Normally by using single crystal x-ray analysis, we get relative stereo chemistry of the organic molecules. How to find the absolute configuration of a molecule?
By Polarimeter an instrument used for know direction of rotation of plane
polarized light, if this rotation towards right will give symbol ( R ) but if this rotation towards lift will give symbol ( S ).
Polarimeter give the configuration of a molecule as a whole. But if the molecule contain more than two stereo centers it is difficult to find the configuration of each stereo centers using polarimeter. If we are using single crystal x-ray analysis, depending on the position of the detector of the x-ray instrument , the configuration may change. That is it give only relative stereo chemistry of each stereo center. If we keep the molecule in one direction it will give one result, keeping in opposite direction give just mirror image of the earlier one. So we can't fix which is the actual one. So it is not the absolute configuration.
Sorry but R and S does have nothing to do with D(+) or L (-)...R and S is a convention. An enantiomer R or diasteroisomer with only R stereogenic centers of a molecule, this can rotate the polarised light into L (-) or vice-versa.
I also agree with prof. Lemos. CD will give the entire configuration of the molecule. In order to get stereo chemistry of each centre in molecule is not practical using the above method.
Hello Preethanuj. Try to interpritate you x-ray results with a FLACK PARAMETR.
The Flack parameter is calculated during the structural refinement using the equation given below:
I(hkl)=(1-x)|F(hkl)|^2+x|F(-h-k-l)|^2
By determining x for all data, x is usually found to be between 0 and 1. If the value is near 0, with a small standard uncertainty, the absolute structure given by the structure refinement is likely correct, and if the value is near 1, then the inverted structure is likely correct. If the value is near 0.5, the crystal may be racemic or twinned.
The technique is most effective when the crystal contains both lighter and heavier atoms. Light atoms usually show only a small anomalous dispersion effect. In this case, the Flack parameter can refine to a physically unrealistic value (less than 0 or greater than 1) and has no meaning.
If so you can modify your structure by adding a heavy atom. That should be work.
Good luck.
Thank you valdimiro, is this method is related to computational chemistry? Is it based on theoretical calculations?
Without any computational chemistry, is it possible to calculate the value between 0 to 1.
Depending on the molecular structure (alpha/beta chiral alcohols/amines/acids..) you can use NMR spectroscopy which is, in my opinion, by far the easiest method.
Chem. Rev. 2004, 104, 17−117
IR and CHN is not good for predicting stereo chemistry...we need a technology which advance the single crystal x-ray instrument using some computational calculations about the obtained parameter in ortep. Then it will be easy for us to find absolute configuration using only one technique.
Hello Preethanuj. I can suggest you the following: 1) try grow a single crystal of your substance 2) make a x-ray analysis of your substance using x-ray diffraction (i usually use Xcalibur R automated four-circle diffractometer (Agilent Technologies) ), and don't forget when you make an experiement - Friedel pairs are not equivalent (beacause of the stereo centers of your molecule) 3) collect all data experiement (.hkl, .cif_od and .ins files) and try to solve and refine it using WinGX for windows (i practically use WinGX and solve by the direct method using SHELXS-97 ) 4) when you will start to solve and refine you structure using SHELXS-97 note a flack parametr as i have written you before. If the value is near 0 than your refinement and stereo chemistry of the structure is correct, if the value is near 1, stereo chemistry of the structure should be inverted (another enantiomer). But sometimes it's rather difficult to refine in a correct way beacause of light atoms. in this case try to synthesize a similar compound which contains a heavy atom (chlorine for example) and make all steps (1-4) again, that should be work. Too many information in my answer, but thanks for your attention. With the best regards, vlad.
Thank you Vladimiro for your information and suggestions....
I see a lot of confusion here. First, the x-ray will give you an absolute, not relative configuration; until recently, it was the only reliable method for establishing the absolute configuration. Recently the VCD has emerged as another method that can be trusted.
Second, the sign of rotation (and CD measurement as well) may only confirm the configuration of the known chiral compound, and its usefulness is often limited to the compounds with just one element of chirality (center, axis, plane).
Third, the (R,S) nomenclature should not be confused with (D,L) - the latter is only describes the absolute configuration of ONE chiral center of sugars and hydroxy and amino acids.
Finally, there are indeed numerous techniques used for establishing the absolute configuration of chiral molecules, based both on instrumental methods and on synthetic chemistry; which one to choose is determined on the suitability as well as on the available resources. Many of the possible approaches are mentioned in the replies here.
Dear Shaina, it is really impossible to determine the stereo chemistry using mass spectrometry. It give idea about mass and fragmentation pattern of the compound.
X-ray method is suitable for direct resolving of absolute configuration : Determination of the Absolute Configuration of Optically Active Compounds by Means of X-Rays , Nature 168, pp.271-272 J. M. BIJVOET, A. F. PEERDEMAN & A. J. van BOMMEL doi:10.1038/168271a0
Topic is considered in March textbook of organic chemistry, some indirect (comparative) methods are highlighted.
I was sure before this discussion that thema is clear for 3-year students but I saw really bullsh💩t answers that mass spectroscopy and elemental analysis could be useful.
I agree with Rogoza... But most of the time we will get relative stereo chemistry.... That's why I asked this question.
Hi;
Absolute configuration of organic compounds are most often obtained by X-ray crystallography and NMR spectroscopy.
https://doiI: 10.1055/b-0035-116330
https://doi.org/10.5059/yukigoseikyokaishi.51.462
Best regards
I agree with Rachida... But most of the time we will get relative stereo chemistry.... That's why I asked this question
https://study.com/academy/.../absolute-configuration-rules-example.h...
Using several spectral devices for each device will demonstrate a specific set of organic compounds (IR, NMR, UV)
I agree with Rogoza... But most of the time we will get relative stereo chemistry.... That's why I asked this question.
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