Chemistry 140A Winter 2014 (K.

Albizati)
What is Organic Chemistry and why is it important?
Old definition chemistry of compounds from living organisms
New definition chemistry of compounds which contain carbon
Nature has selected this element as the base element of life processes because it is able to form very strong covalent bonds to itself and to other
elements. This enables highly complicated compounds, chemical reactions and chemical reaction pathways. Our bodies are just walking bags of
chemicals inter-reacting which allow complex events, like locomotion, vision, speech and thought.
If you want to understand the field of medicine, you must understand Biochemistry and Molecular Biology. To understand Biochemistry and
Molecular Biology, you must have a firm understanding of Organic Chemistry.

Chapter 1 Structure and Bonding

Review Atoms
Most of the mass resides in the nucleus which contains protons and neutrons. The nucleus is surrounded by a cloud of electrons populating orbitals
which describe the probability of where an electron may be found. This cloud is about 2 in diameter which means atoms are about 2 in diameter.

A Molecule is made up of atoms held together by chemical bonds. Why do bonds form?
Two atoms will form a bond only if it is energetically favorable --- that is if energy is released when the bond is formed. Everything in life
tends toward lower energy states in the long run.
So, it makes sense that to break a chemical bond you must put energy into the system.
Two main causes of bonding are related to Coulombs Law:
Opposite charges attract (electrons to protons)
Like charges repel (protons repel protons but more importantly, electrons repel electrons)
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Chemistry 140A Winter 2014 (K. Albizati)

The Two Extremes of Chemical Bonding
Recall that atoms can be viewed as a positively charged nucleus surrounded by a negatively charged electron cloud

When two atoms that can favorably form a bond approach one another from a distance the energy starts to decrease due to the favorable
attraction of one nucleus to the other atoms electrons and vice versa. At some point an optimum distance is reached with respect to the energy
of the system, i.e., the low energy point. This attraction/repulsion follows a familiar curve.
\
Energy
Absorbed
0
Energy
Released

bond length
Interatomic distance

Chemistry 140A Winter 2014 (K. Albizati)

As 2 atoms approach one another from a long distance, attractive forces start to lower the energy of the system until the atoms get to an energetically
optimal distance. If they start to get any closer, the repulsive forces between the 2 nuclei starts to become significant and the energy starts to rise
quickly. The bottom of this energy well corresponds to the bond length. The energy content of the system is at a minimum, its most favorable
state.
The picture shown earlier is a diagram of a covalent bond one in which the electrons are shared equally between the two nuclei. At the other
extreme are ionic bonds total transfer of an electron from one nucleus to another.

So.we have 2 extremes of bonding:

Covalent bonding based on the sharing of electrons between 2 nuclei
Ionic bonding based on the electrostatic attraction of a + charge to a minus charge and formed by transfer of an electron from one nucleus to
another
You have encountered ionic bonds before, as exemplified by salts like NaCl.
Organic chemistry is dominated by covalent bonding, especially between 2 carbon atoms and between carbon and hydrogen. These types of bonds
have substantial covalent character
So..what determines
A. whether two atoms will readily form a bond and
B. which of the two modes (or where in the continuum) the two atoms will exhibit in their bonding?
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Chemistry 140A Winter 2014 (K. Albizati)

It is determined primarily by the atoms electron configuration and individual fundamental physical properties of the atoms themselves.

The Octet Rule

Look at ionic bonding first.
Review:
The elements of the periodic table are listed in order of increasing nuclear protons. In an uncharged element the # of e-s = # protons. Electrons
occupy energy levels (shells) with a fixed capacity (i.e., allowed population of e-s) corresponding to the rows in the Table. The first shell can take
2e-, the second can take 8 and the third can take 18. On the far right of the table are the Noble Gases. These are especially stable elements which
rarely take part in chemical reactions. Their outermost electron shell is filled, with 8 e-s (except for He). This is an especially stable electronic
configuration. When chemical reactions occur electrons are either transferred or shared such that the atoms involved in the new bond have an octet
of electrons around them. Electron dot structures are helpful in visualizing a chemical reaction:

+ . H

H:O:H

H .

Why does NaCl form an ionic bond and H2O forms a covalent bond? It has to do with fundamental physical properties of the individual atoms,
specifically the IONIZATION Potential (IP) and the ELECTRON AFFINITY (EA). These can be measured for every atom and one can calculate the
energetically most favorable bonding mode. However, there is a better way to predict and visualize what type of bonding will occur. First lets look
at covalent bonding a little deeper.

Chemistry 140A Winter 2014 (K. Albizati)

Methane
CH4 formed by combination of 4Hs bonded to a single carbon:

H
:

. H

H:C:H
:

H .

H
.
.
. .
C
.

.
H

Natural Gas is mostly methane.

Carbon and hydrogen tend to form covalent bonds.

Ethane

H H
. H

.
H

H:C:C:H

:
:

H
.
.
. .
C
.

:
:

H .

H
.
.
. .
C
.
.
H

H H

Carbon tends to form covalent bonds with itself.

Chemistry 140A Winter 2014 (K. Albizati)

Carbon can also form multiple bonds
Ethene

C::C

H
.
.
:C
.
.
H

H
.
.
C:
.
.
H

Each carbon is still surrounded by 8 electrons and there is a double bond between the carbons. This is also a covalent bond.
So.what atoms form covalent bonds and which ones form ionic bonds?
Well.using EAs and IPs you can calculate each kind of bond in each kind of molecule. Thats pretty boring. Or you can look at the periodic
table, knowing just one periodic trend in the Table.

Chemistry 140A Winter 2014 (K. Albizati)

ELECTRONEGATIVITY the tendency of an atom to hoard electrons or to donate electrons to other atoms. Recall that the general trends are
that electronegativity increases as you move from left to right and from bottom to top.
In quantitative terms, Table 1.2 shows relative EN values with F being the highest at a relative value of 4.0 with alkali metals at about 1. In general
An EN difference of about 0.3 or less indicates a purely covalent bond and a difference of >2 indicates a purely ionic bond.

However, qualitatively.
-

Fluorine is the most electronegative atom

The alkali metals are the least electronegative and are almost exclusively ionic bonders
Carbon and hydrogen are close in EN and almost always form covalent bonds
The main group elements almost always form covalent bonds to each other.

If the EN difference is between 0.3 and about 2 you have a POLAR COVALENT BOND. These are closer to covalent bonds than they are to ionic
bonds.
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Chemistry 140A Winter 2014 (K. Albizati)

Example:
The carbon to oxygen bond. Carbon has a relative EN of 2.6 while O has a relative EN of 3.4. This is a polar covalent bond with the greater electron
density on oxygen and the lesser electron density on carbon. The bond is POLAR. This can be indicated in the following way:

+ C:O
Other important examples of polar covalent bonds:
C-halogen

C-N

C-S

N-O

N-S

More on the octet rule

The octet rule does not always hold, especially with charged species
Consider.

:
H:O:H

:
H

Each hydrogen brings its electron to the covalent O-H bond which means oxygen has 5 of its 6 valence electrons. The oxygen is missing an
electron which means it has what charge? +1
Note however, that the oxygen is surrounded by 8 electrons. This one follows the octet rule and is a stable species. This is called the hydronium ion,
a very common molecular species which we will see a lot. Its important in acid-base chemistry and is generally written as H3O+.
Now look at

Chemistry 140A Winter 2014 (K. Albizati)

H

:
C:H

:
H

This species has 3 Hs bonded to a single carbon. Since each of the C-H bonds is covalent each H has its required 2 e-s around it which means the
carbon has only 3 of its 4 valence electrons. If 1 electron is missing from carbon what is the charge on the carbon atom? +1 This species is the
methyl carbocation (or methyl cation). We will study such species in detail.
How about..
H

neutral or charged?

O :: C: :O

neutral or charged?

H:N:H

:C:H

:
H:S:H

neutral or charged?

Neutral or charged?

:
:
:

H:N:H

H:C:C: O:H

:
:
:

H H

neutral or charged?

: N : : : N : neutral or charged?

: C : : : O : neutral or charged?

Electron dots are boring and take too long to draw, count and visualize. We use another notation.

H H

neutral or charged?

Chemistry 140A Winter 2014 (K. Albizati)

To better represent a covalent bond we replace the two electrons with a straight line to indicate a chemical bond.
So..
H

O :: C: :O

:
H

:
H

H:N:H

becomes

becomes

H H

:
:
:

H:C:C: O:H
:
:
:

H H

H:N:H

becomes

10

: N : : : N : becomes : N

N:

becomes

becomes

H:S:H

becomes

:
H: O:H

Chemistry 140A Winter 2014 (K. Albizati)

The 3-D Shapes of Molecules
We have seen that methane can be drawn a number of ways:

H :C:H
H

CH4

or

but what is it really shaped like? Flat? Or something else?

Fundamental principal of bonding and molecular topology: Molecules adopt shapes so as to minimize electron repulsion.
Consider BeF2

:
: F
Be

: F

Be

The most favorable electronic arrangement is a linear one. Bent is not quite as good.

Consider BCl3. How do you place the Cls so as to get them as far apart as possible?
:

: Cl

Cl

:
B

: Cl :
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Chemistry 140A Winter 2014 (K. Albizati)

A trigonal arrangement where the bonds point to the corners of a triangle is best. Flat or not?
What about methane?

H
H

Flat? Note the apparent 90 degree bond angles. The H atoms can be farther apart if you point the four bonds to the corners of a
tetrahedron. In this manner the bond angles are 109.5 degrees (greater than 90 and the electrons are as far apart as they can be. Note that this has 4
fold symmetry and that all four bonds are equivalent (same length, same bond strength). This has important implications later.
H

Look at some others

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Chemistry 140A Winter 2014 (K. Albizati)

Nitrogen..consider the ammonium cation

H
H

should be shaped like methane..and it is indeed tetrahedral

What about ammonia?

:

N
H

like BCl3? Nope. The electron pair is like a bond. So it is tetrahedral if you consider it like this. However if you just look at
the nuclei, it is trigonal but bent.

Water?

Same idea. 2 bonds and 2 electron pairs pointed approximately to the corners of a tetrahedron. But if you just look at the nuclei, it appears bent.

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Chemistry 140A Winter 2014 (K. Albizati)

What about CO2?

:
O

linear

How about this one?

O
H

The electrons are farthest apart in a trigonal planar arrangement

O
C
H

The bond angles are approximately 120 degrees.

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Chemistry 140A Winter 2014 (K. Albizati)

Quantum Theory of Bonding for Organic Compounds
So exactly how are electrons arranged around a nucleus?
The movement of an electron around a nucleus is described by a series of equations that approximate the characteristics of waves. The solutions to
these equations are called atomic orbitals and they are literally the probability of finding an electron in a certain region of space around a nucleus.
The shapes of orbitals depend on the energy level of the electron.
Consider the hydrogen atom
-

It has a single electron populating a 1s orbital

S-orbitals in general are spherically symmetric (i.e., they are shaped like spheres)

There is no node

Consider a carbon atom

-

It has a 1s orbital not involved in bonding

It has a 2s orbital which is spherically symmetric which contains a node; this is involved in bonding
o Node region of space where the probability of finding the electron is zero; corresponds to where the wave function has a value of 0.
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Chemistry 140A Winter 2014 (K. Albizati)

-

It has three 2p orbitals, also involved in bonding

o These resemble a figure 8 with + and lobes and are arrayed along the x,y and z axes with the nucleus at the o point.

Molecular orbitals (covalent bonds) are constructed from the overlap of atomic orbitals.

Consider the hydrogen molecule

The in-phase overlap of two 1s orbitals results in a bonding molecular orbital.
+

+
++

1s

1s

++

bonding MO

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Chemistry 140A Winter 2014 (K. Albizati)

And an out-of-phase overlap resulting in an antibonding molecular orbital

node

1s

1s
antibonding MO

In general, the combination of n atomic orbitals gives rise to n molecular orbitals.

An s-orbital can overlap with a p orbital

Two ps can overlap in space in 2 ways:

Overlap of one lobe of each orbital like this is called a sigma bond.

And.
Overlap of both lobes is called a pi bond

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Chemistry 140A Winter 2014 (K. Albizati)

Sosince the s orbital and the p orbitals look so different shape-wise and energy wise, how can all the bonds in methane be identical?
Shouldnt they be different?

Hybrid Orbitals
When atomic orbitals are combined to form molecular orbitals, a mathematical combination can take place to produce orbitals which have the
characteristics of the orbitals being combined but are neither one nor the other. This is called orbital hybridization and it is commonly invoked to
explain many types of covalent bonding.
Consider carbon it has a 2s and three 2p orbitals involved in bonding. These 4 atomic orbitals combine to form four equivalent hybrid orbitals
which have 25% s character and 75% p character. We call these sp3 hybrid orbitals
ANIMATION (See C7SP3 and C8 on laptop in V&S Animations Folder).
- sp3 orbital formation
- Methane formation
Non-bonding electron pairs can also take part in hybridization, such as in ammonia or water which are also sp3 hybridized.

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Chemistry 140A Winter 2014 (K. Albizati)

Pi bonds and hybridization
Consider ethene:

The sigma framework of carbon consists of three sp2 hybridized orbitals in a planar trigonal arrangement. These are bonded to the hydrogen
1s orbitals in a sigma bonding arrangement and in a sigma bond arrangement between the 2 Cs. The H-C-H and H-C-C bond angles are
about 120 degrees as expected.
There is also a pi bond (remember lobe to lobe overlap?) between two carbon 2P orbitals situated above and below the plane of the nuclei.
This kind of double bond between two carbons is called an olefin or a double bond or a pi bond and is a common functional group in
organic molecules. It represents a lot of electron density and this dominates its chemical reactivity. More on this later..

Carbon can also exhibit triple bonding

Ethyne

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Chemistry 140A Winter 2014 (K. Albizati)

-

The sigma framework of carbon consists of two sp-hybridized orbitals in a linear arrangement to minimize electron repulsion.
There is also a pi framework consisting of two pi bonds consisting of overlap of two pairs of carbon 2p orbitals at 90 degree angles to one
another.

To summarize
When carbon is bonded to:
4 other atoms sp3 hybridization
3 other atoms sp2 hybridization
2 other atoms sp hybridization

tetrahedral geometry (shape)

trigonal planar geometry
linear geometry

bond angles approx. 109 degrees

bond angles approx. 120 degrees
bond angles approx 180 degrees

Class quiz hybridization of each carbon? Geometry and bond angles?

O
H

C
C

H
C

H
H

N:

A handy table
# of Atoms Bonded
to a Carbon Atom

Hybridization of
that Carbon Atom

Geometry of that
Carbon Atom

4
3
2

sp3
sp2
sp

Tetrahedral
Trigonal planar
Linear

Bond Angles
Involving that
Carbon Atom
109
120
180

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Chemistry 140A Winter 2014 (K. Albizati)

Drawing Organic Molecules

Several types of drawings are used to represent organic molecules
No one uses electron dot structures
For the next few weeks I will use structures with the bonds drawn out.
We will slowly transition into condensed drawings and then into line structures
Examples:
Pentane major component of gasoline

CH3CH2CH2CH2CH3

Isopropyl alcohol (isopropanol) in lots of stuff

H

OH
OH
H

CH3 CHCH3

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Chemistry 140A Winter 2014 (K. Albizati)

Reading: Skip 1-5 (for now)

Problem Assignment: Skip 1-9, 1-10, 1-11, 1-12, 1-15, 1-18, 1-29, 1-30, 1-31, 1-32, 1-34, 1-47

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