From owner-chemistry@ccl.net Thu Dec 31 09:32:01 2009 From: "Close, David M. CLOSED|,|mail.etsu.edu" To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40981-091231093040-1845-FWHsQgjQQQredKzFaQQKUQ=server.ccl.net> X-Original-From: "Close, David M." Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 31 Dec 2009 09:30:28 -0500 MIME-Version: 1.0 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. On the other hand, there are a few papers that do describe experimental measurements of non-planar adenine and cytosine. See Dong and Miller, Science 298,1227 (2002). Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed=3D=3Detsu.edu#,#ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu#,#ccl.net] On Behalf Of = Sanghwa Han hansh,kangwon.ac.kr Sent: Wednesday, December 30, 2009 10:12 PM To: Close, David M. Subject: CCL: Planarity of an amide group Sent to CCL by: "Sanghwa Han" [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-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt