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Available online at ajdhs.com 

Asian Journal of Dental and Health Sciences 
Open Access to Pharmaceutical and Medical Research 

Copyright  © 2022 The  Author(s): This is an open-access article distributed under the terms of the CC BY-NC 4.0 
which permits unrestricted use, distribution, and reproduction in any medium for non-commercial use provided the 

original author and source are credited 
 

 

 

Review on Molecular Modelling in Chemistry Education 

Itendra Singh Rajpoot, Hemant Patel, Rahul Singh Thakur, Basant Khare,  Anushree Jain, Prateek Kumar Jain, 
Bhupendra Singh Thakur* 

Adina College of Pharmacy, ADINA Campus Rd, Lahdara, Sagar, MP, 470001 

Article Info: 
_______________________________________ 
Article History: 

Received 11 Sep 2022      
Reviewed 06 Nov 2022 
Accepted 23 Nov 2022 
Published 15 Dec 2022 

_______________________________________ 
Cite this article as:  

Rajpoot IS, Patel H, Thakur RS, Khare B, Jain A, 
Jain PK, Thakur BS, Review on Molecular 
Modelling in Chemistry Education, Asian 
Journal of Dental and Health Sciences. 2022; 
2(4):55-58 

DOI: http://dx.doi.org/10.22270/ajdhs.v2i4.26    

_______________________________________

*Address for Correspondence:   

Bhupendra Singh Thakur, Adina College of 
Pharmacy, ADINA Campus Rd, Lahdara, Sagar, 
MP, 470001 

Abstract 
___________________________________________________________________________________________________________________ 

Molecular models derived from results of quantum-chemical calculations present an important category 
of didactic instruments in chemistry education. These models can be used especially as tools for 
supporting the students’ understanding by visual learning, which can adequately address complexity of 
many chemical topics, incorporate appropriate didactic principles, as well as utilize the benefits brought 
up by the actual information technology. The proposed molecular models are non-trivial examples of 
didactic application of computational chemistry techniques in illustration of electron interactions in 
amidic group, namely the interaction of the free electron pair on the nitrogen atom with the carbonyl 
group and also the interaction of atoms in the amide group with other surrounding atoms in the 
molecule. By these molecular models it is possible to explain acid-base properties of amides applying 
knowledge of electron density distribution in the molecules and the resulting electrostatic potential. 
Presentation of the structure and properties of the amides within education is important also for the 
reason that amidic functions are involved in many important natural substances (e.g. proteins, peptides, 
nucleic acids or alkaloids), synthetic macromolecular substances (e.g. Silon) or pharmaceutical 
preparations (e.g. paracetamol). This paper investigated the effect of using different types of models 
while teaching organic chemistry on student understanding of new concepts and the spatial structure of 
new molecules, as well as preference of a particular model type and illustrates the possibilities of 
computer-assisted molecular modelling in supporting chemistry teaching and learning. 

Keywords: Molecular models, Acidity, Amides, Basicity, Electrostatic potential 

 

Introduction 

Chemical concepts are abstract by nature and therefore 
challenging to illustrate in an understandable way. The triple 
mode of representation brings more challenge to chemistry 
learning on the macro level, the submicroscopic level and the 
symbolic level1. At the macro level one can see and observe 
chemical phenomena. The submicroscopic level justifies and 
illustrates the visible properties of a substance with atoms, 
molecules and ions (for example with molecular modelling). 
The symbolic level shows the macro level and micro level 
phenomena using chemical symbols, formulas and equations. 
It is important that teachers understand the threefold 
relationship so that it can be conveyed to their students2. 
While a teacher moves smoothly from one level to another, a 
student might be confused and get a fragmented vision of 
chemistry. According to Gabel (1999), the primary barrier in 
understanding chemistry is that chemistry instruction occurs 
predominantly on the most abstract level, the symbolic level. 
The unobservable submicroscopic level, in which phenomena 
and concepts are difficult to be combined with the students' 
perceptions and the living environment, produces also 
problems for students 3. Therefore students need to use 
different models, analogies or computer graphics to make 
invisible into visible4. Since models and modelling are 
essential in chemical thinking and in the development of 
scientific knowledge they should also be included in chemical 
education. Students should: learn about the nature of models 
and their usage as thinking tools; learn about the scope and 
the limitations of specific chemical models; be encouraged to 

use multiple models for a given phenomenon5. Visualizations 
help students to build mental models when learning about 
difficult concepts and submicroscopic level phenomena. That 
is why the students' visualisation skills, spatial ability 
particularly, should be developed. Computer-based molecular 
modelling has helped a variety of learners to improve their 
visualisation skills and helped them to understand the concept 
of the model, three-dimensional molecular structure and 
chemical bonds6. Molecular modelling software and computer-
assisted learning materials enable new learning environments 
where chemistry concepts and phenomena can be viewed and 
perceived in a new manner. At the same time computer-
assisted methods create new approaches enabling challenging 
chemistry topics to be clarified and simplified. Virtual models 
and visualisations can be modified according to the needs of 
teaching and learning7. Computer-based molecular modelling 
provides a tool for teaching and learning in order to support 
the visualisation of chemical phenomena and the development 
of chemistry teaching8-11. The computer enables to perceive 
things through visual experience which helps memorise things 
and improves learning outcomes9. According to the 
experiences of Finnish school teachers, computer-based 
molecular modelling helps teachers to illustrate and students 
to learn difficult concepts in chemistry in a new way, it 
develops students’ visualisation skills and makes students 
interested in chemistry12. Finnish school teachers have used 
molecular modelling to illustrate the spatial structure of 
molecules, isomerism, atomic and molecular orbitals, chemical 
bonds, electron density, IR-spectroscopy, energy and its 

                       Open Access                                                                                                                                                                                                          Review Article                                                                           

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changes in chemical processes and chemical reactions. 
Molecular modelling can also be applied to biochemistry, 
biology and biotechnology education. According to Pernaa, 
Aksela and Lundell (2009) 10, high school teachers 
experienced that molecular modelling supports the drawing of 
conclusions and the understanding of three-dimensional 
structures and it provides added value for teaching of orbitals, 
chemical bonds and biomolecules. Teachers and students 
generally have positive attitudes towards molecular 
modelling8, 12. The teacher has an important role in the success 
and effectiveness of teaching chemistry through computer-
based molecular modelling, because the use of modelling 
programs should not remain merely as a funny trick, instead 
working with a computer should be tied into teaching. The 
instructions and questions direct the learner's interest and 
activities in order to support learning tasks as well as it is 
possible and to train higher-order thinking skills13. The 
current learning theories highlight learning as a socially 
interactive process based on the students’ experiences. By 
using computer-based molecular modelling it is possible to 
support the understanding of scientific concepts, practice 
different learning skills and to motivate students to investigate 
in an authentic research environment9. There are commercial 
molecular modelling programs e.g. Spartan 
(www.wavefun.com) and HyperChem (www.hyper.com), and 
free programs e.g. ChemSketch (www.acdlabs.com), ArgusLab 
(www.arguslab.com), Symyx Draw (www.symyx-
draw.en.softonic.com), Avogadro 
(www.avogadro.en.softonic.com) and MarvinSketch 
(www.chemaxon.com). Edumol (www.edumol.fi) is an open, 
web-based environment for molecular modelling and 
visualisation. Findings indicate that molecular modelling has 
helped students to understand concepts in molecular 
geometry and bonding8 as well as in model concept, 
isomerism and functional groups14. In the ongoing doctoral 
study, the meaningful teaching model for covalent bonds (as 
opposed to rote learning) is being developed. 

Brief history of the development of molecular 
models 

The history of models15-18 can be traced back to Plato (482-
347 BC), who conceived of the four elements- soil, water, air 
and fire. Nothing much happened in terms of model 
development until in 1808 Dalton published the New System of 
Chemical Philosophy- the first substantial discourse on atomic 
theory. At the same year Malus discovered polarized light. 
Wollaston related it to tetrahedron, but noted that "It is 
perhaps too much to hope that the geometrical arrangement of 
primary particles will ever be perfectly known". In 1811 Dalton 
had a set of models of atoms and simple diatomic molecules 
constructed to help illustrate his ideas. In 1815 Biot observed 
several organic compounds that enable light polarization and 
realized that the rotation of light was due to a property of the 
individual molecule. In 1848 Pasteur found that crystals can 
be separated into two types, and in solution they rotated the 
plane of polarized light equally, but in opposite directions. 
This discovery could not be explained at that time due to lack 
of a proper model. The next indication of actual model 
construction was by Kekule in 1867, who proposed the 
tetrahedral structure of carbon bonds. In 1874 Van’t Hoff used 
models- tetrahedra joined at the apex, sides or faces to 
describe the optical isomers of tartaric acid, which raised 
widespread objection. Sachse was one of the few chemists 
who around 1890 used molecules to make predictions, and 
predicted the ‘boat’ and ‘chair’ forms of cyclohexane. During 
1900-1920 the use of ball-and-stick models became more 
widespread. In 1934 Stuart developed space-filling models 
that gave precise indications of the van der Waals radii of the 
atoms in a molecule. These were preferred over the earlier 

type, and opened the ‘golden age’ of molecular models. In 
1947 Pitzer computed the energy barrier to carbon-carbon 
bond in butane. Later, Pitzer and Hazel, who won Nobel Prize 
in chemistry, demonstrated the axial and equatorial chair form 
of cyclohexane ring. Space filling models were considered an 
indispensable tool for organic chemists during the next 30 
years and enabled the prediction of structural conformations, 
strereochemistry, reactivity and physical properties. Most 
notable was the double helix structure of DNA proposed by 
Watson and Creek in 1953, who later won Nobel Prize in 
chemistry. 

Models in science and science education 

Modeling and simulation are used in research and education 
to describe, explain and explore phenomena, processes and 
abstract ideas. Scientists, engineers and science educators use 
models to concretize, simplify and clarify abstract concepts, as 
well as to develop and explain theories, phenomena and rules. 
A model is considered useful if it is simpler than the natural 
object that it represents. An important value of models in 
science and science education is their contribution to 
visualization of complex ideas, processes and systems. A virtue 
of a good model is that it stimulates its creators and viewers to 
pose questions that take us beyond the original phenomenon 
to formulate hypotheses that can be examined 
experimentally19,20. Experimentation, however, is rarely 
presented as a way of developing, interpreting or evaluating 
explanatory models for the investigated phenomenon21. Ben-
Zvi and Genut (1998) 22 recommended teaching high school 
students about interconnections of history and philosophy of 
science on one hand and the usefulness and limitations of 
scientific models, such as the Periodic Table, on the other 
hand. Gilbert and Boulter (1998) 23 distinguish between target 
systems, mental models, expressed models, consensus models 
and teaching models. Other researchers underscored the need 
for models as enablers of students’ mental transformation 
from two-dimensional to three dimensional representations24-

26. One of the problems that arise while using concrete models 
is that insufficient emphasis is placed on the fact that models 
are theory-based simulations of reality. The theory of 
molecular structure is a kind of intellectual model27. Harrison 
and Treagust (1996) 28 claimed that the use of term "model" is 
a source of considerable semantic variation for science 
students and teachers. Models are often oversimplified and 
therefore cannot tell humans all they may wish to know about 
the real physical system that is being modeled. Teachers and 
students should, therefore, be made aware of the fact that 
models, employed in a variety of research, study and design 
contexts, are not complete representations of the realities they 
are supposed to represent29. Applied to chemistry, physical 
ball and stick models derived from polystyrene spheres and 
plastic straws are not merely enlargements of the molecules 
they are intended to represent. These are analogue models 
that are used to explain new and abstract concepts. Some of 
the properties are similar to aspects of the target they are 
representing. For example, the relative diameter of the 
spheres represents the size of the different atoms. Other 
aspects, however, are not reflected in the model. For example, 
in a ball-and-stick model type, all sticks (straws) are of equal 
length, while "real" molecular bond lengths are not. Other 
analog models focus on different properties of the molecule, 
thereby creating multiple ways of representing the same 
molecule. Teachers frequently use just one type of model, 
limiting students' experience with models and causing their 
model perceptions to be partially or completely inadequate.  

Computerized molecular modelling 

The use of concrete molecular models (made of plastic, wood 
and/or metal) to illustrate phenomena in chemistry teaching 



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has been widespread for a relatively long time30. The choice of 
model type has an impact on the image students create 
concerning the ways in which particles are shaped and how 
they function in the "real" world from a scientific viewpoint. 
Simulating different model types quickly and efficiently is 
achieved in a computerized environment, of which theoretical 
chemists, experimentalists and educators are taking 
advantage. Information technology helps relieving present-
day researchers and students from the laborious task of data 
collection and enables them to engage in creative thinking and 
problem solving. Nakhleh and Krajcik (1994) 31 investigated 
how different levels of information presented by various 
technologies affect secondary students’ understanding of acid, 
base and pH concepts. They found that students using 
microcomputer-based laboratories exhibited a positive shift in 
their concept map scores, indicating greater differentiation 
and integration of their knowledge. The development of 
computerized molecular modeling (CMM) made traditional 
models less favorable in the late 1960’s. Not only are 
computers capable of drawing and manipulating molecules in 
three dimensions. They are also powerful tools for predicting 
molecular spatial structure through energy minimization 
calculations based on quantum mechanics. These capabilities 
have opened the way for advanced research in chemistry, 
resulting, among other things, winning Nobel Prize in 
chemistry (1998). Among the advantages of using information 
technology in science education are the options of providing 

for individual learning, simulation, graphics, and the 
demonstration of models of the micro and macro world32. 
Computer aided instruction enables students to solve a variety 
of problems while carrying out their own research at their 
own pace. The use of computerized models places more 
emphasis on the creation of mental models by students and 
their use to make prediction23. Students need more experience 
with models as intellectual tools that provide contrasting 
conceptual views of phenomena, and more discussion of the 
roles of models in the service of scientific inquiry. Raghavan & 
Glaser (1995) 33 recommend that science educators become 
less concerned with the presentation of facts and concentrate 
on showing the centrality of models in research and education. 
However, most educators use a limited number of static 
models, and do not emphasize the way in which models are 
created, their essential role in science learning, or their 
advantages and limitations. Williamson and Abraham (1995) 

34 studied the effect of computer animations on college student 
mental models of chemical phenomena. Animations were used 
in two treatment situations: as a supplement in large group 
lectures and as both the lecture supplement and an assigned 
individual activity. Both treatments increased the students’ 
understanding. They attributed the improvement to the 
superior formation of dynamic mental models of chemical 
processes that were made possible by the computer 
animation.

 

 

                                                (a) 

 

                                                (b) 

 

                                                 (c) 

Figure 1 (a) Hand-Made primitive cubic unit cell; (b) Hand-Made body centered cubic unit cell; (c) Hand-Made face 
centered cubic unit cell. 



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Conclusion 

Interpretation of symbols, as well as understanding the 
particulate nature of matter and spatial structures are 
essential skills students need for solving problems in organic 
chemistry. However, model perception and understanding the 
spatial structure of organic molecules has been a source of 
difficulty for many chemistry students. A computerized 
molecular modeling (CMM)-based collaborative learning 
environment has been shown to be an effective means to 
overcome certain learning difficulties in chemistry. 

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