From chemistry-request@www.ccl.net Sun Nov 1 14:55:35 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA17578 Sun, 1 Nov 1998 14:55:35 -0500 (EST) Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id OAA16223 for ; Sun, 1 Nov 1998 14:55:31 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA04086; Sun, 1 Nov 98 11:55:08 -0800 Received: from dxg-pc.msi.com(146.202.11.19) by bioc1.msi.com via smap (V2.0) id xma004083; Sun, 1 Nov 98 11:54:48 -0800 Message-Id: <3.0.32.19981101115154.006fe4d4@146.202.0.225> X-Sender: dgregory@146.202.0.225 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sun, 01 Nov 1998 11:51:55 -0800 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:Parameterization Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Howard, Using MSI's Ref_Search web-page (http://www.msi.com/science/online/references/) I found: Maple J.R., Hwang M.-J., Stockfisch T.P., Dinur U., Waldman M., Ewig C.S., Hagler A.T., "Derivation of Class II Force Fields. I. Methodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules", J. Comp. Chem., 15, 162-182, 1994 Hwang M.-J., Stockfisch T.P., Hagler A.T., "Derivation of Class II Force Fields. II. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules", J. Am. Chem. Soc., 116, 2515-2525, 1994 Maple J.R., Hwang M.J., Stockfisch T.P., Hagler A.T, "Derivation of Class II Force Fields. III. Characterization of a Quantum Force Field for Alkanes", Israel J. Chem., 34, 195-231, 1994 Hope this helps. Don Gregory At 05:03 PM 10/30/98 -0600, you wrote: >Hi, > > Several weeks ago I asked some questions about parameterization. I >received several replies, and have been happily (well, sort of) plugging >away at parameterizing Nitromethane. > > I have a further question. I am interested in using Quantum >mechanical calculations to determine some of the intramolecular force >constants, and to that end Craig Burkhart mentioned a paper by Hagler, >Hwang, and Stockfish, which used QM calculations to parameterize (what I >assume is) the DISCOVER 2nd generation force field. Does anyone know >the exact reference? Thanks. > > Howard > >-- > >Howard E. Alper, Ph.D. >Dept. of Chemistry and The Advanced Materials Research Institute >University of New Orleans >New Orleans, LA 70148 >504-280-7216 > > - Helping molecules find happiness for almost a 5th of a century. > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: halper@uno.edu >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 > > > > Dr. Don Gregory (dgregory@msi.com) Japan Science Liaison Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 546-5331 http://www.msi.com From chemistry-request@www.ccl.net Fri Oct 30 03:16:55 1998 Received: from kweetal.tue.nl (kweetal.tue.nl [131.155.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA04932 Fri, 30 Oct 1998 03:16:54 -0500 (EST) Received: from sg10.chem.tue.nl [131.155.80.53] by kweetal.tue.nl (8.9.0) for id JAA14871 (ESMTP). Fri, 30 Oct 1998 09:16:40 +0100 (MET) Received: from tgakrh@localhost by sg10.chem.tue.nl (8.8.5) for chemistry@www.ccl.net id JAA23803. Fri, 30 Oct 1998 09:16:39 +0100 (MET) From: Roelant Harmsen Message-Id: <199810300816.JAA23803@sg10.chem.tue.nl> Subject: Re basisset for Dgauss To: chemistry@www.ccl.net Date: Fri, 30 Oct 1998 09:16:39 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hi everyone, I am looking for a DZVP basisset for Renium in Dgauss format. Does anyone know where to get one, or does anyone have it? Thanks, Roelant ********************************************************************** Roelant Harmsen |tel: ++31 40 2473575/5032 University of Technology Eindhoven |fax: ++31 40 2455054 Schuit Institute of Catalysis |e-mail: R.J.Harmsen@tue.nl P.O. box 513 |e-mail : tgakrh@chem.tue.nl 5600 MB Eindhoven | The Netherlands |AD&D: Xahnar (Wild Mage) Homepage: http://www.tak.chem.tue.nl/personal/rharmsen ********************************************************************** From chemistry-request@www.ccl.net Fri Oct 30 08:24:21 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA06175 Fri, 30 Oct 1998 08:24:20 -0500 (EST) Received: from europe.std.com (europe.std.com [199.172.62.20]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA29412 for ; Fri, 30 Oct 1998 08:24:18 -0500 (EST) Received: from world.std.com by europe.std.com (8.7.6/BZS-8-1.0) id IAA21439; Fri, 30 Oct 1998 08:24:19 -0500 (EST) Received: by world.std.com (TheWorld/Spike-2.0) id AA04273; Fri, 30 Oct 1998 08:24:19 -0500 Date: Fri, 30 Oct 1998 08:24:19 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199810301324.AA04273@world.std.com> To: chemistry@ccl.net Subject: dbx debugger available under Linux? Folks, Is there any way of getting the dbx debugger under Linux? Yeah, I am lazy and would rather not have to learn a new (or gnu?) debugging tool and since I am used to dbx from the SGI... Thanks in advance! Joe jle@world.std.com From chemistry-request@www.ccl.net Fri Oct 30 10:24:31 1998 Received: from earth.ox.ac.uk (darwin.earth.ox.ac.uk [163.1.22.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA08601 Fri, 30 Oct 1998 10:24:22 -0500 (EST) Received: from metropolis.earth.ox.ac.uk (metropolis [163.1.22.59]) by earth.ox.ac.uk (8.9.1a/8.9.1) with SMTP id PAA01155; Fri, 30 Oct 1998 15:24:11 GMT From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <13881.55834.533877.753311@metropolis> Date: Fri, 30 Oct 1998 15:24:10 +0000 (GMT) To: "'chemistry@www.ccl.net'" Subject: CCL:all image convention In-Reply-To: <3639ADA6.4632@antas.agraria.uniss.it> References: <01BE01BC.2E9D6920.johnw@msi.com> <3639ADA6.4632@antas.agraria.uniss.it> X-Mailer: VM 6.62 under Emacs 20.3.1 bruno manunza writes: > Can anybody give some explanation about the 'all image convention'? > It looks like some technique which should be used when the cut-off > radius is larger tha the half cell edge. Is it? I presume you are talking about molecular dynamics simulation in a periodic cell. The "all-image" convention is the natural and correct way of computing interatomic/molecular interactions for an arbitrary cutoff-radius which may be of any length. It really only has a name to contrast with the approximation, the "minimum image convention" which only works for cutoff radii shorter than half the cell edge. Keith Refson -- ------------------------------------------------------------------------------ Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | Spam: root@cyberpromo.com | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------------------ From chemistry-request@www.ccl.net Fri Oct 30 10:58:41 1998 Received: from abacus.ac.BrockU.CA (abacus.ac.BrockU.CA [139.57.65.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA12606 Fri, 30 Oct 1998 10:58:38 -0500 (EST) Received: from [139.57.81.101] ([139.57.81.101]) by abacus.ac.BrockU.CA (8.8.7/8.8.7) with SMTP id KAA10380 for ; Fri, 30 Oct 1998 10:58:37 -0500 (EST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 30 Oct 1998 12:04:36 -0700 To: CHEMISTRY@www.ccl.net From: srothste@abacus.ac.brocku.ca (Stu Rothstein) Subject: Re: CCL:Energy levels of atomic orbitals (calculated/experimental) as functions of nuclear charge. >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 > > A good paper on the issue of transition metal atomic configurations and limitations of the orbital approximation appears in the following: E.R. Scerri, J. Chem. Educ 66 [6] 481 (1989) Stuart M. Rothstein, Chemstry Dept, Brock University, Canada From chemistry-request@www.ccl.net Sat Oct 31 23:30:23 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 XAA16229 Sat, 31 Oct 1998 23:30:22 -0500 (EST) Received: from red5 ([128.97.35.245]) by ewald.mbi.ucla.edu (8.9.1/8.9.1) with SMTP id UAA20146 for ; Sat, 31 Oct 1998 20:30:22 -0800 (PST) Message-Id: <199811010430.UAA20146@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 Date: Sat, 31 Oct 1998 20:36:01 -0800 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Summary: Energy levels of atomic orbitals (calculated/experimental) as functions of nuclear charge. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Thank you for your comments. Individual responses are below. The NIST Physical Reference Data (http://physics.nist.gov/PhysRefData/contents.html) is an excellent resource for electron configurations. I believe the correct way to write electron configurations is to indicate the ground state such that the last orbital represents the highest energy orbital. Giving Titanium as an example: Ti [Ar] 3d^2 4s^2. This clearly shows that Ti+ is [Ar] 3d^2 4s^1. This appears a viable solution until one asks why the 4s^2 in Ti do not enter the lower energy unoccupied 3d orbitals? Laurence >Date: Thu, 29 Oct 1998 10:22:57 +0100 (MET) >From: Habbo Heinze >To: Laurence Lavelle >Subject: Re: CCL:Energy levels of atomic orbitals (calculated/experimental) as functions of nuclear charge. > > >Have a look at > > NIST Physical Reference Data > http://physics.nist.gov/PhysRefData/contents.html > >specifically > > Ground Levels and Ionization Energies for the Neutral Atoms > http://physics.nist.gov/PhysRefData/IonEnergy/ionEnergy.html > >Maybe this data is helpful > >Cheers > >Habbo >Date: Thu, 29 Oct 1998 16:29:31 -0400 (AST) >From: "J. Sichel" > >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 >Date: Thu, 29 Oct 1998 08:00:07 -0500 (EST) >From: Robert Zellmer > >I'm not sure the 3d^1 4s^2 is necessarily written this way because of energy >considerations. Generally, one thinks of the 4s^2 3d^1 configuration as being >correct due to energy considerations and since the 4s is full one would expect >this. > >It may be possible that the 3d is lower in energy than the 4s. However, >I believe that the 3d^1 4s^2 configuration is often written to convey the fact >that the 4s is the valence shell (although most consider the 3d as part of the >"valence" for transition metals since it is only partailly occupied in most cases >and certainly is an important part of the chemistry of these elements). Written >in this way students can "see" the valence shell (shell with highest n value). > >When the configuration is written as 4s^2 3d^1 this shows that the 4s is filled >before the 3d since it is lower in energy. This is also a convienent way to write >the configuration since this is the way it gets filled by using the periodic >table (ns before (n-1)d). So even in cases when the 3d may be lower in energy >it is still written this way. Think of the "exceptions" Cr and Cu in the >first transition metal period which have the config. 4s^1 3d^5 and 4s^1 3d^10, >respectively. These get filled in this way due to shifts in the energies of >these subshells and we usually tell students that 1/2 filled and full subshells >have an "extra" stability. > >I think it would be very confusing to students if you changed the order everytime >these orbitals changed order due to changes in energy. I usually stick with the >4s 3d ordering and tell them they may see it as 3d 4s since in this way the >valence shell is on the "outside". > >I think I have seen a graph of the relative energies of these levels as one moves >through the PT. I will see if I can locate it. > > >Robert J. Zellmer >From: "Huff, Tom" > >I would appreciate a copy of your inputs assuming they are not posted in a >summary on the CCL. My wife teaches first year chemistry and these are her >comments at a first year chemistry level. > >I believe >the problem may simply be that different textbook use different notations in >writing the electron configurations. Some write the electron configurations >by shells (so 3s 3p 3d then 4s etc.); where others are writing the >configuration by energy (3s 3p 4s 3d). On the other hand Judy and I have >discussed several times the fact that the electrons fill in one order (4s >before 3d) but are removed in different order (4s before 3d). I believe >experimental evidence confirms that the 4s fills first (when there are no 3d >electrons) but as you begin adding 3d electrons there will be additional >shielding of the nucleus making the effective nuclear charge less and >therefore higher energy for the 4s when there are one or more 3d electrons. > > >Tom Huff From chemistry-request@www.ccl.net Fri Oct 30 12:01:55 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 MAA19362 Fri, 30 Oct 1998 12:01:54 -0500 (EST) Received: from [194.105.224.226] by pop.isholf.is (NTMail 3.03.0017/4c.acsh) with ESMTP id wa915950 for ; Fri, 30 Oct 1998 17:01:45 +0000 From: "=?iso-8859-1?Q?J=F3n_Valgeirsson?=" To: Subject: Ph.D. study - Guru vs. Hands-on Groups Date: Fri, 30 Oct 1998 17:09:20 -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: <17014552816041@isholf.is> After my message (accidently) was posted on this list Iīve had quite good response and some encouraged me to summarize these for the list. It seems that the overall view is that I should follow my own heart in this matter, for this, one or more of the following reasons were given: 1. The Ph.D. study is a lenghty process itself and should be enjoyed (if possible) by the student. 2. It is difficult to estimate the preference in industry/academia already, let alone in 3-5 years. 3. You will probably have to do some post-doc work anyway - At this point you can simply switch to the algorithm development or medicinal chemistry angle whichever you have the less experience in at that point. 4. If you are doing what you like you are more likely to be successful in your work. 5. It does not matter - your publications and "track-record" matter most. Some on the other hand were either for or against either group. Reasons to join the "hands-on" lesser known group: 1. The industry needs a professional all-rounder who has worked closely with organic/medicinal chemists on real-world drug design problems rather than a specialist. Especially smaller groups who canīt devote much time to method development or software coding. 2. In industry, there is remondous pressure to apply your skills to "practical" problems, not problems that will push back the frontiers of science. 3. You are more likely to use your creativity more in the hands-on lab, and will accquire more problem solving skills - which are essential. 4. If you work in a big specialized lab you can lose sight of the big picture involved in drug design. 5. To much theory detracts from the industry needs. 6. The biggest handicap that most computational chemists have is an inability to "connect" with experimental scientists. It really doesn't matter what calculations you (the computational chemist) can and can't do, or what algorithms you can and can't develop (and program), unless you have a good idea what the people around you need. You have to be able to understand their problems and find ways of helping them solve them. Since these people are chemists, biologists, etc., you need to get whatever exposure you can to these fields. Reasons to join the "guru" group: 1. Larger modelling groups and academia need specialised people who can develope in-house methods and software. 2. Shear vanity would favour hiring a person from a "guru" lab. 3. A Ph.D. from a guru lab offers a sense of Quality to the candidate. 3. Itīs easier to pick up medicinal chemistry than a firm basis in physical chemistry and Computational methods. 4. One should become an expert rather than consult with experts. 5. In a hands-on lab you are more likely to spend time on mundane tasks rather than creating novel approaches. Having shown you all this I apologize to anyone who recognises some part of his/her statements here above. I tried to rephrase most of the statements, and thought it more contraversial if I were to name the contributers. For those interested I will follow the first advice - that is joining the group I favour my self and that this happends to be the "hands-on" group and this has undoubtetly biased my summary presented here. I have to mention that there are some additional personal factors that I took into account in this regard, such as social, economic and geographical reasons that favoured the "hands-on" group. Thank you for your excellent responses, and please do not hesitate to bring forth additional comments on the matter. Jon Valgeirsson jonv@rhi.hi.is