From chemistry-request@www.ccl.net Thu Oct 29 00:41:28 1998 Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA00131 Thu, 29 Oct 1998 00:41:27 -0500 (EST) Received: from red5 ([128.97.35.245]) by ewald.mbi.ucla.edu (8.9.1/8.9.1) with SMTP id VAA23543 for ; Wed, 28 Oct 1998 21:41:29 -0800 (PST) Message-Id: <199810290541.VAA23543@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 Date: Wed, 28 Oct 1998 21:46:35 -0800 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Energy levels of atomic orbitals (calculated/experimental) as functions of nuclear charge. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Greetings, I am looking for recent calculations/experimental data of energy levels of atomic orbitals as functions of nuclear charge. I am teaching first year chemistry and would like recent work on the relative stability of the 4s and 3d orbitals and why they change for the first transition row. Of the four teaching text books I've read two show Sc as 4s^2 3d^1 and two show 3d^1 4s^2 as the ground state. Comments welcome. Appreciated Laurence Lavelle From chemistry-request@www.ccl.net Thu Oct 29 05:32:47 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA01510 Thu, 29 Oct 1998 05:32:41 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id MAA56754 for ; Thu, 29 Oct 1998 12:32:58 +0100 Date: Thu, 29 Oct 1998 12:32:58 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:H2 diss. DFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I calculated the dissociation of H2, by putting the 2 H's at a distance of 10 angstrom. This yielded the following results (STO-3G): RHF = 0.5451863 au RB3LYP = 0.3744394 au Of course, we all know that RHF cannot reasonbly describe this dissociation process. But my question is the following: Why is RB3LYP, which uses the same, bad wavefunction, much better than the RHF value? Of course, correlation, etc. But is there a *physical* explanation for it? Any comments on this topic are most welcome ! Thanks, 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 chemistry-request@www.ccl.net Thu Oct 29 05:52:11 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA01578 Thu, 29 Oct 1998 05:52:06 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id MAA53222 for ; Thu, 29 Oct 1998 12:52:37 +0100 Date: Thu, 29 Oct 1998 12:52:36 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:CC versus CI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all again! Another theoretical point which bothers me: Suppose we perform a CI calculation with all determinants that are normally generated by CCSD (exp(T1+T2)). Would the obtained result be worse or better than the CCSD value? Any comments are welcome? 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 chemistry-request@www.ccl.net Thu Oct 29 07:07:52 1998 Received: from news.uni-kl.de (mmdf@news.uni-kl.de [131.246.137.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA01902 Thu, 29 Oct 1998 07:07:51 -0500 (EST) Received: from iris1.chemie.uni-kl.de ( iris1.chemie.uni-kl.de [131.246.9.107] ) by news.uni-kl.de id aa29812 for ; 29 Oct 98 13:08 MET Received: from oktarin by iris1.chemie.uni-kl.de via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id NAA03553; Thu, 29 Oct 1998 13:07:30 +0100 Received: from localhost by oktarin with smtp (Smail3.1.28.1 #7) id m0zYqrS-0000F9C; Thu, 29 Oct 98 13:07 CET Date: Thu, 29 Oct 1998 13:07:30 +0100 (CET) From: Stefan Konietzny To: "Comp. Chem. List" Subject: Short and urgent question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everyone, is a CI-calc. restartable in g94. I did not find a yes or no about this in the manual. Regards, Stefan. !!!!! reply to: konietz@chemie.uni-kl.de !!!!! finger or talk request: konietz@oktarin.chemie.uni-kl.de **************************************************************** * Stefan Konietzny * *--------------------------------------------------------------* *Fachbereich Chemie, AK Frank | Dept. of Chemistry * *Universitaet Kaiserslautern | University of Kaiserslautern * *Erwin-Schroedingerstr. | Erwin-Schroedingerstr. * *67663 Kaiserslautern | D-67663 Kaiserslautern * *0631/205-2964 (62) | +49-631/205-2964 (62) * **************************************************************** From chemistry-request@www.ccl.net Thu Oct 29 07:46:21 1998 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA02111 Thu, 29 Oct 1998 07:46:15 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.1a/8.9.1) with ESMTP id MAA21082 for ; Thu, 29 Oct 1998 12:47:22 GMT From: Michael Nolan Message-Id: <199810291246.MAA17430@rennes.nmrc.ucc.ie> Subject: Peptide rotation barriers To: chemistry@www.ccl.net (ccl) Date: Thu, 29 Oct 1998 12:46:09 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear all, I'm studying the link formed between p-aminophenol (AP) and p-hydroxybenzoic acid (HBA). The bond formed between the two molecules is the peptide link X O \ / \ / N-----C / \ / \ H X Now according to the biochemists the most stable conformation is the trans configuration (steric reasons etc etc) We computed a rotational barrier (trans->cis for HBA-AP), simply by stepping 15 degree incremenets along the torsion X-N-C-O and calculating single point energies(our resources are so meagre that we cannot do optimisations for each structure). We used B-LYP/6-31G* and also the PCFF force-field. B-LYP gave a large barrier (hundreds of kCal/mol) and the FF gave ridiculous results. At least we could see that the barrier to rotation from trans to cis is very high, which I guess you would expect. I have a couple of questions.... 1: Would it be in people's opinion valid to use PCFF for MD simulations of this system? Bearing in mind for HBA we used the PCFF force-field successfully and I guess we would like to be consistent in our use of force-field. 2: Is it valid to estimate the barrier to rotation around the peptide link only from single point calculations? 3: Has anyone looked at this barrier before? I have looked at a number of databases for AP and only got rubbish and a chemical abstracts search was none too successful. I would appreciate any refs. at all Summary as usual Thanking you for your time Michael ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork IRELAND mail: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/modellingRes.html *****EMRS Call for papers:******** http://nmrc.ucc.ie/groups/AMT/SympMain.html **************************************************************************** From chemistry-request@www.ccl.net Thu Oct 29 08:31:45 1998 Received: from octane.kemi.aau.dk (octane.kemi.aau.dk [130.225.22.149]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA02657 Thu, 29 Oct 1998 08:31:42 -0500 (EST) Received: from octane.kemi.aau.dk (localhost.kemi.aau.dk [127.0.0.1]) by octane.kemi.aau.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA14103; Thu, 29 Oct 1998 14:31:42 -0800 Sender: roberson@kemi.aau.dk Message-ID: <3638ECCE.41C6@kemi.aau.dk> Date: Thu, 29 Oct 1998 14:31:42 -0800 From: MJR Organization: Center for Metal Catalysed Reactions X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: Steven Creve CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:CC versus CI References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Steven Creve wrote: > > Hi all again! > > Another theoretical point which bothers me: > > Suppose we perform a CI calculation with all determinants that are > normally generated by CCSD (exp(T1+T2)). Would the obtained result be > worse or better than the CCSD value? > > Any comments are welcome? > > Steven You ask interesting questions, Steven, and this one I think I can answer. Both CISD and CCSD represent the correlated wavefunction |corr> as a sum over configuration state functions. The difference between them is that CI exploits the variational prinicple to minimise the energy, thus CI: = ensuring a strict upper bound to the total energy, while CC solves the Schroedinger equation within a subspace. As a consequence, the computed CC: H|corr> = E|corr> energy may be greater than or less than the true energy. Use of the cluster operator to parameterise |corr> results in the implicit estimation of contributions from higher excitations ( quadruples, etc ) so the energy in practice tends to be quite accurate. A principle benefit of CC over CI is that it is size consistent: the energy of dimer supermolecule is twice the energy of the constituent monomer, a conventient property when computing binding energies and whenever large numbers of electrons are being correlated. As always, "which method is better" depends upon the problem you are studying and the important features of the solution required. Sometimes the variational principle is critical, sometimes size consistency. Mark ********************************************************************** To reply, replace the danish robersen with the scottish roberson. ********************************************************************** From chemistry-request@www.ccl.net Wed Oct 28 08:51:15 1998 Received: from hotmail.com (f141.hotmail.com [207.82.251.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA17511 Wed, 28 Oct 1998 08:51:01 -0500 (EST) Received: (qmail 17757 invoked by uid 65534); 28 Oct 1998 13:50:22 -0000 Message-ID: <19981028135022.17752.qmail@hotmail.com> Received: from 129.1.198.105 by www.hotmail.com with HTTP; Wed, 28 Oct 1998 05:50:20 PST X-Originating-IP: [129.1.198.105] From: "Xiaomei Yang" To: pueyo@pinon.ccu.uniovi.es Cc: CHEMISTRY@www.ccl.net Subject: Re: Ag Content-Type: text/plain Date: Wed, 28 Oct 1998 08:50:20 EST Look at 1985 handbook by R. Poirier, R. Kari and I.G. Csizmadia: "Handbook of Gaussian Basis Sets", Elsevier Science, New York, 1985. You can also get the MonsterGauss format at ftp://www.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/basis-sets/ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@www.ccl.net Thu Oct 29 15:31:41 1998 Received: from bosoleil.ci.umoncton.ca (sichelj@bosoleil.ci.umoncton.ca [139.103.2.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA17208 Thu, 29 Oct 1998 15:31:40 -0500 (EST) Received: from localhost (sichelj@localhost) by bosoleil.ci.umoncton.ca (8.8.6 (PHNE_15509)/8.8.6) with SMTP id QAA06053; Thu, 29 Oct 1998 16:29:33 -0400 (AST) Date: Thu, 29 Oct 1998 16:29:31 -0400 (AST) From: "J. Sichel" X-Sender: sichelj@bosoleil.ci.umoncton.ca To: Laurence Lavelle cc: chemistry@www.ccl.net Subject: Re: CCL:Energy levels of atomic orbitals (calculated/experimental) as functions of nuclear charge. In-Reply-To: <199810290541.VAA23543@ewald.mbi.ucla.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 28 Oct 1998, Laurence Lavelle wrote: > I am looking for recent calculations/experimental data of energy levels of > atomic orbitals as functions of nuclear charge. I am teaching first year > chemistry and would like recent work on the relative stability of the 4s > and 3d orbitals and why they change for the first transition row. Of the > four teaching text books I've read two show Sc as 4s^2 3d^1 and two show > 3d^1 4s^2 as the ground state. > Comments welcome. According to CE Moore's compilation of Atomic Energy Levels, the experimental ground state is Sc(3d 4s2 2D 3/2). John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada From chemistry-request@www.ccl.net Thu Oct 29 15:55:56 1998 Received: from sigma.ucdavis.edu (sigma.ucdavis.edu [169.237.38.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA21601 Thu, 29 Oct 1998 15:55:55 -0500 (EST) Received: by sigma.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id MAA11731; Thu, 29 Oct 1998 12:56:05 -0800 From: "Dmitry M. Medvedev" Message-Id: <9810291255.ZM11729@sigma.ucdavis.edu> Date: Thu, 29 Oct 1998 12:55:51 -0800 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Biograph file type Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers! I need to convert a .pdb file or .car file (both generated by Biosym InsightII) into .bgf file (MSI Biograph). We have Babel 1.3 which claims to support the .bgf file type but it doesn't. Could you tell me if there is some free program (e.g. some new version of Babel) which can make this conversion? Thanks in advance, Dmitry. From chemistry-request@www.ccl.net Thu Oct 29 17:54:37 1998 Received: from pop.isholf.is (pop.isholf.is [194.105.226.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA02551 Thu, 29 Oct 1998 17:54:34 -0500 (EST) Received: from [194.105.224.97] by pop.isholf.is (NTMail 3.03.0017/4c.acsh) with ESMTP id da912967 for ; Thu, 29 Oct 1998 22:54:11 +0000 From: "=?iso-8859-1?Q?J=F3n_Valgeirsson?=" To: Subject: 98.10.16 US-CT-MEDICINAL/ORGANIC CHEMIST PHARMACEUTICAL Date: Thu, 29 Oct 1998 23:01:44 -0000 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Message-Id: <22541098301844@isholf.is> Dear recipient, I noticed an advertisement from your company on a internet Comp.Chem. joblist (http://www.ccl.net/cca/jobs/joblist). I am sorry to bother you as I am not actually seeking a job as this time, but more to inquire about the industry´s needs. I am about to embark upon a Ph.D. study in Computer aided drug design and am lucky enough to be able to choose between two projects: One is with a relatively well known group in Comp.Chem. and the project would be very specialized, that is optimization of one particular algorithm and would involve little contact with "actual" chemistry and medicinal chemists (very theoretical). The other project is at a Med.Chem./Pharmacology group that does not have the same experience/prestige in Comp.Chem. but has all necessary hardware/software and is prepared to let me consult with whatever experts are in the field at other institutions. This group has also a very active drug design project going on and is "very likely" to produce some active leads in the near future and is very active in publications. So in a nutshell the question is this: In hiring new Comp.Chemist what do you look for ? Is it a very specialised/technical Ph.D. under a "guru" in the field ? or a Ph.D. which involves "hands on" ecperiance on actual comp. drug design albeit from an lesser known group (but with relevant publications of success) ? As you may have guessed I am inclined to join the latter group, but I want to establish that I wont be "shooting myself in the foot" be not joining the most famous professor. Thank you very much for your time, Jon Valgeirsson Holtsgata 31 101 Reykavik ICELAND E-MAIL: jonv@rhi.hi.is From chemistry-request@www.ccl.net Thu Oct 29 18:23:45 1998 Received: from rachmaninov.iq.ufrj.br (rachmaninov.iq.ufrj.br [146.164.30.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA02811 Thu, 29 Oct 1998 18:23:42 -0500 (EST) Received: (jomal@localhost) by rachmaninov.iq.ufrj.br (8.8.5/8.3) id GAA13630; Sat, 31 Oct 1998 06:23:31 GMT From: Joao Otavio M A Lins Message-Id: <199810310623.GAA13630@rachmaninov.iq.ufrj.br> Subject: Re: Biograph file type To: chemistry@www.ccl.net (CCL) Date: Sat, 31 Oct 1998 06:23:31 +0000 (CUT) X-Mailer: ELM [version 2.4ME+ PL43 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Dmitry, You will find the Babel modified sources by Schrodinger Inc. in ftp://ftp.schrodinger.com/schrodinger/babel/babel-v35030.tar.Z (~200KB). -Joao _______________________________________________________________________ Instituto de Quimica da UFRJ email: jomal@iq.ufrj.br Centro de Tecnologia, bloco A, sala 412 voice: +55-21-590-9890 Cidade Universitaria fax : +55-21-290-4746 21949-900 - Rio de Janeiro - RJ BRAZIL _______________________________________________________________________