A Kimball calculation in less than 1 minute gives you energy and structure of L-Alanine. The stereo plot allows to see the proper chirality. However, stereo plots can always be watched with the real image in front or behind the plane of projection. If you choose the 3D-image in front (place the index finger in front of your nose, focus on it by squinting, and move it towards the screen. Stop when the stereoimage hovers in the middle of the picture and in front of it), then you see S-Alanine. The stereo image (slightly) more distant than the plane of the monitor shows R-Alanine. Try it with your hand in front of your nose covering the right image for the left eye and the left image for the right eye and fuse the images by focusing to nearly infinity (it needs some training, but just relax!).
Figure 2:
This second calculation gives a molecule which is 33 kcal/mol more stable than the first. The carboxyl group has been turned around such that a hydrogen bridge N...O-H with the lone pair of the N-atom is formed (the two involved clouds are marked in magenta). You can do this turn-around with the final molecule structure and see directly the energy changes. It needs a short optimization to reach the result shown. By the way, this is now the enantiomer of the first molecule and NCCOOH are here coplanar. Try to view it with the stereoimage slightly behind the monitor screen. The magenta clouds are then in front and you see S-Alanine.
One of the new features of Kimball.exe is to use the Kimball model as a preprocessor for quantum chemistry programs. It supplies the Z-matrix (cartesian structure matrix) and gives results which can be used to check the professional programs. Kimball.exe can now automatically produce inputfiles for Gaussian98, Gamess, and Mopac which may immediately be run. Here alanin.gjf is shown for Gaussian98W:
#p rhf/6-31g scf=tight Alanin generated by Kimball.exe 0 1 C -0.3270316 1.366065 -0.4377297 C 0.1462877 -0.1022132 -0.4377297 N 1.62815 -0.1544847 -0.4377297 C -0.515285 -0.8178274 0.7275701 O -0.3020572 -1.976084 0.9367295 O -1.43661 -0.4913615 1.793383 H -1.443138 1.366065 -0.4377297 H 0.07342323 1.854949 -1.357687 H 0.07342323 1.854949 0.4822277 H -0.170428 -0.6919056 -1.333172 H 1.882076 -1.132707 -0.4377297 H 1.929836 0.2212539 -1.326101 H -1.538646 -1.2967 2.265698The G98W-result, using this file with the Kimball geometry and the indicated model chemistry, is - 321.650819 hartree (in 3' 9"), which compares well with the Kimball result of -321.6233 hartree (in 1', geometry de novo). If the route section is changed to "rhf/6-31g scf=tight opt" the geometry is slightly adjusted and the total energy becomes -321.7164795 hartree (in 18' 49").
For the structure in the 2nd figure G98W gives -321.6395897 and after
optimization (RHF/6-31g scf=tight opt) it becomes -321.7150139 hartree.
The structure and the energy are very similar to that in figure 2. However,
the hydrogen bridge is not "turned on" in the Gaussian result.
The mirror image of the optimized structure is shown as stickframe from RasWin:
This is another new feature of Kimball.exe: The
following file gives the energy partition, a (here empty) list of chosen
geometrical data, and a table of cartesian coordinates which can be extracted
and used as input into various chemical drawing programs, like RasWin
or WebLab viewer:
Alanin (figure 1) - Energies --------------------------------------- measured in Hartree Nucleus-Nucleus Vnn : 245.0874 Electron-Electron Vee : 346.0137 Nucleus-Electron Vne : -1234.3400 Electron potential Vel : -888.3260 Electronic energy Eel : -566.7107 Potential energy V : -643.2386 Kinetic energy T : 321.6154 Total energy Etot : -321.6233 Virial ratio V/T : -2.000024 Alanin - Interatomic Distances and Angles Alanin (figure 1) - Cartesian Coordinates ---------------------------------- use below for RASWIN 13 C -0.3270316 1.366065 -0.4377297 C 0.1462877 -0.1022132 -0.4377297 N 1.62815 -0.1544847 -0.4377297 C -0.515285 -0.8178274 0.7275701 O -0.3020572 -1.976084 0.9367295 O -1.43661 -0.4913615 1.793383 H -1.443138 1.366065 -0.4377297 H 0.07342323 1.854949 -1.357687 H 0.07342323 1.854949 0.4822277 H -0.170428 -0.6919056 -1.333172 H 1.882076 -1.132707 -0.4377297 H 1.929836 0.2212539 -1.326101 H -1.538646 -1.2967 2.265698