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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