From owner-chemistry@ccl.net Wed Feb 8 05:36:00 2012 From: "DJUKIC Jean-Pierre djukic]![unistra.fr" To: CCL Subject: CCL: How can be separate CH-pi and pi-pi interaction? Message-Id: <-46261-120208053314-17559-NRYsRkm/Ng46QJeBdKGX1w##server.ccl.net> X-Original-From: DJUKIC Jean-Pierre Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 08 Feb 2012 11:32:45 +0100 MIME-Version: 1.0 Sent to CCL by: DJUKIC Jean-Pierre [djukic^unistra.fr] Dear RAM, The first thing is to define the physical base of the so-called C-H -pi and pi-pi interactions. Once this is done, the rest is easier. Best regards, JPD Le 07/02/2012 19:22, Ram Shankar S ramchemistry2011]=[gmail.com a écrit : > Sent to CCL by: "Ram Shankar S" [ramchemistry2011|gmail.com] > Dear All, > How can we separate CH-pi and pi-pi interaction into strong, moderate and weak based on the bond distance and bond angles (geometrical parameters) in pure organic substances? Whether is there any reference available for this? > > On what basis this kind of interactions (CH-pi and pi-pi) is separated, and I would like to know how this CH-pi and pi-pi interactions can be classified as strong, moderate and weak.Please help me in this regards. > > Thanks in advance > > With Regards, > RAAM> > > -- From owner-chemistry@ccl.net Wed Feb 8 06:37:00 2012 From: "Guntram Schmidt guntram.schmidt*|*chemie.uni-halle.de" To: CCL Subject: CCL: How can be separate CH-pi and pi-pi interaction? Message-Id: <-46262-120208053443-17727-893QHogO/eTrZvmpWAiUOw(!)server.ccl.net> X-Original-From: Guntram Schmidt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 08 Feb 2012 11:34:27 +0100 MIME-Version: 1.0 Sent to CCL by: Guntram Schmidt [guntram.schmidt[A]chemie.uni-halle.de] Dear RAAM, this surely is not a simple question and there won't be any straigtforward answers. But I can advice you an extremely cool tool for the analysis of your interactions: http://faculty1.ucmerced.edu/ejohnson29/2.cfm?pm=432&lvl=2&menuid=562 based on Johnson, E. R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A. J., & Yang, W. (2010). Revealing noncovalent interactions. Journal of the American Chemical Society, 132(18), 6498-506. doi:10.1021/ja100936w regards, Guntram Am 07.02.2012 19:22, schrieb Ram Shankar S ramchemistry2011]=[gmail.com: > Sent to CCL by: "Ram Shankar S" [ramchemistry2011|gmail.com] > Dear All, > How can we separate CH-pi and pi-pi interaction into strong, moderate and weak based on the bond distance and bond angles (geometrical parameters) in pure organic substances? Whether is there any reference available for this? > > On what basis this kind of interactions (CH-pi and pi-pi) is separated, and I would like to know how this CH-pi and pi-pi interactions can be classified as strong, moderate and weak.Please help me in this regards. > > Thanks in advance > > With Regards, > RAAM> > From owner-chemistry@ccl.net Wed Feb 8 11:59:00 2012 From: "Beatriz C Ramirez beacrm%%gmail.com" To: CCL Subject: CCL:G: Vibrational analysis demon2K Message-Id: <-46263-120208104341-7162-Z14ZLPry3+EE7fzEMGp6rw###server.ccl.net> X-Original-From: "Beatriz C Ramirez" Date: Wed, 8 Feb 2012 10:43:40 -0500 Sent to CCL by: "Beatriz C Ramirez" [beacrm__gmail.com] Hi, I usually look for transition states with Gaussian and I employ the thermochemistry data to calculate the activation energy for the reactions. Now I started to work with the software deMon2k, wich works great, but I'm not sure how to read the thermochemistry in the output file, because the data obtained dont agrees with the experimental data. I think that I'm picking the wrong values. Anyone knows how to read the .out file and the data from the vibrational analysis to calculate activation energies? If somebody can help me I'll be very thankfull Thanks in advance Beatriz R. From owner-chemistry@ccl.net Wed Feb 8 13:01:00 2012 From: "Sten Nilsson Lill stenil[#]chalmers.se" To: CCL Subject: CCL: How can be separate CH-pi and pi-pi interaction? Message-Id: <-46264-120208125951-27231-Wq2ydAW3/OJcJb8tgRlkLA-,-server.ccl.net> X-Original-From: Sten Nilsson Lill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 8 Feb 2012 17:59:42 +0000 MIME-Version: 1.0 Sent to CCL by: Sten Nilsson Lill [stenil a chalmers.se] Dear Ram, as already suggested, NCI-plots are informative to illustrate for example CH-pi and phenyl-phenyl interactions. Based on the "color-coding" of the reduced density gradient isosurfaces generated in the plot you can to some extent quantify the strength of the interaction. For some recent examples, see a study by Jacobsen: E. M. Beck, A. M. Hyde and E. N. Jacobsen, Org. Lett., 2011, 13, 4260?-4263 and some work from our own group: http://pubs.rsc.org/en/content/articlelanding/2012/ob/c2ob06910e The paper on NCI-plot can be found in: J. Contreras?Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J.?P. Piquemal, D. N. Beratan and W. Yang, J. Chem. Theory Comput., 2011, 7, 625?632. Hope that helps, Sten Ph.D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg SE-412 96 Gothenburg, Sweden e-mail: stenil_+_chem.gu.se Phone: +46-31 786 9103 Fax: +46-31-772 3840 ________________________________________ > From: owner-chemistry+stenil==chem.gu.se_+_ccl.net [owner-chemistry+stenil==chem.gu.se_+_ccl.net] on behalf of Ram Shankar S ramchemistry2011]=[gmail.com [owner-chemistry_+_ccl.net] Sent: Tuesday, February 07, 2012 7:22 PM To: Nilsson Lill, Sten Subject: CCL: How can be separate CH-pi and pi-pi interaction? Sent to CCL by: "Ram Shankar S" [ramchemistry2011|gmail.com] Dear All, How can we separate CH-pi and pi-pi interaction into strong, moderate and weak based on the bond distance and bond angles (geometrical parameters) in pure organic substances? Whether is there any reference available for this? On what basis this kind of interactions (CH-pi and pi-pi) is separated, and I would like to know how this CH-pi and pi-pi interactions can be classified as strong, moderate and weak.Please help me in this regards. Thanks in advance With Regards, RAAMhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 8 15:08:01 2012 From: "Patrizia Calaminici pcalamin:_:cinvestav.mx" To: CCL Subject: CCL:G: Vibrational analysis demon2K Message-Id: <-46265-120208125415-7006-utj3n+EtNhiPXOFd6OXpDQ_._server.ccl.net> X-Original-From: Patrizia Calaminici Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 8 Feb 2012 17:52:47 +0000 MIME-Version: 1.0 Sent to CCL by: Patrizia Calaminici [pcalamin###cinvestav.mx] Dear Beatriz, Many thanks for your e-mail. Please, send the output of your calculation directly to me so that we will help you to solve your problem. Kind regards, Patrizia Calaminici :-:===================================:-: Prof. Dr. Patrizia Calaminici Departamento de Quimica, CINVESTAV, Centro De Investigacion Y De Estudios Avanzados, Av. Instituto Politecnico Nacional, 2508 A.P. 14-740 Mexico D.F. 07000 MEXICO Tel: 5255-5-747-3911 (Office) 5255-5-747-3800 Ext. 4411, 4465 (Labs) Fax: 5255-5-747-3389 E-mails: pcalamin:-:cinvestav.mx, calaminicipatrizia:-:gmail.com http://www.quimica.cinvestav.mx/Directorio/Investigadores/DraCalaminiciPatrizia.aspx Secretary: Miss. Lorena Sanchez Mendoza Tel: 5255-5-747-3800 Ext. 4408 E-mail: lsmendoza:-:cinvestav.mx :-:=================================:-: ________________________________________ > From: owner-chemistry+pcalamin==cinvestav.mx:-:ccl.net [owner-chemistry+pcalamin==cinvestav.mx:-:ccl.net] on behalf of Beatriz C Ramirez beacrm%%gmail.com [owner-chemistry:-:ccl.net] Sent: Wednesday, February 08, 2012 9:43 AM To: Patrizia Calaminici Subject: CCL:G: Vibrational analysis demon2K Sent to CCL by: "Beatriz C Ramirez" [beacrm__gmail.com] Hi, I usually look for transition states with Gaussian and I employ the thermochemistry data to calculate the activation energy for the reactions. Now I started to work with the software deMon2k, wich works great, but I'm not sure how to read the thermochemistry in the output file, because the data obtained dont agrees with the experimental data. I think that I'm picking the wrong values. Anyone knows how to read the .out file and the data from the vibrational analysis to calculate activation energies? If somebody can help me I'll be very thankfull Thanks in advance Beatriz R.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt