Acetic acid z-conformation

This overlap density contour plot shows the xy-plane for the Z form of acetic acid after an optimized RHF/6-311G computation with GamessPC using the wine(980913) WindowsNT emulator under Linux (Suse 6.3, kernel 2.2.13). The plotting software is Molden V.3.4. The full red circles in the plane HCCOOH are the Kimball radii of the C(1s2) and O(1s2) cores, while the open red circles depict the Kimball spheres of the CH, CC, C=O(s), C-O, and OH bonds. The superposition on the overlap density gives an idea of the simplification of the Kimball model. The out-of-plane CH-bonds, lone pairs on the O-atoms, and the π-bond of C=O are not drawn. Only the O-C=O angle has been adjusted for the overlay onto the overlap density of Molden, see below. The optimization started from a Kimball structure, shown superimposed on the wireframe of the final structure with the above model chemistry at left. The main difference is a flattening out of the O-C=O angle while all the other structural parameters are nearly equal (demonstrated by the Kimball spheres in the top picture). With actual Kimball.exe one of the two equivalent σ lone pairs of the C=O oxygen in the H-O-C=O plane (not drawn here, but of similar size to the C-O cloud), causes incipient hydrogen bond formation. Look at the density plot again, to observe only two slight bulges at the C=O oxygen atom, perhaps the "vanished" lone pairs. Since the HOC angle is stiffer than the OCO angle (bending freq. 1295 cm-1 versus 620 cm-1), the latter is mainly deformed. Similar structural defects can be seen with Nitric Acid, and S-2-Aminobutyric Acid (go back to table), whereas E- or trans-Nitrous Acid does not exhibit it. One of the ongoing improvements of the Kimball.exe program (still pending 2012!) is the introduction of better and individual shielding parameters.