Geochemistry on the Earth’s surface
for analytical geochemists
1b.
Mineral stability and structure
Tento učební materiál vznikl v rámci projektu Rozvoj doktorského studia chemie
č. CZ.02.2.69/0.0/0.0/16_018/0002593
Topic outline
• Building particles of matter
• Bonds in crystals
– Ionic
– Covalent
• Basic minerals on Earth's surface
IONIC MODEL OF CHEMICAL BONDS
Ionic crystals
• We assume that ions are spherically symmetric particles
• The internal structure of ionic crystals is determined by the
stacking of spherical particles in three dimensions
• There are three rules leading to maximum stabilization:
1. The ions must combine in proportions resulting in an
electrically neutral crystal.
2. The closer the distance of adjacent nuclei of oppositely
charged ions is to the lowest energy equilibrium distance, the
more stable the arrangement (not enough attract when too
far and too much of repel when too close).
3. Each ion should be surrounded by as many oppositely charged
ions as possible - coordination number.
• Decisive effect of size and charge of building particles –
ionic potential (ratio of charge to size).
Energy arrangement
e ... difference in charges
r … the distance between the nuclei
Adapted from Gill (2015)
Total potential energy E p arrangement
is a sum of
A. Attractive forces between
oppositely charged ions
(negative terms)
B. Repulsive forces between ions
with the same charge (positive
terms)
Sizes
20
40
60
80
100
120
140
160
180
3 5 7 9 11 13
koordinační číslo
iontovýpoloměr(pm)
K+
Na+
Ca2+
Fe
2+
Mg
2+
Fe3+
Al3+
Si4+
• The higher the positive charge, the smaller the
ions
- significant attraction by the positive charge of
the nucleus.
• The higher the negative charge, the larger the
ions
- mutual repulsion of electrons.
Arrangement
• When stacking spherical
particles of the same size, the
tightest arrangement is stacks
of regular layers.
• Each layer has hexagonal
symmetry.
• Another layer is placed on top
of it with each particle placed
in a dimple between the three
particles in the lower layer
Layout – 2 layers
Layout – 2 layers
Layout – 3 layers
Layout – 3 layers
Arrangement
• Both types of positions are significantly larger than the spaces
between particles in a monolayer.
• In most crystals, there are cations in these positions.
• C4+ always occupies spaces between three oxygens
(carbonates).
• Si4+ occupies positions in tetrahedral cavities (may also be
substituted by Al3+ – aluminosilicates, exceptionally Ti 4+ –
pyroxenes, amphiboles).
• Other ions (Fe3+, Mg2+, Fe2+, Mn2+, Ca2+, Na+) occupy octahedral
positions in the tightest arrangement of oxygens, while well
substituting in the structures (they occupy the same structural
positions): Fe 3+ –Mg 2+ –Fe 2+ –Mn 2+ , Ca 2+ –Na + .
• K + occupies oxygen positions, as well as OH– groups.
ratio r cat /r O2 Coord. Nr. coord. polyhedron
1 12 centers of the edges of
the cube
0.73 – 1 8 hexahedron
0.41–0.73 6 octahedron
0.22 - 0.41 4 tetrahedron
0.15 – 0.22 3 middle of triangle
Adapted from Misra (2012)
Ionic substitution
1. Ions of one element can normally replace ions of
another element if they differ in size by less than
approx. 15%.
2. If the charge of the ions differs by 1, they can
normally be substituted if the electroneutrality of the
crystal is preserved. Substitution occurs to a much
smaller extent when the charge difference is larger.
3. If two different ions can occupy a position, the ion
with the higher ionic potential forms a stronger bond
with the surrounding ions.
4. Mutual substitution of similar ions can be limited by
different electronegativity and the formation of bonds
of different ionic nature.
COVALENT BONDS
Covalent bond
• Sharing unpaired electrons between
neighboring atoms.
• If the orbitals overlap, a molecular orbital is
formed.
– Shared orbitals have a lower total energy than
each one separately
• Bonds stronger, directional
• Small stable molecules (O2, H2O, CH4 …)
σ and π
• Orbital σ is symmetric according
to the line connecting the nuclei
of the bonded atoms.
– High density of electrons
between nuclei
– Simple bonding
• The orbital axes are parallel and
lie above and below the junction
of the nuclei (nodal plane)
– Electrons above the nodal plane
– Double bond
Adapted from Misra (2012)
Coordination bond
• Link between donor and acceptor:
– The donor has an electron pair.
– The acceptor has an empty orbital.
• Overlapping creates complex compounds.
• A central atom (often a transition metal acceptor)
and several ligands (donors) around
it.
• Complexes are important for the mobility of
metals in the environment.
Covalent crystals
• Structure determined by
the shape of bonds
(hybridization of
orbitals).
• In a diamond, each
carbon is bonded to 4
others in a grid of
tetrahedra.
– Strong bonds, strong
materials
The irregular shape of the water
molecule
The free electron pairs in the water
molecule cause a deformation of the
shape – the molecule is not a linear HOH,
the electron pairs and hydrogens try to fit
into the vertices of the tetrahedron. The
result is a partially deformed (all angles
are not equal) tetrahedron.
AdaptedfromimageByThebiologyprimer-Ownwork,CC0,
https://commons.wikimedia.org/w/index.php?curid=32361523
BONDS IN MINERALS
Non-ideal bonds
• Most compounds fall between the extremes of ionic
and covalent bonding.
• Real ties differ from ideal models.
• In every ionic bond , the occurrence of an electron is
deflected due to the electrostatic force.
– The smaller the cation, the closer it is to the anion and the
greater the effect (Si4+ vs K+).
– The effect of the size of the charge of the cation.
• The difference in electronegativity causes one atom to
attract more of the bonding electrons of a covalent
bond .
– Polarization of the bond causes it to show a certain degree
of "ionicity".
The nature of the bonds
• The nature of the bonds is continuous, and
ionic and covalent bonds represent the
extremes.
Correlation
between the ionic
character of the
bond and the
electronegativity
difference of the
atoms according to
Pauling.
Geologically
significant bonds
are marked.
Adapted from Gill
(2015)
Oxygen compounds
• Carbonates, phosphates, nitrates...
• Ionic bond between anion and cation (e.g.
Ca2+ and CO3
2−).
• Covalent bonds in the anion (in carbonates
between carbon and oxygens).
SILICATE CRYSTALS
A very large group that deserves its own chapter
Silicate bonds
• The Si-O bond has an ionic character of approx. 50% and
thus exhibits approximately equally ionic and covalent
character.
• In the real structure of silicates, the Si cation accounts for
roughly half the charge (Si2+).
• The covalent nature of the bond allows the structural
strength of the silicate chains and structures.
– Silicon determines the construction of silicate structures.
• Other bonds in silicate minerals are of a more ionic nature
(Al-O, Mg-O, Na-O, Ca-O, K-O) – their structure is well
described by the ion model.
– Ions limit the mutual arrangement of Si-O structures in the
mineral.
• Due to its size, aluminum can enter both octahedral and
tetrahedral positions.
Polymerization
• SiO4 tetrahedra share oxygens with each other.
• A polymer structure with chains is formed.
• -Si-O-Si-O-Si-O•
While no oxygen is shared by silicon in olivine,
all oxygens are shared in quartz.
• Great structural diversity of silicate minerals.
Arrangement
group general formula valence
O
Si bonds Cation
bonds
ratio mineral formula
SiO2 4 4 0 4:0 silica SiO2
tecto- MISi3AlO8 16 12 4 3:1 albite NaSi3AlO8
phylo- M3Si4O10(OH)2 22 16 6 2.7:1.3 talc Mg3Si4O10(OH)2
ino- M2Si2O6 12 8 4 2:1 diopside CaMgSi2O6
neso- M2SiO4 8 4 4 1:1 olivine (Fe, Mg)2SiO4
Nesosilicates
• SiO4 tetrahedrahave only half of the oxygen bonds
covered:
• One Si4+ to four O2− => SiO4
4−
• If a free electropositive ion (typically Mg2+) is
abundantly present in the melt, it will bind the SiO4
4−
tetrahedra
• A typical olivine structure (especially forsterite
Mg2SiO4) is formed, which does not contain any direct
bonds between adjacent tetrahedra.
– The cohesion of the crystal is determined by the ionic
bond between Mg2+ and SiO4
4−
• Other examples are garnets (e.g. Ca3Al2Si3O12), zircon
(ZrSiO4) or topaz (AlSiO4F2).
• Typically high temperature crystallization from magma.
Olivine – (Mg, Fe)2SiO4
Olivine – (Mg, Fe)2SiO4
Olivine – (Mg, Fe)2SiO4
Inosilicates
• Pyroxenes
– Each Si shares two oxygens with neighboring
tetrahedra.
– Structurally, we can write it as (SiO3)n , where n is
the number of tetrahedra in the chain.
– The negative charge is mostly balanced by divalent
cations, sometimes also by pairs (Na+ and Al3+ or
Fe3+).
– Common rock-forming minerals (diopside, augite,
enstatite ...).
Pyroxenes – diopside Ca(Mg, Fe)Si2O6
Pyroxenes – diopside Ca(Mg, Fe)Si2O6
Pyroxenes – diopside Ca(Mg, Fe)Si2O6
Inosilicates
• Amphibole
– Half of the tetrahedra share two oxygens, the
other half share three oxygens.
– Two connected pyroxene chains, between which
larger cavities are formed, into which large anions
(OH− or F−) can enter.
• Thanks to them, lower stability at high temperatures.
• Very complex stoichiometry.
– Structurally, we can write it as (Si4O11)n.
– Tremolite, hornblende...
Amphibole – NaCa2(Mg, Fe, Al)5(OH)2(Si, Al)8O22
Amphibole – NaCa2(Mg, Fe, Al)5(OH)2(Si, Al)8O22
Amphibole – NaCa2(Mg, Fe, Al)5(OH)2(Si, Al)8O22
Phyllosilicates
• If all tetrahedra share three oxygens with neighboring
tetrahedra, a continuous planar structure is formed.
– They form sheets, endless planes.
• Anions can again enter the meshes in the network.
• The general formula is Si4O10 or Si2O5.
– Aluminum replaces up to 50% of the tetrahedra, usually less
than 25%.
• Different types of phyllosilicates (chlorites, clay minerals)
differ in the "filling" between the silicate layers.
• The silicate layers are much more cohesive than the filler –
that‘s why they are fissile across the surface (typically
micas).
Phyllosilicates
• Significant absorption capacity (especially
cations).
• Relatively reactive – they significantly affect
the properties of water, soil and sediments.
• 2 main building elements
– Tetrahedral layers
– Octahedral layers
2:1 Phyllosilicates
• "Sandwich" tetrahedral lr.
– octahedral – tetrahedral.
• Between the cations
"sandwiches" – they fit
into the hexagonal "mesh"
of the tetrahedral layer.
• No interlayer – they are
held together by van der
Waals forces. Trioctahedral : 3 Mg2+ in the
octahedral layer per building unit (talc)
Dioctahedral : 2 Al3+ in an octahedral
layer per building unit (pyrophyllite)
AdaptedfromRyan(2014)
Phyllosilicates
pyrophyllite Al2(OH)2Si4O10 (dioctahedral), talc Mg3(OH)2Si4O10 (trioctahedral)
Phyllosilicates – talc Mg3(OH)2Si4O10
Phyllosilicates – talc Mg3(OH)2Si4O10
Phyllosilicates – talc Mg3(OH)2Si4O10
Phyllosilicates – pyrophyllite Al2(OH)2Si4O10
Phyllosilicates – pyrophyllite Al2(OH)2Si4O10
Phyllosilicates – pyrophyllite Al2(OH)2Si4O10
Mica
• Derived from pyrophyllite by replacing one
silicon with aluminum
– One free negative charge in the structure
– The need for cations in the interlayer – the
weakest point of the mineral (that's why they are
layered)
– Typically K+
– Al2Si4O10(OH)2 -> KAl2(Si3Al)O10(OH)2 (muscovite)
1:1 Phyllosilicates
• One octahedral and one tetrahedral sheet is
repeated
• Trioctahedral – 3 Mg2+ in the octahedral layer
per structural unit (serpentines)
• Dioctahedral – 2 Al3+ in an octahedral layer
per structural unit (kaolins)
Phyllosilicates
kaolinite Al4(OH)8Si4O10 (dioctahedral), serpentine Mg6(OH)8Si4O10 (trioctahedral)
Phyllosilicates
Tectosilicates
• Tetrahedra share all oxygens – each oxygen is shared by
two tetrahedra.
• Crystal volume is determined entirely by covalent
bonding and not by ion deposition.
– Poor cleavage.
• The structure contains large spaces and channels
through which cations and whole molecules can
diffuse.
• The basic structure is SiO2.
• When silicon is replaced by aluminum (Al3+), relatively
large ions (Na+, K+, Ba2+) can enter the structure –
feldspars are formed.
Tectosilicates
Tento učební materiál vznikl v rámci projektu Rozvoj doktorského studia
chemie
č. CZ.02.2.69/0.0/0.0/16_018/0002593
Resources
• Images without a specified source are public domain, with a free
license or copyright or used with the permission of doc. Zeman.
• Further, some illustrations come from textbooks:
– Gill, R. (2015). Chemical Fundamentals of Geology and Environmental
Geoscience . 3rd Edition . John Wiley and Sons . 288 p. ISBN: 978-0-
470-65665-5
– Misra , K. (2012). Introduction to geochemistry: principles and
applications. Wiley-Blackwell. 438 p. ISBN 978-1-4443-5095-1.
– Appelo , C. A. J., & Postma, D. (2005). Geochemistry, groundwater and
pollution : (2nd ed.). Leiden: AA Balkema publishers.
– Manahan , S. E. (2005). Environmental chemistry . 8th ed . Boca Raton
, Fla .: CRC Press . ISBN 1-56670-633-5. info
– Ryan, P . (2014). Environmental and low temperature geochemistry .
John Wiley and Sons . 402 p. ISBN 978-1-4051-8612-4 ( pbk .)