From owner-chemistry@ccl.net Sat Sep 9 21:16:01 2006 From: "Kalju Kahn kalju]![chem.ucsb.edu" To: CCL Subject: CCL: sp2 or sp3 for the single-bonded ester oxygen atom Message-Id: <-32509-060908181908-27936-zCDan1xZbpqy/AMomwo+pA- -server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 08 Sep 2006 14:34:46 -0700 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju- -chem.ucsb.edu] Dear Guosheng, One justification behind ester oxygen being sp3 is in bond lengths and angles in esters. The C(sp2)-O bond in esters is about 1.33-1.34 Ang. This is closer to the C-O(sp3) bond in alcohols and ethers (1.41-1.42) than to the C=O(sp2) bond in carbonyl compounds (1.20-1.21). Also, the QM potential-based partial charge on this oxygen is more similar to alcohols than to carbonyls. Liquid simulations with the OPLS-AA force field suggest that Lennard-Jones parameters of ether oxygen should be similar to ether and not to carbonyl oxygen. However, many force fields reconize the uniqueness of this oxygen by using a special atom type for the ether and carboxylic acid oxygens. It in not necessarily true that the coplanar structure of esters arises only from p-pi conjugation. The repulsion of negative charges on the carbonyl oxygen and the two tetrahedrally-arranged electron pairs on sp3 oxygen would also predict planar structures, with Z-conformer (in which both e-pairs point away from the C=O oxygen) much more favorable than the E conformation (e-pairs surrounding C=O oxygen). This is somewhat similar to glyoxal (HOC-CHO), which is planar with a *long* C-C bond. Also note that the classical Lewis resonance structure would make the ester oxygen positively charged, something that would not fit well with the electronegative nature of the oxygen. The ester (sp3) oxygen is known to be weak H-bond acceptor so your finding of limited number of structures is OK. I wonder if anybody has done a gas phase QM study to see the difference between tetrahedrally positioned H-bond acceptor and coplanar one? P.S. Some details about ester force fields are hidden in our own "Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides", in J. Comp. Chem. 23, 977 (2002) Hope this helps, Kalju ------------------- > Sent to CCL by: Guosheng Wu [wu_guosheng2002]^[yahoo.com] > Hi there, > > For the first O atom in ester like CH3OC(=O)CH3, what kind of hybrid state we should assign? > > Certainly it's within the context of molecular mechanics, although I tried a little QM study with > electrostatic potential and electron density calculation, and did not get a clue. (Any QM expert > can help me on it ?) > > I looked up the literature or the web(google), but all I can find out for this problem is that it > has been called sp3 at many occasions. One paper (Kresimir Molcanov et al, Acta Crys. B, 2004, > B60, 424) and some force fields (CVFF, AMBER,...) explicitly call/type it as sp3. > > However, that conflicts my chemistry intuition, since 2 electrons of that O should form so-called > p-pi conjugation with C=O, so it should be in sp2 hybrid state. That also explains the coplanar > structure of ester or simple organic acids. > > Like the paper mentioned above, I did some CSD search for that O as H-bond acceptor, there are > only ~200 hits (dependent on parameter such as resolution, bond length etc), so it's certainly not > much statistically meaningful, but still what I found out is that most of the O..H-X > (X=O or N) H-bonds are more or less in the same plane of the ester. So shall we call it sp2 > oxygen in the future when we talk about molecular mechanics, and apply this concept in any related > study? > > I find this an interesting study, and hope to receive your insights, especially those who work in > QM areas. > > Thanks for your attention, > -Guosheng > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara