Understanding Chemical Structures/Shapes


One of the most useful tools in organic chemists’ tool-kit is the ability to visualize molecular structures and use that information to make predictions about a molecule’s shape and reactivity. This process is called conformational analysis and in the figure above we summarize some of the most common rules for drawing out the “shape” (or most stable conformation) of linear and cyclic molecules. In the figure above, the linear “main-chain” is highlighted in red and the cyclic “main-chain” is highlighted in black.

Some of the most common applications of conformational analysis include:

  • small-molecule/protein interactions (see post on Visualizing Receptor/Ligand Structures)
  • small-molecule/catalyst interaction interactions
  • the most reactive sites on small molecules (i.e. least sterically hindered)
  • the most reactive geometries of small molecules (e.g. cyclization transition-states ~ cyclic conformations



  1. Grossman, R.B. The Art of Writing Reasonable Reaction Mechanisms, Springer 1999
  2. Carey, F.A.; Sundberg, R.J. Advanced Organic Chemistry, Part A: Structure and Mechanisms. Springer 2008


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This work by Eugene Douglass and Chad Miller is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

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