Organic Chemistry - Chapter 14 Notes

Introduction to Spectroscopy

• Spectroscopy involves the interaction between matter and light (electromagnetic radiation).
• Light can be considered as waves of energy or packets (particles) of energy called photons.
• Light waves have properties such as wavelength and frequency.
  • Wavelength is inversely proportional to energy.
  • Frequency is directly proportional to energy.

Electromagnetic Spectrum

• The electromagnetic spectrum is the range of possible frequencies of light.

Spectroscopy Classification

• Different regions of the electromagnetic spectrum are used to probe different aspects of molecular structure.
• Examples:
  • NMR spectroscopy (radio waves): Determines the specific arrangement of all carbon and hydrogen atoms in a compound.
  • IR spectroscopy (infrared): Identifies the functional groups present in a compound.

Quantum Behavior

• Matter exhibits both particle-like and wave-like properties.
• Macroscopic scale: Matter appears to exhibit continuous behavior.
  • Example: A tire can rotate at nearly any rate.
• Molecular scale: Matter exhibits quantum behavior.
  • A molecule will only rotate or vibrate at certain rates (energies).

Vibrational Excitation

• Electrons in covalent bonds have vibrational energy levels separated by gaps (quantized).
• If a photon of light strikes a molecule with the exact amount of energy needed, the light is absorbed, and vibrational excitation occurs.
• Infrared (IR) light generally causes molecular vibration.
• Different types of bonds absorb different IR energies.
• Eventually, the absorbed energy is released from the molecule as heat.

IR Spectroscopy: Bond Stretching and Bending

• Molecular bonds can vibrate by stretching or bending in a number of ways.
• This chapter focuses mainly on stretching frequencies.

IR Spectroscopy: Common Uses

• Night vision goggles can detect emitted IR light.
• IR or thermal imaging is used to detect breast cancer.

IR Spectroscopy: Necessary Energy

• The energy necessary to cause vibration depends on the type of bond.

IR Spectroscopy: Functional Groups

• An IR spectrophotometer irradiates a sample with all frequencies of IR light.
• The frequencies absorbed by the sample indicate the types of bonds (functional groups) present.
• Samples are commonly deposited on a salt (NaCl) plate, dissolved in a solvent, or embedded in a KBr pellet.

IR Spectroscopy: Absorption Bands

• An IR absorption spectrum plots the % transmittance as a function of frequency.
• The “peaks” are called absorption bands.

IR Spectroscopy: Wavenumbers

• Units of frequency in IR are called wavenumbers.
• The values range from 400 to 4000 cm−1.

IR Spectroscopy: Peak Characteristics

• A signal (peak) on the IR spectrum has three important characteristics: wavenumber, intensity, and shape.

Signal Characteristics: Wavenumber

• The frequency (wavenumber) for a stretching vibration depends on:
  • Bond strength: Stronger bond = higher stretching frequency.
  • Mass difference of the atoms bonded together: Larger mass difference = higher stretching frequency.

Signal Characteristics: Wavenumber - Types of Bonds

• The wavenumber formula and empirical observations allow us to designate regions as representing specific types of bonds.

Signal Characteristics: Diagnostic and Fingerprint Regions

• The region above 1500 cm−1 is called the diagnostic region; peaks in this region provide clear information.
• The region below 1500 cm−1 is called the fingerprint region; it typically contains many signals and is difficult to analyze.

Signal Characteristics: Wavenumber - Challenges

• IR spectra for similar compounds (e.g., 2-butanol and 2-propanol) can be virtually indistinguishable due to having the same types of covalent bonds.

Signal Characteristics: Wavenumber - C-H Bonds

• The higher the s character of the carbon, the stronger the C—H bond, and the higher the stretching frequency of the C—H bond.

Signal Characteristics: Wavenumber - C-H Bond Spectra

• Alkyl C—H bonds appear just under 3000 cm−1, while alkenyl and alkynyl C—H bonds are over 3000 cm−1.

Signal Characteristics: Wavenumber - Terminal Alkenes and Alkynes

• It is possible for an alkene or alkyne to have an IR spectra without any signals above 3000 cm−1.

Signal Characteristics: Wavenumber - Resonance

• Resonance delocalization of electrons affects the strength of a covalent bond, and thus the wavenumber of a stretching signal.
• The more delocalized the $p$ electrons, the weaker the $p$ bond, and the lower the stretching frequency.

Signal Characteristics: Wavenumber - Conjugation

• Conjugated carbonyls have lower stretching frequencies.

Signal Characteristics: Intensity - Overview

• The strength (intensity) of IR signals can vary.

Signal Characteristics: Intensity - Dipole Moment

• When a bond undergoes a stretching vibration, its dipole moment also oscillates.
• The oscillating dipole moment creates an electric field surrounding the bond.

Signal Characteristics: Intensity - Polarity

• The more polar the bond, the greater the opportunity for interaction between the waves of the electrical field and the IR radiation.
• Greater bond polarity = stronger IR signals.

Signal Characteristics: Intensity - Example

• The C=O stretching signal is generally stronger than the C=C stretching signal.

Signal Characteristics: Intensity - Symmetrical Bond

• If a bond is completely symmetrical, a stretching frequency is not observed in the IR spectrum.

Signal Characteristics: Intensity - Additional Notes

• Stronger signals are also observed when there are multiple bonds of the same type vibrating.
• Although C—H bonds are not very polar, they often give very strong signals because there are often many of them in an organic compound.
• Sample concentration can affect signal strength. The Intoxilyzer 5000 determines blood alcohol levels by analyzing C—H bond stretching in blood samples.

Signal Characteristics: Shape - Overview

• Some IR signals are broad, while others are very narrow.
• O—H stretching signals are often quite broad.

Signal Characteristics: Shape - O-H Bonds

• O—H bonds can form H-bonds that weaken the O—H bond strength.
• H-bonds are transient, so the sample will contain molecules with varying O—H bond strengths.
• The O—H stretch signal will be narrow if a dilute solution of an alcohol is prepared in a solvent incapable of H-bonding.
• It’s possible to see two signals for an O—H bond: one for the “free” OH and one for those engaged in H-bonding.

Signal Characteristics: Shape - More O-H Examples

• The O—H stretch for a carboxylic acid is broad, and its wavenumber is around 3000 cm−1 rather than 3400 cm−1 for a typical O—H stretch.

Signal Characteristics: Shape - Carboxylic Acids

• H-bonding is often more pronounced in carboxylic acids because they can form H-bonding dimers.

Signal Characteristics: Shape - Amines

• Primary and secondary amines exhibit N—H stretching signals.
• Because N—H bonds are capable of H-bonding, their stretching signals are often broadened.
• 2º amines exhibit only one signal for N—H bonds.
• 1º amines exhibit two signals for the N—H bonds.
• The two N—H bonds vibrate together in two different ways, giving rise to a total of two signals.

Analyzing an IR Spectrum - Step One

• Focus on the diagnostic region (above 1500 cm−1):
  • 1600-1850 cm−1: Check for double bonds.
  • 2100-2300 cm−1: Check for triple bonds.
  • 2700-4000 cm−1: Check for X—H bonds.
• Analyze wavenumber, intensity, and shape for each signal.

Analyzing an IR Spectrum - Step Two

• When looking at the 2700-4000 cm−1 (X—H) region, draw a line at 3000 and focus on the signals that come above it.

Using IR to Distinguish Between Two Compounds

• IR spectroscopy can determine the success of reactions that convert one functional group into another.

Introduction to Mass Spectrometry - Overview

• Mass spectrometry is primarily used to determine the molar mass and formula for a compound.
• In a mass spectrometer:
  • A compound is vaporized, then ionized, and undergoes fragmentation.
  • The masses of the ions are detected and graphed.

Introduction to Mass Spectrometry - Electron Impact

• The most common method of ionizing molecules is by electron impact (EI).
• The sample is bombarded with a beam of high energy electrons (1600 kcal or 70 eV).
• EI usually causes an electron to be ejected from the molecule.

Introduction to Mass Spectrometry - Molecular Ion

• The mass of the radical cation is the same as the parent compound (mass of an electron is negligible).
• If the radical cation remains intact, it is known as the molecular ion (M+•) or parent ion.

Introduction to Mass Spectrometry - Fragmentation

• Most of the radical cations (parent ions) typically fragment into a radical and a cation.
• The ions are deflected by a magnetic field, and their mass-to-charge ratio ($m/z$) is detected.
• Neutrally charged fragments are not detected.

Introduction to Mass Spectrometry - Base Peak

• The mass spectrum shows the relative abundance of each cation that was detected.
• The base peak is the tallest peak in the spectrum and is the most abundant fragment.
• For methane, the base peak is the parent ion, M+•.

Introduction to Mass Spectrometry - Fragments

• Peaks with a $m/z$ less than M+• represent fragments.
• Subsequent H radicals can be fragmented to give ions with $m/z$ = 12, 13, and 14.

Introduction to Mass Spectrometry - Broad Utility

• Mass spec is a relatively sensitive analytical method.
• Many organic compounds can be identified in various fields such as pharmaceutical, biotech, clinical, environmental, geological, and forensic.

Analyzing the (M+•) Peak - Base Peak

• In the mass spec for benzene, the M+• peak is the base peak.
• The M+• peak does not easily fragment.

Analyzing the (M+•) Peak - Parent Ion

• For most compounds, the M+• peak is not the base peak.
• The parent ion for pentane fragments easily.

Analyzing the (M+•) Peak - Molar Mass

• The first step in analyzing a mass spec is to identify the M+• peak.
  • The $m/z$ of the parent ion = molar mass of the compound.
  • An odd-massed M+• peak generally means there is an odd number of N atoms in the molecule.
  • An even-massed M+• peak generally indicates an absence of nitrogen, or an even number of N atoms present.

Analyzing the (M+1)+• Peak - Introduction

• For methane, there is an (M+1)+• peak that is about 1% as abundant as the M+• peak.
• The (M+1)+• peak results from the presence of 13C in the sample.
• Approximately 1% of all carbon atoms are 13C.

Analyzing the (M+1)+• Peak - Number of Carbons

• The more carbon atoms in a compound, the more abundant the (M+1)+• peak is.
• Comparing the heights of the (M+1)+• peak and the M+• peak can allow you to estimate how many carbons are in the molecule.

Analyzing the (M+2)+• Peak - Chlorine

• Chlorine has two abundant isotopes: 35Cl = 76% and 37Cl = 24%.
• So, compounds containing a Cl atom have a 3-to-1 ratio of their M+• to (M+2)+• peaks.

Analyzing the (M+2)+• Peak - Bromine

• 79Br = 51% and 81Br = 49%, so molecules with bromine often have equally strong M+• to (M+2)+• peaks, because these isotopes are equally abundant.

Analyzing the Fragments - Pentane

• MS only detects charged fragments.
• A thorough analysis of the molecular fragments can often yield structural information.

Analyzing the Fragments - Pentane Details

• Clusters around each ion are the result of further fragmentation (loss of H atoms).

Analyzing the Fragments - Most Abundant Fragment

• While all possible fragmentations are possible and observed, the most abundant fragment is the most stable cation possible.
• Since a 3º cation is more stable than 1º or 2º, the M-43 peak will be the most abundant.

Analyzing the Fragments - Alcohols

• Alcohols generally undergo two main types of fragmentation: alpha cleavage and dehydration.
• A stabilized oxonium ion is formed.
• A stable, neutral molecule is formed.

Analyzing the Fragments - Amines

• Amines also undergo alpha cleavage.
• Carbonyls generally undergo McLafferty rearrangement.

Analyzing the Fragments - Summary

• Presence of these characteristic fragments in a mass spectrum confirm the following structural features:
  • M − 15: Loss of a methyl radical
  • M − 29: Loss of an ethyl radical
  • M − 43: Loss of a propyl radical
  • M − 57: Loss of a butyl radical
  • M − 18: Loss of water (from an alcohol)

High-Resolution Mass Spec - Overview

• High-Resolution Mass Spectrometry allows $m/z$ to be measured with up to 4 decimal places.
• Masses are generally not whole number integers:
  • 1 proton = 1.0073 amu
  • 1 neutron = 1.0086 amu
  • One 12C atom = exactly 12.0000 amu (amu scale is based on the mass of 12C)
• All atoms other than 12C will have masses in amu that can be measured to 4 decimal places by a high-resolution mass spec instrument.

High-Resolution Mass Spec - Useful Table

• Relative atomic mass and abundance of several elements.
  • 1H: 1.0078 amu, 99.99%
  • 2H: 2.0141 amu, 0.01%
  • 16O: 15.9949 amu, 99.76%
  • 17O: 16.9991 amu, 0.04%
  • 18O: 17.9992 amu, 0.20%

High-Resolution Mass Spec - Similar Molecular Weights

• Atomic weights on the PTE are based on isotopic abundance.
• High-res MS allows one to distinguish between compounds that have the same MW when rounded to the nearest amu.

Gas Chromatography - Mass Spec - Overview

• Mass Spec is suited for the identification of pure substances.
• MS instruments can be connected to a gas chromatograph so mixtures can be separated prior to MS identification.

Gas Chromatography - Mass Spec - Chromatogram and Mass Spectrum

• GC-MS gives two sets of data:
  • The chromatogram gives the retention time.
  • The mass spectrum.
• GC-MS is a great technique for detecting compounds in complex mixtures, such as blood or urine.

Mass Spec of Large Biomolecules

• To be analyzed by EI mass spec, substances generally must be vaporized prior to ionization.
• In Electrospray ionization (ESI), a high-voltage needle sprays a liquid solution of an analyte into a vacuum causing ionization.
• The molecular ions generally do not fragment… ESI is a “softer” ionizing technique.
• Useful for large molecules that otherwise give complex fragmentation patterns.

Degrees of Unsaturation - Overview

• Mass spec is often used to determine the molecular formula for an organic compound.
• IR can often determine the functional groups present.
• Alkanes (saturated hydrocarbons) follow the formula: $C<em>nH</em>{2n+2}$

Degrees of Unsaturation - Concept

• Degree of unsaturation: a $π$ bond or a ring.
• For every degree of unsaturation in a compound, the number of Hs is reduced by 2.

Degrees of Unsaturation - Isomer Examples

• 1 degree of unsaturation = 1 unit on the hydrogen deficiency index (HDI).

Degrees of Unsaturation - Halogen and Oxygen

• For the HDI scale, a halogen is treated as if it were a hydrogen atom.
• An oxygen does not affect the HDI.

Degrees of Unsaturation - Nitrogen

• For the HDI scale, a nitrogen increases the number of expected hydrogen atoms by one.

Degrees of Unsaturation - Importance

• Calculating the HDI can be very useful. For example, if HDI = 0, the molecule cannot have any rings, double bonds, or triple bonds.