Chemical Biology Lecture
numbers of neutrons, thus giving them
ORGANIC CHEMISTRY
 Organic chemistry is the subject
dedicated to the study of a deceptively
simple set of molecules those based on
carbon.
 Because carbon is central to the
chemistry of life—and serves as the
structural basis for materials of
incredible strength, fuels with
tremendous amounts of stored chemical
energy, and life-saving medicines—we
have honored it with something no other
element has: its own branch of
chemistry, called organic chemistry.
THE STRUCTURE OF ATOM
 Niels Bohr is famous for many
accomplishments but most notably for
his model of the atom.
 Atoms are comprised of three types of
subatomic particles: positively charged
protons, uncharged neutrons, and
negatively charged electrons.
 Positively charged core of protons and
neutrons called the nucleus is orbited by
a cloud of small, fast-moving,
negatively charged electrons. Each of
these three particles plays a role in the
properties of any given atom.
 Protons provide the atom with its
identity. For example, a nucleus with six
protons means carbon.
 Regardless of the number of other
subatomic particles in the structure, a
nucleus containing six protons is always
carbon.
 Neutrons add mass to an atom but do not
alter its identity. For example, a carbon
atom may have six neutrons, as in
carbon 12; seven neutrons, as in carbon
13; or eight neutrons, as in carbon 14.
When atoms have the same number of
protons—meaning that they are the
same element— but have differing
different atomic mass, we refer to them
as isotopes of one another.
 Electrons most directly affect the charge
of an atom. In order for an atom to be
neutral, it must have the same number of
electrons and protons. When the number
of electrons in the electron cloud is not
equal to the number of protons in the
nucleus, a charged species result. We
call these charged species ions.
 If the electrons outnumber protons, the
atoms take on a net negative charge and
becomes what we call an anion. If
instead, protons outnumber electrons, a
cation is formed. As the discrepancy in
the population of electrons and protons
grows, so does the charge on the ion.
For example, a carbon atom with seven
electrons in its cloud would have a net
charge of – 1.
PRINCIPAL ENERGY LEVELS
 If we limit to neutral atoms, the addition
of electrons must match the rate at
which we add protons, each of the first
three rows of the periodic table
represents the filling of different energy
levels by electrons.
 Because energy levels fill from lower
energy to higher, only the highest
energy level in any atom can be unfilled.
We call this outermost energy level the
valence shell.
 By adding protons and neutrons to
hypothetical atom, one pair at a time.
The first pair gives us hydrogen atom.
The first energy level will be the valence
shell for this atom. Currently, it has one
electron in its first energy level.
 Addition of second pair takes us to
helium, which has two electrons in its
first energy level. So, the first level is
still the valence shell.
THE OCTET RULE
 The octet rule is a chemical rule of
thumb that reflects the theory that main-
group elements tend to bond in such a
way that each atom has eight electrons
in its valence shell, giving it the same
electronic configuration as a noble gas.
The noble gasses are the only atoms
with eight valence electrons and
therefore tend not to react or bond with
other atoms and molecules. This lack of
reaction is because they are already at
their most stable state with a full octet of
electrons.
 Hence why other atoms with a full octet
are referred to as in ‘noble-gas
configuration’. The electron
configuration of neon, a noble gas. Neon
has a full octet of eight valence electrons
and therefore tends not to bond with
other atoms.
 The filled valence octet means that the s
and p-orbitals are filled. Therefore, the
electron configuration ends with s2p6
for all atoms with a full octet.
 The octet rule can be obtained through
either ionic or covalent bonds. In
covalent bonds, atoms share electrons.
In ionic bonds, atoms transfer electrons
between each other.
 Generally, metals will lose electrons to
achieve a valence shell of eight
electrons. Non-metals tend to gain
electrons to obtain eight electrons.
 Certain atoms tend to have a certain
number of bonds to meet the octet rule.
For example, carbon will almost always
have four bonds. Nitrogen will almost
always have three bonds plus a lone
pair.
 Oxygen normally has two bonds.
Fluorine normally has one. You should
notice a trend. As you move across the
row of the periodic table, the number of
bonds tends to decrease for those
elements (non-metals) that are
covalently bonding.
 This trend of decreasing the number of
bonds holds true for the rows below the
one discussed above. The further down
you move in the periodic table the more
exceptions to the octet rule there are.
EXCEPTIONS TO THE OCTET RULE
 Transition metals do not normally
follow the octet rule. Instead, because of
the d-block electrons, they can have
more electrons in the valence shell.
 Helium and hydrogen both do not follow
the octet rule, but instead have two
electrons in the valence shell to be
stable. This is because they do not have
p-orbitals, and just need the s2 orbital
filled.
 Lithium often will lose an electron to
have the same configuration as helium
(2 electrons).
 Some compounds disobey the octet rule.
For example, SF6 and XeF2 are two
commonly made gasses in labs. The
further down an atom is in the periodic
table, the more likely it is to not have
eight electrons in the valence shell and
still be stable.
COVALET AND IONIC BOND
 Two periodic trends are important to
understanding the physical and chemical
properties of organic compounds. They
are electronegativity and atomic radius.
 The electronegativity scale is an index
of the attraction of an atom for an
electron. It increases from left to right in
a period and from bottom to top in a
group of the periodic table.
 The order of electronegativities for the
three most common elements in organic
molecules, excluding hydrogen, is C <
N < O. Their electronegativity values
differ by 0.5 between neighboring
elements in this part of the second
 period. There is a more pronounced That is, each atom “owns” the bonding
difference between second and third electrons, so they count toward the total
period elements. of eight for each atom. With the
 Thus, fluorine and chlorine differ by exception of bonds to carbon and to
1.0, as do oxygen and sulfur. The order hydrogen, carbon forms polar covalent
of the electronegativity values of the bonds to other elements.
halogens is I < Br < Cl.  The degree of polarity depends on the
 There are two main classes of bonds. difference in the electronegativity values
Ionic bonds predominate in inorganic of the bonded atoms.
compounds, but covalent bonds are  The direction of the bond moment is
much more important in organic indicated by an arrow with a cross at the
chemistry. end opposite the arrow head. The
 When positive and negative ions symbols δ+ and δ− indicate the partially
combine to form an ionic compound, the positive and partially negative atoms of
charges of the cations and anions must the bonded atoms.
be balanced to give a neutral compound.
For ionic compounds, the cation is
named first and then the anion.
 Thus, ammonium sulfide contains
(NH4)2 and S2− . Two ammonium ions
are required to balance the charge of one
sulfide ion, so the formula of
ammonium sulfide is (NH4)2S.
 Parentheses enclose a polyatomic ion
when a formula unit contains two or
more of that ion, and the subscript is
placed outside the parentheses.
 A covalent bond forms when two nuclei
are simultaneously attracted to the same
pair of electrons. Carbon usually forms
covalent bonds to other elements.
 The stability of Lewis structures is
attributed to the octet rule that states that
second row elements tend to form
associations of atoms with eight
electrons (both shared and unshared) in
the valence shell of all atoms of the
molecule.
 One or more pairs of electrons can be
shared between carbon atoms. Single,
double, and triple bonds are linked one,
two, and three pairs of electrons,
respectively.
 In applying the octet rule, the bonding
electrons are counted twice.