Organic:Model answers

Mandatory Examples

• 
  1.1 Chair: 6.55 kcal, twist-boat 11.919. No pure boat form is normally locatable (13.03) although many a text book on organic chemistry implies that it is a true minimum, albeit somewhat higher in energy than the twist-boat. As noted in the references, it is of course a racemisation transition state connecting the two enantiomeric twist-boat forms. See the relevant section of the lecture course on conformational analysis.
• 1.2 RS/SR = 6.96 (all trans conformation), 7.909 (syn conformation); RR/SS = 6.744 (halogens anti, methyl syn), 7.118 (halogens syn, methyl anti). The MOPAC RM1 values (which take into account stereoelectronic factors) are RR/SS = -29.02 (halogens anti, methyl syn), -28.87 (halogens syn, methyl anti)
  • 
    1.2 Benzene, -0.574, Naphthalene, -4.430, phenanthrene, -3.552 (planar), benzophenanthrene, 7.760 (non planar), Pentahelicene 14.31 (very non planar), hexahelicene, 19.056 (note the problem building this molecule). Note that these increments behave in an interesting fashion, perhaps because at some stage Van der Waals (dispersion) interactions between the newly overlapping layers start to make an effect!
• 1.3
  • 1.3.1 cis-decalin. chair/chair: 14.129, boat/chair: 22.077, boat/boat 27.059
  • 1.3.3 Trans: 14.1, cis 12.9. It appears cis is actually the more stable? Woodward states in his paper that in fact he only isolates 40% of the trans isomer, and comments that the energy difference between cis and trans is likely to be small. So the present result pretty much bears this out!
  • 2.3.4 all-app 29.9, syn 29.7
• 1.4
  • 1.4.1 Axial energies: Me, 12.96, t-Butyl, 77.73, OH, 2.95. Equatorial energies: Me, 2.64, t-Butyl, 32.4, OH, 3.55. The OH appears anomalous in preferring an axial orientation. One presumes the alkoxide will however be heavily solvated, and hence far larger and more akin to t-Butyl.
  • 1.4.4 Thiomethyl, Chair, axial -7.51, equatorial -6.91. Oxamethyl, chair, axial, -2.90, equatorial 1.20
• 1.5 Menthone enol, Thermodynamic 13.6 (obs), Kinetic 28.1 (unobs). B3LYP/6-31G(d) calculation submitted according to instructions in course: Thermo, -467.1222, Kinetic, -467.1201 = 5.5 kJ in favour of former.

Additional Examples

• 2.2 Caryophyllene ketone. Trans: 323.9, Cis 334.9
• 2.3 Germacrene. Divinyl trans: 29.44, cis 39.2,
• 2.4 Xestoquinone: Formed isomer, c + (a/b), 139.4 (global minimum?)

• 2.5 Aldol: Ha+Oa, 323.6, Hb+Ob, 45.4. The third possibility is the formation of a cyclopropene.
• 2.6 Hydride reduction of ketone: 7.19(unobs), 0.89 (obs)
• 2.7 NMR: lhs conformation: 32.98 H23 43° (approx 6Hz), H34 160.3° (approx 11.5 Hz) rhs conformation 30.2 H23 43.4° (6 Hz), H34 92° (1Hz)
• 2.8 Ketone: Isomer 1, 208.5. angles Angle to Hb 88.1, angle to Ha 49.5. Ketone Isomer 2, 196.4. Angle to Hb, 21.2, Angle to Ha 16.9 (these two ketone isomers are almost certainly an artefact of the Tripos force field. An MO calculation (B3LYP/6-31G(d) ) gives only one isomer, with angle to Hb 57.3, angle to Ha, 17.3. This is an ideal candidate for following up with a more accurate calculation according to the instructions given at the end of this course). Enol from Hb: 369.2, Enol from Ha: 491.0.
• 2.9 1-sulfonic acid: 46.6. 2-sulfonic acid 26.2. Wheland intermediate: 1- 29.8. 2- 43.9