This document discusses chemical structures and their relationships. It proposes that chemical structures can be understood as consisting of three ontological categories: (1) the chemical entity as a material object, (2) the chemical graph description as an information object that represents the structure, and (3) the connectivity as a mathematical object that the graph describes. The graph is about the connectivity, which depends on chemical feasibility rather than the existence of real molecules. This approach can account for the relationships between real and predicted chemical structures.

1. What are chemical structures and their relations? Janna Hastings 1 , Colin Batchelor 2 , Christoph Steinbeck 1 and Stefan Schulz 3 1 EBI Cheminformatics and Metabolism, UK 2 Royal Society of Chemistry, Cambridge, UK 3 University Medical Center, Freiburg, Germany

2. What are chemical entities? 20.10.10 Molecules Substances

4. What are chemical relations? 20.10.10

5. Mind and reality 20.10.10 REALITY mostly harmless MIND contents: concepts infinitely subjective, impossible to ensure that different people agree contents: objects descriptions are objective, disagreements between different people can be resolved by empirical investigation

7. What is the problem with this? 20.10.10

9. The chemical graph formalism 20.10.10 hydrogen atoms may be implicit paracetamol

10. 20.10.10 ATP Front view (3D) Side view (3D)

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14. Impossible molecules 20.10.10 Impossible cubane Graphs can be drawn for molecules which are chemically infeasible

25. Thank you for your attention