From dario@rs5.csrsrc.mi.cnr.it Tue Jan 21 03:17:47 1997 Received: from rs5.csrsrc.mi.cnr.it for dario@rs5.csrsrc.mi.cnr.it by www.ccl.net (8.8.3/950822.1) id CAA03264; Tue, 21 Jan 1997 02:27:55 -0500 (EST) Received: by rs5.csrsrc.mi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA10930; Tue, 21 Jan 1997 08:28:23 +0100 Date: Tue, 21 Jan 1997 08:28:23 +0100 From: dario@rs5.csrsrc.mi.cnr.it (Dario Bressanini) Message-Id: <9701210728.AA10930@rs5.csrsrc.mi.cnr.it> To: CHEMISTRY@www.ccl.net Subject: What is EXACTLY a "resonance"? Dear CCLers, What is EXACTLY a "resonance"? Is it correct to say that it is a discrete level of an Hamiltonian embedded in the continuum? By discrete level i mean a stationary state, an eigenfuction belonging to the discrete spectrum of the hamiltonian, a square integrable function.can someone suggest a recent review/article on the subject? thanks Dario Bressanini dario@rs0.csrsrc.mi.cnr.it From zhou@dft.chem.cuhk.edu.hk Tue Jan 21 04:17:48 1997 Received: from iris.chem.cuhk.edu.hk for zhou@dft.chem.cuhk.edu.hk by www.ccl.net (8.8.3/950822.1) id EAA03786; Tue, 21 Jan 1997 04:08:45 -0500 (EST) Received: from dft by iris.chem.cuhk.edu.hk via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@iris.chem.cuhk.hk:CHEMISTRY@www.ccl.net> id RAA01689; Sun, 21 Jan 1996 17:05:45 +0800 Received: by dft (950511.SGI.8.6.12.PATCH526/930416.SGI.AUTO) id RAA25811; Tue, 21 Jan 1997 17:07:58 +0800 Date: Tue, 21 Jan 1997 17:07:57 +0800 (HKT) From: Zhou Ping To: CHEMISTRY@www.ccl.net Subject: Charge input format of G94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, As a novice user of G94, could anyone please tell me how to include point charges in a calculation. I have got the orthogonal coordinates of a complex and the corresponding point charges but I don't understand the instructions of the Gaussian manual: x y z charge point charge format Coordinates are in Bohr and in the standard orientation How should I change the coordinates of the point charges into standard orientation. I will be grateful if anyone could give me a sample input. Many thanks, Zhou Ping The Chinese University of Hong Kong From Steven.Creve@chem.kuleuven.ac.be Tue Jan 21 05:17:48 1997 Received: from hartree.quantchem.kuleuven.ac.be for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.8.3/950822.1) id EAA03949; Tue, 21 Jan 1997 04:39:38 -0500 (EST) Received: from localhost by hartree.quantchem.kuleuven.ac.be with SMTP id AA16980 (5.67c/IDA-1.5 for ); Tue, 21 Jan 1997 10:52:58 +0100 Date: Tue, 21 Jan 1997 10:52:58 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:G:PUNCH Keyword Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Has Anyone already succeeded in applying the PUNCH keyword to punch a GAMESS input file using Gaussian94 ? Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From giovanni@sg2.csrsrc.mi.cnr.it Tue Jan 21 06:17:47 1997 Received: from sg2.csrsrc.mi.cnr.it for giovanni@sg2.csrsrc.mi.cnr.it by www.ccl.net (8.8.3/950822.1) id FAA04166; Tue, 21 Jan 1997 05:21:31 -0500 (EST) Received: from localhost by sg2.csrsrc.mi.cnr.it via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for id CAA08222; Tue, 21 Jan 1997 02:22:01 -0800 Date: Tue, 21 Jan 1997 02:21:58 -0800 (PST) From: Giovanni Scalmani To: Computational Chemistry List Subject: Summary: Electrostatic effects in molecular crystals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear friends, some days ago I submitted a question about "Electrostatic effects in molecular crystals": > >I would like to know if someone has already faced >and (possibly) solved the following problem: > >I would like to model - within an ab-initio calculation - >the crystalline enviroment effect on a single molecule >in a molecular crystal, i.e. I would like to perform a >(possibly high level) calculation of a single molecule's >electronic structure under the influence of a >neighbouring molecules' charge distribution. >An iterative procedure should be necessary to attain >self-consistency between the ab-initio charge distribution >of the reference molecule and the neighbouring molecules' >charge distribution, which will be in turn derived from the >former. > >Since I have no deep knowledge of crystallography, I will >appreciate advises about two issues: >1) Widely speaking: Is such an approach correct? Can you > give me some references in the literature? If I have more > than one molecule (or even molecular species) in the cell > a similar approach on more than one molecule is feasible, > but is it worth while? How should I model the neighbouring > molecules' charge distribution (Mulliken charges, charges > fitted to the molecular electrostatic potential, > Atom-In-Molecule derived charges, orientable atomic > dipoles, ... ) ? >2) More technically: do you know a program which reads the > crystalline structure (for example from the Cambridge > Database) and performs all coordinates manipulation I > will need ? In particular to obtain cartesian coordinates > of any specified molecule in the cell surrounded by all the > neighbouring molecules whose centres of mass are within > a certain radius from the reference molecule's centre of > mass ? > Here I collect the answers I received. Thank you very much to people who have contributed. Giovanni. =Answer 1===================================================================== From: R29CLOSE@ETSU.ETSU-TN.EDU Organization: East Tennessee State University --- Dear Giovanni: I have worked on both these problems. In particular I wrote a program to generate a unit cell (or more) from crystallographic data. I sub- mitted it to CCL last year as DRAWCRYS.FOR. I can help you with all this. In particular, if you send me your xyz coordinates and the space group, I can do the calculations. Then with BABEL I can generate an ALCHEMY file to view the added molecules. The first part is more of a problem. In MOPAC or AMPAC there is a description of "sparkles" These are pseudo charges added to a calculation to simulate the charge of neighbors. But first I need to know what you want to calculate. Often times the easiest thing to do is simulate H-bands between neighboring molecules with water molecules in the right place. ... =Answer 2===================================================================== From: Bart Rousseau Organization: University of Antwerp --- Here are some references on solid state ab initio calculations: Ab-Initio Studies of Crystal Field Effects in Acetylene. P.Popelier, A.T.H. Lenstra, C. Van Alsenoy en H.J. Geise Acta Chemica Scandinavica, A42, 539-543 (1988). An ab-initio study of crystal field effects : Solid and gasphase geometry of acetamide. P. Popelier, A.T.H. Lenstra, C. Van Alsenoy and H.J. Geise Journal of the American Chemical Society, 111, 5658-5660 (1989). An Ab-Initio Study of Crystal Field Effects. Part 3 : Solid and Gas Phase Geometry of Formamide, Modeling the changes in a peptide group due to hydrogen bonds. P. Popelier, A.T.H. Lenstra, C. Van Alsenoy, H.J. Geise Structural Chemistry, 2, 3-9 (1991). Solids Modelled by crystal Fiels ab-initio methods. Part 4 : Thermal Vibrational Parameters and Lattice Expansion Coefficient of the Cubic Phase of Acetylene. K. Verhulst, A.T.H. Lenstra, C. Van Alsenoy, P. Popelier, H.J. Geise. Acta Crystallographica, submitted. Solids Modelled by crystal field ab-initio methods. Part 5 : The phase transitions in biphenyl from a molecular point of view. A.T.H. Lenstra, C. Van Alsenoy, K. Verhulst, H.J. Geise Acta Crystallographica, B50, 96-106 (1994). Solid State Moddeling Part VI : 2,3-diketopiperazine. On the Integration of crystallographic and spectroscopic evidence. A.T.H. Lenstra, B. Bracke, B. Van Dijk, S. Maes, C. Van Alsenoy, Herman O. Desseyn, Spiros P. Perlepes. Acta Crystallographica, submitted. Ab-initio Studies of Crystal Field Effects. Part VII : Structure of 2,3-Diketopiperazine Using a 13-Molecule Cluster, a Calculation involving 1092 Basis Functions. Anik Peeters, C. Van Alsenoy, A.T.H. Lenstra, H.J. Geise International Journal of Quantum Chemistry, 46, 73-80 (1993). Ab-initio studies of crystal field effects. Part 8 : Structure of formamide oxime using a 15-molecule cluster. Anik Peeters, C. Van Alsenoy, A.T.H. Lenstra, H.J. Geise Journal of Molecular Structure (THEOCHEM), 304, 101-107 (1994). Solids Modelled by Crystal Field Ab-Initio Methods. Part 9 : Stereoselective Order-disorder in Tri-ortho-thymotide- 3-Buten-2-ol (2/1) Clathrate. K. Verhulst, A.T.H. Lenstra, C. Van Alsenoy Acta Crystallographica, B51, 1016-1020 (1995). Solids Modelled by Crystal Field Ab-initio Methods. Part 10 : Structure of alpha-glycine, beta-glycine and gamma-glycine using a 15-molecule cluster. A. Peeters, C. Van Alsenoy, A.T.H. Lenstra, H.J. Geise Journal of Chemical Physics, 103, 6608-6616 (1995). Solids Modelled by crystal Fiels ab-initio methods. Part 11 : Integration of Chemical Substitution and Packing Schemes Exploiting Crystallographic and Spectroscopic Evidence Illustrated via Acetamide and Thioacetamide. Koen Verhulst, Stefan Maes, Christian Van Alsenoy, Albert T.H. Lenstra Journal of Molecular Structure (THEOCHEM), submitted. =Answer 3===================================================================== From: Gabriele VALERIO Organization: Ecole Nationale Superieure de Chimie de Montpellier --- Caro Giovanni, I can give you an answer for your second (technical) question. MOLDRAW (http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html) is useful to obtain cartesian coordinates or construct z-matrix from crystalline structural data. =Answer 4===================================================================== From: "Gustavo A. Mercier Jr" --- Hi! I can probably shed some light into your problem. Your problem is analogous to performing a QM computation of an active site of a protein including the electrostatic effects of the surrounding protein "environment". A lot of work went into this area during the 80's when I was doing my Ph.D. work. Check out names like Orlando Tapia, Peter vanDuijnen, Hand Dijkman, Arieh Warshel, Michaeil Levitt,Harel Weinstein, and obviously myself. Warshel and Levitt started the whole thing with a paper in J. Mol. Biol. in the 70's. There is also an early paper by Umeyama where he simply included the effect of the "environment" as a set of point charges in the hamiltonian. Today you are in luck. Many ab initio packages include the ability to incorporate "solvent" effects and you can use this feature for your work. Obviously there are several ways of doing this. - Reaction Field methods (I believe G9x) as originally implemented by O. Tapia (Although he did semiempirical methods). - Multipole Representation. Here you have a set of discrete point charges centered on the atoms, or even higher multipole (some even centered on lone pairs etc.). G9x, Hondo, and even ADF allow for computations with point charges. There is a version of Hondo developed by the the people at the National Bureau of Standards (USA) that incorporates higher multipoles. (Check out the work of Morris Krauss). - Multipole Representation plus polarization. This is probably the most complete treatment. You can check my work and Hans Dijkman's. We never implemented this in a very user friendly manner. Indeed, I was doing serial computations with manual steps in between to do so. I then left the field. Hans and I developed complementary mathematical treatments. All of it is predicated in the group function method of McWeeney. I must point out several caveats. As Hans Dijkman (P. vanDuijnen's grad student at the time) pointed out, you cannot have a direct interaction between the "environment" and the SCF density at each SCF step. You need to have an interaction between the converged density of your molecule and the converged polarized "environment". For example: Run 1 : Qm computation in the presence of point charges. effect 1: polarization of the Qm molecule. Run 2: Use the converge density of 1 to polarize the environment. For example, with atom centered polarizabilities. Run 3: Fix the polarized environment and repeat Run 1 using the new environment, but starting the SCF from the output of Run 1. effect 3: Second order polarization of Qm molecule. Run 4: Repeat 2 with the output of Run 3. Run 5: Repeat 3 with the polarized environment of Run 4. ... The above is a true implementation of the method of group functions by McWeeney when one of the groups is "classical" and the other is Qm. Early work in the area was done by H. Weinstein (my Ph.D. advisor). This is tedious and unfortunately I never automated it because In my case it converged extremely quickly. The polarization of a charged environment is very small. The reason I describe all of this is because people took the wrong turn many times. They simply included the environment during the SCF process and this led to wrong result in thre presence of extended basis sets (no convergence!), but "worked" with minimal basis sets. The effect when you include the environment during the SCF process is to incorporate instantaneous fluctuations in the density of the Qm and environment groups. This resulted in spurious term like a the dispersion term that vanDuijnen described. The densities at each SCF step are not physical observables that can be used to compute interactions between groups, as McWeeney shows. Finally, don't forget the factor of (1/2) that occurs in the energy term because the cost of polarizing the systems is (1/2) the polarization energy computed from the converged polarized system (i.e. Qm + environment). This was also a source of trouble then. ... =Answer 5===================================================================== From: "Donald E. Williams" --- Dear Dr. Scalmani: Your questions raise many different issues. In most of my work I have considered that a given molecule is not polarized by surrounding molecules in the crystal. My procedure is to get a good wavefunction for the gas molecule (I use gaussian-94 for that), calculate the MEP on a geodesic grid around the molecule. Then I fit the MEP, using my program PDM97, with net atomic charges, if possible, or adding additional sites (e.g. lone pairs) if necessary. Then to pursue my interest in ab initio crystal structure prediction I put one or more molecules in an arbitrary cell and minimize the total energy including exchange repulsion and dispersion attraction. This mimization is carried out with my program mpa/mpg. If everything works the observed crystal structure (including space group symmetry) is predicted. For your specific interest in locating molecules around a reference molecule in the crystal, mpa/mpg would of course do that. A recent reference can be found in Acta Cryst. 1996, A52, 326-328. -Donald Williams =Answer 6===================================================================== From: iguana@one.net (Ray Crawford) --- Giovanni, Could you please forward the results of this query to me? We are currently trying to do something similar in that we are trying to estimate the energetic differences between a small molecule crystal conformation and a bound macromolecule/ligand crystal structures. The programs we are using to do this are Gaussian and Spartan. Just a few considerations that you might want to keep in mind are: 1.) crystal structure atomic placements are different than force field/ab initio atom placements. What this means is that if you try to do a Single Point calculation on the single molecule crystal structure, you will get an extremely high energy as compared to a nearby low energy conformation. We found that the majority of this energetic difference in due to the placement of the H's (both bond lengths (which are VERY influential) and bond angles/torsions). Other energetic problems result from the placements of the heavy atoms (although these are not as influential). 2.) not many programs allow you to get around these problems. We are currently using Gaussian because of it's ablility to use very explicative z-matrices. Another option are to use Charmm because of its "restrant" option. I hope these two considerations are useful although they may not be exactly related/relavent to what you are doing... But I do realize that we are examining different aspects of similar problems... Any info you could pass along would be greatly appreciated. =Answer 7===================================================================== From: "Francois GILARDONI - Gp. J.WEBER - Univ. Geneve" (The original message was in Italian. I am sorry to Francois for the errors I will put in this translation!) --- I think that there could be many solutions to your problems: 1. Make use of point charges. Gaussian94 can perform that type of calculations. I used instead the DFT-code deMon and I had good results (J.Chem.Phys., 104 (19), p.7624). The set of charges can be reduced by using Ewald summation technique. In that case, the code I used wasn't able to fit the electrostatic field with the desired precision. 2. Make use of Lennard-Jones, Morse or Buckingham functions to fit the potential energy curve obtained from ab-initio calculations (involving the nearest neighbors). According to my experience, Buckingham functions are the most suited ... but it will strongly depend upon the particular situation. I tried to model Ru(bz)2 and [Ru(cp)2]2+ crystals with this method. 3. The Car-Parinello method and the program MARVIN (pseudo-potential) could also be good choice, but I don't know to much about them. When you are using point charges, don't forget to use a distribution that reflects the symmetry of the crystal. ---------------------------------------------------------------------- ^^^ | SCALMANI Giovanni giovanni@sg2.csrsrc.mi.cnr.it o o | Universita' degli Studi di Milano | | Dipartimento di Chimica Fisica ed Elettrochimica \_/ | via C.Golgi, 19 Phone: ++39-2-26603254 | 20133 Milano (Italy) Fax : ++39-2-70638129 ---------------------------------------------------------------------- From lankau@blubber.chemie.uni-hamburg.de Tue Jan 21 07:17:50 1997 Received: from blubber.chemie.uni-hamburg.de for lankau@blubber.chemie.uni-hamburg.de by www.ccl.net (8.8.3/950822.1) id HAA04496; Tue, 21 Jan 1997 07:00:08 -0500 (EST) Received: by blubber.chemie.uni-hamburg.de (AIX 4.1/UCB 5.64/4.03) id AA12184; Tue, 21 Jan 1997 12:57:45 +0100 Date: Tue, 21 Jan 1997 12:57:44 +0100 (NFT) From: Timm Lankau To: Frage CCL Subject: Summary: broken symmetry in G94 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, thank you very much for your answers. At the end of this mail is an extract from the most helpful answers. Stephan Irle's suggestion seems to the useful but also to be the most tedeous. He suggest to use another element and to redefine it later with the 'massage' command and an external basis set. Once again thank you. Best wishes Timm ========================================================================== Timm Lankau phone (+)40 4123 3686 Institut fuer Physikalische Chemie fax (+)40 4123 3452 Universitaet Hamburg e-mail lankau@chemie.uni-hamburg.de Bundesstr. 45 20146 Hamburg Germany ========================================================================== Summary: ======== Dear Timm, If you have the cartesian coordinates of your computation with the first symmetry, you might just want to change the last digit of the respective coordinates one number, to bring it in accordance with the required symmetry. Since G94 outputs give many digits in the cartesisian coordinates, this changes (let's say for an arbitrary number from 1.2853967 to 1.2853968) changes the symmetry recognition by G94 (see reference manual for the limits that is keeps by default for this recognition), but will not affect the energy itself significantly (often less than a microhartree!). I hope this helps, Han *************************************************************************** ** Dr. Han Zuilhof ** E-mail: ZUILHOF@chem.columbia.edu ** ** Department of Chemistry ** ** ** MC 3156 ** ** ** Columbia University ** ** ** New York, NY, 10027 ** Fax: (212) 932-1289 ** ** USA ** Voice: (212) 854-2179 ** *************************************************************************** Viele Gruesse von Wien nach Hamburg! Meine pragmatische Loesung fuer das Problem ist die Folgende: Gaussian einfach ein anderes chemisches Element fuer das 2. Atom in der Z-Matrix vorsetzen, und dieses dann entsprechend mittels listengesteuertem Basissatz-Input und dem Keyword 'massage' fuer die Kernladung so zu modifizieren, dass de facto zwei identische Atome vorliegen. Fuer N2 hat der Trick auf diese Weise funktioniert. Input: # rhf/gen gfinput n2 full symmetry 0 1 n n 1 r1 r1=1.0 1 2 0 S 3 1.00 .2427660000D+03 .5986570000D-01 .3648510000D+02 .3529550000D+00 .7814490000D+01 .7065130000D+00 SP 2 1.00 .5425220000D+01 -.4133010000D+00 .2379720000D+00 .1149150000D+01 .1224420000D+01 .8589530000D+00 SP 1 1.00 .2832050000D+00 .1000000000D+01 .1000000000D+01 **** --Link1-- # rhf/gen gfinput massage n2 broken symmetry (2nd nitrogen atom massaged) 0 1 n o 1 r1 r1=1.0 1 2 0 S 3 1.00 .2427660000D+03 .5986570000D-01 .3648510000D+02 .3529550000D+00 .7814490000D+01 .7065130000D+00 SP 2 1.00 .5425220000D+01 -.4133010000D+00 .2379720000D+00 .1149150000D+01 .1224420000D+01 .8589530000D+00 SP 1 1.00 .2832050000D+00 .1000000000D+01 .1000000000D+01 **** 2 0 7.0 -Stephan-Irle--stephan@itc.univie.ac.at--------------------------------------- http://www.itc.univie.ac.at/~stephan/ voice:+43/1/40480-679 From korkin@qtp.ufl.edu Tue Jan 21 09:17:50 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id IAA04910; Tue, 21 Jan 1997 08:58:37 -0500 (EST) From: Received: from white7.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id IAA02196; Tue, 21 Jan 1997 08:46:30 -0500 Received: by white7.qtp.ufl.edu (SMI-8.6/SMI-SVR4) id IAA01851; Tue, 21 Jan 1997 08:46:28 -0500 Date: Tue, 21 Jan 1997 08:46:28 -0500 Message-Id: <199701211346.IAA01851@white7.qtp.ufl.edu> To: dario@rs5.csrsrc.mi.cnr.it Subject: Re: CCL:What is EXACTLY a "resonance"? Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: 1cPihZxWM127devri90QnA== Dario, There is no direct correspondence between Hamiltonian and the wave function and the resonance theory. The resonace theory is based rather on bonding concepts developed by organic chemists rather than theoreticians. Certainly, they reflect a "reality" in some way because this theory is based on experimental facts, which can be described by quantum mechanics of molecules. Probably, the most close analogy among the resonance "theory" and quantum mechanics is represented by generalized valence bond (GVB) scheme. But the valence structures in GVB is not exactly what organic chemists mean by "resonance". We can say that a few valence structures in GVB correspond to one structure in resonance theory. You may look in Dewar books. I do not think computational and theoretical chemist care a lot about "resonance" nowdays. Cheers, Anatoli Korki From sichelj@Umoncton.CA Tue Jan 21 10:17:50 1997 Received: from bosoleil.ci.umoncton.ca for sichelj@Umoncton.CA by www.ccl.net (8.8.3/950822.1) id JAA05033; Tue, 21 Jan 1997 09:18:56 -0500 (EST) Received: by bosoleil.ci.umoncton.ca (1.37.109.20/16.2) id AA081226419; Tue, 21 Jan 1997 10:20:19 -0400 Date: Tue, 21 Jan 1997 10:20:18 -0300 (ADT) From: "John-M. Sichel" Sender: "John-M. Sichel" Reply-To: "John-M. Sichel" Subject: Re: CCL:What is EXACTLY a "resonance"? To: Dario Bressanini Cc: CHEMISTRY@www.ccl.net In-Reply-To: <9701210728.AA10930@rs5.csrsrc.mi.cnr.it> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Tue, 21 Jan 1997, Dario Bressanini wrote: > What is EXACTLY a "resonance"? Is it correct to say that > it is a discrete level of an Hamiltonian embedded in the continuum? > By discrete level i mean a stationary state, an eigenfuction belonging > to the discrete spectrum of the hamiltonian, a square integrable function.can someone suggest a recent review/article on the subject? > thanks Dario Bressanini dario@rs0.csrsrc.mi.cnr.it A resonance is _approximately_ a discrete state, but it does interact (perhaps weakly) with the continuum states at nearby energies. The exact states _near_ the resonance energy therefore have some discrete character which makes them different from continuum states at other energies. For example, if absorption to the discrete state is allowed, there will be enhanced absorption to states in this energy region. The observed effect will then be a peak or "resonance" near the energy of the discrete state. John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada E1A 3E9 Tel: (506-)858-4313 E-mail: SICHELJ@UMONCTON.CA I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. (Gaussian92) From rmuller@rcf.usc.edu Tue Jan 21 11:18:07 1997 Received: from usc.edu for rmuller@rcf.usc.edu by www.ccl.net (8.8.3/950822.1) id LAA05942; Tue, 21 Jan 1997 11:16:35 -0500 (EST) Received: from chem2.usc.edu (chem2.usc.edu [128.125.253.153]) by usc.edu (8.8.4/8.7.2/usc) with ESMTP id IAA29720 for ; Tue, 21 Jan 1997 08:16:33 -0800 (PST) Received: from chem2.usc.edu (localhost.usc.edu [127.0.0.1]) by chem2.usc.edu (8.7.6/8.7.3/usc) with SMTP id IAA10412 for ; Tue, 21 Jan 1997 08:16:33 -0800 Sender: rmuller@chem2.usc.edu Message-ID: <32E4EBE1.ABD@rcf.usc.edu> Date: Tue, 21 Jan 1997 08:16:33 -0800 From: "Richard P. Muller" Organization: University of Southern California X-Mailer: Mozilla 3.01Gold (X11; I; AIX 2) MIME-Version: 1.0 To: Computational Chemistry List Subject: CCL: JAVA tools for Chemistry References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I want to put together a web-page linking current JAVA tools for chemistry. I am most interested in applets and applications that come with publically distributed JAVA-source, so that chemists wishing to learn how to program in JAVA may use these resources as starting points. From searching through the CCL archives I've found a couple good links. Can anyone suggest any more? In particular, I would like to see examples of using JAVA applets/applications as front-ends to GAUSSIAN, GAMESS, etc. Any help, references, URL's that anyone can offer will be greatly appreciated. I will of course post the URL of my page when it's finished. Rick -- Richard P. Muller, Ph.D. rmuller@invitro.usc.edu Department of Chemistry, SGM 418 http://www-rcf.usc.edu/~rmuller University of Southern California Office 213-740-7671 Los Angeles, CA 90089-1062 FAX 213-740-2701 From bergerd@bluffton.edu Tue Jan 21 14:17:52 1997 Received: from bc.bluffton.edu for bergerd@bluffton.edu by www.ccl.net (8.8.3/950822.1) id NAA07214; Tue, 21 Jan 1997 13:45:24 -0500 (EST) Received: from [205.133.211.196] by bc.bluffton.edu (SMTPD32-3.02) id AEFB1AAF0032; Tue, 21 Jan 1997 13:46:19 -0500 Received: by bergerd.bluffton.edu with Microsoft Mail id <01BC07A1.57838F20@bergerd.bluffton.edu>; Tue, 21 Jan 1997 13:45:19 -0500 Message-ID: <01BC07A1.57838F20@bergerd.bluffton.edu> From: "Daniel J. Berger" To: "'Computational Chemistry List'" Subject: PM3 parameters for boron Date: Tue, 21 Jan 1997 13:45:13 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Last I checked (just a couple years ago) there weren't any PM3 parameters for boron, but have any been generated recently? Thank you very much! Daniel J. Berger PH: (419) 358-3379 Bluffton College FAX:(419) 358-3323 280 W. College Avenue bergerd@bluffton.edu Bluffton OH 45817-1196 http://cs.bluffton.edu/~berger/ From smb@smb.chem.niu.edu Tue Jan 21 15:17:52 1997 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id OAA08177; Tue, 21 Jan 1997 14:55:02 -0500 (EST) Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA12381 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Tue, 21 Jan 1997 13:55:04 -0600 Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA27305; Tue, 21 Jan 97 13:51:47 -0600 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA16927; Tue, 21 Jan 97 14:01:39 -0600 Received: by smb.chem.niu.edu (940816.SGI.8.6.9/940406.SGI) for CHEMISTRY@www.ccl.net id NAA28319; Tue, 21 Jan 1997 13:53:04 -0600 Date: Tue, 21 Jan 1997 13:53:04 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <199701211953.NAA28319@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: Spring ACS COMP Full program online The Spring 1997 ACS Division of Computers in Chemistry (COMP) full technical program is available now on the divisions' www site: http://hackberry.chem.niu.edu/COMP/ Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From MARYJO@neu.edu Tue Jan 21 15:22:38 1997 Received: from NUHUB.DAC.NEU.EDU for MARYJO@neu.edu by www.ccl.net (8.8.3/950822.1) id OAA07570; Tue, 21 Jan 1997 14:19:11 -0500 (EST) From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01IEH7G3JMY899HQN1@neu.edu>; Tue, 21 Jan 1997 14:18:53 EST Date: Tue, 21 Jan 1997 14:18:53 -0500 (EST) Subject: plant phytochemical computations? To: CHEMISTRY@www.ccl.net Message-id: <01IEH7G3KZ6Q99HQN1@neu.edu> X-Envelope-to: CHEMISTRY@www.ccl.net X-VMS-To: IN%"CHEMISTRY@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi. I am seeking recent references for any quantum calculations on plant phytochemicals I am particularly interested in molecules found in common fruits and vegetables which appear to have health benefits, but are not considered nutrients. I have plenty of references about the phytochemicals and their properties. I simply need to find out what electronic structure calculations have been done on them, so I am seeking references that detail Quantum calculations. Thanks in advance for your references, Mary j.o.