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Is there a way to determine the colour and appearance of a large biomolecule?

If no one had seen chlorophyll, simply knew of its existence, would you, from its formula, be able to determine that it would be green by absorbing every other wavelength? really with any simple molecule/complex biomolecule? for that matter. And from that information, could you determine the colour change of the molecule during any given chemical reaction?

If so, please explain how to predict colour/colour-change of molecules using an explanation/equation. Thanks in advance! (:

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    $\begingroup$ I like this question. I suggest you post it in physics.stackexchange.com and chemistry.stackexchange.com too. For anyone who does not think this is worthy of World Building: I'd totally use this information to look for feasible molecules to tint an atmosphere or a soil. $\endgroup$ – The Square-Cube Law Oct 29 '20 at 18:47
  • $\begingroup$ Structural coloration seems like it would be a major problem. $\endgroup$ – Cadence Oct 29 '20 at 19:01
  • $\begingroup$ It depends on how much computing resources you have. Determining the shape of a large biomolecule is not trivial; there is an entire distributed computing project, called Folding@home, which aims to convince benevolent donors to donate CPU time for solving this type of problems. (And the light-reflecting properies of a material may depend on very much more than its chemical composition; it's a really complicated subject.) (And cholorophyll also absorbs green light; it just absorbs it a little less than red light. Chlorophyll is dark.) $\endgroup$ – AlexP Oct 29 '20 at 19:08
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    $\begingroup$ Seeing as you accepted an answer that is not in the format of answers for hard-science, would you be ok with changing that tag to science-based? $\endgroup$ – The Square-Cube Law Oct 29 '20 at 19:10
  • $\begingroup$ @TheSquare-CubeLaw It is done, my lord. $\endgroup$ – Curly Fries Oct 29 '20 at 19:49
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Yes. But actually, NO.

There are ways to determine the physical properties of a molecule from its composition AND structure. It is similar to predicting the melting point, or predicting the tensile strength of a fiber of the material, or...

But in practice it is much,much,much too complex. It is almost always easier to make a sample of the material, or even a thousand variants of it, and observe and test each.

Bear in mind that for all molecules but especially for large biomolecules, you need to know not only its empiric chemical formula, but also its orientation structure AND how it is folded. The exact same protein molecule, folded one way, is a good neurotransmitter. The same protein, folded in a different way but still having the exact same structure, is a Prion that folds its neighbors into the same shape, and clots together giving the owner Mad Cow Disease!

And yes, the different foldings of the protein are likely to have different physical properties, including color.

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  • $\begingroup$ Adding to this, gemlogy is based on a small subset of rock types that are (in many cases) doped with small amounts of other chemicals, or different crystallizations that change the color. Chalcedony and onyx are a good example, both silicates with drastically different colors. $\endgroup$ – Jackson Dunn Oct 29 '20 at 18:57
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    $\begingroup$ That's why Folding@home is a thing... Computational complexity is a harsh mistress. $\endgroup$ – AlexP Oct 29 '20 at 19:04
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    $\begingroup$ Thank you for clarifying. I was expecting this to be the answer, given the immensity of most biomolecules. $\endgroup$ – Curly Fries Oct 29 '20 at 19:08

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