From owner-chemistry@ccl.net Sun Jan 3 02:52:00 2010 From: "a b c ajohn1234[*]gmail.com" To: CCL Subject: CCL: pbepbe vs. tpsstpss Message-Id: <-40990-100103013411-23476-JXALAelqc2I1ZAonizTumw:_:server.ccl.net> X-Original-From: "a b c" Date: Sun, 3 Jan 2010 01:34:07 -0500 Sent to CCL by: "a b c" [ajohn1234-.-gmail.com] pbepbe versus tpsstpss which is better (esp. when it comes to an inorganic complex with an Fe metal center [say Fe(III) and/or Fe(II)])? thanks, anonymous grad student From owner-chemistry@ccl.net Sun Jan 3 12:26:01 2010 From: "Isaac B Bersuker bersuker\a/cm.utexas.edu" To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40991-100103095512-4954-fyhWZNQKAlIcVgHzneDzpA-#-server.ccl.net> X-Original-From: Isaac B Bersuker Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Sun, 3 Jan 2010 14:54:56 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Isaac B Bersuker [bersuker!^!cm.utexas.edu] Jeff, Any ab initio package can do this job, see, e.g., our papers in J. Phys. Ch= em. A, 111, 10409 (2007), J. Chem. Phys. 129, 114107 (2008), J. Chem. Theor= y Comp., 5, 2679 (2009), etc. Regards I. B. Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker ~~ cm.utexas.edu http://www.cm.utexas.edu/isaac_bersuker ----- Original Message ----- > From: "Jeff Woodford jwoodfor ~~ eou.edu" To: "Isaac B. Bersuker" Sent: Saturday, January 2, 2010 3:25:51 PM GMT -08:00 US/Canada Pacific Subject: CCL: Planarity of an amide group Sent to CCL by: "Jeff Woodford" [jwoodfor::eou.edu] Dr. Bersuker, that is really interesting - do you know what software packages will calculate JTE or PJTE coupling coefficients? Thanks, -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 -----Original Message----- > From: owner-chemistry+jwoodfor=3D=3Deou.edu-x-ccl.net [mailto:owner-chemistry+jwoodfor=3D=3Deou.edu-x-ccl.net] On Behalf Of Isaac= B Bersuker bersuker-.-cm.utexas.edu Sent: Saturday, January 02, 2010 6:18 AM To: Woodford, Jeffrey N Subject: CCL: Planarity of an amide group Sent to CCL by: Isaac B Bersuker [bersuker_+_cm.utexas.edu] Dear CCL people, There is a good tool to find out whether or not the nonplanarity of any molecular system is physical: since ALL instabilities of high-symmetry configurations are due to the Jahn-Teller or pseudo JTE effect (in the case under consideration it should be a pseudo JTE), a direct testing is possiblen by checking with the excited states, see many examples in my latest book on the Jahn-Teller Effect by Cambridge University Press, 2006. Regards I. B.=20 Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker]|[cm.utexas.edu http://www.cm.utexas.edu/isaac_bersuker ----- Original Message ----- > From: "Mariusz Radon mariusz.radon:gmail.com" To: "Isaac B. Bersuker" Sent: Thursday, December 31, 2009 7:56:48 AM GMT -08:00 US/Canada Pacific Subject: CCL: Planarity of an amide group Sent to CCL by: Mariusz Radon [mariusz.radon###gmail.com] Dear Sanghwa: Just few suggestions/questions concerning your question about the non-planarity: - Do you expect the steric interactions between the aminoacids residues could be important for the adopted conformation? If your non-planarity were physical, there must be some reason for it... - Does the non-planarity remain at any correlated level, even simply DFT:B3LYP? Or, ideally, DFT+D (with dispersion correction)? Hope that it can be useful. Best regards and all the best in New Year 2010, Mariusz Radon On Thu, Dec 31, 2009 at 4:11 AM, Sanghwa Han hansh,kangwon.ac.kr wrote: > > Sent to CCL by: "Sanghwa =C2=A0Han" [hansh~~kangwon.ac.kr] > Dear colleagues, > > In Biochemistry textbooks, an amide bond (NH-CO) in a peptide is explaine= d to be planar. > But when I optimize a capped amino acid (e.g. ACE-Amino Acid-NME) using HF/6-31G* for RESP charge derivation, the dihedral HN-CO often deviates > f= rom planarity by as much as 20 degrees. > Do I need to constrain the HN-CO to 0 degrees to obtain an optimized structure that is used in a RESP charge derivation? > Does anybody know if the amide group can be non-planar in experimentally determined structures? > > Thanks. > > Sanghwa Han > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt> > > --=20 Mariusz Radon, PhD student Department of Theoretical Chemistry Jagiellonian University http://www.chemia.uj.edu.pl/~mradon mradon /at/ chemia.uj.edu.pl (PGP public key available on the website) -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemi= str y/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt -=3Dhis is automatically added to each message by the mailing script =3Dhtt= p://www.ccl.net/cgi-bin/ccl/send_ccl_messageJob: htt= p://www.ccl.net/jobs-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt