Department of Chemistry, KAIST

1. Chapter 18. The chemistry of Carbon From Life Science to Physical Science Organic Chemistry is 3D Quantum Mechanics to The Real World 1 Department of Chemistry, KAIST Department of Chemistry, KAIST

2. 18.1 What makes Carbon special Organic chemistry : chemistry of Carbon + H, O, N, etc….. Chemistry of carbon is rich and diverse, as many compounds can form…… More than 90% of all the registered compounds in CA (>26 million) are organic compounds Organic chemistry is the basis of Life Science & modern material science Organic chemistry chemistry of organic compounds Organic compound : substances produced by living matter --- prior to 1828 Inorganic compound : substances obtained from mineral In 1828, Woehler made an organic compound from an inorganic salt

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4. 18.1 What makes Carbon special Carbon provides versatility and stability in making molecules.

5. 18.1 What makes Carbon special Carbon provides versatility and stability in making molecules. Unlimited number of combination is possible with stable C-C, C-H bond formation. compounds Comparison with neighboring elements B : boron Rarely forms B-B bond, does not form multiple bond N : nitrogen N-N bond is exceptionally weak H2NNH2, HN=N=N are only known compounds Si : silicon Si-Si bond is weak, Si is readily oxidized to Si-O elastic silicones oil, grease, rubber siloxanes

6. 18.2 Building Blocks of Organic Chemistry: The Hydrocarbons Organic compounds consisting entirely of hydrogen and carbon Forms structures; so called backbone, skeleton Satruated hydrocarbon : all bonds are single bonds CnH2n+2 “Alkane” paraffin # of structures --- isomers

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8. Example : C5H12 Pentane : b.p. 36oC Isopentane : b.p. 28oC Neopentane : b.p. 9.5oC

9. Newman projection for H3C-CH3 more stable (3Kcal/mol) Stereochemistry Conformational isomers (conformers)

12. Satruated hydrocarbon : Ring structures CnH2n Usually unstable when it’s small Associate with strain energy Cyclic Compounds Most stable cyclic compound Most strained reactive

14. Unsatruated hydrocarbon : Alkenes, Alkynes p bonds are more reactive than s bonds Requires 60Kcal/mol p- bonding Trans isomer is more stable Due to steric effect ***Can be halogenated by the addition of X2

15. Unsatruated hydrocarbon : Alkenes, Alkynes Polyenes

16. 18.3 Derivatives of the Hydrocarbons: Functional Groups

17. 18.3 Derivatives of the Hydrocarbons: Functional Groups

20. R’ = H : aldehyde

22. Ibuprofen (부루펜) Naproxen (낙센)

26. Addition reactions Addition Reactions of Alkenes Br2 Br+······Br - Br+ Br - A nucleophile + :OH2 CH2=CH2 CH3-CH2 CH2CH2OH H2O H2SO4

27. Substitution reactions CH3 Halide to hydroxide C+ t-butyl chloride + OH-  t-butyl hydroxide + Cl- mechanism CH3 CH3 :OH- t-butyl chloride   C(CH3)3OH a SN1 reaction ‘nucleophilic substitution unimolecular’ H (Cl------ OH)- C------- methyl chloride + :OH-  CH3OH a SN2 reaction H H Williamson synthesis (SN2) Esterification (SN2) *C=O is called ‘carbonyl’ group.

28. Pasteur separated two kinds of tartaric acid crystals with different shapes, which corresponded to their mirror images. of • Beginning of Stereochemistry • Basics of Carbohydrates (탄수화물) B C E E C C asymmetric carbon A D A B mirror images an atom that has all four different groups attached to it. asymmetric carbon: Asymmetric carbon is a chiral center. ‘chiral’ means ‘handed’ . Right handed, left handed.

29. ISOMERISM • Structural Isomers • Skeletal Isomers (linear alkane, branched alkane) • Positional Isomers (CH3CH2CH3Br, CH3CH2BrCH3) • Functional Isomers (C2H5OH, CH3OCH3) • Stereoisomers • Geometric Isomers (cis, trans) • Optical Isomer B C E E C C R S A D A B ordinary light  polarized light after passing through calcite crystal  rotated polarized light by passing through sample ( This means that the direction of polarization is rotated after passing though a sample containing an optical isomer. The optical rotation is proportional to the sample conc. and length.

30. Asymmetric carbon atom  chiral molecules (a pair of enantiomers) • “not superimposable’ • Each of the enantiomers causes equal optical rotation in the opposite direction • Racemic mixture: 1:1 mixture of enantiomers • Amino acids in nature : only the L form • Diastereometers: optical isomers of a given compound which are not • mirror images and which are not identical are known • as diastereomers. Assignment of optical isomers (+,-) according to the direction of optical rotation (D,L) according to an arbitrary assignment of one as ‘D” (R,S) clockwise or counterclockwise priority is given by the attached atomic numbers (A: highest, E: lowest). B C E E C C A D A B R S

31. Note that optical isomers of a given compound which are not mirror images and which are not identical are known as diastereomers. (a) = (b) an optical isomer that does not result in optical rotation (a) (b) (c) and (d) are the opposite optical isomers, which exhibit same optical rotations in the opposite directions (c) (d) • and (c): enantiomers to each other • (a) and (d): diastereomers to each other *Diastereomers exhibit different physical. *Enantiomers exhibit same physical properties except for the optical rotation. *Students: please use the definition of diastereomers which is given in this page and the previous page. The definition in our textbook is not clear.

32. asymmetric carbon _ _ _

33. Fig. 9-12, p. 308

34. Fig. 9-13, p. 308

35. 18.4 Benzene and Its derivatives: The Aromatics delocalized p bonding ( see chap. 7 p229) Much less reactive than other unsaturated bonds ---- aromaticity When there are fully delocalized (2n+4)p electrons on the same plane

36. Benzene is very stable due to its aromaticity. H can be substituted by Br. Bz + Br2 PhBr + HBr This is a sort of electrophilic substitution involving a bromonium ion species (Br+). H can be substituted by an alkyl group (Friedel-Craft alkylation).

37. 18.5 Orbitals in Organic Reactions: The Diels-Alder Reaction Diels-Alder cycloaddition reaction (a pericyclic reaction) between diene and dieneophile Electrons do not flow sequentially by arrows. It is a concerted cyclization. p electrons are involved

38. Diels-Alder cycloaddition reaction diene dieneophile Both are plausible in this Figure. In both case, (4n + 2)p is allowed according to the Woodward-Hoffman rule. The rule emphasizes the requirement of phase match between HOMO of diene and LUMO of ene, that is FMO’s. *cis product is obtained from a cis dieneophile.

39. 18.6 Polymers Macromolecules Beyond 26 million known compounds. Polymer : Long chain with a repeating pattern (unit) Repeating unit is called monomer

40. 18.6 Polymers Macromolecules Polymers: long chain with a repeating unit among macromolecules Addition Polymers: HDPE : High Density PolyEthylene R=H, straight chain Container, pipes LDPE : Low Density PolyEthylene R=H, branched chain Plastic bag, Plastic wrap, stretch wrap LLDPE : Liner Low Density PolyEthylene R=H PTFE : Polytetrafluoroethylene Teflon Condensation Polymers: Nylon 66 : copolymer Polyester : ex.) Dacron

41. 18.7 The Molecules of Life: Organic Motif in Biology Carbohydrates Cm(H2O)n n=m=5 for pentose, and 6 for hexose Aldose contains -CHO group. Ketose contains -COR aldose ketose *Fisher projection is convenient for structures having many chiral centers.

42. Haworth projection chair depiction Fischer projection Pyranose ring is formed by C-5 OH attack on C=O. Furanose ring is formed by C-4 OH attack on C=O. Two optical isomers (α and β) are obtained.

43. C-O-C linkage is called ‘glycoside bond’ in polysaccarides Fatty acid: long chain carboxylic acid Fat: triester between glycerol and fatty acid CH2-O-CO-(CH2)16CH3 CH-O-CO-(CH2)16CH3 CH2-O-CO-(CH2)16CH3 Phospholipid: one of the three -O-CO-(CH2)16CH3 is replaced by PO43-

44. 18.7 The Molecules of Life: Organic Motif in Biology Amino acids and proteins Primary structure

45. Amino Acids Disulfide Red.-Ox. Acids

46. Amino Acids Basic

47. Department of Chemistry, KAIST Primary structure of protein (sequence)

48. Secondary structure (α-helix, β-sheet, random coil)

49. Hydrogen bonding is the driving force for the secondary structure formation Department of Chemistry, KAIST

50. Tertiary structure