Undergraduate
  1. General chemistry  1.1. Introduction to Chemistry  1.2. Atomic Structure  1.2.1. Subatomic particles  1.2.2. Atomic Model  1.2.3. Quantum numbers  1.2.4. Electron Configuration  1.2.5. Periodic trends  1.2.6. Isotopes and their applications  1.3. Chemical bond  1.3.1. Ionic bond  1.3.2. Covalent bonds  1.3.3. Metal Bond  1.3.4. Hybridization  1.3.5. Molecular geometry and VSEPR theory  1.3.6. Bond polarity and dipole moment  1.4. Stoichiometry  1.4.1. Mole concept  1.4.2. Empirical and molecular formula  1.4.3. Limiting reactant and excess reactant  1.4.4. Percent Yield and Purity  1.4.5. Dilution calculation  1.5. States of matter  1.5.1. Gas Laws  1.5.2. Matter and Intermolecular Forces  1.5.3. Solid and Crystal Structures  1.5.4. Phase diagram  1.5.5. Plasma and supercritical fluid  1.6. Chemical reactions  1.6.1. Types of Chemical Reactions  1.6.2. Balancing Chemical Equations  1.6.3. Thermochemical reactions  1.6.4. Reaction energy profiles  1.7. Solutions and Mixtures  1.7.1. Concentration units  1.7.2. Syndrome properties  1.7.3. Solubility and Solubility Rules  1.7.4. Henry's Law and Raoult's Law  1.7.5. Partition coefficient  1.8. Chemical equilibrium  1.8.1. Law of mass action  1.8.2. Le Chatelier's principle  1.8.3. Reaction quotient  1.8.4. To use this online calculator for Equilibrium Constant, enter Equilibrium Constant (Eq.) and hit the calculate button. Here is how the Equilibrium Constant calculation can be explained with given input values -> 0.05 = 0.05/0.  1.8.5. Acid-base balance  1.9. Acids and bases  1.9.1. Arrhenius, Brønsted–Lowry, and Lewis definitions  1.9.2. pH and pOH  1.9.3. Acid-base titration  1.9.4. Buffer Solution  1.9.5. Acid-base indicator  1.9.6. Polyprotic Acids and Bases  1.10. Electrochemistry  1.10.1. redox reactions  1.10.2. Galvanic and Electrolytic Cells  1.10.3. Nernst equation  1.10.4. Electrolysis  1.10.5. Faraday's laws of electrolysis  1.11. Thermodynamics  1.11.1. Laws of Thermodynamics  1.11.2. Enthalpy, entropy and Gibbs free energy  1.11.3. Spontaneity of reactions  1.11.4. Thermodynamic cycles (Hess's law, Carnot cycle)  1.12. Kinetics  1.12.1. Rate law and reaction order  1.12.2. Activation Energy and Catalyst  1.12.3. Collision theory  1.12.4. Reaction mechanism  1.12.5. Transition state theory
  2. Organic chemistry  2.1. Structure and relationships  2.1.1. Hybridisation in Carbon Compounds  2.1.2. Resonance and aromatization  2.1.3. Molecular orbitals  2.1.4. Inductive and mesomeric effects  2.2. Hydrocarbons  2.2.1. Hydrocarbons  2.2.2. Alkene  2.2.3. Alkynes  2.2.4. Aromatic compounds  2.2.5. Cycloalkanes and Conformation  2.3. Functional Group  2.3.1. Alcohols and phenols  2.3.2. Ethers and epoxides  2.3.3. Aldehyde and ketone  2.3.4. Carboxylic acids and derivatives  2.3.5. Amin  2.3.6. Esters and amides  2.3.7. Thiols and sulfides  2.4. Stereoscopic  2.4.1. Isomerism in Stereochemistry  2.4.2. Chirality and optical activity  2.4.3. Structural analysis  2.4.4. Diastereomers and Enantiomers  2.5.1. Substitution reactions  2.5.2. Elimination reactions  2.5.3. Addition reactions  2.5.4. Radical reactions  2.5.5. Rearrangement reactions  2.5.6. Pericyclic Reactions  2.6. Spectroscopy and structural analysis  2.6.1. Infrared Spectroscopy  2.6.2. Nuclear magnetic resonance spectroscopy  2.6.3. Mass Spectrometry  2.6.4. UV-visible spectroscopy  2.6.5. X-ray crystallography  2.7. Polymer chemistry  2.7.1. Addition and Condensation Polymers  2.7.2. Polymerization mechanism  2.7.3. Biodegradable Polymer  2.7.4. Conducting and smart polymers
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Ligands and coordination compounds  3.1.2. Crystal field theory  3.1.3. Molecular Orbital Theory in Coordination Compounds  3.1.4. Jahn–Taylor distortion  3.2. Main Group Chemistry  3.2.1. Alkali and alkaline earth metals  3.2.2. Halogens and Noble Gases  3.2.3. Transition metals and their complexes  3.2.4. Lanthanides and Actinides  3.3. Solid state chemistry  3.3.1. Crystal lattices and unit cells  3.3.2. Defects in solids  3.3.3. Electrical and magnetic properties  3.3.4. Superconductivity  3.4. Bio-inorganic chemistry  3.4.1. Metal ions in biology  3.4.2. Enzymatic reactions with metals  3.4.3. Metal poisoning and detoxification  3.4.4. Metalloproteins and Metalloenzymes
  4. Physical chemistry  4.1. Quantum Chemistry  4.1.1. Wave–particle duality  4.1.2. Schrödinger Equation  4.1.3. Quantum Numbers and Orbitals  4.1.4. Atomic and molecular spectroscopy  4.2. Statistical mechanics  4.2.1. Maxwell–Boltzmann distribution  4.2.2. Partitioning functions  4.2.3. Bose–Einstein and Fermi–Dirac statistics  4.3. Chemical thermodynamics  4.3.1. Gibbs Free Energy  4.3.2. Phase transition  4.3.3. Thermodynamic efficiency  4.4. Surface chemistry  4.4.1. Absorption and Catalysis  4.4.2. Colloids and Emulsions
  5. Analytical Chemistry  5.1. Classical methods  5.1.1. Gravimetric Analysis  5.1.2. titrimeter  5.2. Instrumental methods  5.2.1. Chromatography  5.2.2. Spectroscopy  5.2.3. Electroanalytical methods  5.2.4. X-ray diffraction
  6. Industrial Chemistry  6.1. Petrochemistry  6.2. Chemical engineering principles  6.3. Green Chemistry  6.4. Pharmaceuticals and Drug Synthesis
  7. Biochemistry  7.1. Carbohydrates  7.2. Proteins and enzymes  7.3. Lipids and membranes  7.4. Nucleic acids  7.5. Metabolism and Bioenergetics  7.6. Enzyme kinetics and mechanism

Undergraduate → Organic chemistry → Spectroscopy and structural analysis ↓


Mass Spectrometry


Mass spectrometry is a powerful analytical technique used to determine the mass of particles, the composition of a sample, and the structure of molecules. It is used extensively in organic chemistry for structural analysis and to gain insight into the molecular structure of organic compounds. This technique is helpful in identifying the chemical characteristics of unknown substances, and when combined with other techniques, it provides comprehensive details about the molecular and functional groups present within the compound.

Fundamentals of mass spectrometry

In short, mass spectrometry measures the mass-to-charge ratio (m/z) of ions. A mass spectrometer ionizes chemical compounds to produce charged molecules or molecule fragments and measures these ions to determine their mass-to-charge ratios. The main components of a mass spectrometer include:

  1. Ionization source: Converts sample molecules into ions. Common methods include electron impact (EI), chemical ionization (CI), and matrix-assisted laser desorption ionization (MALDI).
  2. Mass analyzer: separates ions based on their m/z ratio. Types include time-of-flight (TOF), quadrupole, and magnetic sector analyzers.
  3. Detector: registers the ions and provides a signal, which is processed to produce a mass spectrum.
Ion Source Mass Analyzer Detectors

Ionization technique

Choosing the right ionization technique is essential because it affects the ionization efficiency of the sample and the resulting mass spectrum. Three main ionization methods are used in organic chemistry:

Electron impact (EI) ionization

In EI, a high-energy electron beam is directed at the sample, knocking out an electron from the sample molecule, resulting in the formation of a positive ion ((M^+)). This process often results in high fragmentation, which can be useful for structural elucidation.

EI: M + e⁻ → M⁺ + 2e⁻

Chemical ionization (CI)

CI uses a reagent gas (such as methane, isobutane, or ammonia) that is first ionized, and the resulting ions react with the sample molecules to ionize them. CI is softer than EI, causing less fragmentation.

CI: MH⁺ + CH₄⁺ → M⁺ + CH₃ + H₂

Matrix-assisted laser desorption ionization (MALDI)

MALDI involves embedding the sample within a matrix that absorbs laser energy, thus stimulating ionization. This technique is extremely useful in the study of large biomolecules and polymers.

Mass analyzer

The mass analyzer sorts the ions produced in the ionization source according to their mass-to-charge ratio. There are several types of mass analyzers:

Time-of-flight (TOF) analyzer

In a TOF analyzer, ions are accelerated through a potential difference, and their time of flight to the detector is measured. Ions with different m/z ratios will have different velocities, and this helps to distinguish between ions.

Relationship:

KE = 1/2 * mv² = z * V

Quadrupole analyzer

These use oscillating electric fields to allow stable trajectories for specific m/z values. Quadrupole analyzers are commonly used due to their accuracy and ability to quickly scan a wide range of masses.

Magnetic field analyzer

These analyzers use magnetic fields to bend the path of ions. The radius of curvature of the ion's path depends on its mass and charge, making separation possible.

Understanding mass spectra

A mass spectrum is a plot that represents ions by their mass-to-charge ratio on the x-axis and their relative abundance on the y-axis. Peaks in the spectrum indicate the presence of ions with specific m/z values.

Here's a basic example of a simple mass spectrum of methane (CH₄):

CH₄⁺ C⁺ CH₂⁺ m/z relative intensity

The highest peak, called the base peak, represents the most abundant ion. The molecular ion peak (or principal peak) represents the intact molecule, which helps identify the molecular weight of the compound.

Interpretation of mass spectra

The process of interpreting mass spectra involves analyzing fragmentation patterns to infer the structure of the parent molecule. Fragmentation patterns can provide valuable clues about functional groups and bonding arrangements within the molecule. Here is a description of common interpretation strategies:

Using fragment peaks

In the mass spectrum, beyond the molecular ion peak, several smaller peaks are typically observed. These correspond to fragment ions and can help predict the structure by suggesting the way the molecule was fragmented.

Analysis of isotopic patterns

The isotopic distribution of elements such as chlorine and bromine gives distinctive patterns. Chlorine, with its isotopes ^{35}Cl and ^{37}Cl, often shows a 3:1 ratio, while bromine shows a 1:1 ratio due to ^{79}Br and ^{81}Br.

Applications in organic chemistry

The importance of mass spectrometry in organic chemistry cannot be overstated. It is vital for identifying unknown compounds, confirming synthesized compounds, and studying complex biomolecules. Major applications include:

Structure explanation

By analyzing fragmentation patterns, organic chemists can detect connectivity and functional groups within the molecule. This process is complementary to nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy, which provide a more complete analysis.

Molecular weight determination

The molecular ion peak in the mass spectrum gives the molecular weight of the compound. Finding this peak correctly is essential to confirm that the correct compound was synthesized or isolated.

Proteomic and metabolomic studies

In biology, mass spectrometry interfaces with a variety of experimental methods to study proteins and metabolites, helping in understanding biological pathways, disease mechanisms, and biomarker discovery.

Conclusion

Mass spectrometry, with its wide range of techniques and capabilities, remains one of the most important instrumental methods in organic chemistry. Its ability to provide detailed molecular information has transformed and advanced the field, giving chemists the ability to unambiguously identify and characterize chemical species. The integration of the technique with biological studies further enhances its utility, solidifying its role as a versatile and indispensable tool in modern scientific applications.


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Mass Spectrometry

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