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 ↓


Natural products chemistry


Natural product chemistry is a major field within organic chemistry. It focuses on the study of chemicals produced by living organisms. These compounds are important components of biological systems, and many of them have beneficial medicinal properties. The study of natural products involves isolating, characterizing, and analyzing these organic compounds.

Introduction to natural products

Natural products are organic compounds that are synthesized by living organisms. Fundamental examples include alkaloids, terpenoids, flavonoids, and polyketides. They serve a wide range of ecological functions, such as defense mechanisms or signaling molecules. Their complexity and diversity make them excellent candidates for pharmaceuticals and other applications.

Historical context

The study of natural products is centuries old. Traditional medical systems such as Ayurveda and Traditional Chinese Medicine used plant extracts and animal products for treatment. With scientific advances, these traditional practices transformed into more systematic research efforts to isolate and identify active ingredients.

Classification of natural products

Alkaloids

Alkaloids are nitrogen-containing compounds, often with important pharmacological effects. Examples include morphine, quinine, and atropine. They are mostly derived from plant sources. Alkaloids typically have complex structures, often containing multiple ring systems.

N

Terpenoids

Terpenoids, or isoprenoids, are derived from isoprene units. They are one of the most diverse classes of natural products, including examples such as menthol, camphor, and the carotenoids. Their structures range from simple monoterpenes to complex polyterpenes and their oxidized derivatives.

C 5 H 8

Flavonoids

Flavonoids are polyphenolic compounds known for their antioxidant activity. They are present in many fruits and vegetables. Examples include quercetin and kaempferol. The basic structure of flavonoids is based on 15 carbon atoms, arranged in a C6-C3-C6 skeleton.

C

Polyketides

Polyketides are a large class of secondary metabolites derived from acetate units. These include important pharmaceutical agents such as erythromycin and tetracycline. Polyketides display a wide range of structures due to variations in their biosynthetic pathways.

CH 3 CO

Isolation methods

It is important to isolate and extract natural products from their biological sources. Different techniques are used depending on the nature of the compound and the source material. Common methods include solvent extraction, steam distillation, and chromatography.

Solvent extraction

It involves using organic solvents to dissolve and separate natural products from plant or animal tissues. The choice of solvent depends on the polarity of the target compound. For example, alkaloids are often extracted using a slightly acidic aqueous solution, followed by an organic solvent.

Step 1: Crush plant material 
Step 2: Add aqueous acid 
Step 3: Filter and phase separate

Steam distillation

This technique is used primarily for volatile oils and essential compounds that are sensitive to high temperatures. The plant material is exposed to steam, which carries the volatile compounds for condensation and collection.

Chromatography

Chromatography is important for the purification and analysis of natural products. Types include paper, thin layer, gas, and high-performance liquid chromatography (HPLC).

Chromatography: 
- Paper/TLC for preliminary analysis 
- HPLC for detailed separation and isolation

Structure explanation

Several spectroscopic techniques are used to determine the structure of natural products, such as nuclear magnetic resonance (NMR), mass spectrometry (MS), and infrared (IR) spectroscopy.

Nuclear magnetic resonance (NMR)

NMR helps to identify the carbon-hydrogen structure of organic compounds. Proton NMR and carbon-13 NMR are widely used to find out the structure.

Mass spectrometry (MS)

MS provides molecular weights and fragmentation patterns, and provides clues to the molecular structure of natural products.

Infrared (IR) spectroscopy

IR spectroscopy is beneficial in identifying functional groups. The peaks in the IR spectrum reveal the presence of bonds such as OH, C=O, and NH etc.

Synthetic approaches

Once a natural product is isolated and its structure elucidated, its total synthesis can be attempted. This allows for large-scale production, structural analogs, and modifications for improved properties.

Total synthesis

Total synthesis reconstructs the entire structure from the original starting materials. This is often complex and requires novel synthesis strategies.

Example: Synthesis of Quinine 
Pathway involves multiple steps including creating quinuclidine moiety

Semi-synthesis

Semi-synthesis involves modifying a natural precursor to form a derivative. This is useful when complete synthesis is impractical but a change to the natural structure is desired.

Applications and significance

Natural products play an important role in the development of medicines, dietary supplements, and agricultural products. Many antibiotics, anti-cancer agents, and other drugs have been derived from natural sources.

Medicines

Natural products such as penicillin, paclitaxel, and artemisinin have revolutionized medicine. They serve as templates for drug development and are leading compounds in drug discovery.

Agriculture

In agriculture, natural products are used as insecticides, herbicides, and growth enhancers. Pyrethrins obtained from chrysanthemum flowers are commonly used as insecticides.

Nutraceuticals and supplements

Nutraceuticals are food-derived products that have medicinal benefits. Compounds such as omega-3 fatty acids, tocopherols, and flavonoids fall into this category.

Challenges and future directions

The field of natural product chemistry faces challenges such as sustainability, sourcing, and maximizing yield from limited sources. Biotechnology advances, such as biosynthetic routes via microbial fermentation, offer promising alternatives for producing natural products on a large scale.

Conclusion

Natural products chemistry is an important branch of organic chemistry, inspiring innovations in many industries. Its rich history and ongoing research lead to new compounds that transform medicine, agriculture, and other fields.


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Natural products chemistry

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