From owner-chemistry@ccl.net Wed Jun 20 00:43:01 2007 From: "Chunyi Sung juneyi1*|*yahoo.com.tw" To: CCL Subject: CCL:G: Fixing distance between point charge and atoms Message-Id: <-34521-070620003905-19549-Oa3FgK2BgJramveFTF6Efw[a]server.ccl.net> X-Original-From: "Chunyi Sung" Date: Wed, 20 Jun 2007 00:39:01 -0400 Sent to CCL by: "Chunyi Sung" [juneyi1(~)yahoo.com.tw] Hi, CCLers I am trying to optimize some molecules in the presence of point charges using the keyword "charge" in Gaussian; however, in my case, some O atom in the molecule always ended up colliding with a positive point charge during geometry optimization. Therefore, I want to somehow set up some constraints on that O atom so that it will stay, say, 2.7 Angstrom away > from the positive point charge, does anyone know how to do that ? Originally, I wanted to put a ghost atom right at the location of the positive point charge, and then use "modredundant" to fix the bond length between the O atom and the ghost atom. However, with the "charge" keyword to include point charges, "Opt" must have "Z-matrix", which does not work with "modredundant". So I am now running out of ideas. I'll appreaciate if anybody has any suggestions on this. thanks chunyi From owner-chemistry@ccl.net Wed Jun 20 05:40:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas() chem.elte.hu" To: CCL Subject: CCL:G: Fixing distance between point charge and atoms Message-Id: <-34522-070620051815-15695-Ph8lMWaIPUMF4XZgN1PYMA###server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 20 Jun 2007 11:12:20 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas^^chem.elte.hu] Hi Chunyi You can try using a pure Z-matrix (it also allows the use of Cartesains) or use redundant internals with some atoms (3 or more) frozen in the Cartesian space. Unfortunately, ghost atoms are not allowed in the definition of redundant internals. Check the manual for the possible options. Good luck, Ödön On Wed, 2007-06-20 at 00:39 -0400, Chunyi Sung juneyi1*|*yahoo.com.tw wrote: > Sent to CCL by: "Chunyi Sung" [juneyi1(~)yahoo.com.tw] > Hi, CCLers > > I am trying to optimize some molecules in the presence of point charges using the keyword "charge" in Gaussian; however, in my case, some O atom in the molecule always ended up colliding with a positive point charge during geometry optimization. Therefore, I want to somehow set up some constraints on that O atom so that it will stay, say, 2.7 Angstrom away > > from the positive point charge, does anyone know how to do that ? > > Originally, I wanted to put a ghost atom right at the location of the positive point charge, and then use "modredundant" to fix the bond length between the O atom and the ghost atom. However, with the "charge" keyword to include point charges, "Opt" must have "Z-matrix", which does not work with "modredundant". So I am now running out of ideas. I'll appreaciate if > anybody has any suggestions on this. > > thanks > > chunyi> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Wed Jun 20 10:25:01 2007 From: "errol lewars elewars+/-trentu.ca" To: CCL Subject: CCL:G: Time dependent DFT calculation of 2-cyclopentenone Message-Id: <-34523-070620102158-32381-fxyu/Hyw8I7JxCpQm+1ALQ%server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Jun 2007 10:22:09 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars|trentu.ca] 2007 June 20 Try this (I did the first 2 singlets): %Mem=100000000 %rwf=a,240mw,b,240mw,c,240mw,d,240mw,e,240mw,f,240mw,g,240mw,h,-1 # B3P86/6-311++G** TD=(Singlets,NStates=2) Maxdisk=15360MB Input: AM1 geom of 2-cyclopentenone. Purpose:UV of lowest two singlets. 0 1 6 0.033991261 0.000000000 -1.325147263 6 1.308376850 0.000000000 -0.560719759 6 1.058639755 0.000000000 0.762984597 6 -0.412938403 0.000000000 1.062157565 6 -1.097109706 0.000000000 -0.310139209 1 2.275045960 0.000000000 -1.066388600 1 1.790420107 0.000000000 1.573793194 1 -0.693565147 0.904847478 1.656934151 1 -0.693565147 -0.904847478 1.656934151 1 -1.737006092 0.904959928 -0.451550862 1 -1.737006092 -0.904959928 -0.451550862 8 -0.095283505 0.000000000 -2.547306416 ------------- Refs: testing 5 funtionals and 5 basis sets K B Wiberg etal, Chem Phys Lett, 1998, 287, 60 they recomended B3P86/6-311++G** How TDDFT is implemented in Gaussian R E Stratman et al, J Chem Phys, 1998, 109, 8218, ---- A much smaller basis set gives results not too different: # B3P86/6-311++G** TD=(Singlets,NStates=2) Maxdisk=15360MB Input: AM1 geom of 2-cyclopentenone. Purpose:UV of lowest two singlets. output: Excitation energies and oscillator strengths: Excited State 1: Singlet-A" 3.6551 eV 339.20 nm f=0.0002 22 -> 23 0.68285 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A' 5.9084 eV 209.85 nm f=0.2884 21 -> 23 0.61415 --------------- # B3P86/6-31G* TD=(Singlets,NStates=2) Maxdisk=15360MB Input: AM1 geom of 2-cyclopentenone. Purpose:UV of lowest two singlets. output: Excitation energies and oscillator strengths: Excited State 1: Singlet-A" 3.6492 eV 339.76 nm f=0.0001 22 -> 23 0.68164 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A" 6.5248 eV 190.02 nm f=0.0001 22 -> 24 0.68936 = E. Lewars ==== Mohamed Z Rishard rishiz{:}hotmail.com wrote: >Sent to CCL by: "Mohamed Z Rishard" [rishiz=-=hotmail.com] >I want to do a TD-DFT calculation for the lowest excited singlet state of the above molecule. The route section is as follows: > >p TD=(nstates=4,root=1) B3LYP/6-311++G(d,p) opt freq pop=full > >However I keep getting a message stating that there is an error. Does anybody have a comment?> > > > > From owner-chemistry@ccl.net Wed Jun 20 11:14:01 2007 From: "Giorgio Maccari giorgio.maccari _ email.it" To: CCL Subject: CCL: Minimizations stopped without convergence Message-Id: <-34524-070620053608-19496-DZuXyjDIq5ZRCSkF9O66hA__server.ccl.net> X-Original-From: "Giorgio Maccari" Date: Wed, 20 Jun 2007 05:36:05 -0400 Sent to CCL by: "Giorgio Maccari" [giorgio.maccari##email.it] Hi I am Giorgio Maccari from the University of Siena (Italy). I have a problem with the minimization with macromodel. I have tried to minimize a big protein. I have setuped my job for stop after 50000 iterations and with a convergence threshold based on the gradient. Then I have started the minimization from the linux shell with the comand 'bmin'. After some iterations (less than the maximum) the minimization stop without any error message and without that the convergence treshold has been caught up. For more clarity I enclose also the com file and the last rows of the log file and the machid file. Thanks COM file: pI_txl_mini6.mae pI_txl_mini6-out.mae MMOD 0 1 0 0 0.0000 0.0000 0.0000 0.0000 FFLD 3 1 0 0 1.0000 0.0000 0.0000 0.0000 SOLV 3 1 0 0 0.0000 0.0000 0.0000 0.0000 BDCO 0 0 0 0 41.5692 99999.0000 0.0000 0.0000 READ 0 0 0 0 0.0000 0.0000 0.0000 0.0000 CONV 2 0 0 0 0.0300 0.0000 0.0000 0.0000 MINI 1 0 500000 0 0.0000 0.0000 0.0000 0.0000 last rows of the LOG file: Iter= 1830 Move(A)= 0.014655 E(kJ/mol)= -308677.2 Grad= 1.050711 Iter= 1840 Move(A)= 0.006781 E(kJ/mol)= -308679.8 Grad= 0.3149876 Iter= 1850 Move(A)= 0.006795 E(kJ/mol)= -308682.0 Grad= 0.5379291 Iter= 1860 Move(A)= 0.000557 E(kJ/mol)= -308682.3 Grad= 0.2615195 Iter= 1870 Move(A)= 0.000002 E(kJ/mol)= -308682.3 Grad= 0.2595331 Total Energy = -308675.0625 kJ/mol Stretch = 10237.7920 kJ/mol Bend = 7214.5508 kJ/mol Torsion = 57681.2422 kJ/mol Improper Torsion = 2272.0823 kJ/mol VDW = -39296.4414 kJ/mol Electrostatic = -167802.2500 kJ/mol Explicit Hydrogen Bonds = 0.0000 kJ/mol Cross Terms = 0.0000 kJ/mol Solvation = -178982.0312 kJ/mol T.E. for cross-checking: -308675.0625 kJ/mol Iterations = 1874 out of 500000 Conf 1 E =-99999.000 ( 0.260) kJ/mol Total number of structures processed = 1 BatchMin: normal termination 19-Jun-2007 20:12:14 real 161m43.825s user 152m41.667s sys 8m37.178s MACHID file: SCHRODINGER: /home/bin/schrodinger uname -a : Linux hydra.smin.unisi.it 2.4.21-4.ELsmp 1 SMP Fri Oct 3 17:52:56 EDT 2003 i686 i686 i386 GNU/Linux Machine name: hydra IP address: 172 16 83 7 Machine id: 244154412 lmutil - Copyright (c) 1989-2004 by Macrovision Corporation. All rights reserved. The FLEXlm host ID of this machine is "000d60d5beac" OS: LINUX 2.4.21-4.ELsmp Distribution: Red Hat Linux 3.2.3-20 CPU: i686 Processors: 2 perl: 5.008 glibc: 2.3.2 Product: macromodel-v86009-Linux-x86 Product: macromodel-v90016-Linux-x86 Product: macromodel-v91111-Linux-x86 Product: maestro-v65008-Linux-x86 Product: mmshare-v13007-Linux-x86 Product: mmshare-v14018-Linux-x86 Product: mmshare-v15112-Linux-x86 From owner-chemistry@ccl.net Wed Jun 20 11:49:00 2007 From: "Christian Stegmann adenozin||googlemail.com" To: CCL Subject: CCL: Announcement: 4th PhD Student Symposium Horizons in Molecular Biology Sept 12th-15th 2007 Message-Id: <-34525-070620071936-30292-sHq9EuynC+sl2JkXaX00lA||server.ccl.net> X-Original-From: "Christian Stegmann" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Jun 2007 12:21:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Christian Stegmann" [adenozin*_*googlemail.com] Dear all, please mark your calendar: You are invited to participate in the 4th Horizons in Molecular Biology Symposium on September 12-15th 2007 in Goettingen, Germany. http://www.horizons.uni-goettingen.de Call for Abstracts: Horizons in Molecular Biology aims to provide deep insights into contemporary life science research and to encourage exchange among people from different biological science branches. We invite distinguished scientists from fields as diverse as structural biology, developmental biology, cell biology and neurobiology. Furthermore, this year's Horizons features a Systems Biology session and a career fair on 12th of September (including company presentations and career workshops). By including a diverse spectrum of topics we hope to broaden horizons and to inspire interdisciplinary discussions. Through the scientific and social events of the meeting we intend to improve the networking of Ph.D. students and young researchers from different parts of the world. The meeting will feature five sessions with invited lectures, two poster sessions, three sessions with student talks and includes an extensive social program. Confirmed invited speakers are: Structural Biology: Hashim Al-Hashimi Nenad Ban Roland Beckmann Kevin Gardner Cell Biology: Jiri Bartek Bernd Bukau Tim Hunt Stefan Müller Phillip Zamore Neuroscience: Jean-Pierre Changeux Joachim Herz Larry Zipursky Developmental Biology: Markus Affolter John Gurdon Andrew McMahon Claudio Stern Systems Biology: Patrick Cramer Friedrich Lottspeich Michael Yaffe Hope to see in September and don't forget to register soon as the number of participants is limited. * Early registration deadline: July 1st, 2007 * Late registration deadline / Abstract Submission deadline: August 1st, 2007 For further details about registration, detailed program, abstract submission and contact information please visit our web page: http://www.horizons.uni-goettingen.de/ Please feel free to download the announcing poster from our website http://www.horizons.uni-goettingen.de/Horizons2007/dl/horizons07.pdf Best regards, Christian Stegmann (On behalf of the the PhD Student Organizing Committee) ----------------------------------------------------------- HORIZONS IN MOLECULAR BIOLOGY International PhD Student Symposium PhD Student Organizing Committee Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Email: horizon%gwdg.de www.horizons.uni-goettingen.de www.gpmolbio.uni-goettingen.de ---------------------------------------------------------- -- Christian Stegmann Max-Planck Institute for Biophysical Chemistry Dept. Cellular Biochemistry / X-ray Crystallography Am Fassberg 11 37077 Goettingen, Germany Phone: +49-551-201-1068 Fax: +49-551-201-1197 From owner-chemistry@ccl.net Wed Jun 20 12:25:00 2007 From: "Vlad vvv900%anusf.anu.edu.au" To: CCL Subject: CCL:G: Java Molecular Editor Released Message-Id: <-34526-070620011920-6068-EfSnuIES4i4+8Elo/U4gZg[*]server.ccl.net> X-Original-From: "Vlad" Content-description: Mail message body Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII Date: Wed, 20 Jun 2007 15:18:59 +1000 MIME-Version: 1.0 Sent to CCL by: "Vlad" [vvv900%%anusf.anu.edu.au] Dear CCLers, We are pleased to announce the release of Java Molecular Editor (JMolEditor). Java Molecular Editor (JMolEditor) is a program for displaying, analyzing, editing, and converting molecular systems. JMolEditor is written in Java, so it is a cross-platform application. It has intuitive interface and inbuilt help system. JMolEditor can be used also for the analysis to display molecular orbitals, electron densities and electrostatic potentials from the Gaussian. A full description of JMolEditor and its documentation are available via the JMolEditor WWW home page: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html System requirements: Java Virtual Machine (JVM) >= 1.5 and Java3d >= 1.3. Key features in JMolEditor include: - molecular builder/editor - ability to read and visualize popular Computational Chemistry formats: - - Gaussian (input and output) - - Gamess (input and output) - - Mopac (input and output) - - QChem (input and output) - - VASP - - Amber (prmtop files) - - PDB, Mol2, MDL molfile, XMol XYZ - visualization of the OOGL off files - visualization of molecular orbitals, electron densities and electrostatic potentials from the Gaussian Cube files Regards, Vlad =============== Dr. Vladislav Vasilyev Supercomputer Facility The Australian National University Canberra, ACT, 0200, Australia From owner-chemistry@ccl.net Wed Jun 20 12:59:01 2007 From: "Gustavo Seabra gustavo.seabra]|[gmail.com" To: CCL Subject: CCL: Time dependent DFT calculation of 2-cyclopentenone Message-Id: <-34527-070620113429-6749-gSlq1Z5AIowg+fgLKvNiNw++server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 20 Jun 2007 11:05:56 -0400 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra:+:gmail.com] > p TD=(nstates=4,root=1) B3LYP/6-311++G(d,p) opt freq pop=full There should be a "#" sign in the beginning of this line. > However I keep getting a message stating that there is an > error. Does anybody have a comment? What is the message? Gustavo Seabra. From owner-chemistry@ccl.net Wed Jun 20 13:34:00 2007 From: "Barbara Jewett barbaraj : ncsa.uiuc.edu" To: CCL Subject: CCL: Computational science advances symposium at ACS in Boston Message-Id: <-34528-070620110700-20907-6mMkEukKmG1GQ3qw8z3OOg:server.ccl.net> X-Original-From: "Barbara Jewett" Date: Wed, 20 Jun 2007 11:06:55 -0400 Sent to CCL by: "Barbara Jewett" [barbaraj^^^ncsa.uiuc.edu] There is an exciting symposium taking place at the upcoming ACS meeting in Boston. Two ACS Divisions, the Division of Computers in Chemistry (COMP) and the Division of Physical Chemistry (PHYS) are co-sponsoring Computational Science & Engineering Advances Supported by NSF Resources. A technical session will be held each afternoon on Monday, Tuesday, and Wednesday, August 20-22 (COMP, section E). The program has been organized by John Towns of the National Center for Supercomputing Applications at the University of Illinois, Urbana-Champaign; details are below. (Program subject to change) Monday, August 20 Engineering Sciences 1:30 178. Multiscale models for biomolecular engineering. Y. Kaznessis 2:00 179. All-atom and multiscale modeling of silicon nanobiodevices. A. Aksimentiev 2:30 180. High-performance, multiscale simulation of engineered tissue mechanics. V. H. Barocas, T. Stylianopoulos, X. Luo, M. S. Shephard 3:00 181. Improvement in structure model accuracy and molecular replacement through highresolution protein structure refinement. B. Qian, D. Baker 3:30 Intermission. 3:45 182. Performing simulations at the terascale today and at the sustained petascale "tomorrow". J. A. Nichols 4:15 183. Screened hybrid DFT and the Mott transition in MnO. R. L. Martin 4:45 184. Advances in ab initio and density functional approaches: From a methodological and basis set perspective. A. K. Wilson Tuesday, August 21 Molecular Sciences 1:00 255. From megaflops to teraflops: From molecules to cells. K. Schulten 1:30 256. Classical and quantum/classical biological modeling using the TeraGrid. A. E. Roitberg 2:00 257. Biomolecular simulation toward the petascale: Performance, workflow, and application to nucleic acid structure and dynamics. T. E. Cheatham III 2:30 258. Multi-terascale molecular modeling of biological systems. R. DeVane, W. Shinoda, J. Henin, M. Dal Peraro, A. Kohlmeyer, M. L. Klein 3:00 Intermission. 3:15 259. Using NSF supercomputer resources to study biomolecular structure and function. J. D. Madura 3:45 260. New discoveries in biomolecular systems enabled by high performance computing. G. A.Voth 4:15 261. Using large-scale computing to investigate dynamic aspects of biomolecular structure and function. C. L. Simmerling 4:45 262. Integrated computational biology: From the molecule to the cell. J. A. McCammon Wednesday, August 22 General Sciences 1:30 420. Where does it all go? How 70M in NSF cyberinfrastructure is leveraged. J. Towns 2:00 421. Atronomy and astrophysics. J. P. Ostriker 2:30 422. Large-scale simulations of complex flow phenomena. S. Dong 3:00 423. Transforming our understanding and prediction of thunderstorms through dynamic adaptation: People and technologies interacting with weather. K. K. Droegemeier, M. Xue 3:30 Intermission. 3:45 424. Numerical study of Quantum Chromodynamics. R. L. Sugar 4:15 425. Petascale computational cosmology. T. Quinn 4:45 426. Using the TeraGrid to advance earthquake system science. P. Maechling From owner-chemistry@ccl.net Wed Jun 20 14:08:01 2007 From: "Gustavo Seabra gustavo.seabra^_^gmail.com" To: CCL Subject: CCL:G: Fixing distance between point charge and atoms Message-Id: <-34529-070620115902-24961-qA9v7MuNM4xnCzcTXoRekQ[a]server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 20 Jun 2007 11:03:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra:-:gmail.com] You can try adding an additional electron-repulsive term to the point charge, as described in the Gaussian webpage: http://gaussian.com/g_ur/k_charge.htm HTH, Gustav Seabra. > -----Original Message----- > From: owner-chemistry%%ccl.net [mailto:owner-chemistry%%ccl.net] > Sent: Wednesday, June 20, 2007 12:39 AM > To: Seabra,Gustavo > Subject: CCL:G: Fixing distance between point charge and atoms > > > Sent to CCL by: "Chunyi Sung" [juneyi1(~)yahoo.com.tw] Hi, CCLers > > I am trying to optimize some molecules in the presence > of point charges using the keyword "charge" in Gaussian; > however, in my case, some O atom in the molecule always ended > up colliding with a positive point charge during geometry > optimization. Therefore, I want to somehow set up some > constraints on that O atom so that it will stay, say, 2.7 > Angstrom away > > from the positive point charge, does anyone know how to do that ? > > Originally, I wanted to put a ghost atom right at the > location of the positive point charge, and then use > "modredundant" to fix the bond length between the O atom and > the ghost atom. However, with the "charge" keyword to include > point charges, "Opt" must have "Z-matrix", which does not > work with "modredundant". So I am now running out of ideas. > I'll appreaciate if anybody has any suggestions on this. > > thanks > > chunyi From owner-chemistry@ccl.net Wed Jun 20 16:12:00 2007 From: "Richard Andrew Huhn huhnra]^[mit.edu" To: CCL Subject: CCL:G: Metal oxidation states and charge separation Message-Id: <-34530-070620160936-8635-wYvFjSzW+By7szwHaIgRWg~!~server.ccl.net> X-Original-From: "Richard Andrew Huhn" Date: Wed, 20 Jun 2007 16:09:32 -0400 Sent to CCL by: "Richard Andrew Huhn" [huhnra#%#mit.edu] I have a crystal structure with two metal-ligand complexes in the unit cell. It is of the type L-M-L L'-M-L'. We are unsure of the oxidation states of the metal: it may be, for example, L-M(0)-L L'-M(II)-L', or L-M(I)-L[+] L'-M(I)-L'[-]. Are comparisons possible of DFT energies / geometries for these two hypothetical species, and if so, how does one specify in G03 the charge separation in the latter species? Literature references to similar calculations would be helpful! Thank you for your help, Rich Huhn From owner-chemistry@ccl.net Wed Jun 20 17:03:00 2007 From: "Mariusz Sterzel m.sterzel^cyf-kr.edu.pl" To: CCL Subject: CCL:G: Time dependent DFT calculation of 2-cyclopentenone Message-Id: <-34531-070620162845-17774-8/WzycO4goSwA5htEffBXA^_^server.ccl.net> X-Original-From: Mariusz Sterzel Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 20 Jun 2007 21:42:47 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Mariusz Sterzel [m.sterzel_._cyf-kr.edu.pl] On Tue, 19 Jun 2007, Mohamed Z Rishard rishiz{:}hotmail.com wrote: > > Sent to CCL by: "Mohamed Z Rishard" [rishiz=-=hotmail.com] > I want to do a TD-DFT calculation for the lowest excited singlet state of the above molecule. The route section is as follows: > > p TD=(nstates=4,root=1) B3LYP/6-311++G(d,p) opt freq pop=full > > However I keep getting a message stating that there is an error. Does anybody have a comment? > Hi, Your input does not work because analytical gradients for TDDTF are not implemented in Gaussian. You can use numerical ones instead. For details take a look at http://www.ccl.net/chemistry/resources/messages/2002/04/11.009-dir/ Analytical gradients are implemented in TURBOMOLE (www.turbomole.com). regards, Mariusz -- Mariusz Sterzel Email: m.sterzel/^at^\cyfronet.pl Academic Computer Centre CYFRONET From owner-chemistry@ccl.net Wed Jun 20 18:31:00 2007 From: "Serge Gorelsky gorelsky:+:gmail.com" To: CCL Subject: CCL:G: Metal oxidation states and charge separation Message-Id: <-34532-070620182507-9052-bw1ZOBd3vWPkFlEC2pXSCg]_[server.ccl.net> X-Original-From: "Serge Gorelsky" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 20 Jun 2007 17:26:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Serge Gorelsky" [gorelsky()gmail.com] > Sent to CCL by: "Richard Andrew Huhn" [huhnra#%#mit.edu] > I have a crystal structure with two metal-ligand complexes in the unit cell. It is of the type L-M-L L'-M-L'. We are unsure of the oxidation states of the metal: it may be, for example, L-M(0)-L L'-M(II)-L', or L-M(I)-L[+] L'-M(I)-L'[-]. > > Are comparisons possible of DFT energies / geometries for these two hypothetical species, and if so, how does one specify in G03 the charge separation in the latter species? Literature references to similar calculations would be helpful! Thank you for your help, this topic has been discussed in the CCL posts before. In a nutshell, you need to give Gaussian 03 the guess wave functions that are the sum of fragment wave functions such as L-M(0)-L L'-M(II)-L', or L-M(I)-L[+] L'-M(I)-L'[-]. This can be easily done by AOMix-CDA (see Appendix II in the AOMix manual at www.sg-chem.net) and GUESS=CARDS keyword in Gaussian 03. -- Best regards, Serge Gorelsky From owner-chemistry@ccl.net Wed Jun 20 20:01:00 2007 From: "Mahalakshmi. S. mlakshmis/a\gmail.com" To: CCL Subject: CCL:G: magentic susceptibility from gaussian program Message-Id: <-34533-070620110306-18896-1e/eNgEBYWZUY6WgOvrDVQ-,-server.ccl.net> X-Original-From: "Mahalakshmi. S." Content-Type: multipart/alternative; boundary="----=_Part_66532_31060911.1182348271721" Date: Wed, 20 Jun 2007 19:34:31 +0530 MIME-Version: 1.0 Sent to CCL by: "Mahalakshmi. S." [mlakshmis(_)gmail.com] ------=_Part_66532_31060911.1182348271721 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL members, In the output of g03 program for calculating the magnetic susceptibility, its given as cgs-ppm. Magnetic anisotropy is obtained by subtracting magnetic susceptibility_parallel and magnetic susceptibility_perpendicular. How do you convert the magnetic anisotropy from cgs-ppm to m3/molecule ? I would like to thank in advance the members who respond to this message. Thanks, Lakshmi ------=_Part_66532_31060911.1182348271721 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL members,

In the output of g03 program for calculating the magnetic susceptibility, its given as cgs-ppm. Magnetic anisotropy is obtained by subtracting magnetic susceptibility_parallel and magnetic susceptibility_perpendicular. How do you convert the magnetic anisotropy from cgs-ppm to m3/molecule ? I would like to thank in advance the members who respond to this message.

Thanks,
Lakshmi
------=_Part_66532_31060911.1182348271721--