Title: Solution Chemistry
1George 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.
2Organic 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 (10
million or more) - Most organic molecules have much more complex
structures than most inorganic molecules
3Organic 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
4Organic 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 orbitals 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
5Organic Chemistry
6Organic Chemistry
Shape of sp3 hybrid orbital different than either
s or p
7Organic 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
8Organic 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
9Organic 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
10Organic 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
11Organic 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
12Carbon 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
13Hydrocarbons
- 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)
14Hydrocarbons
- 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
15Hydrocarbons
- 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
16Hydrocarbons
- Alkanes CnH2n2
- Straight Chained Alkanes
Methane
Propane
Ethane
Butane
17Hydrocarbons
- Branched Chained Alkanes
- Cycloalkanes
3-Ethyl-4-MethylHexane
Cyclobutane
Methylcyclopropane
18Hydrocarbons
- 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
19Hydrocarbons
Straight Chain (n) Alkanes
20Hydrocarbons
Petroleum Fractions
21Hydrocarbons
Cycloalkanes CnH2n
Cyclohexane
Cyclopropane
Cyclobutane
22Hydrocarbons
- 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
23Hydrocarbons
- Structural Isomers of Pentane
C5H12
24Hydrocarbons
- 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
25Hydrocarbons
- 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
26Hydrocarbons
- 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
27Hydrocarbons
- 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.
28Nomenclature 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
29Nomenclature Example
(Cont)
30Nomenclature Example
- Determine the longest chain in the molecule
- 7 Carbons
Substituted Heptane (7 C)
(Cont)
31Nomenclature 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
32Nomenclature 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
33Hydrocarbons
- Reactions of Alkanes
- Combustion (reaction with oxygen)
- C5H12(g) 8 O2(g) ? 5 CO2(g) 6 H2O(l)
- Substitution (for a hydrogen)
- C5H12(g) Cl2(g) ? C5H11Cl(g) HCl(g)
34Hydrocarbons
- 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
35Hydrocarbons
- 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
36Hydrocarbons
- 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
37Hydrocarbons
- 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)
38Hydrocarbons
- 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
39Hydrocarbons
- 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 - Addition Reaction Heat of Formation
-
- Reaction is Exothermic
- Formation of two strong ? bonds from a single ?
bonds and a relatively weak ? bond
40Hydrocarbons
- 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
41Hydrocarbons
- 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
42Hydrocarbons
- 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
43Hydrocarbons
- Nomenclature of Alkenes - Example
- First, find the longest carbon chain containing
the double bond
3-propyl-5-methyl-2-heptene
44Hydrocarbons
- 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
45Hydrocarbons
- 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
46Hydrocarbons
Ethyne or Acetylene
Propyne A Terminal Acetylene
3-Hexyne
47Aromatic 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
48Aromatic Hydrocarbons
Molecular Orbitals of Benzene
49Aromatic 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
50Aromatic Hydrocarbons
Substituted Benzenes
Methylbenzene (Toluene)
3,4-dimethyl-ethylbenzene m,p-dimethyl-ethylbenzen
e
51Aromatic Compounds
Substituted Benzenes
52Aromatic 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
53Reactions 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
54Reactivity 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
55Reactivity 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
56Redox 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
57Redox 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
58Redox 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-)
59Organic 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
60Organic 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
61Functional 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)
62Functional Groups
63Functional Groups
64Alcohols
- 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
65Alcohols
Alcohol Nomenclature Drop final e from
hydrocarbon and add suffix ol
4,6-dimethyl-3-octanol (a secondary alcohol)
66Alcohols
- 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
67Alcohols
- Alcohol Reactions
- Elimination Reactions
- Elimination of a H atoms 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
68Alcohols
- 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
69Haloalkanes
- 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
70Haloalkanes
- 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
71Ethers
- 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
72Ether Nomenclature
OCH2CH3
CH3CH2CH2CH2CH3
4 3 2 1
5 6 7 8
CH2CH2CH2CH3
CH3
4,6-dimethyl-3-ethoxyoctane
73Amines
- 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
74Amine 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
75Amines
- Reactions
- Primary and secondary amines can form H bonds
- 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
76Amines
- 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
77Carbonyl 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
78Aldehydes 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
79Aldehydes 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)
80Aldehydes 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)
81Aldehydes 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)
82Aldehydes 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
83Aldehydes 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
84Aldehydes 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
85Carboxylic 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
86Carboxylic 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
87Carboxylic 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
88Examples
- Straight chain saturated (Aliphatic) carboxylic
acids
89Esters
- 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
90Esters
- 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
91Amides
- 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 -
92Amides
- 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
93Functional 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
94Polymers
- 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
95Addition Polymers
96Addition Polymers
- Free-radical polymerization of Ethene, CH2CH2
,to polyethylene
97Condensation 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
98Biological 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
99Sugars 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
100Sugars 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
101Sugars 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
102Amino 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
103Amino 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
104Amino Acids Proteins
CO
N-H
105Amino 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
106Amino Acids Proteins
107Amino 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
108Amino 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
109Amino 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
110Amino Acids Proteins
Structural Hierarchy of Proteins
111Amino 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
112Amino 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
113Amino 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
114Amino 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)
115Amino 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
116Amino 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
117Practice Problem
- Write the sequence of the complimentary DNA
strand that pairs with each of the following - a. GGTTAC
- Ans CCAATG
- b. CCCGAA
- Ans GGGCTT
118Practice 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
119Nucleic Acids (N-Containing Bases)
Pyrimidines
Thymine
Uracil
Cytosine
120Nucleic acid precursors and their linkage
.
121The Double Helix of DNA
122Amino 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
123Amino 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
124Amino 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
125Amino 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