Posts

Now I’m sure we’ve all been in the situation where, we’re in a lab and we have made our product with very high yield, and we’re happy. But how can we be certain that the product we have is the product we wanted to make in the first place?

 

Well, there are several spectroscopic methods that, when used in conjunction with one another, can paint a very accurate picture of the molecule, from its molecular structure, to the functional groups attached to the molecule. But how do these spectroscopic methods work?

 

Molecular structure determination

 

In order to determine the molecular structure of our sample, we use Nuclear Magnetic Resonance (NMR) spectroscopy. This works based off the principle that some atomic nuclei have nuclear spin, and the presence of this spin makes these nuclei behave like a small magnet. The spinning charge of the nuclei can generate a magnetic dipole, which can interact with an applied external magnetic field.

 

In the absence of the magnetic field, the nuclei are randomly arranged and the energies of the magnetic moments are equal, which doesn’t produce an NMR signal. In the applied magnetic field, the magnetic moments have 1 of 2 possible energy states, one low and one high, and follows a Boltzmann distribution. (1)

Fig 1: Nuclei in the absence and presence of an applied magnetic field (2)

When the sample is irradiated with energy of a suitable frequency, this distribution will change. For example, 1H nuclei will flip from low to high energy states. This is the resonance part of NMR and involves absorption of radiation. The frequency of the irradiated energy depends on the type of nucleus we want to resonate and abides by the following resonance condition:

Where nu is the frequency of the absorbed radiation, gamma is the magnetogyric ratio, which is simply the ratio of the nucleus magnetic moment to its angular momentum (the ratio is unique to each nucleus) and  is the applied magnetic field.

 

From this, we can see that different nuclei absorb energy at different frequencies, and this is due to the electrons surrounding the nucleus “shielding” the nucleus from B0 (2). As the electrons shield the nucleus from the effects of B0, their local diamagnetic shielding can be reduced. This affects the positions of the atom under resonance, the local magnetic field that the nucleus feels and the frequency at which the nucleus resonates. The shielding of the electrons cause each nucleus to experience a different B0, and thus give different peaks for different nuclei, and even the same nuclei with different numbers of electrons, which can inform us about the structure of the molecule.

 

NMR spectroscopy is done multiple times on the same sample, with each successive NMR focusing on a different nucleus in the sample, and the results being used in conjunction with each other to determine the molecular structure. For example, for C3H6O, there are multiple different ways to structure the molecule, with just three being shown below.

 

Figure 2.a) One possible arrangement of C3H6 (a. Acetone)

Fig 2.b : Three possible arrangements of C3H6 ( b. (Z)-1-Propenol)

Fig 2.c : Three possible arrangements of C3H6 (c. (E)-1-Propenol)

If we obtained a 13C and a 1H NMR spectra for all three isomers, we could quickly determine which arrangement is held by our sample. For acetone, if we did 1H NMR, we would see that all the hydrogens are in the same chemical environment

(the electron shielding is the same for all hydrogens), and we would get a single very big peak in the spectrum. If we did 13C NMR, we should see that two of the carbons are in the same chemical environment, but one of the carbons would experience a greater B0 as the attached oxygen effects the electron shielding.

 

For (Z)-1-propenol and (E)-1-propenol, they would be very similar but for one difference in the 13C NMR, as the carbon at the end of the chain, in the (Z)-1-propenol, would experience a slightly greater B0 than the same carbon in the (E)-1-propenol, as the (Z)-1-propenol carbon is closer to the oxygen.

 

Determination of functional groups

 

To determine what is attached to our molecule, we can use infrared (IR) absorption spectroscopy. This works on the principle that molecules absorb frequencies that are unique to their structure. These absorptions happen when the frequency of the absorbed radiation matches the vibrational frequency. The energy of the absorbed radiation is affected by the masses of the atoms, and the associated strength of the bond between the atoms.

 

The IR light is absorbed when the oscillating dipole moment (due to molecular vibrations) interacts with the oscillating electric IR beam, which tells us that the dipole moment at one end of the molecule must be different to the dipole moment at the other end (3). Hence, a molecule that is symmetrical is inactive in the infrared spectrum, for example, N2.

 

The vibrations of the molecule give rises to multiple absorptions that occur between 4000 cm-1 and 400 cm-1, with the region below 1500 cm-1 being known as the fingerprint region, which is generally unique to the molecule in question. When examining an IR spectrum, one would use an IR table, which would tell you approximately the region certain functional groups absorb light in, and by matching the absorption peaks in your spectrum to the IR table, you can determine what functional groups are in your molecule.

 

References

  1. Gunnlaugsson (2022), Analytical and Computational Methods: Lecture 4 https://tcd.blackboard.com/bbcswebdav/pid-2070153-dt-content-rid-12142873_1/courses/CHU33405-202122/Lecture%20Notes%20No%204.%20Organic%20Spectroscopy%202021%20TG.pdf
  2. Gunnlaugsson (2022), Analytical and Computational Methods: Lecture 5 https://tcd.blackboard.com/bbcswebdav/pid-2076008-dt-content-rid-12194659_1/courses/CHU33405-202122/Lecture%20Notes%20No%205.%20Organic%20Spectroscopy%202021%20TG.pdf
  3. Gunnlaugsson (2022), Analytical and Computational Methods: Lecture 3 https://tcd.blackboard.com/bbcswebdav/pid-2070150-dt-content-rid-12142868_1/courses/CHU33405-202122/Lecture%20Notes%20No%203.%20Organic%20Spectroscopy%202021%20TG.pdf

 

Image references

Fig 2.a https://pubchem.ncbi.nlm.nih.gov/compound/Acetone#section=Structures

Fig.2.b https://pubchem.ncbi.nlm.nih.gov/compound/Z_-1-Propenol#section=2D-Structure

Fig 2.c https://pubchem.ncbi.nlm.nih.gov/compound/Prop-1-en-1-ol#section=2D-Structure

In the process of analysing stars, one important factor is their composition.  It is impractical and some could argue impossible with modern technology to gather a representative sample of a star in order to determine which elements are present.  Even if it was possible to execute this task, one could not be certain that the sample obtained would be representative of the entire star; not to mention every star in existence.  One process of determining the composition of a star is through spectroscopy, which is defined in Encyclopedia Britannica as the “study of the emission and absorption of light and other radiation by matter, as related to the dependence of these processes on the wavelength of the radiation” [8].  The processes of emission and absorption occur at the atomic level as a result of radiation being expelled or entering the atom and primarily involves the electrons present in a given atom.

Every atom contains a number of electrons (negatively charged particles) corresponding to its atomic number on the periodic table (if it is neutral) and energy levels where the electrons reside.  For an atom with a charge (referred to as an ion), its number of electrons is indicated by its atomic number and net charge such that a charge of -x indicates the addition of x electrons and +x indicates the removal of x electrons with respect to the atom’s atomic number. A visual representation of the energy levels of an atom (denoted by the quantum number ‘n’ which indicates which level is being considered) is shown below as Figure 1.  One may note that Figure 1 is representative of the Bohr model which depicts the energy levels as circles of increasing radius surrounding the nucleus (containing protons with positive charge and neutrons of no charge).  This model does not accurately show the shapes of the orbitals, but is included for clarity on the concept of energy levels.

Figure 1: The First Four Energy Levels of an Atom (n=1, 2, 3, 4)

When the atom absorbs a photon (radiation of a certain energy), one of these electrons can be promoted or move up in energy levels depending on how much energy was absorbed.  Since the levels are discrete, a certain amount of energy is required to promote an electron from one energy level to another.  The electron will eventually move back down to its previous state, emitting a photon (radiation of a certain energy).  The Electromagnetic Spectrum is a spectrum of all radiation according to wavelength (representing relative length of the radiative wave) shown as Figure 2 below.

What is the electromagnetic spectrum?

Figure 2: The Electromagnetic Spectrum According to Wavelength

When a spectrum is taken of a given body (atoms, stars, etc), there are spectral “lines” referred to as emission or absorption lines (depending on whether the spectrum is emission or absorption) that occur when an electron moves down or up in energy levels respectively (when emitting or absorbing a photon).  Since each atom has a specific amount of electrons, energy levels, and corresponding electronic transitions, the measurement of a star’s spectrum can be used to analyse the star’s composition by relating the wavelength of the radiation to its energy using Equation 1 below where ‘E’ represents the energy of the radiation, ‘h’ is Planck’s constant, ‘c’ is the speed of light in metres per second, and ‘λ’ is the wavelength of the photon (radiation).  Since ‘h’ and ‘c’ are constants, wavelength is the only variable that needs to be determined in order to determine the energy of the photon.  It is worth noting that energy is inversely proportional to wavelength which indicates that a higher energy photon corresponds to lower wavelength (and vice versa).

E=hc/λ

Equation 1

Figure 2 below shows the (absorption) spectrum of a star with absorption lines from certain electronic transitions (denoted as Hα, Hβ, Hγ, and Hδ) above a plot of wavelength vs intensity.  These two plots demonstrate the same information, but the spectrum itself is what would be obtained directly from a spectrometer whereas the intensity vs wavelength plot would be generated from the spectrometer data after it was obtained for analysation.

Figure 3: Absorption Spectrum and Corresponding Intensity vs Wavelength Plot from [2]

The year 1925 marks the first successful prediction of composition of stars through their spectra while also predicting a given star’s temperature and density.  This prediction led to the assumption that stars are primarily composed of hydrogen and helium.  In 1938, it was discovered that the energy of stars comes from the fusion of protons which allows for heavier elements to be generated (since the amount of protons in an atom is equal to the atomic number, and thus by fusing or combining protons the atomic number and corresponding identity of an atom will change).

HydrogenHeliumSodiumAbsorption

Figure 4: Example Star Absorption Spectrum vs Elements Present

In Figure 3, an example absorption spectrum is shown assuming that a given star only contains Hydrogen, Helium, and Sulfur (with their respective emission spectra shown above the star’s absorption spectrum for reference).  Since in reality stars have an abundance of elements and corresponding spectral lines (as shown in Figure 2), the analysation required for determination of composition is much more complex than what is shown in Figure 3.  Nevertheless, it is an adequate visual representation of the process required to determine the composition of a star (or another astronomical body) from its spectrum.

References:

[1] Encyclopedia Britannica. “Stellar spectra.” Encyclopedia Britannica. https://www.britannica.com/science/star-astronomy/Stellar-spectra.

[5] Encyclopedia Britannica. “Evolution of stars and formation of chemical elements.” Encyclopedia Britannica. https://www.britannica.com/science/physical-science/Evolution-of-stars-and-formation-of-chemical-elements.

[8] Encyclopedia Britannica. “Spectroscopy.” Encyclopedia Britannica. https://www.britannica.com/science/spectroscopy.

Image Sources:

[2] (Figure 3) https://casswww.ucsd.edu/archive/public/tutorial/Stars.html

[3] (Featured Image) https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.istockphoto.com%2Fphotos%2Fmilky-way&psig=AOvVaw0neoBxmTLnMwwcFs3EeZ3T&ust=1651660667444000&source=images&cd=vfe&ved=0CAwQjRxqFwoTCNjuvtORw_cCFQAAAAAdAAAAABBP

[4] (Figure 1) https://sites.ualberta.ca/~pogosyan/teaching/ASTRO_122/lect5/lecture5.html

[6] (Figure 4) https://starmappers.wordpress.com/2017/03/30/spectral-lines-and-very-fancy-graphics/

[7] (Figure 2) https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.science-sparks.com%2Fwhat-is-the-electromagnetic-spectrum%2F&psig=AOvVaw2CMBaBStLBaUTQiEXF7qIF&ust=1651661404006000&source=images&cd=vfe&ved=0CAwQjRxqFwoTCJDR96-Uw_cCFQAAAAAdAAAAABAD