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How do analytical methods work? (TLC, UV-Vis Spectrophotometry, GC-MS, LC-MS, etc)

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endlessness said:
Thanks :)

Is there anything that isn't clear or generally could improve? I tried to make it so that people without chemistry knowledge could understand it.

No END<3 it seems to me very straight forward with great thought for a monkey like me..lol
The pic's make it very easy to understand:thumb_up: again great work!!:d
EXCELLENT POST! I have found it extremely difficult to accessible information on thee methods and their appropriate applications. Thank-you SO MUCH!

I do have a question. For a new compound that does not have any reference samples available, how would one confirm the presence and purity of it in a sample?

***** edited to remove any reference to an RC.
^The Nexus, as far as i understand it, does not support discussion of what may be termed 'RC's.
However in the interests of safety and testing it may be required to analyse them.

Unknown compounds without reference require either careful chromatograph data figure comparisons,
or advanced structural determination methods, NMR or X-Ray methods probably beyond this thread or the budget of anyone here?
We do not have any problem discussing RC's, as long as the potential dangers are recognized and info on harm reduction is clearly available. Here are three relevant links:

Regarding analysing these substances, harm reduction organizations such as the one I collaborate with have legal access to reference standards and are constantly working to be up-to-date on the new trends and substances appearing on the market. But in the case that one does not have the standard itself, there are several ways to help identifying a compound. The best is of course if you do several different analysis with different methods to complement each other.

Usually NMR is the method of choice since it gives very good structural information, and is usually what is used when a completely new substance appears and needs to have it's structure described. Before analysing with NMR, the substance needs to be separated through some method like column chromatography or ion exchange, because the NMR results cannot really be 'read' if there's a bunch of substances mixed in, you wont know what peak is from what substance.

Other methods can give some structural info too, like LC-MS/MS (which separates the substance and then bombards the substance with electrons, but instead of just once like normal GC/LC-MS, it does it several successive times, and through the different fragments one can get info on the substance's structure).

Even "simple" GC/LC-MS with access to a database of spectra already can be enough in some cases, since you might not have the standard itself but the spectra may match up perfectly with something already described in the database (which may have been added by a law enforcement agency or a university/research group that had access to the standard). The identification can be done visually or can be done through automated mechanisms like using NIST library, which will search through hundreds of thousands of substances in the database and give you the best guesses with % possibility of match.

Some people/research groups might actually go through the trouble of synthesizing the suspected substance and analysing it, so that they can confirm if the suspected substance is really what they think it is.

There are other methods using X-Ray or FTIR that also give structural information, but since I never worked with them I am not sure how 'complete' the structural info they give by themselves is.

In the case of our organization, up till now it usually has either done with standards, or with access to NIST database and comparing the mass spectra of the unknown substance to the ones in NIST database. Usually when its this second case, we try to confirm through other methods (reagents, TLC, physical properties, etc) to try to diminish possibilities of being a mistaken match, and also we are honest about our limits and uncertainties when giving results.

Now we have just gotten access to LC-MS/MS, which is very good, but we're only doing th first tests, but over time we'll have more experience with that and it should help with identification. We also have the possibility of sending the substance to a university that has NMR (though the whole process of first isolating the substance, sending to the university, having them test it and getting the results, may take long so its only done if really necessary).
Thank you endlessness. The concept of chinese factory compounds disturbed me!
I did a little research on -

X-ray crystallography

Fundamental Concepts
Lecture Supplement: X-ray Crystallography

X-ray Crystallography
• X-rays are diffracted by electrons • Diffraction: constructive or destructive interference of scattered waves • Pattern of diffracted x-rays useful to obtain orientation of atoms in space (molecular
• 1895: discovered by William Röentgen; called x-rays • 1912: von Laue, Friedrich, and Knipping: "Interference Effects with Röentgen Rays"
Experiment: passed x-rays through crystal of sphalerite (zinc sulfide); distinct diffraction pattern observed
Conclusions: (a) Crystals cause distinct x-ray diffraction patterns due to atoms. (b) Crystals are composed of periodic arrays of atoms.
• 1914: English physicists Sir William Henry Bragg and his son Sir William Lawrence Bragg showed that the scattering of x-rays could be represented as a "reflection" by successive planes of atoms within a crystal Implication: diffraction pattern can be used to determine relative positions of
atoms within a single crystal (i.e., molecular structure) First single crystal structure: NaCl
• 1915: Braggs awarded Nobel Prize
Structure Determination: A Simplified Tour
For diffraction to be observed, the wavelength (λ) of radiation must be about equal to the distances between the atoms (about 0-5 Å; 1 Å = 10-10 m); so-called "hard" x-rays correspond to x-rays or neutrons...etc

From: http://www.chem.ed.ac.uk/bunsen_learner/bunsen_xray.html
X-ray crystallography allows us to be able to determine the precise atomic positions and therefore the bond lengths and angles of molecules within a single crystal. X-ray crystallography is a technique in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analysed to reveal the nature of that lattice. Like other techniques, crystallography has its limitations as it only produces an average picture of a structure. However it is extremely powerful in that the results are very accurate, giving bond lengths to a few tens of a pico-metre; (1 Å = 100 pm).

UNIT CELL: Simplest repeating unit - array of lattice points joined together, is fundamental to a particular structure.

CRYSTAL: Stack of unit cells.


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Yes, thank-you again endlessness! That is very comprehensive and I'm gonna take some time now to read over your messages multiple times. I really need to take a basic chem course to get my head straight. I removed the reference to an RC anyway as I don't want to step close to any lines.
Hi endlessness,

Thank you for this wonderful thread!

I found some broken links while reading it so I checked all the links in the OP. Here are the broken links:

Under where to get reagents:
State of Mind | (this one never stopped loading for me, many refreshes later, still nothing)

Under column chromatography:
Link called "silica and alumina". http://orgchem.colorado.edu/hndbksupport/colchrom/images/adsorbents.jpg
Link called "here". http://orgchem.colorado.edu/hndbksupport/colchrom/images/columns.jpg
Embedded photo is missing as well.

Many thanks,

I found two of the photos, the links are new:

P.s. Endlessness, please feel free to delete this post to keep the thread nice and tidy.
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