E Assignment 3 CM6401 Principles of Spectroscopy

Introduction
In today’s age of chemical engineering, drug discovery and molecular analysis, mass spectrometry has emerged as one of the most useful and practical pieces of technology in the realm of chemistry. A technique that helps researchers to determine molecular mass, elemental composition and chemical structure, it involves the vaporization and ionization of molecules into charged particles, followed by the subsequent separation and detection of the aforementioned particles. This particular write-up is dedicated to the discussion of the methods currently utilized in two of the four different phases in mass spectrometry – the ionization of molecules into charged particles and the sequential detection of the particles produced.

Sample Ionization Methods
As the respective molecules and chemicals in question need to be ionized before they can be separated and then detected by the mass spectrometer, the methods in which this is done can be said to be of utmost significance. Three of the more commonly known and used modes of ionization are electron ionization, chemical ionization and electrospray ionization. In this section on sample ionization methods, we will cover and discuss all three methods. Electron ionization (EI) Electron ionization is the antecedent ionization method in history, and is currently still the most commonly used of all ionization methods. In EI, energized high-energy electrons interact with vaporized atoms and molecules to form ions. The formula for this is as follows, with X being the atom or molecule being ionized.

To further delve into the workings of EI, one must go beyond the generalized chemical formula to the diagrammatic representation of the ion source itself. In EI, a wire filament that has an electric current flowing through it is heated. This gives off electrons, which are then accelerated by potential difference towards a positive anode. In Figure 1, this results in a 70eV beam of electrons from the heated wire filament at the left side of the blue structure to the trap electrode at the right side. At the same moment, the vaporized sample to be analyzed is passed through the ion source at an angle that is perpendicular to the electron beam. This causes interactions to happen between the sample molecules and the electron beam, the latter knocking out electrons and energizing the sample molecules. This increase in energy then induces vibration, rotations and molecular

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E Assignment 3 CM6401 Principles of Spectroscopy rearrangements that induce molecular fragmentation and ion formation. The advantages of EI are that it is a purely physical process, with the fragmentation being unimolecular in nature. The mass spectra produced are therefore extremely predictable and reproducible. Also, in EI extensive fragmentation is observed, which provides more information and increases the number of peaks produces. Analysis is therefore improved and simplified. However, fragmentation may occasionally be too extensive, causing the molecular ion peak in the mass spectrum produced to be difficult or even impossible to detect. This is especially so for larger molecules. Another disadvantage of electron ionization is that only volatile samples can be analyzed. Thus, only compounds with low molecular weight can be tested. Radical cations are also formed in EI, which may rearrange and potentially complicated the mass spectra obtained. Chemical ionization (APCI) Atmospheric Pressure Chemical Ionization, or APCI, is another method commonly utilized to ionize samples. Compared to electron ionization, APCI is a considerably lower energy process. It therefore causes less fragmentation, yielding a lower frequency of mass spectra peaks. A simplified representation of the mechanics behind the APCI ion source is depicted in Figure 2. The sample is first diluted with a solvent such as ammonia, methane or isobutane, resulting in the mobile phase being injected into the structure at the far left of Figure 2. This is then sprayed with nebulizer gas travelling at high speeds. The mobile phase then reaches a heater and gets heated to about 400°C. The sample finally reaches the corona discharge electrode, which is a fine needle discharging corona at a current ranging from 2 to 5 µA. It is this corona that ionizes the reagent and solvent molecules in the mobile phase. As the solvent molecules outnumber the sample molecules in the mobile phase, the electrons emanating from the corona will preferentially ionize the solvent. This forms ions from the solvent that collide with other solvent molecules. If methane is the solvent used, the following reactions are expected.

When a molecule of the sample to be analyzed finally comes into contact with one of the ions, the transfer of charge will occur, forming charged particles that can then be scattered and detected.

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E Assignment 3 CM6401 Principles of Spectroscopy As sample ionization is indirect in this method, APCI is considered to be a softer type of ionization which results in reduced fragmentation. The molecular ion is therefore more easily recognizable in the corresponding mass spectra. This can be shown in Figure 3. A potential advantage of APCI is that it is highly sensitive. However, this may also be a disadvantage as purity now becomes increasingly important. Another disadvantage is that the high temperatures involved might decompose some compounds. Electrospray ionization (ESI) Electrospray ionization (ESI) is the last ionization method we will be covering. Similar to the APCI, the sample is dissolved in a large amount of solvent, forming the mobile phase. However, unlike the APCI, volatile acids, bases or buffers are also oftentimes added to the solution, ionizing the sample molecules. The mobile phase is then placed within a very thin and charged metal capillary that faces a metal plate that is charged oppositely to the metal capillary. As the sample molecules are all similarly charged and like repels like, they will repel each other and expel themselves out of the capillary, forming a mist-like aerosol of small droplets. This will land on the charged metal plate as a fine layer of ionized sample. The diagrammatic representation is shown below as Figure 4. This method of ionization is even softer and gentler than APCI, which by itself is already softer than EI, which promotes the retention of molecule integrity and the formation of non-radical and intact ions. Due to the nature of ESI, the size and lability of the product also does not seem to matter, though ESI cannot ionize weakly polar analytes, unlike APCI. Another disadvantage is that ESI is also more susceptible to matrix interferences from salts.

Mass Analyzers
After the successful ionization of our sample, what follows is the separation and detection of the ions produced. Magnetic Sector Mass Spectrometers and Quadrupole Mass Spectrometers are just two of the many mass analyzers currently used that will be covered in the following section.

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E Assignment 3 CM6401 Magnetic Sector Mass Spectrometers Magnetic Sector Mass Spectrometry is the predominant type of mass spectrometry currently used in analytical chemistry. In this ion separation method, the ions are pushed through the flight tube between the poles of a magnet, which then accelerates and deflects the charged ions by virtue of their mass-to-charge ratios, deflecting the faster, lighter and more highly charged ions more, and vice versa. This difference in the degree of deflection provides the ion detector and recorder at the end of the deflection chamber with a spread of ions to work with, from which mass spectra can be produced, depicting both degree of deflection and ion intensity. Using specialized instruments, high resolutions and accuracies are feasible. However, there are several problems with magnetic sectors. First, they are rather expensive compared to other types of mass spectrometers out in the market. They also require skilled operators and high sample purities because impurities could severely compound and confound the mass spectra produced. All these explain why magnetic sector usage is low and presently on the decline. Figure 5 provides some insight into the workings of this equipment. Quadrupole Mass Spectrometers The last piece of technology to be covered is the quadrupole mass spectrometer. It is by far the most widely used mass analyzer due to a variety of advantages it possesses over its counterparts. For one, it is faster, physically smaller, cheaper, and uses much less voltage than other mass analyzers. It is also foolproof and easily constructed. However, it may occasionally underperform with low accuracy and resolution. This mass analyzer is composed of an ion source, 4 uniform cylinder rods (quadrupole), an ion detector and an amplifier. To separate the ions in the sample, a high frequency alternating electrical field is created by applying direct current (DC) to all 4 rods. The ions are then passed through the middle of the quadrupole from the ion source. Only some manage to successfully reach the Faraday cup, which will then channel the gathered electrons to the ion detector. Two factors affect the ability of the ions pass through the quadrupole and reach the Faraday cup at the other end – the radio frequency of the electric field and the DC voltage flowing through the rods. These cause only ions of a particular mass-to-charge ratio to be able to pass through. Varying the electric field and DC voltage will therefore select for the detection (if any) of ions of a specific mass-to-charge ratio. From this, mass spectra can be generated. A diagrammatic representation of the workings behind this engineering marvel is shown in Figure 6. Principles of Spectroscopy

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