Chapter 12: Structure Determination: MS Spectrometry & IR Spectroscopy

Mass Spectrometry

Bombards molecules with high energy electrons & breaks them apart → molecular mass & formula of the molecule itself and various structural units within it

Infrared Spectroscopy

observes the vibrations of bonds and provides evidence of the presence/absence of key functional groups

Mass Spectrometer

ionizes molecule in a high vacuum, sorts the cation ions according to their masses, and records the abundance of cation ions of each mass

Mass Spectrum

a bar graph with masses (m/z values) on the x-axis and intensity, or relative abundance of ions of a given m/x striking the detector, on the y-axis

Base Peak

the tallest peak, assigned an intensity of 100%

Parent Peak

molecular ion (M+); unfragmented radical cation corresponding to the mass of the original molecule

Fragment Peaks

electron bombardment transfers a lot of energy (cation radicals fragment after formation → fragment peaks); bond breaking tends to form the most stable fragments

Isotope Peaks

most elements contain heavier isotopes in varying amounts → small peaks at a higher mass number than than the major M+ molecular ion peak

Fragmentation of Alkenes

cleavage of an allylic bond to give a resonance stabilized allylic cation (m/z 55)

Fragmentation of Aromatic Rings

fragment at the carbon (benzylic carbon) next to the aromatic ring (m/z 91)

Alpha Cleavage

undergone by alcohols, ethers, amines, and carbonyl compounds → neutral radical and resonance-stabilized cation

McLafferty Rearrangement

characteristic fragmentation of the molecular ion of a carbonyl compound containing at least one gamma hydrogen; then transferred to the carbonyl oxygen, C-C bond is broken and a neutral alkene fragment is produced; charge is on oxygen-containing fragment (M-28)

Wavelength and Frequency Relationship

inversely proportional: vλ = c

3 Regions of Electromagnetic Spectrum

Near-IR, Mid-IR, Far-IR

Near-IR

λ (micrometer): 0.78 to 3

energy (kcal/mol): 10 to 37

rotational spectroscopy

Mid-IR

λ (micrometer): 3 to 30

energy (kcal/mol): 1 to 10

rotational-vibrational spectroscopy

Far-IR

λ (micrometer): 30 to 300

energy (kcal/mol): 0.1 to 1

excite overtone or harmonic vibrations

Wavenumber

number of cycles (waves) in a centimeter

ν̃ = 1/λ

IR Spectra

wavenumber (plotted on x-axis) is proportional to energy

percent transmittance (plotted on y-axis): zero transmittance corresponds to 100% absorption of light at that wavelength

Band Positions (ν̃)

4000 cm-1 is the high energy end of the scale, and 400 cm-1 is the low energy end

Band Intensities

expressed either as s (strong), m (medium), or w (weak)

Beer-Lambert Law (Formula)

A = ebc

A: absorbance

e: molar absorptivity

b: path of the length of the sample

c: concentration of the compound in solution

Molecular Vibrations

covalent bonds behave like springs (stretch, bend, twist)

molecule can vibrate in many ways → each way = vibrational node

Degrees of Freedom

a molecule has as many degrees of freedom as the total degrees of freedom of its individual atoms

each atom has 3 degrees corresponding to Cartesian coordinates (x, y, z) in order to describe its position

Linear Molecules (DoF)

2 degrees are notational, 3 are translational, remaining corresponds to vibrations 3n-5

Nonlinear Molecules (DoF)

3 degrees are notational, 3 are translational, remaining corresponds to vibrations 3n-6

IR Active

must be associated with changes in the permanent dipole (the greater the polarity, the stronger its IR absorption)

Conclusions: Fewer Than Theoretical Numbers of IR Bands

absorption is not in the 4000-400 cm-1 range

absorption is too weak to be observed

absorptions are too close to each other to be resolved on the instrument

additional weak bands which are overtones/combinations of fundamental vibrations are observed