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 ↓


Biosynthesis of natural products


In the field of organic chemistry, the biosynthesis of natural products is an exciting topic. Natural products are organic compounds that occur naturally in living organisms. They have specific architectures and functionalities that make them important in many biological processes. Their biosynthesis, which means how they are formed from simple starting materials in nature, involves a series of enzymatic reactions. Let's look at this fascinating process in detail.

What are natural products?

Natural products are small molecules found in nature that are produced by living organisms. These include antibiotics, pigments, and even some toxins. Despite their different roles, they have the same origin because they arise from simple building blocks that undergo complex transformations.

Building blocks in biosynthesis

Biosynthesis typically begins with primary metabolites such as acetate, mevalonate, glycine. These serve as building blocks that lead to more complex structures.

Example: acetate pathway

    Acetyl-CoA + Malonyl-CoA --> Fatty Acids
    Acetyl-CoA + Malonyl-CoA --> Fatty Acids

The conversion of acetyl-CoA and malonyl-CoA to fatty acids is a key step in the formation of a variety of natural products.

Pathway in biosynthesis

The biosynthesis of natural products often involves the following major pathways:

1. Polyketide pathway

Polyketides are biosynthesized from acetate through a series of condensations. These are versatile and result in many antibiotics, antifungals, and anticancer compounds.

Visual example - simplified pathway of polyketide biosynthesis

Acetyl-CoA Polyketide

2. Shikimate route

The shikimate pathway is central in plants and microorganisms, leading to aromatic compounds. These compounds form essential elements such as the amino acids phenylalanine, tyrosine, and tryptophan.

Example: phenylalanine from shikimate

    Shikimate --> Chorismate --> Phenylalanine
    Shikimate --> Chorismate --> Phenylalanine

Visual example - corisite transform

Shikimate Chorismate Phenylalanine

Enzymes in biosynthesis

Enzymes play important roles in biosynthetic pathways, acting as catalysts for reactions. These reactions often require specific 3D structures that enzymes can provide.

Visual example - enzymatic catalysis

Enzymes Substrate

The role of natural products

Natural products are not just fascinating chemical substances. They have a huge role in nature, including defense mechanisms for plants and play a vital role in ecological interactions. Humans have also made extensive use of these compounds.

Medicinal applications

Many natural products are biological compounds used in medicines, such as penicillin from the fungus Penicillium, which revolutionized antibiotics.

Agricultural applications

Various natural products have roles as pesticides and herbicides, making it more important to understand their biosynthesis and effects on nature.

Challenges and opportunities in natural product biosynthesis

The biosynthesis of natural products is a highly complex process. Challenges include understanding the complex enzyme pathways and the ability of synthetic biology to use and manipulate these pathways.

Synthetic biology

Synthetic biology attempts to use biosynthetic pathways to produce complex natural products in the laboratory. This could lead to more sustainable production of needed compounds.

Visual example - synthetic biology potential

DNA Product

Conclusion

The biosynthesis of natural products involves the transformation of a few basic molecules into many complex structures that have enormous ecological and human significance. By understanding these processes, we can appreciate the chemistry that gives rise to phenomena ranging from plant defense mechanisms to life-saving antibiotics. As research continues in this fascinating field, new possibilities for sustainable chemical processes and new drug discovery are emerging, offering new horizons in chemistry and biology. Understanding these processes in easily understood language and examples helps bridge the gap between complex chemistry and everyday applications.


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