From owner-chemistry@ccl.net Tue Oct 4 01:13:01 2005 From: "Per-Ola Norrby pon]-[kemi.dtu.dk" To: CCL Subject: CCL: What keeps a molecule adsorbed? Message-Id: <-29484-051004011039-4220-tfxFq8rE3XUmyCeGZ/U2lw.:.server.ccl.net> X-Original-From: Per-Ola Norrby Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Tue, 4 Oct 2005 07:10:03 +0200 Mime-Version: 1.0 Sent to CCL by: Per-Ola Norrby [pon;;kemi.dtu.dk] To continue on this thread, there are also some important adsorption forces that are NOT captured by standard DFT. The simplest would be the London dispersion (induced dipole-induced dipole). There are also some recent, interesting results by Schwarz and coworkers showing that binding energies change drastically if the gold is treated relativistically. I don't have the reference handy, but I believe I saw numbers like standard relativistic ECP: no binding; fully relativistic calculation: 20 kcal/mol binding (something like that). Of course fully relativistic calculations are out of the question for more than a few atoms. And if your question really was "what constitutes binding in my calculation" as opposed to binding in reality, then both of the above effects are irrelevant, since they wouldn't appear in your calculations. Regards, Per-Ola >Sent to CCL by: Joseph Han [jhh3851/a\yahoo.com] >If the adsorption energy is small (< 5 kcal/mol), it might also be one of the >following: > >(1) Basis set superposition error. You might need to do a counterpoise >correction to address this. > >(2) Dipole-dipole interaction (e.g. van der Waals) where you induce a dipole >in the gold cluster leading to weak electrostaic attraction. > >Joseph > > >--- "Noel O Boyle noel.oboyle2|*|mail.dcu.ie" > wrote: > >> > > Sent to CCL by: "Noel O'Boyle" [noel.oboyle2++mail.dcu.ie] >> Dear all, >> >> I have been trying to explain the results of a DFT study (using G03) >> where a molecule adsorbs onto a gold cluster through its nitrogen atom. >> >> I created an isosurface of the change in the electron density associated >> with the adsorption (by calculating the electron densities of the >> molecule and the gold cluster separately at the geometry of the adsorbed >> system). This shows that electron density *decreases* in the area >> between the adsorbate and the surface. This is the opposite of what I >> expected. >> >> A paper by Bilic, Reimers, Hush and Hafner (JCP, 2002, 116, 8981) shows >> the same effect for ammonia on an infinite surface of gold(111). It >> shows the same result, and says that this is evidence that covalent >> bonding effects are not so important (they also have other evidence). >> >> It seems that I do not understand bonding very well - what keeps the >> molecule stuck to the surface, if it isn't a shared electron or two? >> >> Regards, >> Noel >> -- >> Dr. Noel M. O'Boyle, >> Group of Dr. John Mitchell (http://www-mitchell.ch.cam.ac.uk), >> Unilever Centre for Molecular Science Informatics, >> Dept. of Chemistry, >> University of Cambridge, >> U.K.-- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon^^^kemi.dtu.dk tel +45-45252123, fax +45-45933968 From owner-chemistry@ccl.net Tue Oct 4 14:08:00 2005 From: "Jeff Nauss jnauss|,|accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for November Message-Id: <-29485-051004140714-26878-MmidQXK+hcnisbdZze8wDg_+_server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Tue, 4 Oct 2005 11:07:03 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss^^accelrys.com] Accelrys Inc. are holding the following training workshops during November 2005. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. SAN DIEGO, CA, USA Introduction to MS Modeling 9 Nov Introduction to Nanomaterials Modeling 10-11 Nov Introduction to MS Modeling 14 Nov Introduction to Quantum Mechanics Modeling 15-16 Nov Introduction to Polymer Modeling 17-18 Nov BURLINGTON, MA, USA Introduction to DS Modeling 1.1 2-3 Nov Structure Based Drug Design with DS Modeling 1.2 4 Nov Pharmacophore Generation with Catalyst 8-9 Nov Structure Based Drug Design with Cerius2 10-11 Nov Library Design and Analysis with Cerius2 14-15 Nov QSAR with Cerius2 16-17 Nov ONLINE TRAINING Introduction to General Modeling using Cerius2 2 Nov (4pm GMT) DS ViewerPro 15 Nov (7am PST) GCG Upgrade 28 Nov (3pm PST) GCG Upgrade 29 Nov (7am PST) SeqWeb Upgrade 30 Nov (3 PM PST) SeqWeb Upgrade 1 Dec (7 AM PST) Further details can be found on our website at http://www.accelrys.com/training/general/calendar.html and http://www.accelrys.com/training/general/calendar_online.html Questions regarding scheduling and content should be directed to workshops::accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From owner-chemistry@ccl.net Tue Oct 4 14:43:00 2005 From: "John McKelvey jmmckel{}attglobal.net" To: CCL Subject: CCL: MOPAC QM/MM ...NOTHING TO DO WITH C++/F77 ...[:-) Message-Id: <-29486-051004062427-22775-vyw133qb5RDmH2oX8TGk6g!A!server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 04 Oct 2005 05:22:07 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel[]attglobal.net] Dear Seth, Many thanks for your comments! I had run across DYNAMO while doing a GOOGLE search, but have had no idea about its suitability. I did run across it also at the LINUX4CHEMISTRY web site. I would probably use AM1 for the moment instead of INDO/S as it works better for geometries, and doesn't do horrible for excited states. Fortunately I have a very efficient excited state gradient package thet works for AM1. Many thanks again.. John Dr Seth Olsen s.olsen1[]uq.edu.au wrote: >Sent to CCL by: Dr Seth Olsen [s.olsen1_._uq.edu.au] > >Hi John, > >If you're using Mopac 7, then I think that the MD library 'DYNAMO' has >an interface. I believe also that Ghemical can run QM/MM with Mopac 7. > >If you're optimizing excited state geometries it may be useful to >reparametrize the method against ab initio data. Some common >semiempirical excited state methods (ZINDO) are parametrized against >spectroscopic data - if the excited state dynamics leads out of the >region where the field couples the states than the results might not be >correct. I would refer you to works by Toniolo, Granucci and Martinez >regarding this issue (udoubtedly this list is incomplete, but these >names are at the top of my mind right now). > >Cheers, > >Seth > >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > >Dr Seth Olsen, PhD >Postdoctoral Fellow, Biomolecular Modeling Group >Centre for Computational Molecular Science >Chemistry Building, >The University of Queensland >Qld 4072, Brisbane, Australia > >tel (617) 33653732 >fax (617) 33654623 >email: s.olsen1:+:uq.edu.au >Web: www.ccms.uq.edu.au > >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > > > >----- Original Message ----- > > >>From: "John McKelvey jmmckel#attglobal.net" >> >> >Date: Tuesday, October 4, 2005 4:49 am >Subject: CCL: MOPAC QM/MM ...NOTHING TO DO WITH C++/F77 ...[:-) > > >>Sent to CCL by: John McKelvey [jmmckel**attglobal.net] >>All, >> >>Using MOPAC I would like to optimize excited state geometries of >>molecules imbeded in a solvent cage. Is there such a QM/MM code >>in the >>public domain? I would like to use my own version of MOPAC in such >>a >>program, or modify an existing one. >> >>Best regards, >> >>John McKelvey >> >> >> >>-= This is automatically added to each message by the mailing >>script =- >>To recover the email address of the author of the message, please >>changethe strange characters on the top line to the :+: sign. You can >>also> >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >>+-+-+> > > > > > > From owner-chemistry@ccl.net Tue Oct 4 15:18:00 2005 From: "Eric Scerri scerri]![chem.ucla.edu" To: CCL Subject: CCL: glossary of coined terms Message-Id: <-29487-051004141024-27971-fR/TeFBHCP9sDRk+Y2ekVw++server.ccl.net> X-Original-From: Eric Scerri Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Tue, 4 Oct 2005 11:08:22 -0700 Mime-Version: 1.0 Sent to CCL by: Eric Scerri [scerri a chem.ucla.edu] List members may be interested in the following glossary of coined terms that has just been announced on the chemical education listserver, "Glossary of Coined Names & Terms Used in Science", by Dr. John Andraos, York University (Toronto) --Recently updated. www.careerchem.com/NAMED/Glossary-Coined-Terms.pdf regards, eric scerri -- Dr. Eric Scerri , UCLA, 4077C, Young Hall, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri%a%chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor-in-chief of Foundations of Chemistry http://springerlink.metapress.com/app/home/journal.asp?wasp=503c4f278d734f3f957c34496b6939dc&referrer=parent&backto=linkingpublicationresults,1:103024,1 Also see International Society for the Philosophy of Chemistry http://ispc.sas.upenn.edu/ From owner-chemistry@ccl.net Tue Oct 4 21:02:00 2005 From: "Cesar Augusto MujicaMartinez cesarmujica[*]gmail.com" To: CCL Subject: CCL: W:question about PBC in G03W Message-Id: <-29488-051004181732-11547-/7FbA/XPK+YXQN80/Q18LA++server.ccl.net> X-Original-From: "Cesar Augusto MujicaMartinez" Sent to CCL by: "Cesar Augusto MujicaMartinez" [cesarmujica:-:gmail.com] Dear CCL members, I'm a undergraduate student user of G03W software and I don't know how write the "route section" for a PBC calculation. By default, when the molecule is constructed (in Gaussview using PBC), part of route section appear, but I need energy in some K points for draw a band structure and DOS and I don't know how make this. Would grateful any suggest respect this problem. Thanks in advance. Cesar A. Mujica M. cesarmujica(0)gmail.com Universidad del Valle Cali-Colombia From owner-chemistry@ccl.net Tue Oct 4 21:37:01 2005 From: "Donald James Keidel keided01() student.ucr.edu" To: CCL Subject: CCL: W:Connelly Surface of Cavities Message-Id: <-29489-051004190111-21492-yj41I0he3mUeXjdJN4yGkQ[#]server.ccl.net> X-Original-From: "Donald James Keidel" Sent to CCL by: "Donald James Keidel" [keided01^_^student.ucr.edu] I am looking for a program, free or not, that can fill in the gaps of cavities in proteins with a connelly surface. As i understand it now programs can generate a connelly surface over the protein atoms. I want to be able to visualize the cavities in proteins. Thank you in advance for all replies. Don From owner-chemistry@ccl.net Tue Oct 4 22:12:00 2005 From: "Mark Thompson mark/./arguslab.com" To: CCL Subject: CCL: Chemscore ? Message-Id: <-29490-051004204300-28139-MnBHrtrGKrx3ioJ2o5B+3Q,server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 04 Oct 2005 17:42:40 -0700 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark^^arguslab.com] I'd like to hear from anyone who has an implementation of the ChemScore scoring function. Does anyone know of any open source or freely available sources of this scoring function? Please contact me at mark*|*arguslab.com Thanks in advance, Mark ---------------------------- Mark Thompson mark*|*arguslab.com http://www.arguslab.com ----------------------------