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 → Stereoscopic ↓


Dynamic Stereochemistry


Stereochemistry is the study of how different spatial arrangements of atoms in molecules affect their chemical properties and reactions. While static stereochemistry deals with fixed spatial arrangements, dynamic stereochemistry goes a step further by considering how these arrangements can change over time, often in response to environmental factors such as temperature and pressure.

Introduction to dynamic stereochemistry

Dynamic stereochemistry focuses on the study of stereochemical arrangements in molecules that can change over time. This aspect of stereochemistry is important in understanding the behavior of molecules in biological systems and organic synthesis.

There are several key concepts in dynamic stereochemistry:

  • Molecular structure and conformational changes
  • Atropisomerism
  • Inversion and racemisation
  • Reactivity and stereochemical outcomes

Structure and structural change

One of the simplest forms of dynamic stereochemistry is conformational change. Molecules can adopt different shapes through rotation around the sigma (σ) bond. Consider ethane (C_2H_6), a simple molecule that clearly demonstrates this concept.

Ethane simulation

           
 hhhh
  ,
   CC or CC
  ,
 hhhh

In ethane, rotations around the carbon-carbon bonds lead to different conformations, such as eclipsed and staggered. The energy barrier for rotation is relatively low, meaning that these rotations can occur quickly and often.

Serial forms

The eclipsed conformation has higher energy, as it has steric hindrance and torsional strain, while the staggered conformation is more stable. This dynamic aspect of rolling through structures is fundamental in determining the shape and reactivity of molecules.

Cyclohexane conformations

Chair shape

Cyclohexane is another vivid example. It mainly adopts the chair conformation as it is the most stable configuration avoiding steric strain. However, it can also convert into other forms such as the boat conformation, yet this transformation requires more energy.

Atropisomerism

Atropisomerism is a category of stereoisomerism that is usually caused by restricted rotation around a bond due to steric hindrance. It often involves biaryl compounds where bulky substituents prevent free rotation around the aryl-aryl bond.

Biaryl compounds

In these compounds, because of blocked rotation, the stereochemistry remains stable and distinct atropisomers can be isolated, each with unique properties.

Inversion and racemisation

Another dynamic process is the inversion and racemization of chiral molecules, which describes how one enantiomer of a compound can transform into its mirror image, resulting in a racemic mixture. This process is common in nitrogen and phosphorus compounds.

Nitrogen inversion

Consider the example of ammonia (NH_3). Although ammonia is not chiral, its derivatives, amines with three different substituents and one lone pair, can be chiral. In such compounds, nitrogen can flip to inverse configuration:

Lone pair R S Inverted Pyramid

This dynamic process contributes to rapid interconversion and often leads to equivalent enantiomers, which effectively become nonchiral.

Stereochemical results in reactions

The dynamic nature of stereochemistry significantly affects the outcomes of chemical reactions. Reactants can change their stereochemistry before, during, or after a chemical reaction.

SN1 and SN2 reactions

In the SN1 mechanism, a leaving group leaves before the nucleophile attacks, usually forming a planar carbocation. This allows the nucleophile to attack from either side, forming a racemic mixture if the starting material was chiral:

  R3
    ,
     C+
    ,
  R1 R2

In contrast, in the SN2 mechanism, the nucleophilic attack occurs from the direction opposite to that of the leaving group, leading to an inversion of stereochemistry, called Walden inversion:

NEW: → R1-C-LG → NEW-R1-C
              ,
            R2 R3

E1 and E2 reactions

The E2 mechanism involves a coordinated process in which the base removes a proton while the leaving group moves out. This usually occurs in the anti-periplanar arrangement, which is heavily influenced by stereochemistry.

E2 H LG

In contrast, the E1 mechanism is more similar to SN1, where the formation of the carbocation intermediate allows for a variety of structures.

Kinetic versus thermodynamic control

Stereochemical outcomes in reactions are also controlled by kinetics and thermodynamics. Kinetic control usually yields the fastest-forming product, which is often the least-barrier under standard conditions of temperature and pressure. Thermodynamic control, on the other hand, allows the system to reach equilibrium and favors the more stable stereochemical product.

Kinetic products

Conclusion

Dynamic stereochemistry provides important information about how molecular structures affect chemical and biological systems. This understanding is crucial in fields ranging from drug design to materials science, where the shape and orientation of molecules are critical to their function.

As science progresses, the nuances of dynamic stereochemistry are being unraveled, and a deeper understanding of molecular behavior in different environments is emerging.


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Dynamic Stereochemistry

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