1

Organic Chemistry

Organic molecules are the building blocks of living things all organic
molecules contain carbon (and hydrogen). Organic chemistry is the study of
the chemistry of carbon compounds. Friedhrich Whler
(Wikipedia)
Carbon-containing compounds were once considered organ compounds
available only from living organisms.

The synthesis of the simple organic compound urea in 1828 showed that
organic compounds can be prepared in the laboratory from non-living
material.

O%
heat% C%
H2N% NH2%
silver ammonium silver
isocyanate chloride chloride (used as a fertilizer)%

Today,'organic'natural'products'are'rou3nely'synthesized'in'the'laboratory.'''

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Examples of organic compounds used as drugs 2

Methotrexate, anticancer drug 5-Fluorouracil,

colon cancer drug

AZT, HIV drug Tamiflu, influenza drug Tetracycline, antibiotic

(anti-bacterial drug)
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Note that carbons are often represented as vertices or lines and their bonded 3
hydrogens are not shown.

C%

Methotrexate, anticancer drug

benzene

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Macromolecules studied in MBB 222: DNA, RNA 4

Nucleotides

nucleo0des%

RNA
(ribonucleic acid) DNA (deoxyribonucleic acid)
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Macromolecules studied in MBB 222: proteins 5

amino
acids

peptide

protein

polypeptide
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Textbook used for CHEM 281/282 6

Organic Chemistry,
6th Edition
Paula Yurkanis Bruice

An introduction to organic
compounds: nomenclature,
physical properties and
representation of structure

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Carbon: 2nd row of periodic table, near the middle of the row 7

increasing%electroposi0vity%

increasing%electronega0vity%
increasing%electroposi0vity% increasing%electronega0vity%
(give up e- more easily) (accept e- more easily)
hangs up to e-
Elements on the left side of the periodic table are more electropositive: they tend to give up electrons.
Elements on the right side of the periodic table are more electronegative: they tend to accept electrons.
Elements near the edges of the periodic table give up or accept electrons, becoming charged: these form
ionic bonds with each other because they have opposite charges. Eg. K+Fl- , Na+Cl-
Elements in the middle of the periodic table, like carbon, tend to share electrons, forming covalent bonds
with each other. Eg. CH4
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Chemical bonds: ionic vs. covalent bonds 8

electrons%are%shared%but%not%equally%

unpaired valence electrons

H%
Carbon has 4 valence or
bonding electrons it forms 4
covalent bonds with as many as
4 different atoms very versatile!
The capacity of carbon to form
covalent bonds in this fashion
C%%%+%4%H%%=%%H%%C%%H%
H%
makes it the central component
shared electrons
of all molecules that form living
covalent bond
organisms.
Each of the 4 covalent C-H bonds is made up of an e- pair,
with both C and H contributing one e-.
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
 9
Single (covalent) bonds in carbon: valence electrons and sp3 hybridization
Carbon has a total of six electrons distributed over 5 orbitals and 2 energy levels: two non-bonding electrons
fill its 1s orbital in the lowest energy level (not shown); 4 valence or bonding electrons are distributed in 4
orbitals in the second energy level: one in the 2s orbital and one in each of the 2px , 2py and 2pz orbitals. These
four orbitals are blended or hybridized to generate 4 sp3 orbitals of equal energy, each occupied by one
valence electron.

When carbon undergoes sp3 hybridization it adopts a tetrahedral

geometry due to repulsion of the 4 electrons.
An sp3 carbon forms 4 single bonds, each with one electron
from each of its sp3 orbitals, with orbitals from other atoms the
electrons are shared between the atoms.

Lecture topic 2: Organic chemistry overview Tetrahedral geometry: angle between the C-H bonds is 109.5 o
Sept. 8, 2017
Single (covalent) bonds in carbon: sp3 hybridization , eg. methane, CH3 10

The simplest organic compounds are hydrocarbons,

which are compounds of carbon and hydrogen only.
Methane is the simplest organic compound. It is the major
component of natural gas.
Methane is comprised of a single C atom covalently
bonded to 4 H atoms in a tetrahedral manner: each of the
4 C-H single bonds is identical; the angle between these
Note: each line between C and
bonds is 109.5o.
H in methane represents a
single bond or a pair of shared
C-H bonds are formed by overlap s" e- (one from each atom.
between the sp3 orbitals of C and sp3"
the s orbitals of the Hs. The single The shared orbitals produce a new
e- in each of these orbitals is sigma () orbital the covalent bond
shared between the two atoms. formed by the shared electrons is
sometimes called a bond.
4 sp3 orbitals

Tetrahedral geometry:
angle between the
C-H bonds is 109.5o

Methane, CH4, shown in different representations

Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Some simple hydrocarbons - alkanes 11

Lewis%structure%

Alkanes are hydrocarbons containing only single bonds. They have the general formula: CnH2n+2.
Note that both the C-H and C-C bonds are bonds. The C-C bonds are between sp3 orbitals.
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
More alkanes: hydrocarbons containing only single bonds. They have the 12
general formula: CnH2n+2.

The hydrocarbons listed here are aliphatic compounds, linear or cyclic hydrocarbons that are not
aromatic (i.e. do not contain an aromatic ring). Aliphatic hydrocarbons can also have double, triple bonds
(eg. ethene, ethyne) and can have other elements besides H bound to the carbon (eg. O, N, S, Cl).
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Carbon9carbon'double'bonds:'sp2$hybridiza3on' 13

(cf. 4 hybrid sp3 orbitals

for sp3 hybridization)

The p orbitals between

2 sp2 hybridized
carbons overlap,
forming a pi () bond.
The bond between
the sp2 orbitals makes a
second bond ! double
bond. These two bonds
sp2 orbitals have
are non-equivalent. trigonal geometry ethene%
Double line = double bond or 2 pairs of shaired e-.

Ethene, C2H4, shown in several representations.

Note the difference in C geometry (trigonal sp3 hybridization); ethene is flat.
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Carbon-carbon triple bonds: sp hybridization 14

Two p orbitals overlap between 2 sp hybridized carbons, forming 2 bonds. The bonds between the sp
orbitals makes a third bond ! triple bond.

Ethyne, C2H2, shown in several representations

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Note that rotation can occur across a single bond but not a double or a triple bond
15

ethane ethene ethyne

X' X'

bond bond

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Alkyl substituents 16

Removing a hydrogen from an alkane results in an alkyl group or substituent, which can bond
to other atoms/molecules/groups.

substituents

(from methane) (from ethane) (from propane) (from butane)

(from pentane) (from alkane)

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

 17
If'an'alkyl'group,'R9,'is'bonded'to'another'atom'or'func3onal'group:'
a hydroxyl, OH, the compound becomes an alcohol
an amine (amino) group, NH2, the compound becomes an amine
a halogen (F, Cl, Br or I), the compound becomes an alkyl halide
OR, where R is another alkyl group bound to an O, the compound becomes an ether

-OH, NH2, I and -OCH3 are examples of functional groups substituents that endow special
properties to a compound.

Some'common'names'are'derived'from'the'alkyl'group'plus'the'func3onal'group:''

note the O is part of

the functional group
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Valence shell electrons in C and other elements present in organic compounds 18

Lewis dot structures show valence shell electrons

H% C% N% O%
free (bonding) electrons
bonding pair (shared electrons
1 from each atom) lone e- pairs (non-bonding)

lone pair

Like carbon, nitrogen and oxygen have a 3-dimensional geometry

based on their orbitals. Thus, NH3 and H2O are better represented The lone pair electrons
as follows: give H2O and NH3 a
partial negative charge
NH3 %@%% H 2O %@%% (-) at one end as a
result there is a partial
positive charge (+) at the
%+%% %+% other end. This
asymmetric distribution of
bonds bonds
e- results in polarity.
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Polarity 19

In addition to the presence of lone pair electrons, polar molecules can have an asymmetric charge
distribution due to unequal sharing of bonding electrons. More electronegative atoms like oxygen will
have a greater share of the bonding electrons than more electropositive atoms like hydrogen, forming a
polar covalent bond. This, together with the two lone e- pairs on oxygen (not shown), results in part of
the molecule having a partial negative charge (-) or pole while another part of the molecule has a
partial positive charge (+) - such molecules are said to have a permanent dipole - allows for polar
interactions between molecules where the negative end of one molecule is attracted to the positive end
of another. Water molecules are polar and are thus attracted to each other by polar interactions.
The slight negative charge (-)
at the oxygen pole of one water
molecule is attracted to the
-% slight positive charge (+) at the
+% hydrogen pole of another water
molecule.
Note: the two lone electron
pairs on oxygen contribute to
the partial negative charge at
the - pole.

Non-polar molecules have a symmetric charge distribution for their

bonding electrons. When the bonded atoms are identical (eg. O2) or
of similar electronegativity, the molecules are non-polar.
- O-C and C-H atoms share electrons much more equally than O-H
because O/C and C/H electronegativities are more similar than O/H
- non-polar molecules are not attracted to each other because they O2 (dioxygen) non-polar
lack complementary partial charges
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
Polarity'represented'using'electrosta3c'poten3al'maps,'which'show'the'charge' 20

distribu3on'on'a'molecule'
non@polar% polar%
@%

+% @%

+% +%

H2O'

HF and H2O have charge polarity: they each have an asymmetrical charge distribution where one
end or pole of the molecule has a different partial charge than the other.
In contrast, H2 is non-polar: it has a symmetrical charge distribution.
Lecture topic 2: Organic chemistry overview Sept. 8, 2017
A polar bond has a dipole moment FYI''well'come'back'to'this'' 21

%%
A dipole moment (D or m) is a measure of the polarity of a bond (or molecule). It is the
product of the partial charges of the atoms (q) and the distance (x) between these
charges:
dipole%moment%(D)%=%%=%q%"%x"

The higher the dipole moment the more polar a molecule.

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Molecular dipole moment FYI' 22

The vector sum of the magnitude and the direction of the individual bond dipole determines
the overall dipole moment of a molecule.

O
H H

Note that in
addition to the
bonding electrons
the non-bonding
electrons also
contribute to the
dipole moment.

Lecture topic 2: Organic chemistry overview Sept. 8, 2017

Dipole'Moments'(D'or')' FYI' 23

a%measure%of%the%magnitude%of%a%
molecules%polarity% +% @%
% %=qx%
%%where%x%is%distance%separa0ng%
charges,%q%is%the%magnitude%of%
the%par0al%charge%dierence%
large%x%%large%D%
large%q%%large%D%
%is%a%vector%quan0ty%(is%
direc0onal)%%by%conven0on,%the%
arrow%is%drawn%from%the%par0al%
posi0ve%charge%to%the%par0al%
nega0ve%charge%(think%of%it%
poin0ng%to%the%atom%that%holds%
the%bonding%electrons%most%
0ghtly)%
Note%that%in%physics%the%dipole%
vector%points%in%the%opposite% (diglycine)

direc0on,%from%nega0ve%to%
posi0ve%charge.%
Lecture topic 2: Organic chemistry overview
The%larger%the%dipole%moment%the%more%polar%the%molecule.%
Sept. 8, 2017
Functional groups of simple organic compounds have specific properties and 24
reactivities based on their polarity, electronegativity etc. They are more reactive
than their alkyl substituents.

Alcohols the functional group is a hydroxyl, -OH Thiol the functional group is a
sulfhydryl, -SH
(also called a
thiol)

Acids the functional group is a carboxyl, COOH, comprised of a carbonyl group (a carbon
with a double-bond to an oxygen) bonded to a hydroxyl group via the carbon

carbonyl
COOH = carboxyl
COO- = carboxylate ion

(HCOOH)' (CH3COOH,'vinegar)'
HCOOH%%%%%%%%%%HCOO@%+%H+% CH3COOH%%%%%%%%%%CH3COO@%+%H+%
organic acids can give up a hydrogen, becoming negatively charged
Lecture topic 2: Organic chemistry overview Sept. 8, 2017