Dr Phil King F207

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Introduction to Inorganic Chemistry Module 06510
Dr Phil KingF207
Shapes of Molecules and Complexes
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Why Does The Shape of a Molecule Matter?

• The shape of a molecule determines the following
• What it smells like.
• What it tastes like.
• Its activity as a drug.
• Its role in the chemical processes occurring in
  our bodies.
• Its colour.
• Its solubility.
• Whether it is a gas, liquid or solid.

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• The Lock and Key Hypothesis.
• Virtually all processes in living cells depend on
  enzymes.
• Enzymes speed up reactions by factors of at least
  a million.
• The active sites of enzymes are highly specific.

• Only molecules that are the correct shape to bind
  to the active site of the enzyme may do so.
• Taste and smell receptors in the body use a
  similar lock and key mechanism to bind specific
  molecules.

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• The Lock and Key Hypothesis.
• Aspirin was discovered in 1899 and is derived
  from a compound found in the bark of a willow
  tree.
• The functionality of aspirin is due to its
  chemistry and its molecular shape.

• The aspirin molecule contains a six-membered
  organic ring (needed to cross the non-polar cell
  membrane).
• The acid and ester groups attached do the
  chemistry.

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• The Lock and Key Hypothesis.
• The prostaglandin hormone initiates pain
  signalling in the body and causes inflamation.
• The first step in the synthesis of prostaglandin
  takes place at the active site of the enzyme
  Cyclooxygenase.
• Aspirin has the correct shape to approach and
  bind to the active site of cyclooxygenase.

• The aspirin molecule shields the active site and
  prevents the reagents needed for the synthesis of
  prostaglandin from approaching.

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• The Lock and Key Hypothesis.
• Knowing the shape and structure of aspirin allows
  chemists to synthesise similar molecules and
  investigate their ability to inhibit pain.

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• The Lock and Key Hypothesis.
• The vanilloids shown below are molecules with
  distinctive flavours that are widely used in
  cooking.

Vanillin
Zingerone
Caspaicin

• The molecules have similar chemical structures in
  that they all contain a benzene ring.
• Subtle changes in the sizes or positions of the
  groups attached to the ring change the compounds
  flavour.
• Effectively, we can taste and smell the different
  shapes of the molecules.

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• The Lock and Key Hypothesis.
• Vanillin is a component of vanilla.

Vanillin

• Its low molecular weight and compact shape make
  it volatile, thus, vanilla has a strong aroma.
• When it comes into contact with its receptor in
  the body we experience the taste of vanilla.

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• The Lock and Key Hypothesis.
• Zingerone puts the zing in ginger.

Zingerone

• Its higher molecular weight and less compact
  structure make it less volatile than vanillin so
  the odour of ginger isnt strong.
• The hydrocarbon chain attached to the benzene
  ring makes the zingerone better able to move
  across the non-polar cell membranes.
• The hydrocarbon chain gives the zingerone a more
  intense flavour when it comes into contact with
  its receptor.

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• The Lock and Key Hypothesis.
• Capsaicin accounts for most (but not all) of the
  hot in hot peppers.

Caspaicin

• Very high molecular weight and linear shape make
  it odourless.
• Its intense flavour is due to the long
  hydrocarbon side chain which allows it to bind
  more effectively to its receptor and to pass
  through cell membranes.
• Its ability to pass through membranes makes the
  burning sensation more pervasive and persistent.

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Predicting The Shapes of Main Group Compounds

• Valence Shell Electron Pair Repulsion Theory
  (VSEPR Theory)
• The electrons surrounding the central atom of a
  molecule are in pairs.
• The electron pairs can be of two types- bonding
  pairs or lone pairs.

• The shape of a molecule is determined by spacing
  the electron pairs as far apart as possible to
  minimise the repulsion between them.

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What Shapes Can We Expect?
All of the shapes shown below minimise the
repulsions between the electron pairs.
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The water molecule has four electron pairs (two
bonding and two lone pairs).
The greatest separation of the pairs is in a
tetrahedron. The lone pairs help determine the
shape but do not constitute part of the shape.
The shape is described as angular (or V-shaped).
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How Do We Determine The Number of Electron Pairs
in a Molecule?
Consider the molecule AX2

• The number of bonding pairs of electrons equals
  the number of atoms attached to A (in this case,
  two).
• The number of lone pairs is given by the formula
• ½group number of A - valency of A.
• The group number needed is the old group number
  (i.e. boron is group 3 not group 13).
• The valency is the magnitude of the oxidation
  state (i.e. N3- and N3 both have a valency of 3).

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Consider the molecule BCl3

• The number of bonding pairs of electrons equals
  the number of chlorine atoms attached to boron
  (in this case, three).
• The number of lone pairs is given by the formula
• ½group number of B - valency of B.
• ½3 - 3 0
• Three bonding pairs Zero lone pairs Three
  electron pairs in total.
• Therefore theBCl3 molecule has a trigonal-planar
  shape.

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Excercises

• Determine and draw the shapes of the molecules
  listed below.

SO32-
PCl5
BrF5
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Shapes of Transition Metal Complexes
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• A transition metal complex comprises of a
  transition metal that has a number of
  ions/molecules attached to it.
• The molecules or ions attached to the metal are
  called ligands.
• The number of ligands attached is called the
  co-ordination number.
• Transition metal complexes generally have
  co-ordination numbers of six or four.

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Octahedral Transition Metal Complexes.

• Co-ordination number 6.
• Six ligands surround the central transition metal
  atom.
• One example is the hexacyanoferrate(II) ion shown
  below.
• The octahedral arrangement minimises interactions
  between the ligands.

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Tetrahedral Transition Metal Complexes.

• Co-ordination number 4.
• Four ligands surround the central transition
  metal atom.
• One example is the tetrachlorocobaltate(II) ion
  shown below.
• The tetrahedral arrangement minimises
  interactions between the ligands.

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Square-Planar Transition Metal Complexes.

• Co-ordination number 4.
• Four ligands surround the central transition
  metal atom.
• One example is the tetrachloroplatinate(II) ion
  shown below.
• The square-planar arrangement does not minimise
  interactions between the ligands.

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