Solution Chemistry

1
George Mason University General Chemistry
212 Chapter 15 Organic Chemistry Acknowledgements
Course Text Chemistry the Molecular Nature of
Matter and Change, 6th ed, 2011, Martin S.
Silberberg, McGraw-Hill The Chemistry 211/212
General Chemistry courses taught at George Mason
are intended for those students enrolled in a
science /engineering oriented curricula, with
particular emphasis on chemistry, biochemistry,
and biology The material on these slides is taken
primarily from the course text but the instructor
has modified, condensed, or otherwise reorganized
selected material.Additional material from other
sources may also be included. Interpretation of
course material to clarify concepts and solutions
to problems is the sole responsibility of this
instructor.
2
Organic Chemistry

• Life on earth is based on a vast variety of
  reactions and compounds based on the chemistry of
  Carbon Organic Chemistry
• Organic compounds contain Carbon atoms, nearly
  always bonded to other Carbon atoms, Hydrogen,
  Nitrogen, Oxygen, Halides and selected others (S,
  P)
• Carbonates, Cyanides, Carbides, and other
  carbon-containing ionic compounds are NOT organic
  compounds
• Carbon, a group 4A compound, exhibits the unique
  property of forming bonds with itself
  (catenation) and selected other elements to form
  an extremely large number of compounds about 9
  million
• Most organic molecules have much more complex
  structures than most inorganic molecules

3
Organic Chemistry

• Bond Properties, Catenation, Molecular Shape
• The diversity of organic compounds is based on
  the ability of Carbon atoms to bond to each other
  (catenation) to form straight chains, branched
  chains, and cyclic structures aliphatic,
  aromatic
• Carbon is in group 4 of the Periodic Chart and
  has 4 valence electrons 2s22p2
• This configuration would suggest that compounds
  of Carbon would have two types of bonding
  orbitals each with a different energy
• If fact, all four Carbon bonds are of equal
  energy
• This equalization of energy arises from the
  hybridization of the 2s 2p orbitals resulting
  in 4 sp3 hybrid orbitals of equal energy

4
Organic Chemistry

• Hybrid orbitals are orbitals used to describe
  bonding that is obtained by taking combinations
  of atomic orbitals of an isolated atom
• In the case of Carbon, one s orbital and three
  p orbitals, are combined to form 4 sp3 hybrid
  orbitals
• The Carbon atom in a typical sp3 hybrid structure
  has 4 bonded pairs and zero unshared electrons,
  therefore, Tetrahedral structure
• AXaEb (a b) 4 0 AX4
• The four sp3 hybrid orbitals take the shape of a
  Tetrahedron

5
Organic Chemistry
6
Organic Chemistry
Shape of sp3 hybrid orbital different than either
s or p
7
Organic Chemistry

• The bonds formed by these 4 sp3 hybridized
  orbitals are short and strong
• The C-C bond is short enough to allow
  side-to-side overlap of half-filled, unhybridized
  p orbitals and the formation of multiple bonds
• Multiple bonds restrict rotation of attached
  groups
• The properties of Organic molecules allow for
  many possible molecular shapes

8
Organic Chemistry

• Electron Configuration, Electronegativity, and
  Covalent Bonding
• Carbon ground-state configuration He 2s22p2
• Hybridized configuration 4
  sp3
• Forming a C4 or C4- ion is energetically very
  difficult (impossible?)
• Required energy
• Ionization Energy for C4 - IE1ltIE2ltIE3ltIE4
• Electron Affinity for C4- - EA1ltEA2ltEA3ltEA4
• Electronegativity is midway between metallic and
  most nonmetallic elements
• Carbon, thus, shares electrons to bond covalently
  in all its elemental forms

9
Organic Chemistry

• Molecular Stability
• Silicon and a few other elements also catenate,
  but the unique properties of Carbon make chains
  of carbon very stable
• Atomic Size and Bond strength
• Bond strength decreases as atom size and bond
  length increase, thus, C-C bond strength is the
  highest in group 4A
• Relative Heats of Reaction
• Energy difference between a C-C Bond(346 kJ/mol)
  vs C-O Bond (358 kJ/mol) is small
• Si-Si (226 kJ/mo) vs Si-O (368 kJ/mol) difference
  represents heat lost in bond formation
• Thus, Carbon bonds are more stable than Silicon

10
Organic Chemistry

• Orbitals available for Reaction
• Unlike Carbon, Silicon has low-energy d
  orbitals that can be attacked by lone pairs of
  incoming reactants
• Thus, Ethane (CH3-CH3) with its sp3 hybridized
  orbitals is very stable, does not react with air
  unless considerable energy (a spark) is applied
• Whereas, Disilane (SiH3 SiH3) breaks down in
  water and ignites spontaneously in air

11
Organic Chemistry

• Chemical Diversity of Organic Molecules
• Bonding to Heteroatoms (N, O, X, S, P)
• Electron Density and Reactivity
• Most reactions start (a new bond forms) when a
  region of high electron density on one molecule
  meets a region of low electron density of another
• C-C bond Nonreactive The electronegativities
  of most C-C bonds in a molecule are equal and the
  bonds are nonpolar
• C-H bond Nonreactive the bond is nonpolar
  and the electronegativities of both H(2.1)
  C(2.5) are close
• C-O bond Reactive polar bond
• Bonds to other Heteroatoms Bonds are long
  weak, and thus, reactive

12
Carbon Geometry
The combination of single, double, and triple
bonds in an organic molecule will determine the
molecular geometry
sp3 sp2
sp sp Tetrahedral
trigonal planar linear
linear AX4 AX3
AX2 AX2
Review Chapter 11 Multiple bonding in carbon
compounds
13
Hydrocarbons

• Compounds containing only C and H
• Saturated Hydrocarbons Alkanes
• only single (?) bonds
• Unsaturated Hydrocarbons
• Alkenes Alkynes
• Double () Bonds Triple (?) bonds
• Aromatic Hydrocarbons (Benzene rings)
• (6-C ring with alternating double and single
  bonds)

14
Hydrocarbons

• A close relationship exists among Bond Order,
  Bond Length, and Bond Energy
• Two nuclei are more strongly attracted to two
  shared electrons pairs than to one The atoms are
  drawn closer together and are more difficult to
  pull part
• For a given pair of atoms, a higher bond order
  results in a shorter bond length and a higher
  bond energy, i.e.,
• A shorter bond is a stronger bond

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Hydrocarbons

• Alkanes (Aliphatic Hydrocarbons)
• Normal-chain linear series of C atoms
• C-C-C-C-C-C-
• Branched-chain branching nodes for C atoms
• Cycloalkanes C atoms arranged in rings

Methyl Propane
Cyclohexane
16
Hydrocarbons

• Alkanes CnH2n2
• Straight Chained Alkanes

Methane
Propane
Ethane
Butane
17
Hydrocarbons

• Branched Chained Alkanes
• Cycloalkanes

3-Ethyl-4-MethylHexane
Cyclobutane
Methylcyclopropane
18
Hydrocarbons

• Molecular Formulas of n-Alkanes
• Methane C-1 CH4
• Ethane C-2 CH3CH3
• Propane C-3 CH3CH2CH3
• Butane C-4 CH3CH2CH2CH3
• Pentane C-5 CH3CH2CH2CH2CH3
• Hexane C-6 CH3(CH2)4CH3
• Heptane C-7 CH3(CH2)5CH3
• Octane C-8 CH3(CH2)6CH3
• Nonane C-9 CH3(CH2)7CH3
• Decane C-10 CH3(CH2)8CH3

19
Hydrocarbons
Straight Chain (n) Alkanes
20
Hydrocarbons
Petroleum Fractions
Boiling Point Name Carbon Atoms Use
lt 20 0C Gases C1 to C4 Heating, Cooking
20-200 0C Gasoline C5 to C12 Fuel
200-300 0C Kerosene C12 to C15 Fuel
300-400 0C Fuel oil C15 to C18 Diesel Fuel
gt 400 0C over C18 Lubricants, Asphalt, Wax
21
Hydrocarbons
Cycloalkanes CnH2n
Cyclohexane
Cyclopropane
Cyclobutane
22
Hydrocarbons

• Structural Isomers
• Structural (or constitutional) isomers are
  compounds with the same molecular formula, but
  different structural formulas. Created by
  branching, etc.

Butane
Isobutane
C4H10
C4H10
23
Hydrocarbons

• Structural Isomers of Pentane

C5H12
24
Hydrocarbons

• Chiral Molecules Optical Isomerism
• Another type of isomerism exhibited by some
  alkanes and many other organic compounds is
  called Stereoisomerism
• Sterioisomers are molecules with the same
  arrangement of atoms but different orientations
  of groups in space
• Optical Isomerism is a type of stereoisomerism,
  where two objects are mirror images of each other
  and cannot be superimposed (also called
  enantiomers)
• Optical isomers are not superimposable because
  each is asymmetric there is no plane of symmetry
  that divides an object into two identical parts

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Hydrocarbons

• Chiral Molecules Optical Isomerism
• An asymmetric molecule is called Chiral
• The Carbon atom in an optically active asymmetric
  (l) organic molecule (the Chiral atom) is bonded
  to four (4) different groups.

• Mirror images
• 1C1 1C2 of molecule 1 (left) can be moved to
  the right to sit on top of2C1 2C2 of molecule
  2, i.e.,
• 1C 2C groups can be superimposed
• But, the two groups on C3 are opposite
• ? The two forms are optical isomers and cannot
  be superimposed, i.e., no plane of symmetry to
  divide molecule into equal parts
• C-3 is the Chiral Carbon

Optical Isomers of3-methylhexane
26
Hydrocarbons

• Optical Isomers
• In their physical properties, Optical Isomers
  differ only in the direction each isomer rotates
  the plane of polarized light
• One of the isomers dextrorotary isomer -
  rotates the plane in a clockwise direction (d or
  )
• The other isomer levorotary isomer - rotates
  the plane in a counterclockwise direction (l or
  -)
• An equimolar mixture of the dextrorotary (d or )
  and levorotary (l or -) isomers
• recemic mixture
• does not rotate the plane of light because the
  dextrorotation cancels the levoratation

27
Hydrocarbons

• Optical Isomers
• In their chemical properties, optical isomers
  differ only in a chiral (asymmetric) chemical
  environment
• An optically active isomer is distinguished by
  the chiral atom being attached to 4 distinct
  groups
• If the attached groups are not distinct the
  molecule is NOT optically active
• An isomer of an optically active reactant added
  to a mixture of optically active isomers of an
  another compound will produce products of
  different properties solubility, melting point,
  etc.

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Nomenclature of Alkanes

• Determine the longest continuous chain of carbon
  atoms. The base name is that of this
  straight-chain alkane.
• Any chain branching off the longest chain is
  named as an alkyl group,
• changing the suffix ane to yl
• For multiple alkyl groups of the same type,
  indicate the number with the prefix di, tri,
• Ex. Dimethyl, Tripropyl, Tertbutyl
• The location of the branch is indicated with the
  number of the carbon to which is attached
• Note The numbering of the longest chain begins
  with the end carbon closest to the carbon with
  the first substituted chain or functional group

29
Nomenclature Example
(Cont)
30
Nomenclature Example

• Determine the longest chain in the molecule
• 7 Carbons

Substituted Heptane (7 C)
(Cont)
31
Nomenclature Example

• The base chain is 7 carbons Heptane
• Add the name of each chain substituted on the
  base chain
• methyl groups at Carbon 3 and Carbon 5
• ethyl group at Carbon 4

3,5-dimethyl-4-ethylheptane
32
Nomenclature Example

• Guidelines for numbering substituted carbon
  chains
• The numbering scheme used in developing the name
  of a organic compound begins with the end carbon
  closest to the carbon with the first substituted
  group or functional group

33
Hydrocarbons

• Reactions of Alkanes
• Combustion (reaction with oxygen) Burning
• C5H12(g) 8 O2(g) ? 5 CO2(g) 6 H2O(l)
• Substitution (for a Hydrogen)
• C5H12(g) Cl2(g) ? C5H11Cl(g) HCl(g)

34
Hydrocarbons

• Alkenes
• When a Carbon atom forms a double bond with
  another Carbon atom, it is now bonded to 2 other
  atoms instead of 3 as in an Alkane
• The Geometry now changes from 4 sp3 orbitals
  (Tetrahedral AX4E0) to 3 sp2 hybrid orbitals and
  1 unhybridized 2p orbital (AX3E0 Trigonal
  Planar) lying perpendicular to the plane of the
  trigonal sp2 hybrid orbitals

Review Chapter 10 - Geometry
35
Hydrocarbons

• Alkenes
• Two sp2 orbitals of each carbon form C H sigma
  (?) bonds by overlapping the 1 s orbitals of the
  two H atoms
• The 3rd sp2 orbital forms a C-C (?) bond with the
  other Carbon
• A Pi (?) bond forms when the two unhybridized 2p
  orbitals (one from each carbon) overlap
  side-to-side, one above and one below the C-C
  sigma bond
• A double bond always consists of 1 ? and 1 ? bond

36
Hydrocarbons

• Alkenes CnH2n
• Alkenes substitute the single sigma bond (?) with
  a double bond a combination of a sigma bond and
  a Pi (?) bond
• The double-bonded (-CC-) atoms are sp2
  hybridized
• The carbons in an Alkene structure are bonded to
  fewer than the maximum 4 atoms
• Alkenes are considered unsaturated hydrocarbons

Ethene or Ethylene
Propene
37
Hydrocarbons

• Molecular Formulas of Alkenes
• Ethene CH2CH2
• Propene CH2CHCH3
• Butene CH2CHCH2CH3
• Pentene CH2CHCH2CH2CH3
• Decene CH2CH(CH2)7CH3
• Conjugated Molecules
• Alkene (or aromatic) with alternating Sigma
  bonds and Pi bonds)
• Ex. 2,5-Dimethyl-2,4-Hexadiene
• CH3CH3CH-CHC(CH3CH3)

38
Hydrocarbons

• Reactions of Alkenes
• Addition Reactions
• CH3CHCH2 HBr ? CH3CHBrCH(H2)
• Why does the Bromine (Br) attach to the middle
  carbon?
• Markownikovs Rule
• When a double bond is broken, the H atom being
  added adds to the carbon that already has the
  most Hydrogens
  CH2 ? CH3

39
Hydrocarbons

• An addition reaction occurs when an unsaturated
  reactant (alkene, alkyne) becomes saturated(?
  bonds are eliminated)
• Carbon atoms are bonded to more atoms in the
  Product than in the reactant (Ethene is
  reduced)
• Addition Reaction Heat of Formation
• Reaction is Exothermic
• Formation of two strong ? bonds from a single ?
• bond and a relatively weak ? bond

Reactants (bonds broken Product
(bonds formed) 1 C C 614 kJ 1 C C
347 kJ 4 C H 1652 kJ 5 C
H 2065 kJ 1 H C 427 kJ 1 C
Cl 339 kJ Total 2693
kJ Total 2751 kJ
40
Hydrocarbons

• Elimination Reactions
• The reverse of addition reaction
• A saturated molecule becomes unsaturated
• Typical groups Eliminated include
• Pairs of Halogens Cl2, Br2, I2
• H atom and Halogen HCL, HBr
• H atom and Hydroxyl (OH)
• Driving force Formation of a small, stable
  molecule, such as HCl, H2O, which increases
  ntropy of the system

41
Hydrocarbons

• Substitution Reactions
• A substitution reaction occurs when an atom (or
  group) from an added reagent substitutes for an
  atom or group already attached to a carbon
• Carbon atom is still bonded to the same number of
  atoms in the product as in the reactant
• Carbon atom may be saturated or unsaturated
• X y may be many different atoms (not C)
• Reaction of Acetyl Chloride and
  isopentylalcohol to form banana oil, an ester

42
Hydrocarbons

• Nomenclature of Alkenes
• Alkenes (-CC-) are named just as alkanes, except
  that the ane suffix is changed to ene
• Alkynes (-C?C-) are named in the same way, except
  that the suffix yne is used
• In either case, the position of the double bond
  is indicated by the number of the carbon

43
Hydrocarbons

• Nomenclature of Alkenes - Example
• First, find the longest carbon chain containing
  the double bond

3-propyl-5-methyl-2-heptene
44
Hydrocarbons

• Alkenes Geometric Isomerism
• In Alkanes, the C-C bond allows rotation of
  bonded groups the groups continually change
  relative positions
• In Alkenes with the CC bond, the double bond
  restricts rotation around the bond
• Geometric isomers are compounds joined together
  in the same way, but have different geometries
• The similar groups attached to the two carbon
  atoms of the CC bond are on the same side of the
  double bond in one isomer and on the opposite
  side for the other isomer

trans-2-butene
cis-2-butene
45
Hydrocarbons

• Alkynes
• General Formula - CnH2n-2
• The Carbon-Carbon (-C-C-) bond is replaced by a
  triple bond
• Each Carbon of an Alkyne structure (-C?C-) can
  only bond to one other Carbon in a linear
  structure
• Each C is sp hybridized (sp linear geometry)
• Alkyne compound names are appended by thesuffix
  yne
• The ? electrons in both alkenes (-CC-) and
  alkynes (-C?C-) are electron rich and act as
  functional groups
• Alkenes and alkynes are much more reactive than
  alkanes

46
Hydrocarbons

• Alkynes

Ethyne or Acetylene
Propyne A Terminal Acetylene
3-Hexyne
47
Aromatic Hydrocarbons

• Aromatic Hydrocarbons are Planar molecules
  consisting of one or more 6-carbon rings
• Although often drawn depicting alternating ? and
  ? bonds, the 6 aromatic ring bonds are identical
  with values of length and strength between those
  of C-C CC bonds
• The actual structure consists of 6 ? bonds and 3
  pairs of ? electrons delocalized over all 6
  carbon atoms
• The bond between any two carbons resonates
  between a single bond and a double bond

The orbital picture shows the two lobes of the
delocalized ? cloud above and below the hexagonal
plane of the ?-bonded carbon atoms
48
Aromatic Hydrocarbons
Molecular Orbitals of Benzene
49
Aromatic Hydrocarbons
H
H
C
H
H
C
H
H
C
C
C
C
C
C
C
C
C
H
H
C
H
H
H
H
benzene
benzene
Condensed Resonance Form of Benzene
50
Aromatic Hydrocarbons
Substituted Benzenes
Methylbenzene (Toluene)
3,4-dimethyl-ethylbenzene m,p-dimethyl-ethylbenzen
e
51
Aromatic Compounds
Substituted Benzenes
52
Aromatic Compounds

• Benzene ring naming conventions - ring site
  locations
• Starting at the carbon containing the first
  substituted group, number the carbons 1 thru 6
  moving clockwise
• Alternate names 2 (ortho) 3 (meta) 4 (para)

ortho-toluene 1,2-dimethylbenzene
meta-toluene 1,3-dimethylbenzene
para-toluene 1,4-dimethylbenzene
53
Reactions of Aromatic Compounds

• The stability of the Benzene ring favors
  substitution reactions
• The delocalization of the pi bonds makes it
  very difficult to break a CC- bond for an
  addition reaction

54
Reactivity Alkenes vs Aromatics

• The double bond (-CC-) is electronrich
• ? Electrons are readily attracted to the
  partially positive H atoms of hydronium atoms
  (H3O) and hydrohalic acids (HX), to yield
  alcohols and alkyl Halides, respectively

55
Reactivity Alkenes vs Aromatics

• The pi electrons in an alkene double bond
  represent a localized overlap of unhybridized 2p
  orbitals, where two regions of electron density
  are located above and below the ? bond
• The localized nature of alkene double bonds is
  very different from the delocalized
  unsaturation of aromatic structures
• Although aromatic rings are commonly depicted as
  having alternating sigma (?) and (?) bonds, the
  (?) bonds are actually delocalized over all 6 C
  (?) bonds
• The reactivity of benzene is much less than a
  typical alkene because the ? electrons are
  delocalized requiring much more energy to break
  up the ring structure to accommodate an
  addition reaction
• Substitution is much more likely from an energy
  perspective because the delocalization is retained

56
Redox Processes in Organic Reactions

• Oxidation Number is not applicable for carbon
  atoms
• Oxidation-Reduction in organic reactions is based
  on movement of electron density around Carbon
  atom
• The number of bonds joining a carbon atom and a
  more electronegative atom (group) vs. the
  number of bonds joining a carbon atom to a Less
  electronegative atom (group)
• The more electronegative atoms will attract
  electron density away from the carbon atom
• Less electronegative atoms will donate electron
  density to the carbon atom
• When a C atom forms more bonds to Oxygen or fewer
  bonds to Hydrogen reaction is oxidation
• When a C atoms forms fewer bonds to Oxygen or
  more bonds to Hydrogen reaction is reduction

57
Redox Processes in Organic Reactions

• Combustion Reactions (burning in Oxygen)
• Ethane is converted to Carbon Dioxide (CO2) and
  water (H2O)
• Each Carbon in CO2 has more bonds to Oxygen than
  in ethane (none) and few bonds to Hydrogen
• Reaction is Oxidation
• Oxidation of Propanol
• C-2 has one fewer bonds to H and one more bond to
  O in 2-propanone - Oxidation

58
Redox Processes in Organic Reactions

• Hydrogenation of Ethene
• Each carbon has more bonds to H in Ethane than in
  Ethene
• Ethene is reduced, H2 is oxidized (loses e-)

59
Organic Reactions

• Functional groups
• A functional group is a reactive portion of a
  molecule that undergoes predictable reactions
• The reaction of an organic compound takes place
  at the functional group
• A functional group is a combination of bonded
  atoms that reacts as a group in a characteristic
  way
• Each functional group has its own pattern of
  reactivity
• The distribution of electron density in a
  functional group affects its reactivity
• Vary from carbon-carbon bonds (single, double,
  triple) to several combinations of
  carbon-heteroatom bonds
• A particular bond may be a functional group
  itself or part of one or more functional groups

60
Organic Reactions

• Functional Groups (Cont)
• Electron density can be low at one end of a bond
  and higher at the other end, as in a dipole, an
  intermolecular force
• The Intermolecular Forces that affect physical
  properties and solubility also affect reactivity
• Alkene (-CC-) and Alkyne (-C?C-) bonds have high
  electron density, thus are functional groups with
  high reactivity
• Classification of Functional Groups
• Functional groups with only single bonds undergo
  substitution reactions
• Functional groups with double or triple bonds
  undergo addition reactions
• Functional groups with both single and double
  bonds undergo substitution reactions

61
Functional Groups

• Oxygen containing functional groups
• alcohols, ethers, aldehydes, ketones, esters,
  carboxylic acids, anhydrides, acid halides
• Nitrogen containing functional groups
• amines, amides, nitriles, nitro
• Compounds containing Carbonyl Group (CO)
• acids, esters, ketones, aldehydes,anhydrides,
  amides, acid halides
• Compounds containing Halides
• alkyl halides, aryl halides, acid halides
• Compounds containing double triple bonds
• alkenes, alkynes, aryl structures (benzene rings)

62
Functional Groups
63
Functional Groups
64
Alcohols

• Functional Groups with only single bonds
• An alcohol, general formula R-OH, is a compound
  obtained by substituting an -OH group for an H
  atom in a hydrocarbon
• primary alcohol one carbon attached to the
  carbon with the OH group
• secondary alcohol two carbons attached to the
  carbon with the OH group
• tertiary alcohol three carbons attached to the
  carbon with the OH group

65
Alcohols
Alcohol Nomenclature Drop final e from
hydrocarbon and add suffix ol
4,6-dimethyl-3-octanol (a secondary alcohol)
66
Alcohols

• Alcohol Reactions
• Alcohol structure similar to water
• (R-OH vs H-OH)
• Alcohols react with very active metals to release
  H2
• Alcohols form strongly basic Alkoxide (R-O-)
  Ions
• High melting points and boiling points of
  alcohols result from Hydrogen Bonding
• Alcohols dissolve Polar molecules
• Alcohols dissolve some salts

67
Alcohols

• Alcohol Reactions
• Elimination Reactions
• Elimination of a H atom and a hydroxide ion (OH)
  from a cyclic compound in the presence of acid
  results in the formation of an alkene
• Removal of 2 H atoms from a secondary alcohol in
  the presence of an oxidizing agent, such as
  K2CrO7 results in the formation of a Ketone

68
Alcohols

• Alcohols Reactions
• Oxidation
• For Alcohols with the OH group at the end of a
  chain (primary alcohol) oxidation to an organic
  acid can occur in air
• Substitution Reactions
• Substitution results in products with other
  single bonded functional groups, such as the
  formation of Haloalkanes

69
Haloalkanes

• A Haloalkane (Alkyl Halide) is a Halogen(X F,
  Cl, Br, I) bonded to a carbon atom
• Elimination Reactions
• Elimination of HX in the presence of a strong
  base will produce an Alkene

70
Haloalkanes

• Haloalkanes
• Substitution Reactions
• Halides of Carbon and most other non-metals, such
  as Boron (B), Silicon (Si), Phosphorus (P), all
  undergo substitution reactions
• The process involves an attack on the slightly
  positive central atom, such as C, etc. by an OH-
  group
• -CN, -SH, -OR, and NH2 groups also substitute
  for the halide

71
Ethers

• H-O-H water
• R-O-H alcohol (OH group Hydroxyl group)
• R-O-R ether (R-O group Alkoxy
  group)where R any group
• Ether Nomenclature
• If R-C-O-CH2-CH3 group is part of structure, add
  Ethoxy to name
• If R-C-O-CH3 group is part of structure,add
  Methoxy to name

72
Ether Nomenclature
OCH2CH3
CH3CH2CH2CH2CH3
4 3 2 1
5 6 7 8
CH2CH2CH2CH3
CH3
4,6-dimethyl-3-ethoxyoctane
73
Amines

• An Amine is a compound derived by substituting
  one or more Hydrocarbon groups for Hydrogens in
  Ammonia, NH3
• Naming convention
• Drop the final e from the alkane name and add
  amine (ethanamine) or append amine to alkyl
  name (Methylamine)
• Types
• primary amine one carbon attached to the
  Nitrogen
• secondary amine two carbons attached to the
  Nitrogen.
• tertiary amine three carbons attached to the
  Nitrogen

74
Amine Examples

CH3
CH3
N
CH3
Methylamine (Primary Amine)
Trimethylamine (Tertiary Amine)
Dimethylamine (Secondary Amine)
Trigonal pyramidal Shape AX3E
The pair of unbonded electrons common to all
amines is the key to all amine reactivity Amines
act as bases by donating the pair of unshared
electrons
75
Amines

• Reactions
• Primary and secondary Amines can form Hbonds
• Higher melting points and boiling points than
  Hydrocarbons or Alkyl Halides of similar mass
• Trimethyl Amines cannot form Hydrogen Bonds and
  have generally lower melting points
• Amines of low molecular mass are water soluble
  and weakly basic (donate electrons)
• Reaction with water proceeds slowly and produces
  OH- ions

76
Amines

• Amine Reactions
• Substitution Reactions
• The pair of unbonded electrons on the Nitrogen
  attacks the partially positive Carbon in Alkyl
  Halides to displace the Halogen (X-) and form a
  larger amine

77
Carbonyl Group

• Functional Groups with Double Bonds
• The Carbonyl group is a Carbon doubly bonded to
  an Oxygen (CO)
• Very versatile group appearing in several types
  of compounds
• Aldehydes
• Ketones
• Carboxylic acids
• Esters
• Anydrides
• Acid Halides
• Amides

78
Aldehydes and Ketones

• An Aldehyde is distinguished from a Ketone by the
  Hydrogen atom attached to the Carbonyl Carbon
• If two Hydrogens are attached to the Carbonyl
  atom, the compound is specific Formaldehyde
  (CH2O)

Aldehyde ( - al)
Ketone ( -one)
Formaldehyde
79
Aldehydes and Ketones

• Aldehydes
• In Aldehydes the Carbonyl group always appears at
  the end of a chain
• Aldehyde names drop the final e from the alkane
  names and -al Propanal, Isobutanal, etc.
• Alternate naming conventions
• Benzaldehyde, Propionaldehyde

Butanal (Butyraldehyde)
80
Aldehydes and Ketones

• Ketones
• The Carbonyl Carbon always occurs within a chain
  as it is bonded to two other Alkyl groups (R, R)
• Ketones are named by numbering the carbonyl C,
  dropping the final e from the alkane name, and
  adding -one, 4-Heptanone
• Alternate naming conventions
• Use the Alkyl root and add ketone

4-Heptanone (Dipropylketone)
Methylisopropylketone (3-methyl-2-butanone)
81
Aldehydes and Ketones

• Like the CC bond, the Carbonyl (CO) bond is
  electron-rich
• Unlike the CC bond, the CO bond is highly
  polar
• A - The ? and ? bonds that make up the C-O bond
  of the carbonyl group
• B - The charged resonance form shows that the C-O
  bond is polar (?EN 1.0)

82
Aldehydes and Ketones

• Aldehydes and Ketones are formed by oxidation of
  Alcohols
• The CO is an unsaturated structure, thus,
  carbonyl compounds can undergo addition
  reactions and be reduced (forms more bonds to H)
  to form alcohols

83
Aldehydes and Ketones

• Organometallic compounds
• The Carbonyl group exhibits polarity with the
  Carbon atom bearing a slight positive charge and
  the Oxygen bearing a negative charge
• An addition reaction to the Carbonyl group would
  involve an electron-rich group bonding to the
  positive carbon and an electron-poor group
  bonding to the negative Oxygen
• Organometallic compounds have a metal atom (Li or
  Mg) attached to an R group through a polar
  covalent bond

84
Aldehydes and Ketones

• Organometallic compounds
• The two-step addition of an organometallic
  compound to a Carbonyl group produces an Alcohol
  with a different Carbon skeleton
• Aldehyde Lithium Organometallic
• Acetone (ketone) Ethyllithium

85
Carboxylic Acids

• Carboxylic Acids are formed by adding an
  Hydroxyl group to the Carbonyl Carbon
• Different R groups lead to many different
  carboxylic acids
• Carboxylic Acids have the - oic suffix with
  acid
• Example Ethanoic acid (Acetic acid) C2H4O2

Acidic Hydrogen (Hydroxyl Group)
Carboxyl Group
Carbonyl Group
86
Carboxylic Acids

• Carboxylic Acids are named by dropping the -e
  from the alkane name and adding -oic acid
• Common names are often used
• Carboxylic Acids are Weak Acids in solution
• Typically gt99 of an organic acid is
  undissociated
• Carboxylic acid molecules react completely with
  strong base to form salt water

Carboxylate anion
87
Carboxylic Acids

• Carboxylic acids with long hydrocarbon chains are
  referred to as fatty acids
• Fatty acid skeletons have an even number of
  Carbon atoms (16-18 most common)
• Animal fatty acids have saturated hydrocarbon
  chains
• Vegetable sources are generally unsaturated,
  with the -CC- in the cis configuration
• Fatty acid salts are the soaps, with the
  cation usually from Group 1A of 2A

88
Examples

• Straight chain saturated (Aliphatic) carboxylic
  acids

Name Formula
Methanoic (Formic) Acid HCOOH
Ethanoic (Acetic) Acid CH3COOH
Propionic Acid CH3CH2COOH
Butanoic (Butyric) Acid CH3CH2CH2COOH
Pentanoic Acid CH3CH2CH2CH2COOH
89
Esters

• Esterification is a dehydration-condensation
  reaction between a Carboxylic acid and an alcohol
  to form an Ester
• The Hydroxyl group (OH) from the Alcohol reacts
  with the Carboxyl group to form the Ester and
  Water
• R1COOH R2OH ? R1COOR2 H2O
• Ester group occurs commonly in Lipids, a large
  group of fatty biological substances, such as
  triglycerides

90
Esters

• Hydrolysis is the opposite of Dehydration-Condensa
  tion (Esterification) in which the Oxygen atom
  from water is attracted to the partially positive
  Carbon of the ester carbonyl group, cleaving
  (lysing) the molecule into two parts
• One part gets the OH and one part gets the H
• In Saponification, the process used in the
  manufacture of soap, the ester bonds in animal or
  vegetable fats are Hydrolyzed with a strong
  base

91
Amides

• Amides are derived from the reaction of an Amine
  with a Carboxylic acid or an Ester
• Amides are named by denoting the amine portion
  from the amine and the replacing the -oic acid
  from the Carboxylic acid with -amide

92
Amides

• The partially negative N (2 unbonded e-) of the
  amine is attracted to the partially positive
  carbonyl carbon of the ester
• In the Amine Acid reaction water is lost
• In the Amine Ester reaction an alcohol (ROH) is
  lost
• Amides can be Hydrolyzed in hot water to reform
  the acid and the amine

R1COOH R2NH2 ? R1CONHR2 H2O
93
Functional Groups with Triple Bonds

• Principal Groups with triple bonds
• Alkynes (Acetylenes) -C?C-
• Addition reactions with H2O, H2, HX, X2, others
• Nitriles -C?N
• Produced by substituting a cyanide ion (-C ?N-)
  for a Halide ion (X-) in a reaction with an alkyl
  halide
• Nitriles can be reduced to form amines or
  hydrolyzed to carboxylic acids

94
Polymers

• Polymers are extremely large molecules consisting
  of monomeric repeating units
• Naming polymers
• Add prefix poly- to the monomer name
• Polyethylene Polystyrene Polyvinyl chloride
• Polymer Types
• Addition
• Monomers undergo addition with each other (chain
  reactions)
• Monomers of most addition polymers have the group

95
Addition Polymers
96
Addition Polymers

• Free-radical polymerization of Ethene, CH2CH2
  ,to polyethylene

97
Condensation Polymers

• Condensation polymers have two functional
  groups
• A R B
• Monomers link when group A on one undergoes a
  dehydration-condensation reaction with a B
  group on another monomer
• Many condensation polymers are Copolymer,
  consisting of two or more different repeating
  units
• Condensation of Carboxylic acid Amine monomers
  forms polyamides (nylons)
• Carboxylic Acid and Alcohol monomers form
  polyesters

98
Biological Macromolecules

• Natural Polymers
• Polysaccharides
• Proteins
• Nucleic acids
• Intermolecular forces stabilize the very large
  molecules in the aqueous medium of living cells
• Structures that make wood strong hair curly,
  fingernails hard
• Speed up many natural reaction inside cells
• Defend living organisms against infection
• Possess genetic information organisms need to
  synthesis other biomolecules

99
Sugars Polysaccharides

• Carbohydrates substances that provide energy
  through oxidation
• Monosaccharides
• Glucose simple sugars
• Consist of carbon chains with attached hydroxyl
  and carbonyl groups
• Serve as monomer units of polysaccharides
• Polysaccharides
• Consist mainly of Glucose units with differences
  in aromatic ring position of the links,
  orientation of certain bonds and the extent of
  cross-linking
• Cellulose
• Starch
• Glycogen

100
Sugars Polysaccharides

• Cellulose
• Most abundant organic chemical on earth
• 50 of carbon in plants occurs in stems leaves
• Cotton is 90 cellulose
• Wood strength comes from Hydrogen bonds between
  cellulose chains
• Humans lack enzyme to links to the C1 C4 bonds
  between units making it impossible to digest
• Other animals cows, sheep, termites, however,
  have microorganisms in their digestive tracts can
  digest cellulose

101
Sugars Polysaccharides

• Starch
• A mixture of polysaccharides of glucose
• Energy store in plants
• Starch is broken down by hydrolysis of the bonds
  between units, releasing glucose, which is
  oxidized in a multistep process
• Glycogen
• Energy storage molecule in animals
• Occurs in molecules made from 1000 to 500,000
  glucose units
• The cross-linking between the C1 C4 bonds is
  similar to starch, but is more highly
  cross-linked between the C1 C6 bonds

102
Amino Acids Proteins

• Amino Acids
• An amino acid has a carboxyl group (COOH) and an
  amine group (NH2) attached to an ?-carbon, the
  2nd C atom in a Carbon-Carbon (C-C) chain
• In the aqueous cell fluid, the NH2 (amino) and
  COOH (carboxyl) groups of amino acids are charged
  because the carboxyl group transfers an H ion to
  H2O to form H3O (acid), which transfers the H
  to the amine group

103
Amino Acids Proteins

• Proteins
• Proteins are unbranched polyamide polymers made
  up of amino acids linked together by Peptide
  bonds
• A Peptide (amide) bond is formed by a
  dehydration-condensation reaction in which the
  Carboxyl group of one monomer reacts with the
  Amine group of the next monomer releasing water
• 
  dipeptide
• A Polypeptide chain is a polymer formed by the
  linking of many amino acids by peptide bonds
• A Protein is a polypeptide with a biological
  function

104
Amino Acids Proteins

• Peptide Bonds

CO
N-H
105
Amino Acids Proteins

• About 20 different amino acids occur in proteins
• See Examples on Next Slide
• The R groups are screened gray
• The ?-carbons (boldface), with carboxyl and amino
  groups, are screened yellow
• The amino acids are shown with the charges they
  have under physiological conditions
• They are grouped by polarity, acid-base
  character, and presence of an aromatic ring
• The R groups, which dangle from the ?-carbons on
  alternate sides of the chain, play a major role
  in the shape and function of proteins

106
Amino Acids Proteins
107
Amino Acids Proteins

• Hierarchy of Protein Structure
• Each type of protein has its own amino acid
  composition a specific number and proportion of
  various amino acids
• The role of a protein in a cell, however, is not
  determined by its composition
• The sequence of amino acids determines the
  proteins shape and function in the cell
• Proteins range from 50 to several thousand amino
  acids
• The number of possible sequences of the 20 types
  of amino acid, even in the smaller proteins, is
  extremely large (20n where n is the number of
  amino acids)
• Only a small fraction of the possible
  combinations occur in actual proteins 105 for a
  human being

108
Amino Acids Proteins

• Protein Native Shapes
• Proteins have unique shapes that unfold during
  synthesis in a cell
• Simple Complex
• Long rods Baskets
• Undulating sheets Y-Shapes
• Spheroid Blobs
• Globular Forms

109
Amino Acids Proteins

• Hierarchy of Protein Structure
• Primary (1o) Basic Level (sequence of
  
  covalently bonded amino acids
  in polypeptide chain)
• Secondary (2o) Shapes called ?-helices and
  ?-pleated sheets
  formed as a
  result of H bonding between
  nearby peptide groupings
• Tertiary (3o) 3-dimensional folding of
  whole polypeptide
  chain
• Quarternary (4o) Most complex, proteins
  made up of several
  polypeptide chains

110
Amino Acids Proteins
Structural Hierarchy of Proteins
111
Amino Acids Proteins

• Protein Structure and Function
• Two broad classes of proteins differ in the
  complexity of their amino acid composition and
  sequence, thus, their structure and function
• Fibrous Proteins
• Relatively simple amino acid compositions and
  correspondingly simple structures
• Includes Colagen, the most common animal
  protein (30 glycine 20 proline)
• Globular Proteins
• More complex, containing up to all 20 amino acids
  in varying proportions

112
Amino Acids Proteins

• Nucleotides and Nucleic Acids
• Nucleic Acids Unbranched polymers that consist
  of linked monomer units called mononucleotides
• Mononucleotides consist of
• Nitrogen-containing base
• Sugar
• Phosphate group
• Nucleic Acid Types
• Ribonucleic Acid (RNA)
• Deoxyribonucleic Acid (DNA)
• RNA DNA differ in sugar portions of
  mononucleotides
• RNA contains Ribose, a 5-Carbon sugar
• DNA contains deoxyribose (H substitutes for OH on
  the 2 position of Ribose

113
Amino Acids Proteins

• Nucleic Acid Precursors
• Nucleoside Triphosphates Cellular precursors
  that form a nucleic acid
• Dehydration-condensation reactions between
  cellular precursors
• Releases inorganic diphosphate (H2P2O72-)
• Creates Phosphodiester bonds to form a
  polynucleotide
• Sets up the repeating pattern of the nucleic acid
  backbone
• sugar phosphate sugar phosphate

114
Amino Acids Proteins

• DNA
• Phosphate group
• 2-deoxyribose (a Sugar)
• Base Attached to each sugar is one of four N-
  containing bases, either
• a Pyrimidine (six-membered ring)
• Pyrimidines Thymine (T) Cytosine (C)
• or
• a Purine (six- and five- membered rings sharing a
  side)
• Purines Guanine (G) Adenine (A)
• RNA
• Sugar in RNA is Ribose
• Uracil (U) substitutes for Thymine (T)

115
Amino Acids Proteins

• Nucleic Acid Precursors
• In a cell, nucleic acids are constructed from
  nucleoside triphosphates, precursors of the
  mononucleic units
• Each mononucleic unit consists of
• an N-containing base
• a sugar
• a triphosphate group
• Nitrogen Containing Bases
• Pyrimidines
• Thymine (DNA) Uracil (RNA)
• Cytosine
• Purines
• Guanine
• Adenine

116
Amino Acids Proteins

• Base Pairing
• In the nucleus of a cell, DNA exists as two
  chains wrapped around each other in a double
  Helix
• Each base in one chain Pairs with a base in the
  other through Hydrogen Bonding
• A double-helical DNA molecule may contain many
  millions of H-Bonded bases
• Base Pair Features
• A Pyrimidine (Pyr) is always paired with a Purine
  (Pur)
• Each base is always paired with the same partner
• Thymine (T) (Pyr) with Adenine (A) (Pur)
• Cytosine (C) (Pyr) with Guanine (G) (Pur)
• Thus, base sequence on one chain is the
  complement of the sequence on the other chain
• Ex. A-C-T on one chain paired with T-G-A on
  another

117
Practice Problem

• Write the sequence of the complimentary DNA
  strand that pairs with each of the following
• a. GGTTAC
• Ans CCAATG
• b. CCCGAA
• Ans GGGCTT

118
Practice Problem

• Write the base sequence of the DNA template from
  which the RNA sequence below was derived
• GUA UCA AUG AAC UUG (RNA)
• Ans CAT AGT TAC TTG AAC (DNA)
• (note Uracil (U) substitutes for Thymine (T) in
  RNA)
• How many amino acids are coded for in this
  sequence?
• Ans five (CAT) (AGT) (TAC) (TTG) (AAC)
• Each 3-base sequence is a word, each word
  codes for a specific amino acid

119
Nucleic Acids (N-Containing Bases)
Pyrimidines
Thymine
Uracil
Cytosine
120
Nucleic acid precursors and their linkage
.
121
The Double Helix of DNA
122
Amino Acids Proteins

• Protein Synthesis
• A protein consists of a sequence of Amino Acids
• The Proteins Amino Acid sequence determines its
  structure, which in turn determines its function
• SEQUENCE ? STRUCTURE ? FUNCTION
• The DNA base sequence contains an information
  template that is carried by the RNA base sequence
  (messenger and transfer) to create the protein
  amino acid sequence
• In other words, the DNA sequence determines the
  RNA sequence, which determines the protein amino
  acid sequence
• In Genetic Code, each base acts as a Letter
• Each three-base sequence is a Word
• Each word codes for a specific Amino Acid
• Ex. C-A-C codes for Histidine
• A-A-G codes for Lysine

123
Amino Acids Proteins

• One Amino Acid at a time is positioned and linked
  to the next in the process of protein synthesis
• Outline of Synthesis
• DNA occurs in cell nucleus
• Genetic message is decoded outside of cell
• RNA serves as messenger to synthesis site
• Portion of DNA is unwound and one chain segment
  acts as a template for the formation of a
  complementary chain of messenger RNA (mRNA)
• mRNA made by individual mononucleoside
  triphosphates linking together
• The DNA code words are transcribed into RNA code
  words through base pairing
• mRNA leaves the nucleus and binds, again through
  base-pairing, to an RNA rich-rich particle called
  a Ribosome

124
Amino Acids Proteins

• Synthesis Outline (cont)
• The words (3-base sequences) in the RNA are then
  decoded by molecules of transfer RNA (tRNA)
• The smaller nucleic acid shuttles have two key
  portions on opposite ends of their structures
• A three-base sequence (word) which is a
  complement of a word on the nRNA
• A binding site for the amino acid coded by that
  word
• The Ribosome moves along the bound mRNA, one word
  at a time, while tRNAs bind to the mRNA
• The Amino acids are positioned near one another
  in preparation of peptide bond formation and
  synthesis of the protein

125
Amino Acids Proteins

• Synthesis Outline (cont)
• Net result
• Protein Synthesis involves the DNA message of
  three-base words being transcribed into the RNA
  message of three-base words, which is then
  translated into a sequence of amino acids that
  are linked to make a protein
• DNA Base Sequence ? RNA Base Sequence ?
• Protein Amino Acid Sequence