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 → Stereoscopic ↓


Dynamic Stereochemistry


Stereochemistry is a subfield of chemistry that deals with the three-dimensional arrangement of atoms in molecules and its effect on the physical and chemical properties of those compounds. A fascinating area within this domain is "dynamic stereochemistry", which deals with the study of molecules that can undergo changes in their spatial organization due to kinetic processes. This dynamic aspect can often result in interesting phenomena, such as racemization, enantiomerization, and various stereomutations.

Understanding the basic concepts

Before we delve deeper into dynamic stereochemistry, it is important to have a basic understanding of stereochemistry. Several key terms and concepts need to be clarified:

  • Chirality: A chiral molecule is one that cannot be superimposed on its mirror image. A common example of this in daily life is our hands; the left hand is a non-superimposed mirror image of the right hand. In chemistry, chirality often arises due to the presence of an asymmetric carbon atom, also known as a stereocenter.
  • Enantiomers: These are pairs of chiral molecules that mirror each other but cannot be superimposed on one another. They usually have the same physical properties except for how they rotate plane-polarized light and how they react with other chiral compounds.
  • Racemization: It refers to the process in which an enantiomerically pure compound is converted into an equimolar mixture of enantiomers, known as a racemic mixture.
  • Conformational isomerism: It refers to the different spatial arrangement of atoms that arise as a result of rotation about a single bond.

Dynamic stereochemistry: Key concepts

Dynamic stereochemistry studies the changes in molecular configuration and structure that occur over time. In a dynamic system, transformations between different stereochemical forms can have important implications for the synthesis, behavior, and functionality of molecules.

Kinetic and thermodynamic control

The interconversion of stereoisomers can be effected by kinetic or thermodynamic control, which guides the stereochemical pathway and outcome:

  • Kinetic control: In reactions under kinetic control, the product distribution is determined by the relative rates at which the products are formed. In the context of stereochemistry, this refers to the pathway with the lowest activation energy, often resulting in a non-equilibrium distribution of isomers.
  • Thermodynamic control: Thermodynamically controlled reactions lead to product distributions that reflect the relative stability of the products. In stereochemical terms, this often results in the formation of the most stable isomer, which represents an equilibrium state.

Enantiomerization processes

Enantiomerization involves the transformation of an enantiomer into its mirror image. This can occur through several mechanisms, including:

  • Single-bond rotation: In flexible molecules, rotation around a single bond can convert enantiomers into each other. However, these usually apply to large, unstrained systems.
  • Nucleophilic substitution: It involves inversion of configuration, especially in SN2 reactions where inversion occurs as a result of backside attack.
 Example:
    R-CHBr-CH2-CH3 + NaOH → Enantiomer with inversion

Racemization

Racemization is an essential concept in dynamic stereochemistry because it describes the process in which optically active compounds convert into a racemic mixture:

  • This change can occur through the action of heat, light or chemical reagents.
  • For example, amino acids can racemize upon prolonged heating, which is a significant concern during peptide synthesis.
 Example:
    L-alanine → racemic D,L-alanine (on heating)

Example:
    (S)-(+)-lactic acid → racemic mixture (in presence of strong alkali)

Visual example: Structural change

Case study: Rotation and stereodynamic behavior

A practical example of dynamic stereochemistry can be illustrated by considering biphenyl compounds, where restricted rotation about a single bond connecting the two phenyl rings gives rise to optical activity if the substituents prevent free rotation.

 Example:
    C6H5-C6H4-X with two ortho substituents

Kinetic barrier and energy profile

The rotation barrier – the energy required to convert one conformation to another – can be analyzed via energy profile diagrams:


    
    Transition state
    intermediate
    product

Such diagrams show transitions between energy states, and highlight the stationary and transition states passed through by the molecules.

Applications of dynamic stereochemistry

The principles of dynamic stereochemistry have wide applications in synthetic chemistry, chiral drug development, and biological systems, where controlling the stereochemistry of molecules can produce very different results:

  • Drug development: Many drugs are chiral, and pharmacological effects can differ significantly between enantiomers. Dynamic processes can lead to loss of chiral purity, affecting the efficacy and safety of pharmaceutical agents.
  • Synthesis techniques: Strategies often use dynamic processes to improve yield and selectivity in organic synthesis. For example, dynamic kinetic resolution integrates racemization with stereoselective reactions to access the desired enantiomer.
  • Biochemistry: Enzyme-catalyzed reactions often involve dynamic stereochemical changes. These processes are important in metabolic pathways, where specific stereoisomers are essential for biological activity.

Conclusion

Dynamic stereochemistry provides an interesting perspective on how molecular configurations and conformations change over time. This underscores the importance of understanding both the static and dynamic aspects of stereochemistry in order to effectively manipulate and utilize these properties. By exploring changes in molecular structure and energy profiles, scientists can develop innovative approaches to chemical synthesis, drug development, and beyond.

Further consideration

Researchers continue to explore dynamic stereochemistry to discover new reaction mechanisms, design clever synthetic routes, and develop enantiomerically pure compounds. As the field progresses, it promises to uncover further intricacies of how molecular motion and transformations underlie the chemistry around us.


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Dynamic Stereochemistry

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