Organic Chemistry II Study Notes

Organic Chemistry II CHEM 342 Chapter 14: Infrared Spectroscopy and Mass Spectrometry

Introduction to Structure Determination

• Determining the structure of molecules involves:

  • Probing physical properties

  • Elemental Analysis

  • Finding atomic composition and relative ratios

  • Deriving empirical formula

  • Mass Spectrometry

  • Determining molecular formula

  • Identifying elements and isotopes

  • Understanding molecular connectivity

Mass Spectrometer Components

• Diagram Components:

  • Ionization source (electron beam)

  • Heated filament for sample inlet

  • Ions are deflected based on mass-to-charge ratio (m/z)

  • Magnet and detector

  • CRT display for results visualization

Spectroscopy Overview

• Definition: Involves interaction between matter and electromagnetic (EM) radiation (light).

• Light can exist as:

  • Waves with properties: wavelength and frequency

  • Relationship: Wavelength inversely proportional to energy:
    $E \propto \frac{1}{\text{wavelength}}$

  • Frequency is directly proportional to energy

Electromagnetic Spectrum

• Increasing wavelength, decreasing energy:

  • Ranges from Gamma rays to Radio waves

  • Visible light range is about 400-750 nm

Ultraviolet - Visible Spectroscopy

• Electronic (UV-VIS) Spectroscopy:

  • Used to excite electrons to a higher energy state.

  • More conjugation in molecules results in lower energy absorption.

Infrared Spectroscopy

• Definition: Vibrational spectroscopy to identify functional groups based on molecular vibrations.

• Types of molecular vibrations:

  • Symmetric stretching vibration: Both outer atoms move away from or toward the center.

  • Symmetric bending vibration: Includes scissoring (in-plane) and twisting (out-of-plane).

  • Asymmetric stretching vibration: When one atom moves toward the center, the other moves away.

  • Asymmetric bending vibration: Includes rocking (in-plane) and wagging (out-of-plane).

Nuclear Magnetic Resonance Spectroscopy (NMR)

• Function: Probes spin transitions of atomic nuclei; focuses on interactions in the radio frequency range.

  • Provides information on:

  • Functional groups

  • Atom connectivity

  • Stereochemistry

  • Higher-order structures

• Magnetic Resonance Imaging (MRI): NMR is the basis for MRI for medical imaging.

X-Ray Crystallography

• Technique used to determine the 3D positions of atoms in a molecule based on X-ray diffraction patterns.

Empirical Formula from Elemental Analysis

• Example of calculating empirical formula:

  • Given elemental percentages:

  • C: 63.31%

  • H: 6.28%

  • Cl: 16.99%

  • N: 13.42%

  • Assuming 100g of analyte, convert percentages to moles to find ratios:

  • Moles of C = $\frac{63.31 \text{ g}}{12.01 \text{ g/mol}} = 5.27$

  • Moles of H = $\frac{6.28 \text{ g}}{1.008 \text{ g/mol}} = 6.23$

  • Moles of Cl = $\frac{16.99 \text{ g}}{35.453 \text{ g/mol}} = 0.48$

  • Moles of N = $\frac{13.42 \text{ g}}{14.007 \text{ g/mol}} = 0.96$

  • Empirical Formula: C₁₁H₁₃ClN₂

Units of Unsaturation

• Definition: Degrees of unsaturation refers to the number of rings and pi bonds in a molecule.

  • For saturated hydrocarbons, the formula is:
    $C<em>nH</em>{2n+2}$

  • Adjustments for substituents:

  • For each halogen (X) replacing hydrogen (H), subtract one H.

  • For each nitrogen (N) present, add one H.

• Example calculation for a compound with C₁₁H₁₃ClN₂:

  • UN = (2n + 2) - #H - #X + #N

  • Calculated as: $2UN = (2*11+2) - 13 - 1 + 2 = 6$

Molecular Formula from Mass

• Rule of 13:

  • Based on molecular weight, where $M = 13n + r$ determines the molecular formula from mass (M).

  • Example: For M=164, $\frac{164}{13} = 12 + \frac{8}{13}$ implies potential formula C₁₂H₁₂+₈ or C₁₂H₂₀.

  • When other atoms are present: Subtract their mass equivalents from the formula.

  • Example: For a molecule C₁₂H₂₀O, account for O atom to yield C₁₁H₁₆O.

Identification of a Natural Product: Epibatidine

• Identified using:

  • High-resolution Mass Spectrometry

  • UV Spectroscopy

  • IR Spectroscopy

  • Characteristics:

  • Molecular weight: 210.0764

  • Molecular formula: C₁₁H₁₃N₂Cl

  • Analgesic potency: 500 times greater than morphine.

Structure Elucidation Steps

• Start with pure compound characteristics and gather relevant data:

  • Molecular formula analysis

  • Identification of functional groups

• Use techniques: NMR, IR, UV, X-ray for structural determination.

  • Explore isomers and determine the best possible structural candidates for synthesis.

Infrared Spectroscopy Details

• IR Spectra Interpretation:

• Transmittance percentage (%T) displayed against wavenumber (cm⁻¹):

  • Regions to focus on for specific functional groups:

  • 4000 – 2700 cm⁻¹ for O-H and X-H bonds

  • 1600-1850 cm⁻¹ for C=C double bonds

  • 2100-2300 cm⁻¹ for C≡C triple bonds

Energy of a Photon

• Equations:

  • Energy and frequency relationship:
    $E = h <br>u$

  • Wavenumber relationship:
    $\text{wavenumber (}\text{cm}^{-1}\text{)} = \frac{1}{\lambda (\text{cm})}$

  • Higher wavenumber correlates with higher energy.

Molecular Vibrations

• Types of molecular vibrations:

  • Stretching: Moves atoms along the bond axis.

  • Bending: Changes angles between bonds.

• Main types include: Scott symmetrical and asymmetrical stretching, as well as imaginary bending.

Bond Vibrational Energy Levels

• Illustrated by the Morse Curve:

  • Bonds vibrate at specific frequency levels, even in zero temperature (0K).

  • Quantized energy levels: Lowest is the zero-point energy.

Harmonic Oscillator Model

• For a bond modeled as a harmonic oscillator:

  • Energy of oscillation:
    $E<em>{osc} = h u</em>{osc}$

  • Factors influencing frequency:

  • Mass of atoms and bond stiffness (force constant).

Hooke’s Law in Vibrational Analysis

• Formula:

  • $\nu = \frac{1}{2\pi c} \sqrt{\frac{K}{\mu}}$

  • Where:

  • K = force constant (strength of bond)

  • µ = reduced mass (in atomic mass units)

Approximations Using Hooke’s Law

• Experimental values:

  • sp³: K = 5 x 10⁵ dynes/cm

  • sp²: K = 10 x 10⁵ dynes/cm

  • sp: K = 15 x 10⁵ dynes/cm

Bond Strength Influences

• Factors include:

  • Hybridization

  • Resonance

  • Electronegativity

  • Ring strain

• Stretching frequencies are generally higher energy than bending frequencies.

Dipole Moments and IR Absorption

• A bond must have an oscillating dipole moment to absorb IR radiation.

• Symmetric molecules do not absorb effectively; larger dipoles correlate with stronger absorptions.

Specific IR Stretching Regions

• Summary of C-H stretching regions in IR:

  • Alkanes (C-H) < 3000 cm⁻¹

  • Alkenes/Alkynes > 3000 cm⁻¹

Alcohol and Carboxylic Acid IR Signals

• O-H stretch shows broad characteristic signals due to hydrogen bonding interactions.

• In carboxylic acids, O-H stretching is further broadened.

Amines in IR Spectroscopy

• Primary amines (RNH₂) and secondary amines (R₂NH) show distinct N-H stretches in the IR spectra.

Analyzing IR Spectra

• Tips for functional-group identification:

  • Focus on diagnostic regions:

  • C=C and C≡C ranges and X-H stretching.

Example Problems in IR Analysis

• Assessment of various molecular structures relative to provided IR spectra.

• Consider the functional groups and intensity of signals as clues to structural identification.

Conclusion

• Comprehensive understanding of infrared spectroscopy and mass spectrometry provides foundational tools for organic structure determination in organic chemistry. Students should practice interpreting spectra and correlating functional group presence using IR and mass spectrometric data.