Graduate
  1. Physical Chemistry  1.1. Thermodynamics  1.1.1. Laws of Thermodynamics  1.1.2. Enthalpy and heat capacity  1.1.3. Entropy and free energy  1.1.4. Phase Equilibrium  1.1.5. Statistical thermodynamics  1.1.6. Thermodynamic cycle  1.1.7. Fugacity and activity  1.2. Quantum Chemistry  1.2.1. Principles of quantum mechanics  1.2.2. Schrödinger Equation  1.2.3. Particle in a box  1.2.4. Operators and eigenvalues  1.2.5. Atomic orbitals  1.2.6. Molecular orbital theory  1.2.7. Perturbation theory  1.2.8. Valence bond theory  1.2.9. Hybridization and chemical bonding  1.3. Chemical kinetics  1.3.1. Rate laws and reaction mechanisms  1.3.2. Collision theory  1.3.3. Transition state theory  1.3.4. Enzyme Kinetics  1.3.5. Chain Reactions and Polymerization  1.3.6. Photochemical reactions  1.4. Statistical mechanics  1.4.1. Partitioning functions  1.4.2. Molecular distribution functions  1.4.3. Boltzmann Distribution  1.4.4. Bose–Einstein and Fermi–Dirac statistics  1.5. Spectroscopy  1.5.1. Rotational Spectroscopy  1.5.2. Vibrational Spectroscopy  1.5.3. Electronic Spectroscopy  1.5.4. Nuclear magnetic resonance spectroscopy  1.5.5. Mass Spectrometry  1.5.6. Raman Spectroscopy  1.5.7. Electron paramagnetic resonance spectroscopy  1.6. Surface and colloidal chemistry  1.6.1. Absorption isotherm  1.6.2. Surface tension and wetting  1.6.3. Colloidal Stability  1.6.4. Catalysis  1.6.5. Emulsions and micelles  1.7. Electrochemistry  1.7.1. Nernst equation  1.7.2. Electrochemical cells  1.7.3. Conductivity and mobility  1.7.4. War  1.7.5. Fuel cells  1.7.6. Electrolysis
  2. Organic chemistry  2.1. Reaction mechanism  2.1.1. Nucleophilic substitution reactions  2.1.2. Electrophilic addition reactions  2.1.3. Elimination reactions  2.1.4. Rearrangement reactions  2.1.5. Radical reactions  2.1.6. Pericyclic reactions  2.2. Spectroscopy and structural determination  2.2.1. UV-Vis Spectroscopy  2.2.2. IR Spectroscopy  2.2.3. NMR Spectroscopy  2.2.4. Mass Spectrometry  2.2.5. X-ray crystallography  2.3. Stereoscopic  2.3.1. Chirality and optical activity  2.3.2. Structural analysis  2.3.3. Geometrical isomerism  2.3.4. Dynamic Stereochemistry  2.4. Organometallic Chemistry  2.4.1. Organolithium and organomagnesium reagents  2.4.2. Palladium-catalyzed cross-coupling reactions  2.4.3. Transition Metal Complexes  2.4.4. Metal–carbon bond  2.5. Polymer chemistry  2.5.1. Polymerization mechanism  2.5.2. Polymer Characteristics  2.5.3. Biodegradable Polymer  2.5.4. Conducting polymer  2.5.5. Supramolecular polymers  2.6. Medicinal chemistry  2.6.1. Drug design and development  2.6.2. Pharmacokinetics and pharmacodynamics  2.6.3. Structure-activity relationships  2.6.4. Molecular docking and drug screening
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Crystal field theory  3.1.2. Ligand field theory  3.1.3. Spectrochemical Series  3.1.4. Chelation and stability  3.2. Organometallic Chemistry  3.2.1. Metal Carbonyls  3.2.2. Catalysis by organometallic complexes  3.2.3. Metallocenes  3.3. Bio-inorganic chemistry  3.3.1. Metalloproteins and enzymes  3.3.2. The role of metals in biological systems  3.3.3. Metal ion transport and storage  3.4. Solid state chemistry  3.4.1. Crystal Structures  3.4.2. Band theory of solids  3.4.3. Superconductors  3.4.4. Defects in the crystal  3.5. Lanthanides and Actinides  3.5.1. Electronic configuration in lanthanides and actinides  3.5.2. Coordination chemistry of the lanthanides  3.5.3. Magnetic Properties of Lanthanides
  4. Analytical chemistry  4.1. Chromatography  4.1.1. Gas Chromatography  4.1.2. High Performance Liquid Chromatography  4.1.3. Thin Layer Chromatography  4.2. Spectroscopic Techniques  4.2.1. Atomic absorption spectroscopy  4.2.2. X-ray diffraction  4.2.3. Inductively coupled plasma spectroscopy  4.3. Electroanalytical methods  4.3.1. Potentiometry  4.3.2. Voltammetry  4.3.3. Colometry  4.4. Mass Spectrometry  4.4.1. Ionization Technique  4.4.2. Fragmentation Pattern  4.5. Chemometrics  4.5.1. Multidisciplinary analysis  4.5.2. Machine Learning in Chemistry
  5. Theoretical and Computational Chemistry  5.1. Molecular dynamics simulation  5.1.1. Force fields and energy minimization  5.1.2. Monte Carlo simulation in molecular dynamics simulations  5.2. Quantum chemical methods  5.2.1. Hartree–Fock theory  5.2.2. Density functional theory  5.2.3. Semi-empirical methods  5.3. Computational drug design  5.3.1. Molecular Docking  5.3.2. QSAR Modeling  5.3.3. Virtual Screening
  6. Biochemistry  6.1. Enzyme Kinetics  6.1.1. Michaelis-Menten kinetics  6.1.2. Inhibition mechanism  6.2. Metabolism and Bioenergetics  6.2.1. Glycolysis  6.2.2. Citric acid cycle  6.2.3. Electron transport chain  6.3. molecular Biology  6.3.1. DNA replication and repair  6.3.2. Protein synthesis  6.3.3. Gene Regulation  6.4. Structural Biochemistry  6.4.1. Protein Folding  6.4.2. Membrane Biophysics
  7. Environmental Chemistry  7.1. Atmospheric Chemistry  7.1.1. Greenhouse gases  7.1.2. Ozone depletion  7.1.3. Air pollutants and smoke  7.2. Water Chemistry  7.2.1. pH and water hardness  7.2.2. Wastewater treatment  7.2.3. Aquatic Chemistry  7.3. Soil Chemistry  7.3.1. Heavy metal contamination  7.3.2. Soil pH and Buffering  7.3.3. Nutrient cycling  7.4. Toxicology and Chemical Safety  7.4.1. Toxicokinetics  7.4.2. Risk Assessment in Toxicology and Chemical Safety in Environmental Chemistry  7.4.3. Effects of pollutants on the environment

Graduate → Organic chemistry → Spectroscopy and structural determination ↓


Mass Spectrometry


Mass spectrometry (MS) is a powerful analytical technique used in organic chemistry to determine the molecular mass, structure, and composition of molecules. It plays a vital role in spectroscopy and structural determination, providing detailed information about the chemical nature of substances. In this detailed explanation, we will explore the principles of mass spectrometry, its instrumentation, and its applications in organic chemistry. By the end, you will have a complete understanding of how mass spectrometry works and how it can be used to identify and analyze organic compounds.

Principles of mass spectrometry

Mass spectrometry works on the fundamental principle of ionizing chemical compounds to produce charged molecules or fragments, which are then measured based on their mass-to-charge ratio (m/z). The process involves three main steps: ionization, mass analysis, and detection.

Ionization

The first step in mass spectrometry is ionization, where molecules are converted into ions. Several ionization methods are used, each suitable for different types of samples:

  • Electron ionization (EI): EI involves bombarding the sample with high-energy electrons, causing the molecules to ionize and fragment. It is widely used because of its robustness and ability to produce reproducible spectra.
  • Chemical ionization (CI): In CI the sample is ionized by reacting with a reagent gas (such as methane), resulting in the formation of protonated molecules. This method is gentler than EI, causing less fragmentation.
  • Matrix-assisted laser desorption/ionization (MALDI): MALDI is used to analyze large biomolecules. The sample is mixed with a matrix and then ionized using laser energy.
  • Electrospray ionization (ESI): ESI is a soft ionization technique that produces multiply charged ions and is suitable for large biomolecules, proteins, and polymers.

Mass analysis

After ionization, the ions produced are directed into the mass analyzer. The role of the mass analyzer is to separate these ions based on their m/z ratio. Common types of mass analyzers include:

  • Time-of-flight (TOF): TOF separates ions by measuring the time they take to travel through the flight tube. Ions with different m/z values will travel at different speeds.
  • Quadrupole: Quadrupole mass analyzers use oscillating electric fields to filter ions based on their m/z ratio. This analyzer is widely used due to its ease of use and affordability.
  • Ion trap: These analyzers trap ions using an electric field, allowing sequential removal and detection of ions based on m/z ratio.
  • Orbitrap: Orbitrap determines the m/z values of ions by measuring their frequencies of oscillation. It provides high resolution and accuracy.

Detection

The final step in mass spectrometry is detection, where the separated ions are captured, and their intensity is recorded as a mass spectrum. The data is presented as a plot of ion intensity versus m/z ratio, known as the mass spectrum. This spectrum is used to determine the molecular weight and structure of the analyte.

Instruments in mass spectrometry

A typical mass spectrometer consists of the following components: an ion source, a mass analyzer, and a detector. Additional components such as a vacuum system and a data processing unit are also required.

Ion source

The ion source is the location where ionization of the analyte occurs. The choice of ion source depends on the nature of the sample and the type of analysis. Modern mass spectrometers often include multiple ionization options to accommodate different samples.

Mass analyzer

The mass analyzer is the heart of the mass spectrometer. Different analyzers have different characteristics, such as resolution, mass range, and scanning speed, which affect the choice for specific applications. Understanding these characteristics helps in selecting the appropriate analyzer for the desired analysis.

Detectors

The detector is responsible for capturing and recording the ions passing through the mass analyzer. Common detectors include Faraday cups, electron multipliers, and microchannel plates. The choice of detector affects the sensitivity and dynamic range of the mass spectrometer.

Applications in organic chemistry

Mass spectrometry is integral to the field of organic chemistry, providing many capabilities such as:

Molecular mass determination

One of the simplest applications of mass spectrometry is to determine the molecular mass of a compound. By analyzing m/z value of the molecular ion peak, chemists can determine the molecular weight of the analyte.

Structural explanations

Mass spectrometry can provide information about the structure of organic compounds. Fragmentation patterns in the spectrum reveal functional groups, bond connectivity, and structural motifs. Consider the following example:

        Analysis of the mass spectrum of ethanol (C2H6O):
        
        Molecular ion peak: m/z = 46
        Fragment: CH3CH+OH -> m/z = 31
        Fragment: CH2OH+ -> m/z = 31
        Fragment: CH3+ -> m/z = 15

These fragmentation patterns can indicate the presence of specific structural features within the molecule.

Isotope pattern analysis

Mass spectrometry can be used to determine the isotopic composition of molecules. Elements such as chlorine and bromine, which have multiple isotopes, display characteristic patterns in the mass spectrum. For example:

        The 1-Bromohexane (C6H13Br) spectrum shows peaks at m/z = 164 and m/z = 166 due to Br isotopes (^79Br and ^81Br).

Quantitative analysis

Mass spectrometry is also used for the quantitative analysis of compounds. This technique is sensitive enough to detect and measure trace amounts of substances in complex mixtures.

Interpretation of mass spectra

To interpret mass spectra it is necessary to understand the characteristics of the different peaks in the spectrum. Here are the key elements to consider:

Molecular ion peak

The molecular ion peak is the peak representing the unbroken ion of the analyte. Its m/z value corresponds to the molecular weight of the compound.

Base peak

The base peak is the most intense peak in the spectrum and is given a relative intensity of 100%. Other peaks are measured relative to its intensity. It often corresponds to the most stable segment.

Fragmentation pattern

Examining fragmentation patterns helps to understand the structure of a molecule. By analyzing which fragments are more prevalent, chemists can infer certain structural features.

0 m/z 46 31 15

Sample analysis with mass spectrometry

Consider analyzing a mixture containing caffeine and quinine. Mass spectrometry can be used to identify the components through their unique molecular weights. For example:

        Caffeine (C8H10N4O2)
        Molecular ion peak: m/z = 194
        
        Quinine (C20H24N2O2)
        Molecular ion peak: m/z = 324

The presence of peaks at m/z = 194 and m/z = 324 suggests the presence of caffeine and quinine, respectively, in the sample.

Advanced applications

Mass spectrometry extends beyond basic applications in organic chemistry. Some advanced applications include:

Proteomics

In proteomics, mass spectrometry is used to identify and characterize proteins, allowing the study of biological processes and disease conditions at the molecular level.

Metabolomics

Mass spectrometry aids in metabolomics by analyzing metabolites in biological samples, and provides information about metabolic pathways and their alterations in various diseases.

Pharmaceutical analysis

In the pharmaceutical industry, mass spectrometry is vital for drug development, providing valuable information about drug purity, stability, and metabolic pathways.

Software and data interpretation

Modern mass spectrometry relies heavily on advanced software for data acquisition, processing, and interpretation. Software tools can decompose complex spectra, identify unknowns, and predict fragmentation pathways, increasing the accuracy and reliability of the analysis.

Conclusion

Mass spectrometry is an indispensable tool for molecular mass determination, structural elucidation, and quantitative analysis in organic chemistry. Its versatility and sensitivity make it suitable for a wide range of applications, from basic chemical analysis to advanced biological research. Understanding the principles, instrumentation, and applications of mass spectrometry is important for any chemist in this field, as it provides invaluable information about the nature and behavior of chemical compounds.


Graduate → 2.2.4


U
username
0%
completed in Graduate

← Prev (2.2.3)
NMR Spectroscopy
Next (2.2.5) →
X-ray crystallography

Comments 



Mass Spectrometry

https://www.chemistryelite.com/g/2.2.4?ceal=en