From owner-chemistry@ccl.net Wed Apr 16 03:07:01 2008 From: "Dhurairajan Senthilnathan zenthil03++yahoo.co.in" To: CCL Subject: CCL: Atom freezing Message-Id: <-36746-080416023615-19235-Nf5PjwSFk+2IWgr1YkYgBw[*]server.ccl.net> X-Original-From: "Dhurairajan Senthilnathan" Date: Wed, 16 Apr 2008 02:36:11 -0400 Sent to CCL by: "Dhurairajan Senthilnathan" [zenthil03()yahoo.co.in] Dear CCL'rs I have repeat error during my transition state calculation with atom freezing. this is my input file Errortype: finalizing output problem %chk=modi.chk %mem=156MW %nproc=1 #b3lyp opt=(ts, Addredundant, noeigentest, calcfc) freq Title Card Required -1 1 C -1 3.57687072 -4.13921011 -3.30678087 C 3.09615942 -3.20175132 -2.18353215 O 4.19106378 -2.40224837 -1.72869210 C -1 7.11106271 1.55944777 1.06747883 C 5.88398365 0.71672584 0.67289460 O 4.87047558 0.85342333 1.67240208 C 1.24369758 -1.26676653 0.30210842 C 1.84276596 -0.06332358 -0.39941350 O 2.85161400 -0.72562648 0.19360844 C 1.52338619 1.41022514 -0.08596374 C 0.12181386 1.75688989 -0.62170485 H 3.95504240 -3.55626896 -4.12045513 H 2.75760662 -4.73743959 -3.64711573 H 2.32106628 -2.56568842 -2.55710224 H 2.71798775 -3.78469247 -1.36985789 H 3.89139959 -1.81785848 -1.02848511 H 6.82644205 2.58770963 1.14852593 H 4.10554317 0.32809019 1.42642749 H 0.83212867 -1.14399673 1.28212812 H 1.38270023 -2.32762356 0.31478222 H 1.79540271 -0.11847470 -1.46694106 H 0.09676992 1.60391769 -1.68041742 N -0.34941182 -1.40975080 -0.54503852 N -1.47538282 -1.86218170 0.15317032 N -2.35363532 -2.21509880 0.69776747 H 4.35196386 -4.77527301 -2.93321078 H 7.86942189 1.45716364 0.31959560 H 7.48990511 1.21899762 2.00847411 H 5.50514126 1.05717597 -0.26810069 H 6.16860431 -0.31153602 0.59184751 H -0.60505522 1.12689727 -0.15301451 H -0.10009287 2.78071920 -0.40391833 H 2.25025527 2.04021776 -0.55465408 H 1.54843013 1.56319734 0.97274883 X 1 F X 4 F how can i avoid this error? regards by senthilnathan From owner-chemistry@ccl.net Wed Apr 16 03:42:01 2008 From: "Prof. Stefan Grimme grimmes**uni-muenster.de" To: CCL Subject: CCL:G: DFT for stacking Message-Id: <-36747-080416031006-4297-LyfSOwUtV2vChj9+FXN97g]=[server.ccl.net> X-Original-From: "Prof. Stefan Grimme" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 16 Apr 2008 08:15:17 +0200 MIME-Version: 1.0 Sent to CCL by: "Prof. Stefan Grimme" [grimmes#,#uni-muenster.de] > Sent to CCL by: "Simon Budzak" [budzak-,-fpv.umb.sk] > Dear CLL users, > I am trying to optimize some stacking complexes. Instead of MP2 and CCSD(T) > methods I would like to use for bigger systems DFT. > I know about vdW correction that it is implemented in ORCA (DFT-D) > and MPWB1K in Gaussian. > Are there any other functionals which should I use for correct description of such complexes? Dear All, there are some functionals (LDA, sometimes BHLYP, M06...) that can in special situations extract out of the very small densities in between the fragment some reasonable interaction energies. It is possible to fit heavily parametrized functionals for that purpose. However, asymptotically they are all wrong because the (atom-pairwise) correct R^-6 behavior is not included, i.e., they give the right answer for the wrong reason. This typically leads to severe under-binding with increasing size of the complex (because the densities are much faster [exponentially] decaying than R^-6). In large molecules there are many inter-atomic distances in the range 500-600 pm for which none of the conventional functionals will provide reasonable binding but where R^-6 is still very significant. E.g. for graphite LDA gives only about half of the inter-layer binding energy while it overbinds by orders of magnitude for rare gas dimers. Standard functionals also very often have problems in the balanced description of stacked vs. hydrogen-bonded structures. Currently I see no better approach than DFT-D with GGAs for the optimization of large systems. Binding energies are typically accurate to 5-10 % (often better than 2-3 %) and inter-fragment distances are rarely off by more than 10-20 pm. For recent applications on big systems see: S. Grimme, Do special noncovalent p-p stacking interactions really exist?, Angew. Chem. Int. Ed. 47, (2008), 3430-3434. C. Mück-Lichtenfeld, S. Grimme, Structure and binding energies of the porphine dimer, Molecular Physics, 105, (2007), 2793-2798. S. Grimme, C. Mück-Lichtenfeld, J. Antony, Noncovalent Interactions between Graphene Sheets and in Multishell (Hyper)Fullerenes, J. Phys. Chem. C 111, (2007), 11199-11207. S. Grimme, J. Antony, T. Schwabe, C. Mück-Lichtenfeld, Density Functional Theory with Dispersion Corrections for Supramolecular Structures, Aggregates, and Complexes of (Bio)Organic Molecules, Org. Biomol. Chem. 5, (2007), 741-758. This last reference also contains references to other DFT methods for disperison. Cheers! Stefan Grimme ____________________________________________________________ All theoretical chemistry is really physics and all theoretical chemists know it. (R. P. Feynman) All many-body physics is really chemistry and all theorists know it. (Anonymous) ____________________________________________________________ Prof. Dr. Stefan Grimme (grimmes[]uni-muenster.de) Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) http://www.uni-muenster.de/Chemie/OC/research/grimme/ support QChemistry with your PC http://qah.uni-muenster.de ____________________________________________________________ From owner-chemistry@ccl.net Wed Apr 16 04:36:01 2008 From: "Justin Finnerty justin.finnerty:uni-oldenburg.de" To: CCL Subject: CCL: ubuntu 7.1 + ifort (II) Message-Id: <-36748-080416040254-15961-OZmfBBwiG6cTb3SJppwi2A^^server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 16 Apr 2008 10:02:28 +0200 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty/./uni-oldenburg.de] Hello Pablo, Two points: * Firstly, to set up a compiler or library environment I would recommend that instead of putting MKL_HOME, LD_LIBRARY_PATH in each users .cshrc file that you use the system profile system. This gives all users access to the libraries, compilers and applications. This is particularly useful when you compile/install software as the root, but use/test it as a general user. I use the example of OpenSuse below, but Ubuntu will not be too different. On Suse we have the /etc/profile.d directory where you would place mkl.sh and mkl.csh that contain something like -- mkl.csh -- %< -- if ( ! ${?MKL_HOME} ) then setenv MKL_HOME /path/to/mkl../ endif -- -- mkl.sh -- %< -- if [ "${MKL_HOME}" = "" ]; then export MKL_HOME=/path/to/mkl../ endif -- The intel compiler's bin directory has similar shell scripts for the compiler information (fortran - ifcvars.[csh|sh] and C - iccvar.[csh| sh]). These should be symlinked into the /etc/profile.d You must log-out and then log-in for the changes to /etc/profile.d/* files to take affect. I would also add the libraries to the ld system directly rather than use LD_LIBRARY_PATH. Here I add files to /etc/ld.so.conf.d/ (If this directory does not exist then you can add the lines directly to /etc/ld.so.conf). After adding/changing ld.so.conf... files you need to run 'ldconfig' to make the changes take effect. -- intel.conf -- %< -- /path/to/compiler/lib -- -- mkl.conf -- %< -- /path/to/mkl/lib --- Of course the paths in the examples above must be changed for your system. Also, write these changes into your system administration logbook ;) so you can repeat them when you need to rebuild the system or upgrade the library/compiler. * Secondly, what options do you use with configure. For my 32bit Ifort I would use something like (put all on one line): CC=icc FC=ifc F77=ifc CXX=icc CFLAGS="-I${MKL_HOME}/include -L ${MKL_HOME}/lib" FFLAGS=$CFLAGS ./configure --prefix=/opt/chemie ... When I see " cannot create executables" this usually means that the CFLAGS or FFLAGS are wrong. Check in config.log, go to the end then scroll backwards a long way to get to the compiler error message. BUT, what variables are used when making program may differ. You may also find that after making "configure" work you cannot get the software to compile with other than the GCC compilers. OpenMPI is one package I used that completely ignored the user supplied CFLAGS entry after running "configure" so it was locked into using GCC compilers and compilers that recognised GCC options "-f...". Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Apr 16 05:49:00 2008 From: "Barbara Jagoda-Cwiklik barbara-x-fh.huji.ac.il" To: CCL Subject: CCL:G: basis set Message-Id: <-36749-080416054634-7332-nohVwDhwZP6pzDi9gcj3aw%%server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Apr 2008 12:46:11 +0300 MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara---fh.huji.ac.il] On Tue, Apr 15, 2008 at 10:34 PM, Ioana Sovago isovago]*[chem.ubbcluj.ro wrote: > > Sent to CCL by: "Ioana Sovago" [isovago^chem.ubbcluj.ro] > Who cand help me how to write un input using 2 different baisis set? For more > details pleas send me an email. > > Best regards, Ioana S Hi Ioana, You can try to use keyword GEN. Please, take a look at Gaussian Manual http://www.gaussian.com/g_ur/k_gen.htm and if it is not clear let me know, hope I can provide you some more help :) Best, Basia -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara{=}fh.huji.ac.il From owner-chemistry@ccl.net Wed Apr 16 06:44:01 2008 From: "Anne Rutland ccdc-announce[#]ccdc.cam.ac.uk" To: CCL Subject: CCL: New release of GOLD v. 4.0, software for ligand-protein docking Message-Id: <-36750-080416060920-18044-/8b5BvdJIlMk2i5UqiGWwg%%server.ccl.net> X-Original-From: "Anne Rutland" Date: Wed, 16 Apr 2008 06:09:17 -0400 Sent to CCL by: "Anne Rutland" [ccdc-announce:-:ccdc.cam.ac.uk] The Cambridge Crystallographic Data Centre are pleased to announce the release of GOLD version 4.0 software for ligand-protein docking. GOLD v. 4.0 is supplied as part of the GOLD suite, which also includes the Hermes 1.0 protein visualiser and the post-docking analysis package GoldMine 1.1. New Features included in this version of the GOLD Suite: * A new graphical user interface which includes a Wizard for easy set-up of GOLD dockings. * Protein preparation options for adding hydrogens, deleting unnecessary waters and resetting incorrectly assigned Asn, Gln and His side chains. Raw pdb files no longer need to be preprepared using another package. * A Receptor Density Scaling option for use with ChemScore that more correctly rewards the binding of ligands within tight pockets. * A Server that allows easy docking or re-scoring of subsets of poses from a GoldMine database. * An Arithmetic Descriptor Calculator in GoldMine which can be used to create composite descriptors and set up consensus scoring schemes. * Stereo-view capability on machines that support OpenGL quad-buffered stereo. For further information please visit http://www.ccdc.cam.ac.uk/products/gold_suite For a 60 day evaluation copy, please contact admin::ccdc.cam.ac.uk From owner-chemistry@ccl.net Wed Apr 16 09:05:01 2008 From: "Lukasz Cwiklik cwiklik]|[gmail.com" To: CCL Subject: CCL: Atom freezing Message-Id: <-36751-080416090017-23034-J+nfq/vOWC9qpbSXXB8DZA=server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Apr 2008 15:59:47 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik_._gmail.com] On Wed, Apr 16, 2008 at 9:36 AM, Dhurairajan Senthilnathan zenthil03++yahoo.co.in wrote: > > Sent to CCL by: "Dhurairajan Senthilnathan" [zenthil03()yahoo.co.in] > Dear CCL'rs > I have repeat error during my transition state calculation with atom freezing. this is my input file Dear Dhurairajan, As I have written before, IMO your input file is formally correct (it runs without problems on my machine). I also took a look at source files, this error message seems to be strange. Can you please send us the output file from your job or, at least, the several lines preceding and including the error message? Also, what processor and operating system are you working on? Aren't you using some kind of virtualization? Best regards, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Wed Apr 16 10:47:00 2008 From: "Jens Thomas j.m.h.thomas###dl.ac.uk" To: CCL Subject: CCL: Talks from the "Molecular Modelling: Tools, GUIs and Visualisation" meeting available online. Message-Id: <-36752-080416104016-4136-zrTsHeQ04bxeKO0blvjBhQ(0)server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 16 Apr 2008 14:03:33 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas~!~dl.ac.uk] Hello, A few weeks back we held a CCP1 meeting looking at graphical interfaces, visualisation and tools for molecular modelling. Developers from AgentX, Aten, Avogadro, cclib, the CCP1GUI, GAMESS, GAMESS-UK, GaussSum, Jmol, Molekel, Molpro, Openbabel and Zeobuilder all gave talks at the meeting. A number of people on the CCL expressed interest in the meeting, but were unable to attend. We have therefore put the slides and audio from the talks, as well as a summary of the outcomes, on the Blue Obelisk site. You can find all this on the wiki at: http://blueobelisk.sourceforge.net/wiki/ChemToolsMeet_March_08 If anyone has any questions about the meeting or would like any further information, then please feel free to contact me. Best wishes, Jens -- =================================================================== Jens Thomas, email: j.m.h.thomas!^!dl.ac.uk STFC Daresbury Lab, tel: +44-1925-603849 Warrington, fax: +44-1925-603634 WA4 4AD, UK. http: http://www.cse.scitech.ac.uk =================================================================== From owner-chemistry@ccl.net Wed Apr 16 11:21:00 2008 From: "Negi, Surendra S. ssnegi:_:utmb.edu" To: CCL Subject: CCL: ubuntu 7.1 + ifort (II) Message-Id: <-36753-080416105351-7437-oqEwjiEV4zsx98DZWEnpBg|server.ccl.net> X-Original-From: "Negi, Surendra S." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 16 Apr 2008 09:49:49 -0500 MIME-Version: 1.0 Sent to CCL by: "Negi, Surendra S." [ssnegi..utmb.edu] Try to run following lines in command line source /opt/intel/fce/10.1.015/bin/ifortvars.sh source /opt/intel/cc/10.1.015/bin/iccvars.sh make sure it is fce not fc, check it. -----Original Message----- > From: Pablo A Denis pablod(0)fq.edu.uy [mailto:owner-chemistry===ccl.net] Sent: Tue 4/15/2008 6:06 PM To: Negi, Surendra S. Subject: CCL: ubuntu 7.1 + ifort (II) =20 Sent to CCL by: "Pablo A Denis" [pablod,+,fq.edu.uy] Dear CClers, Thank you very much for your suggestions to make the ifort = work under Ubuntu 7.1. Unfortuatelly, I couldt fix the problem. -I have checked that I am working with bash. -I have added the enviromental variables to the bash -I have tried to rename the bash.bashrc to .bashrc and modified the = .bashrc in /home/usr=20 -I cant compile anything. He just cant see the ifort. The ifort was = installed without problems, also i type man ifort and I can read the = manual. I got the same message when I do the ./configure, cannot create = executable variables... He finds everything gcc, g++, python etc., = latex, but not the ifort. Below you will find a copy of the enviromental variables added to the = bash.basrc... If you have any other suggestion to solve this problem, it will be very = welcome... Many Thanks, Pablo #IFORT #! /bin/bash if [ -z "${PATH}" ] then PATH=3D"/opt/intel/fce/10.1.015/bin"; export PATH else PATH=3D"/opt/intel/fce/10.1.015/bin:${PATH}"; export PATH fi if [ -z "${LD_LIBRARY_PATH}" ] then LD_LIBRARY_PATH=3D"/opt/intel/fce/10.1.015/lib"; export = LD_LIBRARY_PATH else LD_LIBRARY_PATH=3D"/opt/intel/fce/10.1.015/lib:${LD_LIBRARY_PATH}"; = export LD_LIBRARY_PATH fi # DYLD_LIBRARY_PATH is used on MAC OS* if [ -z "${DYLD_LIBRARY_PATH}" ] then DYLD_LIBRARY_PATH=3D"/opt/intel/fce/10.1.015/lib"; export = DYLD_LIBRARY_PATH else = DYLD_LIBRARY_PATH=3D"/opt/intel/fce/10.1.015/lib:${DYLD_LIBRARY_PATH}"; = export DYLD_LIBRARY_PAT H fi if [ -z "${NLSPATH}" ] then NLSPATH=3D"/opt/intel/fce/10.1.015/lib/locale/en_US"; export NLSPATH else NLSPATH=3D"/opt/intel/fce/10.1.015/lib/locale/en_US:${NLSPATH}"; = export NLSPATH fi if [ -z "${MANPATH}" ] then MANPATH=3D"/opt/intel/fce/10.1.015/man":$(manpath); export MANPATH else MANPATH=3D"/opt/intel/fce/10.1.015/man:${MANPATH}"; export MANPATH fi if [ -z "${INTEL_LICENSE_FILE}" ] then = INTEL_LICENSE_FILE=3D"/opt/intel/fce/10.1.015/licenses:/opt/intel/license= s:${HOME}/intel/li censes:/Users/Shared/Library/Application Support/Intel/Licenses"; export = INTEL_LICENSE_FILE else = INTEL_LICENSE_FILE=3D"${INTEL_LICENSE_FILE}:/opt/intel/fce/10.1.015/licen= ses:/opt/intel/lic enses:${HOME}/intel/licenses:/Users/Shared/Library/Application = Support/Intel/Licenses"; export IN TEL_LICENSE_FILE fi #DEB ADDED #! /bin/sh if [ -z "${PATH}" ] then PATH=3D"/opt/intel/idbe/10.1.015/bin"; export PATH else PATH=3D"/opt/intel/idbe/10.1.015/bin:$PATH"; export PATH fi if [ -z "${MANPATH}" ] then MANPATH=3D"/opt/intel/idbe/10.1.015/man":$(manpath); export MANPATH else MANPATH=3D"/opt/intel/idbe/10.1.015/man:${MANPATH}"; export MANPATH fi #MKL ADDED #! /bin/sh if [ -z "${INCLUDE}" ] then export INCLUDE=3D/opt/intel/mkl/10.0.1.014/include else export INCLUDE=3D/opt/intel/mkl/10.0.1.014/include:$INCLUDE fi if [ -z "${LD_LIBRARY_PATH}" ] then export LD_LIBRARY_PATH=3D/opt/intel/mkl/10.0.1.014/lib/em64t else export = LD_LIBRARY_PATH=3D/opt/intel/mkl/10.0.1.014/lib/em64t:$LD_LIBRARY_PATH fi if [ -z "${MANPATH}" ] then export MANPATH=3D/opt/intel/mkl/10.0.1.014/man:$(manpath) else export MANPATH=3D/opt/intel/mkl/10.0.1.014/man:$MANPATH fi if [ -z "${LIBRARY_PATH}" ] then export LIBRARY_PATH=3D/opt/intel/mkl/10.0.1.014/lib/em64t else export = LIBRARY_PATH=3D/opt/intel/mkl/10.0.1.014/lib/em64t:$LIBRARY_PATH fi if [ -z "${CPATH}" ] then export CPATH=3D/opt/intel/mkl/10.0.1.014/include else export CPATH=3D/opt/intel/mkl/10.0.1.014/include:$CPATH fi if [ -z "${FPATH}" ] then export FPATH=3D/opt/intel/mkl/10.0.1.014/include else export FPATH=3D/opt/intel/mkl/10.0.1.014/include:$FPATH fi -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Apr 16 11:56:00 2008 From: "Jerome Kieffer Jerome.Kieffer{=}terre-adelie.org" To: CCL Subject: CCL:G: UV-Vis spectra prediction Message-Id: <-36754-080416081626-18402-uYiJq6mEfAsf4SDpCfpCXw{=}server.ccl.net> X-Original-From: Jerome Kieffer Content-Type: multipart/alternative; boundary="b1_76c1b1e713ad3cde7370a9adcf849d44" Date: Wed, 16 Apr 2008 14:16:05 +0200 MIME-Version: 1.0 Sent to CCL by: Jerome Kieffer [Jerome.Kieffer .. terre-adelie.org] --b1_76c1b1e713ad3cde7370a9adcf849d44 Content-Type: text/plain; charset = "utf-8" Content-Transfer-Encoding: quoted-printable Dear CCLers, I am trying to reproduce experimental UV-spectra of organic molecules : After the conversion wavelength (nm) ->=C2=A0 energy (cm-1)=C2=A0 of the = experimental spectrum,=C2=A0 I deconvoluted it by a sum of gaussian functions (using = FitYK). It fits well. Transitions I obtained using TDDFT are pretty good compared with the = center of the gaussian deconvolution,=C2=A0 but the FWHM of the experimental = spectrum's gaussian varies from 2000 to 8000 cm-1. So my question is: is it possible to calculate the broadening of an absorption band ? some software like gausssum suggest a FWMH of arround 3000cm-1=C2=A0 =C2=A0=20 Thank you for your help Regards -- J=C3=A9r=C3=B4me Kieffer http://www.terre-adelie.org --b1_76c1b1e713ad3cde7370a9adcf849d44 Content-Type: text/html; charset = "utf-8" Content-Transfer-Encoding: quoted-printable Dear CCLers,

I am trying to reproduce experimental UV-spectra of organic molecules :

After the conversion wavelength (nm) ->  energy (cm-1)  of = the experimental spectrum,  I deconvoluted it by a sum of gaussian = functions (using FitYK). It fits well.

Transitions I obtained using TDDFT are pretty good compared with the = center of the gaussian deconvolution,  but the FWHM of the = experimental spectrum's gaussian varies from 2000 to 8000 cm-1.

So my question is: is it possible to calculate the broadening of an = absorption band ? some software like gausssum suggest a FWMH of arround = 3000cm-1   
Thank you for your help

Regards
Jérôme Kieffer
http://www.terre-adelie.org --b1_76c1b1e713ad3cde7370a9adcf849d44-- From owner-chemistry@ccl.net Wed Apr 16 12:33:00 2008 From: "Gonzalo Jim nez-Os s gjimenez[*]unizar.es" To: CCL Subject: CCL: low-spin versus high-spin complexes Message-Id: <-36755-080416113632-2696-/kQqxWRPtXBwAsOfnTCXPg#%#server.ccl.net> X-Original-From: "Gonzalo Jim nez-Os s" Date: Wed, 16 Apr 2008 11:36:28 -0400 Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez,,unizar.es] Dear CCL'ers I have some doubts about the possibility to directly compare the energy of two different spin configurations of a given compound. For instance, one can compute the energy (and hence the optimized geometries) of a neutral dichloro-Co(II) complex in both low-spin (multiplicity 2) and high-spin (multiplicity 4) configurations. In my experience, the high-spin energies are always lower than the low-spin ones by more than 20 kcal/mol but with significant differences depending on the used functional (b3lyp and m05-2x under open-shell conditions). My question is: are these black box energy values comparable? If so, should I safely discard low-spin states and carry out the whole calculations with the high-spin configuration? In connection with this question, are the DFT energies of analogous monocationic Cu(I) (closed-shell, singlet) and dicationic Cu(II) (open-shell, doublet) complexes comparable? I mean, when the only difference between the two species is the oxidation state of the metal atom (and leaving apart the counteranions), is there any sense in comparing the relative stability of each (DFT) calculated structures? Any comment or suggestion to clarify this point will be welcome. Many thanks in advance. Regards, Gonzalo From owner-chemistry@ccl.net Wed Apr 16 13:06:01 2008 From: "qfu-.-kth.se" To: CCL Subject: CCL:G: basis set Message-Id: <-36756-080415190102-11743-OAQXR8xtvmLjG3w+oUwkng/a\server.ccl.net> X-Original-From: qfu_-_kth.se Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 16 Apr 2008 00:34:53 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: qfu+/-kth.se Hi, Ioana, If it is used for Gaussian calculations, you could use the keyword Gen like this: # B3LYP/Gen ... test 0 1 coordinate C 0(it is zero) 3-21G **** H 0(it is zero too) 6-31G **** > > Sent to CCL by: "Ioana Sovago" [isovago^chem.ubbcluj.ro] > Who cand help me how to write un input using 2 different baisis set? For > more details pleas send me an email. > > Best regards, Ioana S> > > From owner-chemistry@ccl.net Wed Apr 16 13:47:00 2008 From: "Prabha Lakshmi prabhalak26(0)yahoo.co.in" To: CCL Subject: CCL: diarylketon conformation Message-Id: <-36757-080416080159-17000-z187qAQwDF80cOIMjlR6Sw- -server.ccl.net> X-Original-From: Prabha Lakshmi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Wed, 16 Apr 2008 17:31:31 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Prabha Lakshmi [prabhalak26{:}yahoo.co.in] Dear CCLers,=0A=0Ain a system similar to phenylCOphenyl, what are dihedral = angles expected involving the carbonyl moiety?=0A=0AThank you,=0A prabhalak= =0A=0AMolecular Biochemistry PhD Student=0A=0A=0A Forgot the famous l= ast words? Access your message archive online at http://in.messenger.yahoo.= com/webmessengerpromo.php From owner-chemistry@ccl.net Wed Apr 16 14:17:01 2008 From: "Prabha Lakshmi prabhalak26::yahoo.co.in" To: CCL Subject: CCL: protein-ligand interactions Message-Id: <-36758-080416075012-15067-DbkfCvGELU+8KEzi7UlWSQ*o*server.ccl.net> X-Original-From: Prabha Lakshmi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Wed, 16 Apr 2008 17:19:56 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Prabha Lakshmi [prabhalak26||yahoo.co.in] Dear Hatice,=0AI would raccommand to use Autodock 4 which is able to accoun= t for some protein flexibility, in addition to well threat small organic mo= lecules.=0A=0ACheers,=0A Prabhalak=0A=0AMolecular Biochemistry PhD student= =0A=0A=0A From Chandigarh to Chennai - find friends all over India. Go= to http://in.promos.yahoo.com/groups/citygroups/ From owner-chemistry@ccl.net Wed Apr 16 14:52:01 2008 From: "Ismael Ortiz Verano ieortizv:+:bt.unal.edu.co" To: CCL Subject: CCL: [CCL] CCL: basis set Message-Id: <-36759-080416003542-27509-FQSa2B4ZdnbBa1+ThqYlDQ[*]server.ccl.net> X-Original-From: "Ismael Ortiz Verano" Content-Type: multipart/alternative; boundary="----=_Part_6884_1399145.1208320532015" Date: Tue, 15 Apr 2008 23:35:31 -0500 MIME-Version: 1.0 Sent to CCL by: "Ismael Ortiz Verano" [ieortizv],[bt.unal.edu.co] ------=_Part_6884_1399145.1208320532015 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Ioana, you must put in your input: Charge multiplicity atom 1 X1 Y1 Z1 . . . . . . . . . . . . atom n Xn Yn Zn element1 element2 element3 ... 0 basis1 **** element 10 element11 element12 ... 0 basis2 **** --=20 Ismael Ortiz Verano Grupo de Qu=EDmica Te=F3rica Universidad Nacional de Colombia Tel: (57)(1) 3165000 ext 10608 ------=_Part_6884_1399145.1208320532015 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Ioana,

you must put in your input:

Charge multiplicity<= br>   atom 1    &nb= sp;  X1   Y1   Z1
   .      =     .    .    .
   .   =        .    .    .=
   . &nb= sp;        .    .    .
 atom n       Xn&nb= sp;  Yn   Zn

element1 el= ement2 element3 ... 0
basis1
****
element 10 element11 element12 .= .. 0
basis2
****

--
Ismael Ortiz Verano
G= rupo de Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608 ------=_Part_6884_1399145.1208320532015-- From owner-chemistry@ccl.net Wed Apr 16 15:27:00 2008 From: "qfu##kth.se" To: CCL Subject: CCL:G: DFT for stacking Message-Id: <-36760-080415190102-11748-2JdGlvhphhFByyZDIPJH4g]=[server.ccl.net> X-Original-From: qfu]*[kth.se Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 16 Apr 2008 00:30:48 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: qfu~~kth.se Hi,Simon! Maybr this paper could help. Chemical Physics Letters, 419,333 (2006) Regards! Qiang Fu > > Sent to CCL by: "Simon Budzak" [budzak-,-fpv.umb.sk] > Dear CLL users, > > I am trying to optimize some stacking complexes. Instead of MP2 and > CCSD(T) > methods I would like to use for bigger systems DFT. > I know about vdW correction that it is implemented in ORCA (DFT-D) > and MPWB1K in Gaussian. > Are there any other functionals which should I use for correct description > of such complexes? > > Thanks for your help in advance > > Simon > > > > > Simon Budzak > Department of Chemistry > Faculty of Natural Science > Matej Bel University > Banska Bystrica > Slovakia> > > From owner-chemistry@ccl.net Wed Apr 16 16:02:00 2008 From: "Ismael Ortiz Verano ieortizv*bt.unal.edu.co" To: CCL Subject: CCL: basis set Message-Id: <-36761-080415213114-29312-Jn78GjSk6F6u7fxt8xgXig#,#server.ccl.net> X-Original-From: "Ismael Ortiz Verano" Content-Type: multipart/alternative; boundary="----=_Part_5893_15532321.1208305737919" Date: Tue, 15 Apr 2008 19:28:57 -0500 MIME-Version: 1.0 Sent to CCL by: "Ismael Ortiz Verano" [ieortizv,+,bt.unal.edu.co] ------=_Part_5893_15532321.1208305737919 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Ioana S, you must put in your input (see at end): Charge multiplicity element 1 X1 Y1 Z1 . . . . . . . . . . . . element n Xn Yn Zn element1 element2 element3 ... 0 basis1 **** element 10 element11 element12 ... 0 basis2 **** --=20 Ismael Ortiz Verano Grupo de Qu=EDmica Te=F3rica Universidad Nacional de Colombia Tel: (57)(1) 3165000 ext 10608 ------=_Part_5893_15532321.1208305737919 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Ioana S, you must put in your input (see at end):



Charge multi= plicity
element 1   &= nbsp; X1   Y1   Z1
   .      &nbs= p;   .    .    .
   .   &n= bsp;      .    .    .    . &nb= sp;        .    .    .
element n     Xn   = Yn   Zn

element1 el= ement2 element3 ... 0
basis1
****
element 10 element11 element12 .= .. 0
basis2
****



--
Ismael Ortiz Verano
Grupo d= e Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608 ------=_Part_5893_15532321.1208305737919-- From owner-chemistry@ccl.net Wed Apr 16 16:40:01 2008 From: "Chem Bio News cbn(a)cambridgesoftemail4.com" To: CCL Subject: CCL: Medicinal Chemistry Structure Browser: Compare structures and properties Message-Id: <-36762-080415205340-11732-uhQ/2i1PnZfP2RtelKC9Vw=server.ccl.net> X-Original-From: Chem Bio News Content-Type: multipart/alternative; boundary="Boundary.11111111.11111111" Date: Wed, 16 Apr 2008 05:19:41 +0600 MIME-Version: 1.0 Sent to CCL by: Chem Bio News[cbn=cambridgesoftemail4.com] --Boundary.11111111.11111111 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit HTML Message - Medicinal Chemistry Structure Browser: Compare structures and properties --Boundary.11111111.11111111 Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Medicinal Chemistry Structure Browser: Compare structures and properties

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This issue of Chem&BioNews includes articles on ChemBio3D, Chem&BioFinder Enterprise, plus a new Chemoku contest.

Medicinal Chemistry Structure Browser: Compare structures and properties
Read ChemBio3D article

For chemists working in drug discovery, it is often useful to analyze a group of small molecules by comparing their structures and properties. ChemBio3D adds the Medicinal Chemistry Structure Browser and the concept of molecular properties in order to make it easier for chemists to examine a set of small molecule structures and their properties.


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Read Informatics Directions article

Auto-generated diagrams should convey structural information, not obscure it. The same concerns apply to manually-drawn structures, but most human chemists “intuitively know” how to do the right thing. ChemDraw 11 has taken several steps forward in addressing these issue and make auto-generated diagrams look better.


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--Boundary.11111111.11111111-- From owner-chemistry@ccl.net Wed Apr 16 17:11:00 2008 From: "Sahar Shamseldden ABDALLA sahar_shams20^hotmail.com" To: CCL Subject: CCL:G: spin multiplicity Message-Id: <-36763-080416121613-1760-rp07L/TcICkK9EsQlZlfRQ.:.server.ccl.net> X-Original-From: "Sahar Shamseldden ABDALLA" Date: Wed, 16 Apr 2008 12:16:10 -0400 Sent to CCL by: "Sahar Shamseldden ABDALLA" [sahar_shams20(0)hotmail.com] Iam doing Mo calculations on some organic molecules using GaussiaN AND I WOULD BE GRATEFUL TO ANYONE CAN HELP ME IN CALCULAtion the spin multiplicity. My method to do that is simply account the total number of electron in the all contributed atoms and devided by two. thank you in advance SAHAR sahar_shams20 . hotmail.com From owner-chemistry@ccl.net Wed Apr 16 17:46:00 2008 From: "Frank Neese neese . thch.uni-bonn.de" To: CCL Subject: CCL: low-spin versus high-spin complexes Message-Id: <-36764-080416133055-25968-udWxfgeDGRMi+fPSFdCxUA_._server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 16 Apr 2008 19:30:33 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese ~~ thch.uni-bonn.de] Gonzalo Jim nez-Os s gjimenez[*]unizar.es wrote: > Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez,,unizar.es] > Dear CCL'ers > > I have some doubts about the possibility to directly compare the energy of two different spin configurations of a given compound. For instance, one can compute the energy (and hence the optimized geometries) of a neutral dichloro-Co(II) complex in both low-spin (multiplicity 2) and high-spin (multiplicity 4) configurations. In my experience, the high-spin energies are always lower than the low-spin ones by more than 20 kcal/mol but with significant differences depending on the used functional (b3lyp and m05-2x under open-shell conditions). My question is: are these black box energy values comparable? If so, should I safely discard low-spin states and carry out the whole calculations with the high-spin configuration? > Yes, these values are comparable but whether or not you should discard one solution is system dependent. There actually is a rich literature on this subject. In most cases DFT tends to overstabilize low spin states but this tends to be critically dependent on the amount of HF exchange - the "optimal value" of %HF exchange - unfortunately - depends on the system. HF itself hugely overstabilizes high spin states. Reiher and co-workers recommend 15% HF exchange in B3LYP instead of the usual 20% for Fe(II). See: M. Reiher, O. Salomon, B. A. Hess, Reparametrization of hybrid functionals based on energy differences of states of di erent multiplicity, Theor. Chem. Acc. 107 2001, 48 See also: Fouqeau, A.; Casida, M.E.; Lawson, L.M.; Hauser, A.; Neese, F. (2005) Comparison of Density Functionals for Energy and Structural Differences Between the High-[5T2g: (t2g4)(eg2)] and Low-[1A1g: (t2g6)(eg0)] Spin States of Iron(II) Coordination Compounds : II. Comparison of Results for More than Ten Modern Functionals with Ligand Field Theory and Ab Initio Results for Hexaquoferrous Dication, [Fe(H2O)6]2+ and Hexaminoferrous Dication [Fe(NH3)6]2+, J. Chem. Phys., 122, 044110/1-13 Fouqueau, A.; Mer, S.; Casida, M.E.; Daku, L.M.L.; Hauser, A.; Mieva, T.; Neese, F. (2004) Comparison of Density Functionals for Energy and Structural Differences between the High [5T2g: t2g4eg2] and Low [1A1g: t2g6] Spin States of the Hexaquo-Ferrous Ion, [Fe(H2O)6]2+, J. Chem. Phys., 120, 9473-9486 and many many others if you look for the authors Reiher, Casida, Harvey, Shaik, Swart, Paulsen among others you will find many papers comparing different functionals. If your Co(II) systems are approximately tetrahedral, high-spin is the chemically sensible multiplicity. > In connection with this question, are the DFT energies of analogous monocationic Cu(I) (closed-shell, singlet) and dicationic Cu(II) (open-shell, doublet) complexes comparable? I mean, when the only difference between the two species is the oxidation state of the metal atom (and leaving apart the counteranions), is there any sense in comparing the relative stability of each (DFT) calculated structures? > The difference between the two energies for Cu(II) and Cu(I) at the same geometry represents the vertical ionization potential and at individually optimized geometries the adiabatic ionization potential. In reality these complexes exist in solution and will have very different solvatization energies. If you would calculate this perfectly you would obtain as the difference in free energy the redox potential of the Cu(II)/Cu(I) couple. Hope that helps, Frank -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese^-^thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Wed Apr 16 18:21:00 2008 From: "Marcelo Puiatti marcelo.puiatti*gmail.com" To: CCL Subject: CCL: basis set Message-Id: <-36765-080416121358-664-FZMx+Dlyw4Wie/JMqjjZWw^server.ccl.net> X-Original-From: "Marcelo Puiatti" Date: Wed, 16 Apr 2008 12:13:54 -0400 Sent to CCL by: "Marcelo Puiatti" [marcelo.puiatti**gmail.com] Hi Ioana, You have to use te gen keyword, as: # B3LYP/gen ... after the geometry you have to write the basis set, to get the format of the basis set you can use gfinput. It prints the basis set in a form suitable for use as general basis set input, and can thus be used in adding to or modifying standard basis sets. Best regards Marcelo From owner-chemistry@ccl.net Wed Apr 16 18:57:01 2008 From: "Frank Neese neese(a)thch.uni-bonn.de" To: CCL Subject: CCL:G: UV-Vis spectra prediction Message-Id: <-36766-080416135819-26129-qg7wiMGDx65Y0TFj817OWw=server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 16 Apr 2008 19:58:01 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese]![thch.uni-bonn.de] For bandshape calculations on larger molecules see: Petrenko, T.; Neese, F. (2007) A general efficient quantum chemical method for predicting absorption bandshapes, resonance Raman spectra and excitation profiles for larger molecules. J. Chem. Phys., 127, 164319 and references therein. In particular works of Robert Berger and Stefan Grimme and their co-workers on larger molecules as published in J. Chem. Phys. as well. Best regards, Frank Jerome Kieffer Jerome.Kieffer{=}terre-adelie.org schrieb: > Dear CCLers, > > I am trying to reproduce experimental UV-spectra of organic molecules : > > After the conversion wavelength (nm) -> energy (cm-1) of the > experimental spectrum, I deconvoluted it by a sum of gaussian > functions (using FitYK). It fits well. > > Transitions I obtained using TDDFT are pretty good compared with the > center of the gaussian deconvolution, but the FWHM of the > experimental spectrum's gaussian varies from 2000 to 8000 cm-1. > > So my question is: is it possible to calculate the broadening of an > absorption band ? some software like gausssum suggest a FWMH of > arround 3000cm-1 > Thank you for your help > > Regards > ------------------------------------------------------------------------ > Jérôme Kieffer > http://www.terre-adelie.org -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese^-^thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Wed Apr 16 19:35:02 2008 From: "David Gallagher gallagher.da{=}gmail.com" To: CCL Subject: CCL:G: UV-Vis spectra prediction Message-Id: <-36767-080416145033-30958-7fC7NX8NTvcbdFZAU2qSAA++server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_20387453==.ALT" Date: Wed, 16 Apr 2008 11:50:39 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da[#]gmail.com] --=====================_20387453==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Bonjour Jerome, The band-width is related to the gradient of the=20 excited state at the transition, i.e. a high=20 gradient allows access to more vibrational levels=20 > from the ground state and hence, a higher=20 band-width, conversely a low gradient gives a=20 narrow peak. I have some Powerpoint slides on=20 UV-spectra that I put together a few years ago=20 explaining the concept . Please let me know if you want a copy of them. Regards, David Gallagher CACheResearch.com At 05:16 AM 4/16/2008, Jerome Kieffer Jerome.Kieffer{=3D}terre-adelie.org= wrote: >Dear CCLers, > >I am trying to reproduce experimental UV-spectra of organic molecules : > >After the conversion wavelength (nm) -> energy=20 >(cm-1) of the experimental spectrum, I=20 >deconvoluted it by a sum of gaussian functions (using FitYK). It fits well. > >Transitions I obtained using TDDFT are pretty=20 >good compared with the center of the gaussian=20 >deconvolution, but the FWHM of the experimental=20 >spectrum's gaussian varies from 2000 to 8000 cm-1. > >So my question is: is it possible to calculate=20 >the broadening of an absorption band ? some=20 >software like gausssum suggest a FWMH of arround 3000cm-1 >Thank you for your help > >Regards > >---------- >J=E9r=F4me Kieffer >http://www.terre-adelie.org --=====================_20387453==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Bonjour Jerome,

The band-width is related to the gradient of the excited state at the transition, i.e. a high gradient allows access to more vibrational levels > from the ground state and hence, a higher band-width, conversely a low gradient gives a narrow peak.  I have some Powerpoint slides on UV-spectra that I put together a few years ago explaining the concept . Please let me know if you want a copy of them.

Regards,
David Gallagher
CACheResearch.com

At 05:16 AM 4/16/2008, Jerome Kieffer Jerome.Kieffer{=3D}terre-adelie.org wrote:
Dear CCLers,

I am trying to reproduce experimental UV-spectra of organic molecules :

After the conversion wavelength (nm) ->  energy (cm-1)  of the experimental spectrum,  I deconvoluted it by a sum of gaussian functions (using FitYK). It fits well.

Transitions I obtained using TDDFT are pretty good compared with the center of the gaussian deconvolution,  but the FWHM of the experimental spectrum's gaussian varies from 2000 to 8000 cm-1.

So my question is: is it possible to calculate the broadening of an absorption band ? some software like gausssum suggest a FWMH of arround 3000cm-1   
Thank you for your help

Regards
J=E9r=F4me Kieffer
http://www.terre-adelie.org
--=====================_20387453==.ALT-- From owner-chemistry@ccl.net Wed Apr 16 20:07:01 2008 From: "Pablo Vitoria Garcia pablo.vitoria[]ehu.es" To: CCL Subject: CCL: diarylketon conformation Message-Id: <-36768-080416185145-15254-VBCIwZFl8bdCgjoAtKMZsA*server.ccl.net> X-Original-From: Pablo Vitoria Garcia Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Thu, 17 Apr 2008 00:51:10 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria Garcia [pablo.vitoria!A!ehu.es] Dear Prabha, A search on the CSD resulted in 56 crystal structures which contain =20 one or more benzophenone moieties. The average dihedral angle between =20 the phenyl and keto groups (0=C2=BA means coplanar) is about 30=C2=BA (sampl= e SD =20 =3D 10=C2=BA). And the two dihedral angles between the keto and phenyls are = =20 inversely correlated, so that the angle between both phenyl groups is =20 centered at about 60=C2=BA. Regards Pablo "Prabha Lakshmi prabhalak26(0)yahoo.co.in" =20 ha escrito: > > Sent to CCL by: Prabha Lakshmi [prabhalak26{:}yahoo.co.in] > Dear CCLers, > > in a system similar to phenylCOphenyl, what are dihedral angles =20 > expected involving the carbonyl moiety? > > Thank you, > prabhalak > > Molecular Biochemistry PhD Student > > > Forgot the famous last words? Access your message archive =20 > online at http://in.messenger.yahoo.com/webmessengerpromo.php > > > > -> > > > From owner-chemistry@ccl.net Wed Apr 16 20:57:00 2008 From: "rachel.crespo-$-uam.es" To: CCL Subject: CCL:G: IRC calculation Message-Id: <-36769-080416161657-30097-XnKohn8YlVvx9BI8GNcv6g+*+server.ccl.net> X-Original-From: rachel.crespo##uam.es Date: Wed, 16 Apr 2008 21:08:58 MET Sent to CCL by: rachel.crespo~~uam.es Dear ccl members I did a calculation of a IRC path employing gaussian03 and I found that the energy profile has a minimun on the TS. What does it means? I don't undestand what happen. Best regards, Rachel -------------------------------------------------------------------------- Mensaje enviado mediante una herramienta Webmail integrada en *El Rincon*: ------------->>>>>>>> https://rincon.uam.es <<<<<<<<--------------