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 ↓


Reaction mechanism


In organic chemistry, understanding the pathways and processes of reactions is crucial to mastering the discipline. Reaction mechanisms provide a detailed, step-by-step explanation of how reactants are transformed into products. This includes the breaking and formation of bonds, the movement of electrons, and the arrangement of atoms throughout the process. Mechanisms not only reveal the sequence of transformations, but also show how the way reactions occur is strongly influenced by the structure and energy of the molecules.

Introduction to reaction mechanisms

The reaction mechanism explains in detail what happens at each step of a chemical reaction. It reveals the types of chemical species involved, including intermediates and transition states. While balanced chemical equations provide insight into the stoichiometry of the reaction, mechanisms provide a deeper understanding of the molecular changes that occur.

Components of the reaction mechanism

Mechanisms are composed of several fundamental components:

  • Reactants: The starting molecules that undergo a change.
  • Products: The final compounds formed after a reaction is complete.
  • Intermediates: Species that appear in the reaction mechanism but not in the overall reaction equation. They are often highly unstable and exist only transiently.
  • Transition states: High energy states through which reactants pass to form products. These cannot be separated.
  • Reaction intermediates: Molecules or ions that are formed in one step and consumed in the next step of a reaction mechanism.

Types of reaction mechanisms

A variety of reaction mechanisms exist in organic chemistry. Here, we explore some of the common types:

Substitution reactions

In substitution reactions, an atom or group of atoms in a molecule is replaced by another atom or group. There are two primary mechanisms of substitution reactions:

1. SN1 mechanism

SN1 mechanism (unimolecular nucleophilic substitution) proceeds via a two-step process:

RL → R+ (carbocation) + L-

The carbocation is then attacked by a nucleophile to form the product:

R+ + Nuc: → R-Nuc

Visual representation:

RL (R+ + L-) slow Fast R-Nuke

The rate determining step is the formation of the carbocation, and this mechanism is favored in polar protic solvents that stabilize the anions. Tertiary carbons usually undergo SN1 reactions.

2. SN2 mechanism

SN2 mechanism (bimolecular nucleophilic substitution) proceeds through a single coordinated step:

Nuc: + RL → Nuc-R + L

Visual representation:

Nuances: RL Attack from behind nuke -r + L

The nucleophile attacks the electrophilic carbon from the opposite direction to the leaving group, causing an inversion of configuration. This mechanism is preferred by strong nucleophiles and occurs most easily at primary carbons.

Elimination reactions

Elimination reactions involve the removal of atoms or groups from a molecule, often resulting in the formation of a double bond. There are two main types of elimination mechanisms:

1. E1 mechanism

E1 mechanism (unimolecular elimination) proceeds via a two-step process involving the formation of a carbocation intermediate:

RL → R+ + L-

After:

R+ → Alkene + H+

Visual representation:

RL (R+) slow alkene + H+

E1 mechanism is similar to SN1, which occurs with tertiary substrates where formation of a stable carbocation is possible.

2. E2 mechanism

E2 mechanism (bimolecular elimination) occurs in a single coordinated step:

Base: + RL → Alkene + BaseH + L

Visual representation:

Base: RL Proton abstraction alkene + BaseH + L

A strong base removes a proton, and the leaving group leaves simultaneously, forming a double bond. E2 is favored by strong bases and bulky leaving groups, and it often occurs at secondary and tertiary carbon positions.

Addition reactions

Addition reactions involve the breaking of multiple bonds and the addition of new atoms or groups. The mechanism may vary depending on the reagents and conditions.

1. Electrophilic addition

In this reaction, an electrophile adds to a pi bond, usually that of an alkene:

C=C + X- → C-CX

The electrophile, usually an acid (e.g., HBr, HCl), first attacks the electron-rich pi bond, resulting in the formation of a carbocation followed by the addition of the nucleophile.

2. Nucleophilic addition

Occurs in carbonyls where a nucleophile attacks the carbon of the double-bonded oxygen:

O=C + Nuc: → HO-C-Nuc

This mechanism is prevalent in ketone and aldehyde reactions, where the nucleophile can attack the partially positive carbon of the carbonyl group.

Conclusion

Understanding reaction mechanisms is essential to explaining how and why reactions occur in organic chemistry. These detailed pathways provide insight beyond the simple shuffling of atoms, revealing the essential intermediates and energy changes involved. Mastery of reaction mechanisms enables chemists to manipulate reactions toward desired results, predict products, and understand side reactions.


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Reaction mechanism

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