From schiffer@h1tw0036.hoechst.com Mon Jul 28 03:13:58 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id CAA11733; Mon, 28 Jul 1997 02:59:07 -0400 (EDT) Received: by backup.hoechst.com id IAA26752; Mon, 28 Jul 1997 08:55:16 +0200 Received: from unknown(134.81.76.36) by backup id sma026731; Mon Jul 28 08:54:26 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id IAA11913; Mon, 28 Jul 1997 08:56:58 +0200 Message-ID: <33DC42B9.41C6@h1tw0036.hoechst.com> Date: Mon, 28 Jul 1997 08:56:57 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: "Dr. Dave Winkler" CC: Computational Chemistry List Subject: Re: CCL:Pi stacking energies References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Dave Winkler wrote: > > Hi, Netters, > > Can anyone give me an estimate of the contribution to ligand binding energy > which may result from an optimum pi-stacking interaction in the active > site? I have a tyrosine forming the base of a site and good ligands > contain aromatic rings which lie ~3.5 A above the aromatic ring of tyrosine. Hi Dave, the interaction energy between two benzene rings in a parallel-displaced arrangement is about 2 kcal/mol, see : P. Hobza et al., J. Phys. Chem. 100 (1996) 18790-18794. See also the discussion in : C. Chipot et al., J. Am. Chem. Soc. 118 (1996) 11217-11224. The last reference does exactly discuss your problem ! Hope, this helps. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From campagne@incm.u-nancy.fr Mon Jul 28 08:14:01 1997 Received: from brown.incm.u-nancy.fr for campagne@incm.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id IAA12610; Mon, 28 Jul 1997 08:05:47 -0400 (EDT) Received: from yellow.incm.u-nancy.fr by brown.incm.u-nancy.fr via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@brown.incm.u-nancy.fr:chemistry@www.ccl.net> id OAA15401; Mon, 28 Jul 1997 14:06:29 +0100 Received: from yellow.incm.u-nancy.fr (localhost [127.0.0.1]) by yellow.incm.u-nancy.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA00886 for ; Mon, 28 Jul 1997 14:06:27 +0100 Sender: campagne@incm.u-nancy.fr Message-ID: <33DC9953.41C6@incm.u-nancy.fr> Date: Mon, 28 Jul 1997 14:06:27 +0100 From: Fabien Campagne Organization: Laboratoire de Chimie The'orique de Nancy X-Mailer: Mozilla 3.0SC-SGI (X11; I; IRIX64 6.2 IP28) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL:Object-oriented means for computational chemist/programs structure and design Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit On Wed, 23 Jul 1997 18:08:13 -0400 David E. Bernholdt wrote: >On Tue, 22 Jul 1997 07:45:08 +0000 "Ping Du" wrote: >> Inheritance is pobably the most important feature of >> OO design if you would like your program to be extensible and >> reusable. >I don't entirely agree. Having done OO _design_ and implemented those >designs in "non-OO" languages, I believe that the other principles of >OO design (abstraction, encapsulation, modularity) are probably more >important and more powerful. I have not encountered a case where I >felt at a serious disadvantage because the languages I was using did >not support inheritance. >But in any case, I must stress the importance of design. Looking A good reference for fortran programers about program structure and design could be: Structured Design Fundamentals of a discipline of Computer Program and Systems Design Edward Yourdon/Larry L. Constantine Yourdon Press Computing Series ISBN 0-13-854471-9 I didn't read this book carrefully myself, but browsed it reading some chapters. This was enough to make me regret that computational chemistry codes have not been design with the principle it describes in mind... :-( This book was written before the idea of object oriented programming ever appeared, with examples in fortran 77. It may still help people who want to go on with fortran to design their code in a reusable way, with less defaults (at the time of development and latter). Because it does not tell you about OO it's certainly more suited to fortran programming. Fortran is a language that does not enable to represent an OO design in a natural way, whatever you could say: you may sill emulate the behaviour of an OO language but you will lose a lot of tools and features available by default in OO languages. This lack could make the implementation of an OO design more difficult. >back, I think that a thorough design phase probably allowed us to find >the right abstractions so that inheritance was really not an issue, >and we could do what inheritance was required "manually". It also may >be a property of the problem to some extent (in our case a broad >spectrum of electronic structure methods). The choice of the language usualy depends on what you're ready to do "manually" or not. I learned a nice assembly language ten years ago, but today, I'm not ready to implement methods well described by the OO formalism using assembly language. It would be painful, and time consuming, even if, of course, that would be possible.. Fabien Campagne -- campagne@incm.u-nancy.fr | Lab. de Chimie Theorique phone: +33 (0)3 83 91 20 00 extension 3236 | Nancy, France. http://www.lctn.u-nancy.fr/viseur/FC.html From schiffer@h1tw0036.hoechst.com Mon Jul 28 12:14:02 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id LAA14085; Mon, 28 Jul 1997 11:30:50 -0400 (EDT) Received: by backup.hoechst.com id RAA11938; Mon, 28 Jul 1997 17:27:04 +0200 Received: from unknown(134.81.76.36) by backup id sma011926; Mon Jul 28 17:26:05 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA12484; Mon, 28 Jul 1997 17:29:00 +0200 Message-ID: <33DCBABB.41C6@h1tw0036.hoechst.com> Date: Mon, 28 Jul 1997 17:28:59 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: search for condensed rings Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear netters, I am looking for a simple algorithm to find all rings in a given molecular structure (given by cartesian coordinates and connectivities). The molecules have less than 100 atoms. I someone of you already have such a program, it would be nice to have a copy of it. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From D.van.der.Spoel@chem.rug.nl Mon Jul 28 16:14:05 1997 Received: from mailhost.rug.nl for D.van.der.Spoel@chem.rug.nl by www.ccl.net (8.8.3/950822.1) id PAA14963; Mon, 28 Jul 1997 15:21:24 -0400 (EDT) From: Received: from rugch4.chem.rug.nl by mailhost with SMTP (XT-PP) with ESMTP; Mon, 28 Jul 1997 21:22:06 +0200 Received: from rugmd4 by rugch4.chem.rug.nl (VAA01189); Mon, 28 Jul 1997 21:21:20 +0200 (DST) Received: (from spoel@localhost) by rugmd4 (950413.SGI.8.6.12/950213.SGI.AUTOCF) id VAA16406 for chemistry@www.ccl.net; Mon, 28 Jul 1997 21:21:19 +0200 Message-Id: <199707281921.VAA16406@rugmd4> Subject: PD FFT routines wanted To: chemistry@www.ccl.net Date: Mon, 28 Jul 1997 21:21:18 +0200 (MDT) Reply-To: D.van.der.Spoel@chem.rug.nl X-Mailer: ELM [version 2.4 PL25] Content-Type: text Hi All. I am looking for public domain 1D, 2D and 3D FFT routines in ansi C. They should be fast and portable. Any clues ? Groeten, David. ________________________________________________________________________ Dr. Ir. David van der Spoel Dept. of Biophysical Chemistry s-mail: Nijenborgh 4, 9747 AG Groningen, The Netherlands. e-mail: spoel@chem.rug.nl www: http://rugmd0.chem.rug.nl/~spoel phone: 31-50-3634327 fax: 31-50-3634800 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From plin@chemvx.tamu.edu Mon Jul 28 16:31:22 1997 Received: from chemvx.chem.tamu.edu for plin@chemvx.tamu.edu by www.ccl.net (8.8.3/950822.1) id QAA15427; Mon, 28 Jul 1997 16:11:04 -0400 (EDT) Received: from warbird.chem.tamu.edu ([165.91.176.59]) by chemvx.chem.tamu.edu (Netscape Mail Server v2.02) with SMTP id AAA159 for ; Mon, 28 Jul 1997 15:10:33 -0500 Sender: plin@chemvx.tamu.edu (Lin Ping) Message-ID: <33DCFCC0.41C6@chemvx.tamu.edu> Date: Mon, 28 Jul 1997 15:10:40 -0500 From: Lin Ping Organization: Department of Chemistry X-Mailer: Mozilla 3.01Gold (X11; I; IRIX64 6.1 IP26) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: CCL:summary:basis set of DFT calculation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, two days ago, I post a queastion asking about the basis set for DFT calculation. >Original question > I am trying to run DFT calculation resently. Since the ordinary basis > sets are optimized for ab initio calculation, I am wondering if there > are basis sets spectially designed for DFT calculation, which will > surely improve the result. > Any hints or references would be greatly appreciated. > Replies can send to me directly, I will summarize to the list. Thanks to those who replied to my question: Bill Davis John Waite Dale Andrew Braden WU Nelson H Morgon *********************************************************************** Dr. William M. Davis As part of my Ph.D. thesis, I reoptimized the Stevens-Basch-Krauss ECP basis sets for the main group elements boron to iodine. The results indicated that, while it is more "theoretically sound" to use a basis set optimized for a particular method (DFT, HF etc.), the results really do not change all that significantly. It is much more important in DFT to chose a good combination of exchange and correlation functionals to improve your predictions. ************************************************************************ Dr. John Waite Dear CCL, I want to thank Dr. George Fitzgerald and Oxford Molecular Group (http://www.oxmol.com/) for a very needed contribution to our community, namely, the DGauss basis sets. These contracted gaussian sets were optimized for DFT calculations and include elements up to Xe. They also include the auxilliary fitting uncontracted gaussian sets for these programs which use them. The latest version of the basis sets for DGauss version 4.0 is available from Oxford Molecular ftp servers: in US: ftp://ftp.oxmol.com/pub/UniChem/UniChem_basis in UK ftp://ftp.oxmol.co.uk/pub/UniChem/UniChem_basis I was also given permission to mirror them in CCL archives: http://www.ccl.net/cca/data/basis-sets/DGauss/dgauss-basis.html or you can get there via ftp://www.ccl.net/pub/chemistry/data/basis-sets/DGauss/ There is also an older version (for DGauss 3.0 and older) in the CCL archives (which contains XC auxilliary fitting sets) in the same directory. The perl scripts are provided to convert these basis sets to other formats: For version 3.0: http://www.ccl.net/cca/software/PERL/basis/DG3_to_deMon/dg2dm.html and for version 4.0: http://www.ccl.net/cca/software/PERL/basis/DG4_to_deMon/dgn2dm.html Again, I put a plug for CCL. Please contribute chemistry related material (software, data, overviews, course materials, etc., etc.) to CCL -- I can mirror your files on our Web server, and also have files on the ftp site. Please contact me for more information (and do not be impatient if you need to wait for a few days for an answer -- but I am catching up usually {;-)}. We are still running old site: http://www.ccl.net/chemistry.html but at some point (when the damned things start to work as we want them!!!) we will open our new site: http://www.ccl.net/ Thank you for you attention... Jan Labanowski Ohio Supercomputer Center jkl@ccl.net ******************************************************************* Dale Braden Have a look at: http://www.emsl.pnl.gov:2080/forms/basisform.html and look through the list for the DFT-optimized basis sets by Godbout, et al. The site gives references for each basis set. ******************************************************************* JH Wu The DZVP (double-zeta split-valence plus polarisation function basis) are optimised for DFT calculation. It is used by Dgauss program (unichem package). I have included a copy of DZVP basis set for C,H,N,O ... in the attachment. From the comment lines, you can search for related reference. I think you can get a whole copy of it from the homepage of unichem3.0 package. (if can't, give me a line) ******************************************************************* NELSON HENRIQUE MORGON Maybe, I could help you, and you can test my basis set. Tell me that basis set you would like, including kind of functional. I can model different basis set. ******************************************************************* LIN Ping -- Department of Chemistry Phone No. : 409-862-9225 Texas A&M University E-mail : plin@chemvx.tamu.edu College Station TX 77843-3255 plin@warbird.chem.tamu.edu URL: http://http.tamu.edu/~p0l1112/ From gillies@cmcnrc.far.ruu.nl Thu Jul 24 12:21:15 1997 Received: from cmcind.far.ruu.nl for gillies@cmcnrc.far.ruu.nl by www.ccl.net (8.8.3/950822.1) id LAA26683; Thu, 24 Jul 1997 11:38:56 -0400 (EDT) Received: from cmcnrc.far.ruu.nl by cmcind.far.ruu.nl via ESMTP (950413.SGI.8.6.12/940406.SGI) for <@cmcind.far.ruu.nl:chemistry@www.ccl.net> id RAA22903; Thu, 24 Jul 1997 17:35:52 +0200 Received: from cmcnrc by cmcnrc.far.ruu.nl via ESMTP (950413.SGI.8.6.12/940406.SGI) for id RAA16700; Thu, 24 Jul 1997 17:35:51 +0200 Message-Id: <199707241535.RAA16700@cmcnrc.far.ruu.nl> To: chemistry@www.ccl.net Reply-To: Malcolm Gillies Subject: Conference Announcement: MGM EC-2 Date: Thu, 24 Jul 1997 17:35:50 +0200 From: Malcolm Gillies Second Electronic Molecular Graphics and Modelling Conference ************************************************************* October 6-17, 1997 World Wide Web: http://www.vei.co.uk/mgmec2/ Email: mgmnorg@vei.co.uk The Second Electronic Molecular Graphics and Modelling Conference (MGM EC-2) will be held on the Internet and World Wide Web >from Oct 6-17, 1997 and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure; Membranes and Membrane Proteins; Protein Folding; Modelling of In Vivo Activity; Knowledge-based Library Design; Surface Science; Host-guest interactions; Carbohydrates and Protein-Carbohydrate Interactions; Enzyme Mechanisms; Conformational Sampling; Nucleic Acids; Quantum Chemistry; Structure-based Design; Visualization; and Perspectives. Presentations of papers or posters must be prepared in Hypertext Markup Language (HTML) with figures in GIF or other Web-compatible formats so that participants can view the papers via the World Wide Web (The presentations may also include enhancements such as 3D structures, VRML, Java, RealAudio, Quicktime movies etc.) Authors may submit WWW presentations for non-permanent display during the conference, or for refereed print or electonic publication in the Journal of Molecular Graphics or the Internet Journal of Chemistry (IJC), http://www.ijc.com/ During the conference, interaction, presentations and discussions will take place via the Internet using a Java-based virtual conference centre, WWW-based discussion forums and an electronic mailing list. Before the conference, a timetable for lectures and discussion sessions for each section will be posted. The Conference will feature a Virtual Exhibition where exhibitors will be able to describe the activities of their organization, display their products and services and interact with registrants. Potential exhibitors should contact the conference organisers. Further information regarding the conference is available from the conference WWW site at http://www.vei.co.uk/mgmec2/ Inquiries may also be sent by email to the conference organisers at mgmnorg@vei.co.uk REGISTRATION ************ If you intend to participate in MGM EC-2 please use the special registration form accessible via http://www.vei.co.uk/mgmec2/. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 45 pounds sterling (75 US dollars) with a special rate for students of 30 pounds sterling (50 US dollars). DEADLINES AND DATES ******************* 1) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is September 1. 2) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is September 15. 3) Refereeing Period The refereeing period will commence upon completion of the conference. Molecular Graphics & Modelling Network (MGMN) mailing list ********************************************************** Conference-related news and announcements will be posted regularly to the MGMN mailing list (mgmn@vei.co.uk). If you wish to subscribe to the MGMN list send the following one line message to mgmn-request@vei.co.uk subscribe mgmn@vei.co.uk your_email@address To unsubscribe send the following message: unsubscribe mgmn@vei.co.uk your_email@address -- Malcolm Gillies Molecular Modelling Coordinator Virtual Environments International http://www.vei.co.uk/ From dalke@ks.uiuc.edu Thu Jul 24 19:21:09 1997 Received: from london.ks.uiuc.edu for dalke@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id SAA28905; Thu, 24 Jul 1997 18:30:09 -0400 (EDT) Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2 [TBG Mods]) id AA132993410; Thu, 24 Jul 1997 17:30:10 -0500 Received: (from dalke@localhost) by bilbao.ks.uiuc.edu (940816.SGI.8.6.9/8.6.9)id RAA00613; Thu, 24 Jul 1997 17:30:04 -0500 Date: Thu, 24 Jul 1997 17:30:04 -0500 From: Andrew Dalke Message-Id: <199707242230.RAA00613@bilbao.ks.uiuc.edu> To: CHEMISTRY@www.ccl.net Subject: Re: Object-oriented means for computational chemist Cc: shenkin@still3.chem.columbia.edu Hello, > The issue I was trying to raise is that regardless of whether one > wants to write the front end in C, C++ or Fortran, or anything else, > the language definition of C++ *precludes* writing a linkable code > libraries in C++ if one ever wants to access the library routines > from another language. That's not quite true. The real requirement is you need a linker that understands how to deal with your C++ compiler . For instance, I can write an interface to a C++ class for C by defining a set of exported functions (in extern "C" context) that are compiled by C++. (I put an example at the end of this email.) There will be two problems: The implementations of 'new' and 'delete' require a special function be linked in, which you will need via the C++ linker. There will also be problems if you use C++'s static variables with class types. All static variables are initialized at before main() is run, so the linker has to add the code that runs the initializations before calling main. The standard linker doesn't do this so here again you need to use the C++ linker (this feature is just not possible with C or Fortran; if variables and arrays are initialized, they are initialized to 0). The biggest limitation is really that I can't link my C++ library created under one compiler with C++ generated from another. But then, all the code I distribute is available in source form so that hasn't been much of a problem. Andrew Dalke dalke@ks.uiuc.edu Here's an example of C wrapper functions for a C++ class. There are three files; the header file includes both the C and C++ APIs. The file 'class.C' contains the class code and does the C-level interface, and main.c is a driver. This uses the 'extern "C"' feature of C++ to turn off name mangling when compiling under C++. = = = = = = = = = class.h = = = = = = = #ifdef __cplusplus class MyClass { int data; public: MyClass(int new_value); ~MyClass(void); int get(void); }; #endif /* for the C interface; doing it this way instead of using a void * */ /* directly lets the compiler do better type checking and keeps the */ /* same "feel" as C++ */ typedef struct MyClass_C { void *class_ptr; } MyClass_C; #ifdef __cplusplus extern "C" { #endif MyClass_C MyClass_new(int new_value); void MyClass_delete(MyClass_C); int MyClass_get(MyClass_C); #ifdef __cplusplus }; #endif = = = = = = = = = =class.C = = = = = = = = = = #include #include "class.h" /* a simple int storage class */ MyClass::MyClass(int new_value) { data = new_value; } MyClass::~MyClass(void) { data = 0; } int MyClass::get(void) { return data; } /* Wrappers for the C interface */ MyClass_C MyClass_new(int new_value) { MyClass_C tmp; tmp.class_ptr = new MyClass(new_value); return tmp; } void MyClass_delete(MyClass_C ref) { delete ((MyClass *) ref.class_ptr); ref.class_ptr = NULL; } int MyClass_get(MyClass_C ref) { return ((MyClass *) ref.class_ptr)->get(); } = = = = = = = = = =main.c = = = = = = /* The driver code -- compile this in C! */ #include #include "class.h" main() { MyClass_C tmp = MyClass_new(5); printf("The value is %d.\n", MyClass_get(tmp)); MyClass_delete(tmp); } = = = = = = Here's how I ran it (using GNU's C++ compiler, SGI's C compiler, and GNU's C++ linker to prove nothing fishy was going on): % g++ -c class.C % cc -c main.c % g++ main.o class.o % ./a.out The value is 5. So it is possible for C routines to call C++ functions and classes. From c72463@s06subz2.uibk.ac.at Fri Jul 25 11:13:29 1997 Received: from ms1.uibk.ac.at for c72463@s06subz2.uibk.ac.at by www.ccl.net (8.8.3/950822.1) id KAA03140; Fri, 25 Jul 1997 10:33:48 -0400 (EDT) Received: from s06subz2.uibk.ac.at (s06subz2.uibk.ac.at [138.232.10.13]) by ms1.uibk.ac.at (8.8.5a) with ESMTP id QAA14343; Fri, 25 Jul 1997 16:33:47 +0200 (CEST); from c72463@s06subz2.uibk.ac.at for Received: from S06SUBZ2/SpoolDir by s06subz2.uibk.ac.at (Mercury 1.31); 25 Jul 97 16:34:00 +0100 Received: from SpoolDir by S06SUBZ2 (Mercury 1.31); 25 Jul 97 16:33:46 +0100 From: "GERHARD BISCHOF" Organization: University of Innsbruck, Austria To: chemistry@www.ccl.net Date: Fri, 25 Jul 1997 16:33:38 +0100 Subject: tungsten parameters for semi-empirical calculations X-Confirm-Reading-To: "GERHARD BISCHOF" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit Content-Transfer-Encoding: 8bit Hallo, I would be grateful to receive any information concerning parameter set for the tungsten atoms available for INDO ( ZINDO/1) quantum chemical calculations. Thank you in advance ! Dr. Renat Nazmutdinov (University of Innsbruck) ************************************************************************** Gerhard Bischof E-mail:Gerhard.Bischof@uibk.ac.at Tel:<0043>512-507-5154 Fax:<0043>512-507-2934 Universit„t Innsbruck Inst. f. Allg., Anorg. und Theor. Chemie Innrain 52 A-6020 Innsbruck Austria *************************************************************************** From support@mathtrek.com Fri Jul 25 12:30:17 1997 Received: from granite.sentex.net for support@mathtrek.com by www.ccl.net (8.8.3/950822.1) id LAA03461; Fri, 25 Jul 1997 11:33:33 -0400 (EDT) Received: from p12a.silicon.sentex.ca (p12a.silicon.sentex.ca [207.245.212.45]) by granite.sentex.net (8.8.6/8.6.9) with SMTP id LAA19664; Fri, 25 Jul 1997 11:42:40 -0400 (EDT) Message-Id: <3.0.16.19970725113112.2dcfd082@mathtrek.com> X-Sender: mathtrek@mathtrek.com (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Fri, 25 Jul 1997 11:31:17 -0400 To: "Paul G. Tratnyek" , chemistry@www.ccl.net From: "W. R. Smith" Subject: Re: CCL:mac program for solving chemical equilibria Cc: i1s@psu.edu (Inge Schuster) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, At last, a "computational chemistry" issue that has nothing too do with QM! >At 09:14 PM 7/24/97 -0800, Paul G. Tratnyek wrote: >>Hi! Does anyone know of any program for the Mac which can do calculations >>associated with simultaneous chemical equilibria, titrations, etc. in >>non-aqueous media ( where pH is not a factor)? > [The most sophisticated speciation programs] >I have seen are for >geochemistry. They can handle lots of species, speciation at solid >surfaces, etc. > >Of course, the concern of geochemists is exclusively with aqueous systems. > >The most recent one I have seen running on a Mac is ChemEQL 2.0. Info at: > > http://www.eawag.ch/soft/chemeql.html I must respond to the comment in [brackets] concerning "sophistication". IMHO, most existing "speciation programs", the one mentioned being an example (the name itself even implies that such calculations are special to the domain of geochemistry) are based on 30-year-old thermodynamic and numerical analysis technology. Lots has happened since then! There abound DOS-based geochemistry programs for aqueous systems dating >from the 60's and early 70's. They generally contain tightly integrated computational algorithms and aqueous-system databases (the latter of which one must usually accept as realistic thermodynamic descriptions of the system). The program mentioned by Tratnyek, although it runs on a Mac (using a little better hardware technology than DOS :-)), appears to one of the more advanced in its class, in that it can accept user thermodynamic data. However, it is still very specific to aqueous systems - and it is likely based on the old numerical analysis technology (but one can't tell >from its description). Most geochemists continue to believe that the computational technology originally developed in the 60's and early 70's for aqueous systems (equilibrium constant equations + Newton-Raphson numerical analysis technology) is the best (and only) appropriate approach for such problems. In reality, aquatic speciation problems are only a special case of general reaction equilibrium problems. Apart from appropriate thermodyamic models, the non-domain-specific technology, in terms of the computational kernel that is central to such calculations, has advanced considerably. This fact is not generally realized in the geochemical community. For example, on page 517 of "Thermodynamics in Geochemistry", G. M. Anderson and D. A. Crerar, Oxford university Press, 1993, there is the following sentences: "There is an important fundamental distinction between the free energy based programs and those using equilibrium constants, and this often determines which method to use in specific applications. The free energy programs actually require much more fundamental thermodynamic information, and this can restrict their usefulness" And on p. 400 of "Geochemical Thermodynamics", 2nd edition, D. K. Nordstrom and J. l. Munoz, Blackwell, 1994: "The only difference worth underscoring here is that a program that accepts only free energy values for the operating database makes it far more difficult to obtain reliable values for aqueous species than it is with a program that uses equilibrium constants. Some free energy values of aqueous species do not exist because the measurements have not been made, whereas the equilibrium constants typically are available:. Both the above statements are widely believed in the geochemistry community - and both are DEAD WRONG. The technology to utilize either type of data (species-specifc free energies or reaction sets with their associated equilibroum constants) has been available since 1982 (section 9.4 of "Chemical reaction Equilibrium Analysis: Theory and Algorithms", W. R. Smith and R. W. Missen, Wiley-Interscience, 1982; Krieger, 1991). An algorithm based on simple linear algebra can be used to convert back and forth between species and reaction data, (This algorithm is incorporated within Mathtrek System's EQS4WIN software - URL below). Comments/discussion on these points are most welcome - any geochemists lurking on the list? How about physical chemists - does anyone like the NASA chemical equilibrium algorithms? -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From dew01@xray5.chem.louisville.edu Fri Jul 25 16:13:34 1997 Received: from xray5.chem.louisville.edu for dew01@xray5.chem.louisville.edu by www.ccl.net (8.8.3/950822.1) id PAA05319; Fri, 25 Jul 1997 15:41:43 -0400 (EDT) Received: (from dew01@localhost) by xray5.chem.louisville.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id PAA04445 for CHEMISTRY@www.ccl.net; Fri, 25 Jul 1997 15:45:09 -0400 From: "Donald E. Williams" Message-Id: <9707251545.ZM4443@xray5.chem.louisville.edu> Date: Fri, 25 Jul 1997 15:45:09 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Nature of the hydrogen bond Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > > >Merethe.Sjovoll@hre.hydro.com writes: >I am interesting in sharing any experience people have with mimicing hydrogen >bonds in forcefields. The main contribution to an O...H bond is obviously the >coulombic interaction. The other thing is dispersion. >The coulombic interaction is usually represented by two point charges and >dispersion by a -C/R**6 term in a forcefield - I have also seen the term >R/R**10 >used. > However, the hydrogen bonds also have a directional character which is not >described by this simple model. >Are really forcefields of the form described above generally able to describe >structures with hydrogen bonds? >I would very much like to know the view of my colleagues on what a hydrogen >bond really is made of and what it takes to describe it. >Best wishes >Merethe Perhaps the most commonly used force field model for the hydrogen bond, especially O-H...O, is the "disappearing hydrogen" model. This intermolecular force field is based on (12-6-1) functional form, representing repulsion, dispersion, and coulombic interaction. This model is non-directional, and assigns *zero* dispersion and *zero* repulsion. Now many say that the main component of h-bond energy is electrostatic. However, in the disappearing hydrogen model, by far the main component is the reduction of hydrogen repulsion. You can test this against crystal structure data. If you restore normal (i.e., hydrocarbon H) repulsion, keeping the electrostatic part, the model fails completely. On the other hand, is you delete the electrostatic part, keeping the zero repulsion, the fit to crystal data become only a little worse. What prevents the h-bond model from collapsing? Of course, it is the repulsion between the oxygens (in an O-H...O bond). What is the significance of the reduced H repulsion in the h-bond? Well this is what always happens when a bond forms. However, there normally is some residual repulsion, say K shell electrons, which prevents the bond from collapsing. Of course, H doesn't have an inner shell to prevent collapse, so maybe the zero repulsion can be rationalized. But there still is a proton there which needs to be considered. I believe that many elementary textbooks give a misleading picture when they describe the h-bond as primarily electrostatic, something akin to an ionic bond. Really the h-bond is more closely related to covalency, with reduced repulsion normally associated with the covalent bond. -Donald Williams -- Dr. Donald E. Williams email:dew01@xray5.chem.louisville.edu Department of Chemistry University of Louisville phone:502-852-5975 Louisville, KY 40292 fax: 502-852-8149 From dsmith@CTCnet.Net Mon Jul 28 17:14:06 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id QAA15603; Mon, 28 Jul 1997 16:21:42 -0400 (EDT) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id QAA10455; Mon, 28 Jul 1997 16:21:33 -0400 Message-Id: <3.0.1.32.19970728162107.009d8020@pop.dasgroup.com> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) X-Priority: 2 (High) Date: Mon, 28 Jul 1997 16:21:07 -0400 To: CHEMISTRY@www.ccl.net From: "Douglas A. Smith Ph.D." Subject: Barrelene Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I need some help, references, etc. I know a number of years ago Lou Allinger did some ab initio calculations on barrelene, i.e., bicyclo[2.2.2]actatriene. I believe these were at the HF/6-31G* level and were published in the Journal of Computational Chemistry. (1) Has anyone published more recent calculations, or using a higher level of theory and/or larger basis set? What about methods including perturbation, correlation, CI, or DFT? (2) Is barrelene aromatic or antiaromatic? I recall the latter, but cannot prove it to myself. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From plin@chemvx.tamu.edu Mon Jul 28 17:22:36 1997 Received: from chemvx.chem.tamu.edu for plin@chemvx.tamu.edu by www.ccl.net (8.8.3/950822.1) id QAA15552; Mon, 28 Jul 1997 16:16:31 -0400 (EDT) Received: from warbird.chem.tamu.edu ([165.91.176.59]) by chemvx.chem.tamu.edu (Netscape Mail Server v2.02) with SMTP id AAA149 for ; Mon, 28 Jul 1997 15:16:24 -0500 Sender: plin@chemvx.tamu.edu (Lin Ping) Message-ID: <33DCFE1F.167E@chemvx.tamu.edu> Date: Mon, 28 Jul 1997 15:16:31 -0500 From: Lin Ping Organization: Department of Chemistry X-Mailer: Mozilla 3.01Gold (X11; I; IRIX64 6.1 IP26) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: CCL:summary:basis set of DFT calculation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, two days ago, I post a queastion asking about the basis set for DFT calculation. >Original question > I am trying to run DFT calculation resently. Since the ordinary basis > sets are optimized for ab initio calculation, I am wondering if there > are basis sets spectially designed for DFT calculation, which will > surely improve the result. > Any hints or references would be greatly appreciated. > Replies can send to me directly, I will summarize to the list. Here is another response from Dr. Georg Schreckenbach. ***************************************************** schrecke@t12.lanl.gov (Georg Schreckenbach) the ADF code is a pure DFT code. It uses Slater type orbitals (STO) as basis functions, and all their basis functions where optimized by the ADF people a long time ago using DFT calculations on atoms. Btw., ADF stands for "Amsterdam Density Functional", and you'll find them at http://tc.chem.vu.nl/SCM or adf@chem.vu.nl ***************************************************** Many thanks for your help. Ping LIN -- Department of Chemistry Phone No. : 409-862-9225 Texas A&M University E-mail : plin@chemvx.tamu.edu College Station TX 77843-3255 plin@warbird.chem.tamu.edu URL: http://http.tamu.edu/~p0l1112/ From SCHMITZ@MARSHALL.EDU Mon Jul 28 19:14:06 1997 Received: from frodo.marshall.edu for SCHMITZ@MARSHALL.EDU by www.ccl.net (8.8.3/950822.1) id SAA16860; Mon, 28 Jul 1997 18:49:58 -0400 (EDT) From: Received: from MARSHALL.EDU by MARSHALL.EDU (PMDF V5.1-8 #20911) id <01ILS3SFQ1HC8WW2ZT@MARSHALL.EDU> for CHEMISTRY@www.ccl.net; Mon, 28 Jul 1997 18:51:27 EDT Date: Mon, 28 Jul 1997 18:49:48 -0400 (EDT) Subject: barrelene To: CHEMISTRY@www.ccl.net Message-id: <01ILS3SFQVMQ8WW2ZT@MARSHALL.EDU> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Douglas A. Smith wrote: < I need some help, references, etc. < I know a number of years ago Lou Allinger did some ab initio calculations < on barrelene, i.e., bicyclo[2.2.2]actatriene. I believe these were at the < HF/6-31G* level and were published in the Journal of Computational < Chemistry. < < (1) Has anyone published more recent calculations, or using a higher level < of theory and/or larger basis set? What about methods including < perturbation, correlation, CI, or DFT? < < (2) Is barrelene aromatic or antiaromatic? I recall the latter, but < cannot prove it to myself. I was involved in the Allinger study you referred to. The reference is: L.R. Schmitz, N.L. Allinger, K.M. Flurchick, J. Comput. Chem. 9, 281(1988). In that study we calculated step-wise heats of hydrogenation of barrelene. The first was unusually large; implying barrelene is less stable than expected for simple alkenes. Note: this study used various empirical schemes from the literature for estimating heats of formation from 6-31G*//3-21G calculations. Later I developed another empirical schemes for estimating heats of formation >from 6-31G*//6-31G* calculations. This gave similar results. The reference is: L.R. Schmitz, Y.R. Chen, J. Comput. Chem. 15, 1437 (1994). Finally, I have developed another scheme that uses MP2/6-31G**//6-31G* energies as a starting point. When applied to the heats of hydrogenation of barrelene, this predicts that heat of hydrogenation of the first double bond is still large. However, the magnitude is reduced from what we calculated using HF energies. This has not been published yet but will be submitted soon. There are experimental heats of hydrogenation (in solution) available and the results are similar to our calculated results. If barrelene is antiaromatic, it would be less stable than expected for simple alkenes. However, the strain in these rings is an alternative explanation. Larry Schmitz Department of Chemistry Marshall University Huntington, WV 25705 schmitz@marshall.edu or chm001@marshall.wvnet.edu From choic@gusun.georgetown.edu Mon Jul 28 20:14:06 1997 Received: from gusun.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.8.3/950822.1) id TAA17007; Mon, 28 Jul 1997 19:26:29 -0400 (EDT) Received: from localhost (choic@localhost) by gusun.georgetown.edu (8.8.5/8.8.5) with SMTP id TAA27426 for ; Mon, 28 Jul 1997 19:24:35 -0400 (EDT) Date: Mon, 28 Jul 1997 19:24:35 -0400 (EDT) From: Cheol Choi X-Sender: choic@gusun To: chemistry@www.ccl.net Subject: NICS ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Is anybody out there how to calculate the NICS (Negative nucleus-independent chemical shift) using G94 results? Thanks, Cheol-Ho Choi Georgetown Univ. From case@scripps.edu Mon Jul 28 20:26:12 1997 Received: from relay1.scripps.edu for case@scripps.edu by www.ccl.net (8.8.3/950822.1) id UAA17136; Mon, 28 Jul 1997 20:06:07 -0400 (EDT) Received: from dirac.scripps.edu (dirac.scripps.edu [137.131.252.42]) by relay1.scripps.edu (8.8.6/TSRI-1.6) with ESMTP id RAA24611 for ; Mon, 28 Jul 1997 17:06:05 -0700 (PDT) Received: (from case@localhost) by dirac.scripps.edu (8.8.5/TSRI-1.4) id RAA12666 for chemistry@www.ccl.net; Mon, 28 Jul 1997 17:00:33 -0700 (PDT) Date: Mon, 28 Jul 1997 17:00:33 -0700 (PDT) From: David Case Message-Id: <199707290000.RAA12666@dirac.scripps.edu> To: chemistry@www.ccl.net Subject: Re: Nature of the hydrogen bond X-Sun-Charset: US-ASCII Donald Williams wrote: > Perhaps the most commonly used force field model for the hydrogen bond, > especially O-H...O, is the "disappearing hydrogen" model. This intermolecular > force field is based on (12-6-1) functional form, representing repulsion, > dispersion, and coulombic interaction. This model is non-directional, and > assigns *zero* dispersion and *zero* repulsion. > Now many say that the main component of h-bond energy is electrostatic. > However, in the disappearing hydrogen model, by far the main component is > the reduction of hydrogen repulsion. I don't know what is the "most commonly used force field", but functions like OPLS and AMBER (or the TIP3 and SPC models of water, etc.) "disappear" the 12-6 (Lennard-Jones) part of the hdyrogen, but *keep* the electrostatic part of the hydrogen in computing the interaction. These force fields do have directionality, since nonlinear geometries have less favorable Coulombic interactions than do linear geometries. This angular dependence is by no means perfect (and is especially questionable for second row acceptors, like sulfur), but does capture much of the flavor of the angular dependence seen in quantum chemistry calculations. So, in this model, one can say (as in Donald Williams' comment) that the main energetic component of the hydrogen bond is the reduction of the hydrogen repulsion that would "otherwise" be there, and that the principal determinant of the angular dependence is electrostatics. ....dave case