ORGANIC
CHEMISTRY
Naming Saturated Hydrocarbons
• The International Union of Pure and Applied Chemistry (IUPAC)
names for the first 12 "straight-chain" or "normal" alkanes are:
Number of Carbons in chain
Prefix
C-C
C=C
C C
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
11
Undec-
Undecane
Undecene
Undecyne
12
Dodec-
Dodecane
Dodecene
Dodecyne
Alkanes and Cycloalkanes
• The simplest saturated hydrocarbons are called alkanes.
• Methane, CH4, is the simplest alkane.
• The alkanes form a homologous series.
– Each member of the series differs by a specific number and
kind of atoms.
Alkanes and Cycloalkanes
• The alkanes differ from each other by a CH2 or methylene group.
• All alkanes have this general formula.
CnH2n+2
• For example ethane, C2H6 , and propane, C3H8 , are the next two family
members.
Alkanes and Cycloalkanes
• Isomers are chemical compounds that have the same molecular
formulas but different structures.
• Two alkanes have the molecular formula C4H10.
– They are a specific type of isomer called structural isomers.
• Branched-chain alkanes are named by the following rules.
Naming Saturated Hydrocarbons
1.
2
3
4
5
6
Choose the longest continuous chain of carbon atoms which gives the
basic name or stem.
Number each carbon atom in the basic chain, starting at the end that
gives the lowest number to the first group attached to the main chain
(substituent).
For each substituent on the chain, we indicate the position in the chain
(by an Arabic numeric prefix) and the kind of substituent (by its name).
 The position of a substituent on the chain is indicated by the lowest
number possible. The number precedes the name of the substituent.
When there are two or more substituents of a given kind, use prefixes to
indicate the number of substituents.
 di = 2, tri = 3, tetra = 4, penta = 5, hexa = 6, hepta = 7, octa = 8, etc.
The combined substituent numbers and names serve as a prefix for the
basic hydrocarbon name.
Separate numbers from numbers by commas and numbers from words by
hyphens.
 Words are "run together".
Naming Saturated Hydrocarbons
•
•
Alkyl groups (represented by the symbol R) are common substituents.
– Alkyl groups are fragments of alkanes in which one H atom has been removed for
the connection to the main chain.
– Alkyl groups have the general formula CnH2n+1.
In alkyl groups the -ane suffix in the name of the parent alkane is replaced by -yl.
– A one carbon group is named methyl.
– A two carbon group is named ethyl.
– A three carbon group is named propyl.
• Three alkanes have the formula C5H12.
– There are three structural isomers of pentane.
n-pentane
2-methylbutane
2,2-dimethylpropane
Alkanes and Cycloalkanes
• There are five isomeric hexanes, C6H14.
n-hexane
2,2-dimethylbutane
2-methylpentane
3-methylpentane
2,3-dimethylbutane
•The number of structural isomers increases rapidly with
increasing numbers of carbon atoms.
•The boiling points of the alkanes increase with molecular weight.
Alkanes and Cycloalkanes
• Cyclic saturated hydrocarbons are called cycloalkanes.
– They have the general formula CnH2n.
• Some examples are:
cyclopentane
cyclooctane
•
1.
2.
3.
•
Alkenes
The three classes of unsaturated hydrocarbons are:
alkenes and cycloalkenes, CnH2n
alkynes and cycloalkynes, CnH2n-2
aromatic hydrocarbons
The simplest alkenes contain one C=C bond per molecule.
– The general formula for simple alkenes is CnH2n.
• The first two alkenes are:
• Each doubly bonded C atom
is sp2 hybridized.
• The sp2 hybrid consists of:
– two s bonds (single
bonds) and
– one s and one p bond
(double bond)
Alkenes
• The systematic naming system for alkenes uses the same stems as alkanes.
• In the IUPAC system, the -ane suffix for alkanes is changed to -ene.
– Common names for the alkenes have the same stem but use the suffix ylene is used.
• In chains of four or more C atoms, a numerical prefix shows the position of
the lowest-numbered doubly bonded C atom.
– Always choose the longest chain that contains the C=C bond.
• Polyenes contain two or more double
bonds per molecule.
• Indicate the number of double bonds
with suffixes:
– -adiene for two double bonds.
– -atriene for three double bonds,
1,3-hexadiene
1,2,5-hexatriene
etc.
• The positions of the substituents are
indicated as for alkanes.
• The position of the C=C bond(s)
is/are given the lowest number(s)
2,3-dimethyl-1,3,5-hexatriene
possible.
Cycloalkenes
• Cycloalkenes have the general formula CnH2n-2.
• Examples are:
• cyclopentene
• cyclohexene
Alkynes
•
•
Alkynes contain CC bonds.
The simplest alkyne is C2H2, ethyne, or acetylene.
– Alkynes with only one C  C bond have the formula CnH2n-2.
•
Each carbon atom in a C  C bond is sp hybridized.
– Each sp hybrid contains two  bonds and two  bonds.
– The carbon atom will have one single bond and one triple bond.
• Alkynes are named like the alkenes except that the suffix -yne is used with
the characteristic stem
– The alkyne stem is derived from the name of the alkane with the same
number of carbon atoms.
3-heptyne
2-octyne
Hydrocarbons: A Summary
Carbon Atom
Hybridization
C uses
C forms
Example
sp3
tetrahedral
4 sp3 hybrids
4  bonds
CH4
sp2
trigonal planar
3 sp2 hybrids &
1p orbital
3  bonds
1  bond
C2H4
sp linear
2 sp hybrids & 2
p orbitals
2  bonds
2  bonds
C2H2
Aromatic Hydrocarbons
• Historically, aromatic was used to describe pleasant smelling substances.
• Now it refers to benzene, C6H6, and derivatives of benzene.
– Other compounds that have similar chemical properties to benzene are
also called aromatic.
• The structure of benzene, C6H6, is:
• Coal tar is the common source of benzene and many other aromatic
compounds.
• Some aromatic hydrocarbons that
contain fused rings are:
• napthalene
Resonance in Benzene
• C–C single bond = 154 pm
• C=C bond = 134 pm
• CC bonds in benzene = 139 pm
• C6H6 has two resonance structures with alternating double bonds.
• The π electrons are delocalized over the ring.
Resonance structures of benzene, C6H6
Abbreviated representation
of resonance structure
π electrons delocalized
Other Aromatic Hydrocarbons
• Many aromatic hydrocarbons contain alkyl groups attached to benzene rings
(as well as to other aromatic rings).
• The positions of the substituents on benzene rings are indicated by the
prefixes:
– ortho(o-) for substituents on adjacent C atoms
– meta(m-) for substituents on C atoms 1 and 3
– para(p-) for substituents on C atoms 1 and 4
m-xylene
o-xylene
p-xylene
General Properties and Reactivity of
Alkanes, Alkenes, and Alkynes
1. Alkanes Consist of C–C and C–H bonds that are strong, not polar, and not
easily attacked by nucleophiles or electrophiles, so reactivity is limited
2. The multiple bond of an alkene produces geometric isomers (cis and trans)
a. Cis and trans isomers of alkenes behave as distinct compounds with
different chemical and physical properties
3. The hydrogen atom of a terminal alkyne can be removed as H+, forming an
acetylide ion (R–CC–)
a. Acetylide ions are potent nucleophiles used for making longer
carbon chains by a nucleophilic substitution reaction
4.
Rotation about the carbon-carbon multiple bonds of alkenes and alkynes
cannot occur without breaking a  bond, which constitutes a large energy
barrier to rotation. Alkenes and alkynes are prepared by elimination
reactions
5. Arenes undergo substitution rather than elimination due to stability from
delocalization of their  electron density, and are poor nucleophiles
Organic Halides
• A halogen atom may replace almost any hydrogen atom in a hydrocarbon.
• The functional group is the halide (-X) group.
• Examples include:
– chloroform, CHCl3
• 1,2-dichloroethane, ClCH2CH2Cl
• para-dichlorobenzene
Alcohols and Phenols
• The functional group in alcohols and phenols is the hydroxyl (-OH) group.
• Alcohols and phenols can be considered derivatives of hydrocarbons in which
one or more H atoms have been replaced by -OH groups.
• Phenols are derivatives of benzene in which one H has been replaced by
replaced by -OH group.
• The stem for the parent hydrocarbon plus an -ol suffix is the systematic name
for an alcohol.
• A numeric prefix indicates the position of the -OH group in alcohols with three
or more C atoms.
• Common names are the name of the appropriate alkyl group plus alcohol.
Alcohols and Phenols
• Ethyl alcohol (ethanol), C2H5OH, is the most
familiar alcohol.
• Phenol, C6H5OH, is the most familiar phenol.
•
1.
2.
•
3.
•
Alcohols and Phenols
Alcohols can be classified into three classes:
Primary (1°) alcohols like ethanol have the OH group attached to a C atom that has
H3
one bond to another C atom.
Secondary(2°) alcohols have the –OH
group
attached to a C atom that has bonds to
H3
2 other C atoms.
For example,2-propanol:
Tertiary (3°) alcohols have the –OH
group attached to a C atom that is
H3
bonded to 3 other C atoms.
For example, 2-methyl-2-propanol
OH
H3
OH
H3
OH
H3
Alcohols and Phenols
•
•
Alcohols are named using the stem for the parent hydrocarbon plus an -ol suffix in
the systematic nomenclature.
A numeric prefix indicates the position of the -OH group in alcohols with three or
more C atoms.
– Common alcohol names are the name of the appropriate alkyl
group plus the word alcohol.
1-pentanol
1-pentyl alcohol
2-pentanol
2-pentyl alcohol
3-pentanol
3-pentyl alcohol
Alcohols and Phenols
• There are several isomeric monohydric acyclic (contains no rings) alcohols
that contain more than three C atoms.
• There are four isomeric four-carbon alcohols.
1-butanol
2-methyl-1-propanol
2-butanol
2-methyl-2-propanol
Alcohols and Phenols
• There are eight isomeric five-carbon alcohols.
Alcohols and Phenols
• Polyhydric alcohols contain more than one -OH group per molecule.
Alcohols and Phenols
• Phenols are usually called by their common (trivial) names.
General Properties and Reactivity of
Alcohols and Ethers
• Alcohols and Ethers
– Have “bent” structures and are able to hydrogen-bond
– Are good solvents for organic compounds
• Alcohols are prepared by
– the addition of water to the carbons of a double bond or by substitution of
an alkyl halide by hydroxide, a potent nucleophile
– he reduction of compounds containing a carbonyl functional group ( CO)
– Undergo two major types of reactions: those involving cleavage of the O–H
bond, which produces an acid, and those involving cleavage of the C–O
bond occurring under acidic conditions where the –OH is first protonated
followed by a nucleophilic substitution
• Phenols are more acidic than alcohols because of interactions between the
oxygen atom and the ring
• Ethers are prepared by
– a substitution reaction in which the highly nucleophilic alkoxide ion (RO–)
attacks the carbon of the polarized C–X bond of an alkyl halide (R´ X)
– Unreactive because they lack the –OH unit
Ethers
• Ethers may be thought of as derivatives of water in which both H atoms have
been replaced by alkyl or aryl groups.
• Ethers are not very polar and not very reactive.
• They are excellent solvents.
• Common names are used for most ethers.
H3C
O
C
H2
CH3
ethylmethyl ether
H3C
O
CH3
dimethyl ether
H2
C
H3C
O
H2
C
diethyl ether
CH3
Aldehydes and Ketones
• The functional group in aldehydes and ketones is the carbonyl group.
Aldehydes and Ketones
• Except for formaldehyde, aldehydes have one H atom and one organic group
bonded to a carbonyl group.
O
H3C
O
O
H
ethanal
or
acetaldehyde
H
H
methanal
or
formaldehyde
H 3C
C
H2
H
propanal
or
propionaldehyde
• Ketones have two organic groups bonded to a carbonyl group.
H3C
O
O
O
C
C
C
CH 3
propanone
or
acetone
H2C
CH 3
CH 3
2-butanone
or
ethylmethylketone
H 2C
CH 3
CH 2
CH 3
3-pentanone
or
diethylketone
Aldehydes and Ketones
• Common names for aldehydes are derived from the name of the acid with the
same number of C atoms.
• IUPAC names are derived from the parent hydrocarbon name by replacing -e with
-al.
Aldehydes and Ketones
• The IUPAC name for a ketone is the characteristic stem for the parent
hydrocarbon plus the suffix -one.
• A numeric prefix indicates the position of the carbonyl group in a chain or
on a ring.
General Properties and Reactivity of
Aldehydes and Ketones
• Aldehydes and ketones
– Contain the carbonyl functional group
– Are prepared by
• the oxidation of alcohols
• reducing a carboxyl group (–CO2H) to a carbonyl group, which
requires a good reducing agent
– Characterized by nucleophilic attack at the carbon atom of the carbonyl
functional group and electrophilic attack at the oxygen atom
– React with organometallic compounds that contain stabilized carbanions
such as the Grignard reagents (RMgX, where X = Cl, Br, ), which
convert the carbonyl functional group to an alcohol and lengthen the
carbon chain
– Aromatic aldehydes have intense and characteristic flavors and aromas,
and many ketones also have intense aromas
– Ketones are found in hormones responsible for sex differentiation in
humans
Amines
• Amines are derivatives of ammonia in which one or more H atoms have been
replaced by organic groups (aliphatic or aromatic or a mixture of both).
• There are three classes of amines.
General Properties and Reactivity of
Amines
• Tertiary amines form cations in which all four H atoms are replaced by alkyl
groups and are called quaternary ammonium salts, which can be chiral if all
four substituents are different
• Alkylamines can be prepared by nucleophilic substitution reactions of polar
alkyl halides with ammonia or other amines
• Reactions of amines are dominated by two properties:
– the ability of amines to act as weak bases and
– their tendency to act as nucleophiles, both resulting from the lone pair of
electrons on the nitrogen atom
• Amines behave as bases by accepting a proton from an acid to form an
ammonium salt
• Amines can react with any electrophile
• Aryl amines are weaker bases than alkylamines because the lone pair of
electrons on nitrogen interacts with the  bonds of the aromatic ring
Carboxylic Acids
• Carboxylic acids contain the carboxyl functional group.
• The general formula for carboxylic acids is:
– R represents an alkyl or an aryl group
• IUPAC names for a carboxylic acid are derived from the name of the
parent hydrocarbon.
– The final -e is dropped from the name of the parent
hydrocarbon
– The suffix -oic is added followed by the word acid.
• Many organic acids are called by their common (trivial) names which
are derived from Greek or Latin.
Carboxylic Acids
O
O
C
H
C
OH
methanoic acid
or
formic acid
H3C
OH
ethanoic acid
or
acetic acid
O
H3C
O
H2
C
C
C
H2
OH
propanoic acid
or
propionic acid
H3C
C
C
H2
OH
butanoic acid
or
butyric acid
Carboxylic Acids
• Positions of substituents on carboxylic acid chains are indicated by
numeric prefixes as in other compounds
– Begin the counting scheme from the carboxyl group
carbon atom.
• They are also often indicated by lower case Greek letters.
–  = 1st C atom
–  = 2nd C atom
–  = 3rd C atom, etc.
Nomenclature of Carboxylic Acids
• Dicarboxylic acids contain two carboxyl groups per molecule.
Carboxylic Acids
• Aromatic acids are usually called by their common names.
• Sometimes, they are named as derivatives of benzoic acid which is
considered to be the "parent" aromatic acid.
Some Derivatives of
Carboxylic Acids
General Properties and Reactivity of
Carboxylic Acids
– Can be prepared from the oxidation of alcohols and aldehydes or through the
reaction of a Grignard reagent with CO2, followed by acidification
– Reactions of carboxylic acids are dominated by their polar carboxyl group
and their acidity
– Reactions with strong bases produce carboxylate salts
– Less susceptible to nucleophilic attack due to delocalization of  bonding
over three atoms (O–C–O)
– Substitution of the –OH of a carboxylic acid produces derivative compounds
with different tendencies to participate in resonance with the CO functional
group
– Resonance structures have significant effects on the reactivity of carboxylic
acid derivatives, but their influence varies, being least important for halides
and most important for the nitrogen of amides
– Two important carboxylic acid derivatives are esters and amides
General Properties and Reactivity of
Ester Carboxylic Acid Derivatives
– Have the general formula RCO2R´, where R and R´ can be any alkyl or aryl group
– Prepared by the reaction of an alcohol (R´OH) with a carboxylic acid (RCO2H) in
the presence of a catalytic amount of strong acid (an electrophile); this protonates
the doubly bonded oxygen atom of the carboxylic acid (a nucleophile) to give a
species that is more electrophilic than the parent carboxylic acid
– The nucleophilic oxygen atom of the alcohol attacks the electrophilic carbon
atom of the carboxylic acid and a new C–O bond is formed
– General overall reaction
OH+
O
R–C
+ R´OH  R–C
+ H2O
OH
OR´
– If an ester is heated with water in the presence of a strong acid or base, the reverse
reaction will occur, producing the parent alcohol, R´OH, and either the carboxylic
acid, RCO2H (under acidic conditions), or the carboxylate anion, RCO2– (under basic
conditions)
General Properties and Reactivity of
Amide Carboxylic Acid Derivatives
– The two substituents on the amide nitrogen can be hydrogen
atoms, alkyl groups, aryl groups, or any combination of two of
those species
O
R1–C–N–R2
R3
– Are prepared by the nucleophilic reaction of amines with other,
more electrophilic carboxylic acid derivatives, such as esters
– Are unreactive because of  bonding interactions between the
lone pair of electrons on nitrogen and the carbonyl group,
which inhibits free rotation about the C–N bond
– Stability of amide bond is important in biology because they
form the backbones of peptides and proteins
When compounds contain more than one functional group, the order of precedence determines
which groups are named with prefix or suffix forms. The highest precedence group takes the
suffix, with all others taking the prefix form. However, double and triple bonds only take suffix
form (-en and -yn) and are used with other suffixes.
Functional group
Formula
Prefix
Suffix
1
Cations
e.g. Ammonium
–NH4+
-onioammonio-
-onium
-ammonium
2
Carboxylic acids
–COOH
carboxy-
-oic acid*
3
Carboxylic acid derivatives
Esters
Acyl chlorides
Amides
–COOR
–COCl
–CONH2
R-oxycarbonylchloroformylcarbamoyl-
-oyl chloride*
-amide*
4
Nitrites
Isocyanides
–CN
–NC
cyanoisocyano-
-nitrile*
isocyanide
5
Aldehydes
Thioaldehydes
–CHO
–CHS
formylthioformyl-
-al*
-thial*
6
Ketones
Thioketones
>CO
>CS
oxothiono-
-one
-thione
7
Alcohols
Thiols
–OH
–SH
hydroxysulfanyl-
-ol
-thiol
8
Amines
–NH2
amino-
-amine
9
Ethers
Thioethers
–O–
–S–
-oxy-thio-
Priority
Isomerism
• Isomers have identical composition but different structures
• Three forms of isomerism
– Conformational
– Constitutional (or structural)
– Stereoisomerism
• Conformational
– Differences in three-dimensional structure resulting from rotation about a  bond
are called differences in conformation, and each different arrangement is called a
conformational isomer
• Constitutional
– Same empirical formula but different atom-to-atom connections
• Stereoisomerism
– Same atom-to-atom connections but different arrangement in space.
• Geometric - Geometric isomers can occur when there is a C=C double bond.
• Optical - Optical isomers are molecules with non-superimposable mirror
images. Such molecules are called CHIRAL. Pairs of chiral molecules are
enantiomers. Chiral molecules in solution can rotate the plane of plane
polarized light.
Conformational Isomers
• Differences between the conformations are depicted in drawings
called Newman projections
– A Newman projection represents the view along a C–C bond axis, with the carbon that
is in front shown as a point and the carbon that is bonded to it shown as a circle; the C–
H bonds to each carbon positioned at 120º from each other; the hydrogen atoms nearest
the viewer are shown bonded to the front carbon, and the hydrogen atoms farthest from
the viewer are shown bonded to the circle
– In one extreme, the eclipsed conformation, the C–H bonds on adjacent carbon atoms are
parallel and lie in the same plane
– In the other extreme, the staggered conformation, the hydrogen atoms are positioned as far
from one another as possible; the staggered conformation is the most stable because
electrostatic repulsion between the hydrogen atoms on adjacent carbons is minimized
Conformational Isomers
• Newman projections are useful for predicting the stability of
conformational isomers
– The eclipsed conformation is higher in energy than the staggered
conformation because of electrostatic repulsions between hydrogen atoms
– The staggered conformation is the most stable because electrostatic repulsion
between the hydrogen atoms on adjacent carbons is minimized
– Longer-chain alkanes can also be represented by Newman projections and
rotation can occur about each C–C bond in the molecule; Newman projections
are useful for revealing steric barriers to rotation at a particular C–C bond due to
the presence of bulky substituents
Structural (Constitutional) Isomers
In the conversion of one
constitutional isomer to another,
at least one bond must be
broken and reformed at a
different position in the
molecule
Stereoisomers: Geometric
Geometric isomers can only occur when there is a C=C double bond.
Geometric isomers differ in the relative placement of substituents in a
rigid molecule; members of an isomeric pair are either cis or trans,
with interconversion between the two forms requiring breaking and
reforming one or more bonds; their structural differences causes them
to have different physical and chemical properties and to exist as two
distinct chemical compounds
Cis-2-butene
Trans-2-butene
Stereoisomers: Optical
Lactic acid
• Optical isomers are molecules with
non-superimposable mirror images.
• Such molecules are called CHIRAL
• An achiral object is one that can be
superimposed on its mirror image
• Pairs of chiral molecules are enantiomers.
• Chiral molecules in solution can rotate the
plane of plane polarized light
• Optical isomers have identical physical
properties, although their chemical properties
may differ
• A chiral solution that contains equal
concentrations of a pair of enantiomers is
called a racemic mixture, where the rotations
cancel one another and the solution is
optically inactive
• Chirality generally occurs when a C atom has 4 different
groups attached.
Chirality: Handedness in Nature
These molecules are non-superimposable mirror images.
Stereoisomers
Stereoisomers
• Interactions of enantiomers with other chiral molecules
– In living organisms, every molecule with a stereocenter is found as a
single enantiomer, not a racemic mixture
– At the molecular level, our bodies are chiral and interact differently with
the individual enantiomers of a particular compound
– Only one enantiomer of a chiral substance interacts with a particular
receptor, initiating a response; the other enantiomer may not bind at all,
or it may bind to another receptor, producing a different response
The Molecules of Life
• All the functional groups described are found in the organic
molecules that constitute and maintain every living organism on
Earth
• Most organic molecules that are chiral have at least one carbon
atom that is bonded to four different groups
– This carbon is designated by an asterisk in structural drawings and is
called a chiral center, chiral carbon atom, asymmetric carbon atom, stereogenic
center, or stereocenter
• The most abundant substances found in living systems belong to
four major classes:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
Carbohydrates
Carbohydrates (also referred to as glycans)
have the basic composition:
Monosaccharides - simple sugars, with multiple hydroxyl groups.
Based on the number of carbons (e.g., 3, 4, 5, or 6) a monosaccharide is a triose,
tetrose, pentose, or hexose, etc.
Disaccharides - two monosaccharides covalently linked
Oligosaccharides - a few monosaccharides covalently linked.
Polysaccharides - polymers consisting of chains of monosaccharide or
disaccharide units (starches and cellulose)
Aldoses (e.g., glucose) have an aldehyde
at one end.
Ketoses (e.g., fructose) have a keto
group, usually at C #2.
Carbohydrates
Nomenclature for stereoisomers: D and L
designations are based on the configuration about the
single asymmetric carbon in glyceraldehyde.
For sugars with more than one chiral center, the D or
L designation refers to the asymmetric carbon
farthest from the aldehyde or keto group.
Most naturally occurring sugars are D isomers.
D & L sugars are mirror images of one another.
They have the same name. For example, D-glucose
and L-glucose are shown at right.
Carbohydrates
• Carbohydrates are the most abundant of the organic compounds found in nature;
they constitute a substantial portion of food consumed to provide energy.
• Carbohydrates are polyhydric aldehydes or polyhydric ketones
– The simplest carbohydrates consist of unbranched chains of three to eight
carbon atoms; one carbon is a carbonyl carbon and the others are bonded to
hydroxyl groups
– The structure of a carbohydrate can be drawn either as a hydrocarbon chain,
known as a Fisher projection, or as a ring, or cyclic form, called a Haworth
projection
– The two cyclic forms in a Haworth projection are called anomers
Haworth projections
represent the cyclic
sugars as having
essentially planar rings,
with the OH at the
anomeric C1 extending
either:
•below the ring ()
•above the ring ().
Sucrose and Ribose
H OH
HO
HO
HO
H
OH
O
H
OH
O
HO
H
H
H
CH2OH
-D-Glucose
H
HO
O
OH
Fructose
H
OH
H
H
H
Deoxyribose, the
sugar in the
DNA backbone.
H
CH2 OH
Sucrose, common table sugar, has a glycosidic bond linking the anomeric hydroxyls of
glucose and fructose. Because the configuration at the anomeric carbon of glucose is 
(O points down from the ring), the linkage is designated (12). The full name is -Dglucopyranosyl-(12)-D- fructopyranose.
Sugars: Related to Alcohols
• Sugars are carbohydrates, compounds with the formula Cx(H2O)y.
CHO
H OH
4
HO
HO
5
3
H
H
OH
2
H
3
H
OH
4
H
OH
5
H
HO
2
HO
1
OH
OH
-D-glucose
H
1
CH2OH
H OH
4
HO
HO
5
HO
1
3
H
H
2
OH
H
OH
-D-glucose
Open chain form
What is the difference between  and  D-glucose?
Glycosidic bonds: The anomeric hydroxyl group (axial) and a hydroxyl
group of another sugar or some other compound can join together, splitting
out water in a condensation reaction to form a glycosidic bond.
R-OH + HO-R' --> R-O-R' + H2O
Lipids
•
Characterized by their insolubility in water
– Form a family of compounds that includes fats, waxes, vitamins, and steroids
– Fatty acids are the simplest lipids and have a long hydrocarbon chain that ends with a
carboxylic acid functional group
1. Saturated fatty acids — the hydrocarbon chains contain only C–C single bonds that
stack in a regular array
2. Unsaturated fatty acids — have a single double bond in the hydrocarbon chain
(monounsaturated) or more than one double bond (polyunsaturated); double bonds give
fatty acid chains a kinked structure, which prevents the molecules from packing tightly
•
Unsaturated fatty acids
– Melting point lower than that of a saturated fatty acid of comparable molecular mass
– Double bonds can be hydrogenated in an addition reaction that produces a saturated fatty
acid or oxidized to produce an aldehyde or carboxylic acid
– Are the starting compounds for the biosynthesis of prostaglandins, hormonelike
substances
• Waxes are esters produced by nucleophilic attack of an alcohol on the carbonyl carbon of a longchain carboxylic acid
• Triacylglycerols are esters that are used by the body to store fats and oils and are formed from one
molecule of glycerol and three fatty acid molecules
• Steroids are lipids whose structure is made up of three cyclohexane rings and one cyclopentane
ring fused together; presence of various substituents on the basic steroid ring structure produces a
family of steroid compounds with different biological activity
– Cholesterol is a steroid found in cellular membranes and is the starting point for the
biosynthesis of steroid hormones, including testosterone, the primary male sex hormone,
and progesterone, which helps maintain pregnancy
Fats and Oils
H2 C
HC
H2 C
O
O CR
O
O CR
O
O CR
What is the
functional group in a
fat or oil?
R = organic group
with NO C=C bonds
C12 = Lauric acid
C16 = Palmitic acid
C18 = Stearic acid
R = organic group
with C=C bonds
C18 = oleic acid
H2 C
HC
H2 C
O
O CR
O
O CR
O
O CR
Fats and Oils
Fats with C=C bonds are usually LIQUDS
Oleic acid: a
monounsaturated
fatty acid
C=C bond
Trans Fatty Acids
•Oleic acid is a mono–unsaturated cisfatty acid
•Trans fatty acids have deleterious health
effects.
•Trans fatty acids raise plasma LDL
cholesterol and lower HDL levels.
C=C bond
Proteins
• Proteins are biologically active polymers formed from amino
acids linked together by amide bonds; in addition to an amine
group and a carboxylic acid group, each amino acid contains a
characteristic R group
– The nature of the R group determines the particular chemical properties
of each amino acid
• All the amino acids found in proteins are chiral compounds
except glycine, which suggests that their interactions with other
chiral compounds are selective
• Some proteins are enzymes that catalyze biological reactions
Alpha-Amino Acids
H2N
H
O
C
C
OH
R
Amine
H
Alanine
H3C
C
Chiral -carbon
NH3
CO2
Acid
Peptides and Proteins
O
H 3N
OŠH CH3
Alanine
HOCH 2
H 3N
+
H
OŠ-
O
Serine
peptide bond
– H2O
H
HOCH2
H
H 3N
O
N
H
O
O
Š
CH3
Adding more peptide links ---> PROTEIN
Nucleic Acids
• Nucleic acids are the basic structural components of DNA and
RNA, the biochemical substances found in the nuclei of cells
that transmit the information needed to direct cellular growth
and reproduction
• Structures are derived from nitrogen-containing cyclic
compounds called pyrimidines and purines, which can hydrogenbond through the lone electron pair on nitrogen (in pyrimidine
and purine) or through the hydrogen of the amine (in purine)
• When a pyrimidine or purine is linked to a sugar by a bond called
a glycosidic bond, a nucleoside is formed; addition of a phosphoric
acid group to the sugar produces a nucleotide
Reactivity of Organic Molecules
• The reactivity of a molecule is affected by the degree of
substitution of the carbon bonded to a functional group; the
carbon is designated as primary, secondary, or tertiary
– Primary carbon is bonded to only one other carbon and a
functional group
– A secondary carbon is bonded to two other carbons and a
functional group
– A tertiary carbon is bonded to three other carbons and a
functional group
• Identifying the transient species formed in a chemical reaction,
some of which are charged, enables chemists to predict the
mechanism and products of the reaction
Reactive Intermediates
• When cleaving a C–H bond, the most common species formed is C+, called a
carbocation, which has only six valence electrons and is electron deficient
– A carbocation is an electrophile, a species that needs electrons to complete
its octet
– A tertiary carbocation is more stable than one that is primary because it
increases electron density at the carbocation
• Adding an electron to a free radical produces a carbanion, a negatively charged
carbon with eight valence electrons
– A carbanion is a nucleophile, an electron-rich species
– Carbanions are destabilized by groups that donate electrons, so a tertiary
carbanion is less stable than a primary one
Common Organic Reactions
• Five common types of organic reactions:
1. Substitution (SN1, SN2)– one atom or group of atoms in a substance is replaced by another
atom or group of atoms from another substance. A typical substitution reaction is the reaction
of hydroxide ion with methyl chloride (nucleophilic substitution reactions):
CH3Cl + OH–  CH3OH + Cl
2. Elimination (E1, E2) – in which adjacent atoms are removed, or “eliminated,” from a
molecule with the formation of a multiple bond and a small molecule are called elimination
reactions
A
B
CH2–CH2  CH2CH2 + A–B
3. Addition – the components of a species A–B are added to adjacent atoms across a carboncarbon multiple bond is called an addition reaction
HCl + CH2CH2  CH3CH2Cl
4. Free-radical reactions – the best known is the reaction of a saturated hydrocarbon with a
halogen:
CH3CH3 + Br2  CH3CH2Br + HBr
• Free radical reactions occur in three stages: initiation, propagation, and termination
–
–
–
At high temperature or in the presence of light, the weak Br–Br bond generates Br atoms
A bromine atom attacks ethane, producing a free radical, which reacts with a bromine molecule
combination of two bromine atoms, of two ethyl radicals, or of an ethyl and a bromine radical
5. Oxidation-reduction reactions – are common in organic chemistry and can be identified by:
–
–
–
An increase in either is an oxidation, whereas a decrease is a reduction
An increase in the number of hydrogens in a hydrocarbon is an indication of a reduction
In compounds with a carbon-nitrogen bond, the number of bonds between the C and N atoms
increases as the oxidation state of the carbon increases
Coordination Compounds
•
Transition metal complexes are important in biochemistry and is an active area of research.
1. Catalytic cofactors: Many reactions require trace elements as catalytic cofactors.
a) Zinc is required in over 200 reactions including synthesis of proteins, taste perception,
prostrate reproductive health, metabolizing alcohol, and protecting against copper and
heavy metal toxicity such as cadmium and lead. Zinc occurs in greater amounts than any
other trace mineral except iron.
b) Manganese is required to synthesize connective tissue and bones (collagen).
2. Oxidation/reduction: Some metal ions, particularly iron, copper, and manganese are involved
in the energy metabolism of cells. Iron is involved in the electron transport that ultimately converts
oxygen to water. Copper participates in electron transport as well as synthesis of nerve membranes
and formation of collagen.
3. Oxygen binding and transport: Oxygen is carried by the red cells of the blood from the lungs
bound to hemoglobin which contains iron at its active heme center. Oxygen is released to the
tissues where it is picked up by a similar protein, myoglobin, before it accepts electrons and
protons to form water.
4. Metabolic regulation: Iron, copper and zinc can regulate the activities of protein and nucleic
acid synthesis. Proper immune response requires these trace elements.
5. Structural integrity: The three dimensional architecture of proteins and nucleic acids depends
upon zinc and manganese as well as iron and copper. These metals bind and hold large molecules
in active configurations. An example is the requirement of zinc for proper conformation of the
taste- bud proteins in the tongue. Without zinc, taste and smell are lost. Iodide is incorporated into
the amino acids which synthesize thyroid hormones.
Important Terms
• A ligand is a Lewis base that coordinates to a central metal atom or ion.
• A donor atom is the atom in a ligand that donate a lone pair of electrons
to form a coordinate covalent bond.
• A unidentate ligand is a ligand that can bind through only one atom.
• A polydentate ligand is a ligand that can bind through more than one
donor atom.
• There are known examples of bidentate, tridentate, quadridentate,
quinquedentate, and sexidentate ligands.
• Chelate complexes are complexes that have a metal atom or ion and
polydentate ligand(s) that form rings.
• The coordination number is the number of donor atoms coordinated to
a metal atom or ion.
• A coordination sphere includes the metal atom or ion and the ligands
coordinated to it. The coordination sphere does not include
uncoordinated counter ions.
Important Terms
• For the complex compound K3[Co(CN)6] the coordination number is
_________, and the coordination sphere is _______.
Nomenclature
1.
2.
3.
4.
5.
6.
7.
Rules for Naming Complex Species
Cations (+ ions) are named before anions (- ions).
Coordinated ligands are named in alphabetical order.
–
Prefixes that specify the number of each kind of ligand (di = 2, tri = 3, tetra = 4, penta = 5, hexa = 6,
etc.) are not used in alphabetizing
–
Prefixes that are part of the name of the ligand, such as in diethylamine, are used to alphabetize the
ligands.
For complicated ligands, especially those that have a prefix such as di or tri as part of the ligand name,
these prefixes are used to specify the number of those ligands that are attached to the central atom.
–
bis = 2 tris = 3 tetrakis = 4 pentakis = 5 hexakis = 6
The names of most anionic ligands end in the suffix -o.
–
Examples of ligands ending in –o are:
•
Cl- chloro
S2- sulfido
O2- oxo
The names of most neutral ligands are unchanged when used in naming the complex.
–
There are several important exceptions to this rule including:
•
NH3 ammine
H2O aqua
The oxidation number of a metal that exhibits variable oxidation states is designated by a Roman numeral in
parentheses following the name of the complex ion or molecule.
If a complex is an anion, the suffix "ate" ends the name.
 No suffix is used in the case of a neutral or cationic complex.
 Usually, the English stem is used for a metal, but if this would make the name awkward, the Latin stem
is substituted. ferrate instead of ironate plumbate instead of leadate
Important Terms
Typical Simple Ligands
Ion/Molecule
Name
Name as a Ligand
NH3
ammonia
ammine
CO
carbon monoxide
carbonyl
Cl-
chloride
Chloro
CN-
cyanide
cyano
F-
fluoride
fluoro
OH-
hydroxide
hydroxo
NO
nitrogen monoxide
nitrosyl
NO2-
nitrite
nitro
PH3
phosphine
phosphine
Nomenclature
• Name the following compounds:
Na3[Fe(Cl)6]
[Ni(NH3)4(OH2)2](NO3)2
Nomenclature
• Write formulas for the following compounds:
potassium hexacyanochromate(III)
tris(ethylenediammine) cobalt(III) nitrate
Structures
• The structures of coordination compounds are controlled primarily by the
coordination number of the metal.
• Usually the structures can be predicted by VSEPR theory (Chapter 8).
– The geometries and hybridizations for common coordination numbers
are summarized in this table.
CN
Geometry
Hybridization
Example
2
Linear
sp
[Ag(NH3)2]+
4
Tetrahedral
sp3
[Cd(NH3)4]2+
4
square planar
sp2d
[Cu(OH2)4]2+
5
trigonal bipyramid
sp3d
Fe(CO)5
5
Square pyramidal
sp2d2
[Mn(Cl)5]3-
6
Octahedral
sp3d2
[Fe(CN)6]4-
Structures
• Sketch the shape of the hexacyanaochromate(III) ion.
Isomerism in Coordination
Compounds
•
Isomers . two or more forms of a compound having the same composition
• Structural isomers involve different atom to ligand bonding sequences.
– hydration isomers isomers
»
–
ionization isomer
»
–
coordination sphere
isomers
exchange ion between ligand and anion
coordination isomers
»
–
exchange water as ligand
and hydrate
denote an exchange of ligands between the coordination spheres of the
cation and anion.
linkage isomers
»
different ligands or different
attachment of ligands
• Stereoisomers (identical bonding)
• geometrical isomers
• optical isomers
Structural (Constitutional) Isomers
• Hydrate isomers are a special case of ionization isomers in which water
molecules may be changed from inside to outside the coordination sphere.
• For example:
– [Cr(OH2)6]Cl3 vs.
.
– [Cr(OH2)5Cl]Cl2 H2O vs.
.
– [Cr(OH2)4Cl2]Cl2 2H2O
• Note whether the water molecule(s) are inside or outside the coordination sphere.
[Cr(OH2)6]Cl3
[Cr(OH2)5Cl]Cl2. H2O
[Cr(OH2)5Cl]Cl2. H2O
[Cr(OH2)4Cl2]Cl2. 2H2O
Structural (Constitutional) Isomers
Ionization (Ion-Ion )Exchange Isomers
[Pt(NH3)4Cl2]Br2 compared to [Pt(NH3)4Br2]Cl2
Note where the Cl’s and Br’s are in the structures, that is what makes these
two species isomers.
• [Pt(NH3)4Cl2]Br2
[Pt(NH3)4Br2]Cl2
Structural (Constitutional) Isomers
• Coordination isomers denote an exchange of ligands between the
coordination spheres of the cation and anion.
• For example look at these two isomers:
[Pt(NH3)4][PtCl6] vs [Pt(NH3)4Cl2][PtCl4]
• The isomeric distinction is whether the ligands are on the cation or the anion.
Structural (Constitutional) Isomers
• Linkage isomerism if a ligand contains more than one atom with a free
electron pair, the ligand may be bound to the central atom via the different atoms.
N
O
C
S C
O
bonding via N
bonding via O
nitronitrito-
N
bonding via C
bonding via N
cyanoisocyano-
bonding via S
bonding via N
thiocyanatoisothiocyanato-
N
[Co(NH3)5ONO]Cl2
[Co(NH3)5NO2]Cl2
Stereoisomers
• Stereoisomers are isomers that have different spatial
arrangements of the atoms relative to the central atom.
• Complexes with only simple ligands can occur as stereoisomers
only if they have coordination numbers equal to or greater than
four.
• Geometrical or positional isomers are stereoisomers that
are not optical isomers.
• Cis-trans isomers have the same kind of ligand either adjacent to each other
(cis) or on the opposite side of the central metal atom from each other
(trans).
• Note where the ligands are positioned relative to the central atom.
• Other types of isomerism can occur in octahedral complexes. Complexes
of the type [MA2B2C2] can occur in several geometric isomeric forms:
trans- trans- transcis- cis- ciscis- cis- trans-
Stereoisomers - Geometric
cis- [Pt(NH3)2Cl2]
trans-[Pt(NH3)2Cl2]
Stereoisomers
trans-diammine-trans-diaqua-trans-dichlorocobalt(III) ion
cis-diammine-cis-diaqua-cis-dichlorocobalt(III) ion
Stereoisomers
trans-diammine-cis-diaqua-cis-dichlorocobalt(III) ion
cis-diammine-cis-diaqua-trans-dichlorocobalt(III) ions
Stereoisomers
cis-diammine-trans-diaqua-cis-dichlorocobalt(III) ions
Stereoisomers
• Octahedral complexes can exhibit another type of geometric isomerism
- mer-fac isomerism.
•mer isomerism involves all three similar ligand lying in the same plane, or
meridianl like a globe.
•fac facial involves a grouping of three similar ligands that are arranged on a
triangular face of the octrahedron
fac and mer-Co(NH3)3Cl3
Stereoisomers
• Optical isomers are mirror images of each other that are not
superimposable.
• The cis-diammine-cis-diaqua-cis-dichlorocobalt(III) ion has two different
forms called optical isomers or enantiomers.
• Separate equimolar solutions of the two isomers rotate plane polarized light
by equal angles but in opposite directions.
– The phenomenon of rotation of polarized light is called optical
activity.
Stereoisomers
• These are the optical isomers of:
cis-diammine-cis-diaqua-cis-dichlorocobalt(III) ion