🥼Organic Chemistry Unit 12 – Mass Spec and IR Spectroscopy in Organic Chem

What's This Unit All About?

• Focuses on two powerful analytical techniques mass spectrometry (MS) and infrared (IR) spectroscopy
• Explores how these techniques provide valuable information about the structure and composition of organic compounds
• Covers the fundamental principles behind MS and IR spectroscopy
  • Includes ionization, fragmentation, and detection in MS
  • Involves absorption of IR radiation and molecular vibrations in IR spectroscopy
• Emphasizes the interpretation of mass spectra and IR spectra to elucidate structural features
• Discusses the complementary nature of MS and IR data in solving structural problems
• Highlights real-world applications of these techniques in various fields (drug discovery, environmental analysis, forensic science)
• Equips you with the skills to analyze and interpret MS and IR data to determine the structure of unknown organic compounds

Key Concepts and Definitions

• Mass spectrometry (MS) analytical technique that measures the mass-to-charge ratio (m/z) of ions
• Infrared (IR) spectroscopy analytical method that probes the vibrational modes of molecules based on their absorption of IR radiation
• Ionization process of converting molecules into charged particles (ions) in MS
  • Common ionization methods electron ionization (EI) and chemical ionization (CI)
• Fragmentation breaking apart of molecular ions into smaller fragments in MS
• Mass spectrum plot of ion abundance versus m/z values
• Base peak most intense peak in a mass spectrum
• Molecular ion peak (M+) represents the intact molecular ion
• Infrared spectrum plot of absorbance or transmittance versus wavenumber (cm^-1^)
• Functional groups specific atomic arrangements (OH, C=O, N-H) that absorb IR radiation at characteristic frequencies
• Fingerprint region (1500-500 cm^-1^) unique pattern of peaks in an IR spectrum characteristic of a specific molecule

Mass Spectrometry Basics

• MS involves three main steps ionization, separation, and detection
• Sample is introduced into the ionization source where molecules are converted into ions
• Ions are accelerated and separated based on their m/z ratios in the mass analyzer
  • Common mass analyzers quadrupole, time-of-flight (TOF), and magnetic sector
• Separated ions are detected and their abundances are measured by the detector
• Resulting mass spectrum displays the relative abundance of ions as a function of their m/z values
• EI is a hard ionization technique that causes extensive fragmentation
  • Produces characteristic fragmentation patterns useful for structure elucidation
• CI is a soft ionization method that generates primarily molecular ions with minimal fragmentation
• Isotopic peaks arise from the presence of naturally occurring isotopes (^13^C, ^2^H, ^15^N) in organic molecules

IR Spectroscopy Fundamentals

• IR spectroscopy measures the absorption of IR radiation by molecules
• Molecules absorb IR radiation when the frequency matches the vibrational frequency of a specific bond or functional group
• Vibrational modes include stretching (symmetric and asymmetric) and bending (scissoring, rocking, wagging, twisting)
• IR spectrum is a plot of absorbance or transmittance versus wavenumber (cm^-1^)
  • Wavenumber is the reciprocal of the wavelength and is proportional to the energy of the IR radiation
• Functional groups absorb IR radiation at characteristic wavenumbers
  • Allows for the identification of functional groups present in a molecule
• Intensity of IR absorption bands depends on the change in dipole moment during the vibration
• Homonuclear diatomic molecules (N≡N, O=O) are IR inactive because they lack a dipole moment
• IR spectroscopy is particularly useful for identifying polar functional groups (O-H, N-H, C=O)

Interpreting Mass Spectra

• Molecular ion peak (M+) corresponds to the unfragmented molecular ion and provides the molecular mass of the compound
• Base peak is the most abundant ion in the spectrum and is assigned a relative intensity of 100%
• Fragmentation patterns arise from the cleavage of specific bonds in the molecule
  • Cleavage occurs at the weakest bonds or those adjacent to a heteroatom (N, O, S)
• Common fragmentation processes include α-cleavage, McLafferty rearrangement, and retro-Diels-Alder reaction
• Isotopic peaks provide information about the number of certain atoms (C, Br, Cl) in the molecule
  • M+2 peak indicates the presence of one Br or Cl atom
• Nitrogen rule states that odd-electron ions (M+) contain an odd number of nitrogen atoms
• High-resolution MS provides accurate mass measurements used to determine the elemental composition of ions
• Interpreting mass spectra involves identifying the molecular ion, recognizing characteristic fragmentation patterns, and piecing together the structural features of the molecule

Analyzing IR Spectra

• IR spectra are divided into two regions functional group region (4000-1500 cm^-1^) and fingerprint region (1500-500 cm^-1^)
• Functional group region contains characteristic absorption bands for common functional groups
  • O-H stretching (3600-3200 cm^-1^), C-H stretching (3000-2800 cm^-1^), C=O stretching (1800-1600 cm^-1^)
• Fingerprint region is unique to each molecule and arises from complex vibrational modes
• Peak shape and intensity provide information about the molecular environment and hydrogen bonding
  • Broad peaks indicate hydrogen bonding, while sharp peaks suggest no hydrogen bonding
• Absence of certain absorption bands can also be informative in structure determination
• Analyzing IR spectra involves identifying functional groups, comparing the spectrum to reference spectra, and using the fingerprint region to confirm the identity of the molecule

Combining MS and IR for Structure Determination

• MS and IR spectroscopy provide complementary information about the structure of organic compounds
• MS gives the molecular mass and fragmentation pattern, while IR identifies functional groups and provides a unique fingerprint
• Combining MS and IR data allows for a more comprehensive structural analysis
  • MS data narrows down the possible structures based on molecular mass and fragmentation
  • IR data confirms the presence or absence of specific functional groups
• Solving spectral problems involves proposing structures consistent with the MS and IR data
  • Requires knowledge of characteristic fragmentation patterns and IR absorption frequencies
• Comparing experimental spectra to reference spectra of known compounds aids in structure determination
• Combining MS and IR is particularly useful for identifying isomers and distinguishing between similar structures
• Advances in hyphenated techniques (GC-MS, LC-MS, GC-IR) allow for the simultaneous acquisition of MS and IR data

Real-World Applications and Cool Stuff

• MS and IR spectroscopy have diverse applications in various fields
• Drug discovery uses MS and IR to identify and characterize new drug candidates
  • Helps in determining the purity, stability, and metabolic fate of drugs
• Environmental analysis employs MS and IR to detect and quantify pollutants (pesticides, PCBs) in air, water, and soil samples
• Forensic science relies on MS and IR for analyzing evidence (drugs, explosives, fibers) and identifying unknown substances
• Food and beverage industry uses MS and IR for quality control, authenticity testing, and detecting contaminants
• Art conservation and archaeology utilize MS and IR to analyze pigments, binders, and degradation products in paintings and artifacts
• Proteomics and metabolomics studies employ MS to identify and quantify proteins and metabolites in biological samples
• Imaging MS techniques (MALDI, DESI) allow for the spatial mapping of molecules in tissue samples
• Portable and handheld MS and IR devices enable on-site analysis and real-time monitoring of chemical threats and environmental hazards