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CHEM 221: Spectroscopy

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image by Sean MacEntee

Mass Spectrometry
A mass spectrometer is a device that is used in analytical chemistry to determine the molecular mass of some unknown molecule. It uses an electric current to ionize the unknown sample. These ions are then accelerated to make sure the right molecule passes through the slits at the end. These unknown ions can be detected at the ion detector, which calculates the mass of that ion. Once the mass data is collected, it can be analyzed by plotting the relative abundance (related to the intensity) versus the mass-to-charge ratio. Notice that if the charge on the ion is equal to +1, the mass to charge ratio simply becomes the mass. The unknown molecule being used is known as the parent molecule and when it is ionized, it is referred to as the parent ion. The peak that the parent ion produces on the mass spectrum is known as the parent peak. The peak directly to the right of the parent peak is known as the p +1 peak and this represents a molecule that has a slightly higher mass. This peak corresponds to the parent molecule that is composed of heavier isotope atoms. Along with these two peaks, there are many other peaks that exist and this entire pattern of peaks is known as the fragmentation pattern. The peak with the highest intensity is called the base peak and it is given a relative abundance of 100%.

McLafferty Rearrangement
Recall that mass spectrometers can be used to determine the mass of a given molecule. The molecule is placed inside the spectrometer and ionized by high-energy electrons. It is then allowed to accelerate through electric and magnetic fields and eventually is detected by an ion detector, which calculates the mass of that ion and creates the mass spectrum. However, during the ionization process, the molecule can also fragment and undergo various types of rearrangements. The American chemist Fred W. McLafferty noticed that when a hydrogen is available at the gamma-position on carbonyl compounds, those carbonyl compounds underwent a specific rearrangement in which the carbonyl transforms into a neutral alkene and the radical cation. This is known as the McLafferty rearrangement.

Infrared Spectroscopy
Infrared spectroscopy is an analytical technique that uses electromagnetic waves in the infrared region to study and determine the types of functional groups that are found in molecules. Just as electrons can gain energy and transition to excited energy quantum states, molecules can also transition to higher molecular energy quantum states if they gain energy in just the right amount. The bonds in molecules can be imagined to vibrate with certain frequency (and therefore energy) values that are specific to that particular chemical bond, just like masses oscillate on springs. When we direct electromagnetic waves onto the chemical bonds with a frequency that does not match the frequency of the chemical bond, then the wave is said to be transmitted and does not affect the chemical bond. However, if the frequency of the infrared electromagnetic wave matches the frequency of the oscillating chemical bond, then the molecule will jump to a higher molecular energy level. In can then return to its normal ground state and in the process release electromagnetic radiation. This electromagnetic radiation can be collected by the IR spectroscopy apparatus and the infrared spectrum can be formed for that particular compound. Since every bond has its own unique frequency of vibration and absorbs electromagnetic waves with a specific amount of energy, we can use the infrared spectrum to determine the types of chemical bonds (and therefore functional groups) found on the molecule.

Infrared Spectroscopy Example
As we previously mentioned, IR spectroscopy can be used to determine the types of chemical bonds (and functional groups) that are found on molecules. Suppose that we are given a set of four different molecules as well as the infrared spectrum that corresponds to one of those four molecules. Our goal is to use this infrared spectrum to determine which one of the four molecules closely matches the data on the graph.

Mass and Infrared Spectrum Example
Suppose that we are given an unknown compound that is said to contain carbon, hydrogen and oxygen. Elemental analysis of this unknown compound shows us that it contains 80% carbon, 13.3% oxygen and 6.7% hydrogen by mass. Using the provided mass and infrared spectrum, we would like to determine the structure of this unknown compound. To solve this problem, we need to first determine the empirical formula and then the molecular formula using the percentages and the mass spectrum. Next we must determine the degree of unsaturation and use this information along with the infrared spectrum to determine the molecular structure.

Proton NMR Spectroscopy
Proton NMR spectroscopy is a technique that is used in organic chemistry to study hydrogen-containing molecules. It uses a principle that comes from nuclear physics known as nuclear magnetic resonance. Just like electrons, protons contain charge that can spin and this will induce a magnetic dipole moment. When the proton is placed into an external magnetic field, the proton's magnetic dipole moment will orient itself along that magnetic field. However, since the proton can spin in one of two ways in any external magnetic field, it has two magnetic dipole moment orientations and so will align with the external magnetic field in one of two ways. One of these orientations will be along the same direction as the magnetic field and this is known as the spin-up (+1/2). This will be the lower in energy and more stable spin state. The other orientation will be along the same axis as the magnetic field but in the opposite direction and this is known as the spin-down state (-1/2). This will be the higher in energy and less stable quantum spin state. If we now direct electromagnetic waves (radiofrequency waves) with just the right frequency at the spin-up state, the spin-up proton will absorb energy and transition (flip) to the spin down state. At this point it is said to undergo resonance and this frequency is known as the resonance frequency or chemical shift. Different hydrogens in molecules can have different chemical shift values and these values can be readily determined by using this nmr technique. This type of technique that uses nuclear magnetic resonance to study the protons (hydrogens) is known as proton nmr spectroscopy.

Parts Per Million in NMR Spectroscopy
The chemical shift of a hydrogen atom is really the frequency at which it is said to undergo resonance. However, when we describe the chemical shift of hydrogen atoms, we do not use Hertz (cycles per second) but rather use units called parts per million or ppm. The reason that we do not express chemical shifts in Hertz is because the chemical shift depends directly on the strength of the magnetic field of the spectrometer that we are using. That means that if two chemists study the same compound but use two different spectrometers with different magnetic field strengths, they will observe two different chemical shifts for that same compound. To fix this problem, we instead use a ratio called parts per million to describe the chemical shift. In order to convert chemical shift from Hertz to ppm, we take the chemical shift in hertz, divide it by the frequency rating of the spectrometer (which depends on the magnetic field strength) and multiply it by one million. This basically allows chemists to express the same chemical shift values regardless of the spectrometer being used.

Parts Per Million in NMR Spectroscopy Example
Chemical shift values depend on the strength of the magnetic field of NMR spectrometers. The greater the magnetic field, the higher the observed chemical shift. In order to correct for this problem, the ppm scale is used instead of hertz. Suppose that one chemist uses a 60 MHz spectrometer and finds that a compound shows a chemical shift of 50 Hz. A second chemist uses a 600 MHz spectrometer and finds that the same compound shows a chemical shift of 500 Hz. Show that the chemical shift in ppm is equal for both cases.

Chemical Shift and Shielding Effect
When the proton inside the nucleus of the hydrogen atom gains just the right amount of energy, it can undergo resonance and the frequency of resonance is known as the chemical shift. The value of the chemical shift for any hydrogen atom depends on its neighboring environment; more specifically, it depends on the magnetic field that it experiences. The external magnetic field can easily influence the electron density found around the nucleus of the hydrogen atom. When the external magnetic field is turned on, the electron density begins to fluctuate as to induce its own magnetic field that opposes the external magnetic field. Therefore, the net magnetic field will be less than the external magnetic field as a result of this induced magnetic field. This is called the shielding effect because the electron density is said to shield the proton in the nucleus from the external magnetic field by decreasing the net magnetic field that is experiences.

Proton NMR Spectrum
Proton nmr spectroscopy uses the principle of nuclear magnetic resonance to determine the chemical shift values of hydrogen nuclei in molecules. Once it collects the data about the chemical shift, it produces a graph known as the proton nmr spectrum. The proton nmr spectrum plots the intensity versus the chemical shift value and the chemical shift is given in units called parts per million (ppm) instead of hertz. Each chemical shift peak is known as a signal. The height (intensity) of the different signals can be used to determine the relative number of hydrogen nuclei that each signal corresponds to. This process of using the height to determine the number of hydrogen atoms each signal corresponds to is known as the integration of the signal. Signals that are found to the right along the x-axis of the spectrum are said to be upfield (well shielded) while signals found to the left are said to be downfield (less shielded).

Electron Shielding Groups
Earlier we saw that a high-electron density around hydrogen nuclei shields them from the external magnetic field. This means that such hydrogen nuclei will require a high applied magnetic field to cause a chemical shift and so these nuclei will be found upfield. Certain types of structures can either increase or decrease the shielding of hydrogen atoms. Alkanes usually contain many hydrogen atoms that are in closely proximity to one another and this tends to increase the shielding of such hydrogen nuclei. Olefinic hydrogens are those hydrogens that are attached directly to carbon-carbon double bonds. The high density of electrons in the double bond area induces a magnetic field that in the end ends up increasing the net magnetic field that the hydrogen atoms feel. This decreases the shielding of hydrogen atoms and puts them relatively downfield. On the other hand, if we examine the hydrogen atoms attached directly to carbon-carbon triple bonds, we see that the electron density induces a magnetic field that decrease the net magnetic field that the hydrogen atoms feel. This places alkyne hydrogens relatively upfield.

Aromatic Hydrogens and Electron Withdrawing Groups
A high electron density around the hydrogen atom will shield the nucleus from the external magnetic field and place it upfield on the nmr spectrum. However, when a very electronegative atom or group of atoms are found in close proximity to the hydrogen, they can act to withdraw the electron density by pulling it closer to themselves. This decreases the electron density around the hydrogen and decreases the shielding. Therefore hydrogens that are attached to these electron-withdrawing groups will be found downfleid. Hydrogen atoms attached to aromatic rings such as benzene will be found significantly downfield. This is because the high electron density around the entire ring creates an electric current around the ring and this in turn induces a magnetic field that adds to the external magnetic field at the location of these hydrogen atoms.

Proton NMR Spectrum Example
Suppose that we are given two pairs of molecules. We would like to match these molecules to their corresponding proton nmr spectra using what we learned so far.

Spin-Spin Coupling
Spin-spin coupling is the splitting of spectral signals on the proton NMR spectrum. This splitting of spectral lines is a result of the interaction between the two different hydrogen atoms found in close proximity to one another. More precisely, it is the interaction between the quantum spins of the nuclei of these hydrogen atoms that causes this spectral splitting.

Spin-Spin Coupling Example
Suppose that we are given the proton NMR spectrum to ethyl chloride. We would like to answer two very important questions about this spectrum. Firstly, what do the two peaks actually correspond to. Secondly, we would like to determine why the first peak region (the one found to the left) contains four signals while the second region (the one to the right) contains three signals.

Spin Coupling Constant
The interaction of the spins of two different hydrogen atoms found in close proximity on a given molecule leads to the splitting of spectral signals and the distance between the split spectral lines is given by the coupling constant, J. The magnitude of the coupling constant is influenced by two factors. Firstly, the distance between the two interacting hydrogen atoms affects the magnitude of the coupling constant. That is, the closer the two hydrogen atoms are to one another, the greater the magnitude of the coupling constant is. Secondly, the orientation (or angle) of the two hydrogen atoms with respect to one another affects the magnitude of the coupling constant. The Karplus curve is a graph that describes how the dihedral angle between two hydrogen atoms affects its coupling constant.

Spin Decoupling of Alcohols
When an alcohol molecule is in the presence of an acid or a base, the alcohol will readily exchange its hydrogen atom attached to the oxygen. As this takes place, the spin of the hydrogen alternates between being spin-up and spin-down. Overtime, this exchange leads to an average spin of zero for that hydrogen. Because the average spin of the exchanging hydrogen is zero, it will not undergo spin-spin coupling with the adjacent hydrogen atoms. This phenomenon is commonly referred to as spin decoupling. The hydrogen is said to be decoupled with respect to its neighboring hydrogen atoms. Decoupling means that the spectral signals on the proton NMR spectrum will not be split.

Decoupling by Irradiation
Previously we said that decoupling takes place as a result of the hydrogen's average spin of zero. In this lecture, we shall see how we can actually use decoupling to remove excess spectral splitting that might appear on the hydrogen NMR spectrum, thereby making the spectrum as clear as possible. By irradiating hydrogen atoms with an electromagnetic wave that has just the right frequency, we can cause the hydrogen nuclei to undergo a change in spin. This gives the hydrogen an average spin of zero, which means it will now be decoupled with respect to adjacent hydrogen atoms of interest.