From chemistry-request@www.ccl.net Tue Feb 23 00:08:05 1999 Received: from mail02.rapidsite.net (mail02.rapidsite.net [207.158.192.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id AAA08597 Tue, 23 Feb 1999 00:08:05 -0500 (EST) Received: from www.mdpi.org (207.158.232.88) by mail02.rapidsite.net (RS ver 1.0.2) with SMTP id 9670 for ; Tue, 23 Feb 1999 00:08:03 -0500 (EST) Message-ID: <36D23801.8E6C53CE@mdpi.org> Date: Tue, 23 Feb 1999 06:09:21 +0100 From: "Dr. Shu-Kun Lin" Reply-To: lin@mdpi.org Organization: MDPI (http://www.mdpi.org) X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Reptints.Net help wanted Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Loop-Detect: 1 It will be a very useful service of indexing with the inclusion of e-mails, websites, as well as tel. and fax numbers, etc. to the author's self made abstracts at http://reprints.net server. Anyone interested in this project please contact me. I need someone to help me or to work on it or agree to serve as a mirror site. Two years ago, I suggested that CAS added authors' e-mail addresses, if available in the original publications, to the chemical abstracts. To include e-mails will be of great help for readers to request for reprints and to for other convenient contacts with the authors. Looking forward to your replies. -- Dr. Shu-Kun Lin MDPI, Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin@mdpi.org URL: http://mdpi.org/lin/ From chemistry-request@www.ccl.net Tue Feb 23 00:25:11 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA09097 Tue, 23 Feb 1999 00:25:10 -0500 (EST) Received: from voxopm-e.csc.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id HAA25648 for ; Tue, 23 Feb 1999 07:25:11 +0200 (EET) Date: Tue, 23 Feb 1999 07:25:10 +0200 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@www.ccl.net Subject: NBO In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Approximately a week ago I send an inquire about NBO (Natural Bond Orbital) analysis within Gaussian98 having warning messages. WARNING: 1 low occupancy (<1.9990e) core orbital found on P 3 1 low occupancy (<1.9990e) core orbital found on C 5 WARNING: Population inversion found on atom P 3 Population inversion found on atom O 4 Population inversion found on atom C 5 Population inversion found on atom C 6 Population inversion found on atom C 7 Population inversion found on atom C 8 Population inversion found on atom C 9 Population inversion found on atom C10 Population inversion found on atom O11 Population inversion found on atom S13 Thank you all for you help. I was asked to summarize this so here all all the answers that I got from you. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Hi! I cannot say much about the warnings you get from G98 in the output. But if it's not normal, it might be caused by the bug in NBO link (l607) which was confirmed to us by Doug Fox three months ago. Unusually, the bug appeared only under Linux. If your G98 works under Linux, and if you purcha- sed G98 more than 3 months ago, you should consider this possibility too. If you have an access to G98 (or G94) on different platforms and if you get the same output everywhere, it's probably not related to the bug. Otherwise, let me know and I'll send you the copy of my correspondence with Doug Fox which also includes the fix for the bug. Sincerely, Darko Babic &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Those WARNINGs are quiet usual. When NBO program prints Natural Atomic Orbitals (1s, 2s, 3s etc. ),it does on the basis of the energy order or on the basis of occupancy. The WARNING message "Population inversion" comes when, the orbital occupancies and energy ordering don't match or don't coincide. suppose, for example when one of 3d orbital lies below in energy, but it's population (occupancy) is lower than 4s or any of 4p orbitals, then population inversion occurs and should print warning massage. For core (NAO treated as unhybridized single center core NBO) orbitals, which in formal Lewis sense should be filled by 2 electrons. Sometimes due to unphysical mixing of core and valence lone pairs, the core occupancy goes below the threshold <1.9990e) and should print worning massage However, your NBO analysis should be ok. Cheers. Jamal &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& I'm quite new to this area but as i heard, an occupancy above 1.99 should refer to a core orbital. Your ones are probably a bit lower than the usual ones (i have no experience in it) but i think they might be correct. However, if you calculate those occupancies to determine which orbitals to use in a multi-reference calculation, they might not be reliable: that is what the warning is for (in the non-dynamic correlation, those determinants/configurations will dominate that have orbitals with low occupancies, thus the outer ones). I have no idea about the warning "population inversion"... Since i'm a beginner to this topic, i'd like to ask you to summarize to the list. Best regards, Tamas Karpati &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Such warnings can usually be ignored. > WARNING: 1 low occupancy (<1.9990e) core orbital found on P 3 > 1 low occupancy (<1.9990e) core orbital found on C 5 In the first case NBO has calculated a couple core orbitals with occupancies slightly lower than threshold. The occupancies reflect delocalizing interactions of the two core orbitals with nearby acceptor functions. But the strengths of these interactions are likely so weak that they can be neglected. Examine the perturbative analysis for interactions involving the two orbitals in question. You'll probably find that the interactions are weaker than a kcal/mol or two and can thus be ignored when developing a qualitative description of the calculated wavefunction. > WARNING: Population inversion found on atom P 3 > Population inversion found on atom O 4 > Population inversion found on atom C 5 > Population inversion found on atom C 6 > Population inversion found on atom C 7 > Population inversion found on atom C 8 > Population inversion found on atom C 9 > Population inversion found on atom C10 > Population inversion found on atom O11 > Population inversion found on atom S13 In the second case NBO has encountered a high energy NAO that has an occupancy somewhat greater than a lower energy NAO. This is a fairly common occurence for extended basis sets for which there are a considerable number of Rydberg orbitals identified by NAO. Examine the output for P3, for example. You might find a 6s NAO with slightly higher occupancy than the 5s, or something similar. However, the occupancies of these orbitals are probably small enough that they can neglected anyway. Eric Glendening &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& the warning about 'Low Occupancy Core Orbitals' is nothing more than a warning with cautious thresholds: just have a look at the occupancies to confirm that they are close to 2 electrons. I also found the 'Population Inversion' warning in some of my outputs and just ignore it if the inversion is between the occupancies of lowly occupied orbitals (that is lower than maybe .02 electrons). The warning is more common with extended basis sets because then there are more unoccupied basis functions and consequently more NAOs with near zero occupancies. The warning about 'Population Inversion' needs a little background: The Natural Population Analysis (NPA) is conducted in the basis of Natural Atomic Orbitals (NAOs). They are created by orthogonalizing the (atom centered) basis set used in GAUSSIAN under the constraint of changing highly populated basis functions as little as possible. On the other hand, lowly occupied basis functions may change much more. During this process the orbitals of the 'Natural Minimal Basis' (consisting of the orbital types that are occupied in the ground state of the atoms, e.g. 1s,2s and _all_ 2p orbitals in the case of boron) and the orbitals of the 'Natural Rhydberg Basis' (the rest) are treated differently. (This has led to some discussion on NPA and transition metals, because their np orbitals are treated as Rhydberg Orbitals by the NPA although they are sometimes populated, e.g. in complexes of late transition metals.) I think that the test for 'Population Inversion' checks if the NAO occupancies are decreasing with increasing NAO energy. Stefan &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Yours, Maija Lahtela-Kakkkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi *************************************** From chemistry-request@www.ccl.net Tue Feb 23 08:06:40 1999 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA21768 Tue, 23 Feb 1999 08:05:08 -0500 (EST) Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.8.5/8.8.5) with SMTP id OAA31501 for ; Tue, 23 Feb 1999 14:05:43 +0100 (MET) Date: Tue, 23 Feb 1999 14:04:29 +0100 (MET) From: Pablo Vitoria Garcia To: ccl Subject: Information about TopMoD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, While surfing the Net, I read about a program to analyze the topology of the Electron Localization Function (ELF), something like "TopMoD". Does anybody know if the program is available and how to get it? Thank you very much for your help Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 -------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Feb 23 11:03:31 1999 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA04568 Tue, 23 Feb 1999 11:03:28 -0500 (EST) Received: from localhost by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id RAA04435; Tue, 23 Feb 1999 17:03:27 +0100 (MET) Date: Tue, 23 Feb 1999 17:03:26 +0100 (MET) From: Anik Peeters X-Sender: anik@inch.uia.ac.be To: chemistry@www.ccl.net Subject: SUMMARY: colour of molecules in the solid state (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ My original question: I am studying molecular crystals using the supermolecule approach: a cluster of 10-15 molecules is described by the wave function and this cluster is surrounded by point charges simulating the other neighbours. The level of theory we are using is Hartree-Fock. The molecule I am studying right now has been observed in three different polymorphic forms. One has a white colour, another one is yellow and a third one is light yellow. I have been trying to relate the yellow and light yellow colour to the band gap between the HOMO and LUMO. However, the energy differences I obtained are too large. I was wondering whether there exists a cheap method (because of the size of the system) to get a better approximation of the band gap. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Summary: Most people suggest to use semi-empirical methods since they are better than Hartree-Fock in estimating the band gap. Other suggestions include the use of a larger basis set (impossible due to the size of my system), the use of pseudopotentials, the use of different boundary conditions, the use of DFT and the inclusion of excited states. Many thanks to Benoit Champagne, Sergio Emanuel Galembeck, Christos Garoufalis, Richard Wheatley, Stefan Konietzny, Ernest Chamot, Jerry Perlstein, Artem Masunov, Andres Aguado and Viorel Chihaia Anik. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ The answers: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Benoit Champagne The best method for such big clusters should be of semi-empirical type like the famous ZINDO. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Sergio Emanuel Galembeck In my opinion the best method for study electronic spectra of large systems is INDO 1/S. This method reproduces very well experimental spectra for organic compounds and it is to use point charges. A nice implementation of this method is ArgusLab 1.0. You can found this program in: http://www.seanet.com/~mthompson/ArgusLab/index.htm +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Christos Garoufalis It almost always happens that HF is overestimating the HOMO-LUMO gap. in my opinion, it is preferable to use some other method for this type of calculation DFT will certainly give smaller gap values, but it depends stronly on the used functional. B3-LYP is a good choise. Even semiempirical methods such as AM1 or MNDO will give you better results. It should also be kept in mind the if you want to the calculate the absorption spectrum the Hartree-Fock level (i.e. the energy differences of the occupied and unoccupied orbitals) is sufficient. In this case C.I. singlets calculation is commonly used. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Richard Wheatley Hello! If you look at my paper in Chem Phys Letts 294, 487 (1998) you will find a way to reduce your calculation to a monomer calculation, including a pseudopotential representing the surroundings. This is approximate but seems to work quite well, and allows better than Hartree-Fock accuracy. Incidentally, you didn't say whether your method is UHF, CIS or CHF. I assume it's UHF; this will certainly overestimate the band gap! +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Stefan Konietzny for my understanding the energy of a LUMO from a HF calculation is not reliable, because the virtuals are not optimized. I think you have to calculate the excited state to get a reliable result. If you are using GAUSSIAN then have a look at the CIS keyword. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Ernest Chamot Short of modeling the system with periodic boundary conditions, your approach seems reasonable: You didn't say whether you are using ab initio or semiempirical HF methods. If you are doing ab initio calculations and aren't using diffuse functions in your basis set, then I strongly suggest that you include them. In my experience you just can't model intermolecular interactions without them, and they must be important here in order for there to be a difference between polymorphs. (But I assume you've already thought of this.) Of course, this would be a pretty big calculation! Have you considered using periodic boundary conditions, and/or DFT? If you are using semiempirical HF methods, I would recommend using Zerner's INDO/S Hamiltonian, as it has been specifically parameterized for predicting electronic spectra. Although you probably want to optimize the geometry with a different method, and just use INDO/S for the spectrum calculation. The drawback with this is that the semiempirical methods are based on minimal basis sets (ie. no diffuse functions), so they have a problem with intermolecular interactions. In either case, however, the crucial thing is to include some level of CI in your calculation. If you don't, the unoccupied orbitals don't get calculated very well, and your band gap will be off. I would expect this to be the major reason that: >I have been trying to relate the yellow and >light yellow colour to the band gap between the HOMO and LUMO. However, >the energy differences I obtained are too large. (All this assumes your system really is "molecules." If it is at all "metallic" or ionic, there will be a BIG surface effect, even with larger "clusters".) +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Jerry Perlstein Anik- I doubt whether the "band gap" has anything to do with the colors you observe. More likely they are either charge transfer transitions or possibly Davydov splittings of the exciton states. Before you do anything fancy why don't you visually looked at the structures to see if there are any molecular interactions which would suggest charge transfer transitions? +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Artem Masunov On Thu, 11 Feb 1999, Jerry Perlstein wrote: > Before you do anything fancy why don't you visually looked at the > structures to see if there are any molecular interactions which would > suggest charge transfer transitions? I wonder what kind of interactions in homomolecular crystals (except conventional pi-pi stacking) could be considered as charge transfer? Are there CT spectra for sigma-interactions? I would appreciate if Jerry Perlstein (and all CCLers) give me some references for the examples and interpretations. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Andres Aguado I have seen your message in the CCL. It is a well known result that HOMO-LUMO differences in a Hartree-Fock approximation lead to too large band gaps. The main problem is not Hartree-Fock theory, but the HOMO-LUMO approach. It gives you the band gap energy without including electronic relaxation of the excited state. You could obtain much better band gaps even within Hartree-Fock by performing a separate self-consistent calculation for the excited state, annd taking a difference between both total energies of the system (excited and ground state). This does not involve any new geometry optimization, because the transition is vertical in the Franck-Condon sense. Anyway, inclusion of correlation is crucial in order to obtain quantitavely accurate results. It changes the magnitude of the gap by approximately 1--3 eV. We have recently studied this problem for the case of typical ionic insulating crystals. This is the reference: Title: Calculation of the band gap energy of ionic crystals Authors: A. Aguado et al. Ref: Rev. Mex. Fis. 44, 550 (1998). It is not a well-known journal and I do not know if you can have it. I could send to you a copy if you are interested. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Viorel Chihaia Firstly I bag you pardon for my bad English. If you try to simulate the molecular crystal I don't use point charges for the rest of the crystal. The correct way to simulate these systems it is to use a periodic condition for the boundary or periodical (like solid state calculation). The cluster method can be used in case of some defects in the molecular crystal. For this you grow the cluster size until you obtaine for the interest properties, the convergence. If you want to simulate some dynamical phenomena you must include your cluster in a clasical field for the rest of crystal. On the other hand the Hartree - Fock calculation fail in the reproduction of the limites for valence band and conduction band. Since you are interested for this values you must use the periodic calculation. I have the CRYSTAL 95 program and if you want to have a idea for the diferences I can help you. From chemistry-request@www.ccl.net Sat Feb 20 12:32:03 1999 Received: from sg1503.chemie.uni-marburg.de (root@sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA28526 Sat, 20 Feb 1999 12:32:02 -0500 (EST) Received: from pc15105 (pc15105.Chemie.Uni-Marburg.DE [137.248.151.180]) by sg1503.chemie.uni-marburg.de (8.9.3/8.9.2/schn) with SMTP id SAA22508 for ; Sat, 20 Feb 1999 18:31:27 +0100 (MET) From: "Stefan Fau" To: "CCL" Subject: Summary: choosing "zero freqs" to be projected out Date: Sat, 20 Feb 1999 18:34:06 +0100 Message-ID: <000001be5cf7$3729b3f0$b497f889@pc15105.chemie.uni-marburg.de> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Importance: Normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id MAA28527 Dear CCLers, I asked how the modes belonging to translational and rotational movements are separated from the vibrational modes in a frequency calculation. Thanks to Frank Jensen and Doug Fox for their answers. The translational and rotational modes are selected on the basis of mechanical considerations, not by the values of the raw frequencies. The separation can be done by a projection technique (e.g. Gaussian, GAMESS-US) or a level-shifting technique (e.g. MOPAC). The original question and answers are given below. Stefan ______________________________________________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de Question: > Dear CCLers, > > Gaussian (like many other programs) projects out the 6 "zero freqs" > that belong to translation and rotation of a non-linear molecule before > diagonalizing the remaining matrix. These "zero freqs" can be of similar > magnitude as the lowest vibrational frequencies if the molecule is very > floppy (I once had a molecule with 7 freqs of |ny|<15cm^-1). > > Does anybody know how the "zero freqs" are selected? Just by the absolute > value of the raw frequency or is there some check for the type of movement > (e.g. all atomic vectors of the mode parallel/orthogonal to the molecular > translation/rotation vector) to avoid projecting out a vibrational > frequency if vibrational and "zero" freqs are intermingled? > > Stefan Answer 1: > Stefan, > as far as I know, there are two common procedures for > removing the 3T+3R modes, projecting and level-shifting. > > The projection technique is described in JCP 72, 99. You > construct 6 cartesian vectors describing the 3T+3R motions > (e.g. Tx is N{1,0,0,1,0,0,1,0,0...}) and form a projection > matrix as P=1-(tx)(tx)dagger- 5 more terms. The force constant > matrix is then projected as PFPdagger before diagonalization. > The 6 TR modes are then zero within the numerical accuracy > of the machine and can easily be picked out. > This is used in e.g. Gaussian and GAMESS-US. > > The level-shifting adds large components to the force > constant matrix corresponding to T+R, such that these > frequencies are no longer close to zero, but very much > larger than any real frequencies. This effectively > decouples them from the real frequencies when the > level-shifted force constant matrix is diagonalized. > Due to their large numerical value they can also easily > be picked out after diagonalization. This is the > techniques used in e.g. MOPAC. > > Frank Answer 2: > Stefan, > > The projectors for translation and rotation can be defined from knowledge > of the moments of inertia and if translational invariance is present the > translational modes will have a zero norm. > > If you have access to the source check out TrVect and VibFrq in utilnz.F. > > Douglas J. Fox > Director of Technical Support > help@gaussian.com From chemistry-request@www.ccl.net Sat Feb 20 17:31:50 1999 Received: from lrz.uni-muenchen.de (root@dialc083.ppp.lrz-muenchen.de [129.187.26.83]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA29739 Sat, 20 Feb 1999 17:31:45 -0500 (EST) Received: (from root@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id XAA01063; Fri, 19 Feb 1999 23:16:28 +0100 Date: Fri, 19 Feb 1999 23:16:28 +0100 Message-Id: <199902192216.XAA01063@lrz.uni-muenchen.de> From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To: Tapas Kar Cc: "Comp. Chem. List" Subject: CCL:Databse for nanotube geometry In-Reply-To: References: X-Mailer: VM 6.22 under 19.15p2 XEmacs Lucid Tapas Kar writes: > I am looking for geometries (Cartesian or Z-matrix form) of simple > Carbon nanotube. Is there any database available for such info? You might want to take a look at ftp://ftp.parc.xerox.com/pub/nano/tube.c Regards, Eugene Leitl From chemistry-request@www.ccl.net Sun Feb 21 09:39:29 1999 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA02601 Sun, 21 Feb 1999 09:39:27 -0500 (EST) Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by mserv.rug.ac.be (8.9.0/8.9.0) with ESMTP id PAA07699 for ; Sun, 21 Feb 1999 15:39:27 +0100 (MET) Received: from dialup.rug.ac.be (pdln1p34.rug.ac.be [157.193.30.34]) by allserv.rug.ac.be (8.9.0/8.9.0) with ESMTP id PAA09131 for ; Sun, 21 Feb 1999 15:39:24 +0100 (MET) Message-Id: <4.2.0.24.19990221151946.00949540@allserv.rug.ac.be> X-Sender: pbultink@allserv.rug.ac.be (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.24 (Beta) Date: Sun, 21 Feb 1999 15:38:13 +0100 To: chemistry@www.ccl.net From: Patrick Bultinck Subject: Reaction Enthalpy and BSSE Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL community, Consider a complexation reaction M + B -> MB (m is a metal ion, B a lewis base e.g.) I want to calculate the reaction enthalpies, so I need H for M, B and MB. This means I also need the vibrational frequencies. These should be calculated for M, B and MB, all in their minimum energy geometry. The geometry of fragment B as present in MB is usually not a minimum energy geometry. Calculation H for MB and M is no problem. However for B has to be studied in it's minimum. Now comes what I am wondering is the way it is done to avoid following TWO problems : a) I can take BSSE into account, but that would mean I need to consider B in it's supermolecule minimum. Optimizing B towards minimum using the supermolecule set is however very ambiguous (who would do conformational analysis of a free ligand with a bunch of ghost orbitals all over the place ?). As pointed out by Mayer et al. (I can send the reference, but don't have it readily available here) studying a supermolecule approach minimum for a monomer yields chemical and mathematical ambiguities. b) I calculate the frequencies for MB in the superset, and for M and B both in their monomer sets. This means that I look at M and B in their true minima, not some minimum in a supermolecule basisset (where the presence of ghost orbitals can influence the geometry of B in a superset in some unpredictable way). However calculating Delta-H as DH=H(MB)-H(M)-H(B) would then cause neglect of BSSE. Note : I am talking BSSE correcting in counterpoise way. I have seen a LOT of articles calculating reaction enthalpies, and it seems most would optimize B in the supermolecule set, but that bothers me more than a bit since I am used to conformational analyses without putting ghost orbitals somewhere (not knowing how they influence molecular geometries e.g.). Can anybody share an opinion, I will gladly summarize. Patrick Bultinck Universiteit Gent-Belgium Quantum and Coordination chemistry group From chemistry-request@www.ccl.net Tue Feb 23 12:30:07 1999 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA07598 Tue, 23 Feb 1999 12:30:06 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with ESMTP id SAA21661 for ; Tue, 23 Feb 1999 18:31:12 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with SMTP id SAA25307 for ; Tue, 23 Feb 1999 18:26:32 +0100 (MET) Received: by styx.bruyeres.cea.fr (CEANET-1.1+) id AA27579; Tue, 23 Feb 1999 17:37:35 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by styx via smap id sma027550; Tue Feb 23 17:37:00 1999 Received: from ripault.cea.fr (brenne.ripault.cea.fr [132.165.32.8]) by ripault.cea.fr. (8.8.7/8.7.3) with ESMTP id RAA26796 for ; Tue, 23 Feb 1999 17:36:31 +0100 Received: from brenne.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.5/8.8.5) with SMTP id SAA18170 for ; Tue, 23 Feb 1999 18:35:46 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <36D2E6F1.59B70A05@ripault.cea.fr> Date: Tue, 23 Feb 1999 18:35:46 +0100 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.30 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: QSPR stability: Cross-valid. coef Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Dear CCLers, I am trying to estimate sublimation enthalpies in terms of a short-range term based on atomic surface tensions (with an additional correction for H-bonds) plus an electrostatic term. I got a fairly good fit for some ~200 molecules, while 8 parameters empirically adjusted. Now I would like to estimate the stability of the model equation wrt the training set. I read in literature (e.g. Katritzky et al. J.Chem.Inf.Commput.Sci.38, 840 (1998)) that a measure of this stability is given by a so-called "cross-validated correlation coefficient". I would be grateful if somebody could give me the exact definition of this coefficient or points to references. BTW, I guess some readers of this request have experience in interpolating experimental data through QSPR. So far I got all data from the NIST Chemistry WebBook, which is a bit cumbersome, especially with a slow access to the web from outside the laboratory. Does anybody know similar extensive compilations of thermodynamical data, on paper or preferably CD-ROM ? I am only aware of the CRC Chemistry Handbook and J.Chem.Phys.Ref.Data. Thanks. -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From chemistry-request@www.ccl.net Tue Feb 23 12:41:57 1999 Received: from curie.syr.edu (curie.syr.edu [128.230.187.116]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA07841 Tue, 23 Feb 1999 12:41:56 -0500 (EST) Received: from syr.edu (curie.syr.edu [128.230.187.116]) by curie.syr.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA95772 for ; Tue, 23 Feb 1999 11:52:50 -0500 (EST) Sender: desingh@syr.edu Message-ID: <36D2DCE1.A7BEF864@syr.edu> Date: Tue, 23 Feb 1999 11:52:49 -0500 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Computational Chemistry List Subject: MOPAC help Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am using mopac97 to minimize the geometry of a structure and I often get the following error message "THE LINE MINIMIZATION FAILED TWICE IN A ROW. TAKE CARE!" Does anyone know what it exactly means...My output telle me that SCF was achieved, but this error is almost always there. Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry & Biochemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@www.ccl.net Tue Feb 23 13:13:32 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA08136 Tue, 23 Feb 1999 13:13:27 -0500 (EST) Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP); Tue, 23 Feb 1999 17:10:09 +0000 From: uccatvm Message-Id: <1436.199902231710@socrates-a.ucl.ac.uk> Subject: polarizability and vdW radius for B To: chemistry@www.ccl.net (CCL) Date: Tue, 23 Feb 1999 17:10:04 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, I would be interested to know if there is a value available for the polarizability and the van der Waals radius for B in a covalently bonded state. I am interested in trivalent boron with two oxygens and one C==C bonded to it in a neutral organic molecule, but any values of covalent B would be useful. We need this information to develop a model potential for a system containing B, but we have had not much luck so far finding reliable values for these. Any suggestions will be greatly appreciated. Best regards, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@www.ccl.net Tue Feb 23 18:36:48 1999 Received: from sungod.ccs.yorku.ca (/7KgVZfS/to8d8E8vOGMNiZopNRmflhV@sungod.ccs.yorku.ca [130.63.236.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA13518 Tue, 23 Feb 1999 18:36:48 -0500 (EST) Received: from mountain.chem.yorku.ca (mountain.chem.yorku.ca [130.63.133.28]) by sungod.ccs.yorku.ca (8.8.7/8.6.11) with ESMTP id SAA10745 for ; Tue, 23 Feb 1999 18:36:48 -0500 (EST) Received: from localhost (waito@localhost) by mountain.chem.yorku.ca (8.8.4/8.6.12) with SMTP id SAA18957 for ; Tue, 23 Feb 1999 18:34:09 -0500 (EST) Date: Tue, 23 Feb 1999 18:34:09 -0500 (EST) From: Wai-To Chan To: chemistry@www.ccl.net Subject: Information about TopMoD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I've never used the program but I can give you the contact address given in the paper by some of its authors. Send your request to Xenophon.Krokidis@lct.jussieu.fr for TopMoD by Noury, Krokidis, Fuster and Silvi Wai-To Chan Department of Chemistry York University, Toronto Ontario, Canada From chemistry-request@www.ccl.net Tue Feb 23 21:36:02 1999 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 VAA14306 Tue, 23 Feb 1999 21:36:01 -0500 (EST) Received: from auric.chem.csiro.au (auric.chem.CSIRO.AU [138.194.44.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id VAA00448 for ; Tue, 23 Feb 1999 21:35:58 -0500 (EST) Received: by auric.chem.csiro.au id AA18552 (5.67b/IDA-1.5 for chemistry@ccl.net); Wed, 24 Feb 1999 13:35:34 +1100 Received: from cpr-46107.chem.csiro.au(138.194.46.107), claiming to be "[138.194.46.107]" via SMTP by auric.chem.CSIRO.AU, id smtpd18548aaa; Wed Feb 24 02:35:33 1999 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 Feb 1999 13:35:32 +1000 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: ethylene oxide structure Hi, Netters, Has anyone seen any work relating to alternate cononical structures for ethylene oxide (oxirane), or to any partial double bond character in the C-O bonds? Please excuse cross postings. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@www.ccl.net Tue Feb 23 23:43:54 1999 Received: from smtp1.fas.harvard.edu (root@smtp1.fas.harvard.edu [140.247.30.81]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA14882; Tue, 23 Feb 1999 23:43:53 -0500 (EST) Received: from login6.fas.harvard.edu (IDENT:daizadeh@login6.fas.harvard.edu [140.247.30.76]) by smtp1.fas.harvard.edu with ESMTP id XAA21162 Received: by login6.fas.harvard.edu with ESMTP id XAA31180 Date: Tue, 23 Feb 1999 23:43:55 -0500 (EST) From: Iraj Daizadeh To: chemistry@www.ccl.net, chemistry-request@www.ccl.net Subject: Wigner Function. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have a time-series and would like to perform a wigner transformation; anyone have a program to do such a thing. Iraj. Iraj Daizadeh, Ph. D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories, Box #140 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@fas.harvard.edu