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 → Analytical chemistry → Mass Spectrometry ↓


Fragmentation Pattern


Mass spectrometry (MS) is a powerful analytical technique used in chemistry to identify compounds and determine their structure, molecular weight, and composition. An essential aspect of mass spectrometry is understanding the fragmentation patterns of ions. These patterns provide important information about the structure of the molecule and aid in its identification.

Fragmentation refers to the process by which molecules break up into smaller ions and neutral fragments in the mass spectrometer. This usually occurs when the molecule ionizes, gaining or losing one or more electrons. The fragmentation pattern is unique to each compound and results in a spectrum containing multiple peaks. Each peak represents ions of different mass-to-charge ratios (m/z), providing a useful “fingerprint” for compound identification.

Ionization and fission process

In mass spectrometry, ionization is the first important step in creating fragments. Common ionization methods include electron ionization (EI), chemical ionization (CI), electrospray ionization (ESI), and matrix-assisted laser desorption/ionization (MALDI). Electron ionization is one of the most traditional and still widely used methods due to its efficiency in creating fragmentation patterns.

In electron ionization, high-energy electrons collide with molecules, knocking an electron out of the molecule and forming a positively charged ion (radical cation):

    a + e⁻ → a⁺ + 2e⁻

This radical cation is often in an excited state, causing further fragmentation in an attempt to stabilize the molecule. Each fragmented bond results in the formation of different fragment ions that contribute to the fragmentation pattern.

Types of fragmentation

Simple bond cleavage

This type of fragmentation involves the breaking of a single bond in the molecule, resulting in the formation of two fragments: one charged and one neutral. For example, consider the fragmentation of butane:

    CH3-CH2-CH2-CH3⁺ → CH3⁺ + CH3-CH2-CH2·

Here, the bond between the two carbon atoms is broken, yielding a charged fragment and a neutral radical.

CH3-CH2-CH2-CH3⁺ → CH3⁺ + CH3-CH2-CH2·

Anagram

Rearrangements involve structural reorganization of the ion prior to fragmentation. The McLafferty rearrangement is a well-known example, particularly in carbonyl-containing compounds. In this process, the gamma hydrogen is transferred to the carbonyl oxygen, followed by splitting:

    R-CH2-CH2-C(=O)-R' → R-CH2-CH=O + R'

This results in the formation of an alkene and a neutral fragment.

R-CH2-CH=O + R'

Loss of small molecules

Another common fragmentation pattern involves the loss of small, neutral molecules such as water, ammonia, or methanol. For example, in alcohols, fragmentation can follow this path:

    2H2O

As a result, the peak corresponding to the ion R⁺ appears in the mass spectrum and the mass of the water molecule is subtracted from the mass of the original molecule.

Interpreting fragmentation patterns

Interpreting fragmentation patterns can be complex. The main thing is to understand what possible bonds can be broken and how these relate to the molecular structure. Analysts often look for certain characteristic peaks, such as:

  • Molecular ion peak ([M]⁺): The mass-to-charge ratio indicates the intact ionized molecule.
  • Base peak: The highest intensity peak in the spectrum, representing the most stable fragment ion.
  • Peaks correspond to common fragments, such as CH3⁺ (mass 15), OH⁺ (mass 17), etc.

Case study: Fragmentation analysis of an organic compound

Let's analyze a simple aromatic compound such as benzene using mass spectrometry. The expected fragmentation pattern includes:

  • Molecular ion peak: The intact benzene ion appears as C6H6⁺ molecular ion peak.
  • Fission of single bonds: Breaking of carbon-carbon bonds leads to the formation of fragment ions of lower mass.

Interpretation of the patterns involves considering possible structures and reasoning about the masses of the resulting ions.

C6H6⁺ pattern

Why fragmentation patterns matter

Understanding fragmentation patterns is essential for several reasons:

  1. Structural elucidation: Fragmentation provides clues about the structure of a molecule, which is especially useful for complex organic molecules.
  2. Compound identification: Each compound has a characteristic pattern, which can be matched to known spectra for identification.
  3. Understanding chemical behaviour: Studies on fragmentation are fundamental to understanding how molecules break down under different conditions, which is useful in areas such as disintegration and stability studies.

Challenges and limitations

One of the main challenges in interpreting fragmentation patterns is the complexity and number of possible fragments that can arise from a single molecule. Additionally, isomers can produce very similar spectra, complicating accurate identification. Unambiguous structural determination often requires the use of complementary techniques such as NMR or IR spectroscopy.

Advanced technologies

Advanced mass spectrometry techniques such as tandem mass spectrometry (MS/MS) help overcome some of the limitations of basic fragmentation analysis. In MS/MS, ions are further fragmented after the initial separation, allowing for more detailed structural analysis.

Overall, mass spectrometry offers unmatched power in structural analysis, and understanding fragmentation patterns is a cornerstone of analytical chemistry. By mastering this field, chemists can gain insights into molecular structure and behavior, which can have applications in research, industry, and beyond.


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Fragmentation Pattern

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