1. Chem 125 Lecture 33 12/1/08 This material is for the exclusive use of Chem 125 students at Yale and may not be copied or distributed further. It is not readily understood without reference to notes or the wiki from the lecture.

2. Ernst Mohr Illustrations (1918) confirm Sachse’s 1890 insight.

3. Ernst Mohr Illustrations (1918) “chair” “boat” bowsprit flagpole “ring flip” by 60° counter-rotation of two parallel bonds Red bonds rotate in & up.Blue bonds rotate in & down. inverted chair www. downunderchicago.com/pics/ol-la-lafuma-recliner--padded--la.jpg http://beothic.blogspot.com/2007/01/dory_13.html

4. Ernst Mohr Illustrations (1918) Drawing chair cyclohexane rings: opposite C-C bonds parallel axial bonds parallel to 3-fold axis equatorial bonds parallel (anti) to next-adjacent C-C bonds What o’clock? ? ? ? ? Z

5. For such problems D.H.R. Barton Invents Conformational Analysis (1950) Baeyer observed only one c-Hexyl-COOH, but in these epimers,  and  OH groups have different reactivity!   “up” ;   “down” (for molecule in conventional orientation, old-fashioned configuration notation, like cis / trans)  Barton redraws Ring A Intermediates in steroid hormone synthesis A B C D (configurationally diastereotopic)

6. (e) “equatorial” (p) “polar” (now axial) Cf. ~1950 Stereochemistry: Bijvoet, Newman, CIP, (Molecular Mechanics) (Nobel Prize 1969 for “development of the concept of conformation and its application in chemistry”) ERRORS?   “up” ;   “down” (for molecule in conventional orientation, old-fashioned configuration notation, like cis / trans) 3-fold axis For such problems D.H.R. Barton Invents Conformational Analysis (1950) ) Ring Flip?

7. Ernst Mohr Illustrations (1918) Ring flip impossible for trans decalin! N.B. During ring flip equatorials become axials and vice versa. anti gauche gauche OK within second ring of decalin, but not anti. fused chairs in "decalin" (decahydronaphthalene) Try with models if you’re skeptical.

8. Mol4D (CMBI Radboud University, Nijmegen, NL) Click for INDEXClick for INDEX or go to http://cheminf.cmbi.ru.nl/wetche/organic/index.html Conformational Jmol Animations (see Wiki to install Jmol)

9. Mol4D (CMBI Radboud University, Nijmegen, NL) Ethane Click to Animate or go to http://cheminf.cmbi.ru.nl/wetche/organic/nalkanesconf/ethane/jmindex.htmlClick to Animate Eclipsed barrier ~5.2 kJ/mol  0.239 = 1.24 kcal/mol Should be ~2.9 kcal/mol. Caveat emptor! Step Keys Click Points Staggered

10. Mol4D (CMBI Radboud University, Nijmegen, NL) Propane Click to Animate or go to http://cheminf.cmbi.ru.nl/wetche/organic/nalkanesconf/propane/jmproprot.htmlClick to Animate Staggered Eclipsed 3.3 kcal/mol

11. Anti  Gauche + 10 13  10 -3/4  3.4 = 10 7.5 /sec OOPS! 10 10.5 /sec Mol4D (CMBI Radboud University, Nijmegen, NL) Butane (central bond) Click to Animate or go to http://cheminf.cmbi.ru.nl/wetche/organic/nalkanesconf/butane/jmindex.htmlClick to Animate Gauche 0.9 kcal/mol (tells how much) eclipsed 3.4 kcal/mol (tells how fast) fully eclipsed ~ 4.4 kcal/mol? (experimentally irrelevant) Anti Gauche / Anti = 10 -3/4  0.9 = 10 -0.68 = 1 / 4.7 Gauche / Anti = 2  10 -3/4  0.9 = 2  10 -0.68 = 1 / 2.4 + + Gauche -

12. Mol4D (CMBI Radboud University, Nijmegen, NL) Ring Flip of c-Hexane Click to Animate or go to http://cheminf.cmbi.ru.nl/wetche/organic/cyclohexane/jm/chxjmol.htmlClick to Animate Flexible or Twist-Boat conformer ~5.5 kcal/mol Barrier (Half-Chair) ~ 11 kcal/mol Chair conformer

13. Mol4D (CMBI Radboud University, Nijmegen, NL) Flexible c-Hexane Click to Animate or go to http://cheminf.cmbi.ru.nl/wetche/organic/cyclohexane/jm/twist_boat.htmlClick to Animate Flexible or Twist-Boat Form Barrier (Boat) ~ 1 kcal/mol

14. Shape, “Strain Energy” & Molecular Mechanics “Hooke’s Law” for Strain Energy

15. Conformational Energy of Ethane 0°120° 240° 360° Torsional Angle Energy 3 kcal/mol

16. Conformational Energy of Butane 0°120° 240° 360° Torsional Angle Energy 4.4 kcal/mol 0.9 kcal/mol 4.4 kcal/mol 0.9 kcal/mol 3.4 kcal/mol CH 3 H H

17. Molecular Mechanics (1946)

18. “Molecular Mechanics” programs calculate (and can minimize) strain assuming that molecules can be treated as mechanical entities. To achieve useful precision they require a very large set of empirical force constants adjusted arbitrarily to make energies match experiment (or reliable quantum calculations).

19. “MM2” Parameters 66 different atoms types (including 14 different types of carbon) 138 different bond stretches (41 alkane carbon-X bonds)

20. “MM2” Parameters 66 different atoms types (including 14 different types of carbon) 624 different bond bendings (41 alkane-alkane-X angles)

21. “MM2” Parameters 66 different atoms types (including 14 different types of carbon) 1494 different bond twistings (37 alkane-alkane - alkane-X twists) 0 0.5 -0.5 Sum: 1-1-1-1 Torsional Contribution to Butane Overall Butane kcal/mole 120°240°360° 180° is low “because of” reduced anti van der Waals repulsion tweaked by torsional energy

22. Contrast with quantum mechanics, where there are no arbitrary parameters. (just particle masses, integral charges & Planck's constant) After simplification “MM3” has >2000 Arbitratily Adjustable Parameters !

23. “Ideal” Cyclohexane (by Molecular Mechanics) 0.33Stretch0.00 0.36Bend0.00 0.09Stretch-Bend-0.000 2.15Torsion2.12 4.681,4 VDW6.32 -1.05Non-1,4 VDW-0.55 6.56TOTAL7.89 Strain (kcal/mol) 1 2 3 4 5 e.g. favorable C … H e.g. (unfavorable) 1 2 3 4 e.g. gauche C-C-C-C Easier (or harder?) to bend a stretched bond

24. Relaxation of Cyclohexane (by Molecular Mechanics) 0.33Stretch0.00 0.36Bend0.00 0.09Stretch-Bend-0.000 2.15Torsion2.12 -1.05Non-1,4 VDW-0.55 4.681,4 VDW6.32 6.56TOTAL7.89 6 gauche butanes Stretches and flattens slightly to reduce VDW 6  0.9 = 5.4 (mnemonic) “Ideal” Minimized gauche butane

25. Axial Methylcyclohexane (by Molecular Mechanics) 0.49Stretch0.00 0.96Bend0.00 0.14Stretch-Bend-0.00 3.08Torsion2.82 -1.31Non-1,4 VDW6.12 5.311,4 VDW7.61 8.66TOTAL16.55  8 gauche butanes ! Axial - Equatorial = 1.8 kcal/mol for CH 3 [ 2 gauche  2 anti ] Relaxed H CH 3 “A-value” a measure of group “size” “Idealized”

26. End of Lecture 33 Dec. 1, 2008