I took a chemistry class in high school, and I kind of still remember the basics of chemistry, but it wasn’t never explained how we know exactly what things are comprised of, and exactly how they bond together.
I know that now we have chromatographs that can analyze samples and give a rundown of the elements contained therein, but what did they do before that?
Would someone care to give me a crash course in the history of modern chemistry?
Er, I should explain. When I say “Exactly how they bond together” I mean, “how we know how they bond together,” as in, how we know that in, say, ethanol, we know that two carbon atoms bond together, and one oxygen atom bonds onto the end of that, and then there’s a handful of hydrogen atoms thrown on for good measure. How are we certain that the oxygen isnt’ in the middle, and then the hydrogens are off to the side, bonded together, and violating the known laws of physics?
Well, one thing that gets you started is figuring out the chemical formula. Let’s say you know that if you burn carbon and hydrogen in oxygen, you get pure methane (I know, you don’t really - this is just a thought experiment). Let’s say you’ve also already figured out the relative weights of carbon and hydrogen. If you measure very very carefully the amounts of carbon and hydrogen you start with, and the amount of methane you end up with, you will see that methane is made up of four parts hydrogen for every part carbon.
So that’s a good start. I’ll let others take it from there.
Well, you could simply burn carbon in pure hydrogen, couldn’t you?
In many cases the structure can be got by xray crystallography. A crystal will scatter (diffract) xrays in a particular way depending on the exact arrangement of atoms - so by a bit of mathematical analysis the exact structure can be got in 3D.
With other methods such as various NMR techniques you can map what atoms lie next to each other. then one can piece together the entire structure like a jigsaw.
I should say that 99.99 % of carbon structures (organic) follow very simple bonding patterns, and much less intensive analysis will give you the structure. Most of the time you dont have to apply the above two techniques, as simpler methods will give a structure that one can be confident of, without extra confirmation at the level you are talking about. If chemistry was as random as your post, then I would give up my job.
With metal based structures one should always get an xray structure as they can be much more varied, and one needs to exactly how things are arranged around the metal.
ps - x ray crystallography is wonderful - I have a new chemical that I have been beating my brains out for a week trying to solve the structure by simple means - managed to grow a crystal on friday and should have a xray structure by tomorrow.
I meant … if chemistry was as random as your post might imply, then …
My few attempts at getting x-ray quality crystals failed. I should’ve just run more 2-D NMRs instead of spending weeks trying to grow crystals.
There are a couple ways that are generally accepted by the journals to get the chemical formula. One is combustion analysis, where the molecule is burned and the combustion products analyzed to give a chemical formula. Another way is high-resolution time-of-flight mass spectrometry. Different compositions will have slightly different weights due to isotopic distribution and this can be seen by HR TOF MS.
NMR is of course a powerful tool. There are lots of techniques out there, especially 2-D techniques, for everything from simple molecules to proteins. Of course, NMR can be done with lots of different elements and on organometallic or inorganic compounds as well. Being an organic chemist, these are the ones I’d be likely to use if needed, as they’re simple, built in to the software, and relatively fast:
COSY (1H-1H correlations): Shows all proton couplings without having to mess around with coupling constants.
HETCOR/HMQC (1H-13C correlations): Two sides of the same coin and which one is used is mostly instrument-dependent, depending on how the probe is set up. Shows which proton signals go with which carbons.
HMBC (1H-13C correlations): Shows the coupling of protons to carbons generally one or two carbons away (though it’s J-value dependent) from the carbon of attachment but not the carbon of attachment.
INADEQUATE (13C-13C correlations): Gives the coupling of every carbon to every other carbon. Highly powerful and the entire carbon skeleton can be pieced together from the INADEQUATE.
Then of course, there’s the other analytical techniques like infrared spectroscopy and even low-resolution MS can be helpful.
And, of course, you’re rarely trying to solve a structure without at least some idea of what you think you’ve got. If nothing else, you knew what you threw into the reaction to begin with. Unless something totally new happens (in which case you’re looking at a paper and possibly a new name reaction) there are only a handful of possibilities.
Nice post, asterion, I learned a lot from it.
It’s very tangential, but I’m dying to know: is INADEQUATE an acronym for something? Who would choose such a… <resist posting the obvious> well, unfortunate choice to describe a software product?
I recommend Asimov’s book Today And tomorrow which contains several essays describing how it got started, beginning with the ancient “elements” of Earth Air Fire and Water, and describing how the first steps in modern chemistry were made. It’s very readable. Asimov had a gift of making the most difficult concepts understandable.
Many NMR experiments have been given names that translate out to cutesy acronyms. INADEQUATE actually stands for Incredible Natural Abundance Double Quantum Transfer. There are many experiments out there, I just listed the ones I would be most likely to use. There’s also the NOESY which uses the Nuclear Overhauser Effect in 2-D to give information about stereochemistry.
To be fair, COSY doesn’t give all couplings, just all couplings within spin systems. TOCSY (total correlation spectroscopy) gives all couplings, but that’s more of a biochemistry technique.
That’s nothing for acronyms. The NMR guys practically a competition for creating memorable acronyms. Among them are:
PENIS Proton-Enhanced Nuclear Induction Spectroscopy (NMR technique)
SECSY: Spin Echo Correlated Spectroscopy
WATERGATE
WURST: Wideband, Uniform Rate, and Smooth Truncation
HOHAHA: Homonuclear Hartmann-Hahn Spectroscopy
And thats just a partial list. The full list is:
http://www.bmrb.wisc.edu/education/nmr_acronym?HOHAHA
As far as how did they know how compounds were connected in the 19th century. The ninteenth century is really where chemists were figuring out how things were bonded. In the early 19th century, it was still not universally accepted that certain elements only had certain numbers of bonds. For example, carbon always has 4 bonds (excepting ions, carbenes, and radicals, but they didn’t make too many of those back then.) It is quite possible that they did not absolutely know the structure of ethanol. On the otherhand, those that accepted the carbon = 4 bonds oxygen = 2 bonds and hydrogen = 1 bond had only a few ways to put ethanol together. The structure you are describing, where the oxygen is in the middle is called dimethyl ether, an isomer of ethanol (isomer means it has the same numbers of elements but arranged differently.) A chemical test would easily distinguish between dimethyl ether and ethanol.
The real brilliance came in the later part of the 19th century. Benzene has the formula C6H6. Just based on this formula this molecule is very unsaturated (meaning lost of double bonds or rings.) Benzene was notoriously unreactive for an unsaturated molecule. When they did get derivatives of this compound a single substitution only produced 1 compound. That meant that every carbon was equivalent so the molecule must have been highly symmetrical. Even more perplexing was that a double substitution produced 3 isomers rather than 5. Eventually they discovered a new bonding method based on conjugated (alternating double and single bonds) rings called aromaticity.
Werner complexes are another example of brilliant chemistry. While carbon strictly adheres to the octet rule metals were very ambiguous about how many things they were bonded to. Based on reactivity, the number of isomers (symetrical bonding motifs have fewer isomers) and such things they were able to definitively prove the structures of these molecules.
Basically, before NMR, X-ray, IR, and mass spectrometry the structure of compounds were detremined using chemical tests to determine functional groups, symmetry, and sheer logic through the process of elimination.
However, as with many rules, there are exceptions. Molecules like non-classical carbocations do exist, and sometimes, exist long enough to be measured. Figuring out their structures took many years. It was only in the 60s and 70s that people could say with any certainty that they really existed, and have more than a vague guess as to what they looked like.
Modern high-resolution NMR was needed to actually visualize them. Methods like spectroscopy only work if you have some theoretical framework to put them in. However, as was said earlier, it’s very rare for you not to have some idea as to what you’re looking at beforehand.
Oh, and another method that’s used more now is de novo computational analysis. You would calculate the quantum chemical structure that is most stable, and then go looking for it experimentally. There have been quantum chemical studies of planar hexacoordinate carbon that suggest it is possible. (Non-planar hexacoordinate carbon has been observed already)
See Exner, Kai, Schleyer, Paul von Rague. Planar Hexacoordinate Carbon: A Viable Possibility. Science 2000 290: 1937-1940