From owner-chemistry@ccl.net Fri Jul 25 05:30:01 2008 From: "allouche allouche[*]lasim.univ-lyon1.fr" To: CCL Subject: CCL:G: Gabedit version 2.1.8 released. Message-Id: <-37413-080725040302-13024-16z9kL59zFg39f1oIYvVsg:server.ccl.net> X-Original-From: allouche Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 25 Jul 2008 09:30:05 +0200 MIME-Version: 1.0 Sent to CCL by: allouche [allouche(~)lasim.univ-lyon1.fr] Dear CCLers, Release 2.1.8 of Gabedit is now available. Gabedit is a free graphical user interface for computational chemistry packages. It's work under Windows, Linux, Mac OSX11 and other UNIX OS. Gabedit makes using Computational Chemistry Packages (CCP) simple and straightforward : * Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. * Set up and submit CCP jobs right from the interface, and monitor their progress as they run. * Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. * Simulated Annealing with Molecular Dynamics is implemented in Gabedit (using Amber 99 molecular mechanics parameters). The computational chemistry packages supported by Gabedit are : Gamess-US , Gaussian , Molcas , Molpro , MPQC , OpenMopac , PCGamess and Q-Chem . ADF and other softwares (through the gabedit and molden format files) are partially supported by Gabedit. Major features * Gabedit can creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, PCGamess and Q-Chem. * Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess, Q-Chem and (partially) ADF calculation results, including the following * Molecular orbitals. * Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. * Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property. * Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the molecular principal axes. * Animation of the normal modes corresponding to vibrational frequencies. * Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the molecular principal axes. * Animation of contours, Animation of planes colorcoded. * Gabedit can display UV-Vis, IR, Raman, ECD, NMR computed spectras. * Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded. * Gabedit can export picture in PDF, PS, EPS, and SVG format * Gabedit can save picture in BMP, JPEG, PNG and PPM format. * Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded). You can download this new version from : http://gabedit.sf.net If you find any bugs or have any problems, please contact me ( allouchear at users.sourceforge.net). Best regards A.R. Allouche Université Claude Bernard Lyon 1 LASIM, UMR 5579 Villeurbanne France From owner-chemistry@ccl.net Fri Jul 25 05:33:00 2008 From: "scerri[#]chem.ucla.edu" To: CCL Subject: CCL: meeting on the reduction of chemistry in Leuven, Belgium Message-Id: <-37414-080724060825-18002-1lXP93zWATjWcqWbiIZ5WA[a]server.ccl.net> X-Original-From: scerri{:}chem.ucla.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 24 Jul 2008 03:08:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: scerri**chem.ucla.edu University of Leuven, Department of Philosophy The Reduction of Chemistry. -------------------- Thursday, July 31 9:30-10:45 Paul Needham, Nagel’s Analysis of Reduction: Comments in Defence as Well as Critique 11:00-12:15 Brian Sutcliffe, Molecular Structure, Chemical Bonding and the Born-Oppenheimer Approximation 14:00-15:15 Robin Hendry, Ontological Reduction and Molecular Structure 15:15-16:30 Robert Bishop, Whence Chemistry? 16:45-18:00 Joachim Schummer, Methodological Pluralism, and the Merits and Limits of Quantum Mechanics in Chemistry 19:30 Conference dinner Friday, August 1 9:30-10:45 Andrea Woody, Persistence meets Resistance: What is at stake in Reduction 11:00-12:15 Peter Mulder, Bohmian Mechanics and the Reduction of Chemistry 14:00-15:15 Eugen Schwarz, Fuzzy Constructions of Autonomous Chemistry versus Clear Definitions with Physical Background 15:30-16:45 Eric Scerri, Reduction of Chemistry in general and Reduction of the Periodic Table in particular -------------------------------------------------------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2007. named as "Outstanding Academic Book for 2007" by Choice Library Magazine. Collected Papers (by Eric Scerri) on Philosophy of Chemistry, Imperial College Press, 2008. From owner-chemistry@ccl.net Fri Jul 25 06:16:01 2008 From: "scerri{}chem.ucla.edu" To: CCL Subject: CCL: Philosophy of Chemistry (Annual Conference of ISPC) in Coburg, Germany Message-Id: <-37415-080725053141-20758-bpIXV2T4DnZqxEt+U50tGw .. server.ccl.net> X-Original-From: scerri]=[chem.ucla.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 25 Jul 2008 02:30:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: scerri-#-chem.ucla.edu International Society for the Philosophy of Chemistry Symposium 2008, Coburg, Germany, August 03.-06. Paper programme (status July 08, 2008) ---------------------------------------- Monday, August 04 09:00 – 09:30 Anke Timmermann, Philadelphia, USA Why, how, what for? Reflections on the possibility and implications of a philosophy of alchemy 09:30 – 10:00 Brigitte Van Tiggelen, Louvain-la-neuve, Belgium A chemistry without hypothesis? Maurice Delacre (1862-1938) and positivist chemistry 10:00 – 10:30 Coffee break 10:30 – 11:00 Michael Akeroyd, Bradford, United Kingdom The philosophical significance of Mendeleev´s successful predictions of the properties of gallium and scandium 11:00 – 11:30 Brigitte Van Tiggelen and Peter Thyssen, Louvain-la-neuve and Leuven, Belgium Accommodating the transition metals in the Periodic Table – Trouble with triads 11:30 – 12:00 Joost Mertens, The Hague, Netherlands Electrolysis by electro synthesis. William Robert Grove´s gas battery (1839-1845) 12:00 – 13:00 Lunch break 13:00 – 13:30 Klaus Ruthenberg, Coburg, Germany Radicals: Their way from noumenon to phaenomenon 13:30 – 14:00 Martin Labarca and Olimpia Lombardi, Buenos Aires, Argentina Why orbitals cannot be observed? 14:00 – 14:30 Mark Leach, Salford, United Kingdom Basic substance, simple substance: An exploration 14:30 – 15:00 Coffee break 15:00 – 15:30 José Antonio Chamizo, Mexico City, Mexico Toulmin´s argumentation diagrams in philosophy of chemistry teaching 15:00 – 16:00 Discussion on philosophy of chemistry in education Tuesday, August 05 09:00 – 09:30 Rom Harré, Oxford and Washington, UK/USA Causality in chemistry 09:30 – 10:00 Eugen Schwarz, Siegen, Germany On relations between chemistry and physics 10:00 – 10:30 Olimpia Lombardi and Mario Castagnino, Buenos Aires, Argentina Matters are not so clear on the physical side 10:30 – 13:00 Excursion 13:00 – 13:30 Paul Needham, Stockholm, Sweden A mereological interpretation of the phase rule 13.30 – 14:00 Eric Scerri, Los Angeles, USA On chemical natural kinds 14:00 – 14:30 Jaap van Brakel, Leuven, Belgium Anomalous anomalous monism: the many sides of chemistry 14:30 – 15:00 Coffee break 15:00 – 15:30 Robin Hendry, Durham, United Kingdom Entropy and chemical substance 15:30 – 16:00 Bahareh Honarparvar, Majid Monajjemi, and F. Mollaamin, Tehran, Iran Conceptual investigation of life and behavior in the viewpoint of entropy Wednesday, August 06 09:00 – 09:30 P. Müürsepp, Talinn, Estonia Chemistry as a physics-like science 09:30 – 10:00 Rein Vihalemm, Tartu, Estonia The autonomy of chemistry: Old and new problems 10:00 – 10:30 Coffee break 10:30 – 11:00 Jürgen Lenz, Austria The emergent properties of matter versus the reduction of chemistry to physics 11:00 – 11:30 Majid Monajjemi, Bahareh Honarparvar, and F. Mollaamin, Tehran, Iran Normal mode analysis and harmonic molecular resonance in the viewpoint of music 11:30 – 12:00 Jens Soentgen, Augsburg, Germany From Pliny's spiritus letalis to climate killer: The history of CO2 ---------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2007. named as "Outstanding Academic Book for 2007" by Choice Library Magazine. Collected Papers (by Eric Scerri) on Philosophy of Chemistry, Imperial College Press, 2008. From owner-chemistry@ccl.net Fri Jul 25 06:42:00 2008 From: "Anatoli Korkin a_korkin*o*yahoo.com" To: CCL Subject: CCL: calculation of the charge transfer complexes Message-Id: <-37416-080725055138-3695-lugRv80TyoU0bQf4CcEi8g:_:server.ccl.net> X-Original-From: "Anatoli Korkin" Date: Fri, 25 Jul 2008 05:51:34 -0400 Sent to CCL by: "Anatoli Korkin" [a_korkin||yahoo.com] Dear CCLers, I would appreciate your advice on selection of the method for calculation of the charge transfer complexes in excited states. I'd like to compute the chemically bound D-A systems with internal charge transfer. Obviously if the LUMO of A(cceptor) is lower the one of D(onor) than D*-A would have a higher energy than D(+)-A(-) and the lowest triplet state should have one electron transfered from HOMO of D to the LUMO of A. I am sure this is an old problem and someone has discussed the technique for getting accurate calculations of such systems. Your advice/references will be highly appreciates. Thanks a lot in advance! Anatoli Korkin From owner-chemistry@ccl.net Fri Jul 25 10:18:00 2008 From: "Anastassia Alexandrova anastassia.alexandrova###yale.edu" To: CCL Subject: CCL: calculation of the charge transfer complexes Message-Id: <-37417-080725085200-5862-bpIXV2T4DnZqxEt+U50tGw,,server.ccl.net> X-Original-From: Anastassia Alexandrova Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Fri, 25 Jul 2008 08:10:19 -0400 MIME-Version: 1.0 Sent to CCL by: Anastassia Alexandrova [anastassia.alexandrova]*[yale.edu] Anatolii, greetings! Ironically, I am also working on charge-transfer excited states right now. One thing I know for sure (though you probably know it too) is that DFT is bad for such problems. The more correlation - the better, obviously; however, if the system is large, constrained DFT may be the best choice. C-DFT is implemented in NWChem by Troy van Voorhis. Best, Anastassia --------------------------------------- Anastassia Alexandrova, Ph.D. Yale University Department of Chemistry 225 Prospect Street New Haven, CT 06520-8107 Phone: 203-432-6288 Fax: 203-432-6068 anastassia.alexandrova#yale.edu http://zarbi.chem.yale.edu/~anastassia/ --------------------------------------- Go one more mile... Quoting "Anatoli Korkin a_korkin*o*yahoo.com" : > > Sent to CCL by: "Anatoli Korkin" [a_korkin||yahoo.com] > Dear CCLers, > > I would appreciate your advice on selection of the method for > calculation of the charge transfer complexes in excited states. I'd > like to compute the chemically bound D-A systems with internal charge > transfer. Obviously if the LUMO of A(cceptor) is lower the one of > D(onor) than D*-A would have a higher energy than D(+)-A(-) and the > lowest triplet state should have one electron transfered from HOMO of > D to the LUMO of A. I am sure this is an old problem and someone has > discussed the technique for getting accurate calculations of such > systems. > > Your advice/references will be highly appreciates. > > Thanks a lot in advance! > > Anatoli Korkin> > From owner-chemistry@ccl.net Fri Jul 25 13:05:00 2008 From: "Pradipta Bandyopadhyay pradipta_b(-)mail.jnu.ac.in" To: CCL Subject: CCL: Ramachandran plot from torsion angles ! Message-Id: <-37418-080724214346-14473-V3d4n1TmY2r55b/z+h+w1g{=}server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=US-ASCII Date: Fri, 25 Jul 2008 07:14:36 +0530 Mime-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta_b-$-mail.jnu.ac.in] Hello, I have calculated the phi and psi torsion angles for my proteins. Can = someone tell me what is the best software to make the Ramachandran plot = > from those values? I have seen many softwares make nice ramachandran plot = > from the PDB file - but I want that from the torsion angles. thanks, Pradipta From owner-chemistry@ccl.net Fri Jul 25 16:40:00 2008 From: "Andrew Francis DeBlase andrew.deblase1*o*marist.edu" To: CCL Subject: CCL:G: How to increase max iterations in a Gaussian 03 IPCM calculation Message-Id: <-37419-080725162942-8916-soKY9vKel0mcYy0+6Wh7Hw a server.ccl.net> X-Original-From: "Andrew Francis DeBlase" Date: Fri, 25 Jul 2008 16:29:38 -0400 Sent to CCL by: "Andrew Francis DeBlase" [andrew.deblase1^^marist.edu] Hello, I am an undergraduate research student who is attempting IPCM calculations to account for solvent effects in cationic pi dimers of thiophene oligomers. My calculations are failing because the maximum number of iterations is exceeded in the SCRF calculation. I've noticed that the job fails after a default of 200 cycles and I was wondering if this number could be increased. After consulting the Gaussian manual, it decided to change the solvent specifications as follows: SCRF(IPCM,Solvent=DiChloroMethane,MXITER=500) I don't understand why I am getting a syntax error and the MXITER keyword is not recognized. I would appreciate any advice on how to increase the max cycles in this calculation. Thanks. From owner-chemistry@ccl.net Fri Jul 25 17:28:00 2008 From: "Wayne Steinmetz WES04747!=!pomona.edu" To: CCL Subject: CCL: Ramachandran plot from torsion angles ! Message-Id: <-37420-080725165738-31355-iSDXAwG9+Y3dcfOOjtc64Q .. server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 25 Jul 2008 13:24:56 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747^-^pomona.edu] Since you have the phi and psi angles, why not use a standard package such as Excel? Wayne E. Steinmetz Professor Emeritus of Chemistry USFS Volunteer Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz[-]pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- > From: owner-chemistry[-]ccl.net [mailto:owner-chemistry[-]ccl.net]=20 Sent: Thursday, July 24, 2008 6:45 PM To: Wayne Steinmetz Subject: CCL: Ramachandran plot from torsion angles ! Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta_b-$-mail.jnu.ac.in] Hello, I have calculated the phi and psi torsion angles for my proteins. Can someone tell me what is the best software to make the Ramachandran plot > from those values? I have seen many softwares make nice ramachandran plot > from the PDB file - but I want that from the torsion angles. thanks, Pradipta -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D From owner-chemistry@ccl.net Fri Jul 25 21:07:01 2008 From: "Jan Labanowski janl[*]speakeasy.net" To: CCL Subject: CCL: Congratulations to CCG Excellence Award Winners Message-Id: <-37421-080725210425-30214-4QDIMzy0U5mzk0ei7W94hQ_._server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 25 Jul 2008 21:04:12 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl/./speakeasy.net] 2008 Press Release Chemical Computing Group Announces Winners of the CCG Excellence Award for the Fall 2008 ACS National Meeting=20 MONTREAL, Canada, July 21, 2008 =E2=80=93 Chemical Computing Group (CCG) an= d the American Chemical Society's (ACS) Division of Computers in Chemistry (COMP) congratulate the winners of the CCG Excellence Awards for the Fall 2008 ACS National Meeting in Philadelphia.=20 CCG will recognize the following winners' works at the award presentation ceremony during the COMP Division Poster Session on Tuesday August 19, 2008. Each winner will receive $1,150 US for travel costs to Philadelphia, as well as a one-year license for the newest version of the Molecular Operating Environment (MOE).=20 The winners are:=20 Satyender Goel, University of Central Florida Pairwise spin-contamination correction and application to 3-D transition metal hydrides from BS-DFT Lucius E. Johnson, University of Louisville Mechanism of electronic stabilization of cyclopropenylidene=20 byamino-substitution In Suk Joung, University of Utah Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations Laveena Muley, University at Buffalo Binding affinity awarded for hydrophobic bonding in scoring functions needs to be context dependent Somisetti V Sambasivarao, Auburn University Systematic development of OPLS-AA force field parameters for ionic liquid simulations About CCG Excellence Award=20 The CCG Excellence Award is granted semi-annually as an opportunity to invest in the future of scientific research and to encourage a new generation of computational chemists. Awardees are selected on the quality and significance of the research to be presented, as well as the strength of the supporting letter and supplemental materials. For more information on the CCG Excellence Awards and eligibility criteria, visit http://www.chemcomp.com/ssupport-academic.htm .=20 Chemical Computing Group Inc. (http://www.chemcomp.com) is a leading suppli= er of scientific software for Life Sciences, headquartered in Montreal, Canada. Chemical Computing Group's software platform is the Molecular Operating Environment (MOE) that integrates visualization, simulation and methodology development in one package. MOE contains a wide variety of built-in applications in the fields of Cheminformatics, Bioinformatics, Computer-Aided Molecular Design and Molecular Modeling. MOE runs on a wide variety of computers including Windows, Linux, Macintosh and Unix systems both for the desktop and in parallel computing clusters. MOE is used by biologists, medicinal chemists and computational chemists in many pharmaceutical companies, biotechnology companies and universities throughout the world.=20 E-mail enquiries can be sent to info]-[chemcomp.com .