MOLECULAR MODEL OF DIFFERENT COMPOUNDS

A PROJECT WORK

Submitted by:

Name: Fran Saru Magar

Roll No.: 324
Grade: 11
Section: C

Submitted to:

i
 Department of Chemistry
St. Xavier’s College, Maitighar
Kathmandu, Nepal

2025

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 CERTIFICATE OF APPROVAL

This project work entitled “Molecular Model of Different Compounds” by Fran Saru
Magar under the supervision of Rudra Rai in the Department of Chemistry, St. Xavier’s
College, is hereby submitted for the partial fulfillment of grade 11 has been accepted.

….…………………
Supervisor
Rudra Rai
Department of Chemistry
St. Xavier’s College
Kathmandu, Nepal

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 Date: 22nd January, 2025

ACKNOWLEDGEMENTS
The successful completion of this project would not have been possible without the
guidance and support of many individuals, and I feel truly fortunate to have received such
excellent supervision. The progress and outcomes of this work are a result of their
valuable assistance, and I take this opportunity to express my heartfelt gratitude to them.

First and foremost, I would like to extend my sincere thanks to St. Xavier’s College for
offering an exceptional platform that fosters research-based learning. I am deeply
thankful to the Department of Chemistry for their consistent guidance, resources, and
unwavering support throughout this project. My heartfelt appreciation goes to Neeva
Rajbhandari for their inspirational leadership and encouragement, which have been a
driving force for me. I am especially grateful to my project supervisor, Rudra Rai,
whose insightful guidance, constructive feedbacks, and constant motivation have been
instrumental in the completion of this work.

Finally, I owe immense gratitude to my family and friends for their steadfast support,
encouragement, and understanding, which helped me overcome challenges and
accomplish my goals. To all of you, thank you for your invaluable contributions to the
success of this project.

Fran Saru Magar

Level: +2
Roll no : 324
22nd January, 2025

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 ABBREVEATIONS

DNA : De-oxy Ribonucleic Acid

VBT : Valence Bond Theory

CPK : Corey-Pauling-Koltun

VSEPR : Valence Shell Electron Pair Repulsion Theory

3-D : Three Dimensional

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 ABSTRACT

Chemistry is a branch of science focused on studying the composition and

transformational properties of matter. This research explores molecular modeling using
both computational and physical methods, including stick-and-clay and ball-and-stick
models, to visualize molecular geometry and bonding. The study highlights the
effectiveness of hands-on models in demonstrating molecular shapes, bond angles, and
interactions. Key findings suggest that physical models enhance understanding of
molecular structure, complementing computational methods. Future research could focus
on advanced modeling tools and applications in education. This benefits easy learning for
primary learning of various students of different grades.

Keywords:
 Stick-and-clay

 Molecular modelling

 Molecular geometry

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 Molecular strucutres

TABLE OF CONTENTS

COVER PAGE……………………………………………………………………………i

CERTIFICATE OF APPROVAL……………………………………………………….ii

ACKNOWLEDGEMENTS………………………………………………………….…iii

ABBREVEATIONS…………………………………..…………………………………iv

ABSTRACT………………………………………………………………..……………..v

TABLE OF CONTENTS………………………………………………………………..vi

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1. INTRODUCTION……………………………………………………………….……1

1.1 Molecule

1.2 Molecular Model

2. OBJECTIVES…………………………………………………………………………3

3. LITERATURE REVIEW……………………………………………………………..4

4. RESULT AND DISCUSSION………………………………………………………...5

4.1 Molecular Modelling

4.2 Preparation of Molecular Model using Stick and Clay

4.3 Structure and Geometry

4.4 Visualization

5. CONCLUSION………………………………………………………………………..8

6. SUGGESTION FOR FURTHER RESEARCH……………………………………..9

7. REFERENCES………………………………………………………………………10

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 CHAPTER - I
INTRODUCTION

1.1 Molecule

The smallest particle of an element or compound having independent existence is called a

molecule. For example, H2O represents one molecule of the compound water, and Cl 2
represents one molecule of the element chlorine. It should be noted that molecules may
be monoatomic (made up of one atom only), diatomic (made up of two atoms), triatomic
(made up of three atoms) or polyatomic. Similarly atoms may be homo-nuclear (made up
of atom of same element, e.g. H2) or hetero nuclear (made up of atom of different
element, e.g. HCl )Biological molecules, such as proteins and DNA, can be made up of
many thousands of atoms.

1.2 Molecular Model

Molecular models can be any physical representation of molecular configuration assigned

to molecular objects that are constructed to understand and explain measurable
characteristics manifested by molecules. A molecule can be represented in the form of

1.2.1 Skeletal Model

A representation of molecular structure in which covalent bonds are shown as

lines. The symbols for all elements other than carbon and hydrogen are
always drawn (unless part of a functional group). Carbon atoms can be
represented with C, or the C omitted. Hydrogen atoms can be omitted only when
bonded to carbon or if part of a group abbreviation; all other hydrogens must be
shown as H. Lone pairs, where present, do not have to shown.

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 1.2.2 Ball and Stick Model

Ball and stick models are three-dimensional models based on VBT theory where
atoms are represented by spheres of different colors and bonds are
represented by sticks between the spheres. Particular atoms are associated
with different colors, for example, black is usually used to represent carbon and
white to represent hydrogen.

1.2.3 Space Filling Models

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 Space-filling models also known as CPK models represent molecules with
spheres proportional to atomic radii, illustrating how atoms occupy space in 3D.
These models provide a realistic view of molecular shape and packing, with
atoms color-coded by element. While they effectively depict molecular volume
and interactions, they don't show bond angles or structures, making them less
useful for detailed bond analysis

CHAPTER - II
OBJECTIVES OF THE STUDY

The objectives of this research work include :

i. To know the molecular shape and geometry of common compounds

ii. To visualize the molecular model in 3-D form

iii. To identify the kind of molecular model representation

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 CHAPTER III
LITERATURE REVIEW

Molecules were first represented using lewis structure. A Lewis Structure is a very
simplified representation of the valence shell electrons in a molecule. It is used to show
how the electrons are arranged around individual atoms in a molecule. Electrons are
shown as "dots" or for bonding electrons as a line between the two atoms. The goal is to
obtain the "best" electron configuration, i.e. the octet rule and formal charges need to be
satisfied. But lewis structure was two dimensional. And then the concept of VSEPR
Theory arose which was 3D. VSEPR theory is a model used to predict 3-D molecular
geometry based on the number of valence shell electron bond pairs among the atoms in a
molecule or ion. This model assumes that electron pairs will arrange themselves to
minimize repulsion effects from one another. [1]

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Traditional ball-and-stick models have been a cornerstone in chemistry education for
decades, providing an accessible means to visualize molecular structures. Turner (1971)
emphasized their utility in demonstrating the basic concept of atomic connectivity and
molecular geometry. These models help students grasp the significance of bond angles
and the arrangement of atoms in space, fostering a deeper understanding of molecular
structures. Their simplicity and visual appeal make them highly effective in introductory
chemistry classrooms.[2]

Magnetic molecular models, incorporating elements like neodymium magnets to simulate

intermolecular forces, represent a significant advancement in model-making techniques.
Ugnu et al. (2023) explored how magnets could be embedded in molecular structures to
demonstrate not just covalent bonds but also weaker interactions such as hydrogen
bonding and electrostatic forces. Their research underscores the value of these interactive
models in enhancing students' understanding of molecular recognition, a concept critical
for fields like biochemistry and drug design.[3]

Fagerberg et al. (2010) introduced a novel molecular model that reflects quantum
mechanical properties of chemical bonds, closely resembling traditional ball-and-stick
models. This advancement enhances the visualization of molecular structures and allows
for a deeper understanding of interatomic interactions. The incorporation of topological
information into the visualization process demonstrates the relevance of ball-and-stick
models in conveying complex molecular information effectively, thus enriching both
educational and research contexts.[4]

CHAPTER IV
RESULT AND DISCUSSION

4.1 Molecular Modeling

Molecular modeling is a computational technique used to visualize the structures,

interactions, and behaviors of molecules. The advancement of molecular modeling has
revolutionized how chemists study molecular properties, offering insights into molecular

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shapes, energies, and reactivity. While traditionally performed using computer software
like Gaussian, AutoDock, or ChemDraw, molecular modeling can also be done using
physical models that provide tangible, hands-on learning experiences.

One of the benefits of molecular modeling is its ability to show molecular shapes in 3D,
making abstract chemical concepts more concrete. Molecular models, whether
computational or physical, facilitate the visualization of molecular conformations and
properties, allowing learners to visualize the geometry and structure alongside exploring
the spatial arrangements of atoms and bonds more effectively than with two-dimensional
diagrams.

4.2 Preparation of Molecular Model using Stick and Clay

The use of physical models made from simple materials like sticks and clay plays a
crucial role in bridging theoretical and practical chemistry concepts. It allows for flexible,
customizable, and tactile representations of molecules. This method is especially useful
for creating models of complex organic compounds, polymers which may be difficult to
conceptualize without a clear and visually representable structure.

Clay models are advantageous because they offer a hands-on approach that encourages
active learning. Sticks are typically used to represent bonds between atoms, while clay is
shaped into spheres to symbolize individual atoms. This combination is particularly
useful for demonstrating basic concepts such as bond lengths, bond angles, and molecular
geometry. Clay-based models enable students to visualize three-dimensional shapes,
which enhances their understanding of molecular flexibility and dynamic movement.

Furthermore, these models can be easily altered to represent different types of bonding
and molecular interactions, such as single, double, or triple bonds, and even hydrogen
bonds. The simplicity of this technique makes it a versatile and cost-effective way for
teachers to teach molecular structure in a variety of educational settings and well as for
students to produce it themselves in the comfort of their homes.

4.3 Structure and Geometry

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Molecular structure refers to the arrangement of atoms and their connectivity within a
molecule.

The VSEPR theory states that electron pairs repel each other whether or not they are in
bond pairs or in lone pairs. Thus, electron pairs will spread themselves as far from each
other as possible to minimize repulsion. VSEPR focuses not only on electron pairs, but it
also focus on electron groups as a whole. An electron group can be an electron pair, a
lone pair, a single unpaired electron, a double bond or a triple bond on the center atom.
Using the VSEPR theory, the electron bond pairs and lone pairs on the center atom will
help us predict the shape of a molecule.

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4.4 Visualization

One of the key concepts in molecular chemistry is the formation of chemical bonds.
Using molecular models to visualize bonding helps learners grasp the different types of
bonds, including covalent, ionic, and metallic bonding. The stick-and-clay models are
particularly effective in illustrating covalent bonds, where atoms share electron pairs. The
sticks represent the shared bonds, and the spheres made of clay represent atoms. This
tactile experience of manipulating the models enhances students' understanding of bond
angles, lengths, and the spatial distribution of electrons.

Ball-and-stick models, in particular, are excellent for demonstrating the three-

dimensional geometry of molecules, which is essential for understanding concepts like
hybridization and molecular orbital theory. For example, the tetrahedral arrangement of
bonds in methane (CH₄) can be more easily understood through a model than through a
textbook diagram. Additionally, these models help students visualize how multiple bonds
interact in larger and more complex molecules, such as proteins and nucleic acids

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 CHAPTER V
CONCLUSION

This research emphasizes the significance of molecular modeling in understanding

molecular structure, geometry, and bonding. The use of both computational and physical
models, such as stick-and-clay representations which are also cost effective, enhances
learning by providing a tangible way to visualize complex chemical concepts. Three-
dimensional models help better understand molecular shapes, bond angles, and atomic
interactions, making abstract concepts more accessible and engaging for students.

Additionally, the study highlights the value of different model types—skeletal, ball-and-
stick, and space-filling models—in illustrating various molecular aspects. By combining
theoretical frameworks like VSEPR theory with practical models, this research
demonstrates how molecular models are essential tools for grasping molecular behavior,
benefiting both educational and research applications in chemistry and related fields.

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 CHAPTER VI
RECOMMENDATION

Future research should integrate advanced computational tools with physical molecular
models to improve the understanding of molecular interactions. Combining software like
Gaussian with hands-on models can enhance accuracy and engagement. Alongside
integrating these methods in theoretical explanations with students to see how they fare
can help advance this research as well as learning how to make this simple and cost
effective. Researchers could also explore the use of digital tools alongside physical
models for better educational outcomes.

Expanding molecular modeling to include biomolecules and developing more cost-

effective materials for physical models would improve accessibility. The findings of this
research could have practical applications in drug design, material science, and chemistry
education.

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 CHAPTER - VII
REFERENCES

This is a list of all the relevant journals, books and all sources of information consulted in
the research work, both print and / or online.

[1] Modern Chemistry Grade 11( Asmita Publication),2024

[2] Martin Turner, Ball and Stick Models for Organic Chemistry,1971

[3] Dewi Ayu Kencana Ungu, Students’ Use of Magnetic Models to Learn
HydrogenBonding and the Formation of Snowflakes, 2023

[4] Jonas H. Fagerberg, Dissolution Rate and Apparent Solubility of Poorly Soluble
Drugs in Biorelevant Dissolution Media, 2010

For information and figures

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1) https://www.chem.ucla.edu/~harding/IGOC/S/
skeletal_formula.html#:~:text=Skeletal%20formula%20(skeletal%20structure%3B
%20line,group%20abbreviation%20such%20as%20Ph).

2) https://manoa.hawaii.edu/exploringourfluidearth/chemical/chemistry-and-seawater/
covalent-compounds/compare-contrast-connect-chemical-structures-visualizing-
invisible

3) https://www.collegesidekick.com/study-guides/trident-boundless-chemistry/
molecular-geometry

4) https://chem.libretexts.org/Bookshelves/
Physical_and_Theoretical_Chemistry_Textbook_Maps/
Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/
Chemical_Bonding/Lewis_Theory_of_Bonding/Geometry_of_Molecules

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