Introduction to Organic and
Biochemistry
(CHE 124)
Reading Assignment
General, Organic, and Biological Chemistry: An Integrated Approach
4th. Ed. Ramond
Chapter 4: Introduction to Organic Compounds
Work Problems
Answers to odd numbered problems in textbook are found in the book’s
index.
Organic and Biochemistry
• Organic Chemistry - the study of the chemistry of the carbon atom.
– 1 element ~ 10 million compounds known.
• Inorganic Chemistry - the study of the chemistry of the other elements.
– 115 elements ~ 1.7 million compound known.
• Biochemistry – the study of the chemical processes that take place in
living organisms.
Carbon
C
Atomic number = 6
Atomic weight = 12.01
Why is Carbon So Important?
• 1. Historically
– Carbon containing compounds were found in living
organisms.
– It was thought that these living organisms contained a
“vital force” that allowed them to synthesis these
compounds.
– Fredrich Wohler (1828) disproved the “doctrine of vital
force” using this reaction.
Ammonium Chloride + Silver Cyanate → Urea + Silver chloride
Why is Carbon So Important? (Cont)
• 2. Number of Organic Compounds
– 85% of known chemical compounds are organic.
• > 10 million known
• ~1.7 million inorganic compounds known
• 3. Carbon is the major element in
biochemical compounds.
– Proteins
– Carbohydrates
– Lipids
– Nucleid Acids (DNA / RNA)
Differences of Organic and
Inorganic Compounds (generalizations)
ORGANIC
Covalent bonds
INORGANIC
Ionic bonds
Low melting point (< 360 C) gases, High melting point solids
liquids and solids
Water insoluble (most, not all)
Water soluble
Soluble in organic solvents (eg
diethyl ether, toluene or
dichloromethane)
Insoluble in organic solvents
Aqueous solutions do not conduct
electricity
Aqueous solvents conduct
electricity
Burn and decompose (most)
Very few burn
Reactions are slow
Reactions are FAST.
Common Elements in Organic Compounds
ELEMENT
NUMBER
OF
COVALENT
BONDS
•
Remember:
–
–
–
HYDROGEN
1
HALOGENS
(F, Cl, Br, I)
1
OXYGEN
2
•
SULFUR
2
•
NITROGEN
3
CARBON
4
PHOSPHORUS
5
•
•
Covalent bonds are formed
by sharing of electrons.
Valence shell (outer shell)
Octet Rule
Draw Lewis dot structure of
each element’s valence shell
Draw Lewis dot structures for
simple molecules.
Draw Bonds / unpaired
electrons for each element
and several simple
molecules
Draw Single Double, Triple
Bonds
Drawing Organic Compounds
• Lewis Dot Structure
• Molecular formulas
– Full diagram
– Line angle diagram
– Three dimensional
•
•
•
•
Water
H2O
Methane CH4
Propane C3H8
Ethanol C2H5OH
1. Count the total number of valence electrons
2. Use single covalent bonds to connect the atoms to one another
3. Beginning with the atoms attached to the central atom, add the remaining
electrons to complete octets
4. If the central atom does not have an octet, move pairs of nonbonding electrons from
attached atoms to form mutliple bonds with the central atoms. Do so until the central
atom has an octet.
Functional Groups
• Functional Group – an atom or group of atoms within a molecule that
shows a characterisitc set of physical and Chemical properties. (p. 66)
– Hydroxyl (alcohols)
-ol
• 1’, 2’ , and 3’ alcohols
–
–
–
–
–
–
–
–
Carboxylic Acid (acid)
-oic acid
Carboxyl group
Aldehyde
-al
Ketone
-one
Arenes (Cyclic Aromatic – benzene ring)
Carboxylic Ester (Ester)
Ethers
Amines
amine
• 1’ 2’, and 3’ amines
–
–
–
–
–
–
Amide
Thiols
Sulfides
Disulfides
Methyl group
Methylene group
-CH3
-CH2-
• Be able to draw and identify in larger molecules.
• R = anything containing carbon.
-
Find and Name Functional Groups
Polar Covalent Bonds
• Covalent bonds are formed by sharing of electrons,
but the electrons are not always shared equally
between the two atoms. This can create a polar
covalent bond. This unequal sharing occurs when
elements with different electronegativities form
covalent bonds. See Fig 4.3 p 106.
Bond
Nonpolar
Covalent
Polar
Covalent
Ionic
Characteristics
Equal sharing of
bonding
electrons
Unequal sharing
of bonding
electrons
Attraction of
opposite
charges
Example
C-C
Electronegativity
difference
< 0.5
δ+
C-O δ-
0.5 – 1.9
Na+ Cl> 1.9
Common Molecular Shapes
•
•
•
•
•
•
•
•
•
Molecules are three-Dimensional structures.
See Table 4.2 p. 108
Tetrahedral
Pyramidal
Bent
Trigonal planar
Bent
Linear
See Fig. 4.5 P. 109 Cholesterol.
Bond Angles.
• Bond angles are important to know.
– 109.5°
– 120 °
– 180 °
Polarity
• Polar molecule
– Molecule in which one side has a partial positive
charge (δ+) and the other has a partial negative
(δ-) charge.
– Must contain one or more polar covalent bonds.
– Some molecules with polar covalent bonds are
nonpolar (e.g. Carbon dioxide) Draw and label
the structure and see why.
Noncovalent Interactions
• 1. Hydrogen bonds
– Interaction of a nitrogen, oxygen, or fluorine atom
with a hydrogen atom that is covalently bonded to
a different nitrogen, oxygen, or fluorine atom
(electronegative atom). This causes the
hydrogen to carry a δ+ charge.
• About 10 fold weaker than a covalent bond.
• Hydrogen bonds are important in the structure of
proteins, and nucleic acids.
• See Fig. 4.7 p. 111
Noncovalent Interactions (Cont’)
• 2. Dipole-dipole forces
– A noncovalent attraction of neighboring polar groups for
one another.
• 3. London forces
– A noncovalent interaction that involves the attraction of
neighboring polar groups for one another.
• Temporary dipole (charge) created due to electrons all being on
one side of the molecule.
Types of Hydrocarbons
• Hydrocarbon - organic compound that contains only
H and C
– Alkanes
-ane
• Saturated (no double or triple bonds) hydrocarbon. Contains
single C –C bonds only.
– Alkenes
-ene
• Unsaturated hydrocarbon containing one or more double bonds
– Alkynes
-yne
• Unsaturated hydrocarbon containing one or more triple bonds
– Arenes (aromatic compounds)
• A compound with one or more benzene rings.
Draw full diagram, line-angle diagram.
Nomenclature (Naming) Of Organic
Compounds
•
IUPAC – International Union of Pure and
Applied Chemistry
– Governs nomenclature of chemical compounds
Naming Unbranched Alkanes
•
Name consists of two parts:
–
–
•
Prefix giving the number of carbons (See counting slide)
Suffix – ane
1. Name the parent compound.
–
–
Use the prefix that designates the number of
carbons.
Add suffix -ane.
Unbranched side chains are named by naming the
alkane, dropping the –ane and adding -yl.
Naming Branched Alkanes
2. Identify and name the longest unbranched carbon
chain which is called “the parent compound”
3. Number carbons in parent compound so carbons
with substituents (also called side chains) have
the lowest possible number (s).
4. Name each substituent and associate with the
carbon number to which it is attached.
5. Write substituents with numbers in alphabetical
order in front of the parent compound. If a side
chain appears more than once, use di = 2, tri = 3,
tetra = 4, penta = 5, hexa = 6 etc. Do NOT use
prefixes such as di, tri, etc. or sec, tert in
alphabetizing side chains.
Learning to Count Carbons in Alkanes
1 = meth2 = eth3 = prop4 = but5 = pent6 = hex7 = hept8 = oct9 = non10 = dec-
11 = undec12 = dodec13 = tridec14 = tetradec15 = pentadec16 = hexadec17 = heptadec18 = octadec19 = nonadec20 = eicos-
Common Alkyl Groups
Alkyl group - a group derived by removing a hydrogen from
an alkane given the symbol R.
Name
methyl
ethyl
propyl
isopropyl
butyl
isobutyl
sec-butyl
tert-butyl
Condensed Structural
Formula
Cycloalkanes
• Cycloalkane – a hydrocarbon that contains
carbon atoms joined to form a ring of carbons
connected by double bonds.
– Cyclopropane
– Cyclobutane
– Cyclopentane
– Cyclohexane
• To name cyclic structures use prefix cyclothen name each substituent. If only one
substituent, do not number it. Use lowest
possible numbers and place in alphabetical
order.
Naming Alkenes / Alkynes
• Identify and name (as alkane) longest parent
chain containing the double or triple bond.
• Drop “–ane” and add “-ene” for double bonds
or “-yne” for triple bonds.
• Number –ene or yne using lowest number
possible. Do not number if parent chain has
less than 3 carbons.
Naming Arenes
• Named as substituted Benzene ring.
– Some substituted benzene rings have common
names
• Methylbenzene = Toluene
• hydroxylbenzene = phenol
• If the ring has a single substituent, then do
not add a number.
• See fig. 4.18 p. 124.
• Disubstituted benzene rings
– 1,2 = ortho
– 1,3 = meta
– 1,4 = para
Naming Arenes (Cont)
• Polycyclic aromatic hydrocarbons (PAHs) –
hydrocarbon containing benzene rings that
are fused to one another.
– Naphthalene
– Anthracene
– PAHs are produced during burning of coal. Most
PAHs are carcinogens.
Constitutional Isomers
• Constitutional Isomers – compounds with the
same molecular formula (same number and
type of atoms), but a different order of
attachment of their atoms.
• C6H14 has 5 constitutional isomers
–
–
–
–
–
Hexane
2-methylpentane
3-methylpentane
2,2dimethylbutane
2,3 dimethylbutane
Conformation
• Conformation – the shapes that a molecule can
take because of bond rotations are called
conformations.
–
–
–
–
Have the same molecules formula
Have the same atomic connections
Have different three-dimensional shapes
Conformations are interconverted by rotation around
a single bond.
• C – C single bonds have free rotation
• C = C double (or triple) bonds are constrained, no
rotation possible.
Geometric Isomers
• Geometic isomers – stereoisomers that result
from restricted bond rotation. Cycloalkanes
and alkenes are molecules that can exist as
cis or trans geometric isomers
• Cis = same side
• Trans = opposite sides
– Cis and trans are also observed near double bonds.
– Have the same molecules formula
– Have the same atomic connections
– Have different three-dimensional shapes
– Are interchanged only by breaking bonds
See fig 4.16 p. 122
Physical Properties of Alkanes
• Polarity = Nonpolar
– Electronegativity of C (2.5) and H (2.1) are similar.
• Boiling point = low
– Boiling point – temperature at which the vapor pressure of a liquid is
equal to the atmospheric pressure. (liquid to gas)
– Bp increases as chain length increases
• Melting point = low
– Melting point – temperature at which a substance changes for a solid
state to a liquid state (solid to liquid).
– Mp increases as chain length increases
• Solubility= Insoluble in water
– Soluble in other alkanes and organic solvents. “like dissolves like”
• Density = 0.7 – 08 g / mL
– Less dense than water (1 g / ml)
– Since alkanes are insoluble and less dense than water, they float on
top of the water.
Products Containing Alkanes
• Natural Gas – mixture of 90 – 95% methane, 5 – 10 %
ethane, and some propane, butane, 2-methyl propane.
• Petroleum (oil) – a thick, viscous liquid mixture of thousand
of compounds formed from the decomposition of ancient
plants and animals.
• Liquified Petroleum gas (LP gas) – propane
• Gasoline – complex mixture of C6 – C12 hydrocarbons
distilled from Petroleum.
• Diesel – complex mixture of C8 – C21 hydrocarbons distilled
from Petroleum
• Chlorofluorocarbons (CFC’s) – hydrocarbons with halogens
attached
– Freons – used in air conditioners, refrigerators.
• CCl3F = freon 11
• CCl2F2 = feon 12
Reactivity of Alkanes