Chapter 11 Structure Determination: Mass Spectrometry, Infrared Spectroscopy, and Ultraviolet Spectroscopy

Introduction Modern techniques for structure determination of organic compounds include: Mass spectrometry What is the size and formula of the compound Infrared spectroscopy What functional groups are present in the compound Ultraviolet spectroscopy Is a conjugated p electron system present in the compound Nuclear magnetic resonance spectroscopy What is the carbon-hydrogen framework of the compound

11.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments Mass spectrometry (MS) measures the mass and molecular weight (MW) of a molecule Provides structural information by finding the masses of fragments produced when molecules break apart Three basic parts of mass spectrometers:

Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments Electron-impact, magnetic-sector instrument Sample is vaporized into ionization source Bombarded by electron beam (70 eV) dislodging valence electron of sample producing cation-radical Most cation-radicals fragment and are separated in magnetic field according to their mass-to-charge ratio (m/z) Since z = 1 for most ions the value of m/z is mass of ion

Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments Mass spectrum of propane (C3H8; MW = 44) Base peak Tallest peak Assigned intensity of 100% Base peak at m/z = 29 in propane mass spectrum Parent peak Unfragmented cation radical – molecular ion (M+) Parent peak only 30% of base peak for propane

11.2 Interpreting Mass Spectra Molecular weight determined from molecular ion peak High resolution double-focusing mass spectrometers are accurate to about 0.0005 amu M+1 peak results from presence of 13C and 2H Fragmentation occurs when high-energy cation radical falls apart One fragment retains positive charge and is a carbocation One fragment is a neutral radical fragment

Interpreting Mass Spectra Mass spectrum of 2,2-dimethylpropane (MW = 72) No M+ peak observed when electron-impact ionization is used “Soft” ionization methods can prevent fragmentation of molecular ion

Interpreting Mass Spectra Base peak in mass spectrum of 2,2-dimethylpropane is at m/z = 57 m/z = 57 corresponds to t-butyl cation Molecular ion fragments to give most stable carbocation

Interpreting Mass Spectra Mass spectrum of hexane (C6H14; MW = 86) All carbon-carbon bonds of hexane are electronically similar and break to a similar extent Mass spectrum contains mixture of ions

Interpreting Mass Spectra M+ = 86 for hexane m/z = 71 arises from loss of methyl radical from hexane cation radical m/z = 57 arises from loss of ethyl radical from hexane cation radical m/z = 43 arises from loss of propyl radical from hexane cation radical m/z = 29 arises from loss of butyl radical from hexane cation radical

Worked Example 11.1 Using Mass Spectra to Identify Compounds Assume that you have two unlabeled samples, one of methylcyclohexane and the other of ethylcyclopentane. How could you use mass spectrometry to identify them?

Worked Example 11.1 Using Mass Spectra to Identify Compounds Strategy Look at the two possible structures and determine how they differ. Then think about how any of these differences in structure might give rise to differences in mass spectra. Methylcyclohexane, for instance, has a –CH3 group, and ethylcyclopentane has a –CH2CH3 group, which should affect the fragmentation process.

Worked Example 11.1 Using Mass Spectra to Identify Compounds Solution The mass spectra of both samples show molecular ions at M+ = 98, corresponding to C7H14, but the two spectra differ in their fragmentation patterns. Sample A has its base peak at m/z = 69, corresponding to the loss of a CH2CH3 group (29 mass units), but B has a rather small peak at m/z = 69. Sample B shows a base peak at m/z = 83, corresponding to the loss of a CH3 group (15 mass units), but sample A has only a small peak at m/z = 83. We can therefore be reasonably certain that A is ethylcyclopentane and B is methylcyclohexane.

11.3 Mass Spectrometry of Some Common Functional Groups Alcohols Fragment by two pathways Alpha cleavage Dehydration

Mass Spectrometry of Some Common Functional Groups Amines Aliphatic amines undergo characteristic a cleavage

Mass Spectrometry of Some Common Functional Groups Carbonyl compounds Ketones and aldehydes with C-H three atoms away from carbonyl group undergo McLafferty rearrangement

Mass Spectrometry of Some Common Functional Groups Ketones and aldehydes also undergo a cleavage of bond between carbonyl group and neighboring carbon

Worked Example 11.2 Identifying Fragmentation Patterns in a Mass Spectrum The mass spectrum of 2-methylpentan-3-ol is shown in Figure 11.8. What fragments can you identify?

Worked Example 11.2 Identifying Fragmentation Patterns in a Mass Spectrum Strategy Calculate the mass of the molecular ion, and identify the functional groups in the molecule. Then write the fragmentation processes you might expect, and compare the masses of the resultant fragments with the peaks present in the spectrum.

Worked Example 11.2 Identifying Fragmentation Patterns in a Mass Spectrum Solution 2-Methylpentan-3-ol, an open-chain alcohol, has M+ = 102 and might be expected to fragment by a cleavage and by dehydration. These processes would lead to fragment ions of m/z = 84, 73, and 59. Of the three expected fragments, dehydration is not observed (no m/z = 84 peak), but both a cleavages take place (m/z = 73, 59).

11. 4 Mass Spectrometry in Biological Chemistry: 11.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments Most biological analyses use “soft” ionization methods: Electrospray ionization (ESI) Sample dissolved in polar solvent and sprayed through steel capillary tube As sample exits tube it is subjected to high voltage producing variably protonated sample ions (M + Hnn+) Matrix-assisted laser desorption ionization (MALDI) Sample is adsorbed onto a suitable matrix compound, such as 2,5-dihydroxybenzoic acid, which is ionized by laser light Matrix compound then transfers energy to the sample and protonates it, forming M + Hnn+ ions Protonated sample ions are focused into small packet and hit with energy from accelerator electrode Ions begin moving with velocity(v) Molecules separate based on different times of flight through analyzer drift tube

Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments MALDI-TOF mass spectrum of chicken egg-white lysozyme Peak at 14,307.7578 daltons (amu) is due to the mono-protonated protein

Spectroscopy and the Electromagnetic Spectrum Absorption spectrum Spectrum of compound’s selective absorption of electromagnetic radiation Infrared absorption spectrum of ethanol

11.6 Infrared Spectroscopy Infrared (IR) region Ranges from 7.8 x 10-7 m to 10-4 m 2.5 x 10-6 m to 2.5 x 10-5 m used by organic chemists Wavelengths given in micrometers (1 mm = 10-6 m) Frequencies given in wavenumbers Wavenumber Reciprocal of wavelength in centimeters Expressed in units of cm-1

Infrared Spectroscopy Molecules stretch or bend at specific frequencies Energy is absorbed if the frequency of the radiation matches the frequency of the vibration IR spectrum What molecular motions? What functional groups?

11.7 Interpreting Infrared Spectra Most functional groups have characteristic IR absorption bands that don’t change from one compound to another

Interpreting Infrared Spectra

Interpreting Infrared Spectra

Interpreting Infrared Spectra Hexane Hex-1-ene Hex-1-yne

Infrared Spectra of Some Common Functional Groups

Infrared Spectra of Some Common Functional Groups