From owner-chemistry@ccl.net Fri Apr 14 10:07:36 2006 From: "Andreas Klamt klamt]![cosmologic.de" To: CCL Subject: CCL: FW: bindings energy with BSSE or in solvent? Message-Id: <-31515-060413164754-28166-K7+Wqw5IaQWIEMvqqgcs8Q[#]server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 13 Apr 2006 21:45:06 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt%a%cosmologic.de] This is an interesting question. I never thought about it in this way. But I do not really believe that the BSSE caculated in the gasphase is relevant for the liquid phase, because solvation as in PCM or COSMO tends to localize the wavefunctions a bit better than in the gasphase. Thus the BSSE should be smaller. My recipe for reaction energies in solution is: 1) desolvate the educts (e.g. with PCM or COSMO, or best with COSMO-RS) 2) apply gasphase reaction QC methods 3) solvate the products (e.g. with PCM or COSMO, or best with COSMO-RS) Shobe, David dshobe#,#sud-chemieinc.com schrieb: > Sent to CCL by: "Shobe, David" [dshobe##sud-chemieinc.com] > You might not be able to combine BSSE and PCM in a single calculation, but you can still calculate a BSSE correction in one calculation and calculate the solvation energy in another. > > --David Shobe, Ph.D., M.L.S. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > -----Original Message----- > >> From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net] >> > Sent: Thursday, April 13, 2006 12:00 PM > To: Shobe, David > Subject: CCL: bindings energy with BSSE or in solvent? > > Sent to CCL by: Goedele Roos [groos- -vub.ac.be] > > Dear list, > It seems one has to choose between the calculation of the bindingsenergy with BSSE or in solvent. Because no BSSE is available for a continuum solvent model (PCM), or am I wrong here? > What would you choose and why: gasphase with BSSE? Or solvent phase without BSSE and calculating all the three components apart: E(complex); E(proteine); E(ligand)? > > Thank you for answering my question! > > Best regards , Goedele > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. > Thank you.> > > > > > -- ----------------------------------------------------------------------------- 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 ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Apr 14 10:08:36 2006 From: "matthieu soulis mathsou_87|,|yahoo.fr" To: CCL Subject: CCL:G: dipole of each molecular orbital Message-Id: <-31516-060411115945-8411-evSruPNsywUXhpMfYYkt0w_+_server.ccl.net> X-Original-From: "matthieu soulis" Date: Tue, 11 Apr 2006 11:59:44 -0400 Sent to CCL by: "matthieu soulis" [mathsou_87#yahoo.fr] I've got a problem: I want to compute the dipole created by each molecular orbital of a molecule with the gaussian 03 code. I have already tried for the CH2O molecule using the "cubman" program (given with G03) but I have obtained some "bizarre" results. I transform the checkpoint file following the user's guide procedure and I obtain the following results I underline that the molecule is in the XY plan and that the molecule is oriented along the y axe: Title Card Required mo=1 Alpha MO coefficients SumAP= 0.7981159190 SumAN= -0.0860337419 SumA= 0.7120821772 CAMax= 5.8359400000 XYZ= 0.0538550000 1.3293060000 0.0538850000 CAMin= -0.0024043000 XYZ= 0.0538550000 0.7932540000 1.6620410000 DipAE= 0.0000305135 -0.9279419621 -0.0000342720 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= 0.0000235135 -0.9279429621 -0.0000342720 Title Card Required mo=2 Alpha MO coefficients SumAP= 1.2455470476 SumAN= -0.1143141935 SumA= 1.1312328542 CAMax= 4.4573500000 XYZ= 0.0538550000 -0.9489150000 0.0538850000 CAMin= -0.0016472100 XYZ= -1.8223270000 -2.2890450000 0.0538850000 DipAE= 0.0000441767 1.2292498933 -0.0000486488 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= 0.0000371767 1.2292488933 -0.0000486488 Title Card Required mo=3 Alpha MO coefficients SumAP= 8.1836724658 SumAN= -0.0901491353 SumA= 8.0935233305 CAMax= 0.4932330000 XYZ= 0.0538550000 0.6592410000 0.0538850000 CAMin= -1.0863000000 XYZ= 0.0538550000 1.3293060000 0.0538850000 DipAE= -0.0004865924 -3.2651757505 -0.0001277952 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= -0.0004935924 -3.2651767505 -0.0001277952 SumAP= 9.8341927996 SumAN= -2.3865627191 SumA= 7.4476300806 CAMax= 0.4301390000 XYZ= 0.0538550000 1.1952930000 0.0538850000 CAMin= -0.6933350000 XYZ= 0.0538550000 -0.9489150000 0.0538850000 DipAE= -0.0009107467 24.3581085701 -0.0000446523 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= -0.0009177467 24.3581075701 -0.0000446523 Title Card Required mo=5 Alpha MO coefficients SumAP= 6.3415780713 SumAN= -6.3435233572 SumA= -0.0019452859 CAMax= 0.3731060000 XYZ= 0.3218810000 1.3293060000 0.0538850000 CAMin= -0.3759850000 XYZ= -0.3481840000 1.3293060000 0.0538850000 DipAE= -21.6482930396 -0.0037676243 -0.0000000422 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= -21.6483000396 -0.0037686243 -0.0000000422 Title Card Required mo=6 Alpha MO coefficients SumAP= 8.3859144358 SumAN= -1.7044680395 SumA= 6.6814463964 CAMax= 0.6596890000 XYZ= 0.0538550000 1.7313450000 0.0538850000 CAMin= -0.5646680000 XYZ= 0.0538550000 1.1952930000 0.0538850000 DipAE= -0.0032863136 0.5291573208 -0.0000749632 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= -0.0032933136 0.5291563208 -0.0000749632 Title Card Required mo=7 Alpha MO coefficients SumAP= 5.7463751075 SumAN= -5.7464097202 SumA= -0.0000346126 CAMax= 0.5229510000 XYZ= 0.0538550000 1.3293060000 0.3219110000 CAMin= -0.5274720000 XYZ= 0.0538550000 1.3293060000 -0.3481540000 DipAE= -0.0000000282 -0.0000347982 -17.6820518448 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= -0.0000070282 -0.0000357982 -17.6820518448 Title Card Required mo=8 Alpha MO coefficients SumAP= 6.1119057473 SumAN= -6.1120541127 SumA= -0.0001483654 CAMax= 0.6018680000 XYZ= 0.3218810000 1.3293060000 0.0538850000 CAMin= -0.6065450000 XYZ= -0.3481840000 1.3293060000 0.0538850000 DipAE= 9.8327911932 0.0038621318 -0.0000000357 DipAN= -0.0000070000 -0.0000010000 0.0000000000 DipA= 9.8327841932 0.0038611318 -0.0000000357 My question is: How can a molecule situated in the XY plan have a molecular orbital mini dipole along the z axe??? please help me i'm desperate!! thank you for your responses Matthieu SOULIS SPCTS facult des sciences et technique de Limoges 123 avenue Albert Thomas 87060 LIMOGES CEDEX e-mail: mathsou_87^^yahoo.fr From owner-chemistry@ccl.net Fri Apr 14 14:02:00 2006 From: "Jan Labanowski janl[a]speakeasy.net" To: CCL Subject: CCL: CCL Tech problems, Support CCL, and Best Wishes Message-Id: <-31517-060414140016-6095-VB1IWMwKp9CaTN+XfQazMg^server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 14 Apr 2006 18:00:13 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl..speakeasy.net] Dear Netters, Some of you may have noticed that CCL has technical problems. I need to buy another computer and hard drives, refresh system installation, etc. Some of you may know that it is not the best time for me to do it. I am also extremely busy lately with another project. So bare with me for a few days or maybe a week or so. In the meantime (and after) please remember to support CCL. I really need your help to run CCL Visit the page: http://www.ccl.net/chemistry/aboutccl/supporting/ Do not hesitate to contact me if you prefer that I would do it rather than going through the Web interface for the services. Again... You may find some of these services useful. And they are not priced high. You will get a regular invoice that you can charge against your project or other funds. Last but not least, you will be helping Computational Chemistry, your fellow Computational Chemists, and me --- the CCL unmoderator who was carrying it for you for over 15 years under many different circumstances. In this Holiday period (for some...) ALL THE BEST!!! Do not eat too much -- rather use the Spring (for some) to enjoy the new life and hope. Jan Labanowski CCL Moderator jkl*o*ccl.net From owner-chemistry@ccl.net Fri Apr 14 20:54:01 2006 From: "Young Leh youngleh|,|gmail.com" To: CCL Subject: CCL: Zeolite Y, Mordenite Unit Cell Structure File Message-Id: <-31518-060414200839-8920-HoDEEnBG54Dl6BhfKvDBdQ#server.ccl.net> X-Original-From: "Young Leh" Date: Fri, 14 Apr 2006 20:08:34 -0400 Sent to CCL by: "Young Leh" [youngleh[*]gmail.com] Dear CCLer, Does anybody could kindly provide the structure files for Zeolite type Y and Mordenite? I am able to look them up through http://www.iza-structure.org/databases/ . However, I am not able to download them. thanks