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Aim: To analyse crystal Structure using various types of Models.

Physical models representing molecular architectures of chemical compounds play

essential roles in understanding Crystallography. The use of molecular models makes
it easier to visualize the structures and shapes of atoms and molecules.Molecular
models are physical models that represent molecules and the processes that occur
with them.

It is because atoms and molecules are so small that they cannot be seen with the
naked eye, we employ physical models to visualize the 3-Dimensional structure of
molecules.

In Crystallographic analysis following types of Models are mainly used for illustration
of various types of Crystal structures.

1. Skeletal model
2. Ball and spoke models/Ball and Stick Model
3. Space-filling models
4. Crystal lattice models

1. Ball and spoke models/ Ball-and-stick Model

Ball and spoke models are a common way of representing molecular structures. Each
atom is represented by a coloured ball that is joined to other atoms using spokes to
represent the bonds between them. This type of model emphasises the bonding
between atoms.

Showing how atoms bond together

Each wooden ball has a number of holes drilled into it. These correspond with the
number of bonds that the atom can form with other atoms. The number of bonds
that can be made depends on how many electrons an atom has, which varies
depending on the element. For example, oxygen atoms can make two bonds, but
hydrogen atoms can only make one.

The chemist Wilhelm August Hofmann first used coloured balls to represent the
elements around 1865. John Dalton, who in the 19th century made great advances in
thinking about the structure of atoms, used ball and spoke models in his lectures.
Some of his models and diagrams of atoms are displayed in the Science Museum in
London.

Ball-and-stick models are three-dimensional models, where the atoms are depicted
as color-coded balls or spheres, specific to different elements. There are models
based on ball and stick that reveal the complete insight of structures, bonding, and
interactions of formula units or molecules. They have helped in understanding
chemistry i.e. The physical properties and chemical reactivities to generate and test
hypotheses.The chemical bonds that connect the atoms are represented by rods and
are easier to visualize. In doing so, the sizes of the balls are made relatively smaller,
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thereby compromising on the proportional correlation with the actual atomic size.
Yet, the ball-and-stick model defines the angles between atoms, clearly depicting the
molecular geometry of simple to more complex structures as compared to other
molecular models.

Ball and stick models are 3D models, with colored “balls” (spheres) representing
specific atoms. The “sticks” are rods that connect the atoms and represent the
chemical bonds. Two and three curved rods represent double and triple bonds
respectively. These models display the relative bond lengths and bond angles,
showing clearly the molecular geometry of most structures with relative ease.

An example is the representation of a carbon atom as a ball with 4 holes at

tetrahedral angles (an angle of 109.5° apart) where the sticks fit into.

Figure-1 Ball and Stick Models

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In addition to tetrahedral holes, there are balls with trigonal, octahedral, and 24
holes that allow rotation about the single bonds. However, the 24 holes type ball
shows molecular flexibility but makes the model slack.

Furthermore, in ball and stick model, the length (diameter) of spheres is much
smaller than the length of rods so that the atoms and bonds can be seen clearly.
Consequently, it fails to demonstrate the actual space occupied by the molecule.

The sticks can also be made flexible since rigid bonds and holes fail to show systems
with inconsistent angles. So is the case especially with double and triple bonds which
are longer and more flexible as compared to single bonds. They can restrict rotation
and support geometric isomerism (cis-trans).

There are other models such as skeletal models, spherical (space-filling) models,
polyhedral models, composite models, and computer-based models, in addition to
the ball and stick model. Ball and stick models can also be virtual computer models,
which serve to illustrate several properties including shape, flexibility, and relative
size.

This model, above all, helps in exhibiting accurate bond angles as compared to other
models.

Color codes for elements

In ball and stick model, atoms (balls) are usually represented in specific colors. These
colors are conventionally used.

Figure-2 Ball and Stick Model Kit

Comparison with Space-filling Mode

Quite often, the ball and stick model is compared to the space-filling model, which
displays molecules using spheres only, to represent atoms. The advantage of this
model is that the radii of spheres are made proportional to the radii of actual atoms,
which gives a clearer perspective on the size of the molecule. In addition, the
distance between the center of spheres is also proportional to the distance between
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atomic nuclei. These spheres are also given different colors to represent specific
atoms.

The main difference between the two is the way chemical bonds are depicted. The
space-filling model utilizes full spheres without any rods whereas the ball and stick
model employs spheres as well as rods.

Moreover, bond angles, double bonds, and triple bonds can be shown using flexible
rods in the ball and stick model while the space-filling model helps more clearly
show the relative dimensions of the molecules.

Table-1 Color Coding for Ball and stick Models

2. Skeletal Model

Simpler two-dimensional representations of chemical compounds are accomplished

using skeletal models. The illustration shows only the molecular framework or bonds
without explicitly showing the atoms. In this representation, many of the carbon
atoms and hydrogen atoms are not explicitly shown. However, the positions of
atoms are implied by the junctions or ends of the bonds.

This model helps to represent larger and more complex chemical structures.Skeletal
models are similar to the ball and spoke kind; they are both classified as 'open'
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structures, as opposed to the 'closed' space-filling type. In skeletal models, the

atoms are not shown as spheres. Instead the atoms are assumed to be at the
intersection of two or more rods, which represent the bonds. The main advantage of
skeletal models that is easy to measure angles and dimensions due to their open
structure. The skeletal models, shown in Image 2.

Figure-3 Skeletal models

3. Space-filling Model

Space-filling models give a representation of the size and shape of the whole
molecule, showing (relatively) how much space each atom occupies. Space-filling
models were first designed by H. A. Stuart in 1934.

Students use space-filling models to help when visualising whether the shape of
certain bulky structures will prevent them reacting with other molecules. However,
space-filling models make it difficult to see how the atoms bond together and
prevents seeing the structure of the whole molecule clearly. Ball and spoke
representations are much better for showing this information.

Space-filling models use a measurement known as the van der Waals radius to give
the accurate size of each type of atom, based on the density of electrons around
them.

Space-filling models are most realistic, where the atoms are scaled up in size to fill
the space between each other. The size and position of an atom in this model are
determined by its bonding properties and van der Waals radius, or contact distance.
The van der Waals radius describes how closely two atoms can approach each other
when a covalent bond does not link them. The spheres in this model illustrate the
relative space occupied by each atom within a compound, while the angles between
atoms are not clearly visible
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Figure-4 Space Filling Models

First designed by chemists Robert Corey and Linus Pauling, and later improved by
Walter Koltun, the CPK coloring convention designates specific colors to atoms of
each element. For example, according to the Corey-Pauling-Koltun (CPK) convention,
all hydrogen atoms are colored white, carbon atoms are black, nitrogen atoms are
blue, oxygen atoms are red, sulfur atoms are deep yellow, and phosphorus atoms
are purple. Alkaline earth metals are represented by dark green, and alkali metals
are indicated by violet.