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Enantiomers have most physical properties exactly same, which makes them hard to seperate from one another. Due to large amounts of physical similarities and chemical similarities (when dealing with optical non active compounds) anyone will assume that if I eat any one of enantiomers of some compound I will get same amount of energy and they will perform exact same task in my body.

Given that many optically active compounds are extracted from nature, why do organisms go through pain of separating enantiomers for their consumption? Why do optical isomers are found in nature that are hard to separate in a lab?

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    $\begingroup$ They don't separate anything. The symmetry has been broken for a long time. Living organisms pretty much deal exclusively with one enantiomer because that's all they are able to make... $\endgroup$ – Zhe Jul 8 '17 at 22:13
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    $\begingroup$ I doubt that eating L-glucose or D-alanine will keep you strong and healthy. $\endgroup$ – Karl Jul 9 '17 at 9:22
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The title is actually a different question than the post, which contains several questions, but I'll answer all of them since they are closely related.

Why are optically active compounds abundant in nature?

Nature needs some kind of complexity to work. To build a living system you need hundreds, thousands or even millions of different molecules, just a few won't do it. If you just draw random molecules you'll end up with a lot of chiral ones. Unless you are sticking to linear chains without functional groups or aromatic (flat) systems you will almost always end up with chiral molecules. It actually would be surprising if there would be no chirality.

Given that many optically active compounds are extracted from nature, why do organisms go through pain of seperating enantiomers for their consumption ?

As Zhe already said in the comment: they don't need to separate those. All the animals and plants basically use only one enantiomer.

Why do optical isomers are found in nature that are hard to seperate in a lab?

Well, you are right. Enantiomers have the same physical properties unless they are in a chiral environment. Organisms on earth are able to produce only one enantiomer because the whole environment is chiral which means both enantiomers have different physical properties.

If we want to separate enantiomers in the lab we are using the same system. We take a chiral phase for chromatography (those are quite expensive) which means both enantiomers behave differently.

We are also able to synthesize enantiomerically pure compounds if we use a chiral environment during synthesis. But this is often expensive and we aren't nearly as good as biological systems doing this.

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    $\begingroup$ It's also important to point out that there are many isomerase enzymes that racemize enantiomers. This coupled with the fact that proteins are chiral and react differently with the different enantiomers sets up a natural version of dynamic kinetic resolution. Rather than separate enantiomers as is common in labs, nature forms pools of racemate starting materials which are drawn from selectively by enzymes. $\endgroup$ – levineds Jul 9 '17 at 3:25
  • $\begingroup$ Why earth become a chiral environment ? What is the benefit in doing so ? $\endgroup$ – user8277998 Jul 9 '17 at 4:33
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    $\begingroup$ @123 First both chiral twins rose from the mud, then one fell off a cliff. Pure chance. $\endgroup$ – Karl Jul 9 '17 at 9:17
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    $\begingroup$ By "chiral environment" I'm assuming you mean an environment with other "chirally imbalanced" chemicals, such as enzymes that only work on D-glucose. Is that correct? $\endgroup$ – user253751 Jul 9 '17 at 10:19
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    $\begingroup$ @immibis Yes. $\qquad$ $\endgroup$ – user8277998 Jul 9 '17 at 17:51

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