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The Molecular Case Study Cycle


Shuchismita Dutta, Ph.D.; Scientific Educational Development Lead, RCSB Protein Data Bank; Associate Research Professor, Institute for Quantitative Biomedicine; Member, Cancer Pharmacology, Cancer Institute of New Jersey; Rutgers, The State University of New Jersey


Molecular visualization and structure-function discussions present a valuable lens for research, practice, and education in chemistry and biology. Currently, molecular structural data, visualization tools and resources are underutilized by students and faculty. A new community, Molecular CaseNet, is engaging undergraduate educators in chemistry and biology to collaboratively develop case studies for interdisciplinary learning on real world topics. Use of molecular case studies will help biologists focus on chemical (covalent and non-covalent) interactions underlying biological processes/cellular events and help chemists consider biological contexts of chemical reactions. Experiences in developing and using molecular case studies will help uncover current challenges in discussing biological/chemical phenomena at the atomic level. These insights can guide future development of necessary scaffolds for exploring molecular structures and linked bioinformatics resources.



 Visualizing shapes and analyzing interactions of biological macromolecules have inspired research, discovery, and technology design in both chemistry and biology. To prepare students for contributing to these fields “Structure and Function” features prominently in various community-determined education standards in both disciplines. For example, it is included in the American Chemical Society (ACS) Guidelines for Bachelor’s Degree Programs (ACS Committee on Professional Training 2015); in American Society for Biochemistry and Molecular Biology (ASBMB)’s “Concept Driven Teaching” (Tansey, Baird et al. 2013); as Threshold Concepts in Biochemistry (Loertscher, Green et al. 2014); and as a core concept in “Vision and Change” for undergraduate biology education (AAAS 2011). Undergraduate educators are constantly looking for suitable lessons/activities that meet the respective disciplinary community standards.

 In the past two decades, collaborative efforts among chemistry and biology educators have made significant progress in incorporating molecular structure-function discussions in undergraduate education. The “Molecular Visualization in Science Education” workshop (NSF 2001) recommended incorporation of molecular visualization into undergraduate chemistry curricula. Inspired by the molecular visualization and pedagogical discussions in the workshop, a series of projects developed courses and assessment strategies for using molecular visualization in chemistry education (Jones, Jordan et al. 2005). These pedagogical approaches and tools have yet to be extensively adapted for biology education. More recently, the BioMolViz group has developed and published a Biomolecular Visualization Framework (Dries et al., 2017) defining themes, goals, and learning objectives for molecular visualization of biomolecules along with relevant assessment instruments. Although many biochemistry and biology courses engage students in interactive biomolecular visualization exercises, rarely do they integrate biology and chemistry knowledge in order to get a deeper understanding of the topic being discussed.

Exploring biomolecular structures in real world contexts can provide opportunities for interdisciplinary learning. Visualizing and discussing biomolecular interactions in atomic detail can provide chemistry students a context for applying chemical knowledge, while biology students can learn how the shapes, properties, and interactions of specific molecular components can provide mechanistic explanations for cellular behavior (van Mil, Boerwinkel et al. 2013, van Mil, Postma et al. 2016). In fact, experts from different subdisciplines in biology explain molecular and cellular mechanisms slightly differently, based on methods used, biological context, analogies, and narration of stories (Trujillo, Anderson et al. 2015). Molecular case studies provide a convenient way to engage students in analyzing challenging real-world problems at the interface of chemistry and biology. Biomolecular structure-function discussions can provide a platform for integrating knowledge and interdisciplinary discussions.


Molecular CaseNet brings together a community of undergraduate educators to collaboratively develop and use molecular case studies at the interface of biology and chemistry. It was initiated in 2018 as part of an NSF RCN-UBE Incubator project (NSF DBI-1827011) to create a few examples of molecular case studies, pilot them, and gather feedback on their usability and relevance in multiple curricular contexts. The main motivation for developing molecular case studies is to engage students in applying 3D spatial reasoning and their knowledge of biology and chemistry. The cases can engage chemistry students in exploring “Biological Structures and Interactions” as part of conceptual topics in biochemistry curricula and introduce biology students to specific core concepts e.g., “Structure and function”; and “Information flow, exchange, and storage” (Brownell, 2017).

Another motivation for developing molecular case studies was to help students learn about science practices. In order to keep up with current science, besides learning about scientific concepts, it is also critical for students to learn about how scientists learn about new systems and topics. The molecular case studies can introduce students to many public biological data resources and help students learn navigate through them to learn about gene and protein sequence data archives [e.g., GenBank (Benson, Cavanaugh et al. 2013), UniProt (UniProt Consortium 2019)]; protein function and interactions with ligands, inhibitors, drugs [e.g., PubMed, DrugBank (Wishart, Feunang et al. 2018), BRENDA (Jeske, Placzek et al. 2019)]; visualize and analyze biomolecular structures available from the Protein Data Bank (Berman et al., 2003); and integrate information from all of these bioinformatics resources and the scientific literature to synthesize new knowledge and/or solve problems. Thus, molecular case studies can introduce students to various science practices and skills (e.g., “process of science”, “modeling”, “interdisciplinary nature of science” and “communication and collaboration”) (Clemmons et al., 2020).

Project Description

The Molecular CaseNet steering committee collaborated on developing the first molecular case study. Discussions began with trying to understand two things: (a) what would educators want their students to learn from the molecular case studies? and (b) how would the cases be incorporated in current curricula? Even in the early phase of these discussions it became clear that chemistry and biology educators (and students) had different interests, expectations, and preparations for navigating through the cases. While chemistry educators did not have a lot of time in their curricula to discuss the central dogma of biology and related concepts, biology educators did not have a lot of time in their courses to review chemical interactions that form the foundation for molecular case studies. To fully participate in case discussions students (and educators) would need scaffolds to learn discipline specific and/or case theme related vocabulary and concepts. Additionally, to engage multidisciplinary educators and students in use of molecular case studies the cases needed to be modular, and open-ended so that they can be adapted to different curricular contexts.

Considerations in Developing a Molecular Case Study

            The first molecular case study, “Nicholas’ Story” (Dutta et al., 2020), was written collaboratively by the seven-member steering committee. Discussions and considerations while writing the case guided the development of a general format for molecular case studies. Key components, resources, tools, and conceptual frameworks considered in developing the first case are described here.

  1. Case theme: this engages the students and educators provides a real-world context for the case study. In order to make it easy to incorporate in the curricula a theme that is common to both biology and chemistry curricula was selected for the first case study. In subsequent cases a broad range of topics were selected to match curricular interests.
  2. A hook: such as a video, narrative, image, story, scientific report, biological phenomenon, newspaper article etc. related to the case theme had to be identified to engage students in the case. The actual case discussion focused on explaining an observation, answering questions, and/or solving a problem posed in the case, all in molecular detail.
  3. Getting to the structure(s): No assumptions were made about students’ prior knowledge of the case theme. So, they were either directly introduced to molecules playing a role in the case or guided through the scientific literature to identify them. Following this, students were asked to identify 3D structures of case-related proteins and complexes in the Protein Data Bank. If no suitable structures were found, structures of molecules that are similar in amino acid sequences, 3D structures, and/or functions, were identified for exploration. A number of public bioinformatics data resources and tools were included in the case to help identify molecules related to the topic of interest. Instructions for how to access and use these bioinformatics resources were included within the case.
  4. Molecular exploration:  A number of free molecular visualization software/platforms are available to explore biomolecular structure(s), e.g., Jmol/JsMol (Jmol Development Group 2008), UCSF Chimera (Pettersen, Goddard et al. 2004), Pymol (DeLano 2002), or iCn3D (NCBI Resource Coordinators 2017). In some instances, the Online Macromolecular Museum (OMM, offered pre-made interactive visualizations. In curricular contexts where limited time is available for active hands-on visualization, pre-made OMM exhibits (if available) were used for molecular exploration. For active visualization and exploration, a web-based tool such as iCn3D was preferred to minimize additional requirements for downloading and installing software. Instructions for accessing and using relevant visualization tools were included within the case.
  5. Modeling: in order to discuss the molecular structure and interactions and answer the case questions students may have to consult the scientific literature and other data resources. By combining information from the literature, various public bioinformatics data resources/tools, and structural explorations, answers for the case study questions can be synthesized.

Experiences from developing the first case underscored the need for a framework to tie together these elements in a molecular case study.

Format for Molecular Case Studies

The Molecular Case Study Cycle was created as a framework for developing, using, and discussing cases at the interface of biology and chemistry. The cycle can help educators and researchers with varied experiences and expertise to meaningfully use and contribute to the case study collection. It can also help authors of molecular case studies organize parallel sets of discipline specific instructions for implementing the case in various curricular settings.

In its current rendition, the Molecular Case Study Cycle (Figure 1) has two halves - one representing the concepts, data resources, and skills commonly discussed in biology curricula (colored pink), while the other half represents knowledge and skills required for discussing and applying chemical concepts (colored blue). Molecular structures are conveniently positioned at the interface of the two halves of this cycle and provide a platform for discussing molecular mechanisms of observations on either side of the cycle. The Molecular CaseNet Steering Committee decided that each molecular case study should be guided by the molecular case study cycle and engage students in navigating through the complete cycle at least once.


Figure 1: Molecular Case Study Cycle showing the biological phenomenon and information about it on the right (colored pink) and chemical interactions and discussions on the left (colored blue).


The Molecular Case Study Cycle was presented at various meetings and workshops to gauge interest in undergraduate educators for developing and using molecular case studies. Within the past year ~10 undergraduate chemistry, biochemistry, and biology educators have collaborated with Molecular CaseNet Steering Committee members to write seven case studies on a variety of topics. All the case studies developed so far, begin with a question related to a biological process, phenomenon, or problem. Initial discussions in the case focus on identifying the protein(s) and/or complexes that play a role in the process/problem being explored in the case. In some instances when the 3D structures of the case specific proteins or complexes are not available, structures of related proteins (e.g., from another organism) may be chosen for case discussion. Once one or more relevant PDB structures are identified the overall 3D shapes and interactions of the molecule can be examined using specific visualization tools and used for explaining cellular, and organismal level functions in molecular detail.


            The molecular case studies were pilot tested to find out if they were useful and relevant to different curricular contexts. In Spring 2020 Molecular CaseNet collaborated with the Quantitative Biology Education and Synthesis (QUBES) network to host a Faculty Mentoring Network (FMN). A group of fifteen undergraduate educators, teaching in a variety of curricular settings, participated in the semester long FMN. They provided feedback on the cases, adapted them to meet their specific curricular needs and used them in their classrooms. Some of these educators used the cases in small classrooms (~5 students), while others in a large classroom (over 100 students). Educators teaching introductory courses had to scaffold the cases they chose to meet their students’ needs, while more advanced students engaged in exploring additional sections developed by the educator teaching the case. A couple of new cases were also written during this FMN. After incorporating feedback from the FMN participants these cases were published on the QUBES platform. The various adaptations that the FMN faculty created were also published on QUBES. The cases themselves are freely available from the Molecular CaseNet website ( for anyone to use and adapt.

            Conversations with chemistry and biology faculty has begun to shed light on barriers that may be preventing educators from using molecular structures in teaching and learning. Informal discussions in various workshops and meetings uncovered the need for developing scaffolds to help students (and educators) learn some discipline specific vocabulary, foundational concepts and skills in order to fully participate in case discussions. For example, introductory chemistry students need to understand concepts in biology such as the central dogma in order to meaningfully navigate through and integrate information from a variety of public biological data resources. Similarly, biology students need a refresher on the properties of covalent and various non-covalent interactions that stabilize biomolecular structures and form the foundation of molecular interactions. Both chemistry and biology faculty and students need to learn about the contents, navigation, and use of data from various bioinformatics resources (including 3D structural data from the PDB). Inclusion of scaffolds may help educators with limited prior experience with molecular structures to gain confidence in teaching their disciplinary content in molecular detail.

Selected members of Molecular CaseNet have initiated a process for addressing the need for scaffolds in facilitating broad use of molecular case studies. In Fall 2020, as part of the Biome Institute organized by QUBES, a small group of undergraduate educators reviewed various education standards in chemistry and biology to identify knowledge gaps and common misconceptions in chemistry and biology instructions. The group has begun developing scaffolds for students (and educators) that can be used in preparation for and/or during the case discussions. Quick refreshers and scaffolds developed here will be suitably integrated with the published molecular case studies at different points of Molecular Case Study Cycle. The and training materials will also be shared on the Molecular CaseNet website for being included in cases developed in the future and/or inclusion in teaching and learning outside of the molecular case studies.


The Molecular CaseNet community is growing. Several undergraduate educators have joined the community and participated in developing/using the cases in a variety of curricular contexts. The Molecular Case Study Cycle provides a foundation for educators to engage in interdisciplinary collaborations to develop and use case studies. It also helps identify and organize knowledge gaps/misconceptions in both disciplines. Use of molecular case studies and creation of training material for explorations at the interface of chemistry and biology will strengthen the foundations for interdisciplinary learning. In addition to learning specific disciplinary contents, use of molecular case studies will help train participating students (and educators) in navigating various public data resources and using bioinformatics tools to acquire skills/experiences that better prepare them for learning, teaching, and research.

The Molecular Case Study Cycle provides a framework for key elements necessary for developing a molecular case study. Some of the important ones include a hook or a story to engage the student/ case study participant; motivation (e.g., observation, question, problem) and guidance (scaffolds) to navigate through relevant biological data resources to learn about and gather information related to the case; PDB structures relevant for the case discussion; and appropriate visualization/analysis tools for modeling the system and discussing the molecular basis of the case theme. Currently, all cases available from the Molecular CaseNet website are motivated by a biological process, question, or problem. Through the case discussions students explain the process, answer the question, or begin solving the problem in molecular detail. However, molecular case studies may begin at any point in the Molecular Case Study Cycle. For example, the motivation for the case may be a chemistry or even a molecular structural observation or question. The Molecular CaseNet welcomes chemistry, structural biology, and other disciplinary educators to collaborate in developing and piloting new case studies for the collection. 

Requesting a Key

All molecular case studies and related resources are freely available online ( Educators can access accompanying teaching notes by requesting for an account by writing to the author (


I am grateful to all members of the first Steering Committee of Molecular CaseNet [Kimberley Cortes (Kennesaw State University, GA), Henry Jakubowski (College of Saint Benedict, St John’s University, MN), Melanie Lenahan (Raritan Valley Community College, NJ), David Marcey (California Lutheran University, CA), Patricia Marsteller (Emory College of Arts and Sciences, GA), and Cassidy Terrell (University of Minnesota, Rochester, MN)] for helping develop the Molecular Case Study Cycle. I also thank all participants in the workshops, presentations, advisory meetings, and undergraduate faculty networks where Molecular CaseNet was presented and piloted for useful discussions and feedback on molecular case studies and its format.


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12/10/20 to 12/12/20


Dr. Dutta,
If this type of case study is used in introductory courses, in your view (and in the view of readers), should the goal be:
A. Teach students to solve a problem by thinking like a scientist?
B. Teach strategies that can be used by students to solve complex problems?
C. Teach strategies that can be used by students to solve simple problems?
D. Ask students to engage in retrieval practice on facts and procedures learned recently that are part of the case study topic?
E. Ask students to attempt to apply facts and procedures they have memorized?
F. Wire context cues into neural networks that help with fact and algorithm recall?
G. Engage students in solving an interesting complex problem -- with lots of help from experts?
Your paper notes that instructors have found “the need for developing scaffolds to help students (and educators) learn some discipline specific vocabulary, foundational concepts and skills in order to fully participate in case discussions.”
This would seem to support the advice to instructors of cognitive scientist Barak Rosenshine. His summary of cognitive research finds that for novice learners, which would include most undergraduates, instructors need to “prepare students for independent practice” and that “hands on activities” should be “always after, not before, the basic material was learned.”
My reading of your findings and Rosenshine would be that in introductory courses, goals C-G above would be appropriate, but for A and B above to be the goals in case studies, students would likely need to be in courses above the introductory level. Is that in line with your experience?
-- rick nelson

Thank you Rick for your thoughtful feedback. I would like to address your question in two parts:

a. Purpose: The case studies are designed to engage students in visualizing, identifying, and discussing biomolecular structures and interactions leading up to understanding biomolecular function. The opportunities for problem solving, thinking like a scientist etc. are added benifits of engaging student in the case studies.

b. Timing: I appreciate your pointing me to Barak Rosenshine's work. I looked up his Principles of Instructions and I totally agree with your analysis. Educators who piloted the cases in introductory courses had to teach some foundational materials before beginning case discussion, whereas case discussion with advanced students did not require a lot of guidance. While it is true that it is important for students to know what hydrogen bonds and disulfide bridges etc. are before they are expected to apply that knowledge in the context of a case, our observation is that knowing the definitions of these types of interactions does not necessarily enable students to recognize them in the context of a biomolecular structure. We are developing additional educational materials (e.g., videos) that can help students learn.

In general the cases are being written so that they can be adapted for a variety of curricular contexts. We welcome more feedback from the community (especially the chemistry educators) regarding improving instructions included in the cases to make them useful in their classrooms.


Hello ConfChem Readers/Participants,

Do you teach about molecular structures and interactions? If you were to try out a molecular case study what would that be about?

Which molecule and what interactions would you like to showcase in your case study? I am not a chemist but am looking forward to learning about your interests.



Hi Shuchi,

As a medicinal chemist who teaches organic chemistry, I reserve the last week of my Organic 2 course for exploration of acetylcholinesterase and chemical warfare. I initally wrote my materials for when Syria was suspected of using Sarin or VX. I have shifted that discussion in recent years towards the Novichok agents that have been suspected in recent espionage. I walk the students through acetylcholine biosythesis, receptor pharmacology, acetylcholine mechanism of action, and eventually get to how serine esterases work at the molecular level. We get to play with cation-pi intermolecular forces, discuss the history of why it is called the anionic binding site and why that is a misnomer. I have developed a number of resources, but would like to work with your team to create a better case base approach, and some really great visualizations of enzyme active site inhibition (either competitive inhibition, or covalent interactions). I would like to also incorporate a dry lab experience with some computational chemistry/visualization. Please let me know if you would like to collaborate on a case based on that material. 

Another molecule of interest that I think unfortunately too many chemists use as an example for chirality and its importance is thalidomide. Too many use this as the example of what can go wrong and "if we only had used the single enantiomer." What I teach is that that chiral center is alpha to a carbonyl and that keto-enol tautomerization makes this argument moot in an in vivo setting. I reference a published study in mice that indicate that it doesn't matter which enantiomer you give, you still wind up with birth defects. 


Hello Ehren,

Thanks for your reply. Both the molecules that you suggested (Sarin and Thalidomide) are great topics for molecular case studies. I see that there are some relevant structures in the PDB and I would greatly appreciate your chemistry educator perspectives in exploring and discussing these molecules. I am definitely interested in collaborating to develop case studies on these topics. Will reach out to you about this by email.



11-Dec-2020 20:00 Rehovot, ISRAEL
Dear Ehren
Thanks sending your msg to Shuchi.
We’d also would be pleased to collaborate with you and Shuchi.
Our group at the Weizmann (Sussman & Silman) solved the first 3D structure of AChE and the first complexes with VX, Sarin & Soman,
as well as a number of the 1st generation Alzheimer’s Disease drugs complexed with AChE.
In addition to standard PyMol type presentations, we could make specific Proteopedia pages to help in your organic chemistry course.
Pls let me know if this would be of interest, and if yes, maybe we could have a Zoom talk on it next week, together with Shuchi.
best regards

Prof. Joel L. Sussman.
Dept. of Structural Biology tel: +972 (8) 934 6309
Weizmann Institute of Science fax: +972 (8) 934 6312
Rehovot 76100 ISRAEL mob: +972 (50) 510 9600

Dear Joel,

Thank you for chiming in. I was thinking about your structures when I read Ehren's suggestion to make molecular case studies on AChE and Sarin. While the presentation and formatting of materials in Proteopedia and Molecular CaseNet may be slightly different, I am happy to collaborate with Ehren and you to develop a case and suitable materials for both projects. 

If you are all willing I am happy to host a meeting to discuss this further in Jan 2021. Please advise.



Dear Shuchi
Sounds terrific, very much would like to participate at your meeting in Jan 2021, pls send me details when you have them
best regards

I am observing the development of these new collaborations with great interest because I would be interested in using the case studies developed by Shuchi, Ehren, and Joel in my classes.  Perhaps someday I would be able to contribute to the development of case studies.  For now I am happy to know about the development of these materials, which I'm confident will spur my students' interest.

Jennifer Muzyka

Centre College

Dear Jennifer,

Thank you for comment. We will surely inform you when the case comes together. I also look forward to collaborating with you at some future date to write cases about topics/stories that interest you, perhaps MurA bound to inhibitors?



Hi all,

I teach a course on chemical weapons at the Middlebury Institute of International Studies at Monterey. My class is for graduate students who are planning careers related more to policy rather than science, but I still might be useful for the development of a case study on sarin.  

Ehren - I'm really interested in the information you provide your students on acetylcholinesterase and nerve agents. Do you have PowerPoint slides or references that you'd be willing to share? If so, could you contact me outside of the conference at

Many thanks


Hello Mark,

Thanks for your interest. We will surely reach out to you when the case is ready.




When I looked at the list of cases on the Molecular Casenet website, I notice that some cases say they are designed for students with a biology background and others for students with a chemistry background.  How do the cases differ between these backgrounds?  I'm wondering if my organic chemistry students would be able to follow the covid-19 case, which suggests it's designed for students with a biology background.  Thanks for sharing these resources with us.



Jennifer Muzyka

Centre College

Dear Jennifer,

The molecular case studies are meant to be modular and are designed to engage both chemistry and biology students. We understand that the preparation and interests of students in these courses may be slightly different. The motivation for the structural discussions may also be different. To address different disciplinary needs and students' prior exposure to some of the foundational concepts, some of the cases were written with slightly different emphasis for biology and chemistry students and follow slightly different pathways for getting to the structures. The structures and interactions remain the same but the questions asked in these versions of the cases may be slightly different.

If there is a specific case (e.g., the COVID case) which you would like to use in your course, I am happy to discuss the possibility of creating an adaptation that meets your curricular needs. Perhaps there will be others in the community who may find the adaptation useful. You may email me at sdutta@rcsb.rutgers. edu to let me know if you would like to discuss this further.



SDWoodgate's picture

I run a large interactive website for chemistry ( and am delighted to be able to use JSMol where appropriate to support learning.  I have been probing understanding by asking questions about the structures and then analysing the student results.  My first attempt was using the structure of alanine to in the context of VSEPR.  I was astounded at how poorly students answered questions where they had to choose the geometry at the particular atoms.  I had colour coding for the atoms, and eventually I put on radio buttons so that the could highlight the atom in questions with no significant improvement (11 500 users).  56% could tell me (from a dropdown) the geometry of the carbons bonded to hydrogen - 49% for the carbon bonded to oxygens - 49% could do the geometry at nitrogen.  

I had have similar results with, for example, deducing the number of branched five-carbon hydrocarbon isomers.  I am posting this as a cautionery tale.  Do no over-estimate in development of your case studies, the ability of students to analyse organic structures, even simple ones.

Dear Sheila,

Thank you for sharing the great resource and your experience with teaching students and structure analysis. I understand that analyzing structures can be challenging and not everyone is able to visualize and analyze molecules easily. My experience is that connecting the structural analysis to a specific story (e.g., in the molecular case study) can engage the students and inspire them to apply themselves a little more. However, I agree that it is important for students to have clear foundational knowledge in order to be able to participate in the case discussions.

I am currently working with other educators to develop educational materials (short videos) to learn about/review some foundational concepts - e.g., the types of covalent and non-covalent interactions commonly seen in biological macromolecules. I may reach out to you with questions, guidance, and feedback as I make headway on this front.



For anyone involved in science instruction, I’d recommend this short online resource from cognitive scientists Carpenter and Agarwal:

How to Use Spaced Retrieval Practice to Boost Learning. (2019).

As Dr. Woodgate reminds us, information students learn tends to be forgotten. UVa. cognitive scientist Daniel Willingham writes that for recall of “new knowledge to become long-lasting, sustained practice [at recall], beyond the point of mastery, is necessary.”

The PDF suggests strategies that help students gain learning that “sticks” in long-term memory, so that when it is forgotten, as new information tends to be, quick recall can be restored by a brief “refreshing of memory.” Which, for careers in the sciences, helps.

-- rick nelson

Thank you Rick for sharing the paper. Great suggestions that I will try to keep in mind in developing the molecular case studies. Appreciated.



SDWoodgate's picture

Videos are great for exposing students to content, but you only know if they have learned if you ask them to use the content and then assess the results.

The great challenge with intermolecular attractions is to persuade them of the importance of the temporary dipole attractive forces.  They are so often referred to by teachers as weak that their importance is lost.  I have done three activities with small molecules.   The organic one (12 500 users link below) was done years ago and is too long and too many words, but the data shows, that even with being led through these ideas, they find it difficult to assess (even if boiling points are given), the relative importance of the types of attractive forces based on the structures of the molecules, let alone subtlties like the high polarity of the C=O and the importance of orientation.

Bestchoice - Demo - Intermolecular organic - Page 1: Review

The data from that activity inspired the two below on really small molecules.  I decided to focus first just on permanent and temporary dipoles and leave hydrogen bonding for a second hit.  Even at the end of all of the self-guided instruction, when asked why is the boiling point of CH3NH2 higher than NH3, only 44% (750 users) chose temporary dipoles. 

Bestchoice - Demo - Temp and Permanent dipoles - Page 1: Review
Bestchoice - Demo - Hydrogen bonding - Page 1: Review

Hello ConfChem Readers/Participants,

Do you use molecular visualization tools in your class? Please share which ones you use? and Why? Is there a particular molecular visualization tool/resource that you would like to use if you included a molecular case study in your class?