From owner-chemistry@ccl.net Tue Sep 9 05:29:00 2008 From: "Uwe Huniar uwe.huniar-#-cosmologic.de" To: CCL Subject: CCL: Excited state calculation Message-Id: <-37726-080909052418-6974-ncoiXkERCR5O6/h1qg88VQ%x%server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 09 Sep 2008 10:47:26 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar/./cosmologic.de] Hello, it depends very much on the accuracy you would like to get. Semi-empirical methods like ZINDO/S can treat very large systems, but since I am not a ZINDO expert, I can not give any comments about the accuracy you can achieve. TDDFT is often the method of choice for the combination of larger systems and reasonable accuracy (or perhaps better: with well-known problems for charge-transfer excitations). Turbomole has a very fast TDDFT part which also includes analytical gradients of excited states and numerical 2nd derivatives at TDDFT level. Together with the RI method (or density fitting or however you like to call it) systems with several thousand basis functions are treatable. I do not have recent benchmarks, but here is an older one (Computational Photochemistry, edited by M. Olivucci, vol. 16 of Theoretical and Computational Chemistry, Elsevier, Amsterdam, 2005, pp. 93–128): C540, 8100 basis functions, SVP basis set, Ih symmetry, a CD spectrum with three excited states took 19 hours on an ancient 440MHz HP workstation. A higher accuracy (on average, but not in every case) can be achieved with coupled cluster methods. There are several ones, but for larger systems you might consider CC2. RI-CC2 is available in Turbomole and (to my knowledge) currently the fastest CC2 implementation available. I know from a talk of Christof Hättig that a full UV/Vis spectrum of Chlorophyll with about 100 atoms and 1000 basis functions (cc-pVDZ) has been calculated. Martin Schütz has published a local RI-CC2 paper (J. Chem. Phys. 2006, 125, 104106) where systems of comparable size have been calculated - but I do not know if that is available routinely within Molpro meanwhile (I guess so). And there are of course plenty of other methods for excited states which can also be used.... Regards, Uwe > Can any one tell me which is the largest molecule for which the excited state is calculated and the method and basis set used for that ? > Thanking you, > Ramachadran From owner-chemistry@ccl.net Tue Sep 9 09:20:01 2008 From: "Craig Lucas craig.lucas-#-nag.co.uk" To: CCL Subject: CCL: HPC Training available for UK Researchers Message-Id: <-37727-080909083049-24842-ULOBJtRtTCXmwBGFO6yQRQ]-[server.ccl.net> X-Original-From: "Craig Lucas" Date: Tue, 9 Sep 2008 08:30:45 -0400 Sent to CCL by: "Craig Lucas" [craig.lucas[#]nag.co.uk] NAG is pleased to announce that we are running free High Performance Computing (HPC) training for UK researchers. NAG provides Computational Science and Engineering (CSE) support for HECToR, the UK Supercomputing Service. You are eligible for training, for which there is no charge, if you are a HECToR user or your work is covered by the remit of either EPSRC, BBSRC or NERC. We provide a regular schedule of courses that cover general HPC topics, such as MPI and OpenMP, as well material specific to HECToR. We can also provide training tailored to your specific requirements and deliver courses at your institution. For further information and our current training schedule and locations please see: http://www.hector.ac.uk/support/cse/schedule/ A full list of available courses and contact details are here: http://www.hector.ac.uk/support/cse/schedule/courselist For more information about NAG, HECToR and the CSE service please see the following links: http://www.nag.co.uk http://www.hector.ac.uk/ http://www.hector.ac.uk/support/cse/ The NAG CSE Team From owner-chemistry@ccl.net Tue Sep 9 11:47:01 2008 From: "mi yang miyang3790.:.gmail.com" To: CCL Subject: CCL: COSMORS optimization Message-Id: <-37728-080909104214-1887-PJAWtyAU9It1tkWpbfaBHA-#-server.ccl.net> X-Original-From: "mi yang" Date: Tue, 9 Sep 2008 10:42:10 -0400 Sent to CCL by: "mi yang" [miyang3790,gmail.com] Hi CCL users I am trying to optimize a fluoride ion complex using B3LYP/6-31G* within COSMORS solvent effects. But the job auto end after giving free energy and do not continue Optimization with out giving any error. How I can optimize such complex in COSMORS..?if any body can help I will be highly thankful Sample of output End part is here ******************************* QIter: Polarization charges converged after 46 iterations. QIter: iQ= 1 Qconv= 0.10000D-08 Erms= 0.15013D-09 Emax= 0.81243D-09 Error on nuclear polarization charges = 0.03795 Error on electronic polarization charges = -0.06614 SCF Done: E(RB+HF-LYP) = -1412.56728334 A.U. after 6 cycles Convg = 0.6872D-08 -V/T = 2.0074 S**2 = 0.0000 KE= 1.402218561123D+03 PE=-6.800504847581D+03 EE= 2.250829574564D+03 -------------------------------------------------------------------- Variational C-PCM results ========================= (a.u.) = -1412.467999 (a.u.) = -1412.567283 Total free energy in solution: with all non electrostatic terms (a.u.) = -1412.541683 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -62.30 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 35.69 Dispersion energy (kcal/mol) = -21.11 Repulsion energy (kcal/mol) = 1.48 Total non electrostatic (kcal/mol) = 16.06 -------------------------------------------------------------------- Partition over spheres: Sphere on Atom Surface Charge GEl GCav GDR 1 C1 13.87 -0.002 -0.03 1.38 -0.79 2 C2 12.71 0.013 -0.50 1.27 -0.63 3 C3 6.88 0.002 -0.09 0.69 -0.38 4 C4 12.07 0.011 -0.40 1.20 -0.67 5 C5 5.83 -0.001 0.00 0.58 -0.28 6 C6 5.87 0.001 -0.07 0.58 -0.28 7 C7 9.74 -0.026 0.55 0.97 -0.53 8 C8 9.68 -0.028 0.64 0.96 -0.51 9 O9 19.39 0.222 -8.18 2.08 -1.21 10 O10 19.64 0.225 -8.87 2.10 -1.22 11 N11 2.53 -0.001 0.01 0.26 -0.05 12 C12 18.77 -0.034 0.53 1.87 -0.97 13 H13 5.56 -0.033 0.52 0.70 -0.37 14 H14 6.48 -0.038 0.52 0.81 -0.56 15 H15 6.48 -0.038 0.51 0.81 -0.56 16 N16 6.14 0.000 0.01 0.64 -0.23 17 H17 1.04 -0.013 0.54 0.13 0.00 18 C18 9.14 -0.010 0.33 0.91 -0.54 19 O19 14.92 0.189 -8.50 1.60 -0.93 20 C20 5.84 0.014 -0.51 0.58 -0.27 21 C21 12.48 0.030 -1.07 1.24 -0.70 22 C22 14.00 0.024 -0.79 1.40 -0.75 23 C23 14.05 0.019 -0.68 1.40 -0.74 24 C24 13.92 0.026 -0.93 1.39 -0.75 25 C25 12.59 0.023 -0.90 1.26 -0.51 26 H26 5.41 -0.026 0.63 0.68 -0.42 27 H27 6.39 -0.038 0.48 0.80 -0.60 28 H28 6.39 -0.039 0.47 0.80 -0.60 29 H29 6.38 -0.037 0.86 0.80 -0.57 30 H30 1.17 0.000 0.01 0.15 0.00 31 H31 4.07 -0.022 0.77 0.51 -0.12 32 H32 6.37 -0.047 1.11 0.80 -0.57 33 H33 2.52 -0.007 0.30 0.32 -0.02 34 Cl34 40.70 0.641 -39.59 4.01 -2.29 -------------------------------------------------------------------- After PCM corrections, the SCF energy is -1412.56728334 a.u. -------------------------------------------------------------------- MiYang Miyang3790 P.R.China From owner-chemistry@ccl.net Tue Sep 9 12:36:01 2008 From: "Barry Hardy barry.hardy|-|vtxmail.ch" To: CCL Subject: CCL: eCheminfo Hyderabad Drug Discovery Workshop & Conference Message-Id: <-37729-080909123322-17740-OxsH9j4H2lwWjHfGhppXfA(0)server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 09 Sep 2008 18:33:04 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy]*[vtxmail.ch] I am pleased to announce that for the first time we will be holding the eCheminfo Hands-on Drug Discovery Design Workshop in India. The workshop will take place at IIIT, Hyderabad 15 - 18 December 2008, and will be followed by an international 2 day symposium. The workshop will be case-study and pharma best practices driven and will cover a variety of core drug discovery informatics and modelling topics including virtual screening, pharmacophore modelling, docking, molecular dynamics of ligand-target complexes, fragment-based design, predictive ADME, predictive toxicology and synthesis design. The workshop leaders are Johann Gasteiger (Molecular Networks), Jeff Wiseman (Locus Pharmaceuticals), Indira Ghosh (JNU, New Delhi), Paul Hawkins (OpenEye), Barry Hardy (Douglas Connect), Peter Oledzki (BioSolveIT), Dhananjay Bhattacharyya (Saha Institute of Nuclear Physics), Ismael Zamora (Pompeu Fabra University and Lead Molecular Design), Madhavi Sastry (Schrodinger),and Wojciech Plonka (Fujitsu Group). The Workshop group will study problems with hands-on examples using numerous leading software packages in a PC-based classroom and will discuss complex issues highlighted by examples and case studies presented by instructors. The symposium will run 19-20 December and will cover the topics of Neglected Diseases, Biophysical Simulations, Drug Discovery Informatics, and Predictive ADME and Toxicology. Invited speakers include: Chandra Verma (Bioinformatics Institute A*STAR, Singapore), Sreedhar Rao (Ranbaxy), Chandrika B-Rao (Piramal Life Sciences), Vellarkad N. Viswanadhan (Jubilant Biosys), R. Narayanan (TCS), Johann Gasteiger (Molecular Networks), Jeff Wiseman (Locus Pharmaceuticals), Indira Ghosh (JNU, New Delhi), Barry Hardy (Douglas Connect), Dhananjay Bhattacharyya (Saha Institute of Nuclear Physics), Ismael Zamora (Pompeu Fabra University and Lead Molecular Design), B. Gopalakrishnan (TCS, IIITH), Abhijit Mitra (IIITH), Avadhesha Surolia (National Institute of Immunology), Achintya Das (Strand Genomics), Pramod Wangikar (IIT Bombay), Mingyue Zheng (Shanghai Institute of Materia Medica) Bursary Award A Bursary Award will be used to help support the attendance of a selection of academic participants, who may be working in any area of research related to drug discovery. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com by 19 September 2008. The recipients of the award will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on their research progress and will be notified by 30 September 2008. CFP We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome. Abstracts (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 19 September 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 30 September 2008. For international registrations, please contact Nicki Douglas, nicki.douglas -[at]- douglasconnect.com, Tel: +41 61 851 0461. If you are located in India, please contact Sunil Chawla at: sunil -[at]- seascapelearning.com, Tel: +91 981 0305 923 or Om Prakash at Tel: +91 971 7040 656. For more information on the program, please visit: http://echeminfo.com/comty_hyderabadworkshop08 or http://seascapelearning.com/echeminfo_reg.html or download the eCheminfo Hyderabad Program as a pdf: http://barryhardy.blogs.com/cheminfostream/files/eChemBrochure-HYD812-v2.pdf best regards Barry Hardy eCheminfo Community of Practice & Research Douglas Connect, Switzerland From owner-chemistry@ccl.net Tue Sep 9 14:01:01 2008 From: "Andreas Klamt klamt[]cosmologic.de" To: CCL Subject: CCL:G: COSMORS optimization (Note: COSMORS keyword does not do COSMO-RS in G03!!!) Message-Id: <-37730-080909134907-27023-uOWDocxg9r0n7dZFHIIIsw*_*server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 09 Sep 2008 19:09:13 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt,,cosmologic.de] Hi Mi Yang, dear Gaussian users, while I (Author of COSMO and COSMO-RS) do not know the details why your job in Gaussian failed, since I did not do the technical implementation of COSMO (C-PCM) in Gaussian, I like to use the occasion to emphazise again, that the keyword "COSMO-RS" in older version of Gaussian03 (Due to a lonely decision of Mike Frisch it does no longer exist in the latest sub-releases) does not trigger COSMO-RS calculations, but it triggers C-PCM calculations with settings which produce a COSMO file suitable for COSMO-RS postprocessing! COSMO-RS is a thermodynamic post-processing based on COSMO files for solutes and solvents!!! Gaussian does not have such functionality! For more details about COSMO-RS see either my publications, my book (Elsevier, 2005) or our website www.cosmologic.de. It is frustrating to receive again and again papers (manuscrips with the word COSMO-RS have an affinity to end up on my desk for review) either for review or as final papers which claim to have done COSMO-RS while they only did C-PCM with COSMO-RS settings. Authors, please do not call such calculations COSMO-RS calculations! Reviewers, please do not let such phrasing pass through a review! COSMO-RS is much more than just COSMO or C-PCM, and we need to keep this difference clear in literature. Best regards Andreas mi yang miyang3790.:.gmail.com schrieb: > Sent to CCL by: "mi yang" [miyang3790,gmail.com] > Hi CCL users > > I am trying to optimize a fluoride ion complex using B3LYP/6-31G* within COSMORS solvent effects. But the job auto end after giving free energy and do not continue Optimization with out giving any error. How I can optimize such complex in COSMORS..?if any body can help I will be highly thankful > > Sample of output End part is here > ******************************* > QIter: Polarization charges converged after 46 iterations. > QIter: iQ= 1 Qconv= 0.10000D-08 Erms= 0.15013D-09 Emax= 0.81243D-09 > Error on nuclear polarization charges = 0.03795 > Error on electronic polarization charges = -0.06614 > SCF Done: E(RB+HF-LYP) = -1412.56728334 A.U. after 6 cycles > Convg = 0.6872D-08 -V/T = 2.0074 > S**2 = 0.0000 > KE= 1.402218561123D+03 PE=-6.800504847581D+03 EE= 2.250829574564D+03 > -------------------------------------------------------------------- > Variational C-PCM results > ========================= > (a.u.) = -1412.467999 > (a.u.) = -1412.567283 > Total free energy in solution: > with all non electrostatic terms (a.u.) = -1412.541683 > -------------------------------------------------------------------- > (Polarized solute)-Solvent (kcal/mol) = -62.30 > -------------------------------------------------------------------- > Cavitation energy (kcal/mol) = 35.69 > Dispersion energy (kcal/mol) = -21.11 > Repulsion energy (kcal/mol) = 1.48 > Total non electrostatic (kcal/mol) = 16.06 > -------------------------------------------------------------------- > Partition over spheres: > Sphere on Atom Surface Charge GEl GCav GDR > 1 C1 13.87 -0.002 -0.03 1.38 -0.79 > 2 C2 12.71 0.013 -0.50 1.27 -0.63 > 3 C3 6.88 0.002 -0.09 0.69 -0.38 > 4 C4 12.07 0.011 -0.40 1.20 -0.67 > 5 C5 5.83 -0.001 0.00 0.58 -0.28 > 6 C6 5.87 0.001 -0.07 0.58 -0.28 > 7 C7 9.74 -0.026 0.55 0.97 -0.53 > 8 C8 9.68 -0.028 0.64 0.96 -0.51 > 9 O9 19.39 0.222 -8.18 2.08 -1.21 > 10 O10 19.64 0.225 -8.87 2.10 -1.22 > 11 N11 2.53 -0.001 0.01 0.26 -0.05 > 12 C12 18.77 -0.034 0.53 1.87 -0.97 > 13 H13 5.56 -0.033 0.52 0.70 -0.37 > 14 H14 6.48 -0.038 0.52 0.81 -0.56 > 15 H15 6.48 -0.038 0.51 0.81 -0.56 > 16 N16 6.14 0.000 0.01 0.64 -0.23 > 17 H17 1.04 -0.013 0.54 0.13 0.00 > 18 C18 9.14 -0.010 0.33 0.91 -0.54 > 19 O19 14.92 0.189 -8.50 1.60 -0.93 > 20 C20 5.84 0.014 -0.51 0.58 -0.27 > 21 C21 12.48 0.030 -1.07 1.24 -0.70 > 22 C22 14.00 0.024 -0.79 1.40 -0.75 > 23 C23 14.05 0.019 -0.68 1.40 -0.74 > 24 C24 13.92 0.026 -0.93 1.39 -0.75 > 25 C25 12.59 0.023 -0.90 1.26 -0.51 > 26 H26 5.41 -0.026 0.63 0.68 -0.42 > 27 H27 6.39 -0.038 0.48 0.80 -0.60 > 28 H28 6.39 -0.039 0.47 0.80 -0.60 > 29 H29 6.38 -0.037 0.86 0.80 -0.57 > 30 H30 1.17 0.000 0.01 0.15 0.00 > 31 H31 4.07 -0.022 0.77 0.51 -0.12 > 32 H32 6.37 -0.047 1.11 0.80 -0.57 > 33 H33 2.52 -0.007 0.30 0.32 -0.02 > 34 Cl34 40.70 0.641 -39.59 4.01 -2.29 > -------------------------------------------------------------------- > After PCM corrections, the SCF energy is -1412.56728334 a.u. > -------------------------------------------------------------------- > > > > > > > > > > > > > > MiYang > Miyang3790 > P.R.China> > > > > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt.:.cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- Please note our COSMO-RS Symposium in 2009 (For details see: http://www.cosmologic.de/Symposium/symposium.html) From owner-chemistry@ccl.net Tue Sep 9 14:36:00 2008 From: "akef afaneh akef_afnh()yahoo.com" To: CCL Subject: CCL: COSMORS optimization Message-Id: <-37731-080909135241-28646-2hQZ+RF71l3bthYGcDRFJA-#-server.ccl.net> X-Original-From: akef afaneh Content-Type: text/plain; charset=us-ascii Date: Tue, 9 Sep 2008 09:52:31 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh|,|yahoo.com] You can not use COSMORS with optimization. Winnipeg, Manitoba, Canada. --- On Tue, 9/9/08, mi yang miyang3790.:.gmail.com wrote: > From: mi yang miyang3790.:.gmail.com > Subject: CCL: COSMORS optimization > To: "Afaneh, Akef Taha " > Date: Tuesday, September 9, 2008, 10:42 AM > Sent to CCL by: "mi yang" [miyang3790,gmail.com] > Hi CCL users > > I am trying to optimize a fluoride ion complex using > B3LYP/6-31G* within COSMORS solvent effects. But the job > auto end after giving free energy and do not continue > Optimization with out giving any error. How I can optimize > such complex in COSMORS..?if any body can help I will be > highly thankful > > Sample of output End part is here > ******************************* > QIter: Polarization charges converged after 46 iterations. > QIter: iQ= 1 Qconv= 0.10000D-08 Erms= 0.15013D-09 > Emax= 0.81243D-09 > Error on nuclear polarization charges = 0.03795 > Error on electronic polarization charges = -0.06614 > SCF Done: E(RB+HF-LYP) = -1412.56728334 A.U. after > 6 cycles > Convg = 0.6872D-08 -V/T = > 2.0074 > S**2 = 0.0000 > KE= 1.402218561123D+03 PE=-6.800504847581D+03 EE= > 2.250829574564D+03 > > -------------------------------------------------------------------- > Variational C-PCM results > ========================= > (a.u.) > = -1412.467999 > (a.u.) > = -1412.567283 > Total free energy in solution: > with all non electrostatic terms (a.u.) = > -1412.541683 > > -------------------------------------------------------------------- > (Polarized solute)-Solvent (kcal/mol) = > -62.30 > > -------------------------------------------------------------------- > Cavitation energy (kcal/mol) = > 35.69 > Dispersion energy (kcal/mol) = > -21.11 > Repulsion energy (kcal/mol) = > 1.48 > Total non electrostatic (kcal/mol) = > 16.06 > > -------------------------------------------------------------------- > Partition over spheres: > Sphere on Atom Surface Charge GEl GCav GDR > 1 C1 13.87 -0.002 -0.03 1.38 -0.79 > 2 C2 12.71 0.013 -0.50 1.27 -0.63 > 3 C3 6.88 0.002 -0.09 0.69 -0.38 > 4 C4 12.07 0.011 -0.40 1.20 -0.67 > 5 C5 5.83 -0.001 0.00 0.58 -0.28 > 6 C6 5.87 0.001 -0.07 0.58 -0.28 > 7 C7 9.74 -0.026 0.55 0.97 -0.53 > 8 C8 9.68 -0.028 0.64 0.96 -0.51 > 9 O9 19.39 0.222 -8.18 2.08 -1.21 > 10 O10 19.64 0.225 -8.87 2.10 -1.22 > 11 N11 2.53 -0.001 0.01 0.26 -0.05 > 12 C12 18.77 -0.034 0.53 1.87 -0.97 > 13 H13 5.56 -0.033 0.52 0.70 -0.37 > 14 H14 6.48 -0.038 0.52 0.81 -0.56 > 15 H15 6.48 -0.038 0.51 0.81 -0.56 > 16 N16 6.14 0.000 0.01 0.64 -0.23 > 17 H17 1.04 -0.013 0.54 0.13 0.00 > 18 C18 9.14 -0.010 0.33 0.91 -0.54 > 19 O19 14.92 0.189 -8.50 1.60 -0.93 > 20 C20 5.84 0.014 -0.51 0.58 -0.27 > 21 C21 12.48 0.030 -1.07 1.24 -0.70 > 22 C22 14.00 0.024 -0.79 1.40 -0.75 > 23 C23 14.05 0.019 -0.68 1.40 -0.74 > 24 C24 13.92 0.026 -0.93 1.39 -0.75 > 25 C25 12.59 0.023 -0.90 1.26 -0.51 > 26 H26 5.41 -0.026 0.63 0.68 -0.42 > 27 H27 6.39 -0.038 0.48 0.80 -0.60 > 28 H28 6.39 -0.039 0.47 0.80 -0.60 > 29 H29 6.38 -0.037 0.86 0.80 -0.57 > 30 H30 1.17 0.000 0.01 0.15 0.00 > 31 H31 4.07 -0.022 0.77 0.51 -0.12 > 32 H32 6.37 -0.047 1.11 0.80 -0.57 > 33 H33 2.52 -0.007 0.30 0.32 -0.02 > 34 Cl34 40.70 0.641 -39.59 4.01 -2.29 > > -------------------------------------------------------------------- > After PCM corrections, the SCF energy is -1412.56728334 > a.u. > > -------------------------------------------------------------------- > > > > > > > > > > > > > > MiYang > Miyang3790 > P.R.China > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the || sign. You > can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search) From owner-chemistry@ccl.net Tue Sep 9 15:16:01 2008 From: "Guenter Grethe ggrethe^^^comcast.net" To: CCL Subject: CCL: 2009 CSA Trust Jacques-Emile Dubois Grants Message-Id: <-37732-080909143111-13317-6osOIYks6qFdJ0ALuMpjXQ-$-server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 9 Sep 2008 14:31:07 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe]|[comcast.net] Applications Invited for CSA Trust Jacques-mile Dubois Grants for 2009 The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. In support of its charter, the Trust has created a unique Grant Program, renamed in honor of Professor Jacques-mile Dubois who made significant contributions to the field of cheminformatics. The Trust is currently inviting the submission of grant applications for 2009. Purpose of the Grants: The Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. A Grant will be awarded annually up to a maximum of three thousand U.S. dollars ($3,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Who is Eligible? Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria. What Activities are Eligible? Grants may be awarded to acquire the tools necessary to support research activities, or for travel to collaborate with research groups, to attend a conference relevant to ones area of research, to gain access to special computational facilities, or to acquire unique research techniques in support of ones research. Application Requirements: Applications must include the following documentation: 1. A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant; 2. The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trusts objectives and the clarity of this statement are essential in the evaluation of the application); 3. A brief biographical sketch, including a statement of academic qualifications; 4. Two reference letters in support of the application. Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-4. Three copies of the complete application document must be supplied for distribution to the Grants Committee. Deadline for Applications: Applications must be received no later than October 24, 2008. Successful applicants will be notified by December 19, 2008. Address for Submission of Applications: Four copies of the application documentation should be forwarded to: Bonnie Lawlor, CSA Trust Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your application by e-mail, please contact Bonnie Lawlor at blawlor{:}nfais.org prior to submission. From owner-chemistry@ccl.net Tue Sep 9 16:23:00 2008 From: "Ghislain Deslongchamps ghislain*UNB.ca" To: CCL Subject: CCL: 2-methyl-tetrahydropyran Message-Id: <-37733-080909154721-20415-K40iFuXtNDW4kFKUxe5wmg_+_server.ccl.net> X-Original-From: Ghislain Deslongchamps Content-Type: multipart/alternative; boundary=Apple-Mail-7-9377336 Date: Tue, 9 Sep 2008 14:43:49 -0300 Mime-Version: 1.0 (Apple Message framework v926) Sent to CCL by: Ghislain Deslongchamps [ghislain-,-UNB.ca] --Apple-Mail-7-9377336 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Hi all, We have encountered very strange results for AM1 calculations on the 2 chair conformers of 2-methyl-tetrahydropyran (CC1CCCCO1). While HF and MP2 give us energy differences in the 3 kcal/mol range between the axial and equatorial chair conformers (OK), the same calculations with AM1 give a 0.17 kcal/mol difference!!! The same result is obtained whether we use MOPAC or GAMESS. This is a huge error on an extremely simple system (C6H12O, ether, no anomeric effect, etc.). Any clues on what is going on with AM1? Cheers, Ghislain ----------------------------------------------------------- Ghislain Deslongchamps, Professor Department of Chemistry University of New Brunswick Fredericton, N.B. CANADA E3B 6E2 phone: (506) 453-4795 FAX: 453-4981 e-mail: ghislain^unb.ca WWW: http://taxane.chem.unb.ca Organic Chemistry Flashware: http://flashchem.nelson.com ----------------------------------------------------------- --Apple-Mail-7-9377336 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Hi all,

We = have encountered very strange results for AM1 calculations on the 2 = chair conformers of 2-methyl-tetrahydropyran = (CC1CCCCO1). While HF and MP2 give us energy differences in = the 3 kcal/mol range between the axial and equatorial chair = conformers (OK), the same calculations with AM1 give a 0.17 kcal/mol = difference!!! The same result is obtained whether we use MOPAC or = GAMESS.
This is a huge error on an extremely simple system = (C6H12O, ether, no anomeric effect, etc.). Any clues on what is going on = with AM1?

=

Cheers,


Ghislain


 Ghislain Deslongchamps, Professor
 Department of Chemistry
 University of New Brunswick
 Fredericton, = N.B.  CANADA  E3B 6E2
 e-mail: = ghislain^unb.ca   WWW:  http://taxane.chem.unb.ca
 Organic Chemistry Flashware:  http://flashchem.nelson.com
=


=

= --Apple-Mail-7-9377336-- From owner-chemistry@ccl.net Tue Sep 9 17:21:00 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007 : yandex.ru" To: CCL Subject: CCL:G: Trying to find a transition state for H2 + N2Zr2Pd2/MgO reaction with Turbomole Message-Id: <-37734-080909171815-4561-Jfy4fiweqo+jfho+dqgbsw++server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 10 Sep 2008 00:35:25 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007++yandex.ru] Dear CCLers, I try to find a transition state for the reaction between gas-phase H2 and N2 adsorbed at Zr2Pd2 cluster which, in turn, is adsorbed at MgO surface. The whole system looks like this: H2 + N2Zr2Pd2/MgO. I use Turbomole 5.10, B3LYP-Gaussian/TZVP level of theory. MgO surface is represented using the embedded cluster approach: Mg13O13(Mg2+)32 cluster surrounded by 14x14x10 array of point charges. I used two different approaches according to 'Turbomole Tutorial', Chapter 7: 1. Running geometry optimizations using 'jobex -ri -c 500 -statpt' command; 2. Running usual geometry optimizations for different values of fixed internal (reaction) coordinate; in this case, I froze different values for the N-H distance. Below is the beginning of my 'coord' file which I used in optimization with a frozen reaction coordinate, in this case R(N-H) = 1.40 A. $coord 2.94269650799085 8.70517256995312 -6.12662777110223 h t 3.18795165995312 8.69023017323135 -4.16985475271014 h t 1.24346929104243 4.66952508859644 -6.81867974430503 n t 1.85514755869715 6.72906299183727 -7.51089310928279 n t 0.49315921621146 1.63177545661267 -3.47573169385390 zr t -2.85469966556776 6.27129664797215 -2.07024114651313 pd t 2.26448474849826 6.72860502838286 -3.33985625474087 zr t 4.81146672690398 2.59188127870774 -1.95584133840447 pd t -1.64765780569636 0.65589780882514 6.53548878831011 mg f -1.03875796590770 3.41041959498460 3.72818956137744 o f -3.94299388891248 -1.40196558549630 4.01842292360774 o f -3.33410249629819 1.35254277554554 1.21117991834791 mg f -6.23825076356201 -3.45985916469058 1.50136538497266 mg f -5.62934072925756 -0.70531234597598 -1.30586730769249 o f 1.54604576628047 -1.34823406228030 5.26170980299269 o f 2.15498555885123 1.40625771444448 2.45442258078541 mg f -0.74926538698186 -3.40611843293943 2.74471717940594 mg f -0.14038863199110 -0.65177377696937 -0.06255879804864 o f -3.04454077059504 -5.46401164965800 0.22762311320849 o f -2.43562634099820 -2.70950812581347 -2.57964196704852 mg f 4.73973774420027 -3.35242818519170 3.98799096601442 mg f 5.34865687937156 -0.59795747135922 1.18073246081783 o f 2.44438751559923 -5.41031261914728 1.47096947823921 o f 3.05334040410747 -2.65580407722876 -1.33628490392127 mg f 0.14913623454979 -7.46815206343715 -1.04611251079960 mg f 0.75810060596027 -4.71364594153782 -3.85341083254211 o f 6.24705006254592 -4.65997339231836 -2.61006583912521 o f 5.63808738999613 -7.41451452578863 0.19720443848056 mg f -6.52781052565389 3.35667156468916 2.48497024080376 o f -7.13669874129849 0.60218933878025 5.29219982320310 mg f -4.73092889673882 -4.76735305138602 -5.09671535499758 o f 4.45027941360410 3.46412001117776 4.97145718378342 o f -5.33984762642259 -7.52187762848530 -2.28945459348295 mg f 3.84133699007477 0.70963530680147 7.77878599317138 mg f 9.44074474664376 -6.66419698257034 -3.88378453590872 mg f 3.95178093634575 -6.71784350909920 -5.12715179684097 mg f -1.53721672926600 -6.77151509209041 -6.37046915690354 mg f -7.02619340471186 -6.82521071830914 -7.61379224995092 mg f -9.72151467196955 5.36080519717668 3.75873050915150 mg f -8.82306207140230 1.29879103874416 -0.03211835900539 mg f -7.92461235284285 -2.76320418409085 -3.82295975021676 mg f -4.23249713250060 5.41458640182631 5.00200551620149 mg f 1.25652345365330 5.46828869116268 6.24524183595528 mg f 6.74554437497941 5.52201956845854 7.48849475486438 mg f 7.64397813705509 1.45993060886613 3.69777275890189 mg f 8.54234682915398 -2.60213163654589 -0.09299978879251 mg f 1.83546699765317 -8.16478517605102 4.27824742115336 mg f -4.55185918267220 -4.15647967484167 6.82569557458534 mg f -3.65349968604081 -8.21851041862997 3.03486530638247 mg f 0.93711555369754 -4.10271922471481 8.06903343472943 mg f $intdef # definitions of internal coordinates 1 f 1.0000000000000 stre 1 4 val= 2.64650 $redundant number_of_atoms 50 degrees_of_freedom 144 internal_coordinates 323 frozen_coordinates 1 Values of frozen coordinates 2.64650000 # definitions of redundant internals . . . However, with both approaches my attempts to find the transition state fail: the geometry optimizations do not converge, energies acquire some wild values, and upon optimization Zr2Pd2 cluster actually starts to 'break apart'. Below, for illsutration, I provide the 'energy' file from the calculation where the above coord file was used: nergy SCF SCFKIN SCFPOT 1 -7296.068737929 6975.991689638 -14272.06042757 2 -7296.778232386 6976.046454267 -14272.82468665 3 -7296.778237618 6976.045515165 -14272.82375278 4 -7304.626661321 6964.224106579 -14268.85076790 5 -7304.570183169 6964.280791980 -14268.85097515 6 -7304.110230526 6964.637134801 -14268.74736533 7 -7303.618275641 6965.088888878 -14268.70716452 8 -7302.817785988 6965.867585718 -14268.68537171 9 -7302.040314371 6966.785363475 -14268.82567785 10 -7301.317276263 6967.845136555 -14269.16241282 11 -7300.690202190 6968.975509339 -14269.66571153 12 -7300.152165210 6970.149115120 -14270.30128033 13 -7299.663959909 6971.401397695 -14271.06535760 14 -7299.274257447 6972.587350278 -14271.86160773 15 -7298.985198441 6973.633912647 -14272.61911109 16 -7298.771595323 6974.517172646 -14273.28876797 17 -7298.587633749 6975.323610256 -14273.91124401 18 -7298.420459703 6976.082314251 -14274.50277395 19 -7298.313181904 6976.656033577 -14274.96921548 20 -7298.196361295 6977.252256625 -14275.44861792 21 -7298.090702828 6977.797583921 -14275.88828675 22 -7297.987411844 6978.338275607 -14276.32568745 23 -7297.885879378 6978.873459102 -14276.75933848 24 -7297.777313753 6979.371389488 -14277.14870324 25 -7297.655418047 6979.902718588 -14277.55813664 26 -7297.512554292 6980.456938386 -14277.96949268 27 -7297.358989750 6981.027905511 -14278.38689526 28 -7297.200292473 6981.603972026 -14278.80426450 29 -7297.043155271 6982.131841291 -14279.17499656 30 -7296.868035994 6982.688447779 -14279.55648377 31 -7296.701331935 6983.194594431 -14279.89592637 32 -7296.524166590 6983.722744185 -14280.24691078 33 -7296.360705390 6984.210813430 -14280.57151882 $end For reference: the total energy of the (H2 + N2Zr2Pd2/MgO) system is about -7300.963 A.U. at the level of theory used. With the "statpt" option I also obtained very strange energies which are even not close to this value. I apologize for such a long post, I understand that finding a transition state for a on-surface reaction using the embedded cluster approach could be a relatively trivial/simple task, but I have been dealing with this issue for quite long time, and still without any success. Could anybody please help me here? Thanks a lot in advance! Sincerely, Aleksey Kuznetsov. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets---euch4e.chem.emory.edu -------------------------------------------