Chapter 1: ATOMIC STRUCTURE

1.1. Subatomic particles

1.2. Quantum theory. Atomic orbitals.

1.3. The periodic table

1.4. The periodicity of atomic properties

1.5. Elements and life

 Matter is made of atoms.

 Atomic structure can be explained by quantum theory which
combines properties of particles and waves.
 The (periodic) properties of atoms are determined by their
electronic structure.

1.1. Subatomic particles

Modern atomic theory is based on two main lines of research:

1- Research on the electrical nature of matter:

It was discovered that atoms are made of fundamental particles

2- Research on the interaction of light with matter:

A detailed understanding of the relative positions of the particles in
atoms can be obtained

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 Properties of the three elementary particles

Particle Mass (uma) Charge (relative)

electron (e-) 0.00054858 -1
proton (p) 1.0073 +1
neutron (n) 1.0087 0

1 uma = 1.66054 x 10-27 kg

• The chemical elements

- Atoms consist of a small, dense nucleus surrounded by a cloud of electrons
at relatively large distances from the nucleus.
- All nuclei contain protons; the nuclei of all atoms except that of the
common form of H, also contain neutrons.

Number of protons: atomic number (Z)

Mass number (A): total no. of protons + neutrons (n)
A=Z+n
- Most elements consist of atoms of different masses, called isotopes.
Isotopes contain the same number of protons and electrons, but
different numbers of neutrons.

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The atomic weight scale is defined from the mass of the isotope 12C:

1 uma = 1/12 mass of one 12C atom

The atomic weight of an element is the weighted average of the
masses of the isotopes. E.g. Atomic mass of carbon: 12.011 uma

Element Symbol Z A Abundance

Hydrogen 1H 1 1 99.985
Deuterium 2H or D 1 2 0.015
Tritium 3H or T 1 3 Radiact. (short life)
Carbon-12 12C 6 12 98.90
Carbon-13 13C 6 13 1.10
Oxygen-16 16O 8 16 99.76

1.2. Quantum theory. Atomic orbitals.

• Fundamentals of wave (quantum) mechanics

• The Schrödinger equation

• Atomic orbitals and quantum numbers

• Electronic structure of hydrogen and multielectronic atoms

• Electron configurations

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 • Fundamentals of the quantum theory

- Wave-particle duality of matter (De Broglie, 1925):

As the electromagnetic radiation, matter has a dual nature. Particles
(electrons) can behave as waves with an associated wavelength that
depends on its mass (m) and speed (v):

h h
 
mv p
- The uncertainty principle (Heisenberg, 1927):
If the location of a particle is known within an uncertainty x, then
the momentum can be known only to within an uncertainty p, so that:
h
p x 
4
This principle is evident at the atomic level. Electrons are not located in
"orbits," we speak of the PROBABILITY of finding the electron in a region of
space.

• The Schrödinger equation

- Electrons behave as standing waves, Schrödinger replaces the exact
trajectory of the particles by a wave function

- is a function of the spatial coordinates and provides information on

the position and energy

- “ square” represents the probability of finding the electron in a

region of space

- The wave functions are obtained from the

Schrödinger equation:
H =E 
where:
E = total energy of the system (kinetic +potential)
H = Hamiltonian operator

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- The Schrödinger equation for the hydrogen atom has the form:

h 2   2  2  2 
      V  E
8 2 m  x 2 y 2 z 2 
 Ze 2
V
r
- This equation can be solved exactly for the hydrogen atom only. Its
solutions are a set of wavefunctions  and their respective energies.

RH Z 2
E 2
n
- A wavefunction describes the state of the electron (atomic orbital) and it
depends on a set of integer numbers called quantum numbers.

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 • Atomic orbitals and quantum numbers

Name Symbol Values Information

Principal quantum n 1, 2, 3, … - Shell or principal level

number - Size
- Related to energy and
distance to nucleus

Secondary or l 0, 1, 2, 3…n-1 - sublevel or subshell

azimuthal quantum - type of atomic orbital
number (orbital l=0, 1, 2, 3, 4…
angular momentum)
s, p, d, f, g…
Magnetic quantum ml -l…0…+l - spatial orientation of an
number orbital in a subshell

Spin quantum number ms ±1/2 - spin direction

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 Shells, subshells and orbitals in an atom
Shell Subshell Orbital

l=2 d +2 +1 0 -1 -2 3d

n=3 l=1 p +1 0 -1 3p
l=0 s 0 3s

l=1 p +1 0 -1 2p
n=2
l=0 s 0 2s

n=1 l=0 s 0 1s
n l ml

Orbitals s, p & d. Boundary surfaces.

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• Electronic structure of hydrogen and
multielectronic atoms

• Hydrogen atom:
- The electron is located in the lowest energy level (ground state), i.e. n=1
- The only orbital with this energy is 1s
- Quantum numbers for an electron in 1s:
n=1, l=0, ml=0, ms= +1/2 or -1/2
- When an atom absorbs energy, it can move to higher levels,n=2, 3,…
(excited states)
- For a given level, all the orbitals are degenerate; the orbital energy
depends only of n. E.g., orbitals 2s and 2p have the same energy.

RH Z 2
E 2
n

• Electronic structure of hydrogen and

multielectronic atoms
• Multielectronic atoms:
- A neutral atom of an element with Z>1 has Z electrons.
- Its electrons occupy orbitals as for H, but with different energies:
1. The nuclear charge is higher → e- attraction increases→ lower energy
2. Each electron is repeled by other electrons → each e- is shielded from the
total nuclear attraction by the other e-, and experiences an effective nuclear
charge:
Zeff= Z - σ (where σ is the shielding constant)

RH Z eff2
- Energy of an electron in a many-electron atom: E
n2
- In a many-electron atom, because of penetration and shielding effects,
the orbital energy depends on n and l. Degeneracy is lost.
For a given level, the order of orbital energies is: s<p<d<f

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 A double rule is useful to sort the energies of the orbitals: “(n + l) rule”
energy levels are ordered from most negative to less negative energies
depending on the value of n + l. If two levels have the same value of n + l,
the lowest energy corresponds to the one having a lower n "
Order (n + l): 1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s
< 4f < 5d < 6p < 7s < 5f < 6d < 7p

0
4s 3p 3d
3s Once we know the orbital energies, we need
2p
Energía

2s to find out how e- are distributed in atoms

1s

Building-up of orbitals

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 • Electron configurations

Electron configuration: it describes the electronic structure of an atom

Orbital filling is performed according to:

1. Building-up principle (“Aufbau”): in the ground state, electrons occupy

atomic orbitals so that the total energy of the atom is a minimal.
Orbitals are occupied from lowest to highest energies.

2. Pauli exclusion principle: no two electrons in an atom can have the same
set of four quantum numbers. Accordingly, each orbital can not contain
more than two electrons whose spins are opposite.

3. Hund's rule: at a subshell, electrons are placed in different orbitals with

parallel spins rather than pairing two electrons in one of the orbitals.

• Electron configurations (cont.)

• H 1s 1
• He 1s 2 [He]
• Li 1s2 2s 1 [He] 2s 1
• Be 1s2 2s 2 [He] 2s 2
• B 1s2 2s 2 2p 1 [He] 2s 2 2p 1
• C 1s 2 2s 2 2p 2 [He] 2s 2 2p 2
• N 1s 2 2s 2 2p 3 [He] 2s 2 2p 3
• O 1s 2 2s 2 2p 4 [He] 2s 2 2p 4
• F 1s 2 2s 2 2p 5 [He] 2s 2 2p 5
• Ne 1s 2 2s 2 2p 6 [He] 2s 2 2p6 = [Ne]

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• Electron configurations (cont.)

• K [Ar] 4s 1
• Ca [Ar] 4s 2 Or this order is OK !
• Sc [Ar] 4s 2 3d 1 [Ar] 3d 1 4s 2
• Ti [Ar] 4s 2 3d 2 [Ar] 3d 2 4s 2
• V [Ar] 4s 2 3d 3 [Ar] 3d 3 4s 2
• Cr [Ar] 4s 1 3d 5 Anomalies
to Filling
• Mn [Ar] 4s 2 3d 5
• Fe [Ar] 4s 2 3d 6 Either order will be OK !
• Co [Ar] 4s 2 3d 7 But it’s normally best to
• Ni [Ar] 4s 2 3d 8 put the one filling last!!!
• Cu [Ar] 4s 1 3d 10 Anomalies
to Filling
• Zn [Ar] 4s 2 3d 10

1.3. The periodic table

The elements are classified according to their electron configuration
Groups: vertical columns 1 to 18
Periods: horizontal lines 1 to 7
Blocks: depending on the last occuppied level they are: s (1-2),
p (13-18), d (3-12), f (rare earth or inner transition elements)

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1.4. The periodicity of atomic properties

• Atomic radii

- increase from top to bottom within groups

- decrease from left to right across periods

Atomic radius

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• Ionic radii

- Cations are smaller and anions are larger

than the respective neutral atoms.
- increase from top to bottom in a group
- decrease from left to right across periods

18/VII
1 2 13/III 14/IV 15/V 16/VI 17/VII I
Li+ Be2+ N3- O2- F-
58 27 171 140 133
Na+ Mg2+ Al3+ P3- S2- Cl- Ionic radius
(pm)
102 72 53 212 184 181
201-250
K+ Ca2+ Ga3+ As3- Se2- Br-
138 100 62 222 198 196 151-200

Rb+ Sr2+ In3+ Te2- I- 101-150

149 116 72 221 220 51-100
Cs Ba2+ Tl3+ 1-50
170 136 88

• Ionization energy

Energy required to remove an electron from an atom or ion in the gas

phase.

X (g) → X+(g) + e- 1st Ionization IE1

X+ (g) → X2+(g) + e- 2nd Ionization IE2

It is an endothermic process IE>0, measured in J/mol, eV…

For successive ionizations IE1<IE2<IE3…

- Examples (in kcal/mol)

IE1 IE2 IE3 IE4

H 314
He 567 1254
Li 124 1744 2823
Be 215 420 3548 5020

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 - Ionization energies increase from left to right across periods and
decrease from top to bottom in a group. Exceptions: Be-B, Mg-Al
N-O, P-S
- Metals have low IE, non-metals have high IE and metalloids show
intermediate values. 18/VIII
H He
1310 2 13/III 14/IV 15/V 16/VI 17/VII 2370
Li Be B C N O F Ne 1st Ionization E
519 900 799 1090 1400 1310 1680 2080
Na Mg Al Si P S Cl Ar Ionization energy
494 736 577 786 1011 1000 1255 1520 (kJ/mol)
K Ca Ga Ge As Se Br Kr 2001-2500
418 590 577 784 947 941 1140 1350
1501-2000
Rb Sr In Sn Sb Te I Xe
402 548 556 707 834 870 1008 1170 1001-1500

Cs Ba Tl Pb Bi Po At Rn 501-1000
376 502 590 716 703 812 1037 1036 1-500

• Electron affinity
- Amount of energy exchanged when an electron is added to an isolated
gaseous atom.
X(g) + e- → X- (g)
It is an exothermic process AE<0 (positive when expressing the tendency
of an anion to lose an electron)
1 18/VIII

High H He
+73 2 13/III 14/IV 15/V 16/VI 17/VII -48
values
Li Be B C N O F Ne Electron
close to F +60 <0 +27 +122 -7 +141 +328 -116 affinity
(kJ/mol)
Na Mg Al Si P S Cl Ar
+53 <0 +43 +134 +72 +200 +349 -96 > 300

K Ca Ga Ge As Se Br Kr 200-300
+48 +2 +29 +116 +78 +195 +325 -96 100-200
Rb Sr In Sn Sb Te I Xe 0-100
+47 +5 +29 +116 +103 +190 +295 -77
-100-0
Cs Ba Tl Pb Bi Po At Rn
< -100
+46 +14 +19 +35 +91 +174 +270 -68

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 • Electronegativity
- A measure of the relative tendency of an atom to attract electrons to
itself when it is chemically combined with another atom.
- It is an empirical parameter, there are different scales.

1 18/VIII
Electronegativity
H He
2.2 2 13/III 14/IV 15/V 16/VI 17/VII
Li Be B C N O F Ne
1.0 1.6 2.0 2.6 3.0 3.4 4.0
Na Mg Al Si P S Cl Ar
0.93 1.3 1.6 1.9 2.2 2.6 3.2 Electronegativity
K Ca Ga Ge As Se Br Kr
4
0.82 1.3 1.6 2.0 2.2 2.6 3.0
3 - 3.9
Rb Sr In Sn Sb Te I Xe
0.82 0.95 1.8 2.0 2.1 2.1 2.7 2 - 2.9

Cs Ba Tl Pb Bi Po At Rn 1 - 1.9
0.79 0.89 2.0 2.3 2.0 2.0 0 – 0.99

SUMMARY OF PERIODIC PROPERTIES

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 • Oxidation states

- Periodic regularities are observed in the oxidation states, since they

depend on the valence electron configuration (last occupied level).

- Many oxidation states correspond to the loss or gain of electrons to

acquire a closed shell electron configuration.

n s2p6 or n d10

1.5. Elements and life

- The most abundant elements in living beings are H, C, N, O (99.3%)
- The remaining 0.7% can be classified as:
- Macrominerals: K, Mg, Na, Ca, P, S, Cl
- Trace elements:

F: in bones and teeth

I: thyroid function
Se: is part of an enzyme
Si: bone growth and connective tissue development
As: growth and reproduction
B: increases the metabolism of Ca, P and Mg
Fe: in hemoglobin and other enzymes
Cu, Zn, Mn, Mo: form enzymes
Co: B12 vitamin
Cr: increases the effectiveness of insulin
Ni: growth and reproduction

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