PHD
  1. Inorganic chemistry  1.1. Coordination chemistry  1.1.1. Ligand field theory  1.1.2. Crystal field theory  1.1.3. Molecular Orbital Theory for Coordination Compounds  1.1.4. Stability of Coordination Compounds  1.1.5. Electronic spectra of coordination compounds  1.1.6. Isomerism in Coordination Compounds  1.1.7. Kinetics and mechanism of coordination reactions  1.2. Organometallic Chemistry  1.2.1. Metal Carbonyls  1.2.2. Metal alkyl and aryl  1.2.3. Fischer and Schrock carbonaceans  1.2.4. Oxidative Addition and Reductive Elimination  1.2.5. Metal Hydrides  1.2.6. Catalysis by organometallic compounds  1.2.7. Metallocenes and Sandwich Complexes  1.2.8. CH activation  1.3. Solid state chemistry  1.3.1. Crystal structures and lattices  1.3.2. Band theory and electrical properties  1.3.3. Defects in the crystal  1.3.4. Synthesis of solid state materials  1.3.5. Magnetic and optical properties of solids  1.3.6. Superconductivity  1.3.7. Solid state ionics  1.4. Bio-inorganic chemistry  1.4.1. Metalloproteins and enzymes  1.4.2. Metal ion transport and storage  1.4.3. The role of metals in medicine  1.4.4. Bioinspired catalysis  1.4.5. Metal–DNA interactions  1.4.6. Metal Complexes in Medical Science  1.5. Lanthanides and Actinides  1.5.1. Electronic configuration and oxidation states in lanthanides and actinides  1.5.2. Spectral and Magnetic Properties in Lanthanides and Actinides  1.5.3. Separation and Extraction of Lanthanides and Actinides  1.5.4. Coordination chemistry of f-block elements  1.6. Main Group Chemistry  1.6.1. Chemistry of boron compounds  1.6.2. Chemistry of Silicon and Germanium Compounds  1.6.3. Chemistry of Phosphorus and Sulfur Compounds  1.6.4. Organosilicon chemistry  1.6.5. Noble Gas Chemistry
  2. Organic chemistry  2.1. Reaction mechanism  2.1.1. Nucleophilic substitution reactions  2.1.2. Electrophilic addition and substitution reactions  2.1.3. Elimination reactions  2.1.4. Rearrangement reactions  2.1.5. Radical reactions  2.1.6. Pericyclic Reactions  2.1.7. Photochemical reactions  2.2. Stereoscopic  2.2.1. Chirality and optical activity  2.2.2. Structural analysis  2.2.3. Stereoelectronic effects  2.2.4. Asymmetric synthesis  2.2.5. Dynamic Stereochemistry  2.3. Organometallic Chemistry in Organic Synthesis  2.3.1. Organolithium and organomagnesium reagents  2.3.2. Transition metal catalyzed coupling reactions  2.3.3. Palladium-catalyzed reactions  2.3.4. Olefin Metathesis  2.3.5. Gold and silver catalysis  2.4. Natural products chemistry  2.4.1. Alkaloids and terpenoids  2.4.2. Steroids and Flavonoids  2.4.3. Total synthesis of natural products  2.4.4. Biosynthesis of natural products  2.5. Supramolecular Chemistry  2.5.1. Host-Guest Chemistry  2.5.2. Self-assembly and molecular recognition  2.5.3. Supramolecular Catalysis  2.5.4. Molecular Machines
  3. Physical Chemistry  3.1. Thermodynamics  3.1.1. Laws of Thermodynamics  3.1.2. Chemical Potential and Equilibrium  3.1.3. Statistical thermodynamics  3.1.4. Non-equilibrium thermodynamics  3.2. Quantum Chemistry  3.2.1. Schrödinger equation and its applications  3.2.2. Molecular orbital theory  3.2.3. Density functional theory  3.2.4. Post-Hartree–Fock methods  3.3. Chemical kinetics  3.3.1. Reaction rate theory  3.3.2. Mechanism and rate laws  3.3.3. Catalysis and enzyme kinetics  3.3.4. Reaction dynamics  3.4. Spectroscopy and molecular structure  3.4.1. Infrared Spectroscopy  3.4.2. UV-visible spectroscopy  3.4.3. Nuclear Magnetic Resonance Spectroscopy  3.4.4. Mass Spectrometry  3.4.5. Raman Spectroscopy  3.5. Surface and Colloid Chemistry  3.5.1. Absorption and Catalysis  3.5.2. Surfactants and micelles  3.5.3. Colloidal Stability  3.5.4. Nanomaterials and Interfaces
  4. Analytical chemistry  4.1. Chromatography  4.1.1. Gas Chromatography  4.1.2. High Performance Liquid Chromatography  4.1.3. Thin Layer Chromatography  4.1.4. Ion Chromatography  4.2. Electroanalytical techniques  4.2.1. Voltammetry and Polarography  4.2.2. Conductometry and potentiometry  4.2.3. Colometry  4.3. Spectroscopic Methods  4.3.1. Atomic absorption spectroscopy  4.3.2. Fluorescence Spectroscopy  4.3.3. X-ray diffraction  4.3.4. Electron paramagnetic resonance spectroscopy  4.4. Chemometrics  4.4.1. Data processing and statistical methods  4.4.2. Multidisciplinary analysis  4.4.3. Machine Learning in Analytical Chemistry
  5. Theoretical and Computational Chemistry  5.1. Molecular dynamics simulation  5.2. Quantum chemistry methods  5.3. Computational drug design  5.4. Machine Learning in Chemistry  5.5. Ab initio molecular dynamics
  6. Biophysics and Medicinal Chemistry  6.1. Drug discovery and design  6.2. Enzyme kinetics and inhibition  6.3. Chemical biology approach  6.4. Protein-ligand interactions  6.5. Bioorthogonal chemistry
  7. Materials chemistry  7.1. Polymer chemistry  7.1.1. Polymerization mechanism  7.1.2. Functional Polymers  7.1.3. Biodegradable Polymer  7.1.4. Conducting and semiconducting polymers  7.2. Nano Chemistry  7.2.1. Nanoparticles and nanostructures  7.2.2. Carbon-based nanomaterials  7.2.3. Quantum dots  7.3. Energy and Environmental Chemistry  7.3.1. Battery and Fuel Cell Chemistry  7.3.2. Green chemistry and sustainable materials  7.3.3. Photocatalysis

PHD → Organic chemistry ↓


Reaction mechanism


A reaction mechanism in organic chemistry is a detailed description of the step-by-step process by which a chemical reaction occurs. In essence, a reaction mechanism divides the process into elementary steps, each of which describes the movement of electrons, changes in molecular structure, and the formation or breaking of bonds. Understanding these mechanisms helps chemists predict the outcomes of chemical reactions, design new reactions, and optimize conditions for desired products.

Importance of the reaction mechanism

Understanding reaction mechanisms is important to the field of organic chemistry because it aids in understanding how reactions begin and are completed. With a solid understanding, chemists can predict potential side products, identify intermediates, and modify reactions to increase yield and selectivity. Reaction mechanisms serve as the basis for synthetic strategies and designing new molecules for a variety of applications, including pharmaceuticals and materials science.

Basic concepts in reaction mechanisms

1. Reaction intermediates

Reaction intermediates are usually short-lived, unstable species that form during the conversion of reactants into products. They are not usually isolated, but can often be detected using spectroscopy or other techniques.

Common types of intermediates include:

  • Carbocations
  • Carbanions
  • Free radicals
  • Carbenes

2. Transitional stages

The transition state is a high energy state through which a chemical reaction proceeds. It is the point of highest energy on the reaction pathway and corresponds to the temporary state where old bonds are partially broken and new bonds are partially formed.

Reactants --(TS1)--> Intermediate --(TS2)--> Products

Visualization using energy profile diagrams helps in understanding the energy changes and activation energies associated with each step of the reaction.

3. Energy profile diagram

These diagrams show the changes in energy during a chemical reaction. The y-axis usually shows the potential energy of the molecules involved, while the x-axis shows the progress of the reaction. Here's an example:

Initial Energy
|--------Activation Energy (Ea)-----------------------
|                                                   |
|                                                   |
|                       Transition State            |
|                            /                     |
|                           /                      |
|                          /                       |
|                         /                        |
|                        /                         |
Reaction Progress--------          ---- Products   |
|                                                   |
|---- Reactants                                      |
|                                                   |
|- Intermediate

4. Role of catalyst

Catalysts are substances that increase the rate of a reaction without consuming themselves. They work by lowering the activation energy (Ea) needed for the reaction to proceed. Catalysts can also provide alternative reaction pathways with lower activation energy or stabilize transition states or intermediates.

Types of reaction mechanisms

1. Nucleophilic substitution (SN)

Nucleophilic substitution reactions involve the replacement of a leaving group by a nucleophile. They are classified into two primary mechanisms: SN1 and SN2.

SN1 mechanism

The SN1 mechanism involves a two-step reaction, where the first step is the slow rate-determining step.

  1. Formation of a carbocation intermediate followed by the departure of the leaving group.
  2. Nucleophilic attack on the carbocation gives the substitution product.
RL --(slow)--> R⁺ (Carbocation) --(fast)--> R-Nu

SN2 mechanism

In contrast, the SN2 mechanism involves a single step where the nucleophile attacks the substrate as the leaving group leaves. This results in a coordinated reaction without intermediates.

Nu + RL --(single step)--> [Nu---R---L] --(converted)--> Nu-R + L

A notable feature is the inversion of configuration at the reaction site, which is similar to the turning of an umbrella from inside to outside.

2. Electrophilic addition (AE)

Electrophilic addition reactions often occur in alkenes and alkynes, where one π-bond is broken and two new σ-bonds are formed. This mechanism usually involves two main steps:

  1. The π-bond of the alkene attacks the electrophile, resulting in the formation of a carbocation.
  2. A nucleophile attacks the carbocation, forming the final product.
H₂C=CH₂ + E⁺ --(step 1)--> H₂C⁺-CH₂-E --(Step 2)--> H₂C-CH₂

3. Elimination reactions (E)

Elimination reactions involve the removal of atoms or groups from a molecule, resulting in the formation of a new π-bond. Two common elimination mechanisms are E1 and E2:

E1 mechanism

E1 is a multistep process similar to SN1. A leaving group departs, forming a carbocation intermediate, followed by deprotonation to yield the alkene.

R-CH₂-L --(slow)--> R-CH₂⁺ + L --(fast)--> R-CH=CH₂

E2 mechanism

E2, on the other hand, involves a coordinated process in which the removal of the residual group and the deprotonation occur simultaneously, leading to the formation of the alkene in a single step.

R-CH₂-L + B⁻ --(single step)--> R-CH=CH₂ + BH + L

4. Aromatic substitution (SA)

Aromatic substitution reactions mainly involve the replacement of substituents on an aromatic ring, with electrophilic aromatic substitution (EAS) being the most common mechanism.

Common mechanisms include the following:

  1. When an electrophile binds to an aromatic ring, an arenium ion (sigma complex) is formed.
  2. Deprotonation to restore the aromaticity of the ring.

Kinetics and thermodynamics of the reaction mechanism

Understanding the kinetics and thermodynamics of reactions is important in determining rate laws and equilibrium conditions.

Kinetics

Kinetics deals with the rates at which chemical processes occur. Reaction mechanisms provide information about potential energy surfaces, molecular interactions, and the sequence of events that lead to product formation.

Rate laws derived from mechanisms predict how reactant concentration affects the reaction rate. For example, the SN1 reaction rate depends entirely on the concentration of the substrate, making it a first-order reaction:

Rate = k [RL]

In contrast, the rate of the SN2 reaction depends on both the substrate and nucleophile concentrations, exhibiting second-order kinetics:

Rate = k [Nu] [RL]

Thermodynamics

Thermodynamics addresses the energy changes and equilibrium conditions of chemical reactions. Equilibrium constants and thermodynamic parameters such as ΔH (enthalpy) and ΔG (Gibbs free energy) help understand reaction feasibility.

Reaction mechanisms help visualize and evaluate which pathways are thermodynamically favorable, thereby determining the stability and reactivity of products and intermediates.

Conclusion

The study of reaction mechanisms in organic chemistry involves unraveling the complex phenomena that occur during chemical reactions. By investigating the kinetic and thermodynamic aspects of intermediates, transition states, and reaction pathways, chemists are better able to understand not only how reactions occur, but also how to control them for a variety of practical applications. The insights gained through reaction mechanisms continue to drive innovation in chemical research and industry.


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Reaction mechanism

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