From elazhary@theochem.uni-stuttgart.de Thu Aug 28 05:20:34 1997 Received: from artemis.rus.uni-stuttgart.de for elazhary@theochem.uni-stuttgart.de by www.ccl.net (8.8.3/950822.1) id FAA05472; Thu, 28 Aug 1997 05:01:45 -0400 (EDT) Received: from tc8.theochem.uni-stuttgart.de (tc8.theochem.uni-stuttgart.de [129.69.55.128]) by artemis.rus.uni-stuttgart.de with SMTP id LAA02231 (8.6.13/IDA-1.6 for ); Thu, 28 Aug 1997 11:01:45 +0200 Message-ID: <199708280901.LAA02231@artemis.rus.uni-stuttgart.de> Received: by tc8.theochem.uni-stuttgart.de (1.38.193.4/16.2/BelWue-2.1) id AA04420; Thu, 28 Aug 1997 11:01:44 +0200 From: "Dr. Adel El-Azhary" Subject: Experimental geometry To: chemistry@www.ccl.net Date: Thu, 28 Aug 97 11:01:44 METDST Mailer: Elm [revision: 70.85] Dear CCL members: I sent an e-mail to ccl yesterday but it looks like that it was not received. So my apologies if you receive it twice. My question is that I am doing some calculation on some small molecules for which effective, substituted, average or equilibrium experimental geometries are available. So which of these is the best to be comapred to the calculated geometry. Best regards, Adel El-Azhary From s9610264@cougar.vut.edu.au Thu Aug 28 06:20:34 1997 Received: from cougar.vut.edu.au for s9610264@cougar.vut.edu.au by www.ccl.net (8.8.3/950822.1) id GAA05669; Thu, 28 Aug 1997 06:11:19 -0400 (EDT) Received: from localhost (s9610264@localhost) by cougar.vut.edu.au (8.8.7/8.8.7) with SMTP id UAA18610 for ; Thu, 28 Aug 1997 20:12:57 +1000 (EST) Date: Thu, 28 Aug 1997 20:12:56 +1000 (EST) From: Adnan Hazar To: CCL Subject: Re: Problem with HyperNMR Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sometime ago I presented a problem I had with HyperNMR. It just was not able to deal with "large" no of protons. Including from HyperChem I have received the following messages: ----------------------------------------------------------------------- From: Wayne Steinmetz One eventually runs out of memory and then has to be sly and crafty. I face the problem with erythromycin. Fortunately, more of the spins are weakly coupled to one another. In order to handle the portion of the spectrum due to the strongly coupled spins, I consider a subspectrum. For example, in the desosamine ring attached to the macrolide ring of erythromycin, the 2' and 3' protons are nearly degenerate so strong coupling is assured. The 2' proton is coupled to the 3' and also a 1'. The 3' is coupled to the 2' and also to the 4'axial and 4'equatorial. The network goes on but to handle the portion of the spectrum due to the 2' and 3' and perform a simulation involving the 1', 2', 3', 4'equatorial, and 4'axial protons. Normally the total spin system of a molecule can be broken down to subsystems, manageable islands of spins. ----------------------------------------------------------------------- From: Serge Pachkovsky This looks very much like an excuse by a sub-standard support droid. There indeed are quite a few spin states in this system. (Not 2^37, however. More like 2^37 * 2^17 * 6^3 * 3^7, if you assume the molecule to consist entirely of H-1, C-13, O-17, and N-14) The nice part, though, is what THIS IS ABSOLUTELY IRRELEVANT. Depending on gory implementation details, a strightforward realization of GIAO-SCF shielding tensors at the INDO level (which, I believe, is the level employed by HyperNMR) may require from about 12*Norb^2 (if the developer in question feels generous) to (9*Natom + 3)*Norb^2 (if he insists on been wasteful) words of memory. In fact, it is possible to go by with much less than this. Coupling constants are a bit more difficult, with something between (3*Natom + 9)*Norb^2 to 12*Natom*Norb^2 for a naive implementation. I do not know enough about HyperNMR to be able to guess how sofisticated its memory handling is. In your particular case, there are 64 atoms and 145 orbitals, so the shilding tensor calculation should need from 2Mb (for a "generous" implementation) to 93Mb (for a "wasteful" one). Coupling constants might need from 32Mb to 132Mb, possibly in addition to the shielding tensor requirements. Keep in mind what these are back-of-the-envelope estimations, actual requirements may differ by a factor of 2 or four in either direction, depending on the actual implementations' quality. Your support contact should be able to provide you with a tighter estimate. In any event, you should be able to compute shielding tensors for a molecule of this size with 64Mb of real memory, provided that the program and operating system you are using do not impose some arbitrary limit on the resources which can be used. Coupling constants may be a bit more problematic, though, both in terms of memory use and calculation time. Regards, /Serge.P ----------------------------------------------------------------------- From: Joel Polowin Hardware level: nothing you can do; that kind of memory simply can't be packed into a PC. Software level: You may be able to reduce the number of spin states by marking some protons as rotationally equivalent, such as the three protons on a methyl group. (Use with caution: for example, the six protons on two different methyl groups are not necessarily all equivalent to each other!) Apart from that, your best bet is probably to calculate the spectrum for only part of the system at a time and then take the total spectrum as being the sum of the spectra of the parts. Joel Polowin joelp@agiss.com ----------------------------------------------------------------------- ********************** Adnan Hazar Chemical Sciences Victoria University Australia ********************** From buyong@ibmnla.chem.uga.edu Thu Aug 28 10:20:44 1997 Received: from ibmnla.chem.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id KAA06784; Thu, 28 Aug 1997 10:18:26 -0400 (EDT) From: Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA19178; Thu, 28 Aug 1997 10:18:06 -0400 Date: Thu, 28 Aug 1997 10:18:05 -0400 (EDT) To: chemistry@www.ccl.net Subject: comparison betweem EXP and Compuation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 28 Aug 1997, Dr. Adel El-Azhary wrote: > Dear CCL members: > > I sent an e-mail to ccl yesterday but it looks like that it was not received. > So my apologies if you receive it twice. My question is that I am doing some > calculation on some small molecules for which effective, substituted, average > or equilibrium experimental geometries are available. So which of these is the > best to be comapred to the calculated geometry. This is a good question. Too often, we compare computed molecular structure with experimental value without concerning whether they are comparable. First of all, WHAT IS A MOLECULE? (see, Gribov, L. A. J. Mol. Struc. 1993,300,415). There is one quite accuarte definition: it is the smallest particle of the substance made up of eletrons and nuclei of a definit mass. This definition can be expressed mathematically by the schrodinger equation. However, we must reduce to classical expresions if we want to compare calculated structure with a real experiment. We have to use classic models, different models for different experiments. Let us start from several experimental procedures obtaining the information of molecular structure. Two kinds of operational bond lengths R(0) and R(s) may be derived directly from rotational and rotation-vibrational spectroscopy. The R(0) structure is derived from the ground state rotational constants B(0) directly, or more usually with assumptions about some of the structural parameters. When the rotational constants for various isotopic species are observed, the substituted structure R(s) can be determined by Kraitchman method. When vibrational (both harmonic and anharmonic) properties are recorded, one may obtained equilibrium structure R(e) with some approximation. Only is the R(e) really comparable with the value from quantum mechanical calculations, which give the distance between equilibrium nuclear position R(e). X-ray or neutron diffraction experiments give the average nuclear positions at thermal equilibrium, and from which the average nuclear position the internuclear distance R(alpha) is defined. When we refer to the structure at 0 K, we get R(z) structure, which may derived from rotational and rotation-vibrational spectroscopy. Gas phase electron diffraction experiments give the thermal average value of internuclear distance: R(g) structure. The relationship and interconversion of those strcutures may be formulated by classical approximation (see reference cited in the end of this message). MM3(96) version will print out all those structures. If you are using molecular mechanical method, MM3(96) is a good option. you can compare your calculated results with comparable experimental data. Other molecular mechanical packages, as I know, do not realized the difference. If you are talking about QM calculation, of course, experimental equilibrium structure is first choice. However, if it is not available, R(s) structure is close to R(e). I have derived a formula R(s) =[R(z) + R(e)]/2 . R(z) comes third, then R(alpha), and finally R(g). Note that QM results are base sets and correlation dependent, and convergence should be considered in the comparison. Refernce: a) Kuchitus, K. in Accurated Molecular Structures, Ed Domenicano, A et al. Oxford Science Publication, 1992. b) Ma, B.; et al. J. Physical chem. 1996, 100, 8763. J. Am. Chem. Soc. 1997, 119, 2570. J. Mol. Struc. In press ( the issure dedicated to Dr. Kuchitsu). ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= From ccl@www.ccl.net Wed Aug 27 08:28:57 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id HAA00626; Wed, 27 Aug 1997 07:21:26 -0400 (EDT) Received: from ACADEMIC.TRUMAN.EDU for sc18@truman.edu by bedrock.ccl.net (8.8.6/950822.1) id HAA06221; Wed, 27 Aug 1997 07:21:23 -0400 (EDT) Received: from MC209E01.truman.edu by ACADEMIC.TRUMAN.EDU (IBM VM SMTP V2R2) with TCP; Wed, 27 Aug 97 06:23:05 CDT Message-ID: <33E3DD42.A1F794C7@truman.edu> Date: Sat, 02 Aug 1997 18:22:11 -0700 From: "K.R.Fountain" Reply-To: sc18@truman.edu X-Mailer: Mozilla 4.0 [en] (Win95; I; 16bit) MIME-Version: 1.0 To: Gregor Fels CC: chemistry@ccl.net Subject: Re: CCL: VRML X-Priority: 3 (Normal) References: Content-Type: multipart/alternative; boundary="------------0B4E6F0EA14736EF7800DF09" --------------0B4E6F0EA14736EF7800DF09 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Gregor Fels wrote: > Dear CCL readers, > we are looking for a way to export Spartan output data to VRML > format, more precise we would like convert data like the color coding > of an electrostatic potential or the result of a HOMO- or > LUMO-presentation to VRML (rather than merely the > coordinates). > > Any suggestion? > > Gregor > > Dr. Gregor Fels > Universitaet-GH-Paderborn > FB 13-Org. Chemie > Warburgerstr. 100 > D-33098 Paderborn, Germany > > Tel. 0049-5251-602181/Fax -603245 > EMail GF@chemie.uni-paderborn.de > > --- > Administrivia: This message is automatically appended by the mail > exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive > search > Web: http://www.ccl.net/chemistry.html Hi, I would also like to be able to ddo this with Spartan or Hyperchem. Please e-mail me any responses you obtain. Sincerely, Ken Fountain > --- --------------0B4E6F0EA14736EF7800DF09 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Gregor Fels wrote:
Dear CCL readers,
we are looking for a way to export Spartan output data to VRML
format, more precise we would like convert data like the color coding
of an electrostatic potential or the result of a HOMO- or
LUMO-presentation to VRML (rather than merely the
coordinates).

Any suggestion?

Gregor

Dr. Gregor Fels
Universitaet-GH-Paderborn
FB 13-Org. Chemie
Warburgerstr. 100
D-33098 Paderborn, Germany

Tel. 0049-5251-602181/Fax -603245
EMail GF@chemie.uni-paderborn.de

---
Administrivia: This message is automatically appended by the mail exploder:
CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
Anon. ftp: www.ccl.net   | CHEMISTRY-SEARCH@www.ccl.net -- archive search
             Web: http://www.ccl.net/chemistry.html

Hi,

   I would also like to be able to ddo this with Spartan or Hyperchem.  Please e-mail me any responses you obtain.
 
 

Sincerely,

Ken Fountain

---

   --------------0B4E6F0EA14736EF7800DF09-- From robert@pauli.utmb.edu Wed Aug 27 14:20:26 1997 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.3/950822.1) id NAA02309; Wed, 27 Aug 1997 13:53:03 -0400 (EDT) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA04082; Wed, 27 Aug 97 13:29:55 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SUN.8.6.12/950213.SUN.AUTOCF) id MAA15752; Wed, 27 Aug 1997 12:52:42 -0500 From: "Robert Fraczkiewicz" Message-Id: <9708271252.ZM15750@pauli.utmb.edu> Date: Wed, 27 Aug 1997 12:52:42 -0500 In-Reply-To: "Gerrit-Jan's Geocities mail" "CCL:Standard Color codes for atoms" (Aug 27, 1:06pm) References: <199708271208.FAA15265@geocities.com> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "Gerrit-Jan's Geocities mail" , Subject: Re: CCL:Standard Color codes for atoms Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Aug 27, 1:06pm, Gerrit-Jan's Geocities mail wrote: > Subject: CCL:Standard Color codes for atoms > Hello all, > > I am looking for the standard color codes for atoms. As far as I can > remember the standard color for Carbon is black, the one for Oxigen is > blue, Nitrogen is Green. But I am not sure, I am just guessing. > I thought that the standard color coding was like this: C black O red N blue S yellow H white Robert Fraczkiewicz University of Texas Medical Branch Galveston, TX 77555 From d3e102@ames2.pnl.gov Wed Aug 27 14:20:33 1997 Received: from pnl.gov for d3e102@ames2.pnl.gov by www.ccl.net (8.8.3/950822.1) id NAA02165; Wed, 27 Aug 1997 13:34:57 -0400 (EDT) Received: from ames2.pnl.gov by pnl.gov (PMDF V5.1-7 #21283) with SMTP id <01IMXJ56TNR48ZFQYQ@pnl.gov> for chemistry@www.ccl.net; Wed, 27 Aug 1997 10:30:02 PDT Received: by ames2.pnl.gov (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA03742; Wed, 27 Aug 1997 10:29:58 -0700 Date: Wed, 27 Aug 1997 10:29:56 -0700 From: d3e102@emsl.pnl.gov Subject: Updated Ab Initio Benchmarks To: chemistry@www.ccl.net Message-id: <9708271029.ZM3740@ames2.pnl.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 06sep94) Content-type: text/plain; charset=us-ascii The third version of the EMSL Ab Initio Benchmark Report is available at http://www.emsl.pnl.gov:2080/docs/tms/abinitio/cover.html. This version includes information on 40 different hardware platforms and 11 different software packages. Compared to the two previous versions our access to some of the "latest and greatest" processors was more restricted. Most significant was the lack of availability of a highspeed Pention II machine, but that defficiency should be rememdied shortly. Please address any comments regarding what you like or don't like to me. -- David Feller | Environmental Molecular Sciences Laboratory | Battelle Pacific Northwest National Lab | Mail Stop K1-90 | e-mail:d3e102@emsl.pnl.gov 906 Battelle Blvd | Fax: (509)-375-6631 Richland, WA 99352 | From jkl@ccl.net Thu Aug 28 17:20:41 1997 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id RAA09256; Thu, 28 Aug 1997 17:10:50 -0400 (EDT) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.6/950822.1) id RAA26561; Thu, 28 Aug 1997 17:10:50 -0400 (EDT) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id RAA03720; Thu, 28 Aug 1997 17:10:49 -0400 (EDT) Date: Thu, 28 Aug 1997 17:10:49 -0400 (EDT) Message-Id: <199708282110.RAA03720@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Molecular Weight Calculator for Windows95 (v4.0) available in CCL archives Cc: jkl@ccl.net Version 4.0 of Molecular Weight Calculator for Windows 95 now available in CCL archives: ftp://www.ccl.net/pub/chemistry/software/MS-WINDOWS95/Molecular_Weight Enjoy and thank Matthew Monroe (Monroem@UNC.Edu) Jan Labanowski jkl@ccl.net