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Title: Solution Chemistry


1
George Mason University General Chemistry
212 Chapter 15 Organic Chemistry Acknowledgements
Course Text Chemistry the Molecular Nature of
Matter and Change, 7th edition, 2011,
McGraw-Hill Martin S. Silberberg Patricia
Amateis 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
2p
sp3
sp3
C-H bonds
2s
Energy
1s
1s
1s
C atom (ground state)
C atom (hybridized state)
C atom (in CH4)
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

15
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

Propane
Methane
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

Physical Properties of StraightChain 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
Pentane
2-Methylbutane
2,2-Dimethylpropane
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

25
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.

28
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

H
H
H
H
C
C
C
C
H
H
H
CH3
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
    Entropy 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

CH2CH3
6
7
CH2CHCH3
H3CHC
C
1
2
3
4
5
3-propyl-5-methyl-2-heptene
CH2CH2CH3
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

H3C
CH3
H3C
H
C
C
C
C
CH3
H
H
H
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
CH2
CH2
C
C
CH3
H3C
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

CH3
CH3
CH3
C2CH3
Methylbenzene (Toluene)
3,4-Dimethyl-ethylbenzene m,p-Dimethyl-ethylbenzen
e
51
Aromatic Compounds
  • Substituted Benzenes

Methoxybenzoate
Nitrobenzene
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)

CH3
1
2 (o)
6 (o)
3 (m)
5 (m)
4 (p)
CH3
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, the compound is oxidized
  • When a C atom forms fewer bonds to Oxygen or more
    bonds to Hydrogen, the compound is reduced

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
OH
CH3CH2CH2CH2CH3
CH2CH2CH2CH3
CH3
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-CH3 group is part of structure,add
    Methoxy to name
  • If R-C-O-CH2-CH3 group is part of structure, add
    Ethoxy to name

72
Ether Nomenclature
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
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

HO
Acidic Hydrogen (Hydroxyl Group)
C
O
CH3
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
    that 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
Purines
Guanine
Adenine
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
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