From owner-chemistry@ccl.net Mon Jul 31 03:11:31 1995 Received: from dingo.cc.uq.oz.au for M.Smythe@mailbox.uq.oz.au by www.ccl.net (8.6.10/930601.1506) id DAA21866; Mon, 31 Jul 1995 03:10:49 -0400 Received: from [130.102.118.72] (zepto.ddd.uq.oz.au) by dingo.cc.uq.oz.au with SMTP id AA28218 (5.67a/IDA-1.5 for ); Mon, 31 Jul 1995 17:10:39 +1000 X-Sender: ddmsmyth@dingo.cc.uq.oz.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 31 Jul 1995 17:16:25 +1000 To: chemistry@ccl.net From: M.Smythe@mailbox.uq.oz.au (Mark Smythe) Subject: pBrBz and tBu parameters Hi all I require para-Bromobenzoyl (pBrBz-CO-NH) and tert-Butoxy (tBu-O-CO) parameters for a peptide crystal simulation (using AMBER). I have done a quick literature search, but no luck. Is anyone aware of the existence of such parameters? Thanks Mark m.smythe@mailbox.uq.oz.au From owner-chemistry@ccl.net Mon Jul 31 07:26:31 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/930601.1506) id HAA23995; Mon, 31 Jul 1995 07:13:03 -0400 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA13372; Mon, 31 Jul 1995 13:06:23 +0200 Date: Mon, 31 Jul 1995 13:06:23 +0200 (DFT) To: TOPPER ROBERT Cc: CHEMISTRY@ccl.net, topper@cooper.edu Subject: Re: CCL:mass spec prediction In-Reply-To: <199507121422.AA02273@zeus> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 12 Jul 1995, TOPPER ROBERT wrote: > > Hello all, > I'm writing on behalf of a colleague who does quite a bit > of mass spectroscopy. He would like to acquire a program > which, given a molecular formula, can "predict" the > mass spectrum. He'd prefer it if it ran on a Mac, but > we also have MS/DOS/Windows and UNIX machines available. > > Does anyone have any recommendations? > > We are aware of the existence of MassSpec 3.0 (Trinity Software) > for Macintosh, but would welcome any comments on the code's > usability, usefulness, etc.. we have a very old version > (1.0) of MassSpec, but it doesn't run under system 7 and it's > pretty clunky under system 6. > > many thanks > rqt > > ************************************************************************ > Robert Q. Topper email: topper@cooper.edu > Department of Chemistry phone: (212) 353-4378 > School of Engineering WWW: watch this space, coming soon! > 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 > ************************************************************************ We have a semiempirical program based on MNDO (it can be run under DOS or UNIX) devoted for predicting primary mass spectrometric fragmentation steps on the basis of quantum chemical calculations. The method was described in I. Mayer and A. Gomory, Int. J. Quant. Chem Symp. 27 ,599 (1993) and, (more advanced version) J. Mol. Struct. (Theochem) 311, 341 (1994). The program is available upon reqest. Yours sincerely, Prof. Istvan Mayer e-mails: mayer@cric.chemres.hu IB13LVIB@HUEARN.sztaki.hu H1376May@ella.hu Central Research Institute for Chemistry of the Hungarian Academy of Sciences H-1525 Budapest, P.O.Box 17 Hungary From owner-chemistry@ccl.net Mon Jul 31 08:41:31 1995 Received: from nih-csl.dcrt.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.6.10/930601.1506) id IAA25108; Mon, 31 Jul 1995 08:31:51 -0400 Received: from [128.231.66.71] (ppc71.od.nih.gov) by nih-csl.dcrt.nih.gov (4.1/1.35(alw-2.4)) id AA01170; Mon, 31 Jul 95 08:31:48 EDT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 31 Jul 1995 08:38:55 -0500 To: chemistry@ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: Gd (and Lanthanide) ECP's Hi! This is the response to my request for Gd (and Lanthanide) basis sets/ECP's. Although an old fashion trip to the library was a bit more helpful than all my electronic searches ;). Something to remember! Cundari and Stevens J.Chem. Phys. 98(7) p. 5555-5565, 1993 ECP's with basis set for Lanthanides using the ECP form available in many common gaussian programs, including HONDO and G9x. Relativistic effects included in an average fashion. Bachelet et. al. Phys. Rev. B 26(8) p. 4189, 1982. Essentially the whole periodic table, but the form of the ECP is not the one supported by gaussian programs, but one seen in Car - Parinello programs using plane waves. The authors claim that the necessary integrals for computations using gaussian functions can be generated using numerical methods without much difficulty (?). good luck! Gustavo A. Mercier, Jr. M.D.-Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-496-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov From owner-chemistry@ccl.net Mon Jul 31 09:26:51 1995 Received: from cacr.ioc.ac.ru for makeev@cacr.ioc.ac.ru by www.ccl.net (8.6.10/930601.1506) id JAA26007; Mon, 31 Jul 1995 09:11:30 -0400 Received: by cacr.ioc.ac.ru (8.6.12/4) id RAA00436; Mon, 31 Jul 1995 17:11:24 +0400 X-NUPop-Charset: Russian Date: Mon, 31 Jul 1995 17:10:42 +0300 (BT) From: "Gennady M. Makeev" Sender: makeev@cacr.ioc.ac.ru Message-Id: <199507311710438561.makeev@cacr.ioc.ac.ru> Return-Receipt-To: makeev@cacr.ioc.ac.ru Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net Subject: MM3 wanted Hi all! Can somebody tell me where I can get MM3 molecular mechanics program for IBM PC? Thanks in forward! Gennady M. Makeev --- Gennady M. Makeev Zelinsky Institute of Organic Chemistry E-MAIL: Moscow, Russia makeev@cacr.ioc.ac.ru (095)-135-90-89 (sometimes I am even available on Saturdays and Sundays) * IRC Channel #Makeev ** IRC NICK Makeev ** PGP key available on request * From owner-chemistry@ccl.net Mon Jul 31 09:31:06 1995 Received: from rzdspc1.informatik.uni-hamburg.de for brock@chemie.uni-hamburg.de by www.ccl.net (8.6.10/930601.1506) id JAA26365; Mon, 31 Jul 1995 09:25:20 -0400 Received: from ocserv.chemie.uni-hamburg.de (ocserv.chemie.uni-hamburg.de [134.100.204.10]) by rzdspc1.informatik.uni-hamburg.de (8.6.12/8.6.12) with SMTP id PAA12639 for ; Mon, 31 Jul 1995 15:24:45 +0200 Received: by ocserv.chemie.uni-hamburg.de (AIX 3.2/UCB 5.64/4.50) id AA05421; Mon, 31 Jul 1995 15:17:11 +0200 From: brock@chemie.uni-hamburg.de (Mathias Brock) Message-Id: <9507311317.AA05421@ocserv.chemie.uni-hamburg.de> Subject: electronic spectra from CAS excited energies To: chemistry@ccl.net Date: Mon, 31 Jul 1995 15:17:10 +0200 (DFT) Cc: brock@chemie.uni-hamburg.de (Mathias Brock) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 549 Dear user of CAS on the net, after calculating excitation energies (by G92), symmetry and spin of the electronic states is needed to arrive to simulated electronic spectra. In particurlar, G92 gives output of the converged states but in general symmtry and spin will not bei given. I suggest some analysis will be required, but have not found an explizit routine yet. For any suggestions, even G92 independent, for evaluation of symmtry and spin data from CSF or SD-type functions, please reply if possible Thank you in advance Mathias Brock From owner-chemistry@ccl.net Mon Jul 31 10:11:38 1995 Received: from login0.isis.unc.edu for shubin@email.unc.edu by www.ccl.net (8.6.10/930601.1506) id KAA28383; Mon, 31 Jul 1995 10:10:35 -0400 Received: (from shubin@localhost) by login0.isis.unc.edu (8.6.12/8.6.12) id KAA119003; Mon, 31 Jul 1995 10:10:33 -0400 Date: Mon, 31 Jul 1995 10:10:31 -0400 (EDT) From: Shubin Liu X-Sender: shubin@login0.isis.unc.edu To: chemistry@ccl.net cc: chemistry@ccl.net Subject: CCL: How to use command "Cube" in Gaussian In-Reply-To: <199507311710438561.makeev@cacr.ioc.ac.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: It is said that to get the density, its gradient and Laplacian of a molecule from Gaussian code directly, one just chooses to use "Cube=density", "Cube=gradient" or "Cube=divergence" in command line and append some data in some format to specify the starting point and grid choice at the end of the input file. I tried several times, unfortunately, they didn't work. For the first command "cube=density", what I obtain is just a unreadable file, while for the later two commands, the program just skips them, with no result at all. Can someone kindly point out what happened and give me helps about how to get them correctly? Thanx a lot! Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu Kenan Hall A207, CB# 3290 sliu@mulliken.chem.unc.edu University of North Carolina Tel : (919) 914-6923 (Home) Chapel Hill, NC 27599-3290 (919) 962-0150 (Office) USA Fax : (919) 962-2388 ............................................................................. From owner-chemistry@ccl.net Mon Jul 31 09:25:33 1995 Received: from rzdspc1.informatik.uni-hamburg.de for brock@chemie.uni-hamburg.de by www.ccl.net (8.6.10/930601.1506) id JAA26365; Mon, 31 Jul 1995 09:25:20 -0400 Received: from ocserv.chemie.uni-hamburg.de (ocserv.chemie.uni-hamburg.de [134.100.204.10]) by rzdspc1.informatik.uni-hamburg.de (8.6.12/8.6.12) with SMTP id PAA12639 for ; Mon, 31 Jul 1995 15:24:45 +0200 Received: by ocserv.chemie.uni-hamburg.de (AIX 3.2/UCB 5.64/4.50) id AA05421; Mon, 31 Jul 1995 15:17:11 +0200 From: brock@chemie.uni-hamburg.de (Mathias Brock) Message-Id: <9507311317.AA05421@ocserv.chemie.uni-hamburg.de> Subject: electronic spectra from CAS excited energies To: chemistry@ccl.net Date: Mon, 31 Jul 1995 15:17:10 +0200 (DFT) Cc: brock@chemie.uni-hamburg.de (Mathias Brock) Dear user of CAS on the net, after calculating excitation energies (by G92), symmetry and spin of the electronic states is needed to arrive to simulated electronic spectra. In particurlar, G92 gives output of the converged states but in general symmtry and spin will not bei given. I suggest some analysis will be required, but have not found an explizit routine yet. For any suggestions, even G92 independent, for evaluation of symmtry and spin data from CSF or SD-type functions, please reply if possible Thank you in advance Mathias Brock From owner-chemistry@ccl.net Mon Jul 31 11:41:38 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/930601.1506) id LAA01796; Mon, 31 Jul 1995 11:28:38 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id UAA04949 for chemistry@ccl.net; Mon, 31 Jul 1995 20:58:44 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA25199; Mon, 31 Jul 95 20:57:43+050 Message-Id: <9507311557.AA25199@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Mon, 31 Jul 95 09:56:21 +0530 Date: Mon, 31 Jul 95 09:56:21 +0530 From: Mrigank To: chemistry@ccl.net Subject: RE: CCL:background message to the first email about urgent messages to X-Vms-Mail-To: UUCP%"shj@sbc2.kist.re.kr" What the hell is this? ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From owner-chemistry@ccl.net Mon Jul 31 12:11:49 1995 Received: from synthesis.chem.arizona.edu for matt@synthesis.chem.arizona.edu by www.ccl.net (8.6.10/930601.1506) id MAA04063; Mon, 31 Jul 1995 12:09:26 -0400 Received: by synthesis.chem.arizona.edu (5.65/DEC-Ultrix/4.3) id AA03563; Mon, 31 Jul 1995 09:06:19 -0700 Date: Mon, 31 Jul 1995 09:06:18 -0700 (MST) From: Matt Stahl To: chemistry@ccl.net Subject: constrained opt's Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Netters, A while back I posted a question about the validity of constrained optimization. The original post and the summary of responses are included in this message. In short, I think constrained opt's are generally accepted as valid in the context of rotation driving studies. There are "better" methods available for reaction path characterization, but as with basis set/level of theory choices it really depends on how much time and effort one wants to spend at that step of the research process. I would like to thank all of the respondants very much. Yet again I have been impressed with the depth of knowledge available in the list. Sincerely, matt __________________________ original post _________________________________ I am working on a project which involves parameterizing molecular mechanics torsion potentials. We used gaussian to generate energy vs. torsion data by performing constrained optimizations. One torsion angle was held constant while the rest of the coordinates in the molecule were optimized. Someone recently made the comment that constrained optimizations with gaussian are not appropriate for such a study because the unconstrained coordinates do not fully optimize. This suggestion seems odd because the literature seems to be repleat with examples of isolating the energetics of a molecular motions (distances, angles, and torsions) through constrained optimization. How far off the mark am i in thinking that constrained opts. are appropriate for this type of work. The alternative method would be to perform an IRC (internal reaction coordinate) calculation to characterize the path between the two minima of interest, but as i understand it IRC calculations are dependant on Linear Synchronous Transit calculations which ESTIMATE the transition state. Can one perform an IRC from a calculated transition state (opt=ts)? If not, how much more "valid" is an IRC calculation than constrained optimization if at any point the IRC has to "guess" the path? ___________________________ responses ___________________________________ >From peon@medchem.dfh.dk Date: Fri, 14 Jul 1995 09:43:26 +0200 From: Per-Ola Norrby To: Matt Stahl Subject: Re: CCL:validity of constrained calcs. Dear Matt, If you are interested in saving CPU-time while doing the torsional parameterization, we have recently published a method that will allow you to do this in a simple and non-ambiguous manner. In short, if you do it correctly, it's actually best to do single point ab initio calculations on several conformations generated by rigid rotations. The trick is doing the MM calculations also as single points on exactly the same confromations, and adjusting the torsion parameters to fit the energy differences at each point. Not only do you save CPU-time, but you decouple possible errors in the remaining force field (except non-bonded interactions) from the current parameterization. The reference is: Norrby et al., J. Comput. Chem., 1995, 16(5), 620. Sincerely, 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, peo@compchem.dfh.dk _________________________________________________________________________ >From FAU@ps1515.chemie.uni-marburg.de Date: Fri, 14 Jul 1995 14:55:10 MDT From: Stefan Fau To: matt@synthesis.chem.arizona.edu Subject: Re: CCL:validity of constrained calcs. Hi Matt, I didn't hear of problems with unconstrained variables that are not fully optimized. G9x determines the convergence of the optimization by the forces along your geometry variables and the displacement(i.e. the change in the value of the variable). You can look at two sections in the G9x output: The displacement for each variable (frozen or not) is listed directly above the line "0 Item Value Converged?" and the corresponding forces are listed under "Internal Coordinate Forces". The units are the same in those two places and below the "0 Item Value Converged?" line. Therefore your partial optimization has converged if all _free_ variables have forces and displacements below the threshhold values. The IRC calcs start with second derivatives (calculated at the beginning of the IRC calc or read in). They are not connected to LST calcs unless you use LST to find your TS. You provide the geometry of the transition state and you can find the TS however you like. It is important to choose a Z-Matrix with enough degrees of freedom to allow symmetry lowering on the way to the minima. The IRC calcs find a steepest descent path from the TS to the minima with the additional restriction that the path is built up from arcs of circles that are smoothly connected (for more details see: C.Gonzalez and H.B.Schlegel, J. Chem. Phys. 90,2154 (1989); J. Chem. Phys. 94,5523 (1990) and J. Chem. Phys. 95,5853 (1991)). Hope it helps, Stefan Stefan Fau, fau@ps1515.chemie.uni-marburg.de FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. D-35032 Marburg fau@ps1515.chemie.uni-marburg.de _________________________________________________________________________ >From alex@mmiris.ab.umd.edu Date: Fri, 14 Jul 95 09:46:51 -0400 From: alex@mmiris.ab.umd.edu To: matt@synthesis.chem.arizona.edu Subject: CCL:validity of constrained calcs. Matt, We have have been doing parameterization for a number of years, much of which was based on the reproduction of ab initio calculated dihedral surfaces. These were obtained from the various version of gaussian by constraining one degree of freedom and minimizing the remainder. I am not aware of any problems with the optimization of the remaining degrees of freedom. If you do think that there are problems you can perform a freqency calculation to determine the number of negative frequencies; ideally you should only obtain one for the constrained degree of freedom. good luck Alex MacKerell, alex@mmiris.ab.umd.edu School of Pharmacy University of Maryland at Baltimore 20 North Pine Street Baltimore, MD 21201 410-706-7442 _________________________________________________________________________ >From polowin@hyper.hyper.com Date: Mon, 17 Jul 95 10:36:22 -0400 From: Joel Polowin To: Matt Stahl Cc: chemistry@ccl.net Subject: Re: CCL:validity of constrained calcs. > Date: Thu, 13 Jul 1995 13:24:12 -0700 (MST) > From: Matt Stahl > Subject: CCL:validity of constrained calcs. > > I am working on a project which involves parameterizing molecular > mechanics torsion potentials. We used gaussian to generate energy vs. > torsion data by performing constrained optimizations. One torsion angle was > held constant while the rest of the coordinates in the molecule were > optimized. Someone recently made the comment that constrained optimizations > with gaussian are not appropriate for such a study because the > unconstrained coordinates do not fully optimize. This suggestion seems > odd because the literature seems to be repleat with examples of isolating > the energetics of a molecular motions (distances, angles, and torsions) > through constrained optimization. How far off the mark am i in thinking > that constrained opts. are appropriate for this type of work. If you add a constraint -- say, a torsion angle -- then none of those atoms have their normal freedom to move; they and their attachments won't be fully optimized. Through non-bonding interactions and propagated bonding interactions, everything else will be slightly distorted as well. If this is what you're talking about, it's a problem inherent in the procedure. In my opinion, it is reasonable to use these results as long as one keeps that problem in mind; in general I think that the structural distortions are not serious. In principle, I suppose it would be possible to get the same results in other ways. Most of my work has involved incrementing a constrained torsion angle to get the barrier to rotation of part of a system with respect to the rest. Instead of doing that, I imagine that one could set up a molecular-dynamics scheme where part of the system was stationary and the rest was started with initial velocities applied to the atoms corresponding to the desired rotation. For sufficiently high velocities, the barrier would be overcome. It would be a matter of repeating the calculations several times with different starting velocities to find out how much "rotational energy" would be necessary to overcome the barrier. I'm not sure how effective such calculations would be compared to the usual procedures. Joel polowin@hyper.com _________________________________________________________________________ >From elewars@alchemy.chem.utoronto.ca Date: Mon, 17 Jul 1995 16:43:33 -0400 From: "E. Lewars" To: matt@synthesis.chem.arizona.edu Subject: CONSTRAINTS I think the use of constraints for your purpose is valid. The optimization will give the other param's optimized *for the particular value of the constraint*, which is what you want, I think. In other words, you will get a slice through the potential energy hypersurface corresponding to the constrained value of one torsional. Of course the other param's won't be fully optimized, but you do not want them to be---you want the values they assume when the molecue is held at some particular dihedral angle (torsional) 9or you want the energy of this contrained, partially optimized geometry). Errol Lewars === >From acp37@rs1.rrz.Uni-Koeln.DE Date: Tue, 18 Jul 1995 10:01:16 +0200 (MST) From: Thorsten Koch To: matt@synthesis.chem.arizona.edu Subject: Re: CCL:validity of constrained calcs. > > Date: Thu, 13 Jul 1995 13:24:12 -0700 (MST) > > From: Matt Stahl > > Subject: CCL:validity of constrained calcs. > > > > The alternative method would be to perform an IRC (internal reaction > > coordinate) calculation to characterize the path between the two minima of > > interest, but as i understand it IRC calculations are dependant on Linear > > Synchronous Transit calculations which ESTIMATE the transition state. Can > > one perform an IRC from a calculated transition state (opt=ts)? If not, how > > much more "valid" is an IRC calculation than constrained optimization if at > > any point the IRC has to "guess" the path? > > As far as I can see, the LST takes the maximum of the linear path between reactants and products as a guess for a transition state. This has to be optimized using opt=ts. If you get a proper transition state from that you can use it for a IRC calculation. Note that in G94 there is a better method to find transition structures. Its invoked by opt=qst2 and input requires the route card, title and molecule specifications of the product and title and molecule specifications of the reactand. Of course, corresponding atoms must be in the same order in the z-matrix. Thorsten /-----------------------------------------------------------------\ | Thorsten Koch | | Institut fuer physikalische Chemie II der Universitaet zu Koeln | | acp37@rrz.uni-koeln.de | | Tel. +49 [0]221 470 4816 | \-----------------------------------------------------------------/ _________________________________________________________________________ >From rgab@trpntech.com Date: 19 Jul 1995 14:07:58 -0800 From: Richard Bone To: Matt Stahl Subject: Re: CCL-validity of constrai Reply to: RE>CCL:validity of constrained calcs Matt A couple of comments for you: you raise a pretty thorny issue of what constitutes the correct 'reaction path'. The general problem with what you have done is that you have assumed that the coordinate system is the same throughout the process. This will not necessarily be the case, i.e., with full relaxation, the proper modes of the system maybe such that the internal coordinate you are interested in does not correspond with anything particularly physical at all points on the path. On the other hand, what you are doing does serve to illustrate particular points effectively because it is easily understandable. Often, at intermediate points on a reaction path, the system is in low symmetry. This allows any motion to be expressed as an l.c. of lots of low-symmetry motions. Put another way, the motion is not 'pure', it is contaminated by other motions of the same (low) symm- etry. This makes analysis fairly tricky. If all you are interested in is the start and end-points, then it probably does not matter too much how you get between them. An IRC (strictly only valid in mass-weighted cartesians) allows you to roll down hill >from a (known) T.S. to wherever the path takes you. How you walk 'uphill' (i.e., do you start by displacing along a normal coordinate?) is still a problem. The whole business of factoring out various degrees of freedom in order to facilitate study of a particular motion introduces all sorts of artifacts and it depends on how much they bother you and the type of motion involved as to what you do about it. Just because the literature is full of anything of a particular nature, doesn't mean it's the best/correct way to go ! What you probably have to do is obtain the (internal) coordinate system at each new point on the path and use the 'mode' which has greatest overlap with the previous mode that you displaced along to make your next step. This is of course, time-consuming and tricky, which is part of the reason why most people don't bother. The subject is a minefield; watch where you tread! Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail rgab@trpntech.com From owner-chemistry@ccl.net Mon Jul 31 12:56:36 1995 Received: from chemsun.chem.umn.edu for schwegle@chemsun.chem.umn.edu by www.ccl.net (8.6.10/930601.1506) id MAA06156; Mon, 31 Jul 1995 12:46:57 -0400 Received: (from schwegle@localhost) by chemsun.chem.umn.edu (8.6.11/8.6.6) id LAA19679 for CHEMISTRY@ccl.net; Mon, 31 Jul 1995 11:42:52 -0500 From: Eric Schwegler Message-Id: <199507311642.LAA19679@chemsun.chem.umn.edu> Subject: Geometrical basis set To: CHEMISTRY@ccl.net Date: Mon, 31 Jul 1995 11:42:51 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 247 Hello, I am trying to locate (in electronic form) the geometrical basis set described by Clementi. I believe the original reference is in: Chem. Phys. Lett. 90, 359 (1982). Any help is appreciated, Eric Schwegler schwegle@chemsun.chem.umn.edu From owner-chemistry@ccl.net Mon Jul 31 13:11:41 1995 Received: from sangam.ncst.ernet.in for parthi@aero.iisc.ernet.in by www.ccl.net (8.6.10/930601.1506) id NAA06491; Mon, 31 Jul 1995 13:07:04 -0400 From: Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by sangam.ncst.ernet.in (8.6.12/8.6.6) with SMTP id WAA17163 for ; Mon, 31 Jul 1995 22:37:20 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA05421; Mon, 31 Jul 95 22:41:06+0530 Date: Mon, 31 Jul 95 22:41:06+0530 Message-Id: <9507311711.AA05421@iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA04190; 31 Jul 95 22:28:36 EDT (Mon) To: vigyan!ccl.net!chemistry@sangam.ncst.ernet.in Subject: NO2+NO3+M ---> N2O5+M Content-Type: text Content-Length: 1381 Dear Netters: We are interested in the rate constant value for the reaction NO2 + NO3 + M ------> N2O5 + M .....(1) and similar reactions as well, using semi-empirical method. To start with, we have constructed a super molecule between NO2 and NO3 wherein the interatomic distance between the two separate moieties was kept very large. NO2 ...... NO3 The potential energy surface (PES) was then traced as a function of the inter atomic distance. From the PES the transition state structure was obtained. Then, we have calculated the rate constant using the Arrhenius rate equation. The frequency factor "A" was assumed to be 10^11 cc mole^-1 sec^-1 (assuming as if a bimolecular reaction). Our question is the following: i) since the reaction (1) is a termolecular reaction, should we have to use some other frequency factor, ii) since the semiempirical method does not consider "M", should we have to add some compensatory factor, iii) can we compare the rate constant of the reaction (1) with other bimolecular reactions which do not involve "M". Thanks in advance for your comments and suggestions. I will summarize after receiving from you. Thank you once again. S. Parthiban Department of Aerospace Engineering, Indian Institute of Science Bangalore-560012, INDIA E-Mail: parthi@aero.iisc.ernet.in From owner-chemistry@ccl.net Mon Jul 31 14:26:37 1995 Received: from SYSWRK.UCIS.Dal.Ca for JWANG@ac.dal.ca by www.ccl.net (8.6.10/930601.1506) id OAA08286; Mon, 31 Jul 1995 14:22:29 -0400 From: Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.3-13 #6307) id <01HTIU1W20FK005DFT@SYSWRK.UCIS.DAL.CA>; Mon, 31 Jul 1995 14:13:07 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.3-13 #6307) id <01HTITYT63B800Y2V4@AC.DAL.CA>; Mon, 31 Jul 1995 14:12:16 -0300 Date: Mon, 31 Jul 1995 14:12:15 -0300 Subject: Simulations of vibrational frequencies for some mixtures To: CHEMISTRY@ccl.net Message-id: <01HTITYT63BA00Y2V4@AC.DAL.CA> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I am interested in the simulations of vibrational motions of some mixtures such as hydrogen fluoride and water, methanol and water. Could someone point to me where to find corresponding experimental results. I will summarize all replies if other people are interested in this topics as well. Jian Wang Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 From owner-chemistry@ccl.net Mon Jul 31 16:26:40 1995 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by www.ccl.net (8.6.10/930601.1506) id QAA14041; Mon, 31 Jul 1995 16:15:12 -0400 From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #7628) id <01HTIY6R9IF48X5MMD@neu.edu>; Mon, 31 Jul 1995 16:17:56 EST Date: Mon, 31 Jul 1995 16:17:55 -0500 (EST) Subject: force const-bond length scaling relations To: chemistry@ccl.net Message-id: <01HTIY6RBDXU8X5MMD@neu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello everybody. Herzberg list a number of empirical equations which relate force constant and bond length, such as (distance)**N x (frequency) = constant where N is 2 or 3, depending on the situation. Does anybody have experience with these? How good are they? Does anybody know if there is a valid expression for metal-ligand bond distances, where the metal atom's charge is variable? Would appreciate any comments, references, insights, etc. Mary Jo From owner-chemistry@ccl.net Mon Jul 31 17:11:46 1995 Received: from bioc1.biosym.com for v_uk@iris92.biosym.com by www.ccl.net (8.6.10/930601.1506) id QAA15099; Mon, 31 Jul 1995 16:59:02 -0400 Received: from iris92.biosym.com by bioc1.biosym.com (5.64/0.0) id AA05730; Mon, 31 Jul 95 13:59:41 -0700 Received: by iris92.biosym.com (931110.SGI.ANONFTP/920502.SGI) for @bioc1.biosym.com:CHEMISTRY@ccl.net id AA12848; Mon, 31 Jul 95 13:55:57 -0700 Date: Mon, 31 Jul 95 13:55:57 -0700 From: v_uk@biosym.com (Masahiko Katagari XPIRE 4-15-96 HOST John Newsam Tohoku University) Message-Id: <9507312055.AA12848@iris92.biosym.com> To: CHEMISTRY@ccl.net Subject: solvation of 3D spherical well Dear CCLers: We are interested in the magnetic properties of metal clusters in zeolite. We would like to use a quantum mechanical program which calculates the eigenstates of the 3-dimensional periodic spherical wells, preferably, a square-wave potential. Or we would like to use the muffin-tin type potential. However the potential we need to use is different from the ordinary muffin-tin potential. In the ordinary muffin-tin potential, the potential falls exponentially (?) at the centers of the atoms. In the potential which we would like to use, the potential is flat at the bottom. Does anyone know a good tool or ideas ? Any help is appreciated. Masa Katagiri BIOSYM Technologies, Inc. 9685 Scranton Road, San Diego, CA 92121, USA v_uk@biosym.com From owner-chemistry@ccl.net Mon Jul 31 22:11:46 1995 Received: from bioc1.biosym.com for behnam@iris134.biosym.com by www.ccl.net (8.6.10/930601.1506) id WAA19413; Mon, 31 Jul 1995 22:07:41 -0400 Received: from iris134.biosym.com by bioc1.biosym.com (5.64/0.0) id AA08627; Mon, 31 Jul 95 19:08:20 -0700 Received: by iris134.biosym.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id TAA03239; Mon, 31 Jul 1995 19:07:08 -0700 Date: Mon, 31 Jul 1995 19:07:08 -0700 From: behnam@iris134.biosym.com (Behnam Vessal) Message-Id: <199508010207.TAA03239@iris134.biosym.com> To: CHEMISTRY@ccl.net Subject: finding voids Dear CCLers: I am in need of a program that finds voids within a structure. Please let me know if you have any programs, tips, or clues. BEst Wishes Behnam P.S. I will summarize if there is enough interest. *********************************** Behnam Vessal, Ph.D. Biosym Technologies, Inc. 9685 Scranton Road San Diego, CA 92121 USA *********************************** e-mail: behnam@biosym.com tel: +1 619 546-5377 fax: +1 619 458-0136 ***********************************