From owner-chemistry@ccl.net Fri Feb 24 02:41:00 2006 From: "Tamas E. Gunda tgunda2005%a%puma.unideb.hu" To: CCL Subject: CCL: superimposing molecules Message-Id: <-30994-060223053657-2007-LRbbDWRzzo+25dnwQ0ritg,,server.ccl.net> X-Original-From: "Tamas E. Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 23 Feb 2006 10:31:56 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas E. Gunda" [tgunda2005-$-puma.unideb.hu] You may want to try Mol2Mol http://web.interware.hu/frenzy/mol2mol It can superimpose and rms compare two molecules, using all atoms or only heavy or selected ones, optionally with different weight factors. Tamas E. Gunda tgunda2005 *AT* puma.unideb.hu > Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd^_^msn.com] > > Hi all, > > Is there a free program out there that runs under Windows and will allow one > to open two pdb files simultaneously, superimpose one on the other easily, > and then save the coordinates of the molecule that has been moved? > > Thanks in advance, > Richard > > From owner-chemistry@ccl.net Fri Feb 24 10:13:01 2006 From: "=?ISO-8859-1?Q?Miquel_Sol=E0?= miquel.sola- -udg.es" To: CCL Subject: CCL: VII Girona Seminar on the Nature of the Chemical Bond, 10-13 July, 2006 Message-Id: <-30995-060224040148-30715-IG5AUtvKmGvPVqouAsGBcw*server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Miquel_Sol=E0?= Content-Type: multipart/alternative; boundary="------------020901030507060602050505" Date: Fri, 24 Feb 2006 09:25:57 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Miquel_Sol=E0?= [miquel.sola~~udg.es] This is a multi-part message in MIME format. --------------020901030507060602050505 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Colleague, On behalf of the Organising Committee, we take great pleasure in announcing you the VII Girona Seminar on the Nature of the Chemical Bond which will be held in Girona (Spain), July 10-13, 2006. The aim of the conference is to give the audience an impression of the recent developments and applications of quantum chemistry to the theoretical analysis of the nature of the chemical bond. This will be the main subject, although, following the philosophy of the six previous Girona Seminars, other aspects such as theoretical chemistry, quantum chemistry, mathematical chemistry, molecular similarity, molecular properties, density functions and density functional theory, and quantitative structure-properties relationships will also be welcome. Deadlines: Student fellowship application: 30 March, 2006 Pre-registration: 30 March, 2006 Student fellowship notification: 15 April, 2006 Acceptance notification: 15 April, 2006 Final registration: 15 May, 2006 Abstract submission: 30 May, 2006 Payment of registration fee: 15 May, 2006 Provisional List of Speakers (all confirmed): W. Allen (University of Georgia, USA) J. Angyan (Université Henri Poincaré, France) P. W. Ayers (McMaster University, Canada) F. M. Bickelhaupt (Vrije Universiteit Amsterdam, The Netherlands) B. Braida (Université Pierre et Marie Curie, France) P. Bultinck (Ghent University, Belgium) R. Carbó-Dorca (Universitat de Girona, Spain/Ghent University, Belgium) E. Chamorro (Universidad Nacional Andrés Bello, Chile) P.K. Chattaraj (Indian Institute of Technology, India) O. Christiansen (University of Aarhus, Denmark) J. Cioslowski (University of Szczecin, Poland) D. L. Cooper (University of Liverpool, United Kingdom) M. Cyranski (University of Warsaw, Poland) G. Frenking (Philipps-Universität Marburg, Germany) C. Gatti (CNR-ISTM Ist. di Scienze e Tecnologie Molecolari, Italy) P. Geerlings (Vrije Universiteit Brussel, Belgium) L. González (Freie Universität Berlin, Germany) R. Havenith (Utrecht University, The Netherlands) K. Hirao (University of Tokyo, Japan) J. Karwowski (University of Torun, Poland) G. Lendvay (Hungarian Academy of Sciences, Hungary) F. J. Luque (Universitat de Barcelona, Spain) I. Mayer (Hungarian Academy of Sciences, Hungary) P. Mezey (Memorial University of Newfoundland, Canada) K. Pernal (University of Szczecin, Poland) R. Ponec (Czech Academy of Sciences, Czech Republic) M. Rafat (University of Manchester, United Kingdom) M. Sodupe (Universitat Autňnoma de Barcelona, Spain) A. Toro-Labbé (Pontificia Universidad Católica de Chile, Chile) J. Ugalde (Euskal Herriko Unibertsitatea, Spain) P. Ugliengo (University of Torino, Italy) J. Zachara (Warsaw University, Poland) More information concerning the Conference (pre-registration, fellowships, fees, accommodation, international and local organizing committees, schedule, social events, etc.) is available in the dedicated VII Girona Seminar WEB site (http://iqc.udg.es/gsncb2006). If you need more information, please do not hesitate to contact us (secretaria,,iqc.udg.es). We are hoping to receive a positive answer to our invitation. Kind Regards, R. Carbó-Dorca, Chairman M. Duran, CoChairman M. Solŕ, Secretary -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Miquel Solŕ Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Phone +34.972.41.89.12 Cellular-Phone: +34.626.163.580 FAX +34.972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel.sola,,udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- --------------020901030507060602050505 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Dear Colleague,

On behalf of the Organising Committee, we take great pleasure in announcing you the VII Girona Seminar on the Nature of the Chemical Bond which will be held in Girona (Spain), July 10-13, 2006. The aim of the conference is to give the audience an impression of the recent developments and applications of quantum chemistry to the theoretical analysis of the nature of the chemical bond. This will be the main subject, although, following the philosophy of the six previous Girona Seminars, other aspects such as theoretical chemistry, quantum chemistry, mathematical chemistry, molecular similarity, molecular properties, density functions and density functional theory, and quantitative structure-properties relationships will also be welcome.

Deadlines:
Student fellowship application: 30 March, 2006
Pre-registration: 30 March, 2006
Student fellowship notification: 15 April, 2006
Acceptance notification: 15 April, 2006
Final registration: 15 May, 2006
Abstract submission: 30 May, 2006
Payment of registration fee: 15 May, 2006 

Provisional List of Speakers (all confirmed):
W. Allen (University of Georgia, USA)
J. Angyan (Université Henri Poincaré, France)
P. W. Ayers (McMaster University, Canada)
F. M. Bickelhaupt (Vrije Universiteit Amsterdam, The Netherlands)
B. Braida (Université Pierre et Marie Curie, France)
P. Bultinck (Ghent University, Belgium)
R. Carbó-Dorca (Universitat de Girona, Spain/Ghent University, Belgium)
E. Chamorro (Universidad Nacional Andrés Bello, Chile)
P.K. Chattaraj (Indian Institute of Technology, India)
O. Christiansen (University of Aarhus, Denmark)
J. Cioslowski (University of Szczecin, Poland)
D. L. Cooper (University of Liverpool, United Kingdom)
M. Cyranski (University of Warsaw, Poland)
G. Frenking (Philipps-Universität Marburg, Germany)
C. Gatti (CNR-ISTM Ist. di Scienze e Tecnologie Molecolari, Italy)
P. Geerlings (Vrije Universiteit Brussel, Belgium)
L. González (Freie Universität Berlin, Germany)
R. Havenith (Utrecht University, The Netherlands)
K. Hirao (University of Tokyo, Japan)
J. Karwowski (University of Torun, Poland)
G. Lendvay (Hungarian Academy of Sciences, Hungary)
F. J. Luque (Universitat de Barcelona, Spain)
I. Mayer (Hungarian Academy of Sciences, Hungary)
P. Mezey (Memorial University of Newfoundland, Canada)
K. Pernal (University of Szczecin, Poland)
R. Ponec (Czech Academy of Sciences, Czech Republic)
M. Rafat (University of Manchester, United Kingdom)
M. Sodupe (Universitat Autònoma de Barcelona, Spain)
A. Toro-Labbé (Pontificia Universidad Católica de Chile, Chile)
J. Ugalde (Euskal Herriko Unibertsitatea, Spain)
P. Ugliengo (University of Torino, Italy)
J. Zachara (Warsaw University, Poland)

More information concerning the Conference (pre-registration, fellowships, fees, accommodation, international and local organizing committees, schedule, social events, etc.) is available in the dedicated VII Girona Seminar WEB site (http://iqc.udg.es/gsncb2006).

If you need more information, please do not hesitate to contact us (secretaria,,iqc.udg.es).

We are hoping to receive a positive answer to our invitation.


Kind Regards,


R. Carbó-Dorca, Chairman

M. Duran, CoChairman
M. Solà, Secretary


 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
 Miquel Solà                           
 Institut de Química Computacional         
 Universitat de Girona                   
 Campus Montilivi
 17071 Girona, CATALONIA (Spain)          
 Phone +34.972.41.89.12
 Cellular-Phone:  +34.626.163.580
 FAX   +34.972.41.83.56                               
 World Wide Web: http://iqc.udg.es/~miquel/mike.html   
 e-mail: miquel.sola,,udg.es                         
 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
--------------020901030507060602050505-- From owner-chemistry@ccl.net Fri Feb 24 11:45:01 2006 From: "Robert J Harrison harrisonrj^ornl.gov" To: CCL Subject: CCL: "Quantitative Quantum Chemistry" March 17-20, 2006 in Santa Fe. Message-Id: <-30996-060224114327-23251-O22h6vxy8zCQ9miA47XvhA ~ server.ccl.net> X-Original-From: "Robert J Harrison" Date: Fri, 24 Feb 2006 11:43:24 -0500 Sent to CCL by: "Robert J Harrison" [harrisonrj..ornl.gov] [Extended hotel registration ends today, Friday, 2/24/2006] On behalf of the organizing committee, I would like to draw everyone's attention to the international symposium "Quantitative Quantum Chemistry" in honor of Dr. Thom Dunning, to be held this March 17-20, 2006, in Santa Fe. All talks are by invitation only, but there is an open poster session on the second evening. A preliminary list of speakers is posted on the web site which includes information about the conference site, schedule and registration. If you wish to attend, please register online as soon as possible and please also note that the block of rooms reserved at the lodge expires today. http://www.csm.ornl.gov/workshops/quant_chem/index.html Please direct questions to Sherry Hempfling at hempflingce__ornl.gov. Sincerely, Robert J. Harrison (UT/ORNL Joint Faculty) PO Box 2008 MS6367, Oak Ridge TN 37831 Tel: (865) 241-3937 (forwards to mobile) Fax__ORNL: (865) 574-0680 Fax__UT: (865) 974 9332 Email: harrisonrj__ornl.gov From owner-chemistry@ccl.net Fri Feb 24 13:22:00 2006 From: "Arvydas Tamulis tamulis .. mserv.itpa.lt" To: CCL Subject: CCL:G: Energy differences between spin states in [Ru(bipyridine)3]+2 Message-Id: <-30997-060224105706-3266-LHHyMzkRl6ckxkvuLVGRLA*|*server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 24 Feb 2006 17:56:52 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis[A]mserv.itpa.lt] Dear Colleagues, We have calculated total energy differences between spin states in [Ru(bipyridine)3)]+2 molecule. Each spin state geometry was optimized by G03 DFT B3LYP/LanL2DZ. Triplet state is 2.29 eV higher in comparison with singlet. Pentet state is 3.23 eV higher in comparison with triplet. Septet state is 2.55 eV higher in comparison with pentet. How realistic are our calculated results? Maybe somebody knows exact ab initio calculation results or experimental data? With best regards, Arvydas Tamulis c/o Vykintas Tamulis From owner-chemistry@ccl.net Fri Feb 24 13:56:00 2006 From: "Josh Bailey mojognome|a|bigfoot.com" To: CCL Subject: CCL: GAMESS - CISD & CISDT polarizability error assistance Message-Id: <-30998-060224040121-30636-eIMTeDLoMEiaNiKKd2vATw*server.ccl.net> X-Original-From: Josh Bailey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 24 Feb 2006 02:30:51 -0500 MIME-Version: 1.0 Sent to CCL by: Josh Bailey [mojognome^^bigfoot.com] In my attempts to compute the polarizability of HCN using CISD and CISDT within GAMESS, I have run into three confusing errors. These errors don't appear to have any direct relationship. The first error I received was actually not an error at all. At the end of a density matrix calculation, GAMESS terminates 'Abnormally' with a fatal error in DDI process . No useful descriptive error was given. This occurs when computing polarizability using CISD and either the cc-aug-pVTZ basis set or a mixture that replaces the hydrogen with 6-31G. The second error I receive is a "problem with previous CI vector file." Within the error a solution of deleting the old civectr file is presented. However, at the end of the run, that file is automatically removed. This occurs with the 6-31G(d,p) basis set and both CISD and CISDT methods. The third error occurs when I attempt to optimize the geometry using CISD and the aug-cc-pVTZ basis set with C4v symmetry. I receive the error "unable to make an unambiguous determination of the spatial symmetry in this nonabelian group." However, if I change to say 6-31G*, the run completes successfully. I am posting my input and output files on the site below. http://www.chemistry.mtu.edu/~jdbailey/gmshelp.html I would appreciate input anyone may have -Josh Bailey -- Josh Bailey MS Candidate Department of Chemistry Michigan Technological University 231.649.6748 jdbailey ~~ mtu.edu mojognome ~~ bigfoot.com From owner-chemistry@ccl.net Fri Feb 24 14:31:00 2006 From: "Ian Hovell HOVELL]|[cetem.gov.br" To: CCL Subject: CCL:G: Transition state for recombination of dibromomercury Message-Id: <-30999-060224133004-27551-su1D+iQtcIDN32QDg+OSuQ{}server.ccl.net> X-Original-From: Ian Hovell Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6393D.C86E54E0" Date: Fri, 24 Feb 2006 09:28:14 -0300 MIME-Version: 1.0 Sent to CCL by: Ian Hovell [HOVELL/./cetem.gov.br] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C6393D.C86E54E0 Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I am assuming a linear transition state for the recombination of a bromine radical with the bromomercury radical forming the dibromo molecule. According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 angstroms produced a transition state calculated using CI methods. I am trying to produce, without much success, a transition state for this recombination reaction at the mpw1pw91 DFT level. In either full or partial (where only one bond is relaxed) optimisations, the radicals either join forming the dibromo molecule, and hence no imaginary frequency, or separate completly according to the starting bond lengths. I am using the built in SDD basis set and G03w. The output produces a warning that the bromine might be hypervalent but has no d functions - could this be the problem or this this level of calculation just not up to finding the transition state for this system? All ideas would be welcome and a summary will be posted if this post generates interest. TIA Ian Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cincia e da Tecnologia- MCT Avenida Ip, No 900 - Cidade Universitaria Ilha do Fundo Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell__cetem.gov.br ------_=_NextPart_001_01C6393D.C86E54E0 Content-Type: text/html; charset="iso-8859-1"
Dear CCLers,
I am assuming a linear transition state for the recombination of a bromine radical with the bromomercury radical forming the dibromo molecule.
According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 angstroms produced a transition state calculated using CI methods.
I am trying to produce, without much success, a transition state for this recombination reaction at the mpw1pw91 DFT level. In either full or partial (where only one bond is relaxed) optimisations, the radicals either join forming the dibromo molecule, and hence no imaginary frequency, or separate completly according to the starting bond lengths.
 
I am using the built in SDD basis set and G03w. The output produces a warning that the bromine might be hypervalent but has no d functions - could this be the problem or this this level of calculation just not up to finding the transition state for this system?
All ideas would be welcome and a summary will be posted if this post generates interest.
TIA
Ian
 
 
Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail hovell__cetem.gov.br
 
------_=_NextPart_001_01C6393D.C86E54E0-- From owner-chemistry@ccl.net Fri Feb 24 20:05:00 2006 From: "Shobe, David dshobe(-)sud-chemieinc.com" To: CCL Subject: CCL:G: Transition state for recombination of dibromomercury Message-Id: <-31000-060224170226-10880-cKmcLDjeBa4+HagYXhcEfA,+,server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Feb 2006 23:02:07 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe,sud-chemieinc.com] Ian, Radical recombination reactions often don't have a TS, and it's not unusual to have a TS at one level of theory and no TS at another. My advice is to run a PES (potential energy scan) varying the Hg-Br distance. If the energy is a monotonic function of the bond length, then there is no transition state (according to whichever level of theory you are using). --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net] Sent: Friday, February 24, 2006 2:44 PM To: Shobe, David Subject: CCL:G: Transition state for recombination of dibromomercury Sent to CCL by: Ian Hovell [HOVELL/./cetem.gov.br] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C6393D.C86E54E0 Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I am assuming a linear transition state for the recombination of a bromine radical with the bromomercury radical forming the dibromo molecule. According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 angstroms produced a transition state calculated using CI methods. I am trying to produce, without much success, a transition state for this recombination reaction at the mpw1pw91 DFT level. In either full or partial (where only one bond is relaxed) optimisations, the radicals either join forming the dibromo molecule, and hence no imaginary frequency, or separate completly according to the starting bond lengths. I am using the built in SDD basis set and G03w. The output produces a warning that the bromine might be hypervalent but has no d functions - could this be the problem or this this level of calculation just not up to finding the transition state for this system? All ideas would be welcome and a summary will be posted if this post generates interest. TIA Ian Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cincia e da Tecnologia- MCT Avenida Ip, No 900 - Cidade Universitaria Ilha do Fundo Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell###cetem.gov.br ------_=_NextPart_001_01C6393D.C86E54E0 Content-Type: text/html; charset="iso-8859-1"
Dear CCLers,
I am assuming a linear transition state for the recombination of a bromine radical with the bromomercury radical forming the dibromo molecule.
According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 angstroms produced a transition state calculated using CI methods.
I am trying to produce, without much success, a transition state for this recombination reaction at the mpw1pw91 DFT level. In either full or partial (where only one bond is relaxed) optimisations, the radicals either join forming the dibromo molecule, and hence no imaginary frequency, or separate completly according to the starting bond lengths.
 
I am using the built in SDD basis set and G03w. The output produces a warning that the bromine might be hypervalent but has no d functions - could this be the problem or this this level of calculation just not up to finding the transition state for this system?
All ideas would be welcome and a summary will be posted if this post generates interest.
TIA
Ian
 
 
Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail hovell###cetem.gov.br
 
------_=_NextPart_001_01C6393D.C86E54E0--