MED-108 Organic Chemistry IR & Mass Spectrometry 2024 PDF

MED-108 Organic Chemistry Infrared (IR) Spectroscopy Mass Spectrometry LOBs covered Discuss the basic principles of organic spectroscopy Interpret infrared absorption spectra of organic compounds Discuss the basic principles of mass spectrometry Identify key spectrometric signals in mass spectra Bas...

MED-108 Organic Chemistry Infrared (IR) Spectroscopy Mass Spectrometry LOBs covered Discuss the basic principles of organic spectroscopy Interpret infrared absorption spectra of organic compounds Discuss the basic principles of mass spectrometry Identify key spectrometric signals in mass spectra Basic Principles of Organic Spectroscopy According to Quantum Mechanics all atoms/molecules have discrete energy levels. This allows transitions to take place from one level to another. When radiation comes into resonance with the difference in energy between the two levels, we get a spectroscopic transition. Either absorption or emission of radiation occurs. Spectroscopy – Basic Principles The principal assumption of spectroscopy is that information on the energy levels can give information about the structure of a molecule Infrared Absorption Spectroscopy Employed to detect the presence of specific functional groups IR Spectroscopy Infrared radiation occurs at wavelengths higher than red light Wavelengths greater than 710 nm IR Spectroscopy Excites modes of vibration in a molecule IR Spectroscopy When the light frequency comes into resonance with the frequency (energy) of a particular molecular vibration, the molecule absorbs the energy and shows a signal IR Spectroscopy Usually we measure % transmittance Interpreting IR Spectra Specific functional groups have specific absorption wavenumbers A similar chart will be provided during assessment Alkanes n-hexane C-C and C-H stretch vibrations Alkanes It is difficult to distinguish between two alkanes using their IR spectra Alkenes 1-hexene =C-H stretch, -C-H stretch, C=C stretch Alkynes 1-hexyne C-H stretch, -C-H stretch, CC stretch 5-Minute Break Aromatic Compounds Toluene Ar-H stretch, -C-H stretch, C=C stretch Alcohols 2-butanol O-H stretch, -C-H stretch, -C-O- stretch Amines There are three types of amines, depending on how many alkyl groups the N atom is connected to Note how many N-H bonds each type has Amines Diethylamine N-H stretch (3300-3500 cm-1) Amines Aniline (primary amine, 2 N-H bonds) Amines Triethylamine No -N-H stretch vibrations Carbonyl Compounds Aldehydes Ketones Carboxylic Acids Esters Aldehydes Butanal -C=O stretch, O=C-H stretch, -C-H stretch Ketones Butanone C=O stretch, -C-H stretch Carboxylic Acids Butanoic acid -O-H stretch, C=O stretch, -C-H stretch, -C-O stretch Esters Ethyl acetate C=O stretch, C-O stretch, -C-H stretch Important Observations for Revision The alkane C-H stretching vibration signal occurs always slightly below 3000 cm-1. Most molecules have alkane-like C-H chemical bonds. This signal therefore does not provide much useful information. Alkene and alkyne C-H stretching vibrations will occur above 3000 cm-1. Alkenes also have the C=C signal near 1600 cm-1, whereas asymmetric alkynes have a CC signal near 2100-2200 cm-1. If the alkyne is symmetric, no such signal will appear in the IR spectrum. Aromatic compounds containing benzene will show =C-H signals just above 3000 cm-1. There will also be a C=C signal near 1600 cm-1. Alcohols show a very distinctive strong, broad O-H signal near 3400 cm-1. The C-O signal is in the fingerprint region and is therefore not very useful. Amines that have N-H bonds will show weak/medium intensity signals near 3300 to 3400 cm-1. There will be as many peaks as there are N-H bonds. If there are no N-H bonds (tertiary amine), this signal will be missing. All compounds containing a carbonyl (C=O) group will shows a strong narrow signal near 1700 cm-1. Aldehydes also show two weak signals at 2700 cm-1 and 2800 cm-1. Ketones show only the C=O signal. Carboxylic acids show a very strong and very broad signal around 3200-3400 cm-1. Esters will also show a strong clear C-O signal near 1200 cm-1 in the fingerprint region. Suspecting the presence of an ester is the only time you should search in this region. WATCH: https://www.youtube.com/watch?v=_TmevMf-Zgs WATCH: https://www.youtube.com/watch?v=Bxo_DQpFh1c 5-Minute Break Mass Spectrometry A technique for measuring the mass of atoms and molecules This was the original method employed to detect isotopes in atoms and determine their natural abundance It can also be employed to measure the masses of fragments of an organic molecule The fragmentation pattern may be useful in determining partially the molecular structure – in this course we will not examine the fragmentation pattern in detail Mass Spectrometer Charged fragments of different mass can be resolved and detected separately Electron Gun – Ionizing Beam Electron gun energy = 70 eV (6700 kJ/mol) First action: remove a valence electron from the molecule RH – e- → RH+. Radical cation is produced – Molecular ion (molar mass) Further actions: molecule is fragmented into sequential radical cations Neutral fragments may also be formed but these are not detected Mass Spectrometer Some fragments are neutral, others are cationic Cations are bent by the electromagnet – neutral fragments cannot be bent by the electromagnet, thus they travel straight and crash into the wall Mass Spectrometer – Explanations for Revision The sample is injected into the ionization chamber on the far left. This chamber is under vacuum so the sample usually turns into a gas. Then it passes through the electron gun, where it is hit by very high energy electrons, which removes electrons also forming positively charged fragments. The positive fragments are then accelerated towards an active electromagnet. This magnet also causes the charged fragments to deflect. Heavier fragments deflect less than lighter fragments. This leads to a separation of the paths of the various fragments according to their mass. Electrically neutral fragments will not be deflected, they will travel straight and will simply crash into the walls of the spectrometer. The fragments then hit the detector on the far right, and the signals enter an interfaced computer where they are stored for further analysis. Mass Spectrometer Output Molecular ion peak – molecular weight Base peak – highest intensity peak – most stable fragment Mass Spectrum – n-Decane Explanations for Revision The peak at m/z = 142 is the molecular ion peak and gives the molecular weight. The successive peaks that differ by 14 mass units experience successive loss of -CH2- pieces, which weigh 14 mass units. The base peak, which is the highest intensity peak with m/z = 43, corresponds to a charged CH3CH2CH2 fragment, which appears to be the most stable fragment. Interpretation Molecular Ion Peak – molar mass (MW) One can use a double-focusing mass spectrometer to achieve resolution of ± 0.0005 amu C5H12 (MM = 72.0575 amu) C4H8O (MM = 72.0939 amu) These two molecules will have a molecular ion peak at m/z = 72 when using a regular mass spectrometer, and it is not possible to tell them apart. Using a double-focusing instrument will allow for their separate detection. Interpretation Sensitive to minor isotopes Carbon: 12C (AM = 12.0 amu) Abundance = 99% 13C (AM = 13.0 amu) Abundance = 1% 13C isotope will give rise to the M+1 peak Interpretation Sensitive to all isotopes Chlorine: 35Cl (AM = 35.0 amu) Abundance = 75% 37Cl (AM = 37.0 amu) Abundance = 25% Signals at m/z = 62 and m/z = 64 have a 3:1 intensity pattern Interpretation Specific pattern for alcohols All alcohols lose a water molecule (mass = 18 amu) and display a M – 18 peak Interpretation Recording of a spectrum of an unknown molecule Computer-based matching on the Registry of Mass Spectral Data This can give the identity of the unknown immediately Human Interpretation First piece of information is the molecular-ion peak – This gives us the molecular weight of the compound – Examine M+1 peak for presence of isotopes – Look for M-18 peak confirming the presence of an alcohol The base peak is the highest-intensity peak – This identifies the mass of the most stable fragment We will not get into the details of fragmentation patterns Nuclear magnetic resonance (NMR) spectroscopy provides more details on the structure of the molecule Summary for Revision Mass spectrometry is used for detecting the masses of atoms or molecules, and can also be used to provide useful information about the structure of a molecule. The mass spectrometer is the instrument used to record mass spectra. Its operation has been explained in the presentation slides. In the mass spectrometer, molecules are shattered into fragments of different sizes. The fragmentation pattern can provide information regarding the structure of the molecule. The highest m/z signal corresponds to the molecular ion, and gives directly the molecular weight. The highest intensity peak is called the base peak and corresponds to the most stable fragment. The presence of 13C atoms in a molecule leads to the presence of the M+1 peak, having one more mass unit than the molecular ion peak. Other peaks in the mass spectrum will also display very weak peaks having one more mass unit than the main peak. If the molecule has chlorine atoms in it, peaks corresponding to the two main isotopes (35Cl and 37Cl) will be present, having a 3:1 intensity pattern. Similar effects can be present for other elements with isotopes. Alcohols are easily dehydrated in the mass spectrometer, and will display a M-18 peak just below the molecular ion peak, 18 being the mass of the lost water molecule.