(12)Organic Chemistry: IR Spectroscopy and Mass Spectrometry - Comprehensive Notes

Organic Chemistry: Infrared Spectroscopy and Mass Spectrometry

Introduction to Spectroscopy

• Spectroscopy is a technique used to determine the structure of a compound.
• Most techniques are nondestructive, meaning they destroy little to no sample.
• Absorption spectroscopy measures the amount of light absorbed by a sample as a function of wavelength.

Types of Spectroscopy

• Infrared (IR) spectroscopy: Measures the bond vibration frequencies in a molecule and is used to determine the functional group.
• Mass spectrometry (MS): Fragments the molecule and measures the mass. MS can give the molecular weight of the compound and functional groups.
• Nuclear magnetic resonance (NMR) spectroscopy: Analyzes the environment of the hydrogens in a compound, providing clues about alkyl and other functional groups present.
• Ultraviolet (UV) spectroscopy: Uses electronic transitions to determine bonding patterns.

Wavelength and Frequency

• The frequency $\nu$ of a wave is the number of complete wave cycles that pass a fixed point in a second.
• Wavelength $\lambda$ is the distance between any two peaks (or any two troughs) of the wave.

Electromagnetic Spectrum

• Frequency and wavelength are inversely proportional, related by the equation: $\nu = \frac{c}{\lambda}$, where $c$ is the speed of light (approximately $3 × 10^{10}$ cm/sec).
• The energy of a photon is given by: $E = h\nu$, where $h$ is Planck’s constant ($6.62 × 10^{-37}$ kJ•sec).

The Infrared (IR) Region

• The IR region is located from just below the visible region to just above the highest microwave and radar frequencies.
• Wavelengths typically range from $2.5 × 10^{-4}$ to $25 × 10^{-4}$ cm.
• Wavenumbers (cm⁻¹) are commonly used units, representing the number of cycles (wavelengths) in a centimeter. They are proportional to frequency and energy.

Molecular Vibrations

• When a bond is stretched, a restoring force pulls the two atoms together toward their equilibrium bond length.
• When a bond is compressed, the restoring force pushes the two atoms apart.
• If a bond is stretched or compressed and then released, the atoms vibrate.

Bond Stretching Frequencies

• Frequency decreases with increasing atomic mass.
• Frequency increases with increasing bond energy.

Vibrational Modes

• A nonlinear molecule with $n$ atoms has $3n – 6$ fundamental vibrational modes.
• Water (H₂O) has $3(3) – 6 = 3$ modes: two stretching modes and one bending mode (scissoring).

Fingerprint Region of the Spectrum

• No two molecules (except enantiomers) will give exactly the same IR spectrum.
• The fingerprint region is between 600 and 1400 cm⁻¹ and contains the most complex vibrations.
• The region between 1600 and 3500 cm⁻¹ has the most common vibrations and can be used to identify specific functional groups.

Effect of an Electric Field on a Polar Bond

• A bond with a dipole moment (e.g., HF) is either stretched or compressed by an electric field, depending on the field's direction.
• The force on the positive charge is in the direction of the electric field ($E$), and the force on the negative charge is in the opposite direction.

Carbon–Carbon Bond Stretching

• Stronger bonds absorb at higher frequencies because they are more difficult to stretch.
• Conjugation lowers the frequency:
  • Isolated C=C: 1640-1680 cm⁻¹ (e.g., cyclohexene at 1645 cm⁻¹)
  • Conjugated C=C: 1620-1640 cm⁻¹ (e.g., cyclohexa-1,3-diene at 1620 cm⁻¹)
  • Aromatic C=C: approximately 1600 cm⁻¹

Carbon–Hydrogen Stretching

• A greater percentage of s character in the hybrid orbitals will make the C—H bond stronger.
• The C—H bond of an sp³ carbon will be slightly weaker than the C—H bond of an sp² or an sp carbon.

IR Spectrum of Alkanes

• An alkane will show stretching and bending frequencies for C—H and C—C bonds only.
• The C—H stretching is a broad band between 2800 and 3000 cm⁻¹, a band present in virtually all organic compounds.
• The absence of other bands indicates the presence of no other functional groups.

IR Spectrum of Alkenes

• The most important absorptions in 1-hexene are the C=C stretch at 1642 cm⁻¹ and the unsaturated C-H stretch at 3080 cm⁻¹.
• The bands of the alkane are also present in the alkene.

IR Spectra of Alkynes

• Terminal alkynes (e.g., oct-1-yne) show:
  • ≡C-H stretch around 3313 cm⁻¹
  • C≡C stretch around 2119 cm⁻¹
• Internal alkynes (e.g., oct-4-yne) may not show a C≡C or ≡C-H stretch.

O—H and N—H Stretching

• Both O—H and N—H stretching occur around 3300 cm⁻¹, but they look different:
  • Alcohol O—H is broad with a rounded tip.
  • Secondary amine (R₂NH) is broad with one sharp spike.
  • Primary amine (RNH₂) is broad with two sharp spikes.
  • There is no signal for a tertiary amine (R₃N) because there is no hydrogen.

IR Spectrum of Alcohols

• Alcohols show a broad, intense O—H stretching absorption centered around 3300 cm⁻¹.
• The broad shape is due to the diverse nature of hydrogen bonding interactions of alcohol molecules.

IR Spectrum of Amines

• Amines show a broad N—H stretching absorption centered around 3300 cm⁻¹.
• Dipropylamine (secondary amine) has only one hydrogen, so it will have only one spike in its spectrum. A primary amine (RNH₂) gives two spikes around 3300 cm⁻¹.

Ketones, Aldehydes, and Acids

• The C=O bond of simple ketones, aldehydes, and carboxylic acids absorbs around 1710 cm⁻¹.
• Usually, the carbonyl is the strongest IR signal.
• Carboxylic acids will also have O—H stretching.
• Aldehydes have two C—H signals around 2700 and 2800 cm⁻¹.

IR Spectrum of Ketones

• 2-Heptanone shows a strong, sharp absorption at 1718 cm⁻¹ due to the C=O stretch.

IR Spectrum of Aldehydes

• Aldehydes have the C=O stretch around 1710 cm⁻¹.
• They also have two different stretch bands for the C—H bond at 2720 and 2820 cm⁻¹.

O—H Stretch of Carboxylic Acids

• This O—H absorbs broadly, 2500–3500 cm⁻¹, due to strong hydrogen bonding.
• Both peaks (C=O and O-H) need to be present to identify the compound as a carboxylic acid.

Conjugated Carbonyl Compounds

• Conjugation lowers the carbonyl absorption to around 1685 cm⁻¹.

Resonance in Amides

• The carbonyl groups of amides absorb at particularly low IR frequencies: about 1640 to 1680 cm⁻¹.

IR Spectrum of Amides

• Amides will show a strong absorption for the C=O at 1640–1680 cm⁻¹.
• If there are hydrogens attached to the nitrogen of the amide, there will be N—H absorptions around 3300 cm⁻¹.

Carbonyl Absorptions Above 1725 cm⁻¹

• Esters typically absorb around 1735 cm⁻¹.
• Strained cyclic ketones absorb at a higher frequency because the angle strain on the carbonyl results in a stronger, stiffer bond.

Carbon-Nitrogen Stretching

• C-N single bond: approximately 1200 cm⁻¹
• C=N double bond: approximately 1660 cm⁻¹
• C≡N triple bond: greater than 2200 cm⁻¹
  • C≡C triple bond: less than 2200 cm⁻¹

IR Spectrum of Nitriles

• A carbon–nitrogen triple bond has an intense and sharp absorption, centered around 2200 to 2300 cm⁻¹.
• Nitrile bonds are more polar than carbon–carbon triple bonds, so nitriles produce stronger absorptions than alkynes.

Summary of IR Absorptions

• Key functional groups and their approximate absorption ranges:
  • O-H: 3300 cm⁻¹ (broad)
  • N-H: 3300 cm⁻¹ (may be broad, sharp, or broad with spikes)
  • ≡C-H: 3300 cm⁻¹ (always sharp, usually strong)
  • =C-H: just above 3000 cm⁻¹
  • -C-H (alkane): just below 3000 cm⁻¹
  • C≡N: approximately 2200 cm⁻¹ (very strong)
  • C=O: approximately 1710 cm⁻¹
  • C=C: approximately 1660 cm⁻¹

Solved Problem Example

• To determine the functional group(s) in a compound, look for peaks outside the fingerprint region that don't look like alkane peaks.
• For example, a weak peak around 3400 cm⁻¹, a strong peak about 1720 cm⁻¹, and C–H stretching peaks around 2720 and 2820 cm⁻¹ suggest an aldehyde.
• The peak at 1720 cm⁻¹ indicates a C=O, and the peaks at 2720 and 2820 cm⁻¹ confirm an aldehyde.

Strengths and Limitations of IR Spectroscopy

• IR alone cannot determine a structure.
• Some signals may be ambiguous.
• The functional group is usually indicated.
• The absence of a signal is definite proof that the functional group is absent.
• Correspondence with a known sample’s IR spectrum confirms the identity of the compound.

Introduction to Mass Spectrometry (MS)

• Molecular weight and molecular formula can be obtained from a very small sample.
• Mass spectrometry is fundamentally different from spectroscopy.
• Destructive technique: The sample cannot be recovered.

Mass Spectrometry Process

• A beam of high-energy electrons breaks the molecule apart.
• The masses of the fragments and their relative abundance reveal information about the structure of the molecule.

Radical Cation Formation

• When a molecule loses one electron, it then has a positive charge and one unpaired electron. This ion is therefore called a radical cation.

Electron Impact Ionization

• Other fragments can be formed when C—C or C—H bonds are broken during ionization. Only the positive fragments can be detected in MS.

Mass Spectrometer Components

• Ion source
• Magnet
• Flight tube
• Detector
• Recorder

Separation of Ions

• The most common mass spectrometer separates ions by magnetic deflection.
• The mixture of ions is accelerated and passes through a magnetic field where the paths of lighter ions are bent more than those of heavier atoms.
• By varying the magnetic field, the spectrometer plots the abundance of ions of each mass.
• The exact radius of curvature of an ion's path depends on its mass-to-charge ratio, symbolized by m/z. In this expression, m is the mass of the ion (in amu) and z is its charge.
• The vast majority of ions have a +1 charge, so we consider their path to be curved by an amount that depends only on their mass.

The Mass Spectrum

• In the spectrum, the tallest peak is called the base peak and it is assigned an abundance of 100%. The % abundance of all other peaks is given relative to the base peak.
• The molecular ion or parent peak (M+) corresponds to the molecular weight of the original molecule.

Gas Chromatography–Mass Spectrometry (GC–MS)

• The gas chromatograph column separates the mixture into its components.
• The mass spectrometer scans mass spectra of the components as they leave the column.

High-Resolution MS

• Masses are measured to an accuracy of about 1 part in 20,000.
• A molecule with a mass of 44 could be C3H8, C2H4O, CO2, or CN2H4.
• Using HRMS, the exact mass can be found and the compound successfully identified.

Masses of Common Isotopes

• ¹²C: 12.000000 amu
• ¹H: 1.007825 amu
• ¹⁶O: 15.994914 amu
• ¹⁴N: 14.003050 amu

Molecules with Heteroatoms

• Isotopes are present in their usual abundance.
• Carbon has a ¹³C isotope present in 1.1% abundance. The spectrum will show the normal M+ and small M+1 peak.
• Bromine has two isotopes: ⁷⁹Br (50.5%) and ⁸¹Br (49.5%). Since the abundances are almost equal, there will be an M+ peak and an M+2 peak of equal height.

Isotopic Abundance

• Key elements and their isotopic composition:
  • Hydrogen: ¹H (100.0%)
  • Carbon: ¹²C (98.9%), ¹³C (1.1%)
  • Nitrogen: ¹⁴N (99.6%), ¹⁵N (0.4%)
  • Oxygen: ¹⁶O (99.8%), ¹⁸O (0.2%)
  • Sulfur: ³²S (95.0%), ³³S (0.8%), ³⁴S (4.2%)
  • Chlorine: ³⁵Cl (75.5%), ³⁷Cl (24.5%)
  • Bromine: ⁷⁹Br (50.5%), ⁸¹Br (49.5%)
  • Iodine: ¹²⁷I (100.0%)

Mass Spectrum with Bromine

• Bromine is a mixture of 50.5% ⁷⁹Br and 49.5% ⁸¹Br. The molecular ion peak M+ (⁷⁹Br) is nearly as tall as the M+2 peak (⁸¹Br).

Mass Spectrum with Chlorine

• Chlorine is a mixture of 75.5% ³⁵Cl and 24.5% ³⁷Cl. Since the ratio is approximately 3:1, the molecular ion peak M+ is three times higher than the M+2 peak.

Mass Spectrum with Sulfur

• Sulfur has three isotopes: ³²S (95%), ³³S (0.8%), and ³⁴S (4.2%).
• The M+ peak will have an M+2 peak that is larger than usual (about 4% of M+).

Mass Spectrum of n-Hexane

• Groups of ions correspond to loss of one-, two-, three-, and four-carbon fragments.

Fragmentation of the Hexane Radical Cation

• Fragmentations often split off simple alkyl groups:
  • Methyl (CH₃): 15
  • Ethyl (C₂H₅): 29
  • Propyl (C₃H₇): 43
  • Butyl (C₄H₉): 57

Mass Spectrum of 2-Methylpentane

• Characteristic fragmentations due to branching, such as loss of methyl (M-15), ethyl (M-29), and propyl (M-43) groups.

Fragmentation of Branched Alkanes

• The most stable carbocation fragments form in greater amounts.

Resonance-Stabilized Cations

• Fragmentation in the mass spectrometer gives resonance-stabilized cations whenever possible. The most common fragmentation of alkenes is cleavage of an allylic bond to give a resonance-stabilized allylic cation.

Mass Spectrum of Alkenes

• Resonance-stabilized cations are favored.

Benzylic Cation

• Compounds containing aromatic rings tend to fragment at the carbon next to the aromatic ring.
• Such a cleavage forms a resonance-stabilized benzylic cation.

Mass Spectrum of Alcohols

• Alcohols often lose water ($H_2O$).

MS of 3-Methylbutan-1-ol

• Loss of water and formation of an allylic cation.

Fragmentation of Ethers, Amines, and Carbonyl Compounds

• Ethers, amines, and carbonyl compounds can also fragment to give resonance-stabilized cations.

EI MS of Di-sec-butyl Ether

• Shows almost no molecular ion.
• Molecular ion formed by loss of an electron from the ether oxygen.
• Next, an ethyl radical is lost via α-cleavage forming the base peak at m/z = 45.