Atomic Structure

Milan Rambukwella, PhD

Development of the atomic theory and the
modern view of the atomic
structure

2
 3
https://slideplayer.com/slide/7477924/

https://en.wikiquote.org/wiki
400 B.C.
Democritus
➢ All matter consists of very
small, indivisible particles,
which he named “atomos”
➢ uncuttable or indivisible
1. Elements are composed of extremely small
particles, called atoms.
2. All atoms of a given element are identical,
having the same size, mass, and chemical
properties. The atoms of one element are
different from the atoms of all other
elements.
3. Compounds are composed of atoms of
more than one element. In any compound,
the ratio of the numbers of atoms of any
two of the elements present is either an
integer or a simple fraction.
https://en.wikipedia.org/wiki 4. A chemical reaction involves only the
Year 1808 separation, combination, or rearrangement
of atoms; it does not result in their creation
John Dalton or destruction.
Hydrogen atoms
Oxygen atom Water compound
4
 Aristotle
• He did not believe in atomic theory → (350 B.C.)
believed that all matter is made of four
things:
Earth
Fire
Water https://en.wikipedia.org/wiki

Air

• "the discovery of elements“

• Although he was wrong his idea persisted for

about 2000 years https://www.playbuzz.com/fionaw10/
5
 The law of conservation of mass
• “matter can be neither created nor destroyed”

Antoine Lavoisier
(1773)
4. A chemical reaction involves only the separation, combination, or
rearrangement of atoms; it does not result in their creation or
destruction.

https://en.wikipedia.org/wiki 6
Proust’s law of definite proportions
• “different samples of the same compound always contain its
constituent elements in the same proportion by mass”
Joseph Proust,
French chemist
(1799)
3. Compounds are composed of atoms of more than one element. In
any compound, the ratio of the numbers of atoms of any two of the
elements present is either an integer or a simple fraction.

https://en.wikipedia.org/wiki
7
General Chemistry, The Essential Concepts, Raymond Chang (2008)
 The law of multiple proportions

• “if two elements can combine to form more than one compound, the
masses of one element that combine with a fixed mass of the other
element are in ratios of small whole numbers.”

8
General Chemistry, The Essential Concepts, Raymond Chang (2008)
 9
https://slideplayer.com/slide/7477924/
The Electron - Cathode ray tube

J. J. Thomson
(1900)

10
• J.J. Thomson, determine the ratio of electric charge to the mass of an
individual electron. The number he came up with is; -1.76 x108 C/g
• R. A. Millikan, an American physicist, found the charge of an electron
to be -1.6022 x 10-19 C

𝑪𝒉𝒂𝒓𝒈𝒆
𝐦𝐚𝐬𝐬 𝐨𝐟 𝐚𝐧 𝐞𝐥𝐞𝐜𝐭𝐫𝐨𝐧 =
𝒄𝒉𝒂𝒓𝒈𝒆/𝒎𝒂𝒔𝒔

−1.6022 x 10−19 C
=
−1.76 x108 C/g

= 9.10x10-28 g

11
• J.J. Thomson “plum-pudding” model →Atoms,
contain electrons, they are electrically neutral.
• Ernest Rutherford → thin foils of gold and other
metals as targets for α particles → protons
• James Chadwick → thin sheet of beryllium with
α particles → neutrons

12
mass number = number of protons = number of neutrons
13
14
 Lewis Structure by Bond Determination

1. Covalent bonds are formed from sharing of electrons by two atoms.

2. The bedrock rule for writing Lewis structures for the first full row of
the periodic table is the octet rule for C, N, O and F: C, N, O and F
atoms are always surrounded by eight valence electrons.
3. For hydrogen atoms, the doublet rule is applied: H atoms are
surrounded by two valence electrons.

15
Write the Lewis structure for the carbonate ion
CO3 2-

16
• In forming compounds; atoms gain, lose, or share electrons to give a
stable electron configuration characterized by 8 valence electrons.
• The octet rule is the most useful in cases involving covalent bonds to
C, N, O, and F.
.. ..
: .. F:
F : ..

17
• Combine carbon (4 valence electrons) and
four fluorines (7 valence electrons each)
. ..
. C.
. F.
: ..

• to write a Lewis structure for CF4.

.. : F:
.. : ..F: .. .. ..
: ..F: C : F
.. : : ..
F C ..F:
..
: ..F:
: ..F:
• The octet rule is satisfied for carbon and
each fluorine.
18
 Double Bonds and Triple Bonds
.. .. .. ..
: O: : C : : O: :O C O:
Carbon dioxide

H : C : :: N: H C N:
Hydrogen cyanide

19
 H H
H
.. H ..
H: C : : C:H Ethylene C C
H H

H : C : :: C:H Acetylene H C C H

20
Step [1] Arrange the atoms next to each other that you think are bonded
together.
• Place H and halogens on the periphery, since they can only form one
bond.

H H
For CH4: H C H not H C H H
H

This H cannot form

two bonds.
21
• Use the common bonding patterns to arrange the atoms.

H H H
For CH5N: H C N H not H C N H
H H H

Place four atoms Place three atoms

around C, since C around N, since N
generally forms generally forms
four bonds. three bonds. 22
Step [2] Count the valence electrons.
• For main group elements, the number of valence
e− is equal to the group number.

• The sum gives the total number of e− that must be

used in the Lewis structure.

For CH3Cl: 1 C x 4e− = 4e−

3 H x 1e− = 3e−
1 Cl x 7e− = 7e−
14 total valence e−

23
Step [3] Arrange the electrons around the atoms.

• Place one bond (two e−) between every two atoms.

• For main group elements (s and p), give no more than 8 e−.

• For H, give no more than 2 e−.

• Use all remaining electrons to fill octets with lone

pairs, beginning with atoms on the periphery.

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For CH3Cl: H
4 bonds x 2e− = 8 e−
H C Cl
+ 3 lone pairs x 2e− = 6 e−
H
e−
2 on 8 e− 14 e−
each H on Cl All valence e− have
been used.

• If all valence electrons are used and an atom still

does not have an octet, proceed to Step [4].

[4] Use multiple bonds to fill octets when needed.

25
 Step [4] Use multiple bonds to fill octets when needed.

Add the bonds and lone pairs.

5 bonds x 2 e− = 10 e−
H C C H + 1 lone pair x 2 e− = 2 e−
H H 12 e−

C still does not All valence e− have

have an octet. been used.

26
 Formal Charges

• The electrical charge difference between the valence electrons in an

isolated atom and the number of electrons assigned to that atom in a
Lewis structure.

number of – number of – number of

Formal charge = - bonds unshared e -
valence e

27
 .. ..
O: O:
.. ..
H O
.. N H O N
..
: O: :O :
.. ..

.. .. ..
O: O: O:
.. .. ..
H O
.. N H O N H O
.. N
..
: O: : O: : O:
.. .. ..
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• Step 1:
The molecular formula and the connectivity are determined by
experiment.
Example:
Methyl nitrite has the molecular formula CH3NO2. All hydrogens are bonded to
carbon, and the order of atomic connections is CONO.

• Step 2:
Count the number of valence electrons. For a neutral molecule this is
equal to the number of valence electrons of the constituent atoms.
• Example (CH3NO2):
Each hydrogen contributes 1 valence electron. Each carbon contributes 4,
nitrogen 5, and each oxygen 6 for a total of 24.

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• Step 3:
Connect the atoms by a covalent bond represented by a dash.

Example:
Methyl nitrite has the partial structure:

H C O N O

H
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 H

H C O N O

H
• Step 4:
Subtract the number of electrons in bonds from the total number of
valence electrons.

Example:
24 valence electrons – 12 electrons in bonds. Therefore, 12 more electrons to
assign.

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• Step 5:
Add electrons in pairs so that as many atoms as possible have 8
electrons. Start with the most electronegative atom.

Example:
The remaining 12 electrons in methyl nitrite are added as 6 pairs.

H
.. ..
H C O N O :
.. .. ..
H
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• Step 6:
If an atom lacks an octet, use electron pairs on an adjacent atom to
form a double or triple bond.

Example:
All the atoms have octets in this Lewis structure.

H
.. ..
H C O
.. N
.. O:

H
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• Step 7:
Calculate formal charges.

Example:
None of the atoms possess a formal charge in this Lewis structure.

H
.. ..
H C O
.. N
.. O:

34
• Step 7:
Calculate formal charges.

Example:
This structure has formal charges; is less stable Lewis structure.

H
+ .. –
H C O N O
.. :
.. ..
H
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36
Periodic Trends in Behold!
s an p block Elements
The Pattern to the Periodic Chart

37
 Periodic Trends in s an p block Elements

• Trends we’ll be looking at:

1. Atomic Radius and Ionic Radius
2. Ionization Energy
3. Electronegativity
4. Reactivity
5. Metallic Character

38
Atomic radius: defined as ½ distance between
neighboring nuclei in molecule or crystal
• Group Trend – As you go down a column, atomic radius increases.
→As you go down, e- are filled into orbitals (energy levels) that are
farther away from the nucleus (attraction not as strong).
• Periodic Trend – As you go across a period (L to R), atomic radius
decreases.
→As you go L to R, e- are put into the same energy level, but more p+
and e- total (more attraction = smaller size).

39
40
 Ionic Radius; size of an atom when it is an ion.
• Metals – lose e-, which means more p+ than e- (more attraction)
SO…
Ionic Radius < Neutral Atomic Radius
• Nonmetals – gain e-, which means more e- than p+ (not as much
attraction) SO…
Ionic Radius > Neutral Atomic Radius
• Group Trend – As you go down a column, atomic radius increases.
• Periodic Trend – As you go across a period (L to R), atomic radius
decreases. 41
 Ionization Energy; energy needed to remove
outermost e-.

• Group Trend – As you go down a column, ionization energy

decreases.
→ As you go down, atomic size is increasing (less attraction), so easier
to remove an e-.
• Periodic Trend – As you go across a period (L to R), ionization energy
increases.
→ As you go L to R, atomic size is decreasing (more attraction), so more
difficult to remove an e-
(also, metals want to lose e-, but nonmetals do not).
42
43
 Electronegativity; ability of atom to attract
electrons in bond

• Noble gases tend not to form bonds, so don’t have

electronegativity values

• Unit = Pauling
• Fluorine: most electronegative element
• = 4.0 Paulings
44
 Electronegativity; ability of atom to attract
electrons in bond

• Group Trend – As you go down a column, electron affinity decreases.

→ As you go down, atomic size is increasing, so less attraction of
electrons to the nucleus.
• Periodic Trend – As you go across a period (L to R), electron affinity
increases.
→ As you go L to R, atomic size is decreasing, so the electrons are more
attracted to the nucleus.

45
 Reactivity; tendency of an atom to react.

• Metals – lose e- when they react, so metals’ reactivity is

based on lowest Ionization Energy (bottom/left corner)
• Low I.E = High Reactivity.
• Nonmetals – gain e- when they react, so nonmetals’
reactivity is based on high electronegativity (upper/right
corner).
• High electronegativity = High reactivity
46
 Metallic Character
• Properties of a Metal;
• Easy to shape (malleable); many are ductile (can be pulled into
wires)
• Conduct electricity and heat
• Shiny
• Group Trend – As you go down a column, metallic character
increases (because ionization energy decreases).
• Periodic Trend – As you go across a period (L to R), metallic
character decreases (because ionization energy decreases) (L to R,
you are going from metals to non-metals).
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48
 Resonance

• The term resonance itself means the use of two or more Lewis
structures to represent a particular molecule.
• Neither resonance structure adequately represents the actual
molecule, which has its own unique, stable structure.

49
Valence Shell Electron Pair Repulsion (VSEPR)
Theory
• Predicts the molecular shape of a bonded molecule.
• Electron pairs in the valence shell of an atom tend to orient
themselves so that the total energy is minimized.
• Electrons around the central atom arrange themselves as
far apart from each other as possible.
• Unshared pairs of electrons (lone pairs) on the central atom
repel the most.
• Greatest at 90o, much weaker at 120o, and very weak at
180o
50
 AXE notation

1) The central atom is called A.

2) All the outer atoms are designated with an X.

3) Any lone pair electrons are designated with an E.

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52
53
 Atomic Spectra
• Classical physics assumed that atoms and
molecules could emit/absorb any arbitrary amount of
radiant energy.
• Planck said that atoms and molecules could
emit/absorb energy only in discrete quantities, like
small packages/bundles.
• Planck gave the name quantum to the smallest
quantity of energy that can be emitted/absorbed in
the form of electromagnetic radiation.

54
 Atomic Spectra
E=hƲ
h is called Planck’s constant
Ʋ is the frequency of radiation
also, Ʋ = C / λ
According to quantum theory, energy is always emitted in integral
multiples of hƲ; for example, hƲ, 2 hƲ, 3 hƲ, . . . etc.

55
Atomic Spectra

56
 Bohr’s theory
• In 1913, Bohr developed a quantum model for the hydrogen atom.

• Proposed the Solar System model of the atom where the electron in a
hydrogen atom moves around the nucleus only in certain allowed circular
orbits.

• RH, the Rydberg constant =2.18 x 10 -18 J

• n is an integer called the principal quantum number; it has the values n
1, 2, 3, . . . .
57
Explanation of Atomic Spectra
• When atoms absorb energy, their electrons move to higher energy
levels.
• These electrons lose energy by emitting light when they return to
lower energy levels.
• The excitation fallback theory explains the visible emission (bright
line) spectrum of element.
• A ground state for the electrons in an atom is an energy state of
lowest energy.
• An excited state is an energy state of higher energy.
58
59
60
 Atomic Spectra of Noble Gases

Helium

Neon

Argon

Krypton

61
Xenon
 Heisenberg’s
Uncertainty Principle

• It is impossible to know simultaneously both the momentum

(mass x velocity) and the position of a particle with certainty.
• H atom→ it is inherently impossible to know simultaneously
both the precise location and precise momentum of the
electron.
• Thus, it is not appropriate to imagine the electron circling the
nucleus in well-defined orbits.
62
• Bohr’s theory did not provide a complete description of
electronic behavior in atoms.
• In 1926 the Austrian physicist Erwin Schrödinger, formulated
an equation that describes the behavior and energies of
submicroscopic particles in general.
• The equation incorporates both particle behavior, in terms of
mass m, and wave behavior, in terms of a wave function ψ
(psi)

63
 Quantum Mechanical View of The Atom

• The Schrödinger equation specifies the possible energy states the

electron can occupy in a hydrogen atom.
• These energy states and wave functions are characterized by a set of
quantum numbers.
• Quantum mechanics tells us that we cannot pinpoint an electron in an
atom, it does define the region where the electron might be at a given
time.
• The concept of electron density gives the probability that an electron
will be found in a particular region of an atom→ square of the wave
function, ψ2. 64
 Quantum Mechanical View of The Atom

• We speak of an atomic orbital, rather than an orbit.

• An atomic orbital can be thought of as the wave function of
an electron in an atom.
• An atomic orbital, therefore, has a characteristic energy, as
well as a characteristic distribution of electron density.

65
 Quantum Numbers
• In quantum mechanics, three quantum numbers are
required to describe the distribution of electrons.
1. principal quantum number
2. angular momentum quantum number
3. magnetic quantum number
• spin quantum number—describes the behavior of a specific
electron and completes the description of electrons in atoms

66
• The principal quantum number (n) can have integral
values 1, 2, 3, etc. → n determines the energy and size of
an orbital.

• The angular momentum quantum number (l) → tells us

the “shape” of the orbitals.

• l has possible integral values from 0 to (n -1).

• If n = 3, there are three values → 0, 1,and 2.
• The value of is generally designated by the letters s, p, d, f,..

67
• The magnetic quantum number (ml) describes the orientation of the
orbital in space.
• The value of ml depends on the value of the angular momentum
quantum number (l).
• For a certain value of , there are (2l +1) integral values of ml as
follows.

• If l = 0, then ml = 0. If l =1, then there are [(2 x1) + 1], or three values
of ml, namely, +1, 0, and 1.
• The electron spin quantum number (ms), which has a value of
+(1/2) or –(1/2).

68
The magnetic quantum number (ml)

69
Write the four quantum numbers for an electron in a 3p orbital.

70
 Pauli Exclusion Principle

• This principle states that no two electrons in an atom can have the
same four quantum numbers.

71
 Aufbau Principle
• The principle dictates that as
protons are added one by one to
the nucleus to build up the
elements, electrons are similarly
added to the atomic orbitals.

72
 Hund’s Rule
• The rule states that the most stable arrangement of electrons in
subshells is the one with the greatest number of parallel spins.

73
 Valence Bond Theory
• A covalent bond forms when the orbitals of two atoms
overlap and a pair of electrons occupy the overlap region.
• The theory assumes that the electrons in a molecule occupy
atomic orbitals of the individual atoms.
• Valence bond theory states that a stable molecule forms
from reacting atoms when the potential energy of the system has
decreased to a minimum;
→the Lewis theory ignores energy changes in chemical bond formation.

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75
 Hydrogen fluoride, HF. Fluorine, F2.

The greater the extent of orbital overlap, the stronger the bond.

76
 Hybridization
• The orbitals that form when bonding occurs are different from the
atomic orbitals in the isolated atoms.
If no change occurred, we could not account for the molecular shapes that are
observed.

• Atomic orbitals “mix” or hybridize when bonding occurs to form

hybrid orbitals.
The spatial orientation of these hybrid orbitals correspond with observed
molecular shapes.

77
1. This is a theoretical model used only to explain covalent bonding.

2. Hybridization is the mixing of at least two nonequivalent atomic

orbitals, for example, s and p orbitals. Therefore, a hybrid orbital is
not a pure atomic orbital. Hybrid orbitals and pure atomic orbitals
have very different shapes.

3. The number of hybrid orbitals is equal to the number of atomic

orbitals that participate in the hybridization process.

4. Hybridization requires an input of energy; however, the system more

than recovers this energy during bond formation.

78
Formation and orientation of sp hybrid orbitals and the bonding in BeCl2

atomic
orbitals

hybrid orbitals

One 2s and one 2p atomic orbital mix to form two sp hybrid orbitals.

79
box diagram with orbital contours

Overlap of Be and Cl orbitals to form BeCl2.

80
 The sp2 hybrid orbitals in BF3

Mixing one s and two p orbitals gives three sp2 hybrid orbitals.
The third 2p orbital remains unhybridized.
81
The three sp2 orbitals point to the corners of an equilateral triangle, their
axes 120° apart.
Each half-filled sp2 orbital overlaps with the half-filled 2p orbital of a F atom.

82
The sp3 hybrid orbitals in CH4

The four sp3 orbitals adopt

a tetrahedral shape ( 109.5 °).

83
The sp3 hybrid orbitals in NH3

The N lone pair occupies an sp3

hybrid orbital, giving a trigonal
pyramidal shape ( 107 °).

84
The sp3d hybrid orbitals in PCl5

The formation of more than four

bonding orbitals requires d orbital
involvement in hybridization.

85
 molecular formula → hybrid orbitals

Molecular Step 1
Formula

Lewis Step 2
structure

Molecular shape and Step 3

e- group arrangement

Hybrid orbitals

86
 Types of Covalent Bonds
A sigma (σ) bond is formed by end-to-end overlap of orbitals.

All single bonds are σ bonds.

A pi (p) bond is formed by sideways overlap of orbitals.

A p bond is weaker than a σ bond because sideways overlap is

less effective than end-to-end overlap.

A double bond consists of one σ bond and one p bond

87
 The s bonds in ethane (C2H6)
both C are sp3 hybridized s bond formed by s-sp3
overlap

End-to-end sp3-sp3 overlap to form a s

bond

A σ bond is cylindrically symmetrical, with its

highest electron density along the bond axis.

88
 The s and p bonds in ethylene (C2H4)
unhybridized 2p orbitals

A p bond has two regions

of electron density.
89
 Describing the Types of Bonds in Molecules

PROBLEM: Describe the types of bonds and orbitals in acetone,

(CH3)2CO.
PLAN: We use the Lewis structures to determine the arrangement of
groups and shape at each central atom. We postulate the hybrid
orbitals, taking note of the multiple bonds present.

SOLUTION: sp2

sp3 sp2
sp3

90
 Molecular Orbital Theory
• The combination of orbitals to form bonds is viewed as the
combination of wave functions.
• Atomic wave functions (AOs) combine to form molecular wave
functions (MOs).

• Addition of AOs forms a bonding MO, which has a region of

high electron density between the nuclei.

• Subtraction of AOs forms an antibonding MO, which has a

node, or region of zero electron density, between the nuclei.

91
An analogy between light waves and atomic wave functions

Amplitudes of wave
functions added

Amplitudes of
wave functions
subtracted 92
Contours and energies of H2 bonding and
antibonding MOs

The bonding MO is lower in energy and the antibonding MO is higher in energy

than the AOs that combined to form them.
93
 Molecular Orbital Diagrams
• An MO diagram, just like an atomic orbital diagram,
shows the relative energy and number of electrons in
each MO.

• The MO diagram also shows the AOs from which each

MO is formed.

Bond order is calculated as follows:

½[(# of e- in bonding MO) – (# of e- in antibonding MO)]

94
 MO diagram for H2

H2 bond order = ½ (2 − 0) = 1
95
 Electrons in Molecular Orbitals

• Electrons are placed in MOs just as they are in AOs.

• MOs are filled in order of increasing energy.

• A MO can hold a maximum of 2 e- with opposite spins.
• Orbitals of equal energy are half-filled, with spins parallel, before pairing spins

• A molecular electron configuration shows the type of MO and the

number of e- each contains. For H2 the configuration is (σ1s)2.

96
 MO diagram for He2+ and He2

He2+ bond order = ½ He2 bond order = 0

(σ1s)2(σ*1s )1 (σ1s)2(σ*1s )2
97
 Predicting Stability of Species Using MO Diagrams

PROBLEM: Use MO diagrams to find bond orders and predict whether H2+ and H2−
exist. If either exists, write its electron configuration.

PLAN: Since the 1s AOs form the MOs, the MO diagrams are similar to the one for H2.
We find the number of electrons in each species and distribute them one at a
time to the MOs following the rules for orbital filling. We calculate the bond order
and predict stability.

SOLUTION:

H2+ has one electron to place in its MOs while H2- has three electrons to place.

98
 For H2-, the bond order is
For H2+, the bond order is
½(2 – 1) = ½;
½(1 – 0) = ½;
so we predict that H2- exists.
so we predict that H2+ exists.
The configuration is (σ1s)2(σ )1
The configuration is (σ1s)1.
*
1s
99
Shapes and energies of s and p MOs from
combinations of 2p atomic orbitals.

100
 Relative MO energy levels for Period 2 homonuclear
diatomic molecules.
without 2s-2p with 2s-2p
mixing mixing

MO energy levels MO energy levels

for O2, F2, and Ne2 for B2, C2, and N2

101
The MO diagram for HF

102
The MO diagram for NO

103
 Take Home Assignment
th
Due by 29 July
1. An electron in the hydrogen atom makes a transition from an energy state of
principal quantum numbers ni to the n =2 state. If the photon emitted has a
wavelength of 434 nm, what is the value of ni?
2. Describe the shapes of s, p, and d orbitals. How are these orbitals related to
the quantum numbers n, l, and ml?
3. Predict the geometries of these ions: (a) NH4+ (b) NH2 - (c) CO3 2- (d) ICl2 -
(e) AlH4 - (f) SnCl5 - (g) H3O+
4. Use molecular orbital theory to compare the relative stabilities of F 2 and F2-.

104
Thank you