Modern techniques for structure determination of organic compounds include: Mass spectrometry Size and formula of the compound Infrared spectroscopy Functional.

Modern techniques for structure determination of organic compounds include:

• Mass spectrometry• Size and formula of the compound

• Infrared spectroscopy• Functional groups present in the compound

• Ultraviolet spectroscopy• Conjugated electron system present in the compound

• Nuclear magnetic resonance spectroscopy• Carbon-hydrogen framework of the compound

Introduction

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:

10.1 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

Fig. 15-5, p. 619

Table 15-3, p. 620

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

Interpreting Mass Spectra

Fig. 15-6, p. 621

Fig. 15-7, p. 622

Fig. 15-8, p. 626

Alcohols• Fragment by two pathways

• Alpha cleavage

• Dehydration

10.3 Mass Spectrometry of Some Common Functional Groups

Amines• Aliphatic amines undergo characteristic 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 cleavage of bond between carbonyl group and neighboring carbon

Mass Spectrometry of Some Common Functional Groups

The mass spectrum of 2-methylpentan-3-ol is shown below. What fragments can you identify?

Worked Example 10.2

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 10.2

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 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 cleavages take place (m/z = 73, 59).

Worked Example 10.2

Identifying Fragmentation Patterns in a Mass Spectrum

Mass spectrum of 2,2-dimethylpropane (MW = 72)

• 2,2-dimethylpropane fragments so easily that 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

MALDI-TOF mass spectrum of chicken egg-white lysozyme• Peak at 14,307.7578 daltons (amu) is due to the mono-

protonated protein

Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments