From tripos!metis!matt@uunet.UU.NET Thu Oct 7 10:42:23 1993 From: tripos!metis!matt@uunet.UU.NET (Matt Clark) Message-Id: <9310072142.AA06977@metis.UUCP> To: uunet!ccl.net!chemistry@uunet.UU.NET Subject: Re: conjugation in mol mech Date: Thu, 07 Oct 93 14:42:23 EDT Neil Ostlund makes an important point about atom types in molecular mechanics, and how different bond types may occur between two atom types. The Tripos force field solves this problem by adding an extra variable to the force field, the bond type. This applies in particular to bond stretch and torsion terms. This allows more flexibility in handling conjugated systems. The single bond length between two sp2 carbons is about 1.47 Angstroms, the double bond length is 1.33 Angtroms. There are different torsion parameters for single and aromatic bonds used in the case of biphenyl torsions, allowing these to be parametrized more accurately. It isn't the same as a pi calculation, but significantly improves the accuracy for conjugated systems. I would encourage anyone developing new force fields to use this idea; it greatly expands the possibilities for future expansion of the force field. Organometallic modeling is much easier with this scheme - you can assign different bond lengths for bridging bonds, dative bonds etc., between the same two atom types. From CTARG@Levels.UniSA.Edu.Au Sat Oct 9 01:25:44 1993 Date: Fri, 08 Oct 1993 15:55:44 +0930 From: CTARG@Levels.UniSA.Edu.Au Subject: ionsiation potentials/electron affinities To: chemistry@ccl.net Message-Id: <01H3VIZGR9YQ9LVEEL@Levels.UniSA.Edu.Au> Hi Netters, The question I have to ask probably falls into the category of simplistic rubbish that I should look up in a school library somewhere but never mind.... I have been trying to reproduce the Gasteiger charge coefficients as used by Chem-X with the view to parameterising some other atoms. The reference paper 'Iterative partial equilization of orbital electronegativity - a rapid access to atomic charges' by Gasteiger and Marsili, Tetrahedron, vol36,(1980) pp 3219 to 3288 gives the a parameter of the electronegativity polynomial as a=1/2(I+E) where I is the ionisation potential and E is the electron affinity. For Hydrogen the text value for a is given as 7.17 eV which is fine using literature values of I and E. However I can't seem to reproduce any of the polynomial parameters for any other atoms. The type of bonding to each atom is obviously taken into account as different a, b and c coefficients are quoted for different bonding arrangements. How is ionsiation potential of an ATOM calculated/measured when it is bonded to something else? Can somebody enlighten me as to how these values are arrived at? Sorry about being so simple minded but somebody has to ask theses questions to make everybody else feel good! Thanks Andy From AJS1@phx.cam.ac.uk Fri Oct 8 12:37:26 1993 From: Anthony Stone Message-Id: <9310081137.AA16677@fandango.ch.cam.ac.uk> Subject: van der Waals radii To: chemistry@ccl.net Date: Fri, 8 Oct 1993 12:37:26 +0000 (BST) A further issue in the context of van der Waals radii is that atoms in molecules are not spherical, so one has to consider whether some sort of spherical average is in fact appropriate, or whether the anisotropy needs to be taken into account. The paper by Nyburg & Faerman in Acta Cryst B41 (1985) 274 gives an analysis of crystal packings that shows the anisotropies very clearly. Sally Price and I have reviewed this issue, among others, in J. Phys. Chem. 92 (1988) 3325. Anthony Stone University Chemical Laboratory, Internet: ajs1@phx.cam.ac.uk Lensfield Road, Phone: +44 223 336375 Cambridge CB2 1EW Fax: +44 223 336362 From MVOUE%BNANDP51.BITNET@phem3.acs.ohio-state.edu Fri Oct 8 14:11:34 1993 Date: Fri, 08 Oct 1993 14:11:34 +0000 (N) From: MVOUE%BNANDP51.BITNET@phem3.acs.ohio-state.edu Subject: Solution of Oernstein-Zernicke equations To: chemistry@ccl.net Message-Id: <01H3VF85XYHE8WWOEJ@BNANDP51> Dear Netters, I was interested if anyone could help me to locate a program which will solve the Oernstein-Zernicke equations for (poly-)electrolyte systems. Any information is welcome. Thanks in advance. Michel Voue Lab. Theoretical Biotechnology University of Namur (Belgium) bitnet%"MVOUE@BNANDP51" From dirk@rulglj.LeidenUniv.nl Fri Oct 8 06:15:21 1993 Date: Fri, 8 Oct 93 13:15:21 -0700 From: dirk@rulglj.LeidenUniv.nl (Dirk Huckriede) Message-Id: <9310082015.AA09000@rulglj.LeidenUniv.nl> To: CHEMISTRY@ccl.net Subject: Volume calculation Hello netters, I'm looking for a program which calculates the volume of a molecule, given the atom types and their coordinates. Can anyone help me ? Bye ! Dirk Huckriede Conformational Analysis Group Gorlaeus Laboratories Leiden University P.O. Box 9502 Phone : +31 71 274505 2300 RA Leiden Fax : +31 71 274488 The Netherlands E-mail : dirk@rulglj.leidenuniv.nl From crawdad@smerdis.ccqc.uga.edu Fri Oct 8 03:56:11 1993 From: crawdad@smerdis.ccqc.uga.edu (Daniel Crawford) Message-Id: <9310081256.AA27060@smerdis.ccqc.uga.edu> Subject: Re: Searching for Duke To: chemistry@ccl.net Date: Fri, 8 Oct 1993 08:56:11 -0500 (EDT) The domain for information on Duke University is: acpub.duke.edu chemistry in particular is, chem.duke.edu Try getting information through those addresses and see if that helps. -Daniel (Duke T'92) -- T. Daniel Crawford Center for Computational Quantum crawdad@smerdis.ccqc.uga.edu Chemistry From young@slater.cem.msu.edu Fri Oct 8 03:53:09 1993 Date: Fri, 8 Oct 93 07:53:09 -0400 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9310081153.AA15065@slater.cem.msu.edu> To: chemistry@ccl.net Subject: Fermi surface vs van der Waals surface Subj: Fermi surface vs Van der Waals surface There was recently a posting asking whether the fermi surface in a solid state calculation is analogous to the van der Waals surface in a molecular scheme. The answer is NO!! The Fermi surface is defined as the surface of all points in k space with the Fermi energy. Here k is a measure of the amount of bonding or antibonding character in a band (think MO for band, roughly). This is not defined in physical space, so it has no analogous properties to a Van der Waals surface. If you would like an analogy for the Fermi surface, think of it as the HOMO, where the Fermi energy is the energy of the HOMO orbital. However, keep in mind that in solids there is a continum of states defined by a band, thus several bands may cross the Fermi energy, thus the HOMO can not be defined as ONE orbital. Dave Young young@slater.cem.msu.edu youngdc@msucem From msjones@whale.st.usm.edu Sat Oct 9 37:42:53 1993 From: msjones@whale.st.usm.edu (Michael Sean Jones) Message-Id: <9310081726.AA20559@whale.st.usm.edu> Subject: REGULATIONS To: CHEMISTRY@ccl.net (chemlist) Date: Fri, 8 Oct 1993 12:26:53 +22304916 (CDT) Netters, I am writing in response to a letter that we all received from Jan Labonowski(spelling???). It stated that he/she would not allow messages of the type "...searching for...", etc. to be broadcast on the list. This seems illogical to me, since the whole purpose of the internet is to improve and raise the efficiency of communications. In particular, this list should serve as an extension of the purpose of the internet; that is, to improve the efficiency of communications between scientists interested in computational chemistry. This allows a very specialized list of individulals to view the message. The messages, in fact, would not make much sense to anyone outside of the computational chemistry field. It is to the benefit of everyone involved with the list to allow such communications as "...searching for..." to be posted. Sure, like Jan stated in the letter, anyone could go to a library, even a high school library, to find addresses of people around the world. However, very few libraries will keep internet or bitnet addresses on file, as they change very often, and would be too hard to keep up with. This is the very reason why a successful "Internet White Pages" has yet to appear. Sure, there are services available for finding file names, and people, but the lists are kept for only a limited number of machines around the world. Furthermore, as was stated earlier, the purpose of the internet is not facilitate efficient information exchange. This list, being a part of the internet, should respect the purposes of the internet by allowing such messages. It is easily understood why messages such as "... searching for an art professor by the name of..." would be banned from the list, but the searches I have seen have been relevant to the field of computational chemistry. What a better group to ask for an address of a computational chemistry researcher's address than this list? I might also add, that even though Jan CRUDELY suggested that everyone who did not want messages like that sent send me a message telling me not to do it anymore on this list. Jan also mentioned that once I got 2000 messages, I might not do it anymore. Well Jan, such a suggestion goes outside of even your own guidelines for the use of this list. Read the rules. Even after the suggestion that everyone who did not want me to send messages like that send me a message telling me not to, noone did. Obviously, the VAST majority of the 2000 subscribers enjoy the ability to ask colleagues for addresses. Maybe you should to. I do enjoy the use of this list, but the guidelines seem to be contradictory to the whole purpose of the internet. If anyone else feels the way that I do, please subscribe to the list. I might also suggest simply glancing at the name of the sender and the subject of the message before reading it. Using ELM this is possible. Then, if you are not interested in the message, simply delete it. It works well for deleting messges that you do not know much about, such as requests for addresses that that you do not know. Mike msjones@wave.st.usm.edu From CHAMH@INDSVAX1.INDSTATE.EDU Fri Oct 8 09:34:00 1993 Date: Fri, 8 Oct 1993 14:34 EST From: CHAMH@INDSVAX1.INDSTATE.EDU Subject: Problem with MECI in MOPAC93 To: chemistry@ccl.net Message-Id: <01H3VG67OV2C0017ER@INDSVAX1.INDSTATE.EDU> I am running MOPAC93 on the RS/6000 and find that when I use MECI on a system, the .out file builds up to a point (e.g. in the middle of the Cartesian coordinates or interatomic matrix), and the job hangs. The MECI (and related keywords) works fine for 'smaller' systems, but above a certain number of atoms the above problem occurs. The problem is not with DIMSIZES becasue larger systems work without MECI. If anyone has experienced this problem and identified a workaround, or otherwise has a suggestion for a fix, please contact me. Many thanks, Arthur M. Halpern Department of Chemistry Indiana State University Terre Haute, Indiana (812) 237-2182 BITNET: CHAMH@INDSVAX1 INTERNET: chhalp@scifac.indstate.edu From adrian@silver.chem.nwu.edu Fri Oct 8 10:31:47 1993 From: adrian@silver.chem.nwu.edu (Adrian Roitberg) Message-Id: <9310082031.AA08068@silver.chem.nwu.edu> Subject: Extended Huckel To: chemistry@ccl.net Date: Fri, 8 Oct 93 15:31:47 CDT Dear netters, Does somebody out there know about extended huckel parameters for charged Ru atoms ?? I have found them for neutral Ru, but need them for Ru(II) and Ru(III) if possible. Also, does Prof. Roald Hoffman have an e-mail address were to reach him ?? Thanks a lot. Adrian E. Roitberg ============================================================================= Dept. of Chemistry | Phone: (708) 491-3423 Northwestern University | Fax : (708) 491-7713 2145 Sheridan Road. Evanston, IL |E-mail:adrian@silver.chem.nwu.edu 60208-3113 | ============================================================================= From arne@escher.mbi.ucla.edu Fri Oct 8 06:49:43 1993 Message-Id: <9310082049.AA01652@escher.mbi.ucla.edu> To: msjones@whale.st.usm.edu (Michael Sean Jones) Subject: Re: REGULATIONS Date: Fri, 08 Oct 93 13:49:43 -0700 From: "Arne Elofsson (arne@uclaue.mbi.ucal.edu)" I do not agree with (Michael Sean Jones) Actually I think it is quite anoying to read all these messages, Do you know the adress to ... etc etc Even if this is usefull it takes a lot of time for the othr 1999 subscribers who not is interested in finding the adress to prof X. I think there is a huge difference between a mailing list and the use of usenet archives. In these archives I search for the kind of information I want, while in a mailing list the information is forced onto after a subscription. These mails are mixed up with all other (personal) mails, therefore it is necessary to keep the number of mails you get to a (rather) small number. You can not get only 10 % interesting mails. therefore I suggest: Either 1. Use sci.chem or so for asking these questions or. 2. Create another mailing list "comp-chem-where-are-you" I'm sure Jan is willing to give away his scripts for the mailinglist. arne. PS. another good (?) idea might be to set up a FAQ available through ftp or mailserver, as the same questions appear again and again, as people not uses the excellent search routines. But I guess this is a lot of work. From JKONG@ac.dal.ca Fri Oct 8 15:23:44 1993 Date: Fri, 08 Oct 1993 18:23:44 -0300 From: JKONG@ac.dal.ca Subject: Reply directly to the original sender? To: chemistry@ccl.net Message-Id: <01H3VO5Z07MA000MY2@AC.DAL.CA> Dear netters, A few days I used up my disk quota and I guess I missed some parts of the discussions about reviewing/publishing and DFT and I should apologize to some fellows who may get bounced messages. Most of my files are mails. Most of the mails I get from this list are replys to questions. I suppose the senders just type reply command to answer. I usually use VAX/4500 to receive mails and the reply command sends the message directly to the original sender. But I think on some machines reply utility sends the message to the list and everybody gets a copy. (Usually reply sends messages to the address at the fist line of the message you are reading.) I thought it would be better to send replies of technical questions to the original sender instead of the list unless you think other people will be interested too and the original sender is supposed to summarize the replies in a few days. You can request the replies from the original sender if you are interested in the topic. How is that? Jing From WALKERG@cofc.edu Tue Oct 8 12:49:43 1993 Date: 08 Oct 1993 17:49:43 -0500 (EST) From: WALKERG@cofc.edu Subject: Working on Eley-Rideal modeling... To: chemistry@ccl.net Message-Id: <01H3VMUYUFVM006G5P@cofc.edu> Organization: College of Charleston Hi. I'm totally new to this list, so I'll keep this as brief as possible. I'm an undergraduate at the University of Charleston working on a research project in computational chemistry. The project is an attempt to model and propose new theories about the Eley-Rideal mechanism for gas/ surface reactions. This post is merely an attempt to shake out anyone working on similar problems. I could certainly use your advice. -Gary E. Walker Junior, University of Charleston Charleston, SC Walkerg@ashley.cofc.edu From scott@paganini.biocad.com Fri Oct 8 05:23:46 1993 Date: Fri, 8 Oct 93 12:23:46 -0700 From: scott@paganini.biocad.com (Scott Kahn) Message-Id: <9310081923.AA13196@paganini.biocad.com> To: CHEMISTRY@ccl.net Subject: United atom summary Here is a summary of the responses received for my question on untied atoms. Many thanks to all that relied! *>> I would like to locate any/all references that discuss the derivation *>> and/or calibration of united atom forcefield parameters, and would *>> appreciate any help that those participating in this list can offer. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From dan@omega.chem.yale.edu We use united atom force field parameters quite a bit. Unfortunately they are not useful in all cases. We found that the only way to get the proper free energy of hydration for benzene was to use an all atom model; you cannot include charges on a 6 site model due to the need to preserve the 6-fold symmetry of the molecule. It's not so much of a problem. Here's the reference for the OPLS force field for proteins: The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. W. L. Jorgensen and J. Tirado-Rives J. Am. Chem. Soc., 110, 1657 (1988). The current version of the parameter set has replaced the united atom aromatic rings with all atom ones. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From wk01189@worldlink.com In addition to the "classical" AMBER and OPLS references you may want to look at the work of Dunfield et al. in Scheraga's lab describing UNICEPP (J. Phys. Chem. 82, 2609 [1978]). It is one of the few cases I am aware where they put some effort into trying to reproduce the all-atom version of the potential function (in this case, ECEPP). Also, Hall and Pavitt in their comparative study of different force fields found a hybrid version of UNICEPP to be one of the most accurate (the reference is J.Comp.Chem. 5, 441-450 [1984]). It is unfortunate that Scheraga and co-workers did not keep up with UNICEPP and almost never used in publications after the original description; however, the group of N. Go in Japan (and his followers) have used this potential function in a number of papers (some of the most recent in the latest issue of Proteins). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From grootenhuis@akzo.akzo.400net.nl (Dr. Peter D.J. Grootenhuis) I have a paper in press (in Molecular Simulation, it may be already out) that is concerned with the parametrisation of a united atom representing carbohydrate hydroxyl groups. The whole procedure is described in detail. We call the approach CHEAT (Carbohydrate Hydroxyls represented by Extended AToms). I hope it will be of use ... ------ Scott D. Kahn, BioCAD Corporation (415) 903-3917 Email : scott@biocad.com From sslagle@silibio.ncsa.uiuc.edu Fri Oct 8 15:14:11 1993 Date: Fri, 8 Oct 93 20:14:11 -0500 From: sslagle@silibio.ncsa.uiuc.edu (Stuart Slagle) Message-Id: <9310090114.AA03996@silibio> To: chemistry@ccl.net Subject: Re: regulations Some individuals have voiced conflicting opinions regarding the admission of "in search of ..." requests on this list. To state it simply, the requests are highly bothersome. These requests reduce the signal to noise on this mailing list. The amount of *crap* on this list is often frustrating enough that I erase all mail from osc without reading them. By avoiding the "in search of ..." requests, will someone on the net do my library research for me requests, and the other inane posts on this group, it is difficult to find the truly informative or thought provoking posts. I have personally unsubscribed/resubscribed to this list multiple times for this very reason. Only the announcements of new software keeps me on this list. The question is for how long? To Jan and Mike: please fight this out of the list. To all: flame to me not the list -- please! Stuart Slagle U of Illinois@U-C sslagle@ncsa.uiuc.edu From mckelvey@Kodak.COM Fri Oct 8 09:26:26 1993 Date: Fri, 8 Oct 93 13:26:26 -0400 Message-Id: <9310081726.AA03687@Kodak.COM> From: mckelvey@Kodak.COM To: osc@Kodak.COM Subject: MOPAC 6 on PC We run it routinely...NDP compiler...33MHZ-486 = 12 % of 25MHZ RS6000 John McKelvey