Molecular Modeling

Part I: Lewis Structures

In your lab notebook, each of the following compounds or ions should have at least 1/9
of a page devoted to it, as you will return to the lab and add subsequent data at a later
date. If you write large, you may want even more room for each substance. For each of
the following: Write the formula for the ion or molecule, and determine the Lewis
structure, indicating appropriate resonance structures if needed.
1. methane 14. carbonate ion
2. carbon disulfide 15. sulfur dioxide

3. chloromethane 16. sulfate ion

4. borate ion 17. tellurium tetrachloride

5. carbon tetrachloride 18. carbon dioxide
6. titanium (IV) chloride 19. iodine pentafluoride

7. oxalate ion 20. iodate ion

8. xenon difluoride 21. sulfur hexafluoride
9. sulfur trioxide 22. sulfite ion
10. phosphoric acid 23. dichloroethyne
11. arsenic pentafluoride 24. boron trichloride

12. hydrogen peroxide 25. SnF62-

13. ICl4-1

Part II: Molecular Geometry

According to the Valence Shell Electron Pair Repulsion Theory (VSEPR) the electron
pairs occupying the valence shell of an atom repel each other due to their like negative
charges. In order to minimize the repulsion, the electron pairs position themselves
around the atom so that they are far apart as possible from each other. This results in a
symmetric arrangement of the electron pairs. Two pairs results in a linear arrangement,
three pairs take a trigonal arrangement, and so on.

In forming a covalent molecule, one or more of the electron pairs is shared between two
atoms. Pairs that are involved in forming the bond are known as bonding pairs. The
pairs of electrons which are not involved in forming a bond with another atom are called
lone pairs. The total number of pairs around an atom is the sum of the bonding pairs
plus the lone pairs.
The geometry of the molecule is determined by the spatial arrangement taken by all of
the electron pairs, both bonding and lone pairs. However, when describing the shape of
the molecule, one describes only the arrangement of the atoms. For example: water
has four pairs of electrons around the oxygen atom. Two of these pairs are involved in
bonding the hydrogen atoms to the oxygen while the other two pairs are lone pairs. The
four pairs of electrons take a tetrahedral arrangement however, the two hydrogen atoms
and the oxygen atoms take a bent or "V" arrangement. Thus, the water molecule is said
to be bent.

Some atoms are bonded together using double (two pairs) or triple bonds (three pairs).
Since these multiple sets of pairs of electrons lie between the same two atoms they are
considered as one pair when determining the geometry taken by the electron pairs. For
example: carbon dioxide has two oxygen atoms each doubly bonded to the carbon
atom. Around the carbon atom are four pairs of electrons, however, two pairs are
involved in bonding each oxygen atom and there are no lone pairs. We count each
double bond as one pair so the total number of pairs around the carbon atom is two, not
four. These "two" pairs take a linear arrangement. The molecule is also linear.

In this lab activity you will examine models of several possible combinations of electron
pairs, both bonding and lone pairs, and bonded atoms. You will then describe the
geometric arrangement of the atoms in the molecule.

Materials:
Set of molecular models labeled A through R

Procedure:
Prepare a table similar to the one below in which to record data:

Model #Bonding #Lone Total 3-d Bond Name

Code Pairs Pairs Pairs Sketch Angle

For each model, examine it and identify the number of lone pairs, the number of bonded
pairs, and the total number of electron pairs on the central atom. Record this information
in your data table. Sketch the three-dimensional geometry of the molecule. Use the
following terms for describing the molecular shape: linear, trigonal planar, angular or
bent, tetrahedral, pyramidal, trigonal bipyramidal, seesaw, T-shaped, octahedral, square
planar, or square-based pyramid. The bond angle is the angle formed when one draws
a line from one bonded atom to the central atom and then to the nearest neighboring
atom. For each model determine the bond angle(s). The angle should be one of the
following: 180o, 120o, 109o, 90o.

Return to the Part I write up. For each of the Lewis Structures you draw, indicate the
number of bond pairs and the number of lone pairs. Finally, indicate the name of the
molecular geometry associated with the molecule or ion and sketch the 3-d geometry of
the molecule or ion.

Analysis
1. We assumed that all of the bonded atoms were identical. Would the molecular
shape change if they were not identical? Explain with examples.

2. We assumed that double and triple bonds were exactly like single bonds. In what
ways are they not, and what effect does this have on the shape of the molecule?

3. We assumed that the repulsion by all pairs of electrons is exactly the same.
However, it has been determined that the strength of repulsion is not exactly the
same. L.P.-L.P. > L.P.-B.P. > B.P.-B.P. (L.P. = lone pair, B.P. = bonding pair) What
effect does this have on the shape of the molecules, particularly the bond angles?
Part III: Polarity of Bonds and Molecules

The concept of bond polarity is useful in describing the sharing of electrons between
atoms. A non-polar bond is one in which the electrons are shared equally between the
two atoms. In a polar covalent bond, one of the atoms exerts a greater attraction for the
electrons than the other. If the difference in relative abilities to attract electrons is great
enough, an ionic bond is formed. The ability of an atom to attract electrons to itself in a
chemical bond is called electronegativity.

The electronegativity difference between two atoms is a measure of the polarity of the
bond between them; the greater the difference, the more polar the bond. For example,
the bonding in HF: the electronegativity difference between H and F is 4.0 - 2.2 = 1.8.
Consequently, the sharing of electrons is unequal, with the more electronegative fluorine
attracting electron density off the hydrogen. We represent this situation in the following
two ways:

δ + δ - ---->
H ― F or H―F

The δ + and δ - are meant to represent partial positive and negative charges,
respectively.
The shape of a molecule and the polarity of its bonds together determine the charge
distribution of the molecule. A molecule whose centers of positive and negative charges
do not coincide is described as being polar. The degree of polarity is measured by the
dipole moment of the molecule. To have a dipole moment, a polyatomic molecule must
have polar bonds. However, even if polar bonds are present, the molecule itself might
not have a dipole moment if the bonds are arranged so their polarities cancel. This
situation is found in the linear CO2 molecule.

<--- --->
O=C=O
Remember that the arrow points toward the more electronegative atom. In this lab you
will examine models of several possible combinations of polyatomic molecules. You will
then describe the polarity of the molecules for which you have drawn Lewis Dot
Structures in Part I, based on some derived rules for dipole moments (molecular
polarity).
Procedure:
Examine the models of polar and non-polar molecules provided by your teacher. Sketch
the examples of each in your lab notebook. Notice that different colored balls represent
different atoms. From these, develop a series of rules to identify polar and non-polar
molecules. For example: For a molecule to be polar __________ and/or _________
must be true.

Go back to Part I and apply the rules you generated to identify the molecules drawn as
polar or non-polar. Finally, state the reason for each classification.

Follow up:

1. Explain the difference between "bond polarity" and "molecular polarity".

2. In spite of the larger electronegativity difference between bonded atoms, BeCl 2 has
no dipole moment, whereas SCl2 does posses one. What is the origin of this
difference in properties?

3. How is the dipole moment of a diatomic molecule A - B expected to vary as a

function of the electronegativity difference between A and B?

Part IV: Hybridization, Sigma, and Pi Bonding

Various combinations of atomic orbital sets can be mixed, or hybridized to obtain

different geometries of orbitals about the central atom. The purpose in formulating
hybrid orbitals is to provide a convenient model in which we can imagine the electrons to
be localized in the region between two atoms. It makes no difference whether the pair of
electrons in a hybrid is involved in bonding or is a lone pair. In addition, none of these
have considered multiple bonds. The concept of hybridization can also be applied to
molecules containing multiple bonds. For example, C2H4, ethylene, possesses a
carbon-carbon double bond, and is planar about each carbon atom.

In this activity you will identify the type of hybrid orbitals and the number of sigma and pi
bonds associated with each structure drawn for Part I.

Procedure:
Sketch and identify the models shown of sp, sp2, sp3, sp2d, and sp3d2 hybridization.
For each, indicate how many unhybridized p orbitals are present in the atom. Sketch the
models of molecules demonstrating sigma and pi bonding.

Assign hybrid notation to each of the central atoms of the structures you have drawn
electron dots for in Part I. Indicate by labeling the sigma and pi bonds in each of the
structures drawn for Part I.

Analysis

1. Do all the pairs of electrons in hybrid orbitals need to be involved in bonding?

Explain using water as an example.
2. In arsine, AsH3, the bond angle predicted using VSEPR theory would be less than
(yet close to) 109.5o. The actual bond angle turns out to be very close to 90o. Does
this correspond to the predicted hybrids? Why or why not? Suggest an alternative
theory to describe the bonding in AsH3.

3. The Lewis structure of allene is:

H H
C=C=C
H H

a. Make a sketch of the molecule showing the sigma and pi bonding, analogous to
those in the introduction.

b. Is the molecule planar? Explain.