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 → Biophysics and Medicinal Chemistry ↓


Chemical biology approach


Introduction to chemical biology

Chemical biology is an exciting field that lies at the intersection of chemistry and biology. It uses the tools and techniques of chemistry to address and solve biological questions. Through this field, researchers can investigate biological systems, understand interactions at the molecular level and create new therapeutic strategies to combat diseases.

Basic concepts of chemical biology

At its core, chemical biology uses chemical techniques such as synthesis, molecular modeling, and analytical tools to study biological systems. Here are some fundamental concepts:

  • Synthesis of bioactive molecules: Scientists design and synthesize small molecules that can interact with biological pathways.
  • Investigation of biological mechanisms: Small molecules are used to investigate and explain the mechanisms of biological processes.
  • Drug discovery: Chemical biology plays a vital role in the identification and optimization of potential drug candidates.

Techniques in chemical biology

A number of techniques are used in chemical biology to facilitate the exploration of complex biological systems:

Chemical probes

Chemical probes are small molecules designed to interact with select proteins or pathways. They can be used to monitor and alter biological processes. For example:

(CH3)2CH-CH2-OH

The formula above refers to isopropyl alcohol, which can be a starting material in the synthesis of chemical probes.

Bioorthogonal chemistry

This involves using chemical reactions inside living organisms, without interfering with the original biochemical processes. A classic reaction used in bioorthogonal chemistry is the Huisgen cycloaddition.

Cu(I) + Alkyne + Azide → 1,4-disubstituted 1,2,3-triazole

In the above reaction, copper(I)-catalyzed alkyne–azide cycloaddition produces triazoles, which are useful for tagging biomolecules.

Applications in biophysical chemistry

Biophysical chemistry combines principles of physics and chemistry to study biological systems. Approaches from chemical biology are particularly valuable in this area:

Study of protein dynamics

Chemical biology provides tools for observing protein dynamics. For example, fluorescent probes enable real-time monitoring of protein conformation.

Protein A

In the above view, the circle represents a protein whose structural change is monitored by a fluorescent probe.

Membrane interactions

Using chemical probes, biophysical chemists can determine how drugs interact with cell membranes, providing information about a drug’s efficacy and mechanism of action.

Applications in medicinal chemistry

Medicinal chemistry focuses on the design, synthesis, and development of medicines. Approaches from chemical biology are invaluable in this field:

Lead compound identification

Small molecules are screened against biological targets to find lead compounds for further development:

IC50 < 10 nM

The IC50 value represents the concentration of the inhibitor where the response (or binding) is reduced by half. A lower IC50 suggests a more potent compound.

SAR study

Structure-activity relationship (SAR) studies explore the relationship between the chemical structure of a compound and its biological activity.

For example, variations in the length of the alkyl chain can affect the ability of a molecule to bind to a biological target, thereby affecting its pharmacological properties:

R-CH2-OH R-CH2-NH2

In the above example changing -OH to -NH2 has drastic effect on the activity and physicochemical properties.

Future perspectives

As technology and scientific knowledge continue to advance, chemical biology will undoubtedly grow in importance and utility, providing even more sophisticated tools for analyzing biological systems and formulating new therapies. Emerging trends include:

  • Integration with computational approaches: Advances in machine learning algorithms will help predict chemical interactions and drug efficacy.
  • Personalized medicine: Chemical biology is the key to developing tailored therapies based on individual genetic and environmental factors.
  • Better understanding of disease mechanisms: Novel chemical probes can provide insight into diseases at the molecular level, allowing for more precise interventions.

Conclusion

Chemical biology is a powerful discipline that continues to enhance our understanding and manipulation of biological systems. By linking chemistry and biology, it provides invaluable insights that drive innovation in both biophysical and medicinal chemistry. As we continue to unravel the mysteries of life at the molecular level, chemical biology will remain an indispensable tool in science and medicine, leading to new breakthroughs and treatments that improve health and quality of life for humanity.


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Chemical biology approach

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