From chemistry-request@server.ccl.net Mon Apr 17 12:00:03 2000 Received: from vectraC.total.com (vectrac.total.com [146.249.254.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18575 for ; Mon, 17 Apr 2000 12:00:02 -0400 Received: by vectraC.total.com; id RAA03467; Mon, 17 Apr 2000 17:57:47 +0200 (MET DST) Message-Id: <200004171557.RAA03467@vectraC.total.com> X400-Received: by mta mtaMHUB in /c=FR/admd=ATLAS/prmd=TOTAL/; converted ( (1)(0)(10021)(7)(1)(0)(100), (1)(0)(10021)(7)(1)(0)(6), (1)(0)(10021)(7)(1)(0)(1)); Relayed; 17 Apr 2000 17:48:28 +0200 X400-Received: by mta TOTAL-HUB in /c=FR/admd=ATLAS/prmd=TOTAL/; Relayed; 17 Apr 2000 17:57:10 +0200 X400-Received: by mta RAF-NORMANDIE in /c=FR/admd=ATLAS/prmd=TOTAL/; Relayed; 17 Apr 2000 17:57:09 +0200 X400-Received: by /c=FR/admd=ATLAS/prmd=TOTAL/; converted ( (1)(0)(10021)(7)(1)(0)(100), (1)(0)(10021)(7)(1)(0)(6), (1)(0)(10021)(7)(1)(0)(1)); Relayed; 17 Apr 2000 17:57:09 +0200 X400-MTS-Identifier: [/c=FR/admd=ATLAS/prmd=TOTAL/; ISOCOR-38f7d313-RAF-NO|TRq] Content-Identifier: Molecule adsorpt Content-Return: Prohibited X400-Content-Type: P2-1988 ( 22 ) Original-Encoded-Information-Types: Undefined, IA5-Text, Teletex X-Priority: 1 Priority: urgent Disclose-Recipients: Prohibited X400-Originator: Francois.HUTSCHKA@total.com X400-Recipients: non-disclosure; Importance: high Date: 17 Apr 2000 17:57:09 +0200 From: HUTSCHKA Francois To: chemistry@server.ccl.net cc: HUTSCHKA Francois Subject: Molecule adsorption on silica MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id MAA18576 Hello, I am looking for theoretical studies (MM or QM) of molecule adsorption on a silica surface. Any references or suggestion would be appreciated. Regards. ******************************************************** Dr. François HUTSCHKA TOTALFINA - CERT European Research and Technical Center Department Processes and Refining Molecular Modeling BP 27 76700 HARFLEUR Email: francois.hutschka@total.com Voice: (33).02.35.55.13.53 Fax: (33).02.35.55.12.99 Frombroad ignore "0" in "02" ******************************************************* From chemistry-request@server.ccl.net Mon Apr 17 18:36:12 2000 Received: from ns-mx.uiowa.edu (ns-mx.uiowa.edu [128.255.56.78]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA20818 for ; Mon, 17 Apr 2000 18:36:11 -0400 Received: from [128.255.72.43] (his.chem.uiowa.edu [128.255.72.43]) by ns-mx.uiowa.edu (8.9.3/8.9.1/ns-mx-1.7) with ESMTP id RAA38468 for ; Mon, 17 Apr 2000 17:36:10 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Date: Mon, 17 Apr 2000 17:36:08 -0500 To: CHEMISTRY@ccl.net From: "Jan H. Jensen" Subject: 33rd Midwest Theoretical Chemistry Conference +++++++++++++++++++++++++++++++++++++++++++++ FINAL ANNOUNCEMENT 33rd Midwest Theoretical Chemistry Conference University of Iowa Iowa City, IA May 25-27, 2000 +++++++++++++++++++++++++++++++++++++++++++++ The 33rd MWTCC will be held at the Iowa Memorial Union at the University of Iowa, Iowa City, IA from May 25 to May 27, 2000. The conference covers all areas of theoretical chemistry. It will feature two plenary lectures by Don Truhlar (U. Minnesota) and Mark Gordon (Iowa State U.) as well as a varied mix of short presentations and posters from undergraduate and graduate students, postdocs, faculty, corporate and government scientists. Traditionally the conference has been a forum for graduate students and postdocs to present their research and their participation is especially encouraged. For a preliminary program see http://www.uiowa.edu/~mwtcc/sched.html. The registration fee is $30.00 for abstracts submitted before May 1. After May 1 the registration fee increases to $50.00. To register, download the registration form at http://www.uiowa.edu/~mwtcc/Regform.pdf, fill it out, and send it to the address indicated on the form, together with your abstract. More information on the conference, including the registration form, can be obtained at the WWW site http://www.uiowa.edu/~mwtcc. I look forward to seeing you this May. Jan H. Jensen, Organizer =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Assistant Professor Department of Chemistry jan-jensen@uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~chemdept/faculty/jensen/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Tue Apr 18 09:17:15 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA24854 for ; Tue, 18 Apr 2000 09:17:11 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Tue, 18 Apr 2000 15:17:24 +0200 Message-ID: <002a01bfa938$a90c94e0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "chinapong kritayakornupong" CC: References: Subject: Re: CCL:van der walls radius Date: Tue, 18 Apr 2000 15:18:57 +0200 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0027_01BFA949.6A5AB720" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0027_01BFA949.6A5AB720 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 8bit Chinapong wrote: > Dear all, > What's program that can calculate van der walls radius of > functional groups such as CH3, i-Pr, t-Bu group? How can I find van der > walls radius of functional from expermental data? > Sincerely Your, > Chinapong As with the exception of the most simple groups, the exact shape depends on the conformation of the moiety in question, I think that no simple answer exists on the vdW radius of a group, However, something similar called to Verloops's Sterimol parameters was developed in the seventies. Maybe it could be interesting to you: Verloop's steric parameters for QSAR (L and B1 to B5), originally were calculated by the program Sterimol. These parameters characterize the shape of a molecule or substituent, the geometrical features which might significantly influence the biological activity. L is the length of the molecule/substituent, B1-B4 is the measure of the width in four rectangular directions, B5 is the maximum width perdendicular to L (taking into account the vdW radii of the atoms)(see the attached sterimol.gif image). The farthest extension in the X direction of the group is calculated as L, the atoms are represented as spheres with their van der Waals radii. Next the group is rotated around the X axis (atoms #1-#2). During the rotation the minimum and maximum distances to the X axis in the XY and YZ planes are calculated. When the absolute minimum is found, it will be B1, and the corresponding other three distance values, in ascending order, B2 - B3; the absolute maximum is taken as B5. For a detailed description of these parameters consult : Verloop, A., Hoogenstraaten, W., Tipker, J.: Development and Application of New Steric Substituent Parameters in Drug Design in: Drug Design (E.J. Äriens, ed), vol VII., chapter 4, Academic Press, N.Y.,1976. The program Mol2Mol can calculate these sterimol parameters Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. 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Tue, 18 Apr 2000 11:42:32 -0400 Received: from wchuwr.chem.uni.wroc.pl ([156.17.103.1]) by gerwazy.chem.uni.wroc.pl (8.8.8+Sun/8.8.8) with ESMTP id RAA00871 for ; Tue, 18 Apr 2000 17:48:17 +0200 (MET DST) Received: from WCHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.44); 18 Apr 00 17:43:48 MET Received: from SpoolDir by WCHUWR (Mercury 1.44); 18 Apr 00 17:43:28 MET From: "Adrian Radomir Jaszewski" Organization: University of Wroclaw (Chemistry) To: chemistry@server.ccl.net Date: Tue, 18 Apr 2000 17:43:25 MET Subject: SUMMARY:SOMO of the radical Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Message-ID: Dear CCL'ers, Last week I asked this question on the CCL : >From N linearly independent basis functions of the radical >(S=1/2) one can construct N alpha and N beta orbitals: >N alfa = (n-1) CORE + 1 SOMO occupied + (N-n) VIRTUAL >N beta = (n-1) CORE + 1 SOMO unoccupied + (N-n) VIRTUAL >where n denotes the number of electrons. > >Unrestricted DFT wavefunctions of the radicals are usually >constructed using identical (or almost identical) spatial >orbitals for different spins (alpha, beta) in the case of >CORE and VIRTUAL MO. Lowest energy (occupied) alpha-spin >SOMO and highest energy (unoccupied) beta-spin SOMO can be >also very similar to each other but sometimes they are >strongly asymmetrical. A knowledge of the SOMO contour can >be helpful in the analysis of the spin density distribution >as well as the values of the calculated hyperfine coupling >constants for the radicals. > >My question is: >When SOMO occupied (alpha) and SOMO unoccupied (beta) are >dissimilar which of them (or what combination of these SOMOs) >can be used to aid spin density analysis? In some cases I >have observed that the spin density contours were similar >to the highest energy beta-spin SOMO (unoccupied!!) contour >rather than to the occupied alpha-spin SOMO; and what is >the energy (in Hartree) of that SOMO when: >E(lowest energy VMO)= -0.06916(alpha) -0.06008(beta) >E(highest energy SOMO)= -0.12635(beta) >E(lowest energy SOMO)= -0.26301(alpha) >E(highest energy DOMO)= -0.24908(alpha) -0.24319(beta)? > I summarize below the replies I obtained very quickly to my question. They have been very helpful. I thank very much all those who supplied information. With my best regards, Adrian +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ This is pretty normal behavior and has a fairly simple explanation. Imagine a molecule with 3 electrons (2 alpha and 1 beta) and imagine orbital energy increases #1 < #2 < #3 ... This makes the occupied orbitals MO #1 alpha, MO #2 alpha and MO #1 beta, and the unoccupied orbitals MO #2 beta, MO #3 (alpha or beta) and so on. The orbitals that you are called "SOMO occupied (alpha)" and "SOMO unoccupied (beta)" are MO #2 alpha and MO #2 beta in my nomenclature. Now consider two cases: Case #1: MO #1 alpha looks like MO #1 beta. In this case, the spin density distribution looks like MO #2 alpha (this will be true even if MO #2 alpha and MO #2 beta do not look like each other). Case #2: MO #1 alpha looks like MO #2 beta, and MO #2 alpha looks like MO #1 beta. In this case, the spin density distribution looks like MO #1 alpha, and because of the similarity between MO #1 alpha and MO #2 beta, it also looks like MO #2 beta. Bigger molecules can behave the same way. The point here is that UNrestricted wavefunctions allow different energy orderings for the alpha and beta orbitals (even when each alpha orbital looks like a beta orbital). This can lead to situations where the spin density distribution resembles an alpha orbital (or a group of orbitals) other than the alpha HOMO (what you call the alpha SOMO). Hope this helps. Good luck, -Alan -------------- Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan Alan.Shusterman@directory.reed.edu +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ It may happen that the nth alpha orbital resembles the n-1th beta orbital and that the nth beta orbital resembles the n-1th alpha orbital. That could be the explanation for the similarity you noticed between the lowest beta unoccupied orbital and the total spin density. If you are using Gaussian, you might try calculating the unrestricted wavefunction as usual, and then read in that wavefunction as the guess for a restricted open-shell calculation, that is, use Guess(Read,Only). You can do the population analysis, but you won't find orbital energies. If you really want those orbital energies, a restricted open-shell calculation can be done. Curt Hoganson University of Delaware hoganson@dplus.net +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Your orbital energies indicate that there might be a heavy mixing of the alpha-spin "DOMO" and "SOMO". Is there any reason not to perform a spin-restricted DFT calculation? This makes your analysis much easier since the spin-density comes from the SOMO alone. -- ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I'm happy to share my feelings about this subject with you. In my opinion the only way to properly calculate hyperfine couplings and spin densities is to evaluate the spin up and spin down densities, subtract them from each other and calculate the hyperfine coupling as the expectation value of the appropriate operator using this spin density. Using the unoccupied beta-MO is rather unphysical and maybe quite basis set dependent. Using the alpha MO is also unphysical because any (unitary) mixing of alpha MOs produces the same total wavefunction. Thus, if another MO is close in energy to the spin up "SOMO" it will mix with it and thereby obscure the picture. However, the physics contained in the total electron and spin density matrices are not affected by this mixing. Having said all this, many people have observed in open shell transition metal complexes that the unoccupied spin down orbitals give a clearer picture of the bonding. This is because the corresponding spin-up orbitals maybe deeply buried under or within ligand based orbitals due to strong exchange stabilization. Noodleman refers to this as 'inverted bonding'. In a pictorial sense it might be o.k. to look at the unoccupied MOs but for calculation of observables I would personally certainly not rely on anything else but the densities themselves. Best regards, Frank Frank.Neese@uni-konstanz.de +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ You appear to assume alpha means lower energy. I think most progems just arbritarilly assign alpha and beta spins. Hence in your case what the program calls the lowest unoccupied beta is actually the SOMO i.e where the unpaired electron (density) is. Patrick J O'Malley patrick.o'malley@umist.ac.uk ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue Apr 18 18:30:43 2000 Received: from mallard.duc.auburn.edu (mallard.duc.auburn.edu [131.204.2.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA27598 for ; Tue, 18 Apr 2000 18:30:42 -0400 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id RAA16288 for ; Tue, 18 Apr 2000 17:30:41 -0500 (CDT) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Tue, 18 Apr 2000 17:30:41 -0500 (CDT) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: About G3 energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's I did G3 calculation for H and found G3 energy summary at the end of the ouptput. Temperature= 298.150000 Pressure= 1.000000 E(ZPE)= 0.000000 E(Thermal)= 0.001416 E(QCISD(T))= -0.498233 E(Empiric)= -0.001185 DE(Plus)= 0.000000 DE(2DF)= 0.000000 E(Delta-G3)= -0.001585 E(G3-Empiric)= -0.001185 G3(0 K)= -0.501003 G3 Energy= -0.499587 G3 Enthalpy= -0.498642 G3 Free Energy= -0.511657 However, I am confused which G3 energy can be used to estimate the heat of formation for the isodemic reaction between G3 Enthalpy and G3 energy. I would appreciate it if anybody give me some advice on this matter. Thank you. yours Ohyun Kwon Department of Chemistry Auburn University Auburn, AL 36849 From chemistry-request@server.ccl.net Tue Apr 18 13:31:30 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA26476 for ; Tue, 18 Apr 2000 13:31:05 -0400 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA15049 for ; Tue, 18 Apr 2000 13:30:49 -0400 (EDT) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id NAA08296; Tue, 18 Apr 2000 13:24:47 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id NAA14566; Tue, 18 Apr 2000 13:06:33 -0400 (EDT) Date: Tue, 18 Apr 2000 13:06:33 -0400 (EDT) From: Steve Heller To: lists , amber@cgl.ucsf.edu, APPLSPEC@listserv.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.uwf.edu, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, molecular-dynamics-news@mailbase.ac.uk, pdb-l@rcsb.org, PHILCHEM@VM.SC.EDU, PLASMACHEM-L@LISTSERV.SYR.EDU, POLYMER@TECHUNIX.TECHNION.AC.IL, SAFETY@LIST.UVM.EDU, ToxList@esc.syrres.com, ucair-lib@twu.edu Subject: Chemistry Search Engine web site Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is a new and free chemistry web site, with over 15,000 different url's of chemistry web sites - www.chemindustry.com This web site is trying to become the Yahoo of chemistry. Steve