From chemistry-request@server.ccl.net Tue Feb 22 04:02:13 2000 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03585 for ; Tue, 22 Feb 2000 04:02:12 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id XAA29854 for ; Mon, 21 Feb 2000 23:55:27 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma029852; Mon, 21 Feb 00 23:55:26 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id XAA50256; Mon, 21 Feb 2000 23:55:25 -0800 (PST) Received: from mdli.com (lchen-95h.mdli.com [191.254.19.100]) by shepherd.mdli.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id FK4MGWDS; Mon, 21 Feb 2000 23:55:24 -0800 Message-ID: <38B23E73.5835121B@mdli.com> Date: Mon, 21 Feb 2000 23:44:51 -0800 From: Lingran Chen X-Mailer: Mozilla 4.5 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Summary: References on exact solutions to Schroedinger equations? References: <38979D79.66201E63@mdli.com> Content-Type: text/plain; charset=iso-8859-1 X-MIME-Autoconverted: from 8bit to quoted-printable by puffin.mdli.com id XAA50256 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA03586 Dear CCLers: Some days ago I asked the following question: > Dear CCLers: > > I'm looking for the references about the mathematically *exact* > solutions to Schroedinger equations for any chemical systems. > Thanks in advance. > > -Lingran I have received many replies, which are summarized below. First, let me cite the answers of my question from Ira N. Levine's book "Quantum Chemistry" (5th edition, 2000) I just bought and received today: P.78: "We solved the Schroedinger equation exactly for the particle in a box and the harmonic oscillator." P.163: "The Schroedinger equation for the one-electron atom is exactly solvable. However, because of the interelectronic repulsion terms in the Hamiltonian, the Schroedinger equation for many-electron atoms and molecules is not separable in any coordinate system and cannot be solved exactly. " P.376: "The electronic Schroedinger equation for H2+ is separable, and we can get exact solutions for the eigenfunctions and eigenvalues." The answers I received are listed (in the order I received) below. Thanks a lot! -Lingran > *********************************** > Lingran Chen, Ph.D. > Senior Scientific Programmer > MDL Information Systems, Inc. > 14600 Catalina Street > San Leandro > CA 94577 > U.S.A. > > Phone: (510) 895-1313 > FAX: (510) 614-3616 > > Email: LCHEN@MDLI.COM > Web: http://www.mdli.com > *********************************** ----------------------------------------------------------------------------------- Subject: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 09:31:46 +0100 (CET) From: Jochen =?UNKNOWN?Q?K=FCpper?= To: Lingran Chen CC: "chemistry@ccl.net" References: 1 As far as I understand there are none :-( You could look at textbooks-solutions of H-atoms, though ). Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43.02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.jochen-kuepper.de ---------- Subject: Re: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 11:40:35 +0200 (EET) From: John Kerkines To: Lingran Chen Dear Lingran, That's a very interesting question you sent to the list. Can you please forward to me (or to the list) any responses? With Regards, John Kerkines ---------- Subject: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 15:50:19 +0100 From: Thomas Bligaard Pedersen Organization: Physics Department, Techn. Univ. of Denmark CC: Lingran Chen , "chemistry@ccl.net" References: 1 , 2 The only molecules, for which there exists exact analytical solutions, are the molecular ions of homonuclear diatomics with only one electron: H2(+), He2(3+), >... "Where as the equation for the H atom is separable in sperical polar coordinates, the equation for the molecule-ion is separable in ellipsoidal coordinates in which the two nuclei are the foci of the ellipses." quote P.W.Atkins, Molecular Quantum Chemistry 2nd ed. p 250-251 An actual derivation is not made in this book, but I have seen one in lecture notes by Jens Peder Dahl. These might be difficult to obtain, but he is very helpfull, and can probably direct you to the original references if you contact him on jpd@kemi.dtu.dk I hope this helps Thomas ---------- Subject: mathematically exact Date: Wed, 02 Feb 2000 08:02:06 -0800 From: vmohan@isisph.com To: LCHEN@MDLI.COM Hi, I would think that Quantum Monte Carlo method yields the mathematically exact solutions to Schrodinger equation. The advantage of this method is that the correlation term [exp(-rij)] can be directly used in the wavefunction. Conventional variational methods include the electron correlation indirectly. The exactness of QMC on a number of chemical systems thas been published by Jim Anderson [Penn.State]. Hope this helps, -mohan ---------- Subject: Re: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 08:14:03 -0800 From: wsteinmetz Organization: Pomona College To: Lingran Chen References: 1 Mathematically exact solutions? The list of closed-form analytic solutions is VERY short. The list of chemical problems includes the H atom, the harmonic oscillator, the rigid rotor, possibly the Morse potential, and the ESR/NMR problem. Consult Pauling and Wilson, Introduction to Quantum Mechanics. Another good practical book with solutions is S. Flueege, Practical Quantum Mechanics, Springer-Verlag. Any good book on NMR will outiline the application of angular momentum theory to the calculation of the spectrum of a system of coupled spins. The classic was written by Pople, Schneider, and Bernstein. The solution involves the diagonalization of N x N matrices. ---------- Subject: Re: CCL: References on exact solutions to Schroedinger equation Date: Wed, 02 Feb 2000 11:54:39 -0500 (EST) From: Stefan Fau To: lchen@mdli.com Hi, it may not be what you are looking for, but maybe two years ago some mathematician found an exact solution to the three body interaction problem, I think by developing it in an infinite series. I believe I read it as a short note in Scientific American. Stefan ______________________________________________________________________ Dr. Stefan Fau fau@qtp.ufl.edu Quantum Theory Project University of Florida Gainesville FL 32611-8435 ---------- Subject: Re: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 09:41:55 -0800 From: "Richard P. Muller" To: Lingran Chen , "chemistry@ccl.net" References: 1 , 2 , 3 Thomas Bligaard Pedersen wrote: > > The only molecules, for which there exists exact analytical solutions, are the > molecular ions of homonuclear diatomics with only one electron: H2(+), He2(3+), > >... > > "Where as the equation for the H atom is separable in sperical polar coordinates, > the equation for the molecule-ion is separable in ellipsoidal coordinates in which > the two nuclei are the foci of the ellipses." > quote P.W.Atkins, Molecular Quantum Chemistry 2nd ed. p 250-251 > An actual derivation is not made in this book, but I have seen one in lecture > notes by Jens Peder Dahl. These might be difficult to obtain, but he is very > helpfull, and can probably direct you to the original references if you contact > him on > > jpd@kemi.dtu.dk > > I hope this helps If you're interested in close-to-exact solutions, I would suggest looking at the papers of Hylleraas or Pekeris for the He atom (I can send you software that reproduces Pekeris' work, if you'd like). I also highly recommend Flugge's _Practical_Quantum_Mechanics_, which has a wide variety of problems solved analytically. Bethe and Jackiw'w _Intermediate_Quantum_Mechanics_ is also quite good for this. -- Richard P. Muller, Ph.D. rpm@wag.caltech.edu http://www.wag.caltech.edu/home/rpm ---------- Subject: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 18:52:28 +0100 From: Eberhard von Kitzing To: Thomas Bligaard Pedersen CC: Lingran Chen , "chemistry@ccl.net" References: 1 , 2 At 15:50 Uhr +0100 02.02.2000, Thomas Bligaard Pedersen wrote: >The only molecules, for which there exists exact analytical solutions, are the >molecular ions of homonuclear diatomics with only one electron: H2(+), >He2(3+), >>... > >"Where as the equation for the H atom is separable in sperical polar >coordinates, >the equation for the molecule-ion is separable in ellipsoidal coordinates >in which >the two nuclei are the foci of the ellipses." You may find something in Hund Z Phys 36, 657 (1926) Mulliken J Chem Phys 3, 375 (1935) Coulson Trans Farad Soc 33, 1479 (1937) ========================================================== Eberhard von Kitzing Abteilung Zellphysiologie Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69120 Heidelberg Tel: +49 6221 486 467 Germany FAX: +49 6221 486 459 email: vkitzing@mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/ ---------- Subject: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 13:27:49 -0600 From: "Robert E. Harris" To: Chemistry References: 1 , 2 The H2 molecule positive ion solution is discussed on pp. 201-203 of Eyring, Walter, and Kimball's book, "Quantum Chemistry". They refer to work; E. Teller, Z. Physik, 61, 458 (1930), O. Burrau, Kgl. Danske Videnskab. Selskab., 7, 1 (1927), E. Hylleras, Z. Physik, 71, 739 (1931), and G. Jaffe, Z. Physik, 87, 535 (1934). It is also discussed on pp. 134-136 of Pitzer's "Quantum Chemistry". See also pp. 1-40 of Slater's "Quantum Theory of Molecules and Solids, Volume 1, Electronic Structure of Molecules". Slater says quite complete numerical information about the solution is given by D. R. Bates, K. Ledsham, and A. L. Stewart, Phil. Trans. Roy. Soc. London, 246, 215 (1953). One should note that the solution for the ground state is not closed form in terms of elementary transcendental functions. REH Robert E. Harris Phone: 573-882-3274 Fax: 573-882-2754 Department of Chemistry, University of Missouri-Columbia Columbia, Missouri, USA 65211 ---------- Subject: CCL:References on exact solutions to Schroedinger equations? Date: Wed, 02 Feb 2000 13:40:54 -0600 From: "Robert E. Harris" To: chemistry@ccl.net References: 1 , 2 I neglected Pauling and Wilson's "Introduction to Quantum Mechanics", pp. 327-340 in the Dover reprint. The exact solutions for H2+ ion are of course numerical solutions; these are exact in the sense that the exponential solution for the H atom is exact. The exponential function is well-know and frequently tabulated, while the solutions to the H2 + ion are not familiar. So, some would say the H atom is solved "exactly" while the H2 + ion isn't, but really, is a mutt more of a dog than an Afgan ound jsut because mutts are more familiar? REH Robert E. Harris Phone: 573-882-3274 Fax: 573-882-2754 Department of Chemistry, University of Missouri-Columbia Columbia, Missouri, USA 65211 ---------- Subject: Exact Solutions to "Chemical Systems" Date: Wed, 02 Feb 2000 15:44:11 -0500 (EST) From: Brian Williams To: lchen@mdli.com I don't know if this is exactly what you are after, but at the moment I think I have a way to define analytically solvable potentials resembling diatomic or Morse potential curves. I am at the moment attempting to see if these analytically exact solutions can be fit to experimental data for diatomics. I do not have this work written up, but would be happy to send you notes if you are interested. Brian Williams, Chemistry Bucknell University ---------- Subject: Exact solutions. Date: Thu, 03 Feb 2000 01:35:43 +0100 From: Thomas Bligaard Pedersen To: lchen@mdli.com I was wrong in saying that only homonuclear diatomics are solved analytically. These were solved in G. Jaffé, Z. Phys. 87:535 (1934) Heteronuclear diatomic molecular ions with one electron are also solved: W.G.Barber and H.R.Hassé, Proc. Camb. Phil. Soc. 31:564 (1935) Thomas ---------- Subject: CCL:Nuclear Attraction Integrals Date: Thu, 03 Feb 2000 09:42:45 +0100 (MET) From: Christoph.van.Wuellen@ruhr-uni-bochum.de To: rpm@wag.caltech.edu (Richard P. Muller) CC: chemistry@ccl.net A nuclear attraction integral is just a special case of a two-electron integral: = (ij | kk) where k is a normalized s-Funktion centered at c with "infinitly high" exponent. Some simplifications arise naturally, so if you have a text on two-electron integrals, it also covers nuclear attr. integrals. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ ---------- Subject: CCL:Re, References on exact solutions ... Date: Thu, 03 Feb 2000 09:49:32 +0100 (MET) From: Christoph.van.Wuellen@ruhr-uni-bochum.de To: chemistry@ccl.net I wonder if during this discussion is has been pointed out that H2+ is a three-body system. The "exact" solution discussed so far is however the solution of a one-body Schroedinger equation with the clamped nuclei hamiltonian. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ ---------- Subject: CCL:Re, References on exact solutions ... Date: Thu, 03 Feb 2000 23:18:22 +0200 (EET) From: Tom Sundius To: Christoph.van.Wuellen@ruhr-uni-bochum.de CC: chemistry@ccl.net On Thu, 3 Feb 100 Christoph.van.Wuellen@ruhr-uni-bochum.de wrote: > I wonder if during this discussion is has been pointed out that H2+ is > a three-body system. The "exact" solution discussed so far is however the > solution of a one-body Schroedinger equation with the clamped nuclei > hamiltonian. Of course there is no analytical solution to a three-body problem. But a complete numerical solution by separation of the variables was already given in 1927 by Oyvind Burrau in Denmark. His solution to the problem in the book by Pauling and Wilson (Introduction to Quantum Mechanics, sect. 42c). This solution was later improved by Hylleraas and Jaffe. The results were in very close agreement with experiment. Tom Sundius University of Helsinki, Department of Physics phone +358-9-191 8339 P.O.Box 9, FIN-00014 Helsinki, Finland fax +358-9-191 8680 ---------- Subject: CCL:Re, References on exact solutions ... Date: Fri, 04 Feb 2000 11:32:36 +0100 From: Ramon Crehuet Organization: C.S.I.C. To: chemistry@ccl.net References: 1 There is system that can be considered somehow chemical: Hooke's atom. It consists of an atom with two Coulomb interacting electrons bounded to a nucleus by an harmonic potential. This is very briefly described by Burke, Perdew and Ernzerhof in J. Chem. Phys, Vol. 109, No. 10, p. 3760 and the mathematical solution can be found in references therein. SORRY!!! Vol. 109, No. 10, p. 3760, 1998 Ramon ---------- Subject: CCL:Re, References on exact solutions ... Date: Fri, 04 Feb 2000 12:15:46 +0100 From: assfeld@host23.lctn.u-nancy.fr To: chemistry@ccl.net, rcsqtc@iiqab.csic.es Any FULL CI calculations are *exact* solutions, at least for the basis set considered. And there is a lot of litterature about it. Just my 2 cents... ...Xav http://www.lctn.u-nancy.fr/Chercheurs/Xavier.Assfeld From chemistry-request@server.ccl.net Tue Feb 22 09:04:40 2000 Received: from mail4.nycap.rr.com (mail4-1.nyroc.rr.com [24.92.33.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA05522 for ; Tue, 22 Feb 2000 09:04:39 -0500 Received: from claessen.nycap.rr.com ([24.161.16.156]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com; Tue, 22 Feb 2000 08:00:17 -0500 Reply-To: From: "Rolf Claessen" To: "Chemistry@Ccl. Net" Cc: "Scheila" Subject: RE: X-ray data converter- I need a free software Date: Tue, 22 Feb 2000 07:54:37 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Dear Scheila, a very good and free program is BABEL. You can find a download site at http://www.eyesopen.com/download/babelwin.zip or at ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ (also win and mac and unix) It handles over 50 different formats. Find other related chemistry software in my chemistry software list (>300 in categories) at http://www.claessen.net/chemistry/soft_en.html Regards, Rolf Claessen > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Scheila > Sent: Monday, February 21, 2000 10:53 AM > To: chemistry@ccl.net > Subject: CCL:X-ray data converter- I need a free software > > > I’m a student and I’m working with molecular structure and > proprieties in my > doctoral course. > I need a help to convert some x-ray data disposed in a paper. This paper > shows the data group, the a, b and c parameters and the atomic coordinates > in the format: > x y z > C1 7866(3) 3480(6) -1818(4) > C2 7641(2) 4107(6) -2989(4) > C3 7896(2) 5715(6) -3240(4) > : > : > OMEI 9490(2) 7341(7) 3845(4) > CMEI 9845(5) 5894(15) 3795(10) > W1/2* 9230 923 2984 > W2/2* 8963 2070 3358 > > > *occupancy factor f=0.5 > > In fact I don’t know witch format is it and I want to know if > there are any > free software that could convert this data to a FDTA format, to > be imported > by the Spartan software. > It is important to remember that it is the x-ray atomic coordinates of a > crystallized molecule. > Thanks for any help. > > Scheila F. Braga > > ________________________ > Scheila Furtado Braga > IFGW-DFA-UNICAMP > Campinas – Brazil > e-mail : scheila@ifi.unicamp.br > _________________________ > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Feb 22 10:20:08 2000 Received: from prserv.net (out1.prserv.net [32.97.166.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA06096 for ; Tue, 22 Feb 2000 10:20:08 -0500 From: jmmckel@attglobal.net Received: from attglobal.net ([32.100.232.115]) by prserv.net (out1) with SMTP id <2000022214131725202j9q6te>; Tue, 22 Feb 2000 14:13:17 +0000 Message-ID: <38B256A8.9AA0BCCF@attglobal.net> Date: Tue, 22 Feb 2000 09:28:08 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Error Function [ERF] Code Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! I'm aware that most gaussian function based ab initio codes make copious use of ERF in the calculation of Vee and Ven, and that most codes have their own way of computing this information. Can someone please point me to a source for a fortran code to do compute ERF, however slow it might be? Many thanks! John McKelvey From chemistry-request@server.ccl.net Tue Feb 22 12:08:11 2000 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06859 for ; Tue, 22 Feb 2000 12:08:11 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id JAA04959; Tue, 22 Feb 2000 09:01:16 -0700 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: jmmckel@attglobal.net, chemistry@ccl.net Subject: Re: CCL:Error Function [ERF] Code Date: Tue, 22 Feb 2000 08:59:53 -0700 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <38B256A8.9AA0BCCF@attglobal.net> In-Reply-To: <38B256A8.9AA0BCCF@attglobal.net> MIME-Version: 1.0 Message-Id: <00022209011500.00324@ice> Content-Transfer-Encoding: 8bit The slatec/fnlib functions derf, derfc, initds, dcsevl, and d1mach (available from netlib) should fix you up. Note that the d1mach is used also by lapack, and you can get inappropriate machine values if you are not careful. Cheers, Matt On Tue, 22 Feb 2000, jmmckel@attglobal.net wrote: > Hello! > > I'm aware that most gaussian function based ab initio codes make copious > use of ERF in the calculation of Vee and Ven, and that most codes have > their own way of computing this information. Can someone please point > me to a source for a fortran code to do compute ERF, however slow it > might be? > > Many thanks! > > John McKelvey > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Tue Feb 22 12:11:15 2000 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06915 for ; Tue, 22 Feb 2000 12:11:14 -0500 Received: from lekha (lekha.cam.msi-eu.com [172.27.64.201]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian/GNU) with ESMTP id QAA07339 for ; Tue, 22 Feb 2000 16:02:17 GMT Message-Id: <4.2.0.58.20000222155858.00a70d80@mailhost> X-Sender: katriona_knapman@mailhost X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Tue, 22 Feb 2000 16:02:17 +0000 To: chemistry@ccl.net From: Katriona Knapman Subject: New website for computational materials science Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed MatHub is a new website dedicated to materials science modeling and informatics. The URL is http://www.mathub.com/ MatHub has been developed to provide current and background information about computational materials science, including the theory behind the software, the applications to different industries, plus features, events, links, jobs, games and puzzles, and more. Contributions from the computational chemistry community are welcome in the form of comment and opinion, feature articles, links, references, or book reviews. If you are interested in contributing, please contact Katriona Knapman at knapman@mathub.com ----------------------------------- Katriona Knapman Editor, MatHub knapman@mathub.com From chemistry-request@server.ccl.net Tue Feb 22 12:28:25 2000 Received: from basfegw1.basf-ag.de (basfegw1.basf-ag.de [141.6.1.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA07048 for ; Tue, 22 Feb 2000 12:28:25 -0500 From: wolfgang.hoeffken@basf-ag.de Received: from basfigw1.fw.basf-ag.de (actually host dmz-igw1) by basfegw1.basf-ag.de with SMTP (MMTA) with ESMTP; Tue, 22 Feb 2000 17:21:32 +0100 Received: from pluto1.zx.basf-ag.de by basfigw1.fw.basf-ag.de with SMTP (MMTA); Tue, 22 Feb 2000 17:21:28 +0100 Received: by pluto1.zx.basf-ag.de(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id C125688D.00593F8B ; Tue, 22 Feb 2000 17:14:49 +0100 X-Lotus-FromDomain: BASF-AG To: CHEMISTRY@ccl.net Message-ID: Date: Tue, 22 Feb 2000 17:21:15 +0100 Subject: Symposium on PROTEIN STRUCTURE ANALYSIS FOR BIOMEDICAL RESEARCH Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline ----------------------------------------------------- 2nd International DGK-Symposium on PROTEIN STRUCTURE ANALYSIS FOR BIOMEDICAL RESEARCH ----------------------------------------------------- in MURNAU, Germany, from 30 March - 1 April, 2000 DEAR PARTICIPANT: We would like to draw your attention to the webpage http://www.mpasmb-hamburg.mpg.de/bartunik/dgk/murnau_2000.html It gives the titles of the invited lectures, and it will soon show the complete scientific program of the meeting. The website further contains a (downloadable) picture of the participants of the 1st Murnau Symposium in March 1999. FOR THOSE WHO HAVE NOT YET REGISTERED: If you are quick we can still accept abstracts for posters or oral contributions until the >>> Final DEADLINE FOR ABSTRACTS: 28 FEBRUARY, 2000. <<< Please visit the webpage for further information and online registration. Looking forward to seeing you in Murnau, the organisers Hans Bartunik, Wolfgang Hoeffken, Rolf Hilgenfeld. From chemistry-request@server.ccl.net Tue Feb 22 11:54:40 2000 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06764 for ; Tue, 22 Feb 2000 11:54:38 -0500 Received: from lpbcsun.lpbc.jussieu.fr (lpbcsun.lpbc.jussieu.fr [134.157.132.1]) by shiva.jussieu.fr (8.9.3/jtpda-5.3.3) with ESMTP id QAA88343 for ; Tue, 22 Feb 2000 16:47:46 +0100 (CET) Received: from VieuxPC (155.ext.jussieu.fr [134.157.81.155]) by lpbcsun.lpbc.jussieu.fr (8.6.11/jtpda-5.1) with SMTP id QAA06355 for ; Tue, 22 Feb 2000 16:33:37 +0100 Message-ID: <002f01bf7d4b$f5d290e0$0300a8c0@VieuxPC> From: "Alexandre Hocquet" To: Subject: NBO intermolecular interactions Date: Tue, 22 Feb 2000 16:46:11 +0100 Dear CCLers, As I was browsing the Weinhold NBO web page as recently advised (courtesy of Alexei Khalizov), i was puzzled to see in the reference list a publication : a.. Intermolecular Interactions From A Natural Bond Orbital, Donor-Acceptor Viewpoint. A. E. Reed, L. A. Curtiss, and F. Weinhold, Chem. Revs. 88, 899 (1998) which i eventually could not find at this reference. Does any CCLer have a rational explanation for this ? Does a publication on this topic actually exist ? Thanks in advance Alexandre HOCQUET Laboratoire de Physicochimie Biomol=E9culaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 33 144277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05, France From chemistry-request@server.ccl.net Tue Feb 22 12:36:02 2000 Received: from sos1.chem.iupui.edu ([134.68.137.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA07164 for ; Tue, 22 Feb 2000 12:36:02 -0500 Received: from localhost (dgao@localhost) by sos1.chem.iupui.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA45748; Tue, 22 Feb 2000 11:27:19 -0500 (EST) Date: Tue, 22 Feb 2000 11:27:18 -0500 From: Daquan Gao To: chemistry@ccl.net cc: "Dr. Sudhir A. Kulkarni" , Renxiao Wang Subject: Summary: Surface and volume algorithms Message-ID: Hi everyone, Let me summarize the responses again since there have been much more yestoday. Thanks to everyone and especially Robert Pearlman from Austin. My origianl question, > Dear CCLers, > > I would like pointers to fast algorithms(preferentially analytical) of > computing the surface areas of molecules? Any idea is also > appreciated. > First is a quest for answers, From: Renxiao Wang On Fri, 18 Feb 2000, Daquan Gao wrote: > Dear Gao, I will appreciate it if you give me a copy of all the answers you got. As far as I know, there is few analytical algorithms for calculating surface and volume. Good luck! ------------------------------------------------------------------------ | Dr. Renxiao Wang | ------------------------------------------------------------------------ | Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104 | | University of California Los Angeles | Los Angeles, CA90066 | | Los Angeles, CA 90024 | U.S.A | | Phone: 310-8250269 (Lab) | Phone: 310-3904638 (Home) | ------------------------------------------------------------------------ | E-mail: renxiao@chem.ucla.edu | | WWW: http://zimbu.chem.ucla.edu/~arthur/ | ------------------------------------------------------------------------ Answer 1, ##############________________ From: "Martin,Yvonne" Try the programs by Robert Pearlman. Savol2 I think is the most recent one. You can get it from QCPE. Yvonne Martin Another request , ##________________ From: "Dr. Sudhir A. Kulkarni" Hello, Please summarize answers you get for the list or send copies to me. Thanks. Sudhir Answer 2, #################_____________ From: Thomas Huber Daquan, I think your question was a bit too general for the list. Depending on your problem there are several approaches to do surf/vol calculations. In Protein systems the program suite of Mike Connolly is quite popular, and it is analytical, but it costs some $500. If you need fast analytical surfaces for visualization, try to look at the VMD program system from Klaus Schulten's lab. There is an interface to a program called surf. Quite fast, analytical and free. Please specify your needs. There might be other tools (eg my molgeom6 software, but it is not yet ready for public release). Hope this helps! Thomas ----------------------------------------------------------------------------- Dr. Thomas Huber Institut fuer Stoffwechselbiochemie Tel.: +49(89)5996-462 der Universitaet Muenchen FAX: +49(89)5996-415 Vorstand Prof.Ch.Haass email thuber@physik.tu-muenchen.de Schillerstrasse 44 D-80336 Muenchen Answer 3, #######################_______________ From: PEARLMAN@VAX.PHR.UTEXAS.EDU Hello from sunny Austin, TX -- Recently, there have been a number of inquiries regarding software for calculating molecular surface areas, molecular volumes, and atomic contributions thereto. The most recent posting (from Daquan Gao) was: > This is the only response I got. Thanks to Yvonne Martin! I believe > now that QCPE is the first place to look for this info. > > Daquan Gao > > Try the programs by Robert Pearlman. Savol2 I think is the most recent > one. You can get it from QCPE. Our community owes a lot to Yvonne Martin, both for her own contributions and for the frequency with which she replies to such inquiries by offering pointers to a wide variety of useful software. In this case, however, the pointer is out-dated. Please do *NOT* use the old version of our surface area and volume software from QCPE. It has not been updated (or fixed) in many years. Instead, please send a request to me (pearlman@vax.phr.utexas.edu) and I will reply with instructions for down-loading a much newer, much nicer version called "Savol3". Savol3 provides extremely rapid, analytic calculation of both surface area and volume for molecular surfaces and solvent-accessible surfaces. In addition to partitioning both the surface area and volume into rationally defined atomic contributions, Savol3 also partitions the surface area and volume into polar/non-polar contributions (based either on user-specified charge thresholds or on the standard but crude hetero/non-hetero basis). We currently provide Savol3 for use on SGI workstations (but could be talked into providing it on other platforms if broad-based need exists). We will soon offer a version which will operate on SMILES or 2D MDL SDfile input. Meanwhile, please note that Savol3 currently requires 3D molecular structures as input. These can be provided in PDB format or in Tripos' mol2 or mol1 format. I/O can be specified using unix command-line options or can be provided in response to prompts issued by the program. Alternatively, since we provide an object library and source code for an example calling routine, the 3D structure and other I/O issues could be handled via an argument list (without concern for 3D file format). Best wishes, -- Bob Pearlman Answer 4, ########################________________ From: jmmckel@attglobal.net Also try GEOPOL from QCPE. It is used in several other programs, including solvated geometry optimizations. John McKelvey From: ReichertD@mir.wustl.edu Daquan, Now I feel guilty I'd meant to reply to your original post. The original Connolly surface program is available from QCPE (#429) another possibility is MSMS for solvent excluded surfaces (www.scrips.edu/pub/olson-web/people/sanner/html/msms_home.html). hope this helps, -david David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd@mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940