From chemistry-request@ccl.net Sat Jun 19 16:44:53 2004 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5JLipF7004144 for ; Sat, 19 Jun 2004 16:44:52 -0500 Received: from 192.168.0.101 (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i5JLnMPu028984; Sat, 19 Jun 2004 14:49:22 -0700 Date: Sat, 19 Jun 2004 14:49:20 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <3210337657.20040619144920=at=uci.edu> To: Qiang Lu CC: Errol Lewars , chemistry=at=ccl.net Subject: Re: CCL:Re[2]: how to calculate proton dissociation energy in GAUSSIAN03 In-Reply-To: <996418025.20040618185904=at=uci.edu> References: <6039937.20040617140858=at=uci.edu> <40D36714.7090100=at=trentu.cA> <996418025.20040618185904=at=uci.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Errol, I think I understand now. There is no need to calculate the single point calculation of H+. The difference BH-B between different B is what we care and that will cancel the energy come from H+. -- Best regards, Qiang mailto:qiangl=at=uci.edu =================Original message text=============== Hi Errol, Thank you for you reply. That is what I mean. And for the energy of H+, can I simply do a single point calculation of H+? -- Best regards, Qiang mailto:qiangl=at=uci.edu =================Original message text=============== Hello, You mean deltaE for the reaction BH --> B- + H+ , where BH is imidazole coordinated to Zn++? You calculate the energy of the optimized structure BH, and the energy of the optimized B-, and take the difference in E of the of thr reactant and the products. The level of the calc may be mnportant, so work your way up. EL === Qiang Lu wrote: >Dear CCL-ers, > >I want to calculate the proton dissociation energy of imidazole when >it is a ligand of ZN. Could you tell me some hint about how to perform >it? Any suggestion will be helpful. Thank you in advance. > > > > > ==============End of original message text=========== -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY=at=ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST=at=ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ==============End of original message text=========== From chemistry-request@ccl.net Sat Jun 19 06:09:59 2004 Received: from mail.mans.edu.eg (mail.mans.edu.eg [193.227.50.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5JB9vF7016558 for ; Sat, 19 Jun 2004 06:09:58 -0500 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C455ED.ECD245B0" Subject: optimizing subset in a supermolecule X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Sat, 19 Jun 2004 14:09:44 +0300 Message-ID: <095F5EDC6A006F41AFF7804586108ACF38E541=at=mail.mans.edu.eg> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: optimizing subset in a supermolecule Thread-Index: AcRV7ezSknMkJBySR1mGPkh1COpHDQ== From: "Tarek M. El-Gogary" To: X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C455ED.ECD245B0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 RGVhciBDQ0wtZXJzLA0KDQpJIHdhbnQgdG8gcGVyZm9ybSBhIGdlb20uIG9wdHouIGNhbGN1bGF0 aW9uIGZvciBhIG1vbm9tZXIgaW4gYSB0cmltZXIgc3VwZXJtb2xlY3VsZSBzeXN0ZW0gbWFpbnRh aW5pbmcgdGhlIHRyaW1lciBzdGFydGluZyBzdHJ1Y3R1cmUgKHdoaWNoIGlzIGNvbWluZyBmcm9t IHgtcmF5IHN0dWR5KS4gQ291bGQgeW91IHRlbGwgbWUgc29tZSBoaW50IGFib3V0IGhvdyB0byBw ZXJmb3JtIGl0PyBBbnkgc3VnZ2VzdGlvbiB3aWxsIGJlIGhlbHBmdWwuIFRoYW5rIHlvdSBpbiBh ZHZhbmNlLg0KDQogDQoNCg0KQmVzdCByZWdhcmRzLA0KIHRhcmVrDQo= ------_=_NextPart_001_01C455ED.ECD245B0 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj48SFRNTD48SEVBRD48TUVUQSBIVFRQLUVRVUlWPSJDb250ZW50LVR5cGUiIENPTlRFTlQ9 InRleHQvaHRtbDsgY2hhcnNldD11dGYtOCI+PC9IRUFEPjxCT0RZPjxESVY+PEZPTlQgc2l6ZT0y PkRlYXIgQ0NMLWVycyw8QlI+PEJSPkkgd2FudCB0byBwZXJmb3JtIGEgCmdlb20uIG9wdHouIGNh bGN1bGF0aW9uIGZvciBhIG1vbm9tZXIgaW4gYSB0cmltZXIgc3VwZXJtb2xlY3VsZSAKc3lzdGVt Jm5ic3A7bWFpbnRhaW5pbmcgdGhlIHRyaW1lciBzdGFydGluZyBzdHJ1Y3R1cmUgKHdoaWNoIGlz IGNvbWluZyBmcm9tIAp4LXJheSBzdHVkeSkuIENvdWxkIHlvdSB0ZWxsIG1lIHNvbWUgaGludCBh Ym91dCBob3cgdG8gcGVyZm9ybSBpdD8gQW55IApzdWdnZXN0aW9uIHdpbGwgYmUgaGVscGZ1bC4g VGhhbmsgeW91IGluIGFkdmFuY2UuPEJSPjxCUj4mbmJzcDs8QlI+PEJSPjxCUj5CZXN0IApyZWdh cmRzLDxCUj4mbmJzcDt0YXJlazwvRk9OVD48L0RJVj48L0JPRFk+PC9IVE1MPg== ------_=_NextPart_001_01C455ED.ECD245B0-- From chemistry-request@ccl.net Sat Jun 19 11:33:28 2004 Received: from nova.its.msstate.edu (nova.its.msstate.edu [130.18.2.42]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5JGXRF7028846 for ; Sat, 19 Jun 2004 11:33:27 -0500 Received: from localhost (archive.msstate.edu [130.18.80.18]) by nova.its.msstate.edu (iPlanet Messaging Server 5.2 HotFix 1.17 (built Jun 23 2003)) with ESMTP id <0HZK004G8DLH4Z*at*nova.its.msstate.edu> for chemistry*at*ccl.net; Sat, 19 Jun 2004 11:24:53 -0500 (CDT) Received: from ws209-37.arbouracres.dynamic.msstate.edu (ws209-37.arbouracres.dynamic.msstate.edu [130.18.37.209]) by webmail.msstate.edu (IMP) with HTTP for ; Sat, 19 Jun 2004 11:24:53 -0500 Date: Sat, 19 Jun 2004 11:24:53 -0500 From: pr4*at*ra.msstate.edu Subject: Summary: Relativistic Effect X-Originating-IP: 130.18.37.209 To: chemistry*at*ccl.net Message-id: <1087662293.40d468d50fb85*at*webmail.msstate.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT User-Agent: Internet Messaging Program (IMP) 3.2.3 X-Spam-Status: No, hits=2.1 required=7.5 tests=FVGT_m_MULTI_ODD2,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I would like to thank everyone who replied to my question. The following is a summary of the responses. I hope this summery can also help others. This is my original question: I want to study geometries of some molecules with Pb and Sn. I know that for heavy atoms I need to include the relativistic effect in my calulation but I do not know what method and basis set is the best for these heavy atoms. I have several articles discussing relativistic effect but would like suggestions of articles and books also. Best regards, Pornpun Rattananakin -- Sorry for the self-promotion, but I might suggest the new cc-pVnZ-PP (n=D-5) basis sets for these elements that use very accurate relativistic effective core potentials. These sets are described in JCP 119, 11099 (2003) and JCP 119, 11113 (2003) and are available for download on the EMSL basis set website (http://www.emsl.pnl.gov/forms/basisform.html) regards, Kirk Peterson -- Hi, If you wanted to cut down on calculation time, I can tell you that the Stuttgart pseudopotentials have included spin-orbit coupling effects in the parameterization. They work reasonably well. Look for papers by Dolg, Stoll and Preuss. Hope that helps, Sean Hughes Centre for Research in Molecular Modeling (CERMM) Dept. Chemistry and Biochemistry Concordia University 7141 Sherbrooke St. West Montreal, Quebec Canada H4B 1R6 Tel: (514)-848-2424 ext.4260 Fax: (514)-848-2868 -- Dear Pornpun Rattananakin, Perhaps Erik van Lenthe's Ph.D. thesis on the relativistic ZORA method, as implemented in ADF, could be of interest to you: http://www.scm.com/Doc/vlenthe.pdf I hope this is relevant for you. If you want more info on this, let me know. Best regards, Stan van Gisbergen -- I study Ruthenium complexes using B3LYP/LanL2DZ. The LanL2DZ basis set includes a pseudopotential for the inner electrons of the Ru - this takes care of the relativistic effect as well as speeds up the calculation. I find the books by C. Cramer and F. Jensen very useful: "Introduction to Computational Chemistry" and "Essentials of Computational Chemistry" (both > from Wiley). Noel -- "So the LanL2DZ basis set is the best one for B3LYP method, isn't it?" Well, I don't know if that's true. I think you need a basis set with an effective core potential (ECP). If you look at http://www.gaussian.com/g_ur/m_basis_sets.htm and search the page for the word ECP you find the following basis sets: SHC, CEP-4G, CEP-31G, CEP-121G, LanL2MB, LanL2DZ, SDD. Which is best?? Well, LanL2DZ is better than LanL2MB. And all of the CEPs are the same after the second row (so they are probably not good for you). Some people using the SDD ones. I recommend testing LanL2DZ and SDD versus a crystal structure, or finding some reference where results from different ECPs are compared. Noel -- Dear Pornpun I good idea is to use ECP potentials for your studies. Their computational cost is reasonable and offer good results. A very good book on relativistic effects is the one of Krishnan Balasubramanian, Relativistic effects in Chemistry.Also the Review article of P. Pyyko, Chem. Rev 88, 563 1988, describes in brief topics concerning the effect of Relativity on Molecular Gem. and other Properties. Also you will find a reach source of articles based on relativity. The best Aggelos Avramopoulos PHD --