Purity and identification methods of synthesized molecules besides using expensive equipment?

[Genecks]

As I have some organic chemistry knowledge, I've become interested in the synthesis of a variety of chemical compounds, primarily because I'm interested in their usage to observed behavioral outputs from deliberate input of a drug into an animal system (aka I want to make drugs for experimental purposes). However, I do not readily have the resources to buy an infrared spectroscopy machine. I suspect it would not be too difficult to setup some kind of thin-layer chromatography setup to analyze whether or not I have obtained the particular substance I am interested in. However, even then, I would be unsure about the results unless I had an IR and some kind of way of analyzing the purity of what I have generated.

 

As such, I have the following questions:

 

1) What are inexpensive alternatives to identifying a molecule without the usage of an IR spectroscopy machine?

2) Say that I was interested in generating modafinil or similar drugs with its pharmocological attributes, how do I test whether or not I have generated the drug I desire (assume I already have a tablet of modafinil on me).

 

On a related note, something in the back of my mind tells me that this goes into the realm of analytical chemistry, of which there are particular substances that can be generated to bind to particular domains of a molecule in order to signify that the desired product has been generated. Furthermore, such analytical techniques could be used to separate the impurities from the desired molecule. Is this right? How practical is such a thing in the realm of organic chemistry? In the realm of inorganic chemistry, I'm familiar with the idea of simply decanting a solution and further refining the obtained products for a greater yield of the desired product.

 

Also, let's assume I'm not working in an academic lab and working with invertebrate species (completely legal). I could be working with mice, but a variety of neuroscientists have become interested in invertebrates because of the myriad of chemical receptors they have (they are slightly entertaining to tease apart and research).

Edited October 8, 2011 by Genecks

[mississippichem]

There are many wet techniques to test for specific functionalities. However mass spec and NMR are usually required top draw definitive conclusions about structure. What kind of equipment do you have access to? any good handbook of analytical chemistry would be super beneficial. I do lots of spectroscopy (its kind of inherently the nature of my work) so Im probably not the best person to ask. John Cuthber seems to be knowledgeable of many wet techniques, perhaps he will chime in here.

[Genecks]

There are many wet techniques to test for specific functionalities. However mass spec and NMR are usually required top draw definitive conclusions about structure. What kind of equipment do you have access to? any good handbook of analytical chemistry would be super beneficial. I do lots of spectroscopy (its kind of inherently the nature of my work) so Im probably not the best person to ask. John Cuthber seems to be knowledgeable of many wet techniques, perhaps he will chime in here.

 

 

In reply to your question, I have no personal access to any materials at the moment. A lot of this is arm-chair thinking and to quench my curiosity about a topic I have been thinking about for a little over a month.

 

As I read that IR spectroscopy machines can cost over $20,000 USD, I am not particularly interested in buying one for personal usage. I'd be more inclined to be an electrophysiology rig or laser electrode puller with that kind of cash.

 

Hmm, perhaps I'm wrong about the cost of these IR machines.

I'm looking at this: http://www.ebay.com/itm/Perkin-Elmer-Spectrum-RX-FT-IR-Infrared-Spectrometer-/370547984682?pt=LH_DefaultDomain_0&hash=item564661892a

 

Are machines like this simple enough to do the chemical work I'm interested in? It looks decently affordable for an up-start chemist. $300 USD is non-significant compared to 25k. I'm not sure what the benefits and consequences of getting a machine like that is. Nor am I aware of why people would want to buy more up-to-date expensive models that cost well over $5000 USD.

 

From what I can recall, these machines use various kinds of materials to pass the light through, such as diamond or some other prism. As diamonds can be mighty expensive depending on the quality, I can see why the materials used can reflect the cost of the IR machine.

 

Input on these thoughts?

Edited October 8, 2011 by Genecks

[hypervalent_iodine]

1) What are inexpensive alternatives to identifying a molecule without the usage of an IR spectroscopy machine?

 

As mississippi said, the best way to identify compounds is to use NMR. IR really doesn't cut it in terms of structural elucidation/confirmation, unless your compound is well characterised and you can reference the fingerprint region to a library. Given that you can't really buy an NMR machine (practically speaking), it might be worth your while taking a trip to the chemistry department of your university (if I'm not mistaken, you still attend university, yes?) and ask whoever is in control of the NMR equipment if they could help you run a few samples. I'm not sure if this will work given that this is private research, but there's no harm in asking and it's probably your best option.

 

There are of course a million different chemical tests to help you identify structures (NMR hasn't always existed, after all), however these are usually only diagnostic for certain functional groups. If you're doing this for biological application, purity is of utmost importance and while chemical tests certainly have their benefits, they aren't going to tell you if you have byproducts in your samples.

 

 

2) Say that I was interested in generating modafinil or similar drugs with its pharmocological attributes, how do I test whether or not I have generated the drug I desire (assume I already have a tablet of modafinil on me).

 

As above, you will need to get NMR data.

 

On a related note, something in the back of my mind tells me that this goes into the realm of analytical chemistry, of which there are particular substances that can be generated to bind to particular domains of a molecule in order to signify that the desired product has been generated. Furthermore, such analytical techniques could be used to separate the impurities from the desired molecule. Is this right? How practical is such a thing in the realm of organic chemistry? In the realm of inorganic chemistry, I'm familiar with the idea of simply decanting a solution and further refining the obtained products for a greater yield of the desired product.

 

Yes, however (as I mentioned above) this won't necessarily tell you that you don't also have something else in your compound. You may generate byproducts that have the same functional groups you are testing for, but in a different position. The standard way to purify compounds is by silica gel chromatography (aka flash column chromatography). Depending on your compounds, there are also simpler ways to purify them similar to what you are describing. For example, if you are converting an azide to an amine you can remove any starting material and purify your amine simply by doing an acid base work up.

 

Also, let's assume I'm not working in an academic lab and working with invertebrate species (completely legal). I could be working with mice, but a variety of neuroscientists have become interested in invertebrates because of the myriad of chemical receptors they have (they are slightly entertaining to tease apart and research).

 

I'm assuming C. elegans?

 

Anyway, I hope that answers your immediate questions. Feel free to come back with any more specific questions related to your compounds

 

P.S. A simple FT-IR like that would probably be a sufficient in terms of getting data for simple organic compounds. To be honest though, and as I said before, IR is not really going to be that useful to you if your compounds aren't already known or if there hasn't already been IR data recorded for it in the literature.

[John Cuthber]

The simple + cheap way to check if you have a pure compound is to measure the melting point.

If the melting point is sharp you probably have a pure compound. If you recrystallise it and check again and get the same MP then it's almost certainly pure.

Identity is another matter. Even a cheap IR will give you a good clue but they are at their best for comparing a known with an unknown compound, rather that establishing an ID from scratch. That's not a problem if you can get a genuine sample to compare it with. (But remember that some tablets contain more filler than drug)

 

If you are careful, you can even check things like molar mass by titration.

For details you could do a lot worse than get an old (say 1960s or 1970s) copy of the British pharmacopoeia. They won't have a method for modafinil but they will have a method for the sulfa drugs which are somewhat similar.

 

Incidentally, while it's true that some set ups use diamond, because it's transparent to IR and hard and inert, if you don't plan to use it with reactive materials under pressure, you can use rock salt- which is rather cheaper.