From owner-chemistry@ccl.net Sat Jan 2 05:03:01 2010 From: "Mariusz Radon mariusz.radon:gmail.com" <owner-chemistry[a]server.ccl.net> To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40985-091231105700-2301-1Jy9AKAxtkH7ND+FZNkLqQ[a]server.ccl.net> X-Original-From: Mariusz Radon <mariusz.radon _ gmail.com> Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Thu, 31 Dec 2009 16:56:48 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon###gmail.com] Dear Sanghwa: Just few suggestions/questions concerning your question about the non-plana= rity: - 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 <owner-chemistry..ccl.net> 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 H= F/6-31G* for RESP charge derivation, the dihedral HN-CO often deviates from= planarity by as much as 20 degrees. > Do I need to constrain the HN-CO to 0 degrees to obtain an optimized stru= cture 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) From owner-chemistry@ccl.net Sat Jan 2 13:11:00 2010 From: "Isaac B Bersuker bersuker-.-cm.utexas.edu" <owner-chemistry%%server.ccl.net> To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40986-100102095713-15532-DQ/h3OYyXBx1lH4ngpi8kQ%%server.ccl.net> X-Original-From: Isaac B Bersuker <bersuker|cm.utexas.edu> Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Sat, 2 Jan 2010 14:17:49 +0000 (UTC) MIME-Version: 1.0 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 mol= ecular system is physical: since ALL instabilities of high-symmetry configu= rations 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 th= e 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" <owner-chemistry__ccl.net> To: "Isaac B. Bersuker" <bersuker__mail.cm.utexas.edu> 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-plana= rity: - 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 <owner-chemistry:_:ccl.net> 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 H= F/6-31G* for RESP charge derivation, the dihedral HN-CO often deviates from= planarity by as much as 20 degrees. > Do I need to constrain the HN-CO to 0 degrees to obtain an optimized stru= cture 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/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Jan 2 13:59:00 2010 From: "case case ~~ biomaps.rutgers.edu" <owner-chemistry,,server.ccl.net> To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40987-100102094540-14697-pjuh/hyP8WupL6/v5iqeiA,,server.ccl.net> X-Original-From: case <case . biomaps.rutgers.edu> Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sat, 2 Jan 2010 09:45:20 -0500 Mime-Version: 1.0 Sent to CCL by: case [case^^^biomaps.rutgers.edu] On Wed, Dec 30, 2009, Sanghwa Han hansh,kangwon.ac.kr wrote: > > In Biochemistry textbooks, an amide bond (NH-CO) in a peptide is > explained 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 from 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? The "standard" idea is that environmental effects (especially H-bonding) stabilize the Lewis structure with a C=N double bond (relative to the structure with a single bond), and hence that gas-phase peptides will be more prone to pyramidalization about N than will peptides in solution. Here is a somewhat dated but still useful article on this subject: %A B.E. Mannfors %A N.G. Mirkin %A K. Palmo %A S. Krimm %T Analysis of the Pyramidalization of the Peptide Group Nitrogen: Implications for Molecular Mechanics Energy Functions %J J. Phys. Chem. A %V 107 %P 1825-1832 %D 2003 ...good luck...dave case From owner-chemistry@ccl.net Sat Jan 2 23:08:00 2010 From: "Jeff Woodford jwoodfor ~~ eou.edu" <owner-chemistry]*[server.ccl.net> To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40988-100102185756-12248-QQy4IEwT9EjYoHn+quN3Bw]*[server.ccl.net> X-Original-From: "Jeff Woodford" <jwoodfor^^^eou.edu> Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 2 Jan 2010 15:25:51 -0800 MIME-Version: 1.0 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*ccl.net [mailto:owner-chemistry+jwoodfor=3D=3Deou.edu*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" = <owner-chemistry]|[ccl.net> To: "Isaac B. Bersuker" <bersuker]|[mail.cm.utexas.edu> 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 <owner-chemistry:_:ccl.net> wrote: > > Sent to CCL by: "Sanghwa =A0Han" [hansh~~kangwon.ac.kr] > Dear colleagues, > > In Biochemistry textbooks, an amide bond (NH-CO) in a peptide is = explained 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 = > from 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-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =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/che= mistr y/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Jan 2 23:50:02 2010 From: "Mihaly Mezei Mihaly.Mezei||mssm.edu" <owner-chemistry .. server.ccl.net> To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40989-100102014741-30573-Z++kACqIuFv0PqdvZsMcig .. server.ccl.net> X-Original-From: Mihaly Mezei <Mihaly.Mezei|,|mssm.edu> Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Sat, 02 Jan 2010 00:06:57 -0500 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei * mssm.edu] ----- Original Message ----- > From: "Close, David M. CLOSED|,|mail.etsu.edu" <owner-chemistry%ccl.net> Date: Thursday, December 31, 2009 9:30 am Subject: CCL: Planarity of an amide group > > Sent to CCL by: "Close, David M." [CLOSED]^[mail.etsu.edu] > Sanghwa: > With the methods you describe, the optimized structures will contain > non-planar amides. This is commonly observed, and the non- > planarity can > be as much as 20 degrees. This is seen a lot in nucleic acid bases. > The question remains, is this physically real? > Certainly the peptide bond is planar. In crystals of nucleic acids, > the amides are planar. You can look this up in the summary papers by > Helen Berman from the PDB. Also when nucleic acids base pair, the > nitrogens form planar H-bonds. I am wondering if the planarity of the peptide bond seen in most crystal structures is not the result of a constraint built in the refinement process. Years ago, at a Gordon Research Conference one talk discussed some conclusion drawn from the geometry of a crystal structure, until the crystallographer, who was also present, stood up, and confessed that this particular feature was arbitrarily introduced, for lack of more detailed information. > On the other hand, there are a few papers that do describe > experimental measurements of non-planar adenine and cytosine. See > Dongand Miller, Science 298,1227 (2002). I am not surprised. I think that a deviation of 10-20 degrees is quite reasonable to expect as the environments of each peptide bind is quite different in a protein. > Regards, Dave Close. Best regards, and Happy New Year! Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu