ACTIVITY # 1 more important tool for both chemists and

biochemists. Biological compounds can be

MOLECULAR MODELING IN
modeled on the computer along with the
ORGANIC CHEMISTRY
pharmaceutical candidates to study potential
interactions between the molecules.

ABSTRACT Applications such as these illustrate why this

powerful tool has now become ubiquitous in
There’s a lot of important structure
science.
in the field of science, and one of them is the
structure of molecules in a compound. In this experiment, you will be

Scientist and Chemist used molecular model trained to construct molecular models using

to illustrate the positions and functions of balls and sticks and Hyperchem software.

the elements. The Molecular Model is a The software can be downloaded from the

collection of (computer based) techniques internet.

for deriving, representing and manipulating II. OBJECTIVES

the structures and reactions of molecules,
1. To construct structures of
and those properties that are dependent on
compounds using molecular models.
these three-dimensional structures.
2. To determine properties of covalent
In this activity, we will use a bonds using the Hyperchem
software that surely help in constructing software.
molecular model and determining its
III. METHODOLOGY & SET-UP
properties.
Materials:
I. INTRODUCTION
 Ball and Stick Models
Chemists have been using molecular
 Computer
models of one kind or another for more than
a century. Building representations of  Hyperchem Software

molecules in three dimensions helps to How to use the Hyperchem:

illuminate both the structure and function of
1. Be familiar with the important features of
a compound. With the advent of computers,
the software.
molecular modeling has become an even
2. To build a molecule from scratch, begin
by double clicking on the draw key. This
will open a periodic chart for you.
3. Select carbon C and place a carbon
somewhere in the black are. Notice that you
might have to click twice to get the carbon
to show (it will appear as a small blue
circle): this is because when you click on the
periodic chart that becomes the active
window. The first time you click on the
black background, it makes the Hyperchem
window the active screen so the second click
is required to place the carbon.
4. To attach a second carbon to our first,
begin by clicking on the carbon already
there and drag a line a little ways to
represent the bond. Yu will find that the
circle disappears and all that remains is the
line. This is OK: the default rendering (that
is how the program displays molecules) os a
short hand “stick” form. This line represents
the single line between the two carbons,
with a carbon on each end. If the line does
not draw the first time, try it again.
5. If you want to connect another carbon,
simply click on one end of the line, and
draw another line.
6. If you want to draw 2-propane, all you
have to do is select Oxygen (O) from the
periodic table (click draw twice) and then
point the cursor to the middle carbon and
draw a line to represent oxygen. Notice
again that we will only get a line but this
time the line is blue on one side (whether the
carbon is) and red on the other (to represent
oxygen on the other side)
7. If you accidentally clicked on the middle
carbon twice, you will notice that it changed
from blue to red. Hyperchem assumed you
wanted to change the identity of that atom.
Just choose Carbon in the periodic chart and
double click the red bend to turn it back to
blue then click on Oxygen, click and drag
the line from the middle carbon to put the
oxygen on just as before.
8. To generate a double bond on oxygen,
click the middle line between the carbon and
oxygen. You will see it changes from a
single line to two lines, to represent a double
bond.
9. To show the number of hydrogens, close
the periodic chart and under “Build” choose
“Add H and Model Build”. This
automatically completes your molecule by
adding hydrogen to any “open valences”
(the location where iit is expecting another
bond but there is none) and selecting the
best bond lengths and angles for all atoms in
the molecule.
10. If you want to change the feature, simply 1. COMPOUND NAME:
go to “Display” and choose “Rendering” and Isopropyl Alcohol

click on “Balls and cylinders” which will BOND ANGLE: 109°

BOND LENGTH: 154 pm
make the molecules like balls.
Balls and Cylinders
11. To do theoretical calculations for energy,
click on Molecular Dynamics or MD. It
simulates the motions of molecules by
taking into account attraction and repulsion
of every atom in the system with every
atom. To run MD simulations on 2-propane
begin by going to “Set-up” and choosing
Sticks
“Molecular dynamics”. Once in there, select
one of the options, AMBER. There are two
basic ways to run MD calculations, “In
Vacuo” or in water. If you want to add
water, under “set-up” choose “periodic Balls

box”.

12. To run the calculation, go to “Compute”

and “Molecular Dynamics”. Hyperchem will
remember your choices from the previous
step. For example, MD will run using
2. COMPOUND NAME: Toluene
AMBER force field. You will notice that
BOND ANGLE: 109°
there are more choices here such as step size
BOND LENGTH: 134 pm
and time of stimulation. Typically, the
smaller the step size and the longer the run Balls and Cylinders
the more accurate the results.

13. To display results, go to “Compute” ad

you will see several options that were not
available before (such as properties).

IV. DATA RESULTS

Sticks Balls

Balls
4. COMPOUND NAME:
2.2 Dimethylpropane
BOND ANGLE: 109°
BOND LENGTH: 109 pm

Balls and Cylinder

3. COMPOUND NAME:
Benzaldehyde
BOND ANGLE: 109°
BOND LENGTH: 120 pm

Balls and Cylinder

Sticks

Sticks Balls
 5. COMPOUND NAME: 6. COMPOUND NAME:
Ethyl acetate Salicylic acid
BOND ANGLE: 120° BOND ANGLE: 109°
BOND LENGTH: 143 pm BOND LENGTH: 109 pm

Balls and Cylinders Balls and Cylinders

Sticks

Sticks

Balls Balls
 7. COMPOUND NAME: V. DISCUSSION
Benzoic acid
Molecular Modeling techniques are
BOND ANGLE: 120°
considered as useful techniques that have
BOND LENGTH: 134 pm
been proven by chemists and biochemists
Balls and Cylinders for the investigation of structure and
dynamics of molecules in organic
compounds. As graphical illustrations, with
the use of molecular modeling one can
identify the molecular dynamics
investigations and calculations of an organic
compound. For this purpose, the molecular
models will provide such information like
the central atoms of compounds,
hybridization of central atoms, bong lengths
Sticks
and bond angle.

Through the Hyperchem software, it

provides an intelligent and flexible
environment for displaying, manipulating
and analyzing molecules, compounds, their
atoms, bonding patterns, bonding angles,
covalent bond properties and their
interaction with each other. This software

Balls program is suitable for any chemistry-

related work. The operation of this software
and with the combined use of default values
and tasks wherever the user input is required
which makes it very easy to use for any new
users while keeping its full flexibility for
chemists and biochemists that are using the
software for further studies. In Hyperchem,
molecules are displayed as one or more
illustrations which embody a scheme. It
provides a complete graphical user interface
for program control, as well as a text
interface that allows complex scripts with
variable substitution, control loops, and
function calls. Also using this software with
unique features, it can be incorporated that
everything you need to study
molecular modeling is integrated in this
program which makes it as a unique tool
with many purposes that is helpful for any
type of user.
VI. CONCLUSION
In this activity, we have concluded
that the structure of compounds in molecular
models help people to understand deeper on
how to illustrate and identify the compounds
of elements. It can help in understanding
their functions and structure and
properties.
With the help of Hyperchem
software, it is much easier to construct a
compound. Also, we determined
different properties of covalent bond using
this application such as the boiling point and
melting points, specify their atom type and
other properties, specify bong lengths,
angles and the bonding geometry regarding
a selected atom.
VII. ANSWERS TO QUESTIONS
1. Explain why c-c and c=c bond lengths
in benzene have the same value?
It is because Benzene is a planar molecule
(all atoms lie in one plate), C-C in single and
double lengths are of different, C-C is
0.154nm and C=C is 0.134nm. In the
about Kekule Structure however in real benzene
all the bonds are the same because they are
intermediate in length between single bond
and double bond is at 0.139nm.
Also, C=C double bond is not constantly
positioned in any specific carbon. As they
always spinning round the six carbons in
benzene compound.
2. Arrange the following in increasing
bond lengths?
Increasing bond lengths:
its
C=O with 120 pm, C=N with 129 pm, C-O
with 143 pm, C-N with 147 pm and C-C
with 154 pm
3. Explain the difference in angle between
the
H-C=O and H-C-O?
H-C-O is 109° it is functional groups of
electrons around the middle atom the bond
gives 109°. The orbital points to the corner
of tetrahedron H-C=O 120°. It is three
groups of electrons around the middle atom
of bond give an angle of 120°.

This is to certify that the following

members of the group participated in the
preparation of this report.

Rochelle Joyce O. Bersamin

Christine Infante

Khyscia Judenly R. Lagarto