How can an inexperienced chemist determine the chemical structure of a molecule?

Question

I'm a fairly inexperienced, but nonetheless interested chemist, currently planning a small project for the coming summer: I want to isolate an unknown chemical from a plant and determine it's chemical structure.

I have ample access to Carex grayi, a sedge plant, and have chosen this plant for a few reasons.

1. Of the plants growing near where I live, I can definitively identify Carex grayi. I am relatively inexperienced in taxonomy and plant identification, and I want to know which species I am working with.
2. As far as I can tell, the plant is relatively unresearched, and may or may not contain alkaloids.

This brings me to my next point. I know it may seem immature or disheartening, but my interest in chemistry stemmed from my interest in neuroscience and neurotransmitters. From countless hours of reading, I have learned much about the pharmacological (and sometimes psychoactive) tendencies of alkaloids. I realize that ingesting unknown alkaloids is extremely dangerous, and I do not intend to ingest anything. However, due to their numerous applications in medicine and recreational use, there is a massive amount of information on the internet regarding their extraction and isolation. I am entirely open to the idea of isolating a chemical from another group, but as I am inexperienced and my interest stems from neuroscience, I only really know about alkaloids. I am only somewhat familiar with terpenoids, and know little about any other group.

So, assuming I am able to extract an unknown chemical of some specified group from a plant, is there any way for me to determine the chemical's structure? The Chemical structure Wikipedia page lists the following methods for determing chemical structure:

• X-ray diffraction
• Proton NMR
• Carbon-13 NMR
• Mass spectrometry
• Infrared spectroscopy

I don't really have access to these tools as student over the summer. I am willing to spend a small amount of money on this project, but no more than about one hundred dollars. Is it too much or too difficult for a student to determine a chemical's structure over the summer? Should I do anything differently (as in, is there a certain group of chemicals that would make this project possible or easier)?

Also, is there a "classical" chemical extraction similar to this that most fledgling chemistry students would conduct? This is obviously a ridiculous made-up example: extract dandylionine from a dandy lion flower.

Answer 1

So, assuming I am able to extract an unknown chemical of some specified group from a plant, is there any way for me to determine the chemical's structure?

Yes.

I don't really have access to these tools as student over the summer. I am willing to spend a small amount of money on this project, but no more than about one hundred dollars.

Then probably no (at least not with the same accuracy you would if there weren't these constraints).

Mass spectrometry and nuclear magnetic resonance are the two most powerful analytical tools to identify completely unknown substances. This doesn't mean it's as trivial as putting your purified substance in the equipment and finding its structure. For reliable results you need a purified substance, an optimized experimental routine and of course the instrument properly set up.

In fact, before trying to determine the structure of the substance, you must purify it, and that alone is a challenge. As I'm sure you are aware, the plant contains thousands, millions of different molecules. How are you going to extract something you haven't defined? The first step would have to be defining what is it that you're looking for.

Let's consider you're looking for whatever makes plants green:

You could macerate the plant, add some water, filter the mixture, check the colors of the filtrate and of the residue, and you would notice most of the green wasn't extracted. You would find different results with different solvents though, and a better option would be ethanol. Even then, it wouldn't mean you have a pure chlorophyll solution, so several other steps would probably be required to purify the substance*. Generally speaking, you would use some kind of chromatography.

For your project, I suggest you try to first precisely define what is it you're looking for. The substance that gives the plant its color? Its smell? Its pharmacological effects? You must use this property to analyze your experimental results. You can visually inspect the color, you can smell extracts, and perhaps test physiological effects (this is obviously dangerous and shouldn't be done unless you really know what you are dealing with!). Use the target substance properties' to decide what's the best way of extracting and purifying it.

Then, considering you did purify something, without the high-tech analytical tools mentioned, there are some experiments which can indicate what you have, but they require a reference substance and usually can't be used to say that a substance is the same as another, but rather that a substance isn't the same as the reference. For example, you can compare boiling/melting points and/or thin layer chromatography retardation factors, both which can be done at home home (to some extent), and also UV/Visible light absorption/emission, which might not be trivial to do at home but require instruments that are a lot easier to find in chemistry teaching labs.

For precise tips on the extraction and identifications, it would be necessary to know what you're looking for.

It's also important to note that there's a lot you can do besides determining a chemical structure. There are several properties of a substance you can study in order to characterize it. Some examples are solubility (in different solvents, at different conditions (temperature, pH, salinity)), density, reactivity (in face of pretty much anything you find at home) and physical properties such as texture, color, smell, etc.

Finally, do not think I'm saying you should give up, your wish to discover what something is made of is what made chemistry a science, but you need to have a clearer problem to be solved. Decide precisely what it is you're looking for (in terms of macroscopic properties, chemical group or something like that), and then research (and ask!) what could you do about that without a full lab.

*Chlorophyl is actually a group of substances which have a critical role in photosynthesis, and are, of course, green.

In summary:

1. You already have your sample. Now choose your analyte, the molecule(s) you want to study.
2. Do research. Look for information on how people usually study this (group of) substances. You'll have better luck looking in education-related sources, which usually have simpler experiments.
3. Once you've found something that fits your interests and available material, do experiments. Observe the results. Change parameters, do them again, try to understand what's happening.
4. If you can't explain the results, do research, check your references, and of course, ask here. We'll be glad to help.