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KCL Biomedical Science 4BBY1020 Chem For Biosciences
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Lecture 2Atoms, compounds and chemical bonding
Dr A. James Mason
Recall the simple model of atomic structure in terms of protons, neutrons and electrons
• Movement from one orbital to
another leads to
absorption/emission of
electromagnetic radiation
• Energy levels determine types of
bonding, determine structure and
shape
• See using light energy is emitted or
absorbed at discrete wavelengths
• Electrons at discrete positions from nucleus, different levels of
energy which separate them
Describe the shapes, arrangements and relative energies of s, p and d atomic orbitals
• Electrons are confined within specific volumes of
space called orbitals.
• Orbitals grouped into shells: s, p, d, f
• 4s orbital of lower energy level therefore fills up
before 3d orbital
,Predict the electron configuration of isolated atoms of the major elements commonly found in
biological molecules (H, C, N, O, P, S) and relate this to their valence and reactivity
• Valency - “The maximum number of univalent atoms (originally hydrogen or chlorine atoms)
that may combine with an atom of the element under consideration, or with a fragment, or
for which an atom of this element can be substituted.” – IUPAC
• Valency determined by Valence shell = the highest occupied shell
• Oxygen electron arrangement (2, 6) ; Highest occupied is shell 2 therefore it is the valence
shell
• 2 more electrons required to fill oxygen valence shell (to make 8 electrons in the shell)
• Therefore, Valency is how many electrons are required to fill valence shell
• Valency:
H=1
C=4
N=3
O=2
P=3
S=2
,Define the term “electronegativity”, describe electronegativity trends in the periodic table, and
use electronegativity values to predict whether ionic or covalent bonding will occur between two
atoms.
• Electronegativity - Ability of an atom to attract electrons towards itself
• Always something in between (indicated by red area); can have covalent bonds with partial
ionic character and covalent bonds with partial ionic character, All dependent on
electronegativity of both atoms
, Understand the nature of ionic, covalent and dative covalent bonds, and lone pairs of electrons,
and depict these using Lewis dot symbols
Outline how molecular orbitals are formed from atomic orbitals and distinguish between bonding,
anti-bonding and non-bonding orbitals
• 2 atoms come together, therefore atomic orbitals come together, form a new molecular
orbital
• Each atomic orbital takes a place in the molecular orbital. One forms a low energy bonding
orbital, the other forms a high energy bonding orbital
• Look at example on right:
• The orbital at the bottom is filled
therefore high density therefore
Anti – Bonding orbital.
• The orbital at the top is empty
therefore low density therefore Bonding orbital
• Electrons naturally occupy the bonding orbital, which is lower in energy
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