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1 Organic Chemistry Courtney Eichengreen 719.321.4187 1.

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Presentation on theme: "1 Organic Chemistry Courtney Eichengreen 719.321.4187 1."— Presentation transcript:

1 1 Organic Chemistry Courtney Eichengreen

2 2 Organic Chemistry I From atoms to molecules and beyond Functional Groups Bonding and Molecular Structure Resonance and Isomers Intermolecular interactions Hydrocarbons Substitution and Elimination Reactions Oxygen Containing Compounds Amines 2

3 3 Lewis Dot Structures Rules for writing Find total # valence e - 1 e - pair = 1 bond; Arrange remaining e - per octet rules Except: Period 3 can have expanded octet (vacant d orbital required for hybridization) Formal Charge # valence e - (isolated atom) - # valence e - (lewis structure) Sum of formal charge for each atom is the total charge on the molecule ACTUAL charge distribution depends on electronegativity 3

4 4 Structural Formulas Dash Formula Condensed Formula Bond-line Formula Fischer projection Newman projection Dash-line-wedge Ball and stick All Images courtesy of Exam Krackers 4

5 5 Functional Groups List #1- Critical for the MCAT Alkane C-C AlkeneC=C AlkyneCΞC AlcoholR-OH EtherR-O-R AmineR-N-R 2 AldehydeR-CHO KetoneR 2 C=O Carboxylic AcidRCOOH EsterRCOOR AmideRCONH 2 5

6 6 Functional Groups List #2- Also Useful Alkyl Halogen Gem-dihalide Vic dihalide Hydroxyl Alkoxy Hemiacetal Hemiketal Mesyl group Tosyl group Carbonyl Acetal Acyl Anhydride Aryl Benzyl Phenyl Hydrazine Hydrazone Vinyl Vinylic Allyl Nitrile Epoxide Enamine Imine Nitro Nitroso 6

7 77

8 Bonds Types: Ionic Covalent Coordinate covalent Polar covalent Hydrogen Bonds complete transfer of electrons shared electrons One atom provides both electrons in a shared pair. unequal sharing of electrons bonds between polar molecules containing H and O, N, or F 88

9 9 Covalent Bonds Sigma Between s orbitals Small, strong, lots of rotation Pi Between p orbitals Discreet structure, weaker than sigma, no rotation 9

10 Covalent Bonds 10

11 11 Bonds In the pi bond of an alkene, the electron pair have: A. 33% p character and are at a lower energy level than the electron pair in the bond. B. 33% p character and are at a higher energy level than the electron pair in the bond. C. 100% p character and are at a lower energy level than the electron pair in the bond. D. 100% p character and are at a higher energy level than the electron pair in the bond. 11

12 12 Hybridization 12

13 Hybridization Remember: All pi bonds are between P orbitals Leftover P and S orbitals hybridize, participate in sigma bonds Ex: H 2 C=CH 2 13

14 14 Hybrid Bonds SuffixC bondsHybridiz ation Percent S:P Bond Angle Bond Length Bond Strength -ane -ene -yne -yl 14

15 15 Hybrid Bonds SuffixC bondsHybridiz ation Percent S:P Bond Angle o Bond Length (pm) Bond Strength (kJ/mol) -aneC-Csp325: eneC=Csp233: yneC=CC=Csp50: yl Side chain

16 16 Special Cases – O and N Know typical bonding for C, N, O Bond angles in N compounds Lone pair occupies more space than sigma bond Bond angles Bond angles in O compounds Bond angles

17 17 A) sp2, sp2 B) sp2, sp3 C) sp3, sp3 D) sp3, sp2 For the molecule 1,4 pentadiene, what type of hybridization is present in carbons # 1 and # 3 respectively? 17

18 18 VSEPR: molecular geometry valance shell electron pair repulsion GEOMETRY = Minimize electron repulsion 18

19 19 moleculeLewis structureShapemoleculeLewis structureShape BeCl 2 Linear, sp SF 4 SeesawSO 3 Trigonal planar, sp 2 ICl 3 T shapedNO 2 - Bent CH 4 Tetrahedral, sp 3 NH 3 Trigonal Pyramidal PCl 5 Trigonal bipyramidal, dsp 3 SF 6 Octahedral, d 2 sp 3 IF 5 Square PyramidalICl 4 - Square Planar VSEPR 1. Draw the Lewis dot structure 2. Place electron pairs as far apart as possible then large atoms, then small atoms 3. Name the molecular structure based on the position of the atoms 19

20 NOW LETS MOVE STUFF AROUND! Weve seen static properties of atoms and molecules… 20

21 21 Delocalized e - and Resonance Resonance forms differ only in location of e - To be a significant resonance form, must be stable Remember octet rule, and consider formal charge Real structure = blend of possible resonance structures, resonance hybrid 21

22 22 Resonance: Acids and Bases Conjugate stabilized by RESONANCE Organic Acids- Presence of positively charged H+ present on a OH such as methyl alcohol present on a C next to a C=O such as acetone (alpha C) Organic Bases- Presence of lone pair e to bond to H Nitrogen containing molecules are most common Oxygen containing molecules can act as bases w strong acids 22

23 23 Stereochemistry Isomers: same molecular formula, different spatial arrangements Different spatial arrangements different physical and chemical properties! 23

24 Stereochemistry: Isomers CONNECTIVITY Structural (constitutional) isomers: Different connectivity. C 4 H 10 - Isobutane vs n-butane Same connectivity, different spatial arrangement: Stereoisomers 24

25 Stereochemistry: Isomers ROTATION Conformational isomers: Different spatial arrangement of same molecule, but doesnt require bond breaking to interconvert! rotational isomers Chair vs. boat, Staggered vs Eclipsed, Gauche vs Anti DOES require bond breaking to interconvert: configurational isomers 25

26 Stereochemistry: Isomers DOUBLE BOND Geometric isomers: differ in arrangement about a double bond Cis vs. trans Stereoisomers that are not rotational and have no double bond: OPTICAL isomers 26

27 27 Stereochemistry: Isomers CHIRAL ARRANGEMENT Enantiomers: non-superimposable mirror images Same physical properties (MP, BP, density, solubility, etc.) except rotation of light and reactions with other chiral compounds Chiral centers that are all opposite each other (R/S) Diastereomers: chiral molecules with other than exactly opposite stereocenters (not mirror images) 27

28 28 Stereochemistry: Isomers What kind of isomers are the two compounds below? A. Diastereomers B. Enantiomers C. Constitutional isomers D. Geometric Isomers 28

29 29 Enantiomers differ in rotation of plane-polarized light Excess of one enantiomer causes rotation: Right, clockwise, dextrarotary (d), or + Left, counterclockwise, levarotary (l), or – Specific rotation [a] = a / (l*d) Racemic: 50:50 mixt of enantiomers, NO net rotation Same as R and S? NO Meso molecule – NO net rotation, internal symmetry 29 Stereochemistry: Rotating Light

30 Stereochemistry: Chirality R and S: 1. Assign priority by atomic number If attachments are the same, look at the atoms 2. Orient lowest priority (#4) away from the observer 3. Draw a circular arrow from 1 to 2 to 3 R = clockwise S = counterclockwise E and Z: Different than cis and trans Z= same side of high priority groups E=opposite side of high priority groups 30

31 WHAT ABOUT BETWEEN MOLECULES? Now we know everything about what happens WITHIN molecules… 31

32 Intermolecular interactions Due to DIPOLE MOMENTS Charge distribution of bond is unequal Molecule with dipole moment = polar Molecule without dipole moment = nonpolar Possible to have nonpolar molecules with polar bonds Induced Dipoles Spontaneous dipole moment in nonpolar molecule Occurs via: polar molecule, ion, or electric field Instantaneous Dipole Due to random e- movement 32

33 Intermolecular interactions London Dispersion Forces Between 2 instantaneous dipoles Dipole-dipole interactions Dipole-dipole or dipole-induced dipole Hydrogen Bonds Strongest dipole-dipole interaction 33

34 34 When albuterol is dissolved in water, which of the following hydrogen-bonded structures does NOT contribute to its water solubility? 34

35 HYDROCARBONS The first and simplest class of molecules we need to get friendly with for Test Day: 35

36 36 IUPAC Naming Conventions IUPAC Rules for Alkane Nomenclature 1. Find + name the longest continuous carbon chain. 2. Identify and name groups attached to this chain. 3. Number the chain consecutively, starting at the end nearest highest priority (oxidation) substituent group. 4. Name the compound listing groups in alphabetical order, preceded by their number in the compound. (di, tri, tetra etc., dont count for alphabetizing). MCAT secret: on Test Day, youll only ever have to MATCH to the correct name! 36

37 37 Hydrocarbons # of CRoot Name# of CRoot Name 1meth6hex 2eth7hept 3prop8oct 4but9non 5pent10dec 37

38 38 Hydrocarbons Saturated: C n H (2n+2) Unsaturated: one or more pi bonds; each pi bond decreases # of H by 2 Primary, secondary, tertiary, and quaternary carbons Know and be able to recognize the following structures n-butylsec-butyl iso-butyltert-butyl n-propyl Iso-propyl 38

39 39 Alkanes Physical Properties: Straight chains: MP and BP increase with length Branched chains: BP decreases (less surface area, vDW forces) MP – a little more complicated due to crystal structure When compared to the straight chain analog, the straight chain will have a higher MP than the branched molecule. BUT, amongst branched molecules, the greater the branching, the higher the MP. 39

40 40 Alkanes-Important Reactions Pretty Darn Unreactive Combustion: Alkane + Oxygen + High energy input (fire) Products: H 2 O, CO 2, Heat Halogenation Initiation with UV light Homolytic cleavage of diatomic halogen Yields a free radical Propagation (chain reaction mechanisms) Halogen radical removes H from alkyl Yields an alkyl radical, which can make more radicals Termination Radical bonds to another radical Reactivity of halogens: F > Cl > Br >>> I Selectivity of halogens (How selective is the halogen in choosing a position on an alkane): I > Br > Cl > F more electronegative means less selective Stability of free radicals: more substituted = more stable, so most subd C aryl>>>alkene> 3 o > 2 o > 1 o >methyl 40

41 41 Cycloalkanes General formula: (CH 2 ) n or C n H 2n Nomenclature: Its the same! As MW increases BP increases; MP fluctuates (crystal stacking with different geometry) Ring strain in cyclic compounds: Zero for cyclohexane (All C-C-C bond angles: 111.5°) Increases as rings become smaller or larger (up to cyclononane) 41

42 42 Cycloalkanes Cyclohexane Exist as chair and boat conformations Chair conformation preferred because it is at the lowest energy. (WHY?) Substituents can occupy axial and equatorial positions. Axia (6) - perpendicular to the ring Equatorial (6)- roughly in the plane of the ring Big substituents prefer to be equatorial – less crowding! When the ring reverses its conformation, substituents reverse their relative position 42

43 43 Cyclohexanes In a sample of cis-1,2-dimethylcyclohexane at room temperature, the methyl groups will: A. Both be equatorial whenever the molecule is in the chair conformation. B. Both be axial whenever the molecule is in the chair conformation. C. Alternate between both equatorial and both axial whenever the molecule is in the chair conformation D. Both alternate between equatorial and axial but will never exist both axial or both equatorial at the same time 43

44 REACTIONS!! Things start getting more exciting once we start substituting H for more interesting functional groups… so lets get ready for some 44

45 45 Substitutions Substitution: one functional group replaces another Electrophile: wants electrons, has partial + charge Nucleophile: donates electrons, has partial – charge 45

46 46 Eliminations Elimination: functional group lost, double bond made Often, a Lewis base is responsible for taking H leaving behind an extra pair of e - for the = The opposite of elimination is addition 46

47 47 Substitution and Elimination SN1: substitution, nucleophilic, unimolecular Mechanism: two-step 1. spontaneous formation of carbocation (SLOW) 2. Nucleophile attacks carbocation Kinetics: rate depends only on the substrate, R=k[reactant] Stereochemistry: racemization of chiral substrates Favored with weak or bulky Nu, good LG, stable carbocation Protic solvents stabilize carbocation Can see carbocation rearrangement 47

48 48 Substitution and Elimination E1: elimination, unimolecular Mechanism: two-step 1. spontaneous formation of carbocation (SLOW) 2. Base abstracts beta H Kinetics: rate depends only on the substrate, R=k[reactant] Favored with good LG, stable carbocation, weak base Protic solvents stabilize carbocation Can see carbocation rearrangement 48

49 49 Which of the following carbocations is the most stable? A.A.CH 3 CH 2 CH 2 CH 2 B.B.CH 3 CH 2 CH 2 CHCH 3 C.C.(CH 3 ) 3 C D.D.CH 3 49

50 50 Substitution and Elimination SN2: substitution, nucleophilic, bimolecular Mechanism: CONCERTED Kinetics: rate depends on substrate+nucleophile, R=k[Nu][E] Stereochemistry: inversion of configuration (but watch your R and S!) Favored with poor LG, small + strong Nu Polar, APROTIC solvents dont obstruct Nu 50

51 51 Substitution and Elimination E2: elimination, bimolecular Mechanism: CONCERTED Anti-peri-planar transition state determines stereochemistry Kinetics: rate depends on substrate+base, R=k[substrate][B] Favored with strong bulky base If you see HEAT, think Elimination E2 reactions often run in solvent of conjugate acid (WHY?) 51

52 52 Benzene A special molecule, a special case of substitution! Actually, its addition and then elimination. Aromatic molecule, Stabilized by resonance Undergoes net substitution not addition (WHY?) Substituents determine subsequent reactivity: Electron donating groups activate the ring and are ortho-para directors Electron withdrawing groups deactivate the ring and are meta directors Halogens are electron withdrawing BUT are ortho-para directors 52

53 53 Benzene: Substituent Effects 53

54 In what order were the substituents added? How can you tell? 54

55 OXYGEN-CONTAINING COMPOUNDS Another class of molecules we need to be familiar with: 55

56 56 Oxygen Containing Compounds Alcohols Aldehydes and Ketones Carboxylic Acids Acid Derivatives Acid Chlorides Anhydrides Amides Keto Acids and Esters 56

57 57 Alcohols One of the most common reactions of alcohols is nucleophilic substitution. Which of the following are TRUE in regards to S N 2 reactions: I. Inversion of configuration occurs II. Racemic mixture of products results III. Reaction rate = k [S][nucleophile] A. I only B. II only C. I and III only D. I, II, and III 57

58 58 Alcohols Physical Properties: Polar High MP and BP (WHY?) More substituted = less acidic (CH3)3COH: pKa = CH3CH2OH: pKa = CH3OH: pKa = Electron withdrawing substituents stabilize alkoxide ion and lower pKa. Tert-butyl alcohol:pKa = Nonafluoro-tert-butyl alcohol:pKa = 5.4 General principles H bonding Acidity: weak relative to other O containing compounds 58

59 59 Alcohols Naming Select longest C chain containing the hydroxyl group and derive the parent name by replacing –e ending of the corresponding alkane with –ol. Number the chain beginning at the end nearest the –OH group. Number the substituents according to their position on the chain, and write the name listing the substituents in alphabetical order. 59

60 60 Alcohols-Oxidation & Reduction Oxidation Reduction 60

61 61 Alcohols-Oxidation & Reduction Common oxidizing and reducing agents Generally for the MCAT Oxidizing agents have lots of oxygens Reducing agents have lots of hydrogens Oxidizing AgentsReducing Agents K 2 Cr 2 O 7 LiAlH 4 KMnO 4 NaBH 4 H 2 CrO 4 H 2 + Pressure O2O2 Br 2 61

62 62 Making Alcohols: reduction synthesis Aldehydes, ketones, esters, and acetates can be reduced to alcohols w strong reducing agents such as NaBH 4 and LiAlH 4 Electron donating groups increase the negative charge on the carbon and make it less susceptible to nucleophilic attack. Reactivity: Aldehydes>Ketones>Esters/acetates Only LiAlH 4 is strong enough to reduce esters and acetates 62

63 63 Alcohols to Alkylhalides via a strong acid catalyst R-OH + HCl RCl + H 2 0 -OH is converted to a much better leaving group when protonated by a strong acid For tertiary alcohols: HCl or HBr Primary/secondary alcohols are harder, need SOCl 2 or PBr 3 63

64 64 In the reaction above, if the reagents in the first step were replaced with LiAlH 4, what product would result? a)c) b)d) 64 OH O HO

65 65 Carbonyls Carbon double bonded to Oxygen Planar stereochemistry Partial positive charge on Carbon (susceptibility to nucleophilic attack) Aldehydes & Ketones (nucleophilic addition) Carboxylic Acids (nucleophilic substitution) Amides 65

66 66 Aldehydes and Ketones Physical properties: Carbonyl group is polar Higher BP and MP than alkanes (WHY?) More water soluble than alkanes (WHY?) Trigonal planar geometry, reduction yields racemic mixtures General principles: Effects of substituents on reactivity of C=O: e - withdrawing increase the carbocation nature and make the C=O more reactive Steric hindrance: ketones are less reactive than aldehydes Acidity of alpha hydrogen: carbanions, unsaturated carbonyls: resonance structures 66

67 67 Aldehydes and Ketones Naming – lalala its the same rules! Naming Aldehydes Replace terminal –e of corresponding alkane with –al. Parent chain must contain the –CHO group The –CHO carbon is C1 When –CHO is attached to a ring, we say carbaldehyde Naming Ketones Replace terminal –e of corresponding alkane with –one. Parent chain is longest chain containing ketone Numbering begins at the end nearest the carbonyl C. 67

68 68 Aldehydes and Ketones- Acetal and Ketal Formation nucleophilic addition at C=O bond 68

69 69 Aldehydes and Ketones Keto-enol Tautomerism: Keto tautomer is preferred (alcohols are more acidic than aldehydes and ketones). 69

70 70 Guanine, the base portion of guanosine, exists as an equilibrium mixture of the keto and enol forms. Which of the following structures represents the enol form of guanine? 70

71 71 Aldehydes and Ketones- reactions at adjacent positions Aldol (aldehyde + alcohol) condensation: Occurs at the alpha carbon Pi electrons in enol act as nucleophile Base catalyzed condensation (removal of H2O) Can use mixtures of different aldehydes and ketones 71

72 72 Aldehydes are easy to oxidize because of the adjacent hydrogen. In other words, they are good reducing agents. Examples used as indicators: Potassium dichromate (VI): orange to green Tollens reagent (silver mirror test): grey ppt. Fehlings or benedicts solution (copper solution): blue to red Ketones (no adjacent H) are resistant to oxidation. Aldehydes and Ketones-Oxidation (Aldehydes Carboxylic acids) 72

73 73 Aldehydes and Ketones Organometallic reagents: Nucleophilic addition of a carbanion to an aldehyde or ketone to yield an alcohol 73

74 74 Carboxylic Acids General Principles: Electrophilic carbonyl C susceptible to nucleophilic attack! Fairly strong acids (compared to other organic Oxygen containing compounds) Acidity of terminal H increases with EWG, decreases with EDG – always consider stability of conjugate base Planar, polar, H bonding 74

75 Which class of compounds would have a higher boiling point, Acyl Chlorides or Carboxylic Acids? Why? 75

76 76 Carboxylic Acids Naming Carboxylic acids derived from open chain alkanes are systematically named by replacing the terminal –e of the corresponding alkane name with –oic acid. Compounds that have a –CO2H group bonded to a ring are named using the suffix –carboxylic acid. The –CO2H group is attached to C #1 and is not itself numbered in the system. 76

77 77 Carboxylic Acids-important reactions Carboxyl group reactions: Nucleophilic attack: Carboxyl groups and their derivatives undergo nucleophilic substitution. Aldehydes and Ketones undergo addition (WHY?) Must contain a good leaving group or a substituent that can be converted to a good leaving group. 77

78 78 Carboxylic Acids-important reactions Reduction: Form a primary alcohol LiAlH 4 is the reducing agent CH 3 (CH 2 ) 6 COOH CH 3 (CH 2 ) 6 CH 2 OH LiAlH4 78

79 79 Carboxylic Acids-important reactions Carboxyl group reactions: Decarboxylation: know that it happens (-CO 2 ) 79

80 80 Carboxylic Acids-important reactions Fischer Esterification Reaction: Alcohol + Carboxylic Acid Ester + Water Acid Catalyzed- protonates –OH to H 2 O (excellent leaving group) Alcohol performs nucleophilic attack on carbonyl carbon These bonds are broken H+H+ 80

81 81 Carboxylic Acids- reactions at two positions Substitution reactions: keto reactions shown, consider enol reactions To make - > SOCl 2 or PCl 3 Heat, -H 2 O R'OH, heat, H+ - R 2 NH heat HO - 81

82 82 Carboxylic Acids- reactions at two positions Halogenation: enol tautomer undergoes halogenation 82

83 83 Acid Derivatives Naming Acid Halides (RCOX) -oyl halide instead of -oic acid ex: ethanoyl chloride Acid Anhydrides (RCO2COR) Just replace the word acid with anhydride. 2 acetic acid acetic anhydride Unsymmetrical anhydrides are named by citing the two acids alphabetically. Acetic acid + benzoic acid acetic benzoic anhydride Esters (RCO2R) Name R (on the –O– side) with -yl, R (on the =O side) with -oate ex: isopropyl propanoate Amides (RCONH2) Just use the suffix amide Acetic acid acetamide If the Nis further substituted, first identify the substituent groups and then the parent amide. The substituents are preceded by the letter N. Propanoic acid + methyl amine N-Methylpropanamide 83

84 84 Acid Derivatives- Relative Reactivity A more reactive acid derivative can be converted to a less reactive one, but not vice versa Only esters and amides commonly found in nature. Acid halides and anhydrides react rapidly with water and do not exist in living organisms 84

85 85

86 86 Acid Derivatives- Reactions of Derivatives Hydrolysis- +water carboxylic acid Alcoholysis- +alcohol ester Aminolysis- +ammonia or amine amide Reduction- + H- aldehyde or alcohol Grignard- + Organometallic ketone or alcohol 86

87 87 Acid Derivatives Transesterification Transesterification: exchange alkoxyl group with ester of another alcohol Alcohol + Ester Different Alcohol + Different Ester 87

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