Carbon Backbone, Nomenclature, Physical & Chemical Properties Chapter 2 Introduction to Hydrocabons Carbon Backbone, Nomenclature, Physical & Chemical Properties

HYDROCARBONS Compounds composed of only carbon and hydrogen atoms (C, H). Each carbon has 4 bonds. They represent a “backbone” when other “heteroatoms” (O, N, S, .....) are substituted for H. (The heteroatoms give function to the molecule.) Acyclic (without rings); Cyclic (with rings); Saturated: only carbon-carbon single bonds; Unsaturated: contains one or more carbon-carbon double and/or triple bond

HYDROCARBONS Alkanes contain only single ( ) bonds and have the generic molecular formula: [CnH2n+2] Alkenes also contain double ( + ) bonds and have the generic molecular formula: [CnH2n] Alkynes contain triple ( + 2) bonds and have the generic molecular formula: [CnH2n-2] Aromatics are planar, ring structures with alternating single and double bonds: eg. C6H6

Types of Hydrocarbons Each C atom is tetrahedral with sp3 hybridized orbitals. They only have single bonds. Organic molecules can be divided into four categories. Alkanes have only single bonds. Alkenes contain a C-C double bond, and alkynes contain a C-C triple bond. Benzene is an example of an aromatic hydrocarbon. Each C atom is trigonal planar with sp2 hybridized orbitals. There is no rotation about the C=C bond in alkenes.

Types of Hydrocarbons Each C atom is linear with sp hybridized orbitals. Organic molecules can be divided into four categories. Alkanes have only single bonds. Alkenes contain a C-C double bond, and alkynes contain a C-C triple bond. Benzene is an example of an aromatic hydrocarbon. Each C--C bond is the same length; shorter than a C-C bond: longer than a C=C bond. The concept of resonance is used to explain this phenomena.

It is easy to rotate about the C-C bond in alkanes. Propane It is easy to rotate about the C-C bond in alkanes. The structures of propane show that adjacent carbon atoms are able to rotate freely around C-C single bonds.

Naming Alkanes C1 - C10 : the number of C atoms present in the chain. Each member C3 - C10 differs by one CH2 unit. This is called a homologous series. Methane to butane are gases at normal pressures. Pentane to decane are liquids at normal pressures.

Nomenclature of Alkyl Substituents

Examples of Alkyl Substituents

Constitutional or structural isomers have the same molecular formula, but their atoms are linked differently. Naming has to account for them.

C7H16 can be any one of the following: A compound can have more than one name, but a name must unambiguously specify only one compound C7H16 can be any one of the following:

Alkanes (Different types of sp3 carbon atoms) Primary, 1o, a carbon atom with 3 hydrogen atoms: [R- CH3] Secondary, 2o, a carbon atom with 2 hydrogen atoms: [R- CH2-R] Tertiary, 3o, a carbon atom with 1 hydrogen atom: [R-CH- R] R Quaternary, 4o, a carbon atom with 0 hydrogen atoms: CR4

Different Kinds of sp3 Carbons and Hydrogens

Nomenclature of Alkanes 1. Determine the number of carbons in the parent hydrocarbon 2. Number the chain so that the substituent gets the lowest possible number

3. Number the substituents to yield the lowest possible number in the number of the compound (substituents are listed in alphabetical order) 4. Assign the lowest possible numbers to all of the substituents

5. When both directions lead to the same lowest number for one of the substituents, the direction is chosen that gives the lowest possible number to one of the remaining substituents 6. If the same number is obtained in both directions, the first group receives the lowest number

7. In the case of two hydrocarbon chains with the same number of carbons, choose the one with the most substituents 8. Certain common nomenclatures are used in the IUPAC system

Cycloalkane Nomenclature CnH2n Cycloalkane Nomenclature 26

Cycloalkanes Cycloalkanes are alkanes that contain a ring of three or more carbons. Count the number of carbons in the ring, and add the prefix cyclo to the IUPAC name of the unbranched alkane that has that number of carbons. Cyclopentane Cyclohexane 6

Cycloalkanes Name any alkyl groups on the ring in the usual way. A number is not needed for a single substituent. CH2CH3 Ethylcyclopentane 6

Cycloalkanes Name any alkyl groups on the ring in the usual way. A number is not needed for a single substituent. List substituents in alphabetical order and count in the direction that gives the lowest numerical locant at the first point of difference. CH2CH3 H3C CH3 3-Ethyl-1,1-dimethylcyclohexane 6

For more than two substituents,

2.17 Physical Properties of Alkanes and Cycloalkanes 4

Crude oil Naphtha Kerosene (bp 95-150 °C) (bp: 150-230 °C) C5-C12 Light gasoline (bp: 25-95 °C) C15-C25 Gas oil (bp: 230-340 °C) Refinery gas C1-C4 Residue 2

Fig. 2.15

Example of Intramolecular Forces: Protein Folding 15-16 Title: Tertiary Interactions Caption: The four distinct interactions that stabilize tertiary protein structures. Notes: Note that the disulfide bridge is a covalent bond. Ion-dipole (Dissolving) 40-600kJ/mol 10-40kJ/mol 150-1000kJ/mol 0.05-40kJ/mol 700-4,000kJ/mol

Intermolecular Forces Ion-Dipole Forces (40-600 kJ/mol) Interaction between an ion and a dipole (e.g. NaOH and water = 44 kJ/mol) Strongest of all intermolecular forces.

Ion-Dipole & Dipole-Dipole Interactions: like dissolves like Polar compounds dissolve in polar solvents & non-polar in non-polar

Intermolecular Forces Dipole-Dipole Forces (permanent dipoles) Dipole-Dipole Forces Dipole-dipole forces exist between neutral polar molecules. Polar molecules need to be close together. Weaker than ion-dipole forces. There is a mix of attractive and repulsive dipole-dipole forces as the molecules tumble. If two molecules have about the same mass and size, then dipole-dipole forces increase with increasing polarity. 5-25 kJ/mol

Intermolecular Forces Dipole-Dipole Forces

Boiling Points & Hydrogen Bonding Hydrogen Bonding Special case of dipole-dipole forces. By experiments: boiling points of compounds with H-F, H-O, and H-N bonds are abnormally high. H bonded to an electronegative element : F, O, and N. H-bonds are strong. Eg. Ice Floating Solids are usually more closely packed than liquids; Therefore, solids are usually more dense than liquids. However, Ice is an exception due to H-bonding. Ice (solid) is less dense than water (liquid). The H-O bond length is 1.0 Å. The O…H hydrogen bond length is 1.8 Å. Ice has waters arranged in open, regular hexagons.

Hydrogen Bonding Hydrogen bonds, a unique dipole-dipole (10-40 kJ/mol).

Intermolecular Forces Hydrogen Bonding

DNA: Size, Shape & Self Assembly http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm Views & Algorithms 10.85 Å 10.85 Å 15-23 Title: Base Pairs Caption: Representation of the base pairings of thymine and adenine, and cytosine and guanine, in line as well as ball-and-stick models. Notes: Base pairs occur through hydrogen bonding.

Intermolecular Forces London or Dispersion Forces An instantaneous dipole can induce another dipole in an adjacent molecule (or atom). The forces between instantaneous dipoles are called London or Dispersion forces ( 0.05-40 kJ/mol). London Dispersion Forces Weakest of all intermolecular forces. It is possible for two adjacent neutral molecules to affect each other. The nucleus of one molecule (or atom) attracts the electrons of the adjacent molecule (or atom); a dipole forms. London dispersion forces increase as molecular weight increases. London dispersion forces exist between all molecules. London dispersion forces depend on the shape of the molecule.

van der Waals Forces The boiling point of a compound increases with the increase in van der Waals force..and the Gecko!

Gecko: toe, setae, spatulae 6000x Magnification Full et. al., Nature (2000) 5,000 setae / mm2 600x frictional force; 10-7 Newtons per seta Geim, Nature Materials (2003) Glue-free Adhesive 100 x 10 6 hairs/cm2 GECKOS tiny tropical lizards are able to run up walls and along ceilings extremely fast, yet they can stick to a sheet of polished glass with only one foot. The secret of their success lies in the rows of tiny hairs on the bottom of their feet. Thousands of these hairs, called setae, are arrayed like the bristles of a toothbrush across a gecko’s toes. Microscopy reveals that the tip of each seta is divided into hundreds of tiny“spatulae”, each pointing in a different direction and tipped with a cone-shaped structure. This shape suggests a suction mechanism, but suction relies on air pressure—and gecko feet are known to stick to walls even in a vacuum. Robert Full of the University of California, Berkeley, Nature 2000. Using a tiny micro-electro-mechanical force sensor, they conducted various experiments to measure the stickiness of a single seta. The maximum adhesive force that could be exerted by a single seta had already been estimated, by measuring the total force exerted by a foot and dividing by the number of setae (around 5,000 per square millimetre). But to their surprise, researchers found that a single seta can actually exert ten times as much force as this. Setae are, in other words, even stickier than expected—giving thegecko a surprisingly large safety margin.adhesive force is about 600 times greater than the simple frictional force between lizard skin and the surface. And a seta will stick to a surface most firmly if it is first pushed into the surface and then pulled along it by a few millionths of a metre. These findings suggest that setae operate at a molecular level, and exploit intra-molecular forces, called van der Waals forces, for their stickiness. They detach by curling up the tips of their toes before moving, forming a sort of reverse fist. This allows them to peel their feet off the surface gently at a critical angle without damage, much like peeling a sticky label off a jar withot tearing it. The researchers found that setae reliably detach from the surface at an angle of about 30°. http://micro.magnet.fsu.edu/primer/java/electronmicroscopy/magnify1/index.html

Boiling Points of Alkanes governed by strength of intermolecular attractive forces alkanes are nonpolar, so dipole-dipole and dipole-induced dipole forces are absent only forces of intermolecular attraction are induced dipole-induced dipole forces 6

Induced dipole-Induced dipole Attractive Forces + – + – two nonpolar molecules center of positive charge and center of negative charge coincide in each 5

Induced dipole-Induced dipole Attractive Forces + – + – movement of electrons creates an instantaneous dipole in one molecule (left) 5

Induced dipole-Induced dipole Attractive Forces – + + – temporary dipole in one molecule (left) induces a complementary dipole in other molecule (right) 5

Induced dipole-Induced dipole Attractive Forces – – + + temporary dipole in one molecule (left) induces a complementary dipole in other molecule (right) 5

Induced dipole-Induced dipole Attractive Forces – – + + the result is a small attractive force between the two molecules 5

Induced dipole-Induced dipole Attractive Forces – – + + the result is a small attractive force between the two molecules 5

Boiling Points Increase with increasing number of carbons more atoms, more electrons, more opportunities for induced dipole-induced dipole forces Decrease with chain branching branched molecules are more compact with smaller surface area—fewer points of contact with other molecules 8

Intermolecular Forces London Dispersion Forces Which has the higher attractive force?

Boiling Points Increase with increasing number of carbons more atoms, more electrons, more opportunities for induced dipole-induced dipole forces Heptane bp 98°C Octane bp 125°C Nonane bp 150°C 8

2,2,3,3-Tetramethylbutane: bp 107°C Boiling Points Decrease with chain branching branched molecules are more compact with smaller surface area—fewer points of contact with other molecules Octane: bp 125°C 2-Methylheptane: bp 118°C 2,2,3,3-Tetramethylbutane: bp 107°C 8

2.18 Chemical Properties: Combustion of Alkanes All alkanes burn in air to give carbon dioxide and water. 10

Heats of Combustion Heptane 4817 kJ/mol 654 kJ/mol Octane 5471 kJ/mol Nonane 6125 kJ/mol What pattern is noticed in this case? 11

Heats of Combustion Increase with increasing number of carbons more moles of O2 consumed, more moles of CO2 and H2O formed 8

Heats of Combustion 5471 kJ/mol 5 kJ/mol 5466 kJ/mol 8 kJ/mol What pattern is noticed in this case? 13

Figure 2.17 5471 kJ/mol 5466 kJ/mol 25 + O2 5458 kJ/mol 2 5452 kJ/mol 8CO2 + 9H2O 14

Heat of Combustion Patterns Increase with increasing number of carbons more moles of O2 consumed, more moles of CO2 and H2O formed Decrease with chain branching branched molecules are more stable (have less potential energy) than their unbranched isomers 8

Important Point Isomers can differ in respect to their stability. Equivalent statement: Isomers differ in respect to their potential energy. Differences in potential energy can be measured by comparing heats of combustion. (Worksheet problems) 12

2.19 Oxidation-Reduction in Organic Chemistry Oxidation of a carbon atom corresponds to an increase in the number of bonds to the carbon atom and/or a decrease in the number of hydrogens bonded to the carbon atom. See examples on the board. 15

increasing oxidation state of carbon OH HO O C OH H increasing oxidation state of carbon O C H H C OH H C -4 -2 +2 +4 16

increasing oxidation state of carbon HC CH increasing oxidation state of carbon C H C H -3 -2 -1 16

But most compounds contain several (or many) carbons, and these can be in different oxidation states. CH3CH2OH C2H6O 18

Working from the molecular formula gives the average oxidation state. But most compounds contain several (or many) carbons, and these can be in different oxidation states. Working from the molecular formula gives the average oxidation state. CH3CH2OH C2H6O Average oxidation state of C = -2 18

How can we calculate the oxidation state of each carbon in a molecule that contains carbons in different oxidation states? CH3CH2OH C2H6O Average oxidation state of C = -2 18

Table 2.5 How to Calculate Oxidation Numbers 1. Write the Lewis structure and include unshared electron pairs. •• 21

Table 2.5 How to Calculate Oxidation Numbers • • •• 2. Assign the electrons in a covalent bond between two atoms to the more electronegative partner. 21

Table 2.5 How to Calculate Oxidation Numbers • • •• 3. For a bond between two atoms of the same element, assign the electrons in the bond equally. 21

Table 2.5 How to Calculate Oxidation Numbers • • •• • 3. For a bond between two atoms of the same element, assign the electrons in the bond equally. 21

Table 2.5 How to Calculate Oxidation Numbers • • •• • 4. Count the number of electrons assigned to each atom and subtract that number from the number of valence electrons in the neutral atom; the result is the oxidation number. Each H = +1 C of CH3 = -3 C of CH2O = -1 O = -2 21

Generalization Oxidation of carbon occurs when a bond between carbon and an atom which is less electronegative than carbon is replaced by a bond to an atom that is more electronegative than carbon. The reverse process is reduction. C oxidation C X Y reduction X less electronegative than carbon Y more electronegative than carbon 20

Examples CH3Cl HCl CH4 Cl2 + Oxidation + 2Li LiCl CH3Cl CH3Li Reduction 21

Functions, Nomenclature, Chapter 4 Alcohols & Halides Functions, Nomenclature,

Common Functional Groups Class General Formula Halohydrocarbons RX Alcohols R Ethers RR Amines

Nomenclature of Alkyl Halides In the IUPAC system, alkyl halides are named as substituted alkanes

Structures of Alkyl Halides

Different Kinds of Alkyl Halides

Nomenclature of Ethers ??? As substituents:

Structures of Alcohol and Ether

Nomenclature of Alcohols In an alcohol, the OH is a functional group A functional group is the center of reactivity in a molecule 1. Determine the parent hydrocarbon containing the functional group

2. The functional group suffix should get the lowest number 3. When there is both a functional group suffix and a substituent, the functional group suffix gets the lowest number

4. If there is more than one substituent, the substituents are cited in alphabetical order

Nomenclature of Amines The substituents are listed in alphabetical order and a number or an “N” is assigned to each one

Structures of Amines

Naming Quaternary Ammonium Salts

Other Common Functional Groups Class General Formula Aldehydes Ketones Carboxylic Acids Esters Amides

Dipole–dipole interaction Attractive Forces Ionic bonds Covalent bonds Hydrogen bonds Dipole–dipole interaction Ion-dipole Dispersion Forces van der Waals force The greater the attractive intermoleclar forces between molecules, the higher is the boiling point of the compound, eg. water.

Protein Shape: Forces, Bonds, Self Assembly, Folding (Intramolecular forces) 15-16 Title: Tertiary Interactions Caption: The four distinct interactions that stabilize tertiary protein structures. Notes: Note that the disulfide bridge is a covalent bond. Ion-dipole (Dissolving) 40-600kJ/mol 10-40kJ/mol 150-1000kJ/mol 0.05-40kJ/mol 700-4,000kJ/mol

A hydrogen bond is a special kind of dipole–dipole interaction

Dipole–Dipole Interaction Dipole–dipole interactions are stronger than van der Waals force but weaker than ionic or covalent bonds

van der Waals Forces The boiling point of a compound increases with the increase in van der Waals force

Ion-Dipole & Dipole-Dipole Interactions: like dissolves like Polar compounds dissolve in polar solvents & non-polar in non-polar

Chapter 3 Alkanes & Cycloalkane Conformations

Conformations of Alkanes: Rotation about Carbon–Carbon Bonds

Conformational Analysis Drawing Acyclic Molecules Newman Projections

Conformational Analysis Drawing Acyclic Molecules Sawhorse Drawings

Different Conformations of Ethane A staggered conformer is more stable than an eclipsed conformer Torsional strain: repulsion between pairs of bonding electrons

Conformations of n-Butane Steric strain: repulsion between the electron clouds of atoms or groups

Cycloalkanes: Ring Strain Angle strain results when bond angles deviate from the ideal 109.5° bond angle

The Shapes of Cycloalkanes: Planar or Nonplanar? 1

Adolf von Baeyer (19th century) Assumed cycloalkanes were planar polygons. Believed distortion of bond angles from 109.5° gives angle strain to some cycloalkanes. One for two is great in baseball. 2

Types of Strain • Torsional strain strain that results from eclipsed bonds (measure of the dihedral angle) • Van der Waals strain or (Steric strain) strain that results from atoms being too close together. • Angle strain results from distortion of bond angles from normal values, for a tetrahedron 109.5o 3

Measuring Strain in Cycloalkanes Heats of combustion can be used to compare stabilities of isomers. But cyclopropane, cyclobutane, etc. are not isomers. All heats of combustion increase as the number of carbon atoms increase. 4

Measuring Strain in Cycloalkanes Therefore, divide heats of combustion by number of carbons and compare heats of combustion on a "per CH2 group" basis. 4

Heats of Combustion in Cycloalkanes Cycloalkane kJ/mol Per CH2 Cyclopropane 2,091 697 Cyclobutane 2,721 681 Cyclopentane 3,291 658 Cyclohexane 3,920 653 Cycloheptane 4,599 657 Cyclooctane 5,267 658 Cyclononane 5,933 659 Cyclodecane 6,587 659 4

Heats of Combustion in Cycloalkanes Cycloalkane kJ/mol Per CH2 According to Baeyer, cyclopentane should have less angle strain than cyclohexane. Cyclopentane 3,291 658 Cyclohexane 3,920 653 The heat of combustion per CH2 group is less for cyclohexane than for cyclopentane. Therefore, cyclohexane has less strain than cyclopentane. 4

Conformations of Cyclohexane Heat of combustion suggests that angle strain is unimportant in cyclohexane. Tetrahedral bond angles require nonplanar geometries. The chair and boat conformations. 5

6

The chair conformation of cyclohexane is free of strain

Chair is the most stable conformation of cyclohexane All of the bonds are staggered and the bond angles at carbon are close to tetrahedral. 6

Boat conformation is less stable than the chair 180 pm All of the bond angles are close to tetrahedral but close contact between flagpole hydrogens causes strain in boat. 6

Boat conformation is less stable than the chair Eclipsed bonds bonds gives torsional strain to boat. 6

Skew boat is slightly more stable than boat Skew or Twist Boat Less van der Waals strain and less torsional strain in skew boat. 6

Generalization The chair conformation of cyclohexane is the most stable conformation and derivatives of cyclohexane almost always exist in the chair conformation 2

Axial and Equatorial Bonds in Cyclohexane 11

Drawing Cyclohexane

The 12 bonds to the ring can be divided into two sets of 6.

6 Bonds are axial Axial bonds point "north and south" 12

The 12 bonds to the ring can be divided into two sets of 6.

6 Bonds are equatorial Equatorial bonds lie along the equator 12

Conformational Inversion (Ring-Flipping) in Cyclohexane 16

Conformational Inversion chair-chair interconversion (ring-flipping) rapid process (activation energy = 45 kJ/mol) all axial bonds become equatorial and vice versa 17

18

Half- chair 18

Half- chair Skew boat 18

Half- chair Skew boat 18

Half- chair Skew boat 18

45 kJ/mol 45 kJ/mol 23 kJ/mol 18

The Conformations of Cyclohexane and Their Energies

Conformational Analysis of Monosubstituted Cyclohexanes most stable conformation is chair substituent is more stable when equatorial 19

Steric Strain of 1,3-Diaxial Interaction in Methylcyclohexane

Methylcyclohexane axial CH3 CH3 equatorial 5% 95% Chair chair interconversion occurs, but at any instant 95% of the molecules have their methyl group equatorial. An axial methyl group is more crowded than an equatorial one. 20

Methylcyclohexane 5% 95% Hydrogen atoms closer than 2.4 Angstroms will cause steric strain. This is called a "1,3-diaxial repulsion" a type of van der Waals strain or Steric strain. 20

Fluorocyclohexane F F 40% 60% Crowding is less pronounced with a "small" substituent such as fluorine. Size of substituent is related to its branching. 20

tert-Butylcyclohexane C(CH3)3 C(CH3)3 Less than 0.01% Greater than 99.99% Crowding is more pronounced with a "bulky" substituent such as tert-butyl. tert-Butyl is highly branched. 20

tert-Butylcyclohexane van der Waals strain due to 1,3-diaxial repulsions 24

The larger the substituent on a cyclohexane ring, the more the equatorial substituted conformer will be favored Keq = [equatorial conformer]/[axial conformer]

Disubstituted Cyclohexanes Cis-trans Isomerism 16

Cyclic Alkanes Stereochemistry Cis -Trans Isomers

The Chair Conformers of cis-1,4-Dimethylcyclohexane

1,2-disubstituted-cis-cyclohexane Stereochemistry axial equatorial

Cyclohexane Stereochemistry Drawings: Cis isomers & the need for perspective Are the methyl groups axial or equatorial? What is the actual conformational shape of the cyclohexane ring?

The Chair Conformers of trans-1,4-Dimethylcyclohexane

Cyclohexane Stereochemistry Trans isomers

1-tert-Butyl-3-Methylcyclohexane

Cyclohexane Stereochemistry Cis -Trans Isomers e,e or a,a a,e or e,a e,a or a,e e,e or a,a Complete the Table: a = axial; e = equatorial

Conformations of Fused Rings Trans-fused cyclohexane ring is more stable than cis-fused cyclohexane ring