From noda@zsu.zaporizhzhe.ua Fri Nov 21 06:34:29 1997 Received: from frya.zgik.zaporizhzhe.ua for noda@zsu.zaporizhzhe.ua by www.ccl.net (8.8.3/950822.1) id FAA20313; Fri, 21 Nov 1997 05:53:30 -0500 (EST) Received: from k1.zsu.zaporizhzhe.ua by frya.zgik.zaporizhzhe.ua with SMTP id MAA21363; (8.8.8/vak+evp/1.8e) Fri, 21 Nov 1997 12:26:57 +0200 (EET) Received: from pp200-nt-01 by k1.zsu.zaporizhzhe.ua with SMTP id MAA07645; (8.6.11/vak/1.8e) Fri, 21 Nov 1997 12:24:37 +0200 Date: Fri, 21 Nov 1997 12:24:37 +0200 Message-Id: <199711211024.MAA07645@k1.zsu.zaporizhzhe.ua> X-Sender: noda@win-serv.k1.zsu.zaporizhzhe.ua X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: "Eugene G. Noda" Subject: HF and EC bond lengths At 06:35 PM 11/19/97 -0800, Jason Perry wrote: > >2) HF is biased toward the metal s orbital over the metal d orbital. The >s orbital is more diffuse than the d orbitals and requires less correlation >to describe properly. You can test this by calculating the metal s2dn-2, >s1dn-1, and dn state spittings of the metal. You get much better agreement >with experiment when correlation and good basis sets are used. Otherwise, >there is a bias in favor of the s2dn-2 and s1dn-1 states. Because of this >bias, HF descriptions of metal-ligand covalent bonds often have too much >s character in them. With the addition of correlation more d character >is introduced into the bond. Since the s orbital is larger than the d >orbital, reducing s character and introducing more d character coincides >with a shortening of the bond. > Dear Jason No one is against to discuss correlation shortening bonds in organometallics using different methods. However, I am strongly against to involve so-called "s-d mixing" argument. In my opinion, this is the case when poor computational model leads to the bad physics. Take a look at Fig. 5 from my recent article http://www.zsu.zaporizhzhe.ua/~noda/ccl_disc.html which I specially to the present discussion placed on the web. Of course, some portion of s-p density in the bonding region is really existed. However, my calcs show that this density comes from 3s and 3p orbitals at least for the first row transmetals. Even if you ignore this, I will be insisted that many decades speculations in the frame of "mixing" were completely unfruitful and totally misleading. I tend to classify such models as a plausible physics. Sincerely, Eugene %----------------------------------------------------------------------- % Eugene G. Noda Head of Lab % Faculty of Mathematics Parallel Computing Laboratory % Zaporizhia State University Tel.: +380-(61)-264-3656 % 66 Zhukovski Street Fax: +380-(61)-262-7161 % Zaporizhia, 330600 E-mail: noda@zsu.zaporizhzhe.ua % Ukraine http://www.zsu.zaporizhzhe.ua/~noda/ %----------------------------------------------------------------------- From metz@phindigo.oci.uni-heidelberg.de Fri Nov 21 10:34:34 1997 Received: from phindigo.oci.uni-heidelberg.de for metz@phindigo.oci.uni-heidelberg.de by www.ccl.net (8.8.3/950822.1) id JAA21242; Fri, 21 Nov 1997 09:55:47 -0500 (EST) Received: by phindigo.oci.uni-heidelberg.de (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id PAA11575; Fri, 21 Nov 1997 15:57:27 -0100 From: "Markus Metz" Message-Id: <9711211557.ZM11573@phindigo.oci.uni-heidelberg.de> Date: Fri, 21 Nov 1997 15:57:12 +0000 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: atom in molecules Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello ! I am using GAUSSIAN 94 to calculate the properties of atoms in molecules (1) using the SCF density.(keywords: AIM=ALL, DENSITY=LAPLACIAN) For example the attractors, critical points on attractor interaction lines, zero flux surfaces, bond paths and the second derivative of the electron density of cyclopropane were calculated. What I am interested in are the bent bonds in this molecule. Does anybody know, how to visualize this data? Thanks in advance, Markus Metz. (1) R. F. W. Bader, Atoms in Molecules: a quantum theory, Clarendon Press, Oxford, 1990. metz@phindigo.oci.uni-heidelberg.de -- -------------------------------------------------------------------------------- Markus Metz Universitaet Heidelberg Tel.: 06221-54-6066 Organ.-Chem. Institut Lehrstuhl III Fax: 06221-54-4885 Im Neuenheimer Feld 270 69120 Heidelberg -------------------------------------------------------------------------------- From schrecke@t12.lanl.gov Fri Nov 21 11:34:35 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id LAA21850; Fri, 21 Nov 1997 11:18:43 -0500 (EST) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.8/(cic-5, 10/28/97)) with SMTP id JAA06815 for ; Fri, 21 Nov 1997 09:18:40 -0700 (MST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 21 Nov 1997 09:22:04 -0700 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: atomic symmetry in G94 Dear CCL, I am trying to run a few atoms or ions (e.g., Fe_+) in Gaussian 94, restricted open shell. My incentive is to compare orbital energies as they come out of different methods and / or basis sets. Now, when I run such an atom, the program turns off symmetry. This would not bother me too much if the subsequent SCF had not mixed up states. However, it does so, and I do not get, for instance, 5 degenerate d orbitals of the same energy. I tried to enforce some symmetry by placing other nuclei into symmetric positions far away but then I run into SCF convergence problems. Any advice or tricks? Best regards, Georg -- ============================================================== Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ ============================================================== From martin@saluki-mail.siu.edu Fri Nov 21 13:34:35 1997 Received: from saluki-mail.siu.edu for martin@saluki-mail.siu.edu by www.ccl.net (8.8.3/950822.1) id NAA22407; Fri, 21 Nov 1997 13:27:09 -0500 (EST) Received: from 131.230.89.21 (harpo.thchem.siu.edu [131.230.89.21]) by saluki-mail.siu.edu (AIX4.2/UCB 8.7/8.7) with SMTP id MAA157040 for ; Fri, 21 Nov 1997 12:26:25 -0600 (CST) Message-Id: <199711211826.MAA157040@saluki-mail.siu.edu> X-Mailer: Microsoft Internet Mail & News for Macintosh - 3.0c (405) Date: Fri, 21 Nov 1997 12:29:02 -0600 Subject: Excited state benzene studies From: Martin Cuma To: chemistry@www.ccl.net Mime-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7bit Hello, I am trying to find some references to the calculations of excited states of benzene, especially lowest pi-pi* singlets and triplets. Is there anybody aware of the source I could look at? Thanks, MC Martin Cuma Dept. of Chemistry Southern Illinois University at Carbondale From hinsen@lmspc1.ibs.fr Fri Nov 21 13:48:19 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id NAA22232; Fri, 21 Nov 1997 13:01:40 -0500 (EST) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id TAA13068; Fri, 21 Nov 1997 19:00:27 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id SAA09053; Fri, 21 Nov 1997 18:58:40 +0100 Date: Fri, 21 Nov 1997 18:58:40 +0100 Message-Id: <199711211758.SAA09053@lmspc1.ibs.fr> From: Konrad Hinsen To: Lutz.Ehrlich@EMBL-Heidelberg.de CC: richard@TC.Cornell.EDU, chemistry@www.ccl.net In-reply-to: <199711170932.JAA05368@cuckoo.embl-heidelberg.de> (Lutz.Ehrlich@EMBL-Heidelberg.de) Subject: Re: CCL:Rigid body dynamics > > 2. How does it compare with SHAKE type constraint methods: > > faster/slower or just different? > > Just different would be a better description, as you constrain the bond > angles and dihedrals as well (dependent of course, on the way you choose > your rigid bodies). > Second, in the SHAKE approach, each atom still experiences the force due to > it's interaction with the rest of the system. In VRDB (as proposed by > Head-Gordon) , a force/torque acting on a rigid body is derived from the > forces acting on it's constitutive atoms. > Third, Head-Gordon in her work enforces planarity of the peptide bond by > turning it into a rigid body. Thus, your dynamics will differ > from a plain bond-length SHAKE simulation. I have no practical experience with VRBD, but with other treatments of rigid-body and constrained systems, which may be of interest. First of all it is necessary to distinguish between the consequence of applying certain constraints and the limitations/efficiency of particular methods to do so. Obviously keeping a peptide group rigid is a stronger constraint than fixing just the bond length, but it also comes with a higher reduction of fast degrees of freedom, which is after all the reason for applying mechanical constraints. For a discussion and an explicit comparison for helix dynamics, see K. Hinsen, G.R. Kneller Influence of constraints on the dynamics of polypeptide chains Phys. Rev. E 52, 6868 (1995) Once you have chosen the constraints you want to apply (that's a physical choice), you must then pick a method to implement them (that's an algorithmic choice). In this choice you must consider the limitations and efficiency criteria for each method. For SHAKE these are - limitation: no rigid groups of more than three atoms (planar) or four atoms (non-planar) (at least for the commonly implemented original version of SHAKE, a generalization has been published, but is not in general use) - efficiency problem: strongly interdependent constraint cause a long iteration For VRBD: - limitation: no constraints between rigid units - efficiency consideration: most efficient for large rigid units Note that many other techniques for implementing constraints have been proposed and/or tested. In principle, the results for a given set of constraints should be identical irrespective of the method used, but I am not aware of any practical comparison. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From boufer@cennas.nhmfl.gov Fri Nov 21 14:34:36 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id OAA22626; Fri, 21 Nov 1997 14:03:34 -0500 (EST) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id OAA14100 for ; Fri, 21 Nov 1997 14:03:24 -0500 (EST) Date: Fri, 21 Nov 1997 14:03:24 -0500 (EST) From: Ahmed Bouferguene X-Sender: boufer@cennas To: CHEMISTRY@www.ccl.net Subject: Second order correction of the energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings all, Does anyone know how to evaluate the polarization energy of a molecule in the field of a point charge ? ahmed P.S. A good reference will be of great help. From alexei@palladium.enscm.fr Fri Nov 21 14:42:52 1997 Received: from palladium.enscm.fr for alexei@palladium.enscm.fr by www.ccl.net (8.8.3/950822.1) id OAA22719; Fri, 21 Nov 1997 14:28:53 -0500 (EST) Received: from localhost (alexei@localhost) by palladium.enscm.fr (8.8.7/8.8.7) with SMTP id UAA26770; Fri, 21 Nov 1997 20:37:58 +0100 (MET) Date: Fri, 21 Nov 1997 20:37:58 +0100 (MET) From: "Dr. Alexei Arbouznikov" X-Sender: alexei@palladium To: Georg Schreckenbach cc: CCL Subject: Re: CCL:G:atomic symmetry in G94 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Georg, Unfortunately, if you use restricted Hartree-Fock within the Gaussian program, you can not get the correct degeneracy of the open shells, except for the simplest case of exactly half-filled open shells (try, e.g., Mn++ ion - d5 configuration, and you will obtain 5 degenerate d-orbitals). To get the correct degeneracy in some more complicated configurations (non-half-filled one open shell or several open shells, e.g., 3d and 4s with occupation numbers other than 1/2 for at least one of them), you have to use GVB(0) option in the Gaussian, and specify explicitely the vector coupling coefficients for the desired state (the way to do it should be indicated in the G94 manual). Other solution of this problem is using another ab initio programs with well-elaborated ROHF techniques, such as, e.g., Monstergauss-92. If you are interested in, please, ask some additional questions. Best regards, Dr. Alexei Arbouznikov Ecole Nationale Superieure de Chimie, Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula, 8, rue de l'Ecole Normale 34296 Montpellier, Cedex 5 FRANCE Telephone: (33) 4-67-14-72-68 Fax: (33) 4-67-14-43-49 E-mail: alexei@palladium.enscm.fr