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The standard way of representing molecules with letters like $\ce{C}$ for Carbon, $\ce{O}$ for Oxygen etc.; and a lot of lines and double lines like a graph from Graph theory where each letter is a 'vertex', the lines like edges. I forget what this chemical notation system is called. Yet it is 2-dimensional. The formula for '$\ce{H2O}$' ,water doesn't indicate the 'angle' of 'separation' between the two Hydrogen atoms that are bonded with the Oxygen atom. Similarly a formula for some molecule like a protein might not indicate all the 'involved angles' in 3-dimensional space that 'allow' it to be folded in a precise way. So does the 2-dimensional notation system for molecules miss details of how a molecule is twisted in 3-D space? Also can two distinct molecules 'look' the same in 2-D notation?

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  • $\begingroup$ I see some inconsistencies there. $\ce{H2O}$ does not even represent topology, do you mean $\ce{H-O-H}$ ? $\endgroup$
    – mykhal
    Jun 7, 2020 at 18:00

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Below is 2 types of sugars; glucose and mannose.
Glucose an mannose
If you know how to interpret the lines, then you can determine which one is which.

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  • $\begingroup$ Very useful info. , but can two distinct molecules have exactly the same 2-D representations, with the same array of lines? $\endgroup$
    – user128932
    Sep 1, 2014 at 6:19
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    $\begingroup$ @user128932, any schematic representation is not going to be fully precise. Molecules can exist in various conformations with disparities that no generic type of projection or formula can encompass down to an arbitrary level of detail. In skeletal formulae, for example, bond angles of tetrahedral atoms are rendered as $120^{\circ}$, making the mental reservation that this is not usually the true angle. However, no two distinct molecules have the same skeletal formulae, as long as the stereochemistry is correctly depicted with wedges/dashes. $\endgroup$
    – Greg E.
    Sep 1, 2014 at 7:23
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    $\begingroup$ @GregE. Not entirely true. First, chemical formulas do not have generic notion to include electronic configuration, in rare cases it may lead to ambiguity. Also, topological features (like knots) may be impossible to figure from 2-d structure if drown without explicitly preserving them. Last, skeletal formulas fail in case the molecule has significant amount of non-covalent interactions, like ionic and dipole interaction. Luckily, all above is in full effect mostly in cases of 1) very big molecules 2) active particles 3)when it doesn't matter. $\endgroup$
    – permeakra
    Sep 1, 2014 at 8:18
  • $\begingroup$ So 2-D representations of molecular formula do not necessarily capture topological features in 3-d space important in protein folding which is very important in cellular 'mechanics'. Why do most chemistry and biochemistry books ( that I have seen) tend to focus on the 2-D notation system for molecules when explaining molecular 'activity'? $\endgroup$
    – user128932
    Sep 2, 2014 at 6:58
  • $\begingroup$ Are there two molecule that are identical except one is the mirror image of the other yet according to their 2-D representations this 'chiral' quality ( if that's the right word) is hard to see? $\endgroup$
    – user128932
    Sep 8, 2014 at 4:31

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