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


Biophysical and medicinal chemistry is defined as the study of chemicals and their physical properties, as well as the interactions they have with biological systems in the context of medicine. This field bridges the gap between physical chemistry and biology, playing a vital role in drug development. Topics in this domain cover diverse aspects such as protein structure, enzyme kinetics, thermodynamics, and the interaction between drugs and biological membranes.

Understanding biophysical chemistry

Biophysical chemistry focuses on the application of the principles of physical chemistry to understand the structure, dynamics, and interactions of biological molecules. At its core, it combines the principles of physics and physical chemistry with biological systems.

Classical biophysical techniques include:

  • Crystallography
  • Nuclear Magnetic Resonance (NMR)
  • Mass Spectrometry
  • Fluorescence Spectroscopy

All of these methods are used to study the structure and dynamics of proteins, nucleic acids, membranes, and other biological complexes.

Protein folding and dynamics

The process by which a protein structure assumes its functional shape is known as protein folding. Proteins are made up of long chains of amino acids and can fold into specific three-dimensional structures that determine their function.

        // Basic formula to represent protein fold stability
        ΔG = ΔH – TΔS

Here, ΔG is the change in Gibbs free energy, ΔH is the change in enthalpy, T is the temperature, and ΔS is the change in entropy.

Protein folding pathways

Enzyme kinetics

Enzymes are biological catalysts that speed up chemical reactions. Understanding the kinetics of enzyme catalysis helps in designing inhibitors for therapeutic purposes. The Michaelis-Menten equation is a fundamental equation in enzyme kinetics.

        v = (Vmax [s]) / (km + [s])

In this equation, v is the rate of the reaction, Vmax is the maximum rate, [S] is the substrate concentration, and Km is the Michaelis constant.

Enzyme saturation curve

Role of medicinal chemistry

Medicinal chemistry involves the design, development, and synthesis of medicinal compounds. The aim of this field is to discover new drugs and improve the efficiency and safety of existing drugs. It includes several sub-disciplines such as pharmacokinetics, pharmacodynamics, and toxicology.

Drug-target interactions

Drugs exert their effects by interacting with specific biological targets, usually proteins or nucleic acids. Understanding these interactions at the molecular level is important for drug development.

Consider the interaction between a drug and an enzyme. The binding can be described by the equation:

        [e] + [s] ⇌ [es] → [e] + [p]

where [E] is the enzyme, [S] is the substrate or drug, [ES] is the enzyme-substrate complex, and [P] is the product.

Enzymes Medicine

Quantitative structure-activity relationship (QSAR)

QSAR models predict the activity of chemical compounds based on their chemical structure. This approach helps identify promising drug candidates.

A simple QSAR model can be represented as:

        Activity = a + bX + cY + dZ

where a, b, c, and d are constants, and X, Y, and Z are descriptors derived from the chemical structure.

Integration into drug discovery

The interrelationship between biophysical and medicinal chemistry is vital in modern drug discovery. Integration of these fields helps to understand the detailed mechanisms by which drugs exert their action, metabolism, and toxicity.

Consider the process of lead optimization, where potential drug candidates are refined to improve their efficacy and safety profile. It involves a cyclical process of design, synthesis, testing, and analysis.

Computational chemistry techniques

In today's biomedical research, computational chemistry techniques facilitate the understanding and prediction of molecular interactions and properties. Some of the widely used methods include:

  • Molecular dynamics simulation
  • Docking studies
  • Quantum chemistry calculations

These techniques provide information about the structural flexibility of molecules, binding affinity to biological targets, and electronic properties of drugs.

Conclusion

Biophysics and medicinal chemistry serve as a fundamental pillar in the elucidation of biochemical mechanisms and the development of therapeutic agents. Understanding the interplay between molecular dynamics, structure-activity relationships, and drug-target interactions is crucial for advances in health and medicine.


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Biophysics and Medicinal Chemistry

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