Download BioN02 Introduction to organic chemistry Summer 2014

Introduction to organic
chemistry
Dr. Mamoun Ahram
Nursing
Summer semester, 2015
Organic compounds
Organic chemistry the chemistry of carbon
compounds.
They consist of one or more elements covalently
bonded to carbon atoms
"Organic" means carbon-containing
Functional groups
The distinctive properties of organic molecules depend
on:
arrangement of carbon skeleton,
the presence of functional groups.
Functional groups: groups of atoms attached to carbon
skeleton, which have a characteristic structure and
chemical reactivity.
Or Aromatic
Anhydride
Hydrocarbons
Contain only carbon and hydrogen
Aromatic
Second group
Single bonds + a carbon bonded to an
electronegative atom
Third group
Contain C=O
Anhydride
Alkanes
They contain carbon and hydrogen only in single
bonds.
Examples: methane (CH4), ethane (CH3CH3),
propane (CH3CH2CH3)
Straight versus branched alkanes
Carbons can be connected in a row or in branches
Note that with more branching, physical properties are
different.
boiling point is lower
Note that different drawings can be used
Condensed structures do not show bonds
Isomers
Isomers are molecules that have same molecular
formula, but different structures
Constitutional isomers (also known as structural
ismers): isomers of different atom connectivity (note
boiling point)
Structural
Formulas for
C4H10O
Isomers
Conformations
Organic molecules have different conformations.
(three-dimensional arrangement of atoms)
This is because C-C bonds can rotate.
These are called geometric isomers (or stereoisomers).
Naming organic molecules
Prefix-parent-suffix
If two or more functional
groups, order ot priority:
Parents: number of
carbon molecules
1. Carboxylic acid
Prefix: where substituents 2. Aldehyde
are located (methyl, ethyl, 3. Ketone
etc.)
4. Alcohol
Suffix: family (alkane,
5. Amine
alcohol, ether, etc.)
6. Alkyne = alkene
7. Alkane
Number of carbon molecules
Example
pentane
2,2-dimethylpropane
2-methylbutane
“Common" names for simple alkanes
The iso structural unit consists of two methyl groups attached
to a common carbon (When this unit is present in an alkane or
alky group, the common name starts with the prefix iso)
Number of carbons attached
to branch point
D
D
Sec: secondary
Tert: tertiary
Classification of carbon atoms
“R” indicates a general abbreviation of any organic substituent
Naming an alkanes
Name the parent (look for longest hydrocarbon chain)
Number the carbon atoms (begin near the branch
point)
Identify and name the branch points
Write the name as a single name
Substituents
If there are substituents of the same kinds, identify their
positions, and then use the prefixes di-, tri-, tetra, etc. to
indicate how many are present.
If there are substituents of different kinds present, name them
in alphabetical order (e.g. ethyl before methyl)
Prefixes such as di-, tri-, tetra-, etc. are ignored when
alphabetizing
Cycloalkanes
Ring structures of alkanes
These have the general formula, CnH2n
Name the longest continuous carbon chain, with the
prefix “cyclo”
If it has a substituent attached to one of the carbons,
then this carbon is number 1
If two substituents are attached, then you start with
the one that has alphabetical priority.
Examples (practice at home)
What are they?
Alkenes are hydrocarbons that have carbon-carbon
double bond functional groups
Alkynes are hydrocarbons that have carbon-carbon
triple bond functional groups
They are said to be unsaturated
Alkanes are saturated
Formula and structure
Alkane R–CH2–CH2–R
CnH2n+2
This is the maximum H/C ratio for a given number of
carbon atoms
Alkene R–CH=CH–R CnH2n
Each double bond reduces the number of hydrogen
atoms by 2
Alkyne R–C≡C–R
CnH2n-2
Each triple bond reduces the number of hydrogen
atoms by 4
Naming alkenes and alkynes
The –ene or -yne suffix indicates an alkene or alkynes (cycloalkene or
cycloalkynes)
The longest chain chosen for the root name must include both carbon
atoms of the double bond
The root chain must be numbered from the end nearest a double (or
triple) bond carbon atom.
If the double (or triple) bond is in the center of the chain, the
nearest substituent is used to determine the end where numbering
starts
The smaller of the two numbers designating the carbon atoms of the
double bond is used as the double bond locator. If more than one double
bond is present the compound is named as a diene, triene or equivalent
prefix indicating the number of double bonds, and each double bond is
assigned a locator number
In cycloalkenes (or cycloalkynes) the double bond carbons are assigned
ring locations #1 and #2. Which of the two is #1 may be determined by
the nearest substituent rule
Examples
Examples
Cis vs. trans of 2-butene
In the cis isomer the methyl groups are on the same
side; whereas they are on opposite sides in the trans
isomer
Isomers that differ only in the spatial orientation of
their component atoms are called stereoisomers
Alkene polymers
Polymers are large molecules made from repetitive
units called monomers
Benzene
An aromatic cyclic hydrocarbon
Naming of benzene (1)
Molecule is named by attaching the name of the
substituent as a prefix to benzene
Naming of benzene (2)
The prefix ortho signifies a 1,2-disubstituted benzene ring
meta signifies 1,3-disubstitution
para signifies 1,4-disubstitution
The prefixes o, m, and p can be used when a substance is
named as a benzene derivative
Common aromatic compounds
Naming of benzene (3)
The benzene ring is named as a phenyl group when it is
a substituent
phenylethyne
What is an alcohol?
A hydrocarbon derivative in which one or more
hydrogens of a parent hydrocarbon have been
replaced by a hydroxyl or alcohol functional group, OH
Naming alcohol
Select the longest carbon chain containing the hydroxyl group.
Derive the parent name by replacing the -e ending of the
corresponding alkane with –ol.
Number the chain from the end nearer the hydroxyl group.
The position of the hydroxyl group(s) on the parent chain is(are)
indicated by placing the number(s)
Number substituents according to position on chain, listing the
substituents in alphabetical order
OH
OH
OH
t-butanol
2-pentanol
heptanol
Naming alcohols
If there is more than one hydroxyl group (-OH), the suffix is
expanded to include a prefix that indicates the number of
hydroxyl groups present (-anediol, -anetriol, etc.)
Numbering order of compounds with more
than one functional group
1.
2.
3.
4.
5.
6.
7.
Carboxylic acid
Aldehyde
Ketone
Alcohol
Amine
Alkyne = alkene
Alkane
Naming alcohols
The hydroxyl group takes precedence over alkyl groups and
halogen substituents, as well as double bonds, in the numbering
of the parent chain
Alcohols may also be classified as primary, 1º, secondary, 2º &
tertiary, 3º (carbons attached to the carbon with –OH)
Reactions of alcohols (1)
Dehydration
If OH is attached to a
secondary carbon,
the major product has
the greater number of
alkyl groups directly
attached to the
double-bond
carbons.
Reactions of alcohols (2)
Oxidation
The product depends on the class of alcohol, 1o, 2o or 3o
1o alcohol
2o alcohol
3o alcohol
What are phenols?
Derivatives of hydroxybenzene
2-bromophenol
2-chloro-5-methylphenol
2-chlorophenol (o-chlorophenol)
2-methylphenol
3-methylphenol
4-methylphenol
What are ethers?
Ethers are compounds having two alkyl or aryl groups bonded to
an oxygen atom, as in the formula R1–O–R2
Ethers contain a H-bond acceptor, O, but no H-bond donor
Dimethyl ether is soluble in water
Diethyl ether is miscible in water
Ethers with larger alkane groups are water insoluble
Diethyl ether is anesthetic
Naming ethers
The smaller, shorter
alkyl group
becomes the alkoxy
substituent. The
larger, longer alkyl
group side
becomes the alkane
base name.
Alkyl Group
Name
Alkoxy
Group
Name
CH3–
Methyl
CH3O–
Methoxy
CH3CH2–
Ethyl
CH3CH2O–
Ethoxy
(CH3)2CH–
Isopropyl
(CH3)2CHO–
Isopropoxy
(CH3)3C–
tert-Butyl
(CH3)3CO–
tert-Butoxy
C6H5–
Phenyl
C6H5O–
Phenoxy
What re they?
Sulfur analogs of alcohols
are called thiols or
mercaptans
Strong odor
Nomenclature
The parent is the longest chain that contains the -SH
group
change the suffix -e to -thiol
when -SH is a substituent, it is named as a sulfanyl
group
2-butene-1-thiol
SH
SH
1-Butaneth iol
2-Methyl-1-prop anethiol
(Butyl mercaptan)
(Isobutyl mercaptan)
OH
HS
2-Sulfanylethan ol
(2-Mercap toeth anol)
Naming alkyl halides
Thyroxine
What are amines?
Amines are derivatives of ammonia with alkyl groups
substituting for hydrogen atoms.
Amines are characterized by the number of R groups
bound to the nitrogen.
Naming amines
1o amines are given the family name of the alkyl group and
amine is added as a suffix:
CH3NH2 (a primary amine): methyl amine
Secondary and tertiary amines are named by alphabetizing the R groups and then adding amine
This is a 2o amine with two different R groups,
ethyl and methyl. This is ethylmethylamine.
This is a 3o amine. This is ethyldimethylamine
Naming amines
For amines with other functional groups, the amine is
considered a substituent amino group.
Naming amines
Secondary and tertiary amines with the same
substituents (symmetrical) are named as di- and trialkyl amines:
Naming secondary and tertiary amines
If the two groups are different, then they are named as
substituent amines with the parent molecules being the
largest
Secondary amines can be named by replacing the -e of the
parent group with the word amine and then using an upper
case N to designate that the second alkyl group is on the
nitrogen atom
N-methyl-1-propanamine
N,N-dimethylethanamine
Naming amines
Rings that contain atoms
other than carbons are called
heterocycles.
There are a number of
important heterocyclic
amines.
In each case the nitrogen is
assigned the number 1 in the
ring.
There are only a few common
names for amines
Properties of amines
Amines are polar
Primary and secondary amines have H-bond donors and
acceptors, so they are held together by H-bonds.
Tertiary amines have no H-bond donor, since they have three
alkyl groups on the nitrogen.
Basicity of amines
Amines are significantly more basic than water. They
produce hydroxide ion and ammonium ions when dissolved
in water.
In blood, amines exist as ammonium ions.
Amine salts
Reaction of an amine
with an acid produces
an alkylammonium
salt.
Salts of amines are
named by changing
“amine” to
“ammonium” and
adding the name of
the negative ion to the
end of the word.
Quaternary amines
Nitrogen can also have a fourth alkyl group attached.
When nitrogen is attached to four groups, it is called
amino cation.
This gives a positively-charged compound known as a
quaternary amine.
They will always carry a
positive charge, regardless
of the pH of the
surrounding solution.
Quaternary ammonium salts
Quaternary ammonium salts are salts of quaternary
ammonium cations with an anion.
Carbonyl groups
Aldehyde
Ketone
Carboxylic acid
Ester
Amide
-al
-one
-oic acid
-oate
-amide
What are they?
Belong to the carbonyl group (C=O)
Polar
The carbonyl carbon of aldehydes has at least one
hydrogen bonded to it
Ketones have two alkyl groups bonded to the carbonyl
carbon
Naming aldehydes and ketones
The longest C chain containing
the C=O is the parent
compound
The parent compound is given
the suffix "-al" for aldehyde or
"-one“ for ketone
C-1 is always the C=O carbon
in aldehydes. In ketones, C=O
carbon is lowest number
possible.
C=O has precedence over -OH
groups
When the aldehyde group is
attached to a ring it is named
as a -carbaldehyde
Properties
This group is polar
The carbonyl group has a H-bond acceptor but no H-bond
donor
This makes aldehydes and ketones slightly soluble in water
and having lower boiling point that alcohols
Low toxicity (ketones)-highly toxic (small aldehydes like
formaldehyde)
(R)
(R)
Reactions of aldehydes and ketones (1)
Oxidation
Both are synthesized from oxidation of alcohols
Aldehydes are oxidized to carboxylic acids
RCH=O + [O]  RC(OH)=O
Ketones do not get oxidized because they do not have
hydrogen
Reactions of aldehydes and ketones (2)
Reduction
Aldehydes and ketones are reduced to alcohols
Reactions of aldehydes and ketones (3)
Addition (conversion C=O to C-O)
forming hemiacetals (having both an –OH group and an
ether –OR group) and acetals (having two –OR groups)
Reversible reaction
Stability of hemiacetals
These are also generally unstable, but hemi-acetals can
be stabilized if they form a ring structure (e.g. glucose)
Addition of another alcohol forming acetal
What is carboxylic acid?
The active group of carboxylic acids is called a carboxyl
group
Properties of carboxylic acid
Both parts of the carboxyl group are polar
The C=O of carboxylic acids is highly polar, and is a hydrogen
bond acceptor
The O-H of the carboxyl group is also highly polar, and
contains a hydrogen bond donor, Hd+, as well as a hydrogen
bond acceptor, Od-
They have higher boiling
points than similar
alcohols, due to dimer
formation.
Naming carboxylic acids
The carboxyl group always occurs at the end of the
molecule, making it C1
Family name is longest chain containing the carboxyl group
Suffix is "-oic acid"
Carbonyl groups appearing in carboxylic acids are called
"oxo" and hydroxy groups are named "hydroxy“
Simple dicarboxylic acids have the general formula HO2C–
(CH2)n–CO2H (where n = 0 to 5) and end with “-dioic acid”
Examples
Formula
HCO2H
Common Name
formic acid
IUPAC Name
methanoic acid
CH3CO2H
acetic acid
ethanoic acid
CH3CH2CO2H
propionic acid
propanoic acid
CH3(CH2)2CO2H
CH3(CH2)3CO2H
CH3(CH2)4CO2H
butyric acid
valeric acid
caproic acid
butanoic acid
pentanoic acid
hexanoic acid
CH3(CH2)5CO2H
enanthic acid
heptanoic acid
CH3(CH2)6CO2H
caprylic acid
octanoic acid
CH3(CH2)7CO2H
pelargonic acid
nonanoic acid
CH3(CH2)8CO2H
capric acid
decanoic acid
Examples
Acidity of Carboxylic Acids
Carboxylic acids are weak acids
The name of the ionic form of carboxylic acids ends of
“-ate”
Salts of Carboxylic Acids
Carboxylic acids are neutralized by bases forming salts
O
CH3
C OH
NaOH
HCl
O
CH3
_
+
Na
C O
Important drugs are carboxylic acids
Aspirin (salicyclic acid)
Ibuprofen
Anesthetics (lidocaine and benzoncaine)
Reactions of carboxylic acids
Formation of esters (esterification) by substitution of
the hydroxyl Group with either the –OR of an alcohol
(reversible reaction)
Esters
In esters, the –OH group of the carboxyl end is
converted to –OR.
Naming esters
Esters are named with the alkyl group from the
alcohol, followed by the acid name changed to "oate”.
The group attached to (C=O) is the parent.
Hydrolysis of esters
Formation of carboxylic acid and an alcohol
Amides
Amides are derived from carboxylic acids
The -COOH group of carboxylic acid is replaced by an NH2 group
Naming amides
The name is derived from the acid
by replacing the "oic acid" ending
by "amide“
A common amide is ethanamide,
CH3CONH2 (acetamide)
The simplest amide is
methanamide (HCONH2)
If the chain is branched, the carbon
in the -CONH2 group counts as the
number 1 carbon atom.
Naming amides 2
Amides are classified as 1º, 2º or 3º, depending on the
number of alkyl groups bonded to the nitrogen
With N substituted amides the attachment to the
nitrogen must be indicated
CH3CONHCH3 is N-Methylacetamide
CH3CONH(CH2CH3)2 is N,N-Diethylacetamide
Examples
Properties of amides
The melting points of
unsubstituted amides are
high because they can
form hydrogen bonds.
Formation of amides
Formation of amides by substitution of the hydroxyl
Group with the NR2 of an amine
Hydrolysis of amides
Formation of carboxylic acid and an amine
Acetaminophen
It is an amide that also contains a hydroxyl group.
It reduces fever, but unlike aspirin, it is not an anti-inflammatory
agent and does not induce internal bleeding.
It is used in individuals prone to bleeding or recovering from
surgery or wounds.
Overdoses of acetaminophen can cause kidney and liver
damage.
Phosphoric acid
Phosphoric acid can form three ionized forms
Phosphoester
Alcohols react with phosphoric acid to produce a
phosphate ester, or phosphoester
Anhydride linkage
Two phosphorioc acids can form a phosphoric acid
anhydride called pyrophosphate or diphosphoric acid
A third phosphate can react with them forming a
triphosphoric acid
Diphosphate and triphosphate esters
Diphosphate and triphosphates can form esters
Hydrolysis of phosphate
Pyrophosphate and triphosphoric acids can be
hydrolyzed easily
This is just the reverse reaction of forming them
Phosphorylation
Phosphorylation is the transfer of phosphate from one molecule
to an alcohol group of another molecule.
This is an important reaction in biochemistry because and
energy-rich molecule is formed.
Hydrolysis of pyrophosphate and triphosphoric acids, releases
energy.