Chapter 2: Structure and Properties of Organic Molecules

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1 Chapter 2: Structure and Properties of Organic Molecules

2 Atomic Orbitals ( ) Wave functions that represent the probability of finding electrons in a specific region of space s, p, d, f orbitals In organic chemistry, need to concentrate only on s and p orbitals 33

3 p orbitals have a nodal plane Area of space where the probability of finding electrons is almost zero 34

4 Molecular orbitals (2.2) are produced when atomic orbitals (either native or hybridized) of different atoms interact Produces bonding and anti-bonding orbitals Molecular Orbitals for H 2 * antibonding molecular orbital relative energy s atomic orbital of hydrogen s atomic orbital of hydrogen bonding molecular orbital 35

5 In the case of p orbitals, the overlap can take place in two different forms 36

6 37

7 Single Bonds (2.3) All single bonds are sigma bonds and all double or triple bonds contain only one sigma bond Sigma bonds can be formed from atomic orbitals, hybridized or native or a combination 38

8 2 other types of bonds in organic molecules: Pi (π) bond Hydrogen-bond (H-bond) 39

9 π-bond: cannot exists if a σ-bond is not already present Result from the overlap of p orbitals of two atoms. The π-bond is always perpendicular to the sigma bond connecting the nuclei. Occur in sp 2 and sp hybridized atoms (double/triple bonds) 40

10 Double bond 4 electrons in the bonding region between the nuclei * first pair forms the sigma bond * second pair forms the pi bond Normal combination for a double bond such as the one found in ethylene Example: Ethene or ethylene H H C C H H 41

11 Triple Bond 6 electrons in the bonding region between the nuclei * first pair forms the sigma bond * second/third pairs form the pi bonds Normal combination for a triple bond such as the one found in acetylene 42

12 Hybridization and Molecular shapes (2.4) Molecular shapes are related to hybridization of central atom sp 3 : only single bonds; o angle (methane) sp 2 : double bond; 120 o angle (ethylene) sp: triple bond; 180 o angle (acetylene) 43

13 Atomic orbitals can combine to generate new orbitals: * Hybridization: combination of atomic orbitals of the same atom producing new orbitals of lower energy * sp, sp 2 and sp 3 These orbitals explain the geometry of molecules Shape of sp Hybrid Orbitals in phase s out-of-phase p sp 3 one s orbital combines with 3 p orbitals to form 4 new sp 3 hybrid orbitals 44

14 45

15 46

16 Only 3 general shapes are normally found in organic molecules: 47

17 Rotation of Single Bond vs Rigidity of Double Bond (2.7) Consider ethane: CH 3 -CH 3 Each carbon is sp 3 Many structures of ethane are possible. They differ only by the position of one methyl group in relation to the other one: 48

18 CONFORMATIONS: Structures that differ only by rotation along a single bond Ex: ethane Both forms exist, and all other structures in between. In fact a real ethane molecule rotates through all the conformations, but the staggered conformation is favoured. 49

19 Consider ethylene: CH 2 =CH 2 Ethylene is quite rigid and rotation along the C=C is not allowed. 50

20 In ethylene, rotation does not affect the sigma bond, but the pi overlap is broken RULE: Rotation is allowed along single bonds, but double/triple bonds are rigid and cannot be twisted 51

21 Because of this rigidity, compounds with different substituent arrangements on a double bond are different: 52

22 these 2 compounds are different and have different chemical/physical properties. They are called: Isomers Compounds having the same molecular formula, but different structures 53

23 Structural Isomers (2.8) Also known as constitutional isomers, they differ only by their bonding sequence 54

24 Example 2: C 5 H 12 pentane has 3 structural isomers CH 3 CH 3CH 2CH 2CH 2CH 3 CH 3CHCH 2CH 3 CH 3 CCH 3 CH 3 CH 3 pentane isopentane neopentane 55

25 Problem: How many structural isomers with a molecular formula C 6 H 14 can you draw? 56

26 Stereoisomerism (2.8) compounds that differ by the 3D arrangements of atoms (or groups) in space. They are called: Stereoisomers 57

27 Problem: what is the relationship between A/B, A/C and B/C? H H H CH 3 H CH 3 H 3 C CH 3 H 3 C H H A B C CH 3 58

28 Problem: Draw all the possible isomers of formula C 5 H 10 and identify the structural and stereoisomers. 59

29 Polarity of molecules(2.9) Bond polarity can range from: Non-polar covalent (C-C) Polar covalent (C-O) Ionic (NH Cl) The polarity of bonds is related to electronegativity of atoms 60

30 Electronegativity of some important elements (for more examples see Figure 1-7) 61

31 Example: Bond polarity is the most important topic to remember in order to understand organic chemistry 62

32 The dipole moment the dipole moment of a bond is the measure of its polarity Ǻ (in Debye: D) 63

33 For example: 64

34 The molecular dipole moment is the dipole moment of the molecule taken as a whole. It is a good indicator of the overall polarity of molecules. Its value is the vector sum of individual bond dipole moments 65

35 Examples: H O H formaldehyde 2. 3D O C O carbon dioxide 0 D 66

36 Because of bond dipole, partial positive and negative charges are induced within a neutral molecule. These induced charges will be important in reactivity as well as in interactions that exist between molecules. H Cl H O H N H H H 67

37 Intermolecular Forces (2-10) 3 major kinds of attractive forces cause molecules to associate into solids or liquids: dipole-dipole forces (polar molecules) London forces (affect all molecules) Hydrogen bonds (for molecules with NH or OH groups) 68

38 Dipole-dipole forces: attractive intermolecular forces resulting from the attraction of the positive and negative ends of polar molecules The greater the forces, the higher will be the boiling point of a given compound 69

39 O cyclopentane no dipole moment bp: 49 o C tetrahydrofuran dipole moment exists bp: 65 o C 70

40 London dispersion forces: In non-polar molecules (alkanes), this is the principal attractive force They arise from temporary dipole moments created by the proximity of other molecules 71

41 Result: molecules with larger surface area will have a higher boiling/melting point 72

42 Hydrogen bonding Not a true bond, but a very strong form of dipole-dipole attraction. An H atom can participate in H-bonding if it is bonded to O or N (-OH, -NH) 73

43 Hydrogen bonds form between the hydrogen and the lone pair of the heteroatom from another molecule result: the stronger the H-bond, the higher the boiling/melting point alcohols (OH) have higher boiling points than amines (NH) of similar molecular weights, because the OH bond is more strongly polarized than NH OH Ethanol bp= 78 o C NH 2 Propyl amine bp= 49 o C 74

44 Nomenclature (will be covered as we introduce new functional groups Types of Functional Groups The following slides are to help you recognize organic compounds See Inside Front Cover of Book 75

45 3 general classes of organic compounds: A) Hydrocarbons (contains only C, H) B) Compounds containing O C) Compounds containing N 76

46 Hydrocarbons: compounds composed only of carbon and hydrogen. They include: alkanes (saturated hydrocarbons) alkenes (double bond) alkynes (triple bond) Aromatics (double and single bonds in conjugation) 77

47 Alkanes: General formula C n H 2n + 2 Names: ends with the suffix anes First part of the names refer to the number of carbon atoms. All other compounds are named based on the corresponding alkanes 78

48 #C Name Formula 1 methane CH 4 2 ethane C 2 H 6 3 propane C 3 H 8 4 butane C 4 H 10 5 pentane C 5 H 12 6 hexane C 6 H 14 7 heptane C 7 H 16 8 octane C 8 H 18 9 nonane C 9 H decane C 10 H 22 79

49 pentane heptane If the alkane molecule forms a ring, it is a cycloalkane and is formula is: C n H 2n (same as an alkene) 80

50 If a molecule contains a non alkane part, the non alkane portion is referred to as: Functional group The alkane portion is then referred to as the alkyl Alkyl group OH pentanol functional group 81

51 Alkyl group: the alkane portion of a molecule minus one H atom which was removed to allow bonding to the functional group Names of Alkyl groups: derived from the alkane [alkane name - ane] + yl = alkyl 82

52 When the structure of the alkyl group is of no concern, it is often replaced by R as a generalization 83

53 Alkenes: hydrocarbons with a C=C General formula C n H 2n (same as cycloalkanes) The C=C is the most reactive part of an alkene: it is the functional group Names: [alkane ane] + ene =alkene ethane ethene cyclohexane cyclohexene 84

54 Alkene may have stereochemistry and can be labeled as cis or trans. In small rings (4-8 carbon atoms) containing a double bond, the term cis is omitted since the double bond is always in that geometry. 85

55 In alkenes where there is more than one possibility for the position of the double bond, the location of the C=C must be specified 86

56 Alkynes Hydrocarbons with a C-C triple bond The triple bond is the functional group Names: [alkane ane] + yne = alkyne 87

57 Aromatic Hydrocarbons: Aromatic hydrocarbons are derived from benzene Benzene is a 6-carbon cyclic structure containing 3 double bonds. Each double bond is separated from the next one by a single bond a conjugated system where the electron are delocalized 88

58 Names: alkyl group first + benzene The symbol Ar represents aryl groups the same way R represented alkyl groups 89

59 Compounds Containing O Alcohols Ethers Aldehydes and Ketones Carboxylic Acids Carboxylic Acid Derivatives 90

60 Alcohols: compounds containing the OH group, the hydroxyl group Names: [alkane e] + ol = alkanol Position of the OH group must be specified 91

61 Ethers: made of 2 alkyl groups bonded to the same O Names: [alkyl + alkyl] + ether or [dialkyl] + ether If alkyl groups are different, use alphabetical order. 92

62 Aldehydes and Ketones For both of these compounds, the functional group is the carbonyl group: C=O Ketones: 2 alkyl groups attached to C=O Aldehydes: 1 alkyl group and one H attached to C=O 93

63 Ketones: [alkane e] + one = alkanone C=O position must be specified Aldehydes: [alkane e] + al = alkanal OR [alkane e] + aldehyde = alkanaldehyde not necessary to specify the position of C=O (always #1 unless with an acid derivative) O O O O propanone (acetone) 2-pentanone H ethanal (acetaldehyde)) H butanal 94

64 Carboxylic acids: molecules containing the carboxyl group O OH COOH carboxyl group CO 2 H Names: [alkane e] + oic acid = alkanoic acid 95

65 Carboxylic acid derivatives All acid derivatives contain the carbonyl group bonded to an heteroatom (Cl, O, N). 96

66 Compounds Containing N Amines Amides Nitriles 97

67 Amines: alkylated derivatives of ammonia (NH 3 ) Amines are basic. They are classified based on the number of alkyl groups attached to N. R NH 2 primary amine R NH R secondary amine R R R N R N + R R R tertiary quaternary amine ammonium salt 98

68 Names: [alkyl + alkyl] + amine OR (di) or (tri) + amine 99

69 2-35 Study Problems: What is the relationship between the following pairs of compounds (same, structural or stereoisomers). 100

70 2-41 Which compound in each of the following pair has the higher boiling point? Why? 101

71 2-42 Circle and name the functional groups in the following compounds. O Cl OH CHO 102

72 2-37 Predict whether the following compounds have a dipole moment or not. Use an arrow to show the direction of the dipole when present. O 103

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