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Conformations

Dear Reader,

The joys of organic chemistry continue. Now we have conformations of molecules.

This is all about how molecules arrange themselves, while sigma bonds can rotate and spin around. Unless you heat to an almighty temperature or use light the pi bonds in a double bond will not rotate.

Graphs of energy as a function of the torsion angle for three two carbon compounds

Graph of the energy as a function of the torsion angle for the central part of a butane molecule.

Cyclohexane the six membered round thing which has a lot of great chemistry, note that it has been used in the past as a starting material for nylon

Axial and equatorial groups, for steric reasons it is normally better to put a large group in the equatorial site

Now we should look for a moment at the conformation of tert-butyl cyclohexane which has the alkyl group in the axial site. Here is a ball and stick view.

Tert-butyl cyclohexane with the tert butyl in the axial site

Now some of you might see that the tert butyl is bumping into the axial hydrogens. Now it is more clear if we look at the space filling version of the molecule.

Space filling view, note that the hydrogens of the tert butyl are bumping into the axial hydrogens of the cyclohexane ring

 

A problem for you to do at home

Two six membered rings, this is made by the hydrogenation of naphthalene

We have the molecular coordinates for you so that you can see the two isomers.

28

XYZ file : cis isomer

C(1)               1.2474           5.0087           2.8314

C(2)               2.4348           5.9740           3.0188

H(3)              2.4576           6.6612           2.1335

H(4)              0.3305           5.6281           2.6513

C(7)               3.7832           5.2314           3.0243

C(8)               1.4517           4.1239           1.5877

C(9)               2.8023           3.3945           1.5917

C(10)             3.9592           4.3896           1.7524

C(11)             2.2371           6.8490           4.2705

C(12)             0.9699           4.1857           4.1025

C(13)             1.9494           6.0249           5.5333

C(14)             0.7459           5.0979           5.3170

H(23)            4.6195           5.9667           3.1001

H(24)            3.8632           4.5648           3.9125

H(25)            1.4031           4.7671           0.6758

H(26)            0.6193           3.3863           1.5010

H(27)            2.9259           2.8230           0.6406

H(28)            2.8323           2.6467           2.4179

H(29)            3.9982           5.0620           0.8625

H(30)            4.9304           3.8403           1.7900

H(31)            3.1319           7.4954           4.4316

H(32)            1.3747           7.5373           4.0966

H(33)            1.8173           3.4969           4.3194

H(34)            0.0686           3.5455           3.9492

H(35)            1.7491           6.7085           6.3930

H(36)            2.8445           5.4207           5.8094

H(37)            -0.1728          5.7113           5.1584

H(38)            0.5730           4.4804           6.2308

 

trans-Decalin

 

28

XYZ file : trans isomer

C(1)               -2.5300          3.2148           -2.2822

C(2)               -3.8215          3.0791           -3.0831

C(3)               -3.9242          4.1335           -4.1834

C(4)               -3.7568          5.5502           -3.6185

C(5)               -2.4239          5.6761           -2.8542

C(6)               -2.3413          4.6290           -1.7364

C(7)               -3.8497          6.6029           -4.7305

C(8)               -3.6598          8.0140           -4.1778

C(9)               -2.3535          8.1443           -3.4005

C(10)             -2.2453          7.0943           -2.2968

H(11)            -4.5890          5.7363           -2.9032

H(12)            -1.5922          5.4845           -3.5685

H(13)            -2.5605          2.5016           -1.4283

H(14)            -1.6780          2.9922           -2.9629

H(15)            -3.8505          2.0690           -3.5496

H(16)            -4.6765          3.2247           -2.3855

H(17)            -3.1268          3.9482           -4.9375

H(18)            -4.9328          4.0583           -4.6479

H(19)            -3.1373          4.8366           -0.9868

H(20)            -1.3326          4.6929           -1.2703

H(21)            -4.8513          6.5342           -5.2111

H(22)            -3.0423          6.4042           -5.4702

H(23)            -3.6479          8.7346           -5.0259

H(24)            -4.5009          8.2303           -3.4817

H(25)            -1.5011          8.0161           -4.1046

H(26)            -2.3315          9.1506           -2.9254

H(27)            -1.2423          7.1721           -1.8205

H(28)            -3.0517          7.2829           -1.5532

Steroid drugs, these are very important for both good things and bad things.

The steric effect of the tert butyl group is important, note that it makes it harder for a nucleophile to get close to the carbon bearing the tosylate group.

Epoxide chemistry, both what they do and how they are formed.

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