From owner-chemistry@ccl.net Fri Nov 11 02:33:00 2005 From: "Brian Salter-Duke b_duke{=}octa4.net.au" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-29938-051111011946-19087-eIHOxR2X4oPLGLCCW9UTNw~~server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 11 Nov 2005 17:19:26 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke^^^octa4.net.au] On Thu, Nov 10, 2005 at 06:17:07PM -0500, Eric Scerri scerri__chem.ucla.edu wrote: > Sent to CCL by: Eric Scerri [scerri!^!chem.ucla.edu] > > > > In teaching qualitative molecular orbital theory one encounters the > question of the crossing of the sigma 2p and pi 2p bonding orbitals > in homonuclear diatomics. > > > This is such that N2 has the pi orbitals of lower energy than sigma > whereas for O2 the energies are reversed. This is an interesting point. The statement about N2 is false. At all basis sets greater than minimum basis the sigma level lies lower than the pi level. This means that a Koopmans Theorem prediction of the ordering of the lowest PES ionisation levels is wrong. The lowest ionisation is from the sigma orbital, but this does NOT mean that the sigma orbital is the highest occupied. To predict the correct PES ordering one has to go beyond Hartree-Fock level. Even the delta-SCF method where the total energy of the N2 molecule and the N2+ ion are determinated at Hartree-Fock level gives the wrong ordering. Introduction of correlation at MP2 or beyond is required to predict the correct order of the ion states. I discussed this with Brian O'Leary in:- Non-Koopmans' Molecules. B. J. Duke and B. O'Leary. Journal of Chemical Education, 72, 501 - 504, 1995. For an earlier discussion of the orbital energy ordering see "Atoms and Molecules" by Martin Karplus and Richard Porter. The diagram is on page 349 in my edition (1970). I do not know of a later text that looks at this in anything like this way. At all levels of teaching we should not draw conclusions about the ordering of molecular orbitals from experimental PES data. Theory should predict experiment and be modified or improved if the predictions are wrong. Experiment should not predict theory. Eric, I'm happy to run any of these diatomics if you want, but be rather clearer about what sort of calculation you want. Brian. > But what about heteronuclear diatomics where each of the atoms ? > > > The ordering given in general chemistry textbooks shows a wide > variation. See for example Oxtoby, Zumdahl or Olmsted and Williams, > all three of which contradict each other. > > Herzberg's, Spectra of Diatomic Molecules specifically states the > configurations of CO and NO. > > For CO the ordering is as in the case of N2 whereas for NO the > ordering is as in O2. > > However Herzberg's book is now a little out of date (1950). > > Do more recent calculations on these two molecules suggest anything > different? Would anyone be prepared to run these calculations and > tell me the results? > > How about experimental evidence such as PES on CO and NO? > > > > regards, > eric scerri -- Brian Salter-Duke (Brian Duke) b_duke * octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ. From owner-chemistry@ccl.net Fri Nov 11 03:07:00 2005 From: "Crous Werner wcrous]*[sun.ac.za wcrous]*[sun.ac.za" To: CCL Subject: CCL:G: Multi-step ONIOM Message-Id: <-29939-051111022224-28719-gccLWVHxExQ0RrOUIeEBBw-*-server.ccl.net> X-Original-From: "Crous Werner " Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Fri, 11 Nov 2005 09:22:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Crous Werner [wcrous::sun.ac.za]" Hi I do not think there is something wrong with the original input except for the link1 part as Wei Deng pointed out. I do not agree that one must use a linking atom in this case. Here we are dealing with IMOMO and not IMOMM. Therefore the interactions, covalent and electrostatic between the two systems will automatically be incorporated in the extrapolated ONIOM energy due to the nature of the ONIOM calculation. When making use of a force field for the MM-part and you have a bond that stretches from the MM to the QM you need to use a linking atom as the MM calculations states that bonded atoms should have bonds specified. When using QM you do not have to specify any bonds. Werner -----Original Message----- > From: owner-chemistry*|*ccl.net [mailto:owner-chemistry*|*ccl.net] Sent: 10 November 2005 05:24 To: Crous, Werner Subject: CCL:G: Multi-step ONIOM Sent to CCL by: Wei David Deng [weidavid.deng===yale.edu] There are at least two parts are wrong. On the first step, you didn't specify the link atom and where the hydrogen should be put in the model system. You need to add "H" at the end of the chloride input. On the second step, you already said "geom=check", then you shouldn't enter the H and L levels again. It will automatic extract from the checkpoint file. I am attaching my input below. I hope this works in your system, since I am using a later version of Gaussian. Sincerely David Deng ================================================= %Chk=NaCl #T oniom(hf/6-31g(d):hf/3-21g*) sp Title Card Required 0 1 Na Cl 1 2.000 L H --Link1-- %Chk=NaCl #T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read NaCl SinglePoint-2 Na(High) Cl(Low) 0 1 ===================================== Wei David Deng wrote: > > Sent to CCL by: "Telkuni Tsuru" [telkuni]-[venus.dti.ne.jp] > Hello, CCLers. > > I like to ask the description of multi-step ONIOM job on Gaussian98W. > For example, the following input is correct? > > ======= input ======== > %Chk=NaCl > > #T ONIOM(HF/6-31G(d):HF/3-21G(d)) SP > > NaCl SinglePoint-1 Na(High) Cl(Low) > > 0,1 0,1 > Na 2.000000 0.000000 0.000000 H > Cl 0.000000 0.000000 0.000000 L > > --Link1-- > %Chk=NaCl > > #T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read > > NaCl SinglePoint-2 Na(High) Cl(Low) > > 0,1 0,1 > Na H > Cl L > > ======= end of input ======= > > If you don't mind, please point out the wrong part and teach me correct > description. > Any responses I'll appreciate. I will summarize them and upload to this ML. > > > Sincerely yours, > ---------------------------------------------------- > Telkuni Tsuru telkuni:venus.dti.ne.jp > Bunshi Gijyutu > [this "venus" means the planet "venus".]> > > > > -- Wei Deng (David), Ph.D. Post-doctoral Researcher Department of Chemistry, Yale University 225 Prospect St., P.O. Box 208107 New Haven, CT 06520-8107 Tel: (203) 284-2501 Email: weidavid.deng]-[yale.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 11 04:04:01 2005 From: "Lubos Vrbka shnek**tiscali.cz" To: CCL Subject: CCL: water melting simulation Message-Id: <-29940-051111031244-26555-jKXyb/fcQsdm5DtgMxa8EA::server.ccl.net> X-Original-From: Lubos Vrbka Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Fri, 11 Nov 2005 08:19:34 +0100 MIME-Version: 1.0 Sent to CCL by: Lubos Vrbka [shnek%%tiscali.cz] > Masakazu Matsumoto, Shinji Saito and Iwao Ohmine > Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing > Nature 416, 409-413 (28 March 2002) > > http://www.nature.com/nature/journal/v416/n6879/abs/416409a.html you may also check the work of szleifer or kusalik. you might find some useful references in our recent paper in Phys Rev Lett 95 (2005) 148501 (that is however not concerning exactly your topic). regards, -- Lubos _---_" From owner-chemistry@ccl.net Fri Nov 11 08:50:00 2005 From: "Evgeniy Gromov Evgeniy.Gromov|,|tc.pci.uni-heidelberg.de" To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29941-051111054035-9500-OuRVGla+UnjWOzBfzWcJqQ{}server.ccl.net> X-Original-From: Evgeniy Gromov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 11 Nov 2005 11:40:24 +0100 MIME-Version: 1.0 Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] Dear All, Does someone know a soft which allows one to simulate solvent by explicitly setting up (coordinates of) certain number of solvent molecules (e.q. water molecules) surrounding a solute system. For instance I'd like to add say 10 water molecules around some other system. Is it possible to do this "automatically" using some soft? Thanks a lot, Evgeniy -- _______________________________________ Dr. Evgeniy Gromov Theoretische Chemie Physikalisch-Chemisches Institut Im Neuenheimer Feld 229 D-69120 Heidelberg Germany Telefon: +49/(0)6221/545263 Fax: +49/(0)6221/545221 E-mail: evgeniy,tc.pci.uni-heidelberg.de _______________________________________ From owner-chemistry@ccl.net Fri Nov 11 10:54:00 2005 From: "Marcel Swart m.swart[#]few.vu.nl" To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29942-051111101901-25252-m3s89A4AO6zSXjQVF+3R5g~~server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-2-943732236 Date: Fri, 11 Nov 2005 16:17:51 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Marcel Swart [m.swart\a/few.vu.nl] --Apple-Mail-2-943732236 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Yes, included in ADF2005 is pdb2adf, which can do just that; I've also got a rangenconf program to do this, but it's a bit more involved. On Nov 11, 2005, at 3:06 PM, Evgeniy Gromov =20 Evgeniy.Gromov|,|tc.pci.uni-heidelberg.de wrote: > Sent to CCL by: Evgeniy Gromov =20 > [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] > Dear All, > > Does someone know a soft which allows one to simulate > solvent by explicitly setting up (coordinates of) certain > number of solvent molecules (e.q. water molecules) surrounding > a solute system. For instance I'd like to add say 10 water > molecules around some other system. Is it possible to > do this "automatically" using some soft? > > Thanks a lot, > > Evgeniy > -- =20 > _______________________________________ > Dr. Evgeniy Gromov > Theoretische Chemie > Physikalisch-Chemisches Institut > Im Neuenheimer Feld 229 > D-69120 Heidelberg > Germany > > Telefon: +49/(0)6221/545263 > Fax: +49/(0)6221/545221 > E-mail: evgeniy**tc.pci.uni-heidelberg.de > _______________________________________ > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please =20 > change> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=20= > +-+ > > > > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart::few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2-943732236 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Yes, included in ADF2005 is pdb2adf, which can do just that; I've also got a rangenconf program to do this, but it's a bit more involved. On Nov 11, 2005, at 3:06 PM, Evgeniy Gromov Evgeniy.Gromov|,|tc.pci.uni-heidelberg.de wrote: Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] Dear All, Does someone know a soft which allows one to simulate solvent by explicitly setting up (coordinates of) certain number of solvent molecules (e.q. water molecules) surrounding a solute system. For instance I'd like to add say 10 water molecules around some other system. Is it possible to do this "automatically" using some soft? Thanks a lot, Evgeniy --=20 _______________________________________ Dr. Evgeniy Gromov Theoretische Chemie Physikalisch-Chemisches Institut Im Neuenheimer Feld 229 D-69120 Heidelberg Germany Telefon: +49/(0)6221/545263 Fax: +49/(0)6221/545221 E-mail: evgeniy**tc.pci.uni-heidelberg.de _______________________________________ -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job advertisements: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt= Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart::few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2-943732236-- From owner-chemistry@ccl.net Fri Nov 11 11:29:00 2005 From: "Ulrike Salzner salzner{:}fen.bilkent.edu.tr" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-29943-051111105422-2843-xjzmDL7/S1jO0TH0++ZsCA__server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 11 Nov 2005 17:54:15 +0200 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner##fen.bilkent.edu.tr] I was thinking about this a lot. I am still puzzled. The first year textbooks give the orbital diagram usually without reference. I did HF calculations, and as it was stated in the other mails, the order of sigma and pi for N2 is different. Interestingly, with DFT sigma and pi orbitals change place. But DFT orbitals are quite controversial. Experiment measures the order of states not of orbitals, and correlated methods reproduce the correct ordering of states but they do not produce molecular orbitals either. So where do those orbital interaction diagrams come from in the first place? Have experimental states been mapped onto matching MOs? It would be great if someone could provide a reference regarding this mattter. Thanks, Ulrike On Thu, 2005-11-10 at 18:13 -0500, Eric Scerri scerri__chem.ucla.edu wrote: > Sent to CCL by: Eric Scerri [scerri!^!chem.ucla.edu] > > > > In teaching qualitative molecular orbital theory one encounters the > question of the crossing of the sigma 2p and pi 2p bonding orbitals > in homonuclear diatomics. > > > This is such that N2 has the pi orbitals of lower energy than sigma > whereas for O2 the energies are reversed. > > But what about heteronuclear diatomics where each of the atoms ? > > > The ordering given in general chemistry textbooks shows a wide > variation. See for example Oxtoby, Zumdahl or Olmsted and Williams, > all three of which contradict each other. > > Herzberg's, Spectra of Diatomic Molecules specifically states the > configurations of CO and NO. > > For CO the ordering is as in the case of N2 whereas for NO the > ordering is as in O2. > > However Herzberg's book is now a little out of date (1950). > > Do more recent calculations on these two molecules suggest anything > different? Would anyone be prepared to run these calculations and > tell me the results? > > How about experimental evidence such as PES on CO and NO? > > > > regards, > eric scerri> > > > -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Fri Nov 11 12:04:01 2005 From: "Rafael R. Pappalardo rafapa#us.es" To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29944-051111112040-15171-yt7IfumKgnEwkdgg6KdHbg- -server.ccl.net> X-Original-From: "Rafael R. Pappalardo" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 11 Nov 2005 16:20:25 +0100 MIME-Version: 1.0 Sent to CCL by: "Rafael R. Pappalardo" [rafapa]=[us.es] On Friday 11 November 2005 14:50, Evgeniy Gromov Evgeniy.Gromov|,| tc.pci.uni-heidelberg.de wrote: > Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] > Dear All, > > Does someone know a soft which allows one to simulate > solvent by explicitly setting up (coordinates of) certain > number of solvent molecules (e.q. water molecules) surrounding > a solute system. For instance I'd like to add say 10 water > molecules around some other system. Is it possible to > do this "automatically" using some soft? > > Thanks a lot, > > Evgeniy I have really good experiences with PACKMOL. http://www.ime.unicamp.br/~martinez/packmol/index.html Hope this help. Rafael -- Dr. Rafael R. Pappalardo Physical Chemistry Dept., Univ. de Sevilla (Spain) e-mail: rafapa[a]us.es From owner-chemistry@ccl.net Fri Nov 11 12:39:00 2005 From: "David Santos Carballal david.:.fq.uh.cu" To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29945-051111113504-27130-1oayn+DcuXTPNn4vRaCnRg|,|server.ccl.net> X-Original-From: David Santos Carballal Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 11 Nov 2005 11:27:51 -0500 (CST) MIME-Version: 1.0 Sent to CCL by: David Santos Carballal [david---fq.uh.cu] Yes, could add water molecules with the tool xyzedit and simulate your sistem with the tool dynamic of TINKER, a free software for windows and linux at http://dasher.wustl.edu/tinker/ David Santos Carballal On Fri, 11 Nov 2005, Evgeniy Gromov Evgeniy.Gromov|,|tc.pci.uni-heidelberg.de wrote: > Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] > Dear All, > > Does someone know a soft which allows one to simulate > solvent by explicitly setting up (coordinates of) certain > number of solvent molecules (e.q. water molecules) surrounding > a solute system. For instance I'd like to add say 10 water > molecules around some other system. Is it possible to > do this "automatically" using some soft? > > Thanks a lot, > > Evgeniy > -- > _______________________________________ > Dr. Evgeniy Gromov > Theoretische Chemie > Physikalisch-Chemisches Institut > Im Neuenheimer Feld 229 > D-69120 Heidelberg > Germany > > Telefon: +49/(0)6221/545263 > Fax: +49/(0)6221/545221 > E-mail: evgeniy**tc.pci.uni-heidelberg.de > _______________________________________> > > From owner-chemistry@ccl.net Fri Nov 11 13:14:00 2005 From: "Victor Belousov vihtor:-:don.tula.net" To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29946-051111121947-16287-a0dPj+j/Ps1+C8DiQ+lPuw-,-server.ccl.net> X-Original-From: Victor Belousov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 11 Nov 2005 19:17:49 +0300 MIME-Version: 1.0 Sent to CCL by: Victor Belousov [vihtor_+_don.tula.net] Dear Evgeniy, You may use HyperChem. Build your system (or import it) and select Setup/Periodic Box... in main menu. Regards, Victor vihtor!!a!!don.tula.net You wrote: > Sent to CCL by: Evgeniy Gromov > [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] > Dear All, > Does someone know a soft which allows one to simulate > solvent by explicitly setting up (coordinates of) certain > number of solvent molecules (e.q. water molecules) surrounding > a solute system. For instance I'd like to add say 10 water > molecules around some other system. Is it possible to > do this "automatically" using some soft? > Thanks a lot, > Evgeniy From owner-chemistry@ccl.net Fri Nov 11 14:10:00 2005 From: "janl\a/speakeasy.net" To: CCL Subject: CCL: CCL Manager out of town till Tue Message-Id: <-29947-051111130817-19879-hFgECIwWDYZP0MXN2RoY9w*server.ccl.net> X-Original-From: janl~!~speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 11 Nov 2005 18:08:13 +0000 MIME-Version: 1.0 Sent to CCL by: janl^-^speakeasy.net Dear CCL, I will be out of town until Tue. While I plan to be on the Internet, things may be slower (e.g., with authorizing you to post a message or processing your requests). You have been forewarned... Jan CCL Unmoderator jkl-.-ccl.net From owner-chemistry@ccl.net Fri Nov 11 16:48:00 2005 From: "Wayne Steinmetz WES04747*pomona.edu" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-29948-051111140327-12234-vJiL/gGK9oFU/oCQHQ6T6Q++server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 11 Nov 2005 11:02:20 -0800 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747:pomona.edu] You have asked a host of questions around one theme, qualitative MO theory. An excellent summary of experimental data can be found in P. Krupenie, The Band spectrum of Carbon Monoxide. This was published by the US Government Printing Office as NSRDS-NBS 5. The government periodicals desk at the UCLA library may help you track down this document. Krupenie also published a critical review of spectroscopic data for N2 and O2 in the Journal of Physical Chemical Reference Data. What is your audience for the qualitative use of MO theory? I have been convinced that MO theory provides a good reason for bringing back the index (Index censorum librorum). The index was not established as an absolute prohibition to reading materials but as a warning. Only those who are mature enough to understand the materials should be exposed to it. When I teach General Chemistry, I ask the students to burn the section on the MO treatment of diatomic molecules. It is usually a swindle. I do use MO theory in the examination of the properties of transition-metal complexes. In this case, crystal field theory is a swindle and VB doesn't explain much. I do use MO theory to discuss H2 as the treatment provides insights into the nature of bonding. Period. I found that the extension to homonuclear and heteronuclear diatomic molecules to be counterproductive. One has to be well versed in quantum mechanics to use MO theory correctly. Alexander Pope was right in stating "A little knowledge is a dangerous thing; drink deeplyu or not at all of the Pyrean (sic) spring". In the right context, qualitative MO theory can be used as a framework for interpreting experimental data. The simplistic approach in most textbooks cannot be used in most cases to predict the results. Given the low cost of programs such as Spartan that are based on good physics, why should we bother with the old, flawed approaches at all? In this case, the availability of good software should change the way we teach! Molecular orbitals are a means to an end. They are not observables. The electron density and the total energy are measurable. This is one of the reasons why DFT is so successful. I have found that the spacing between the orbital energies and in some cases the order depend critically on the basis set. Hence, if very sophisticated methods yield different results for these intermediate pieces, why should we encumber students with them? I would be pleased to continue this discussion if you wish. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz .. pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] Sent: Thursday, November 10, 2005 3:12 PM To: Wayne Steinmetz Subject: CCL: question on molecular orbitals in CO and NO Sent to CCL by: Eric Scerri [scerri!^!chem.ucla.edu] In teaching qualitative molecular orbital theory one encounters the question of the crossing of the sigma 2p and pi 2p bonding orbitals in homonuclear diatomics. This is such that N2 has the pi orbitals of lower energy than sigma whereas for O2 the energies are reversed. But what about heteronuclear diatomics where each of the atoms ? The ordering given in general chemistry textbooks shows a wide variation. See for example Oxtoby, Zumdahl or Olmsted and Williams, all three of which contradict each other. Herzberg's, Spectra of Diatomic Molecules specifically states the configurations of CO and NO. For CO the ordering is as in the case of N2 whereas for NO the ordering is as in O2. However Herzberg's book is now a little out of date (1950). Do more recent calculations on these two molecules suggest anything different? Would anyone be prepared to run these calculations and tell me the results? How about experimental evidence such as PES on CO and NO? regards, eric scerrihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Fri Nov 11 17:22:00 2005 From: "Wayne Steinmetz WES04747],[pomona.edu" To: CCL Subject: CCL: Soft for adding (solvent) molecules around some other system Message-Id: <-29949-051111132347-31603-tf95/L6URAONwJYYxRFMTw(~)server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 11 Nov 2005 10:19:13 -0800 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747++pomona.edu] SYBYL which is marketed by Tripos has a number of tools for solvating molecules. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz%pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] Sent: Friday, November 11, 2005 9:21 AM To: Wayne Steinmetz Subject: CCL: Soft for adding (solvent) molecules around some other system Sent to CCL by: "Rafael R. Pappalardo" [rafapa]=[us.es] On Friday 11 November 2005 14:50, Evgeniy Gromov Evgeniy.Gromov|,| tc.pci.uni-heidelberg.de wrote: > Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov()tc.pci.uni-heidelberg.de] > Dear All, > > Does someone know a soft which allows one to simulate > solvent by explicitly setting up (coordinates of) certain > number of solvent molecules (e.q. water molecules) surrounding > a solute system. For instance I'd like to add say 10 water > molecules around some other system. Is it possible to > do this "automatically" using some soft? > > Thanks a lot, > > Evgeniy I have really good experiences with PACKMOL. http://www.ime.unicamp.br/~martinez/packmol/index.html Hope this help. Rafael -- Dr. Rafael R. Pappalardo Physical Chemistry Dept., Univ. de Sevilla (Spain) e-mail: rafapa/./us.eshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software.