AI and Chemistry some observations

Chemical structures can be a big problem for LLMs

AI and Chemistry is an increasingly popular topic for research and discussion. I thought it would be interesting to see how Large Language Models (LLMs) e.g. Gemini coped with carbon-13 NMR which is highly dependant on molecular symmetry. I asked first about cyclohexane and I got a near perfect answer – one peak due to high symmetry. For some reason I then asked about morpholine (another six -membered ring) and the trouble started.
Gemini offered a really poor chemical structure of morpholine albeit with a caveat about checking the results.

Then, when I used dictation, morpholine became morphine and a worse structure of morphine was offered.

I was not the first to draw attention to this shortcoming. Chem. Eng. News has a cautionary tale about AI and caffeine.

Text-based queries – a different story

Following some discussion on BlueSky, I wanted to give Gemini a chance to do better with a text-based query. The results were impressive and I quote them with absolutely no subsequent edits.

What is ChemTube3D ? Who would find it useful?

ChemTube3D is a free, web-based resource developed by the University of Liverpool that provides interactive 3D chemistry animations and structures along with supporting information. It covers a wide range of topics relevant to advanced school chemistry and university chemistry courses.

Key features of ChemTube3D include:

• Interactive 3D Visualizations: Users can manipulate and explore molecular structures and reaction mechanisms in three dimensions. They can rotate, zoom, and change the display style (e.g., space-filling, ball-and-stick, wireframe).
• Animations of Reaction Mechanisms: Complex organic reaction mechanisms are brought to life with animated curly arrows showing the movement of electrons.
• Coverage of Diverse Topics: The site covers areas like organic reactions, organic structure and bonding, inorganic chemistry, polymers, solid-state chemistry, and even A-level (advanced high school) topics.
• Supporting Information: Each animation and structure is accompanied by relevant text and explanations to aid understanding.
• Integration with Textbooks: Many pages include icons indicating associated textbook page numbers for further reading.
• Search Functionality: A search feature allows users to quickly find specific topics or molecules.
• Full-Screen View: Molecules and reactions can be viewed in full-screen mode for better immersion.
• Mobile App: A mobile app is available (primarily focused on organic chemistry) for learning on the go.

  ChemTube3D is a valuable resource for a wide range of individuals, including:

  • Undergraduate Chemistry Students: It helps visualize abstract chemical concepts, understand reaction mechanisms, and explore molecular structures in detail.
  • Advanced High School (A-Level or equivalent) Chemistry Students: It provides a more engaging and interactive way to learn complex topics.
  • Chemistry Educators (Teachers and Lecturers): They can use the animations and structures in their lessons and lectures to enhance student understanding. The resource can also be embedded in virtual learning environments.
  • Practicing Chemists: It can serve as a quick reference for visualizing molecules and reaction pathways.
  • Anyone Interested in Chemistry: Individuals with a general interest in chemistry can use it to explore the molecular world in an accessible way.

  In summary, ChemTube3D is a powerful and free tool that utilizes interactive 3D visualizations to enhance the learning and teaching of chemistry for students and educators at various levels.

  This would almost be suitable as a press release with no human effort!

I am told there are some good examples of additional tools that can overcome these limitations
https://www.nature.com/articles/s42256-024-00832-8
https://pubs.rsc.org/en/content/articlehtml/2025/sc/d4sc03921a but I haven’t been able to test them for myself.

Siri/ChatGPT was not so detailed.

In conclusion, my advice to our Education Secretary at this time would be not to use LLMs to mark Chemistry homework but colleagues in text-based subjects might find it very useful.