Channel Molecule: The power of spectroscopy

I was once asked by a friend why the world is so colourful if it is entirely materialistic without a divine designer.
Well, it isn’t colourful.
The part of the entire range of electromagnetic waves that we may recognise as ‘light’ or ‘colours’ is just a tiny segment. And all the other members of the electromagnetic wave family: radio waves, microwaves, infrared, ultraviolet, and so on, all pass us without being detected by the eye. The world is dark and dull indeed.
And the sole reason why we do see something which we call ‘visible light’ is that it is good for our survival. The Sun radiates the strongest at wavelengths that correspond to yellow and green, and it is vital for our hunter-gatherer ancestors to detect radiations in this and nearby ranges, so as to differentiate objects from their different interactions with the Sun’s radiation. This is vital for tasks like locating food, spotting dangerous beasts, and so on.
So we see visible light-EM waves of wavelengths in the range 400-700nm.  Evolution has limited us to seeing nothing more than these. Our biological selves never get what is more than needed for survival.
I am reminded of Robert Hooke, a major developer of microscope and a rival of Issac Newton. When talking about his motivation of studying microscopy, he said, ‘Since the Fall of Man, mankind has lost the ability of seeing and knowing everything, and science is to strive to get that ability back.’
How similar the matter is in the case of spectroscopy! In spectroscopy, we see the world under all sorts of electromagnetic waves, not only the visible light. Surprisingly, what appears under light in the hidden ‘invisible ranges’ reveal much, much, valuable information about our building blocks – molecules. Corresponding to different segments of the entire EM wave range are different sorts of spectroscopy, each telling us a rather independent aspect of the molecule in question.

Here I just list the spectroscopies from wavelength longest to shortest:
Radio wave: An H-1 or C-13 nucleus is like a little compass with only two directions. In a strong magnetic field, the energy required for its transition from aligned with to aligned against the field corresponds to the energy of radio waves. Nuclear Magnetic Resonance (NMR), using radio waves, provides us with information of how the nuclei (H-1 or C-13) of a molecule behave under an external magnetic field. As these nuclei also experience internal magnetic field resulting from its own electrons and neibouring atoms inside the molecule, their different behaviours in NMR tells us how atoms in a molecule are linked.
Microwave: The energy of microwave correspond to the energy required for a molecule to rotate from a slower speed to a higher speed. The amount of energy needed depends on the ‘moment of inertia’ of the entire molecule: moment of inertia to rotation is mass to translation. It describes how much the molecule resists rotating, and in turn depends on the mass distribution of the entire molecule. Therefore, by studying the spectra of the microwave region, we can obtain information about the symmetry of the molecule and the lengths of its bonds (that roughly determines the size of the molecule), as well as detecting whether there are unusually heavier or lighter atoms, or what we call isotopes.
Infrared: Under the infrared region of EM wave, the bonds of a molecule begin to vibrate (stretch, bend or twist) at higher rates than usual. As the vibrational frequence depends on the bond length and the weight of atoms on either end of the bond (Think of a chemical bond as a spring with 2 balls attached to its ends.), infrared (IR) spectroscopy tells us what kind of bonds are present in a molecule, and a bit information about how they are connected. IR spectra differs from Microwave Spectra in that it reports on individual bonds instead of the molecule as a whole.
Visual light and Ultraviolet:  These wavelengths of EM wave exite electrons in a molecule from one energy level to another. As the electronic energy levels of an individual atoms is different from that of a molecule, UV-vis spectroscopy presents an intriguing field of study- Molecular Orbital Theory, which enables us to investigate how exactly atoms form bonds, or how exactly they share their electrons to lower the energy of the system as a whole.
X-ray: X-ray is too high in energy to correspond to any energetic transition of individual molecules. However, its behaviour as a wave is remarkable. Crystals diffract X-rays: that is, crystals interact well with X-rays because their inter-layer distances is comparable to the wavelength of X-rays. Reading the diffraction pattern of X-ray crystallography is an excellent way to decode the almost exact locations of atoms in a crystal. The structure of DNA was revealed by X-ray crystallography.

As we can see, molecules interact so much with EM waves and in such various modes, that even though we cannot directly see them ourselves, studying their spectra is already enough to reveal their identities. Here I have the H-NMR and IR spectra for banana oil (the sample for the NMR spectrum is synthesised myself. The one for IR is borrowed from a classmate, because my yield was too low to carry out IR spectroscopy.).
图片
Here is how we decode them:
In the IR spectrum, the peak at 1793cm-1 is characteristic for a carbonyl group, and the peak at 1227cm-1 is characteristic for a C-O single bond. Now in the H-NMR spectrum, the 2H triplet at chemical shift 4.091ppm strongly suggest that this is a methylene(CH2) group at the alkoxyl side of an ester (1.3 for CH2,+3 for attaching to an ester), thus explaining the carbonyl and the C-O bond. So we are pretty sure that this compound is an ester.
Furthermore, because the peak just mentioned is a triplet, this methylene group probably attaches to another methylene(CH2) group. (Due to some effect called ‘coupling’, a n-plet arrises when there are n+1 identical or similar neighbours to the H in question…) Therefore, part of our molecule can already be determined:
-COOCH2CH2-
What is on the carboxylic side of the ester? The 3H singlet at 2.038ppm suggests that the carbonyl is simply attached to a methyl(CH3) group (0.9 for CH3, +1.0 for attaching to a carbonyl). The protons on this methyl does not have any proton neighbours, so it appears as singlet. Our molecule is now:
CH3COOCH2CH2-
Now the protons on rightmost CH2 appears as a distorted quartet at about 1.5ppm, the normal postion for CH2. This suggests that this is attached to a CH group on the right, so that 2 neighbours on the left and 1 neighbour on the right gives the quartet. The 1H peak at 1.7ppm (apparently highly influenced by coupling because it has too many neighbouring protons) confirms this. Now the rightmost 6H doublet is unquestionably two methyl groups attached to this CH. Thus, the structure of the entire molecule is determined.
CH3COOCH2CH2CH(CH3)2
This must be the correct formula for banana oil! Because we synthesised it from acetic acid and iso-pentanol. 🙂 However, with spectroscopy, we can determine the structure of a molecule even if we don’t know how it is made.

I hope now you can grasp a little bit of how powerful spectroscopy is in chemistry! Reading information from what infrared or radio waves tells us is as interesting as enjoying the colourful world of visible light we live in. Though we can’t directly ‘see’ the molecules, who says deducing the molecular structrue from spectra is not another way of ‘seeing’? Evolution or sorts of devinity fail to give us the insight into our tiny building blocks, but science, technology, and logic succeed.
In Clayden’s Organic Chemistry, the authors claim that the single most important achievement of chemistry in the 20th Century is spectroscopy, with which comes the great certainty of molecular structures’ determination. Das glaube ich. I believe so.

0 comments