170 replies to this topic

[Destiny]

Why would that happen

[Chyros]

Because of the sheer amount of heat coming off of it.

[Destiny]

I thought you'd mean that the glow and the UV rays will irradiate or something the PC's parts

[Chyros]

Destiny, on 6 Dec 2010, 8:34, said:

I thought you'd mean that the glow and the UV rays will irradiate or something the PC's parts

What the hell, a UV lamp isn't radioactive or something .

[Chyros]

Vid on TLC or thin layer chromatography today, chappies.



TLC is one of the most basic means of analysing a reaction mixture. New reactions are generally monitored by TLC every x minutes to check their progression, and TLC functions as a rudimentary way of checking a compound's purity and to compare against other compounds to check what the impurities may be. It also paves the way for follow-up methods such as PLC, column chromatography etc.

TLC works by using a stationary phase, i.e. a powdery solid, through which the compounds may pass at variable speed. They are pulled through the solids by use of an eluent, a mixture of solvents with a specially designed polarity, that pulls the compounds you apply on the TLC paper to varying degrees. Using stronger eluents (more polar mixtures, such as 5% HCOOH in MeOH, to name a very polar one) will pull compounds along more strongly, while weaker eluents (very apolar ones, for example 2% DCM in hexane, to name a very apolar one) will make compounds move very little. Different compounds will, due to their varying polarity, move through the stationary phase with different speeds, and through this, separation is achieved, showing you how many compounds are (at least) present in the mixture, and if you have a reference, you can identify if a certain compound is in the mixture or not.

There are many subtleties, tips, tricks and traps to TLC, which despite seemingly a very simple analytical method, will catch the unwary synthetic organic chemist off guard. In the interests of time and accessibility of the information, I didn't cover these aspects.

More to come on subjects related to TLC.

[TheDR]

Cool stuff.

So what would use does TLC have in a real life situation?

[Chyros]

TheDR, on 8 Dec 2010, 22:04, said:

Cool stuff.

So what would use does TLC have in a real life situation?

Analogs of TLC are used for testing DNA in crime scene situations, for example. They use a different stationary phase (slime) and a different moving phase (electricity) and they call it "gel electrophoresis" but the principle remains the exact same. You also get a whole bunch of spots that differ per DNA, so if two samples give the same set of spots, it's the same DNA.

[CJ]

Chyros, on 8 Dec 2010, 22:03, said:

TheDR, on 8 Dec 2010, 22:04, said:

Cool stuff.

So what would use does TLC have in a real life situation?

Analogs of TLC are used for testing DNA in crime scene situations, for example. They use a different stationary phase (slime) and a different moving phase (electricity) and they call it "gel electrophoresis" but the principle remains the exact same. You also get a whole bunch of spots that differ per DNA, so if two samples give the same set of spots, it's the same DNA.

I'd like to point out that electrophoresis was first used to run prenatal diagnoses on fetuses in order to determine whether they had any hereditary disease

[Destiny]

That's kinda cool Chyros, so red marker ink is not red...



...say, do you have problems doing the videos with other dudes around?

[Chyros]

Destiny, on 9 Dec 2010, 2:19, said:

That's kinda cool Chyros, so red marker ink is not red...



...say, do you have problems doing the videos with other dudes around?

It varies per brand of marker, but most marker colours are not one-dye formulae. Black is sometimes composed of blue, red, green etc. or a very deep purple, and rarely actually black.

About the second thing; what do you mean?

[Destiny]

The vids you do are all alone by yourself If there were other dudes in the lab, would you still film?

[Chyros]

Destiny, on 9 Dec 2010, 8:19, said:

The vids you do are all alone by yourself If there were other dudes in the lab, would you still film?

No. I go to the lab early to avoid it, because that means a lot of re-takes and noise from the radio for example. Half the takes I did for this vid had one or more people going "hey, Thomas!" in them .

[deltaepsilon]

Chyros, on 9 Dec 2010, 17:25, said:

Destiny, on 9 Dec 2010, 8:19, said:

The vids you do are all alone by yourself If there were other dudes in the lab, would you still film?

No. I go to the lab early to avoid it, because that means a lot of re-takes and noise from the radio for example. Half the takes I did for this vid had one or more people going "hey, Thomas!" in them .

Keep the ruined takes so we can hear you telling them to shut up.

[Destiny]

You should show these outtakes

[Chyros]

deltaepsilon, on 9 Dec 2010, 10:27, said:

Chyros, on 9 Dec 2010, 17:25, said:

Destiny, on 9 Dec 2010, 8:19, said:

The vids you do are all alone by yourself If there were other dudes in the lab, would you still film?

No. I go to the lab early to avoid it, because that means a lot of re-takes and noise from the radio for example. Half the takes I did for this vid had one or more people going "hey, Thomas!" in them .

Keep the ruined takes so we can hear you telling them to shut up.

Meh, it's not usually something like that. I just record a whole vid, and afterwards I decide if I didn't stutter too much or forgot to mention anything too substantial or made some kid of ridiculous misspeak or forgot to show something I wanted to etc. I do the whole speech improvised on the spot, so sometimes it goes a bit wrong, though not too often. The most exciting thing you'd get to hear if I did is half a dozen instances of "hi Thomas" "hiya" etc.

Besides, I don't know how to do video editing so it would be too much of a bother to in the first place . As it is, I copy the vid directly from my phone and leave it exactly like it is because I don't know how to edit it.

Edited by Chyros, 09 December 2010 - 13:30.

[Chyros]

New vid on column chromatography, a method I practice very often.



Column chromatography is a separation method based on the same principles as thin-layer chromatography; see my previous video on this subject for more information: http://www.youtube.c...h?v=1rt25dy_hxw

Note that unlike TLC, column chromatography is not an analytical method, but a preparatory one; not qualitative but quantitative. You use it to purify a mixture, not determine what it's composed of. Nonetheless, column chromatography is practically always accompanied by TLC'ing the fractions to determine the compounds in them and therefore, their composition and purity.

The method employs a gel of a stationary phase in an eluent through which the compounds in a mixture may pass at variable speed. They are pulled through the solids by use of more eluent sitting on top of the stationary phase, with the polarity and properties of the eluent designed around separating any impurities as well as possible from your target compound. The eluent (with any compounds in solution) drips out at the tap at the bottom of the column and this is collected in small containers as fractions of the column. This allows you to test all the fractions for which compounds are in them, and when you know this, you can take the fractions which contain ONLY your product and discard and that contain impurities. Combination of these pure fractions and consecutive removal of the solvent will then yield your product in a pure fashion.

Thanks to TheDR for rotating the video for me: it was originally turned 90 degrees from what it is now.

[Zhao]

[Chyros]

Dat good or bad? Can't really tell from the face .

[Ghostrider]

Chyros, on 11 Jan 2011, 15:54, said:

New vid on column chromatography, a method I practice very often.

*video*

Column chromatography is a separation method based on the same principles as thin-layer chromatography; see my previous video on this subject for more information: http://www.youtube.c...h?v=1rt25dy_hxw

Note that unlike TLC, column chromatography is not an analytical method, but a preparatory one; not qualitative but quantitative. You use it to purify a mixture, not determine what it's composed of. Nonetheless, column chromatography is practically always accompanied by TLC'ing the fractions to determine the compounds in them and therefore, their composition and purity.

The method employs a gel of a stationary phase in an eluent through which the compounds in a mixture may pass at variable speed. They are pulled through the solids by use of more eluent sitting on top of the stationary phase, with the polarity and properties of the eluent designed around separating any impurities as well as possible from your target compound. The eluent (with any compounds in solution) drips out at the tap at the bottom of the column and this is collected in small containers as fractions of the column. This allows you to test all the fractions for which compounds are in them, and when you know this, you can take the fractions which contain ONLY your product and discard and that contain impurities. Combination of these pure fractions and consecutive removal of the solvent will then yield your product in a pure fashion.

Thanks to TheDR for rotating the video for me: it was originally turned 90 degrees from what it is now.

So can you customize the eluent to the compound you want to separate by adjusting the polarity/other properties of it?

[Chyros]

Ghostrider, on 12 Jan 2011, 9:35, said:

Chyros, on 11 Jan 2011, 15:54, said:

New vid on column chromatography, a method I practice very often.

*video*

Column chromatography is a separation method based on the same principles as thin-layer chromatography; see my previous video on this subject for more information: http://www.youtube.c...h?v=1rt25dy_hxw

Note that unlike TLC, column chromatography is not an analytical method, but a preparatory one; not qualitative but quantitative. You use it to purify a mixture, not determine what it's composed of. Nonetheless, column chromatography is practically always accompanied by TLC'ing the fractions to determine the compounds in them and therefore, their composition and purity.

The method employs a gel of a stationary phase in an eluent through which the compounds in a mixture may pass at variable speed. They are pulled through the solids by use of more eluent sitting on top of the stationary phase, with the polarity and properties of the eluent designed around separating any impurities as well as possible from your target compound. The eluent (with any compounds in solution) drips out at the tap at the bottom of the column and this is collected in small containers as fractions of the column. This allows you to test all the fractions for which compounds are in them, and when you know this, you can take the fractions which contain ONLY your product and discard and that contain impurities. Combination of these pure fractions and consecutive removal of the solvent will then yield your product in a pure fashion.

Thanks to TheDR for rotating the video for me: it was originally turned 90 degrees from what it is now.

So can you customize the eluent to the compound you want to separate by adjusting the polarity/other properties of it?

Yeah, definitely . There are a few things you can do with your eluent: you test the eluent with TLC because what happens on TLC will be roughly the same as that which happens in the column (at least in theory ), so if you want a dot on a TLC to move faster, use a more polar eluent (for example MeOH in DCM) while if you want it to move less quickly you can use a less polar eluent (EtOAc in hexane for example). Ideally, the dot with your product is well-separated from other dots and is located between 1/3rd to 1/2 of the pathway on a TLC. If it moves too fast, it may overlap with other dots without you being able to see it, and if it moves too slowly, you're going to be columning forever or it might not even come off at all.

If you want to catch multiple dots, for example one that elutes very quickly and one that elutes very slowly, you can use a gradient in your eluent: start off with a very apolar eluent such as Et₂O in hexane and when you have that compound off the column, you slowly add a higher concentration of a very polar eluent such as MeOH or HCOOH.

Sometimes, like in my case, the column actually reacts with your compound. Silica, the most often-used stationary phase, is acidic and can therefore form hydrogen bonds with certain compounds (which means the compound will be bound very strongly to the column and regardless of how polar your solvent is, you may not get it off your column at all) or it may protonate your compound which can sometimes destroy the compound. To prevent this, you can for example use a few percents of Et₃N in your eluent, which is a weak, non-nucleophilic base (which happens to reek of semen :s) that neutralises the acidity of your column. In my case, I use complicated phosphine oxides which are impossible to get off without some base as I found the oxides are retained very strongly retained by the acidic silica:

Si-O-H ..... O=P-R

An alternative would be to use MeOH in the eluent (though this makes my compounds elute too quickly):

MeO-H ..... O=P-R

[Chyros]

Here's a photo of a very long column I ran a while ago where I took 144 fractions including TLCs for them (which took me basically all day):


Now here's a column I ran once which had an interesting effect:

The reaction mixture I tried to purify here turned out to contain all colours and separating them via column chromatography produced a very nice rainbow effect in my column.

[Destiny]

Chyros...I really really really want to make that huge tray of test tubes fall...do it for us and see what happens when all of them inside mixes!





...but that's pretty chromatography. I wonder if you shined UV or something light on it, what'll happen...

[Chyros]

Destiny, on 15 Jan 2011, 12:28, said:

Chyros...I really really really want to make that huge tray of test tubes fall...do it for us and see what happens when all of them inside mixes!

Tbh, you'd be disappointed... Remember that column chromatography is a way to separate compounds in a mixture, so when you mix all the fractions all you're doing is putting them together again .

Quote

...but that's pretty chromatography. I wonder if you shined UV or something light on it, what'll happen...

Funny you should say that, it reminded me of the following pics I took once:

A friend of mine in FOC works with pyrene () derivatives. These molecules are highly UV-active because of their extensive delocalised pi-electron system which allows them to reorganise electrons and emit photons in the form of visible light and even the tiniest contamination with them makes something very UV-active. He ran a column on them a while ago and I took some pictures. Because his molecules are so UV-active this allows him to actually see the compounds move through the column using a handheld UV lamp.

This is what the column looked like:


And this is what the eluent looked like; the minor contamination from his compounds was enough to make the entire eluent body light up like a Christmas tree:

Edited by Chyros, 15 January 2011 - 11:08.

[Destiny]

No really, it's cool! The first one looks...really...well...hmm...how do I phrase it...

[Chyros]

Blue?