Bonding and Packing in Minerals: GY 111 Lecture Note Series

GY 111 Lecture Notes
D. Haywick (2007-08)
GY 111 Lecture Note Series

Bonding and Packing in Minerals
Lecture Goals:
A) Bonding
B) Packing of atoms/ions in crystals
Reference: Press et al. (2003), Chapter 3; Grotzinger et al. (2007) Chapter 3
A) Bonding
Last time we met, we were discussing basic chemistry. This was necessary in order to
examine the chemical characteristics of the mineral groups. Chemical reactions are
largely driven by movements of electrons between different atoms. Ions result when
electrons are gained (anions) or lost (cations) during these reactions. Ions are different
sizes than their parent atoms. In general, atoms that become cations become smaller and
atoms that become anions become larger. The size of the ions/atoms is one of the
principle factors regulating how crystals form. I am jumping ahead just now. Lets get
back to the first topic of today; chemical bonding.
There are 3 major types of chemical bonds that glue together atoms and ions in
minerals: 1) Ionic bonding, 2) covalent bonding and 3) metallic bonding. A 4th type,
van der waal or hydrogen bonding, is relatively weak but does play an important role in
some of the minerals (e.g., the micas).
Ionic bonding is electromagnetic and occurs when ions bond together (consider this a
bond resulting from the exchange of electrons). Remember the mineral halite from last
time? This mineral is composed of Na+ and Cl- and the resulting ionic bond is very
strong because of the charge difference between the two ions. Other minerals
characterized by ionic bonding include fluorite, calcite and many others.
Covalent bonding is another very strong type of chemical bond. This type, electrons are
shared between 2 or more ions. The classic examples illustrating this type of bonding are
the molecules H2 and O2 (hydrogen gas and oxygen gas).
Many of the sulfide and silicate minerals display covalent bonding. A very simple (and
largely incorrect) way to view the covalent bonding in silicate minerals like quartz is as
follows:
The third type of bonding (metallic) is relatively weak. As the name applies, it is
characteristic of metals such as gold, silver and copper. It also occurs in several other
types of native elements, most of which you will not see in GY 111. In metallic bonding,
there is free movement of electrons around atomic nuclei and it is this property that
makes most metals conduct electricity. To explain how the electrons were associated with
the nuclei, my High School chemistry teacher asked us to first imagine a pipe packed
with gumballs (the atomic nuclei), and then to imagine sugar (electrons) passing through
the spaces between the gumballs. Once again, the analogy isnt all that accurate, but it
more or less captures the gist of metallic bonding (it also did wonders for gumball sales
in the school store).
Hydrogen bonding results from weak attraction between ions of opposite charge such as
illustrated below. As previously stated, it is a very weak bond and results in some
interesting mineral properties where it occurs. The minerals that were produced at least in
part due to hydrogen bonding include the micas (biotite and muscovite), other platy
minerals such as chlorite and most of clays (e.g., kaolinite).
Bonding does more than simply glue atoms/ions into minerals; it also dictates some of the
physical properties of those minerals. Note: the following are generalized properties.
They are not inclusive.
Bond
Ionic
Covalent
Metallic
Mineral properties
-strong bond
-high melting points
-vitreous lusters
-higher solubility
- strong bonds
- hard minerals
- very high melting points
- vitreous adamantine lusters
- weak bonds
- low to high melting points
- metallic lusters
-electrically conductive
B) Packing of atoms/ions (crystallography):

I hate teaching this section to GY 111 students as it requires artistic skills which I simply
do not have. The problem is that we need to envision 3D space. A chalk board only
permits 2D drawings of 3D objects. If you have a good eye for perspectives you will
probably be okay. If not. well, Google Crystal Systems.
All objects are made of atoms and ions. In minerals, these particles are put together in a
precise manner depending upon 1) the amount of space you have and 2) the relative size
of the atoms/ions that are bonded together. It is largely the ionic ratio that determines
how the particles are packed in space. For ions that are the same size, the packing is
relatively easy to envision. Picture again the gumballs that I discussed earlier in this
lecture. Picture a glass filled with them. All of the gumballs will shift slightly to best fill
the space provided by the glass. There will be space between them, but not nearly as
much as if the packing were random.
Unfortunately, ions are seldom the same size in a mineral, and consequently, the way
they pack together is seldom as simple as that portrayed above. Take halite again. Na+ is
much smaller than Cl- meaning that rather than the perfect packing in gum balls, the
packing in halite looks rather more like this:
Note that the Cl- ions largely dictate the size of the resulting package. Incidentally,
crystallographers (those geologists who study how crystals form) call these packages
unit cells. The actual definition of a unit cell goes something like this: the smallest
reproducible structure that records both chemical composition and packing arrangement
of ions/atoms in a mineral. Real crystals are nothing but stacked together identical unit
cells. The unit cell of halite is this:
Many of you may have envisioned this as the unit cell:
If so, youd be wrong. This cell is not identical and repeatable (the corner ions are
different). The correct cell can be stacked with others to make larger and larger identical
assemblages. It is ultimately this stacking that gives rise to the macroscopic crystal forms
that we see in nature. The unit cell of halite has a face-centered structure. Fluorite's unit
cell is also cubic, but it is different from halite's. It is said to be body-centered because
the fluoride ions which comprise part of the mineral are wholly contained within the unit
cell.
Note: Dr. Haywick will show 3D

models to illustrate the
crystallography of halite and
fluorite in the lecture.
A lot of this stuff is pretty abstract, but if you are following it, you probably have several
questions about mineral chemistry. One that I asked when I was a student was: Why is the
formula of halite NaCl if the unit cell has a bunch of Na+ and Cl- ions? Well first of all,
it is important that you realize that each unit cell actually shares parts of ions with other
unit cells. In halite, the 8 Na+ ions at the corners are shared between 8 other unit cells. In
effect, each of these ions can only be counted as 1/8 Na+. Ions at the edges are shared
between 4 other cells (1/4). Ions in the sides of cells are shared with another cell (1/2).
Only those ions wholly contained within a unit cell count as 1. If you take the time to add
up all of the partial counts, this is what you get for Halite:
Na+:
8 ions at corners (8 x 1/8) = 1

6 ions at sides (6 x 1/2) = 3
4
Cl :
12 ions at edges (12 x 1/4) = 3
1 ions in center (1 x 1 =
1
4
So technically, if you based the formula of a mineral on its unit cell, halite would be
Na4Cl4. Those of you who want to refine your understanding of unit cells may wish to do
the same type of math on the Fluorite unit cell.
Before we leave unit cells, please note that ionic/atomic packing in minerals is highly
variable. Consequently the crystals morphologies that can arise are also highly variable.
You will see this variability very shortly when we deal with the silicate minerals, but you
should note that the variability at the unit cell level is well documented and well studied
by cleaver geologists.
Geologists (actually crystallographers) recognize 7 distinct crystal systems. They are
defined and distinguished from one another on the basis of the dimensions and angular
relations of crystallographic axes that define the unit cells. Here is a sketch of one of
those crystal systems that show you what Im on about:
Axes are called a, b, c

Angles are called alpha("), beta ($), gamma (( )
* a 4th axis occurs in the Hexagonal crystal

systems
In the cubic system, there are 3 axes of equal length that are separated from one another
by right angles (a=b=c, "=$=( = 90 ). If you think about it, this must define a cube (as
well as an octahedron, a dodecahedron and a few other shapes). All minerals of the cubic
class are highly symmetrical. In fact, it is symmetry that allows you to identify the crystal
system of a particular mineral.
The other crystal systems (listed in order of decreasing symmetry) are distinguished
criteria listed on the table and diagram on the next page.
All of the stuff that we have just discussed comprises the core of one of our sophomorelevel courses (GY 342). In GY 111, you do not have to be all that familiar with crystal
systems. But you do have to know about the way minerals (especially the silicates) are
put together.
You also have to know that sometimes you get minerals with the same chemical
composition that have completely different crystal structures. A classic example of these
polymorphs are the minerals diamond and graphite (chemical formula for both is C).
Graphite has a platy arrangement of carbon atoms. Diamond has a very complex rigid
(which is hard to draw; see diagrams on the top of the next page).
Diamond (Chemical comp = C)
Graphite (Chemical comp = C)
Here are a couple nice models of the other minerals that we discussed today.
Halite (NaCl)
Fluorite (CaF2)
Mineral Crystal Systems (You do NOT need to know this for GY 111)
Crystal System
Axes
Angles between axes
Mineral examples
Cubic
a=b=c
" =$ =( =90
Halite, Galena, Pyrite
Tetragonal
a=bc
" =$ =( =90
Zircon
Hexagonal
a= a1=b c
" =$ =120 , ( =90
Apatite
Trigonal
a= a1=b c
" =$ =120 , ( =90
Quartz, Calcite
Orthorhombic
abc
" =$ =( =90
Aragonite, Staurolite
Monoclinic
abc
" =$ =90 , ( 90
Gypsum, Orthoclase
Triclinic
abc
" $ ( 90
Plagioclase
Crystal structures (you do NOT have to know this for GY 111 either). This figure is included for
those of you interested in the mathematically-precise aspects of geology) From Price and Harte
(1974)
Important terms/concepts from todays lecture

(Google any terms that you are not familiar with)
polymorph
bonding
unit cell (face centered vs body centered)
bonding (metallic, ionic, covalent, hydrogen)
crystallography
crystal systems (cubic/isometric, tetragonal, hexagonal, trigonal, orthorhombic,
monoclinic, triclinic)

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GY 111 Lecture Notes

GY 111 Lecture Note Series

GY 111 Lecture Notes

GY 111 Lecture Notes

B) Packing of atoms/ions (crystallography):

GY 111 Lecture Notes

Many of you may have envisioned this as the unit cell:

GY 111 Lecture Notes

Note: Dr. Haywick will show 3D

8 ions at corners (8 x 1/8) = 1

GY 111 Lecture Notes

Axes are called a, b, c

* a 4th axis occurs in the Hexagonal crystal

GY 111 Lecture Notes

Diamond (Chemical comp = C)

Graphite (Chemical comp = C)

GY 111 Lecture Notes

Angles between axes

Halite, Galena, Pyrite

" =$ =120 , ( =90

" =$ =120 , ( =90

GY 111 Lecture Notes

Important terms/concepts from todays lecture

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