Download Document

Introduction to
Organic Chemistry
BIOB111
CHEMISTRY & BIOCHEMISTRY
Session 7
Session Plan

Introduction to Organic Compounds

Differences between organic and inorganic compounds

Functional Groups

Nomenclature

Structural Isomers

Stereo isomers
Organic Compounds
Organic compounds:
•
All compounds or molecules containing the elements carbon and hydrogen.
–
•
Organic compounds found in living organisms needed for life’s processes
–
•
Carbohydrates, lipids, proteins, and nucleic acids, fats, plastics, and fuels
Many common organic compounds contain:
–
•
A compound that contains carbon is a organic compound
Oxygen, nitrogen, or sulphur atoms
Hydrocarbons:
Organic compounds containing only carbon and hydrogen atoms are called
–
Sources of organic compounds:
•
•
Nature
Laboratory synthesis
Organic vs Inorganic Chemistry
• Organic Chemistry
– Study of the compounds of the element carbon
– The study of hydrocarbons & their various derivatives.
– Examples: natural gas (methane CH4), petroleum, plastics, rubbers,
paper, carbohydrates (sugars, starches), proteins, enzymes, fatty acids,
vitamins, drugs, textiles, etc.
• Inorganic Chemistry
– Study of the compounds of the other 117 elements
– The study of all substances other than hydrocarbons & their derivatives.
– Examples: water, sulfuric acid, nitric acid, ores & minerals, air, baking powder,
caustic soda, table salt, metal alloys (brass, bronze), etc.
Stoker 2014, Figure 12-1 p340
Organic vs Inorganic Compounds
(Properties)
0
Diversity of Organic Compounds
• What is the basis for the huge diversity of
organic compounds?
– The ability of carbon to from covalent bonds with
other elements (e.g. H, O, N and S) and itself
– Each carbon has 4 unpaired electrons in it’s valence
shell >>> each can be involved in one covalent bond
• Total covalent bonds formed by a carbon atom = 4
Bonding of Carbon Atoms
• Organic Chemistry is based on Carbon &
its ability to form chains.
– Carbon belongs to Group IV.A & has 4 valence electrons
– Carbon shares these 4 valence e- with other atoms to acquire a noble gas
arrangement of 8 valence e-
• To form a stable compound:
– Carbon always forms 4 covalent bonds (= shares 4 pairs of of e-)
Stoker 2014, p119
Basis for Formation of Organic Compounds
• What is the basis for the formation of organic
compounds?
– Ability of constituent atoms (within compound) to
achieve a stable configuration (octet rule)
– To achieve complete valence shell (satisfy octet rule):
•
•
•
•
•
Carbon forms four covalent bonds
Nitrogen forms three covalent bonds
Oxygen forms two covalent bonds
Hydrogen will form one covalent bond
Halogens (F, Cl, Br, I) form one covalent bond
Hydrocarbons
• Hydrocarbon
– Organic compounds that contain only H & C atoms
• Saturated Hydrocarbons
– Have only single covalent bonds between C atoms
– Are saturated with Hydrogen atoms
– Include Alkanes (straight chains) & Cycloalkanes (carbon rings)
Hydrocarbons
• Saturated Hydrocarbons
–
–
–
–
Have only single covalent bonds between C atoms
Alkane: Propane
Chemical formula: C3H8 >>> CH3CH2CH3
Ends of the chain have CH3, whereas the middle has CH2
Hydrocarbons
• Saturated Hydrocarbons
–
–
–
–
–
Have only single covalent bonds between C atoms.
Cycloalkane: cyclohexane
Chemical formula: C6H12 >>> CH2CH2CH2CH2CH2CH2
No ends to the chain all connected, all are CH2
Has two less hydrogens than comparable alkane (due to lack of ends)
Hydrocarbons
Unsaturated Hydrocarbons
–
–
–
–
Have 1 or more double or triple covalent bonds between C atoms
Alkene: Propene
Chemical formula: C3H6 >>> CH2CHCH3
Extra carbon-carbon = two less hydrogens in structure
Alkene
Alkane
H
H
C
C
H
Propene
C
H
H
H
H
H
H
H
C
C
H
Propane
C
H
H
H
Hydrocarbons
Unsaturated Hydrocarbons
–
–
–
–
Have 1 or more double or triple covalent bonds between C atoms
Cycloalkene: cyclohexene
Chemical formula: C6H10 >>> CHCHCH2CH2CH2CH2
Extra carbon-carbon = two less hydrogens in structure
CH
CH2
CH2
CH
Alkene
CH 2
CH2 Cyclohexene
CH2
CH2
CH2
Alkane
CH2
CH 2
CH2
Cyclohexane
IUPAC Nomenclature common
Hydrocarbons
Number of Carbon Atoms
Prefix
Alkanes
Alkenes
Alkynes
CnH2n+2
CnH2n
CnH2n-2
(Single bonds)
(Double bonds)
(Triple bonds)
1 Meth-
Methane
-
-
2 Eth-
Ethane
Ethene
Ethyne
3 Prop-
Propane
Propene
Propyne
4 But-
Butane
Butene
Butyne
5 Pent-
Pentane
Pentene
Pentyne
6 Hex-
Hexane
Hexene
Hexyne
7 Hept-
Heptane
Heptene
Heptyne
8 Oct-
Octane
Octene
Octyne
9 Non-
Nonane
Nonene
Nonyne
10 Dec-
Decane
Decene
Decyne
Important rules
for distinguishing
between alkanes,
alkenes and
alkynes
Nomenclature and Structure of First 10 Alkanes
(Saturated Hydrocarbons)
• Biob
Stoker 2014, Table 12-2 p350
Summary of Organic Compounds
• Biob
Stoker 2014, Figure 12-2 p342
Key concept: valence shell, octet rule, atom/compound stability
When an atom adopts it’s most stable state,
how full is it’s valence (outer) shell?
What is the octet rule? What does the octet rule say about
the electron arrangement within an atom’s valance shell?
Are each of the atoms that make up an organic compound
more stable within the compound or as individual atoms?
G
Multiple atoms come together to form compounds, where the multiple atoms
are attached to one another via chemical bonds. For example, to form a H2O
molecule, an oxygen atom forms a covalent bonds to two separate hydrogen
atoms. Are the oxygen and hydrogen atoms more stable within the H2O
compound or as separate atoms and why?
a)
The atoms are more stable as individual atoms, as all of their electrons
are paired, whereas as within compounds the atom are more reactive as
some of the electrons are unpaired
b)
The atoms are equally stable when in the compounds and as
individual atoms
c)
The atoms are more stable within the compound, as all of their electrons
are paired, whereas as within the individual atoms some of the electrons
are unpaired and reactive
d)
The atoms are more stable as individual atoms as they can move about
more freely than when they are a part of a compound
The outer shell of a carbon atom contains four unpaired valence
electrons. The number of unpaired valence electrons an atom contains
is equal to the number of covalent bonds the atom is capable of forming.
Which of the following accurately describes the covalent bonding of a
carbon atom?
a)
Each of the four unpaired valence electrons must form a
covalent bond with another carbon atom to become more stable
b)
Each of the four valence electrons within the carbon atom can
covalent bond to each other to become more stable
c)
Each of the four valence electrons of a carbon atom can form a covalent
bond via electron sharing with other atoms such as hydrogen and carbon
d)
Each of the four valence electrons of a carbon atom can covalent bond
to more than one different atom simultaneously
Key concept: Saturated and unsaturated hydrocarbons
What is the functional group
of a saturated/unsaturated hydrocarbon?
How is a unsaturated hydrocarbon
different from a saturated hydrocarbon?
For two compounds with an equal number of carbons,
does a saturated or unsaturated hydrocarbon
contain more atoms in total? Why?
Compounds composed of carbon and hydrogen are referred to as hydrocarbons.
Hydrocarbon derivatives can also have additional atoms such as nitrogen and
oxygen. Hydrocarbons are grouped into those that are saturated and those that
are unsaturated. Which of the following best describes the difference between a
saturated and an unsaturated hydrocarbon?
d
a)
The carbons within saturated hydrocarbons are connected to other carbons
by single bonds, whereas at least one carbon in an unsaturated hydrocarbon
connects to another carbon atom through a double or triple bond
b)
Saturated hydrocarbons contain only single carbon-carbon bonds,
whereas unsaturated hydrocarbons contain only double or triple
carbon-carbon bonds
c)
The carbons within unsaturated hydrocarbons are connected to other carbons
by single bonds, whereas at least one carbon in an saturated hydrocarbon
connects to another carbon atom through a double or triple bond
d)
Unsaturated hydrocarbons contain only single carbon-carbon bonds,
whereas saturated hydrocarbons contain only double or triple carbon-carbon bonds
Even though hydrocarbons only contain carbon and hydrogen they belong to one of three
functional groups, either the alkanes, alkenes or alkynes. One of the major differences
between these functional groups is the ratio between the carbon and hydrogen atoms, as
more double and triple carbon-carbon bonds within a compound reduces it’s number of
hydrogens. Which of the following best describes the differences between the
hydrocarbon functional groups?
d
d
a)
Both alkanes and alkenes contain the same number of hydrogen atoms, but alkynes
contain less hydrogen atoms due to the presence of one or more triple carbon-carbon
bonds
b)
Alkanes contain the most hydrogen atoms attached to the carbon atoms, as there as
only single carbon-carbon bonds, whereas alkenes and alkynes contain less hydrogen
atoms due to the presence of double or triple carbon-carbon bonds
c)
Alkanes contain the most hydrogen atoms as they contain only single carbon-carbon
bonds, whereas alkynes do not contain any hydrogen atoms, only carbon atoms
d)
Alkyne compounds contain the most hydrogen atoms due to their triple carbon-carbon
bonds, alkenes have the next most hydrogen atoms and alkanes have the least hydrogen
atoms, due to the presence of only single carbon-carbon bonds
Common Functional Groups in Organic
Chemistry
• What are functional groups?
– Carbon combines with other elements to form functional groups.
•
Sites of chemical reactions/key structural components that define how
organic molecules react
–
–
Particular functional groups undergo similar chemical reactions
E.g. Alcohols (contain OH functional group) have certain chemical properties
Alcohol
•
Functional groups are used to classify and name organic compounds.
Functional groups in macromolecules
Carbohydrate
Glucose
Alcohol
Lipid
Triacylglycerol (TAG)
Ether
Ester
Carboxylic
acid
Alcohol
Protein
Amino Acid
Carboxylic acid
Nucleic acids:
DNA/RNA
Stoker 2014, p695
Nucleotide
Amide
Amine
Amine
Ether
Stoker 2014, p650
Alcohol
Common Functional Groups
#More detail in coming slides#
Common Functional Groups
#More detail in coming slides#
Alkane & Alkyl Groups
• Alkanes are saturated hydrocarbons:
Alkanes:
Propane is used as a
fuel for cars (LPG gas)
Contain single Carbon-Carbon bonds (CH4)
• Alkyl groups:
•
Carbon branches that has one H less than the parent
•
•
Replace the -ane ending of the corresponding alkane name with yl.
Can form a covalent bond with another atom e.g. C or N
methane = methyl
—CH3
ethane = ethyl
—CH2—CH3
propane = propyl
—CH2—CH2—CH3
Alkyl Groups
• Biob
Stoker 2014, Table 12-3 p351
Alkenes and Alkynes
• Alkenes contain a double bond between
adjacent carbon atoms.
C
Alkenes:
Many, many units of ethene
combine to make polyethylene
(most common plastic)
C
• Alkynes contain a triple bond.
C
C
Alkynes:
Ethyne is used to generate
temps of 3000 degrees
used to weld metal
• Aromatic compounds contain a
benzene ring.
Aromatic compounds:
Benzene found in crude oil is used
to make many industrial products
(e.g. synthetic rubber)
Alcohols, Thiols and Ethers
• An alcohol contains the
hydroxyl (–OH) functional
group.
Thiol
Alcohols:
Ethanol is present in
alcoholic beverages
• Thiols contain a thiol (–SH)
functional group.
• In an ether, a central oxygen
atom is bonded to two carbon
atoms (–C–O–C–).
Thiols:
Butenethiol is one of the
compounds responsible
for the smell of a skunk
Ethers:
Diethyl ether was used
as an aesthetic in the
past
Aldehydes and Ketones
•
•
Carbonyl group:
A carbon atom with a double bond to
an oxygen atom
An aldehyde contains a carbonyl group
(C=O), attached to at least one hydrogen
atom Aldehydes:
O
H3C
Formaldehyde (Methanal) is used to preserve
biological specimens (e.g. cadavers)
•
In a ketone, the carbon of the carbonyl
group is attached to two other carbon
atoms
Ketones:
Acetone (propanone) used in paint and nail
polish removers
C
H
O
H 3C
C
CH3
Stoker 2013, p356
Carboxylic Acids and Esters
O
• Carboxylic acids contain the
carboxyl group
– A carbonyl group attached to a hydroxyl
group.
Carboxylic acids:
Acetic acid (ethanoic acid) is
found in vinegar
• An ester contains the carboxyl
group between carbon atoms.
Esters:
Triacylglycerol (single
unit of a fat and oil)
contains three esters
C
H3 C
OH
O
H3C
C
CH3
O
Amines and Amides
• In an amine, the functional
group is a nitrogen atom with
one or more carbon atoms.
H3C
N
H
H3C
N
CH3
H
H
H3C
N
H3C
C
NH2
CH3
CH3
• In an amide, the hydroxyl
group of a carboxylic acid is
replaced by a nitrogen group.
O
Amines:
Butandiamine responsible
for the smell of decaying fish
Amides:
Methanamide used to
make paper
Functional groups in macromolecules
Carbohydrate
Glucose
Alcohol
Lipid
Triacylglycerol (TAG)
Ether
Ester
Carboxylic
acid
Alcohol
Protein
Amino Acid
Carboxylic acid
Nucleic acids:
DNA/RNA
Stoker 2014, p695
Nucleotide
Amide
Amine
Amine
Ether
Stoker 2014, p650
Alcohol
IUPAC Nomenclature vs. Common Names
• IUPAC (International Union of Pure and Applied
Chemistry) has developed a system of nomenclature
which allow each organic compound to be assign a
unique name.
– Prefixes are used to name hydrocarbon molecules
according to the number of carbons present in the
longest continuous chain of carbon bonds.
Structural Representation of Organic
Compounds
• How are the structures of organic compounds represented?
– The structure of organic compounds can be represented
by:
• Molecular Formula C3H8
– Indicate the number and types of atoms present in
a molecule but contain no information about their
arrangement.
• Structural Formula
– Complete
– Condensed CH3CH2CH3
– Line Bond Formula
Stoker 2014, pp.358
Isomers
• What are structural isomers?
– Molecules that have the same molecular formula, but different bonding
arrangements/ structural formulas.
– e.g. ethanol vs dimethyl ether
propanal vs propanone
– Isomers do not necessarily share similar properties.
– There are two main forms:
• Structural isomerism
• Stereoisomerism (spatial isomerism)
Conformational and Stereo Isomers
•
The C-C single bonds enable free rotation of
the alkane chain
–
•
Different conformational structures result from C-C
single bond rotation but no bonds are broken
The groups attached to a C-C single bond
can:
–
Rotate around the bond, giving different relative
arrangements called conformational isomers
–
In the stereoisomers the two methyl group are
positioned differently:
•
•
cis isomer = the methyl groups are on the same side of
the c-c bond
trans isomer = methyl groups on opposite sides
of the c-c bond
Stereoisomers
cis
trans
Structural (Constitutional) Isomers
•
Structural isomers are compounds that have the
same molecular formula but different structural formulas
–
Different arrangement of atoms in space
•
Different structural isomers result from different connectivity of atoms, which
requires breaking & re-formation of bonds in the same molecule
•
Continuous-chain alkane
–
–
•
C atoms are connected in a continuous non-branching chain.
E.g. Butane: CH3 – CH2 – CH2 – CH3
Branched-chain alkane
–
–
1 or more branches
are attached to a continuous chain.
E.g. 2-methylpropane
2-methylpropane
CH3
I
CH3 – CH – CH3
Methyl group
Three carbon chain
Structural Isomers of C5H12
•
Pentane
CH3 – CH2 – CH2 – CH2 – CH3
•
2-methylbutane
CH3
I
CH3 – CH – CH2 – CH3
•
2,2-dimethylpropane
CH3
I
CH3 – C – CH3
I
CH3
Stoker 2014, Table 12-1 p348
Readings & Resources
•
•
•
•
•
•
•
•
Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn,
Brooks/Cole, Cengage Learning, Belmont, CA.
Stoker, HS 2004, General, Organic and Biological Chemistry, 3rd edn,
Houghton Mifflin, Boston, MA.
Timberlake, KC 2014, General, organic, and biological chemistry:
structures of life, 4th edn, Pearson, Boston, MA.
Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008,
Molecular biology of the cell, 5th edn, Garland Science, New York.
Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H.
Freeman, New York.
Dominiczak, MH 2007, Flesh and bones of metabolism, Elsevier Mosby,
Edinburgh.
Tortora, GJ & Derrickson, B 2014, Principles of Anatomy and Physiology,
14th edn, John Wiley & Sons, Hoboken, NJ.
Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology,
10th edn, John Wiley & Sons, New York, NY.