Molecular Modelling Problem.

Electrophilic substitution in furan can be modelled by protonation. At least three possible protonated isomers are possible; two are shown below (what is the third?)
  1. Calculate the energies of the three protonated forms of furan at various levels of theory, including MM2 Mechanics (ChemBio3D), Semi-Empirical (PM6), RHF Ab initio and correlated B3LYP density functional. Which technique(s) agree with the known electrophilic substitution pattern of furans in the 2-position. How "expensive" in terms of computer time are the various techniques?
  2. What happens with other heterocycles, i.e. pyrroles (N), thiophenes (S), oxazoles (NO)?
  3. Does benzo substition on the heterocycle (i.e. benzofuran or indole) change the pattern?
  4. Do you get the same prediction if you inspect merely the HOMO (highest occupied molecular orbital) of the reagent?
  5. If you have performed a Gaussian calculation, you will have the .fchk file. From this you can generate a molecular electrostatic potential, using the DOS command cubegen 0 potential=scf indole.fchk test.cube. The cube file can then ve viewed using ChemBio3D or Gaussview. Does the MEP give the same result as the other techniques?
  6. If you apply a transition state model by using a reaction coordinate and an electrophile such as nitronium cation, do the results change?

Instructions and Manuals for using Programs

The problems can be attempted using Gaussian 03 (Ab initio) and the Chemistry SCAN resource. Details on how to prepare a program input are found here.
(c) Copyright H. S. Rzepa, 1999-2009.