger's MM2 = versions. Of course they are thousands if one counts as a new version a MM2 to which were added a few parameters. For the purposes of my inventory, i will define a *different* version, one that differs in : - the equations of the force field terms (stretch, Van der Waals...) - the definitions of the nonbonded terms (point charges for bonds dipoles) - the treatment of conjugation - evaluating parameters that are not defined - recognizing substructures - treatment of strucures with more than 4 bonds attached to an atom Taking (Gundertofte et al., J.Comput.Chem., 1996, p429) as a starting point, i can name : MM2*(Macromodel) : Mohamadi et al., J.Comput.Chem., 1990, p440 "MM2" (Chem3D) : no reference MMX (PC model) : Gajewski et al., Advances in Molecular Modeling, Liotta Ed, JAI Press, Greenwich, CT, 1990 **If someone has a reprint of this reference, i am highly interested** an MMP2 variant : Liljefors et al., J.Comput.Chem., 1985, p478 Furthermore i can quote : MM+ (Hyperchem) : no reference MM2X (Optimol) : Holloway et al., J.Med.Chem., 1995, p305 If you know others, please let me know. Also, if you know other criteria that could be pertinent to define a *different* version, do not hesitate either. ---------------------------- Dear Alexandre, I have completed this task by analysing and comparing of the original MM2, MMX within the PCMODEL, MM2 within Spartan and MM2 within the OFF of the Cerius2 by MSI. The work will be published soon. = The main conclusion was that each implementation has something special what the others does not have (conjugation, treatment of vdW interactions, source of the atomic point charges and/or bond dipole moments or increments). = Therefore, if you want to move from one software to another you should take care for the parameters. Well, it will be a really hard work - I know - and let me know if you need any help or you want to have the results of the Open Force Field within Cerius2 or the Spartan. Furthermore, if you are not aware from working together via electronically I am happy to join to you! -- = = ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi Mueller Laboratory ph.d. student Dept. Organic Chemistry University of Veszprem szilagyi@mm2.vein.hu Veszprem, H-8201 POB. 158; Egyetem u. 10. Phone: +36 88 422022 extn. 395 HUNGARY Mobile: +36 20 461413 Fax: +36 88 427492 http://mm1.vein.hu/ = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Para aniadir a tu lista: MM2 (Molgen) Molgen es un programa de modelizacion molecular que funciona bajo MS-DOS. Entre sus capacidades se cuenta la minimizacion con el campo de fuerzas MM2. Hasta hace poco era distribuido en los USA por Eric Slone, pero recientemente ha pasado a ser de dominio publico y puede obtenerse en los archivos del CCL: http:/www.ccl.net/ccl/software.html Un saludo. Jose I. Garcia The list of MM2s you gave is a good starting point. I do have a few additions. First, I think you should list all the cases where Allinger himself drastically changed the functional form. The original version is MM2(77), and MMP2 came as a separate program in 1980 (I think, I'm not entirely sure of all dates I'll give below). The MM2(85) combined MM2 and MMP2 into one program, so that is a functional change. With this version, MM2 reached a kind of maturity plateau. There were later changes, but not any drastic improvements in overall performance. There were new versions in 1987 and 1991, and at least the MM2(87) version included changes in functional form. There are many "minor" functions in MM2, like electronegativity effect and anomeric effect, I cannot say for sure when they were added, but I believe that all were in MM2(87). I think MM2(91) was just a parameter update, but I'm not sure. In 1994 was published the parameter estimator for MM2 (and MM3), "J. Mol. Struct (THEOCHEM) 312 (1994) 69-83", but I haven't seen an implementation for MM2 (it is in MM3[94]). Other implementations: TINKER, from Jay Ponder (info at http://dasher.wustl.edu/) The Chem3D parameters were originally from TINKER You lacked a reference for Chem3D, see: http://www.camsci.com/ CAChe from Tektronix has an "augmented" MM2. Spartan from Wavefunction includes an MM2 with the original parameter set, but no conjugated calculations! A bit dangerous, but... See: http://www.wavefun.com/ In the MacroModel manual I also found references to Osawa, "Tet, 2769 (83)", and Kroon-Batenburg, "JMolStr, 417 (83)", I don't know if both qualify as separate implementations according to your rules. I know that several workers in the inorganic/organometallic field have extended MM2 to higher coordination. You could use the review by Benjamin Hay as a starting point, "Coord. Chem. Rev. 126, 177-236 (1993)". Many (I'm among them) have also solved special coordinations in MM2 without changes to the functional form using tricks like dummy atoms and fixed atoms, I don't know if that qualifies ( MM2 definitely wasn't INTENDED to be abused so, that's for sure... :-). Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * 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/ Dear Alexandre Hocquet, I can tell you something about one "family" of MM2 versions. The code distributed as "MM2" in the Chem3D package is actually my code written completely from scratch and based on MM2 circa 1987. It is IDENTICAL to "real" MM2 in all basic functional forms with the following exceptions: (1) It adds a quartic term to the bond stretch (just the next term in the Taylor expansion of the Morse potential, "real" MM2 uses the first two, harmonic and cubic, while we added the quartic). This has essentially no effect on minimum energy structures and energies (often less than 0.0001 kcal difference), but was added to make molecular dynamics stable, exp. at high temperature. Allinger's group has added this same term to MM3. (2) Our "MM2" uses the identical dipole-dipole term to real "MM2", but it also allows (in addition) use of partial charges (needed, for example to get the correct formal charge on a carboxylate, etc.). Then our code actually does electrostatics as a sum of the dipole-dipole, charge-charge and charge-dipole interactions. Again this same mechanism was subsequently implemented in MM3. (3) Our code uses a "hybrid" method for conjugated systems that is somewhat intermediate between the old MMPI and "real" MMP2. We use a straight PPP MO method instead of the "variable electroneg" style method, and we have calibrated the internal parameters to give good results on a number of kinds of heterocycles. The overall differences in results from MMP2 are small, but not zero. (4) Our code does not implement any of the special "parameter tweaking" terms that are in MM3 and in some versions of MM2, things like the electronegativity effect, anomeric effect, Bohlmann effect, etc. A later version of our MM2 (as well as an MM3 semi-clone) is available in the free molecular mechanics/dynamics package TINKER, which can be obtained with source code from http://dasher.wustl.edu/tinker. We have added many, many other options, parameter sets, etc., but it is possible to get TINKER to give a pretty authentic rendition of MM2 by turning off the bells and whistles. Hope this helps, Jay Ponder -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ Dear Alexandre Hocquet, I do not know whether this belongs to the list you plan to make. I have one version of the MM2 program with conformational search procedure, MC-MM2, Tetrahedron, 51, 6789 (1995). The force field (equations and constants) is inchanged original MM2(87). The DRIVER subroutine is supplemented by Monte Carlo type routine to enable searching of the conformational space by random variation of randomly selected torsional angles. Besides I think that Osawa published MM2' in Tetrahedron with some new parameters. Best regards. Sincerely, Ljiljana Dosen-Micovic, e-mail: LMICOVIC@hf01.chem.bg.ac.yu Faculty of Chemistry University of Belgrade Belgrade, Yugoslavia -- = Alexandre Hocquet Laboratorio de Cristalograf=EDa Facultad de Ciencias F=EDsicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro Chile fono : 56 2 678 45 19 fax : 56 2 696 73 59 email : ahocquet@cec.uchile.cl >From jkl@ccl.net Wed Mar 26 00:58 EST 1997 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.3/950822.1) id AAA01171; Wed, 26 Mar 1997 00:58:19 -0500 (EST) Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id AAA09490; Wed, 26 Mar 1997 00:58:19 -0500 (EST) From: Jan Labanowski Date: Wed, 26 Mar 1997 00:58:19 -0500 (EST) Message-Id: <199703260558.AAA09490@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Call for Abstracts (Internet in Chem - LasVegasACS - Sept.97) Cc: jkl@ccl.net CALL FOR ABSTRACTS ================== American Chemical Society Computers in Chemistry Division (COMP) "Internet for the Practicing Chemist" 214th National American Chemical Society Meeting Las Vegas, NV, September 7-11, 1997 Division of Computers in Chemistry (COMP) of the American Chemical Society cordially invites you to present a paper at the symposium "Internet for the Practicing Chemist" to be held at the National ACS Meeting in Las Vegas, Sept. 7-11, 1997. ABSTRACT MUST BE RECEIVED BEFORE APRIL 18, 1997. The scope of the symposium is broadly defined as "Use of Internet in Chemistry" and possible topics include (listed here without any priority in mind): Internet in education and distance learning, legal and business aspects of the Internet, standards and applications for publishing and presenting information on the Internet (e.g., CGI, CML, HTML, Java, JavaScript, MIME, VRML, etc., etc.), tools for conferences and collaboration over the Internet, managing information resources on the Internet, research uses of the Internet, and studies on the impact of Internet in chemistry. Please indicate how much time should be allocated for your presentation, and what special equipment you may require. I would like to encourage authors to prepare material for their presentation in Web form. The details of depositing this material will be provided to the authors at a later date. The abstracts should be submitted on the original abstract form (please submit 4 copies). You can obtain this form electronically (an MS-WORD template) from: http://www.acs.org/meetings/abstract/abinfo.html or request the hardcopy >from ACS via e-mail (abstract@acs.org) or Web (http://www.acs.org/meetings/abstract/abrqst.html). If nothing works, I may try to retype a few abstracts (Max. 150 Words!!!) on the original form if I get them early enough and in an electronic form (plain text). Include all additional information requested on the form, i.e., names and addresses of all coauthors, presenting author phone, FAX, and e-mail, and ACS Division membership. The COMP Division does not provide financial support for travel expenses for speakers. However, if you have some prospective sponsors, they will get due credit and acknowledgment during the symposium, their support will be acknowledged in the Web site resulting from the symposium, and I will be more than willing to write a solicitation letter as a Session Chairman to the prospective sponsor. Please contact me if such an opportunity exists in your case. Jan Labanowski Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43212 e-mail: jkl@ccl.net FAX: 614/292-7168 Phone: 614/292-9279 From jeonghy@camd1.kkpcr.re.kr Wed Mar 26 03:31:52 1997 Received: from camd1.kkpcr.re.kr for jeonghy@camd1.kkpcr.re.kr by www.ccl.net (8.8.3/950822.1) id DAA11183; Wed, 26 Mar 1997 03:15:43 -0500 (EST) Received: (from jeonghy@localhost) by camd1.kkpcr.re.kr (8.6.12h2/8.6.12) id BAA09581 for chemistry@www.ccl.net; Thu, 27 Mar 1997 01:33:00 GMT From: Ho Young Jeong Message-Id: <199703270133.BAA09581@camd1.kkpcr.re.kr> Subject: basic book for the application? To: chemistry@www.ccl.net Date: Wed, 26 Mar 1997 17:33:00 -0800 (PST) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! I am looking for the basic books or papers to show the application of quantum calculation. I have seen books to explain the basic concept of quantum mechanics, but it is hard to find a book or a paper to teach the application by quantum calculation program such as gaussian94. Since I am a beginner in this field, I need a good teacher! Thank you in advance. Ho Young Jeong. jeonghy@camd1.kkpcr.re.kr From fiona@rsc.anu.edu.au Wed Mar 26 06:31:52 1997 Received: from anugpo.anu.edu.au for fiona@rsc.anu.edu.au by www.ccl.net (8.8.3/950822.1) id GAA12165; Wed, 26 Mar 1997 06:15:58 -0500 (EST) From: Received: from rsc (rsc.anu.edu.au [150.203.35.129]) by anugpo.anu.edu.au (8.8.5/8.8.5) with SMTP id WAA22216 for ; Wed, 26 Mar 1997 22:15:19 +1100 (EST) Received: from [150.203.148.155] by rsc (SMI-8.6/SMI-SVR4) id WAA14996; Wed, 26 Mar 1997 22:20:56 +1100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Mar 1997 22:15:43 +1100 To: chemistry@www.ccl.net Subject: Anisotropic Hyperfine Constants Dear Netters, I recently asked a question of you regarding the theoretical determination of the nuclear magnetic dipolar-electronic magnetic dipolar anisotropic hyperfine coupling constants. I thank everybody for there responses. I was about to post a summary of everyone's responses as well as my own summary, but decided to hold off until I could get the following point cleared up which has been nagging me for the past week or so. I've been able to verify that the hyperfine constants, A_ab, are, in fact, proportional to the expectation values of the electric field gradient, _averaged_over_spin_density_, rather than charge density as is the case for the actual electric field gradient, ONLY for A_zz, A_zx and A_zy. In the case of A_xx, A_yy and A_xy the electronic spin operator appearing in the hyperfine Hamiltonian is _only_ s_x or s_y, i.e., s_z does not appear for these terms, yet the same "averaged over spin density" expressions are used to calculate these constants as well. My question is, how is this possible, i.e., why does it seem that s_z was substituted for s_x and s_y? Thanks in advance, Fiona Bettens. From lars@lmspc3.ibs.fr Wed Mar 26 09:31:55 1997 Received: from ibs.ibs.fr for lars@lmspc3.ibs.fr by www.ccl.net (8.8.3/950822.1) id JAA13002; Wed, 26 Mar 1997 09:13:20 -0500 (EST) Received: from lmspc3.ibs.fr (lars@lmspc3.ibs.fr [192.134.36.143]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id PAA09237 for ; Wed, 26 Mar 1997 15:13:59 +0100 Received: (from lars@localhost) by lmspc3.ibs.fr (8.8.5/8.8.5) id PAA14949 for chemistry@www.ccl.net; Wed, 26 Mar 1997 15:10:34 +0100 Date: Wed, 26 Mar 1997 15:10:34 +0100 From: Lars Hemmingsen Message-Id: <199703261410.PAA14949@lmspc3.ibs.fr> To: chemistry@www.ccl.net Subject: MM parametres for NO3-, CO3--, SO4--, PO4---, HPO4-- Hello all ! Does anyone have MM parameters or references where parameters may be found (atomic charges, force constants, van der Waals) for NO3-, CO3--, SO4--, PO4--- or HPO4-- ? All answers will be greatly appreciated. I will summarise if there is an interest in such a summary (judging >from the replies I get). Thanks in advance, yours Lars Hemmingsen From korkin@qtp.ufl.edu Wed Mar 26 10:31:55 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id KAA13381; Wed, 26 Mar 1997 10:01:02 -0500 (EST) Received: from red by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id KAA22542; Wed, 26 Mar 1997 10:00:15 -0500 Date: Wed, 26 Mar 1997 10:00:14 -0500 (EST) From: Anatoli Korkin Reply-To: Anatoli Korkin Subject: Re: CCL:G:basic book for the application? To: jeonghy@camd1.kkpcr.re.kr Cc: chemistry@www.ccl.net, bartlett@qtp.ufl.edu, piotr@qtp.ufl.edu, aces2@qtp.ufl.edu Message-ID: MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: WaGlRCrCYraxkdRYyu6jkQ== X-Mailer: dtmail 1.2.0 CDE Version 1.2_14 SunOS 5.6 sun4d sparc > > I am looking for the basic books or papers to show the application of > quantum calculation. I have seen books to explain the basic concept of > quantum mechanics, but it is hard to find a book or a paper to teach the > application by quantum calculation program such as gaussian94. Since I am a > beginner in this field, I need a good teacher! > > Thank you in advance. > > Ho Young Jeong. > jeonghy@camd1.kkpcr.re.kr Dear Young Jeong, A good book book is Tim Clark's "Handbook of Computational Chemistry". It is a bit old, and may be I missed some good new books on this topic. Send your summary to me, if you are not going to send it to CCL. If you get ACES program, the Bartlett's group provides a good technical support and you may get answers to some basic questions. Our new company provides a scientific consulting in addition. If there is enough of demand we organize workshops (in Florida and in other States and in other countries) and the internet courses in teaching how to use the quantum chemistry programs and how to apply quantum theory to solve chemical problems. Of course, the basic quantum theory is explained too. You may visit the Aces program and the ACES Q.C. company webb sites: http://www.qtp.ufl.edu/Aces2/ and http://www.emtron.com/aces_qc/ Good luck in your studies and future research! Anatoli Korkin From luo@seas.marine.usf.edu Wed Mar 26 11:31:57 1997 Received: from seas.marine.usf.edu for luo@seas.marine.usf.edu by www.ccl.net (8.8.3/950822.1) id LAA14271; Wed, 26 Mar 1997 11:31:33 -0500 (EST) Received: from localhost (luo@localhost) by seas.marine.usf.edu (8.8.5/8.8.5) with SMTP id LAA24988 for ; Wed, 26 Mar 1997 11:32:26 -0500 (EST) Date: Wed, 26 Mar 1997 11:32:26 -0500 (EST) From: Yu-Ran Luo To: chemistry@www.ccl.net Subject: On pKa data and prediction Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know : (1) Where can we find a complete data collection on pKa (in water and DMSO) of organic compounds? (2) Which software can predict pKa ? The Company name? Many thanks in advance. Dr. Yu-Ran Luo, (O) 813-553-3922, Fax: 813-893-9189, e-mail: luo@seas.marine.usf.edu From elewars@alchemy.chem.utoronto.ca Wed Mar 26 11:37:22 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id KAA13897; Wed, 26 Mar 1997 10:53:05 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id KAA29504 for chemistry@www.ccl.net; Wed, 26 Mar 1997 10:53:03 -0500 (EST) Date: Wed, 26 Mar 1997 10:53:03 -0500 (EST) From: "E. Lewars" Message-Id: <199703261553.KAA29504@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: GETTING STARTED WITH GAUSSIAN ETC 1997 March 26 H Y Jeong recently asked how he could get started using programs like Gaussian. 1 General information on computational chemistry: "Quantum Chemistry", by Ira N. Levine, 4th ed., Prentice Hall, 1991. Very good introduction to QC, with problems (some answered). Chapters 15 and, especially, 16 and 17 give a nice, brief overview of current computational chemistry (a new edition may be out in a year or so). 2 A very useful introduction to comp. chem., oriented toward Gaussian: "Exploring Chemistry with Electronic Structure Methods" J. B. Foresman, A. Frisch; Gaussian Inc., Carnegie Office Park, Building 6, Pittsburgh, PA 15106 2nd edition, (1996); for info about the book, email explore@gaussian.com Although this book is oriented toward Gaussian (94; the first Ed. to G92), it has information that would be useful to beginners using any kind of quantum mechanical molecular structure program. MMX and semiempirical methods are mentioned only in passing, and more stress is placed on Z-matrices than, perhaps, modern practice warrants. 4. "A Handbook of Computational Chemistry", Tim Clark; Wiley (1985). A nice feature of this book is that it deals with MMX, semiemp. and ab initio. As expected for a book 12 years old, there is much discussion on how to write Z-matrices and only passing reference to the use of interactive molecule-building programs to create input. 6. There are a series of VERY useful books on _using_ computational chemistry, published by: Wavefunction Inc., (18401 Von Karman, Suite 210, CA 92715, USA); FAX (714)955-2118); sales@wavefun.com They are interested in promoting the teaching of computational chemistry, and have produced books oriented toward their SPARTAN program, which is a nice integrated MM-semiempirical-ab initio package. Finally, a beginner might try finding some published papers on topics related to his research and try repriducing the results. =============================================================================== elewars@trentu.ca E. Lewars FAX (705)748-1625 Chemistry Dept Trent University Peterborough, Ontario Canada K9J 7B8 =============================================================================== From sanjoy@sscu.iisc.ernet.in Wed Mar 26 12:31:57 1997 Received: from milan.doe.ernet.in for sanjoy@sscu.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id LAA14342; Wed, 26 Mar 1997 11:36:09 -0500 (EST) Received: from iisc.ernet.in by milan.doe.ernet.in (4.1/SMI-4.1) id AA23763; Wed, 26 Mar 97 15:54:11+050 Received: from sscu.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-4.1) id WAA24840; Wed, 26 Mar 1997 22:05:57 +0530 Received: by sscu.iisc.ernet.in (ERNET-IISc/SMI-4.1) id VAA01812; Wed, 26 Mar 1997 21:48:10 +0600 Date: Wed, 26 Mar 1997 21:48:10 +0600 From: sanjoy@sscu.iisc.ernet.in (Mr.Sanjoy ) Message-Id: <199703261548.VAA01812@sscu.iisc.ernet.in> To: chemistry@www.ccl.net Subject: CCL: Parameters for SDS Dear Netters, I am trying to simulate SDS micelle in water. Can anyone tell me where can I find accurate parameters such as charges, bond lengths, bond angles, force constants and van der Waals for SO4-- and CH2/CH3 groups. Thanks in advance. Sanjoy Bandyopadhyay (sanjoy@sscu.iisc.ernet.in) From dqujfm0@PS.UIB.ES Wed Mar 26 12:36:31 1997 Received: from lofre for dqujfm0@PS.UIB.ES by www.ccl.net (8.8.3/950822.1) id LAA14478; Wed, 26 Mar 1997 11:58:58 -0500 (EST) X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Wed, 26 Mar 1997 17:57:37 UTC+0100 Date: Wed, 26 Mar 1997 17:57:37 UTC+0100 X400-Originator: dqujfm0@PS.UIB.ES X400-Recipients: non-disclosure:; X400-Content-Type: P2-1984 (2) X400-MTS-Identifier: [/PRMD=iris/ADMD=mensatex/C=es/;970326175737] Content-Identifier: 353 From: Juan Frau To: Message-ID: <353*dqujfm0@PS.UIB.ES> Subject: MM recopilation MIME-Version: 1.0 (Generated by Ean X.400 to MIME gateway) Hi everybody, We are trying to develop a course in our univesity about MM. It can be divided in two parts, a general description about MM and the second one some examples of application of this methodology. Therefore, I would like to recopile some papers about applications of molecular mechanics methods. I am taking about five, six papers, o reviews where I could find some spectacular applications (agreement with theory about conformational energies, free energry calculations, ,.). I know it is a very general question. But I was wondering if you have some list about it. Thanks in advance ***************************************************************** Juan Frau Universitat Illes Balears Palma de Mallorca. Islas Baleares. Spain. E-mail: dqujfm0@ps.uib.es From maiden@RedBrick.DCU.IE Wed Mar 26 13:32:03 1997 Received: from tolka.dcu.ie for maiden@RedBrick.DCU.IE by www.ccl.net (8.8.3/950822.1) id MAA14763; Wed, 26 Mar 1997 12:41:51 -0500 (EST) Received: from Nurse.RedBrick.DCU.IE by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA19429; Wed, 26 Mar 1997 17:41:49 GMT Received: (from maiden@localhost) by RedBrick.DCU.IE (SomeMTA) id RAA15569; Wed, 26 Mar 1997 17:39:33 GMT Organisation: DCU Networking Society X-Disclaimer: The DCUNS is not responsible for the content of this message Date: Wed, 26 Mar 1997 17:39:33 +0000 (GMT) From: michael nolan To: chemistry@www.ccl.net Subject: CMn{CO)3...coordinates Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCl. Is there any way of getting the CARTESIAN coordinates of CpMn{CO}3..... thanking you in advance michael ****************************************************************************** Michael Nolan (nearly BSc.) Dublin City University (quantum chem.) 41 Woodview Chemistry + German Year 4 Lucan Co. Dublin Ireland / Republic of Ireland / ROI / Eire Email: Maiden@redbrick.dcu.ie ***************************************************************************** From pughj@ucs.orst.edu Wed Mar 26 13:40:01 1997 Received: from ucs.orst.edu for pughj@ucs.orst.edu by www.ccl.net (8.8.3/950822.1) id MAA14820; Wed, 26 Mar 1997 12:53:29 -0500 (EST) Received: by ucs.orst.edu; (5.65v3.2/1.1.8.2/13Sep96-1023AM) id AA24389; Wed, 26 Mar 1997 09:53:25 -0800 Date: Wed, 26 Mar 1997 09:53:24 -0800 (PST) From: James Pugh To: chemistry@www.ccl.net Subject: Graphical Interface for Gaussian Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCL: Our lab is heavily involved in using Gaussian calculations for various projects. Recently we have need of some method to graphically view the output from such calculations for the purpose of gaining bond distances, angles, dihedral angles etc.. If anyone has knowledge of a program that can easily take Gaussian output and graphically display it, the information would be greatly appreciated. We do have Spartan v. 4.1.1, but there seems to be difficulty in using it for this purpose. I can be reached by direct e-mail at the following address: pughj@ucs.orst.edu Thank you in advance for your assistance. Jim Pugh Department of Chemistry Oregon State University From jlye@tx.ncsu.edu Wed Mar 26 13:42:48 1997 Received: from ds10.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.8.3/950822.1) id NAA15224; Wed, 26 Mar 1997 13:31:20 -0500 (EST) Received: by ds10.tx.ncsu.edu (5.65/Eos/C-U-09Sep93) id AA22033; Wed, 26 Mar 1997 13:31:07 -0500 From: "Jason Lye" Message-Id: <9703261331.ZM22031@unity.ncsu.edu> Date: Wed, 26 Mar 1997 13:31:04 -0500 X-Mailer: Z-Mail (3.2.1 15feb95) To: chemistry@www.ccl.net Subject: Re: ZINDO Energy Units Cc: cache@pacificu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Netters, I recently asked how what the energy units were from Zindo, and how to convert them into something more spectroscopically meaningful such as cm-1. Thanks to all who replied. I have appended Ernest Chamot's reply, although others made the following clear: The energy units can be directly converted in the CAChe editor by looking at the Internals (in the EDIT menu.) The energy units from a Zindo CI calculation are already in cm-1. Thanks once again, Jason Lye ________________________________________________________________ Hi Jason, Converting the energy units in ZINDO is straightforward. All the Quantum Mechanical methods like to use "fundamental" units, in this case, Hartrees. One Hartree equals 627.51 kcal. You will notice immediately, that if you multiply the ZINDO numbers by 627.1, however, that you get a very large number that doesn't look anything like a heat of formation. That is because electronic energies are calculated relative to the completely separated electrons and nuclei as the reference state, rather than relative to the elements in their standard state. This doesn't matter if you are looking at differences in energies: just subtract one from the other. I would warn you about the likely accuracy of these energies, however. ZINDO does okay coming up with energy differences between orbitals for calculating UV spectra, but it is too crude to calculate good optimized geometries and corresponding molecular energies. (Some of the best results have been obtained by using DFT to calculate geometries, and then ZINDO to calculate spectra.) In fact, if you try to calculate heats of formation by using a ZINDO optimized geometry and subtracting the energies of a ZINDO optimized molecules of the elements (try something like H2O vs H2 and O2, for instance) you will find errors in heats of formation on the order of 100-200 kcal/mol! I'm not sure which energy differences you are looking for. If you are looking for vertical excitation energies (in effect just the difference between how the electrons are distributed at the same geometry, with the same set of orbitals), then you may be okay, judging by ZINDO's success in predicting UV absorbances. If you want to compare the ground state singlet energy to the energy of the optimized geometry in the triplet state, etc. I don't think ZINDO will give you a usable accuracy. Good luck. EC --- Ernest Chamot Chamot Labs, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (630)637-1559 echamot@chamotlabs.com http://www.chamotlabs.com/cl ---End of forwarded mail from "Ernest Chamot" -- _______________________________________________________________________________ Jason Lye, | Dye Synthesis Research Group, | College Of Textiles, Box 8301, | "Lifes' cheap, but North Carolina State University, | the accessories will kill you!" Raleigh, N.C. 27695 - 8301 | | Ph: (919) 515-6615 | jlye@tx.ncsu.edu | _______________________________________________________________________________ From jlye@tx.ncsu.edu Wed Mar 26 14:32:00 1997 Received: from ds10.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.8.3/950822.1) id NAA15398; Wed, 26 Mar 1997 13:41:11 -0500 (EST) Received: by ds10.tx.ncsu.edu (5.65/Eos/C-U-09Sep93) id AA22033; Wed, 26 Mar 1997 13:31:07 -0500 From: "Jason Lye" Message-Id: <9703261331.ZM22031@unity.ncsu.edu> Date: Wed, 26 Mar 1997 13:31:04 -0500 X-Mailer: Z-Mail (3.2.1 15feb95) To: chemistry@www.ccl.net Subject: Re: ZINDO Energy Units Cc: cache@pacificu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Netters, I recently asked how what the energy units were from Zindo, and how to convert them into something more spectroscopically meaningful such as cm-1. Thanks to all who replied. I have appended Ernest Chamot's reply, although others made the following clear: The energy units can be directly converted in the CAChe editor by looking at the Internals (in the EDIT menu.) The energy units from a Zindo CI calculation are already in cm-1. Thanks once again, Jason Lye ________________________________________________________________ Hi Jason, Converting the energy units in ZINDO is straightforward. All the Quantum Mechanical methods like to use "fundamental" units, in this case, Hartrees. One Hartree equals 627.51 kcal. You will notice immediately, that if you multiply the ZINDO numbers by 627.1, however, that you get a very large number that doesn't look anything like a heat of formation. That is because electronic energies are calculated relative to the completely separated electrons and nuclei as the reference state, rather than relative to the elements in their standard state. This doesn't matter if you are looking at differences in energies: just subtract one from the other. I would warn you about the likely accuracy of these energies, however. ZINDO does okay coming up with energy differences between orbitals for calculating UV spectra, but it is too crude to calculate good optimized geometries and corresponding molecular energies. (Some of the best results have been obtained by using DFT to calculate geometries, and then ZINDO to calculate spectra.) In fact, if you try to calculate heats of formation by using a ZINDO optimized geometry and subtracting the energies of a ZINDO optimized molecules of the elements (try something like H2O vs H2 and O2, for instance) you will find errors in heats of formation on the order of 100-200 kcal/mol! I'm not sure which energy differences you are looking for. If you are looking for vertical excitation energies (in effect just the difference between how the electrons are distributed at the same geometry, with the same set of orbitals), then you may be okay, judging by ZINDO's success in predicting UV absorbances. If you want to compare the ground state singlet energy to the energy of the optimized geometry in the triplet state, etc. I don't think ZINDO will give you a usable accuracy. Good luck. EC --- Ernest Chamot Chamot Labs, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (630)637-1559 echamot@chamotlabs.com http://www.chamotlabs.com/cl ---End of forwarded mail from "Ernest Chamot" -- _______________________________________________________________________________ Jason Lye, | Dye Synthesis Research Group, | College Of Textiles, Box 8301, | "Lifes' cheap, but North Carolina State University, | the accessories will kill you!" Raleigh, N.C. 27695 - 8301 | | Ph: (919) 515-6615 | jlye@tx.ncsu.edu | _______________________________________________________________________________ From ahocquet@tamarugo.cec.uchile.cl Wed Mar 26 15:32:53 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id PAA16161; Wed, 26 Mar 1997 15:17:10 -0500 (EST) Received: from [146.83.10.18] by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA24437; Wed, 26 Mar 1997 17:16:07 +0400 Date: Wed, 26 Mar 1997 17:16:07 +0400 Message-Id: <9703262116.AA24437@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Alexandre Hocquet Subject: MMOK : A summary... Dear CCLers, Please find enclosed the summary of my question regarding the MOPAC keyword MMOK. Thanks to all that answered and especially to Thomas Strassner Dear Alexandre, for some information about the performance of that correction and about ureas you could take a look at: "A semiempirical AM1, MNDO and PM3 study of the rotational barriers of various ureas, thioureas, amides and thioamides", M. Feigel, T. Strassner, J. Mol. Structure, 283 (1993) 33. Ab initio and molecular mechanics calculations of various substituted ureas - rotational barriers and a new parametrization for ureas, T. Strassner, J. Mol. Mod., 2 (1996) 217. There was another publication dealing with peptide bond rotations and MOPAC, where you might take a look on: Ludwig, Schinke, Brandt, J.Mol.Mod. 1996, V2 N9 341-350 If you do have specific questions I will be happy to help you. You can email me at strasner@xenon.chem.ucla.edu Best regards Thomas Strassner >Dear CCLers, > >As i am getting interested in ureas, i am more and more encountering the >keyword MMOK >in my literature searching. I understood that this is a MOPAC keyword (is >it really ?) >, that it is concerned with an amide structural correction for >semiempirical methods, > >I dont know MOPAC, and the description of a similar keyword in the SPARTAN >software >(a molecular mechanics correction) is rather....rather spartan. > >Does someone know a reference (possibly other than the MOPAC manual) that >describes >the functionality of that strange keyword ? On what (published) structural >results >was it founded ? > >I will of course summarize the answers... > >Thanks in advance > >Alexandre Hocquet ************************************************************************ ***** Dr. Thomas Strassner ***** ***** UCLA, Department of Chemistry and Biochemistry ***** ***** 405 Hilgard Avenue ***** ***** Los Angeles, CA, 90024 ***** ***** ***** ***** Phone : (310) 825-0269 ***** ***** Fax: (310) 206-1843 ***** ***** ***** ************************************************************************ Alexandre Hocquet Laboratorio de Cristalografia Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro Chile fono : 56 2 678 45 19 fax : 56 2 696 73 59 email : ahocquet@cec.uchile.cl From bruno@antas.agraria.uniss.it Wed Mar 26 18:31:59 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id RAA17427; Wed, 26 Mar 1997 17:55:38 -0500 (EST) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA172726942; Wed, 26 Mar 1997 23:55:43 +0100 Date: Wed, 26 Mar 1997 23:55:48 +0100 (NFT) From: "Dr. Bruno Manunza" To: James Pugh Cc: chemistry@www.ccl.net Subject: Re: CCL:G:Graphical Interface for Gaussian In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 26 Mar 1997, James Pugh wrote: > > CCL: > > Our lab is heavily involved in using Gaussian calculations for various > projects. Recently we have need of some method to graphically view the > output from such calculations for the purpose of gaining bond distances, > angles, dihedral angles etc.. > > If anyone has knowledge of a program that can easily take Gaussian output > and graphically display it, the information would be greatly > appreciated. We do have Spartan v. 4.1.1, but there seems to be > difficulty in using it for this purpose. I can be reached by direct > e-mail at the following address: > > pughj@ucs.orst.edu > > Thank you in advance for your assistance. > > Jim Pugh > Department of Chemistry > Oregon State University > Dear Jim, A similar question was posed a few days ago, you may either try molden at http://camms1.caos.kun.nl/~schaft/molden/molden.html or try converting your output with babel (ftp://joplin.biosci.arizona.edu/pub/Babel/) our site also keep a list of software useful to the computational chemist so you may also have a look at http://antas.agraria.uniss.it hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From bruno@antas.agraria.uniss.it Wed Mar 26 19:32:02 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id SAA17635; Wed, 26 Mar 1997 18:44:15 -0500 (EST) Received: from user1 (dial1.uniss.it) by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA173189867; Thu, 27 Mar 1997 00:44:27 +0100 Message-Id: <3339B4A8.2DC9@antas.agraria.uniss.it> Date: Thu, 27 Mar 1997 00:43:36 +0100 From: bruno Organization: University of Sassari X-Mailer: Mozilla 3.0Gold (Win95; I) Mime-Version: 1.0 To: Lars Hemmingsen Cc: chemistry@www.ccl.net Subject: Re: CCL:MM parametres for NO3-, CO3--, SO4--, PO4---, HPO4-- References: <199703261410.PAA14949@lmspc3.ibs.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lars Hemmingsen wrote: > > Hello all ! > > Does anyone have MM parameters or references where parameters may be found > (atomic charges, force constants, van der Waals) for NO3-, CO3--, SO4--, > PO4--- or HPO4-- ? > All answers will be greatly appreciated. > > I will summarise if there is an interest in such a summary (judging > from the replies I get). > > Thanks in advance, yours Lars Hemmingsen There have been a couple of postings regarding this subject today, yours an one from Sanjoy Bandyopadhyay asking for MM parameter for SO4-- and CH2/CH3. You'll probably have to compute charges fitting the Electrostatic potential of your molecules according to a strategie like RESP (gopher://www.ccl.net:73/11/software/SOURCES/FORTRAN/resp) (see also the AMBER page at this regard (http://www.amber.ucsf.edu/amber/amber.html). You may keep in mind also that either GAUSSIAN.XX, GAMESS and MOPAC have options which allow to compute the partial atomic charges according to this philosophy. The force constants and van der Waals parameters for CH2, CH3, PO4, CO3 may be taken from the Cornell et al. AMBER force field (http://www.amber.ucsf.edu/amber/ff94.html)or from the MM3 force field (http://europa.chem.uga.edu/cgi-bin/mm3para) (strike 8-9 blanks in the form field to obtain a complete list). By the way we are trynk to keep update a list of force field links on ur site and you may have a lok to the molecular databases page on http://antas.agraria.uniss.it. Hope it helps Regards Bruno -- Dr Bruno Manunza DISAABA - Environmental Sciences Dept. V.le ITALIA 39 07100 SASSARI, ITALY phone 39 79 229215 fax 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it http://antas.agraria.uniss.it From tanhs@sps.nus.sg Wed Mar 26 23:32:02 1997 Received: from sps.nus.sg for tanhs@sps.nus.sg by www.ccl.net (8.8.3/950822.1) id XAA19255; Wed, 26 Mar 1997 23:14:06 -0500 (EST) Received: from localhost (tanhs@localhost) by sps.nus.sg (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id MAA17689 for ; Thu, 27 Mar 1997 12:05:26 +0800 Date: Thu, 27 Mar 1997 12:05:26 +0800 (SST) From: Tan Howe Siang To: chemistry@www.ccl.net Subject: DFT vs. HF (Vib. Freq.) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL I wonder if anyone out there knows of any literature regarding the the DFT and HF method and the comparison between the 2 methods for the computing of the vibrational frequencies of simple molecules (especially organic molecules like CCL4). Thank you.