Week 3 Chemical Detectives Workbook - Monash S2 2024 PDF

8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 Week 3: Chemical detectives - workbook Site: Monash Moodle1 Printed by: Kaltham Alzaabi...

8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 Week 3: Chemical detectives - workbook Site: Monash Moodle1 Printed by: Kaltham Alzaabi Unit: CHM1022 - Chemistry II - S2 2024 Date: Sunday, 4 August 2024, 9:49 AM Book: Week 3: Chemical detectives - workbook https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 1/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 Table of contents 1. Pre-workshop material 1.1. Mass spectroscopy 1.2. Microanalysis 1.3. Index of hydrogen deficiency 1.4. IR Spectoscopy 1.5. IR spectroscopy video 1.6. NMR spectroscopy 2. Summary 3. Preparation quiz 4. Online lectures https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 2/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1. Pre-workshop material From the laboratory exercises, you will have seen that we can use chemical experiments to differentiate compounds. Today, chemists rely almost exclusively on instrumental methods of analysis for structure determination. This week we will explore several analytical techniques, namely mass spectrometry (MS), infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy. Please read Sections 20.1-20.4 of Chemistry, Blackman et al. (4th ed.) https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 3/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1.1. Mass spectroscopy Watch the first 2 minutes of the following mass spectroscopy video, followed by 4:53-5:50 min (if you’re interested, you can watch the whole thing). Mass Spectrometry MS https://www.youtube.com/watch?v=J-wao0O0_qM Electron impact ionisation (EI) mass spectrometry EI mass spectroscopy is routinely used to determine the molecular weight of a compound. A sample of the molecules of interest are passed through an electron beam, ionising the molecules. Imagine a hammer being the electron beam smashing the molecules. The impact removes electrons from the molecule to make it charged (ionised). These charged molecules are then accelerated to a constant velocity and passed through the magnetic region. In this zone they are deflected, with the degree of deflection related to the m/z ratio. This allows the mass to be determined. One simple design is shown in Figure 3. Figure 3: One type of EI Mass spectroscopy instrument. The charged molecule is subjected to a strong magnetic field which causes it to change its path. The degree to which its path changes (known as deflection) is based on the mass of the molecule. (Blackman et al. 4th ed.) The output from the detector is called a mass spectrum which is a plot of signal intensity against a mass:charge (m/z) ratio (which is simply calculated by dividing the mass of the species by its total charge). For CHM1022, you can assume the charge will always be 1. Therefore m/z will be the mass. https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 4/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 Figure 4: Mass spectrum example for carbon Mass spectrometry – resolution and isotope distributions Mass spectrometry can be either high or low resolution, which can be incredibly important for distinguishing compounds of similar mass. Consider: Carbon monoxide (CO) m/z Nitrogen (N2) m/z Low resolution 28 28 High resolution 27.99491 28.00614 You could only tell the difference at high resolution! Furthermore, certain elements produce unique patterns due to their inherent isotope distributions. For example, in nature, chlorine occurs as a mixture of 75.77% 35Cl and 24.23% 37Cl (a 3:1 ratio). Likewise, Br naturally exists as a 1:1 ratio of 79Br:81Br. This appears in the mass spectra as such: Figure 5: Isotope distributions in MS for Cl and Br Bromine is particularly easy to recognise by the presence of two signals of equal intensity and a mass difference of 2, due to the 79Br (M+ ion) and 81Br [(M + 2)+ ion] isotopes, which are nearly equally abundant. The presence of a chlorine atom in a molecule will give rise to an (M + 2)+ signal one-third the height of the M+ signal (the ratio of 35Cl to 37Cl is 3 : 1). https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 5/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1.2. Microanalysis Microanalysis and molecular formula determination Microanalysis is the process in which a compound is combusted and the specific percentage of C, H, and O measured (NB: Some more advanced equipment can even measure other elements). Molecular formula can then be determined from this data, normally with the use of the mass spectrum. Worked Example MS indicates m/z = 108 and microanalysis gives C, 78%, H, 7.4%, O = 14.6%. Determine the molecular formula of the unknown. Step one Convert percentage ratios using molar masses Hence the empirical formula is C7H8O. Step two Match the empirical formula to the molecular mass. Therefore, the molecular formula is the same as the empirical formula - C7H8O. Note: Empirical formula and molecular formula should be written in the following the convention CxHyOz. https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 6/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1.3. Index of hydrogen deficiency Index of hydrogen deficiency (double bond equivalents) Information about the presence of rings or unsaturation (double or triple bonds) can be obtained from the molecular formula. Index of hydrogen deficiency Consider the following examples: Figure 2: Examples for index of hydrogen deficiency For compounds containing elements other than C and H, adjust H in reference hydrocarbon: Group Rule Example Index of hydrogen deficiency Group 15 Add 1H to (N, P, etc.) reference Group 16 No correction (O, S, Se, etc.) Group 17 Subtract 1H from (F, Cl, Br, etc.) reference https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 7/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1.4. IR Spectoscopy Fundamentals of IR spectroscopy The absorption of infrared radiation provides information regarding functional groups in a molecule. This radiation can be absorbed directly by the bonds within a given molecule so long as those bonds have a dipole moment (difference in electronegativity between the two atoms causes the electrons to be closer to one atom - resulting in an unequal distribution of the charge). These bonds are then known as IR active. The simplest vibrational motions in molecules giving rise to the absorption of infrared radiation are stretching and bending motions (Figure 6). Figure 6: The 6 different types of motions detected in IR As mentioned in the video, IR spectroscopy uses wavenumber (cm-1) as the scale. Wavenumber is 1/λ, where λ is wavelength in cm. You will not be required to convert between wavenumber, wavelength and frequency for CHM1022. The 6 different motions in Figure 6 can lead to the absorption of infrared radiation over a range of energy levels and wavelengths. How much radiation is absorbed from 450-4000 cm-1 (which matches the infrared region of the electromagnetic spectrum) gives rise to the IR spectrum, an example of which is shown below: Figure 7: Example IR spectrum. Note 4000cm-1 on LHS represents 2500nm. (Blackman et al. 4th ed.) Dips in the graph indicate energy levels where bonds in the molecule have absorbed the IR energy. Results in the 1550-3800 cm-1 region are the most informative whereas those below 1400 cm-1 are generally too complex to be of use. Interpreting IR spectra Stretching vibrations for most functional groups are found in the region from 1500-3800 cm-1. Some common functional groups and their absorption frequencies are: https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 8/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 Figure 8: IR absorption ranges for common functional groups (Blackman et al. 4th ed.) In particular, aldehydes, ketones and carboxylic acids (and derivatives such as amides and esters) have a characteristic strong infrared signal between 1630-1800 cm-1 due to the stretching vibration of C=O. As many functional groups contain a carbonyl, it is difficult to determine the functional group from the C=O stretch alone (Figure 10). Figure 9: Example of a carbonyl IR absorption. Note the C=O stretch is around 1700cm-1 (Blackman et al. 4th ed.) Figure 10: IR absorbance’s of functional groups containing C=O (Blackman et al. 4th ed.) There are also some common rules to predicting the frequency at which bonds will absorb IR radiation: Bending usually occurs at a lower wavenumber than stretching The stronger the bond the higher the wavenumber. Note: the more bonds between the atoms increases the strength of the bond. Figure 11: IR absorbance Vs bond strength (Blackman et al. 4th ed.) https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 9/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 The C-Y stretching wavenumber decreases with an increase in the mass of Y Figure 12: IR absorbance Vs atom mass (Blackman et al. 4th ed.) Hybridisation effects cause the stretching wave number to decrease from sp to sp3. Figure 13: IR absorbance Vs hybridisation (Blackman et al. 4th ed.) https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 10/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1.5. IR spectroscopy video Watch the first 2 minutes of the following IR spectroscopy video (if you’re interested, you can watch the whole video). Infrared spectroscopy (IR) https://www.youtube.com/watch?v=DDTIJgIh86E https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 11/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 1.6. NMR spectroscopy Watch the NMR spectroscopy video for an introduction to 1H NMR spectroscopy. Proton Nuclear Magnetic Resonance (NMR) https://www.youtube.com/watch?v=uNM801B9Y84 https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 12/16 8/4/24, 9:51 AM Week 3: Chemical detectives - workbook | MonashELMS1 2. Summary This week we have been chemical detectives and solved unknown structures by applying the spectroscopy techniques of NMR spectroscopy, IR spectroscopy and mass spectrometry (MS). With a microanalyses result, we have been able to derive an empirical formula and use it to determine a molecular formula on consultation with mass spectrometry data. Calculation of the Index of Hydrogen Deficiency (IHD) was then used in conjunction with spectroscopic data to confirm, or refute, the structure of an unknown organic molecule. We have also increased our knowledge of NMR spectroscopy and you should now be able to answer the following questions: What is multiplicity (coupling) and why is it useful? What information does chemical shift tell us about the environment of nuclei? What is integration and what is its relationship to the number of protons? In conclusion, using NMR, IR, microanalysis and MS together provides the toolkit we need to elucidate the structure of a compound. Explore the 3D representation and corresponding 1H NMR spectra for propanone and ethyl acetate illustrated in ChemTube 3D (click the links) (Note: Spectrum (singular) and spectra (plural)). Use the controls located at the right hand corner of the image of the molecule to rotate it. Right-click the images for more options. https://learning.monash.edu/mod/book/tool/print/index.php?id=2779886 13/16