Experiment #30 - Aqueous Phase pKa's of Organic Acids

Construct the 14 molecules. Since many of them have similar substructure, use one structure & then edit it to make another. For example, construct 8 & MINIMIZE. In the FILE menu, SAVE AS /Expt30/8, then QUIT. The structure of 8 will still show on the green screen. Use the BUILD menu & choose EDIT STRUCTURE. Alter 8 to give 1. MINIMIZE. From the FILE menu, SAVE AS /Expt30/1 & QUIT. Then repeat above to alter 1 to give 2, etc. (Be sure that 6, 7, & 12 are trans, as in the figure, & that 1 is cis.)

Once the molecules are constructed, run an AM1 geometry optimization on each, followed by a calculation of the electrostatic potential on the total electron density surface. For example, in the FILE menu, OPEN 1. In the SETUP menu, choose SEMIEMPIRICAL with a TITLE, GEOMETRY OPTIMIZATION AM1. SAVE this & SUBMIT the job. When it has completed, do the SURFACE calculation. To do a SURFACE calculation, go to the SETUP menu & choose SURFACE. In the SURFACE box, choose DENSITY (i.e. the total electron density surface will be calculated). In the PROPERTIES box, choose ELPOT (i.e. the molecular electrostatic potential. It will be calculated from the wavefunction of the optimized geometry structure on the total electron density surface). Choose ADD & see that this description of the calculation gets added into the box. then SAVE. Go to the SETUP menu & choose SUBMIT. When the calculation is done, go to the DISPLAY menu & choose SURFACE. In the DISPLAY SURFACE AS box, choose mesh (dots are hard to see; solid is slow to rotate; but try these to see result). Select the MAP PROPERTY box; the maximum & minimum values of the electrostatic potential will be given. Record the maximum value for comparison to the pKa's. SAVE these choices. The map will be displayed. To prove that the maximum in the molecular electrostatic potential occurs around the carboxylic hydrogen, compare the color of blue around this H (i.e. dark blue) to that around other H's (i.e. lighter blue). To quantitatively make a comparison, go to the DISPLAY menu & choose PROPERTIES; select SURFACE. Position the cursor at a location on the surface & click with the left mouse button. A ball will appear on the surface & the value of the electrostatic potential at that point will be given. You can do this at several sites on the surface.