Organic Chemistry
Atomic structure and bonding
Dr. Talal Ahmed Awad
Department of Chemistry
Atomic Structure and Orbitals
• Atoms are made up of protons, neutrons, and
electrons. Protons are positively charged and
are found together with (uncharged)
neutrons in the nucleus.
• Electrons, which have a negative charge that
is equal in magnitude to the positive charge
on the proton, occupy the space surrounding
the nucleus.
• Protons and neutrons have similar masses,
about 1800 times the mass of an electron.
• Almost all the atom’s mass is in the nucleus,
but it is the electrons that take part in
chemical bonding and reactions.
Atomic Structure and Orbitals
• Atoms with the same number of protons but different
numbers of neutrons are called isotopes.
• The most common kind of carbon atom has six protons and
six neutrons in its nucleus.
• Its mass number (the sum of the protons and neutrons) is 12,
and we write its symbol as 12C.
• About 1% of carbon atoms have seven neutrons; the mass
number is 13, written 13C.
• A very small fraction of carbon atoms have eight neutrons
and a mass number of 14. The 14C isotope is radioactive.
Electron Shells and Orbitals
• An element’s chemical properties are determined by the
number of protons and number of electrons around the
nucleus.
• The electrons form bonds and determine the structure of
the resulting molecules.
• Electrons show properties of both particles and waves; in
many ways, the electrons in atoms and molecules behave
more like waves than like particles.
• Electrons are found in orbitals.
• Orbitals are mathematical descriptions that chemists use to
explain and predict the properties of atoms and molecules.
• Atomic Orbital: is an allowed energy state for an electron,
with an associated probability function that defines the
distribution of electron density in space.
Electron Shells and Orbitals
• An atom has a dense, positively charged nucleus surrounded by
a cloud of electrons.
• The electron density is highest at the nucleus and drops off
exponentially with increasing distance from the nucleus in any
direction.
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Electron Shells and Orbitals
• Atomic orbitals are grouped into different “shells” at different
distances from the nucleus. Each shell is identified by a
principal quantum number n, with n = 1 for the lowest-
energy shell closest to the nucleus.
• As n increases, the shells are farther from the nucleus, are
higher in energy, and can hold more electrons.
• The first electron shell contains just the 1s orbital.
• All s orbitals are spherically symmetrical, meaning that they
are nondirectional.
• The electron density is only a function of the distance from
the nucleus.
• The second electron shell consists of the 2s and 2p orbitals.
• The 2s orbital is spherically symmetrical like the 1s orbital.
2s Orbital
The 2p Orbitals
• There are three 2p orbitals, oriented at right angles to each other.
• Each p orbital consists of two lobes.
• Each is labeled according to its orientation along the x, y, or z axis.
Chapter 1 8
Electronic Configurations
• The aufbau principle states to
fill the lowest energy orbitals
first.
• Hund’s rule states that when
there are two or more orbitals
of the same energy
(degenerate), electrons will go
into different orbitals rather
than pairing up in the same
orbital.
Chapter 1 9
Electronic Configurations of Atoms
• Valence electrons are electrons on the outermost shell of the atom.
Chapter 1 10
Bond Formation: The Octet Rule
• A filled shell of electrons is especially stable.
• Atoms transfer or share electrons in such a way as to attain a
filled shell of electrons.
• A filled shell of electrons is simply the electron configuration
of a noble gas, such as He, Ne, or Ar.
• This principle has come to be called the octet rule because a
filled shell implies eight valence electrons for the elements in
the second row of the periodic table.
Ionic Bonding
• There are two ways that atoms can interact to attain noble-
gas configurations.
• Sometimes atoms attain noble-gas configurations by
transferring electrons from one atom to another.
• For example, lithium has one electron more than the helium
configuration, and fluorine has one electron less than the
neon configuration.
• Lithium easily loses its valence electron, and fluorine easily
gains one:
• The resulting ions have opposite charges, and they attract
each other to form an ionic bond
Covalent Bonding
• Is the most common type of bonding in organic compounds.
• In which electrons are shared rather than transferred,
• Hydrogen, for example, needs a second electron to achieve
the noble-gas configuration of helium.
• If two hydrogen atoms come together and form a bond, they
“share” their two electrons, and each atom has two electrons
in its valence shell.
Bonding in H2, The Sigma (σ) Bond
• Electron density lies between the nuclei.
• A bond may be formed by s—s, p—p, s—p, or hybridized
orbital overlaps.
• The bonding (σ) molecular orbital (MO) is lower in energy
than the original atomic orbitals.
• The antibonding (σ*) MO is higher in energy than the atomic
orbitals.
s Bonding MO
Formation of a σ bonding
MO: When the 1s orbitals of
two hydrogen atoms overlap
in phase with each other,
they interact constructively
to form a bonding MO.
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s* Antibonding MO
Formation of a σ*
antibonding MO: When
two 1s orbitals overlap out
of phase, they interact
destructively to form an
antibonding MO.
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H2: s—s Overlap
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Cl2: p—p Overlap
• When two p orbitals overlap along the line between the
nuclei, a bonding orbital and an antibonding orbital result.
• Most of the electron density is centered along the line
between the nuclei.
• This linear overlap is another type of sigma bonding MO.
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s and p Orbital Overlap
• Overlap of an s orbital with a p orbital gives a σ
bonding MO and a σ* antibonding MO.
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Pi Bonding and Antibonding
The sideways overlap of two parallel p orbitals leads to a bonding MO and
a antibonding MO. A pi () bond is not as strong as most sigma bonds.
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Multiple Bonds
• A double bond (two pairs of
shared electrons) consists of a
sigma bond and a pi bond.
• A triple bond (three pairs of
shared electrons) consists of a
sigma bond and two pi bonds.
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