Chapter 15Organic Chemistry

Source: Science, Jan 9, 2009, “On the origins of life on earth”

Life is chemistry.

Organic chemistry is enough to drive one mad. - Friedrich Wöhler What is an organic compound?

Organic compound – contains carbon, nearly always bonded to other C and H, and often other elements

Vitalism: Organic molecules were yhought to arise spontaneously (Spontaneous Generation) and couldnot be synthesized from inorganics

Wöhler’s experiment changed that

Urea synthesized from ammonium cyanate.(2 compounds – same molecular formula)

Vitalism

A major misconception that stifled organic chemistry research in early 19th Century.

Resulted in the basic distinction between organic and inorganic substances

An unobservable spiritual energy existed within organic compounds of living things, making them impossible to synthesize and fundamentally different from inorganic compounds (compounds of the “mineral world” – mostly, what we have studied so far)

Reading for today: Did life originally arise from inorganic chemicals?

Classes of organic molecules

I. Hydrocarbons – simplest type of organic compound-functional groups & reactivity-polymers

Classes of organic molecules

II. Biomolecules – natural polymers-polysaccharides, proteins, nucleic acids

Section 15.1: What’s so special about Carbon?

Atomic properties of carbon (and bonding behavior) make it special.

Structural complexity of organic compounds

Always bonds covalently – moderateEN makes formation of C ions energetically impossible under ordinary conditions.

Why? – REVIEW

Ionization energy (IE) – Chap 8Energy required for the complete removal of 1 mole of e- from 1 mole of gaseous atoms or ions (E to overcomeattraction between protons & e-)

C’s location in the periodic table tells you a lot

Ionization energy (IE) – Chap 8 As size decreases, more E to removean e-

C is small and forms 4 covalent bonds

Structural complexity of organic compounds

Ionization energy (IE) – Energy required to get C4+ ion = IE1 + IE2 + IE3 + IE4

A lot of energy to remove an e- ……..and to add e-’s Electron affinity (EA):

The energy change accompanying the addition of1 mole of e-’s to 1 mole of gaseous atoms or ions.

EA1 is negative (exothermic): Energy releasedEA2 – EA4 are positive (endothermic): Energy required

Energy is required to get C4- ion = EA1 + EA2 + EA3 + EA4

Carbon has the ability to catenate – form chains of atoms (= large, complex molecules)

Due to the sp3 hybridization: C forms 4 bonds in nearly all of its compounds

C forms short, strong bonds:Small size allows close approach of another atom

Structural complexity of organic compounds

Carbon easily forms double and triple bonds: C – C bond is short enough to allow side-to-side overlap

Double bond

Triple bond

Structural complexity of organic compounds

Double and triple bonds:

Restricts rotation

=

MORE variety

Structural complexity of organic compounds

So why don’t Si, Ge and Sn also form organic compounds? In same Group 4A as C.

C’s location in the periodic table tells you a lot – Periodic Trends

(1) Atomic size and bond strengthi.e. C – C bonds = 347 kJ/mol Si – Si bonds = 226 kJ/mol

(2) ∆Hreaction

i.e. C – C (347), C – O (358) Si – Si (226), Si – O (368)

(3) Orbitals available for reactioni.e. C has s and p orbitals Si has s, p, and d orbitals

d orbitals can be attacked by lonee- pairs of incoming reactants

Ethane (CH3-CH3): Stable in waterand air

Disilane (SiH3-SiH3): Breaks down inwater, spontaneous ignition in air

Structural complexity of organic compounds

Chemical diversity of organic compounds

CRC Handbook of Physics and Chemistry - # of C-based compounds dwarfs the # ofcompounds formed from all of the other elements combined

Chemical diversity also a result of atomic and bonding behavior of carbon.

Bonding to heteroatoms: Organic compounds contain atoms other than C and H (also N, O, S, P and halogens)

Example:

23 organic molecules

4 singley bonded C 1 O Filled in with H

Chemical diversity of organic compounds

Electron density and reactivity

Most chemical reactions start (and new bonds form) when a region of high e- densityon one molecule meets a region of low e- density on another

Regions of high e- density can be due to: (1) Multiple bonds(2) Partial charges(3) Lone pairs

4 bonds commonly found in organic molecules:

C – C: Generally, unreactive – EN values equal and bond is nonpolar

C – H: Largely unreactive – EN values close (C = 2.5, H = 2.1) – bond is short (strong) C and H are both small atoms

C – O: Reactive – Highly polar (∆ EN = 1.0) O end of bond is e- rich

Bonds to other heteroatoms (S, P, Br): Reactive – bonds longer (S, P, Br large relative to H)

Chemical diversity of organic compounds

Functional Group – a specific combination of bonded atoms that reacts in a characteristic way, no matter what organic molecule it occurs in

In fact, reactions in organic molecule nearly always take place at functional groups.

Example: Structure of amino acids

20 amino acids differonly by functional group

Section 15.2: Hydrocarbons

Organic Molecule-Animal Analogy for Hydrocarbons:

• C – C bonds form the skeleton

• H atoms are the skin covering the skeleton

• Functional groups are limbs protruding from body ready to “grab” (react with) reactants

Hydrocarbons – a large group of organic compounds containing only H and C atoms

Example: Natural gas and gasoline are hydrocarbon mixtures

Section 15.2: Hydrocarbons

Carbon skeletons – What different possible arrangements exist for C atoms?

For example: If you have two carbon atoms, there is one possible arrangement

C – C

As the number of carbon atoms increases, the number of arrangements increases.

Section 15.2: Hydrocarbons

Practice Drawing Hydrocarbons

Purpose: Get a sense of the number of possibilities for a given formula (i.e. C6H14)

Steps: #1: Are there single, double, or triple bonds? How many of each? #2: Figure out the arrangement of C atoms #3: Add the H skeleton

(1) Six C atoms, no multiple bonds, no rings

(2) Four C atoms, one double bond, no rings

(3) Four C atoms, no multiple bonds, one ring

Section 15.2: Hydrocarbons

Hydrocarbon classification – 4 main groups:

(1) Alkanes – single bonds(2) Alkenes – double bonds(3) Alkynes – triple bonds(4) Aromatic Hydrocarbons - rings

Alkanes – CnH2n+2

Each carbon is sp3 hybridized

Each C is bonded to the maximum number of other atoms – saturated hydrocarbons

Naming: Each chain, branch or ring has a name based on the number of carbons Prefix + root + suffix

Root: # of carbon atoms in the longest continuous chain in the molecule (Table 15.1)Suffix: type of organic compound (identifies key functional group) -ane for alkanesPrefix: groups attached to the main chain

Example: Table 15.2

Section 15.2: Hydrocarbons

Different ways to depict molecules

Section 15.2: Hydrocarbons

Cyclic Hydrocarbons – Rings

Cycloalkanes – 2 H’s are lost when ring forms from straight chain – CnH2n

Section 15.2: Hydrocarbons

Isomers – two or more compounds with the same molecular formula but with different properties

Constitutional Isomers – different arrangements of bonded atoms

Section 15.2: Hydrocarbons

Physical Properties of Alkanes

Why do we see this trend in boiling point?

Section 15.2: Hydrocarbons

Chiral Molecules and Optical Isomerism

Optical isomers – molecules are mirror images of each other

Most naturally proteins are composed of L-amino acids: L-leucine, L-glutamine.Opposite for naturally occuring carbohydrates: D-glucose metabolized, L-glucose excluded

Often indicated with L and D:

L-alanine D-alanine

Section 15.2: Hydrocarbons

Alkenes – CnH2n

Each carbon is sp2 hybridized

Each C is bonded to fewer than max # of other atoms – unsaturated hydrocarbons

Naming: Each chain, branch or ring has a name based on the number of carbons Prefix + root + suffix

Root: # of carbon atoms in the chain that contains the double bonds (even if not longest)Suffix: type of organic compound (identifies key functional group) -ene for alkenesPrefix: groups attached to the main chain

Name these alkenes:

Section 15.2: Hydrocarbons

Geometric Isomers: Cis-Trans Isomerism – because π bonds restrict rotation

Section 15.2: Hydrocarbons

Alkynes – CnH2n-2 Each carbon is sp hybridized

Alkanes1 σ bond

Alkenes1 σ bond1 π bond

Alkynes1 σ bond2 π bonds

Section 15.2: Hydrocarbons

Aromatic hydrocarbons – one or more rings of 6 carbons atoms

Benzene is simplest example

Naming = attached groups + -benzene suffix

Section 15.3: Organic Reaction Types

Notation: R – CH2 – Br where R is an alkyl group (a saturated hydrocarbon chain)

Functional Group – a specific combination of bonded atoms that reacts in a characteristic way, no matter what organic molecule it occurs in

Three main reaction types:

1) Addition reactions: unsaturated reactant saturated product

Generic reaction Example: Ethylene

Characteristics: • common for double and triple bonded C’s, and C = O bonds • π bonds break, σ bonds remain • reaction occurs b/c it is energetically favorable

Show why is this reaction energetically favorable

Section 15.3: Organic Reaction Types

2) Elimination reactions: opposite of addition reactionssaturated reactant saturated product

Generic reaction Example

Characteristics: • Typically eliminates:

2 halogens (i.e. Cl2), H and halogen (i.e. HBr), or H and –OH group (i.e. H2O) • Driving force of this reaction is formation of small, stable molecules

Addition Reaction example

Elimination Reaction example

Reactants Bond Energy

Products Bond Energy

2693 kJ 3098 kJ

4410 kJ 4373 kJ

What is wrong with this picture?

Thermodynamics in a Nutshell

G – Gibbs free energy – in chemistry, the “force” that causes chemical reactions – can tell us whether or not a reaction will occur

H – enthalpy – keeps track of the quantity of energy – in chemical reactions, it is the energy change during a reaction (∆Hreaction, ∆Hlattice)

You can ask: Will the reaction occur spontaneously? ∆H is negative exothermic (energy lost) = more stable = YES ∆H is positive endothermic (energy required) = less stable = NO

Addition Reaction example

Elimination Reaction example

Reactants Bond Energy

Products Bond Energy

2693 kJ 3098 kJ

4410 kJ 4373 kJ

S – entropy – keeps track of the distribution of energy in a system Rule: Energy becomes distributed more uniformly (more disordered) with time

Hot Cold

Heat flow Dissolution (Chap12)

Thermodynamics in a Nutshell

G – Gibbs free energy – in chemistry, the “force” that causes chemical reactions – can tell us whether or not a reaction will occur

DiffusionProton Pump

(non-spontaneous)

Summary: Thermodynamics in a Nutshell

G – Gibbs free energy – in chemistry, the “force” that causes chemical reactions – can tell us whether or not a reaction will occur

H – enthalpy – keeps track of the quantity of energy – in chemical reactions, it is the energy change during a reaction (∆Hreaction, ∆Hlattice)

You can ask: Will the reaction occur spontaneously? ∆H is negative exothermic (energy loss as heat) = more stable = YES ∆H is positive endothermic (energy needs to be added) = less stable = NO

You can ask: Will the reaction occur spontaneously? uniformity/disorder increases YES uniformity/disorder decreases NO

S – entropy – keeps track of the distribution of energy in a system – energy becomes distributed more uniformly (more disordered) with time

Addition Reaction example

Elimination Reaction example

Reactants Bond Energy

Products Bond Energy

2693 kJ 3098 kJ

4410 kJ 4373 kJ

3) Substitution reactions:

Section 15.3: Organic Reaction Types

Generic reaction

Example

Characteristics: • C involved in bonding can be saturated or unsaturated (involved in double, triple bonds)

Section 15.3: Redox Process in Organic Reactions

Oxidation-reduction reactions in O-chem: Do NOT monitor change in O.N. of various C atoms in a compound. Rather, note movement of e- density around C based on # of more/less EN atoms

More EN atom takes e- density from C (oxidation)

Example: C – C bonds replaced with C – O bonds

2 CH3-CH3 + 7 O2 4 CO2 + 6 H2O

Less EN atom gives e- density to C (reduction)

Example: C – H bonds replaces a C – O bond

CH3O CH4

In O Chem: Focus is usually on the organic reactant only.

Oxidation: C forms more bonds to O, Br, F, etc or fewer to H

Reduction: C forms fewer bonds to O, Br, F, etc or more bonds to H

Nature’s Redox:

Photosynthesis(Reduction)

Respiration(Oxidation)

Section 15.4: Properties & Reactivities of Functional Groups The distribution of e- density in the functional group affects the reactivity

(1) Functional groups with single bonds onlyalcohols, haloalkanes, amines

(2) Functional groups with double bonds alkenes, carbonyl group (aldehydes & ketones)

(3) Functional groups with both single and double bonds carboxylic acid, ester, amide

(4) Functional groups with triple bonds nitrile, alkynes

Section 15.5: Monomers & Polymers – Synthetic Macromolecules

Polymers – many monomer units bonded together

Section 15.5: Monomers & Polymers – Synthetic Macromolecules Petroleum-based products – there will be a shortage of raw materials soon

bisphenol A (BPA)

- used in synthesizing DGEBA, a building block for an epoxy resin

Addition polymers – as each monomer adds to the chain, it forms a new reactive site.Section 15.5: Monomers & Polymers – Synthetic Macromolecules

Section 15.6: Monomers & Polymers – Biological Macromolecules

Section 15.6: Polysaccharides

Glucose is a monosaccharide – alcohol and aldehyde groups react to make cyclic formsPolysaccharide chains formed from cyclic forms that undergo dehydration reactions.

Different disaccharides formed from different monosaccharides:sucrose (table sugar): glucose (C-1) + fructose (C-2)lactose (milk sugar): glucose (C-1) + galactose (C-4)maltose (beer): glucose (C-1) + glucose (C-4)

3 main groups of polysaccharides:

Cellulose – most abundant organic chemical on earth, structural function (plant cell walls), long chains of glucose, humans cannot digest this (cows, sheep, termites)

Starch – energy storage in plants (amylose and amylopectin)

Glycogen – energy storage in animals

Section 15.6: Polysaccharides

(C6H10O5)n

Section 15.6: Amino Acids and Proteins

Section 15.6: Amino Acids and Proteins

valine tyrosineleucinetyrosine

Ionic bonds

Hydrogen bonds

Disulfide bonds (covalent)

+ hydrophobicinteractions

between –CH3

Section 15.6: Nucleic Acids, DNA, and RNA

Pyrimidines:Thymine (T) [Uracil (U)], cytosine (C)

Purines:Guanine (G), Adenine (A)

A – T(U) , G – C