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


Stereochemistry is a fundamental domain within organic chemistry that deals with the three-dimensional arrangement of atoms in molecules. It is important for understanding the behavior and properties of molecules. In this explanation, we will explore various aspects of stereochemistry, its importance, and how it affects the physical and chemical properties of compounds.

Introduction to stereochemistry

Stereochemistry involves the study of the spatial arrangement of atoms within molecules. Unlike constitutional isomers that differ in the connectivity of atoms, stereoisomers have the same connectivity but differ in the orientation of their atoms in space. This spatial arrangement can significantly affect a molecule's melting point, boiling point, solubility, and, most importantly, its biological activity.

Types of isomerism

Isomerism is a phenomenon in which compounds have the same molecular formula but different structural or spatial arrangements. Isomers can be broadly classified into two main types: structural isomers and stereo isomers. Stereo isomers can be further divided into enantiomers and diastereomers.

Structural isomers

Structural isomers differ in the valency of atoms. The physical and chemical properties of each structural isomer can be completely different.

Example: C4H10 can exist as: 
- n-butane: CH3-CH2-CH2-CH3 
- isobutane (or 2-methylpropane): (CH3)2CH-CH3

Stereoisomers

Stereoisomers have the same order of bonded atoms, but differ in the three-dimensional orientation of these atoms. There are two main types of stereoisomers:

  • Enantiomers: superimposed mirror images.
  • Diastereomers: are not mirror images and are not superimposable.

Chirality and chiral centers

Chirality is an important concept in stereochemistry. A molecule is chiral if it is not superimposable on its mirror image. The presence of a chiral center, usually a carbon atom bonded to four different groups, often confers chirality.

Chiral center

Chiral centers are designated with an asterisk (*) and typically involve a carbon atom bonded to four different substituents. This unique arrangement results in two different configurations, usually denoted as 'R' or 'S' depending on the priority rules set forth in the Cahn-Ingold-Prelog (CIP) system.

Example: CH3-CH(OH)-COOH 
In this lactic acid molecule, the central carbon bonded to OH, COOH, H, and CH3 is a chiral center.

Optical activity

Optical activity refers to the way chiral molecules interact with plane-polarized light, causing the molecules to rotate in the plane either to the right (dextrorotatory) or to the left (levorotatory). This optical rotation is a characteristic of chiral substances and is measured using polarimeters.

Enantiomers and optical activity

Enantiomers are pairs of molecules that are non-superimposable mirror images. They exhibit identical physical properties except for the direction in which they rotate plane-polarized light. Enantiomers rotate light by equal amounts but in opposite directions.

Example: (R)-2-Butanol and (S)-2-Butanol

Fischer projections

Fischer projections are a two-dimensional way of depicting three-dimensional molecules. They are particularly useful for studying carbohydrates and amino acids. In a Fischer projection, vertical lines represent bonds going into the plane, and horizontal lines represent bonds coming out of the plane.

Viewing the Fischer projection

To explain the Fisher projection consider the following:

  • The intersections represent carbon atoms.
  • Functional groups are drawn with horizontal and vertical lines.
Example: 
  H   OH
     /
    C
   / 
COOH  H3C

Configuration and naming

The R/S nomenclature system assigns labels to chiral centers based on the priority of the attached substituents. Labeling involves the CIP priority rules:

  1. Identify the chiral centre.
  2. Assign priority based on atomic number; higher atomic number will get higher priority.
  3. Arrange it in such a way that the lowest priority group is away from you.
  4. Determine the sequence 1-2-3; if it is clockwise, it is R. If counterclockwise, it is S.
Example: Assigning R/S configuration to 2-bromo-1-chloropropane:
1. Br > Cl > CH3 > H
2. Configuration is R.

Diastereomers

Diastereomers are stereoisomers that are not mirror images. They can arise in molecules with multiple chiral centers. Diastereomers often have different physical properties and reactivities.

Example: Tartaric acid can exist as: 
- D-(+)-tartaric acid 
- L-(-)-tartaric acid 
- meso-tartaric acid

Mesocompounds

Meso compounds contain multiple chiral centers, but they can be superimposed on their mirror images because of the internal plane of symmetry. Although they contain chiral centers, meso compounds are achiral.

Example: meso-2,3-butanediol

Geometrical isomer

Geometric isomers, a subgroup of diastereomers, arise from restricted rotation about double bonds or ring structures. They are usually referred to as cis-trans isomers.

Cis-trans isomerism

Cis-trans isomers occur in compounds with restricted rotation, where different groups are attached to the carbon of a double bond or in ring structures.

Example: But-2-ene: 
- Cis: CH3 on the same side
- Trans: CH3 on opposite sides

Importance of stereochemistry

Stereochemistry plays an important role in the pharmaceutical industry, where the activity of a drug can depend largely on its stereochemistry. One enantiomer may be therapeutic, while another may be harmful or inactive. Synthetic chemists must therefore ensure that the correct enantiomer is produced.

Chirality in biology

Biological systems are inherently chiral and often interact with only one enantiomer of a chiral molecule. This specificity highlights the importance of stereochemistry in the design and action of drugs.

Conclusion

Stereochemistry is a vast and complex field that has profound implications in a variety of fields ranging from fundamental organic chemistry to drug development. By understanding the principles of stereochemistry, chemists can more effectively predict, understand, and manipulate the properties and reactions of organic compounds.


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Stereoscopic

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