Stereocenter vs stereoisomers vs chirality

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lotus0618
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Stereocenter vs stereoisomers vs chirality

Post by lotus0618 » Sun Jan 19, 2020 6:46 pm

I'm still quite confused about stereocenter vs stereoisomers vs chiral.

This is my understanding so far: stereocenter can be connected to 3 compounds (for example: E-butene) but it doesn't have to be a chiral center. so a stereocenter has to connect to at least 3 compounds?
STereoisomers is a stereocenter in which you can flip the compounds while keeping the connectivity of carbons and you can find stereoisomers only across double bonds? ex: E-butene vs Z-butene

Also, only chiral centers can rotate plan-polarized lights (R or S) but there's no connection b/t R, S and d, l (or +/-)

and What's exactly the difference b/t D/L vs R/S?

Please speak to me like a child.
NS_Tutor_Mathias
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Re: Stereocenter vs stereoisomers vs chirality

Post by NS_Tutor_Mathias » Sun Jan 19, 2020 8:24 pm

Stereocenter:
Anything that can have a configuration. A configuration means "I can have the same guys but arrange them in different ways". This includes all chiral centers, but also includes things like double bonds with asymmetric substituents (those get the E/Z or cis/trans naming scheme).

Stereoisomer:
A version of something with a stereocenter. So if I say "Cysteine has a stereocenter" then I can also say "S-cysteine and R-cysteine are two stereoisomers".

Optical activity versus absolute and relative configuration:
Chiral centers in asymmetric molecules will cause it to be optically active. Symmetric molecules with chiral centers are called meso compounds and are not optically active.

Optical activity in turn is quantified as either d/l and/or +/-, and both just describe what happens to plane polarized light when it hits these compounds. It tells you nothing about the structure of the compound!

However, configuration (how substituents are attached to a chiral center) can either be described in a relative way (D/L, a clunky system that compares things to glycerol - don't worry about it, draw Fischer projections and know that right = D and left = L) or in an absolute way (R/S, a somewhat verbose but very accurate and consistent system that assigns each substituent a CIP priority).


Let me know if this is a good start. I have tons of examples on hand, so if there are any sticking points with these descriptions, I am more than happy to pull up some relevant images and illustrations!
lotus0618
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Re: Stereocenter vs stereoisomers vs chirality

Post by lotus0618 » Mon Jan 20, 2020 3:59 pm

Stereocenter: So pretty much anything can be a stereocenter then?


Optical activity versus absolute and relative configuration:
-d, l (+/-) tells us NOTHING ABOUT THE STRUCTURE OF the compound. ex: a R chiral center can be l or d
-R,S and D,L tell us about the configuration of the compound, but nothing about what happens if the polarized light hits the compound. R and S describe relative configuration, which means that it tells me if each chiral center in a molecule rotates clockwise or CCW. D and L tells us about the absolute configuration, which means the OVERALL of a molecule, not each chiral center of the molecule.
ex: a D molecule (the last OH is on the right) can have 2 chiral centers -one is R and the other is S

Have I nailed this down yet?
NS_Tutor_Mathias
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Re: Stereocenter vs stereoisomers vs chirality

Post by NS_Tutor_Mathias » Mon Jan 20, 2020 4:30 pm

As long as it can actually be configured in some alternate way (so you can't just rotate one way of writing the structure to get the other), it is a stereocenter. That means primarily stuff with 4 different substituents (chiral centers) and atoms with one double bond and two different substituents along their single bonds. As you study carbohydrate chemistry you'll run into more sub-types of stereocenters.

A last thing worth keeping separate is the concept of conformation and configuration: Conformations are just ways of rotating and smushing the same old bonds around without breaking ANY. These are unrelated to stereochemistry.

Everything you said about optical activity versus configurations is correct. Except this:
D and L tells us about the absolute configuration, which means the OVERALL of a molecule, not each chiral center of the molecule
D and L are descriptors of relative configuration, which means rather than assigning priorities every compound is treated as a homolog of glyceraldehyde, a maximally simple chiral aldehyde (since only C2 in glyceraldehyde can ever be chiral). This is pretty antiquated, and not a terribly sensible system, but you essentially just look at whether the next-to-last carbon (simply: the last chiral carbon) in a Fischer projection of the given molecule is pointing to the right or left. This of course won't help you name the rest of the molecule (if it has several chiral centers, as like carbohydrates tend to have), but that is fine - you'll simply have to know the names of a few specific pentoses and hexoses.

For reference:
https://en.wikipedia.org/wiki/Absolute_configuration


As an exercise, look up the structures of valine, methionine, proline and cysteine. Don't read any spoilers, just draw them. Then assign D/L and R/S to each. Let me know what you find!
lotus0618
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Re: Stereocenter vs stereoisomers vs chirality

Post by lotus0618 » Wed Jan 22, 2020 9:52 pm

I encountered tiny bit of a problem while answering your question.
First) i drew out the structure of the valine amino acid.
2nd) I drew out my Fisher projection with my eyes looking down at the CH3 and H -> CH3 and H point towards me so in my fisher projection, I have them on the horizontal line 'hugging me' and since teh NH3 and COOH group are away from me, I have them on the vertical line. My absolute configuration is S for valine (I got R and then flipped to S due to H as the last priority is towards me instead of being away from me).
However, I cannot indicate the D or L for valine because my NH3 is on the vertical line, instead of horizontal line for me to determine if NH3 is on the left or right..I know it's kind of silly but how do you do this then?
And without drawing the structure, I know that all amino acids in living cells are in the L configuration. lol
NS_Tutor_Mathias
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Re: Stereocenter vs stereoisomers vs chirality

Post by NS_Tutor_Mathias » Thu Jan 23, 2020 1:25 am

You are right that it is clunky, but it is totally fair to use what you know about homology and that all physiological AAs are L-enantiomers (provided they are chiral at all) to answer this.

I've attached an image that explains the D/L system visually pretty intuitively. Use that, and go ahead and try this exercise again. I promise it will produce some interesting and memorable results.
Attachments
homology_to_glycerol.png
(31.5 KiB) Not downloaded yet
lotus0618
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Re: Stereocenter vs stereoisomers vs chirality

Post by lotus0618 » Thu Jan 23, 2020 3:09 pm

Can you please resend the attachment? when I opened it, it's super dark so I can barely see it
NS_Tutor_Mathias
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Re: Stereocenter vs stereoisomers vs chirality

Post by NS_Tutor_Mathias » Thu Jan 23, 2020 4:11 pm

If you have this problem in the future: The easiest thing to do to avoid these problems is to right click on the link, select 'save as' and open the *.png file directly in any other viewer after downloading.

In the meantime, I've added a copy with transparency explicitly removed.
Attachments
homology_to_glycerol.png
(38.18 KiB) Not downloaded yet
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