Visualization of molecular structures and their interactions

Posted by Natasa Brouwer, Krištof Kranjc, Franc Perdih, on Jan. 20, 2022, 9:52 a.m.

Franc Perdih, Krištof Kranjc*

University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia;

* e-mail:


Challenge and goal

Lecturers can find (and use) an abundance of 2D teaching material (as figures in books, on-line sources available on screens etc.), thus these materials predominate in teaching practice. However, as we all know, molecules are 3D objects and the interactions between them take place in a 3D environment; besides we should not forget about the time component. Thus, to fully comprehend a structure of a molecule or a process (reaction, interaction) taking place between two molecules it is necessary to overcome the 2D world and step into additional dimensions. How can we imagine this? How can teachers help their students to imagine this? It is well known that this step from 2D paper (or screen) to 3D "real world" represents an enormous challenge and obstacle for the majority of students. Teachers thus often use various models, like conventional, made of plastic or wood, some of them being more advanced and using 3D printing to make their own models. But all these approaches generally present only static pictures ("frozen photos") of molecules, they are cumbersome, lack versatility, their production is time-consuming, expensive, and the final results may not be applicable for use at students' home or when courses are taking place on-line. Computer simulations of structure and interactions between the molecules can solve most of the above-mentioned drawbacks of classical approaches, thus a shift to dynamic 3D representations (models) is of paramount importance. Let's call this "molecular videos".

To conclude, we believe that the the "flat earth syndrome" is a very true problem in chemistry teaching, Many students have (or are used to) only depthless vision and therefore need “3D glasses” to understand many chemical concepts (not only molecular structures).

Topic of the user case

visualization of molecular structure

Local context (specific)

The proposed approaches toward development and application of 3D computer-generated models of molecules showing their structures and also interactions between them (including the time component of such processes) are of extreme importance for gaining profound understanding of the fundamental principles governing structure of inorganic and organic compounds and their reactions (which is a necessary fundamental knowledge to understand all further topics in these areas and in fields connected with them). However, teachers in HE rarely use such approaches, mostly they still use conventional models (if at all) and expect their students have above-average 3D comprehension, albeit it is self-evident that many lack exactly this crucial competence. This is also true at UL FKKT, where lectures of inorganic and organic chemistry are often conducted without recourse to models, due to above mentioned drawbacks. Thus, the proposed application of computer-generated models and development of an appropriate open on-line repository (library) for them would certainly encourage lecturers to use them whenever necessary and thus substantially improve their teaching performance.

Local CPD goals

Areas of initial application would be in the selected field of chemistry (organic, inorganic, and biochemistry) but would be in subsequent steps broadened to the other department of FKKT, where materials and polymer sciences, and chemical engineering would be included as well. With positive results achieved locally at our FKKT, we could proceed further, to the other faculties dealing with STEM disciplines in connection with molecules and their shapes (biology, physics, pharmacy etc.).


Needs defined in STEM-CPD Roadmap

19 design active learning classes / sessions using digital technology
4 engage students and arouse interest for the discipline in the class
24 use blended learning approach
5 be interested in their students' progress.
2 attending presentations about teaching approaches.
4 attending hands-on workshops on specific continuous professional development (CPD) topics.
5 following online courses / MOOC about teaching and learning.

CPD activities at the local university

A. Promote awareness of importance of 3D visualization of molecular structures, their polarization and changes in time (depending on the environment) thus benefiting students learning at the HE level.

  1. The examples of 3D visualization provided (and ideas on how to produce them) will inspire other lecturers to follow these good practices and develop additional models necessary for successful teaching in their own field.
  2. The idea that 3D visualization helps understanding and mastering the principles of molecular structures and interactions, is based on a plethora of literature data. Its broader application will result in establishment of good practices that will be shared and emulated, thus promoting their use throughout the STEM community as a worthwhile CPD goal.

B. Developing a 3D visualization protocol to improve teaching effectivness of university teachers at UL FKKT and to promote implementation of this protocol in as broad areas as possible, representing a better alternative to the conventional (2D) representations of molecular structures. Upon completion of the microMOOC (to be prepared) teachers will recognize the benefits of computer generated 3D (interactive) visualization techniques and be ready to incorporate them in their teaching practice.

C. Teachers that will generate their sets of 3D models will be able to deposit them in a virtual open-source library enabling other participants sharing and using of all generated structures.

Teaching and learning materials


CPD activities at the local university

  • organizing an introduction lecture on the topic, gaining an initial group of teachers that will be ready to use these protocols in their teaching practice
  • if possible, providing lectures of foreign (and domestic) experts (non chemists) on 3D visualization, computer graphical design and simulations for chemistry and other STEM HE teachers...


Teaching and learning materials

  • development of a set of microMOOCs: how to generate and develop 3D structures of molecules with open-source computer programmes; how to handle them in virtual 3D space; how to represent interactions between them in 3D space and in time (4D space).

Sustainable implementation


Expected impact of the CPD User Case

- to enable easy construction of personalized (tailored) dynamic 3D representations (models) of molecules, their interactions and transformations

- to improve the 3D perception among the users of such dynamic representations and increase the recognition of their importance

- to establish an open on-line repository of such 3D representations

Plans for eventual continuation of the CPD within the same topic

To extend these representations to other STEM disciplines where 3D objects and their transformations are also relevant (i.e. topology, knot theory, structure of atoms and nuclei, quantum chemistry and physics, transformatons of elementary particles, astronomy, structure of the Universe etc.).

Competence design interactive teaching, Engagement and motivation, facilitation discipline specific learning, Blended learning (type P1-2b, P1-3b, P1-4b)

This CPD scenario describes a User case in which lecturers develop their competence in designing interactive teaching and how to engage and motivate students and how to facilitate discipline specific thinking and how to use blended learning and develop attitudes in supporting student development and enabling students’ well-being in a learning process and inclusivity.
In this CPD scenario the participants are using a very short open online course, a micro mooc (μmooc) and professionalize in a close connection to their own teaching practice (at their workplace) and meet in person on location with the training staff and with other participants.

Learning environment

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