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 → Supramolecular Chemistry ↓


Molecular Machines


Molecular machines are complex structures made up of a group of molecules that work together to perform a specific function, just like macroscopic machines. The study of these machines involves concepts of supramolecular chemistry, a branch of chemistry that focuses on the study of intermolecular forces and the assemblies they form. This fascinating field combines aspects of chemistry, biology, and physics to design functional molecular structures that can mimic the operation of conventional machines.

Introduction to supramolecular chemistry

Supramolecular chemistry is often described as "chemistry beyond the molecule." While traditional chemistry focuses on the bonds between atoms, supramolecular chemistry deals with the non-covalent interactions between molecules. These interactions include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, and electrostatic effects.

Key concepts

  • Host-guest chemistry: This involves the interaction of two or more molecules, where one acts as a host and the other as a guest. Typical examples include crown ethers that bind alkali metals and cyclodextrins that capture small organic molecules. Host-guest interactions are fundamental to the construction of molecular machines.
  • Self-assembly: Molecules arrange themselves into structured, functional architectures without any external guidance. This phenomenon is important for the development of molecular machines because it allows complex structures to form spontaneously.

Understanding molecular machines

Molecular machines are able to perform work when provided with an energy input. These functions can include motion, switching, transport of molecules, and control of chemical reactions. Similar to the way engines and conveyor belts work in the macroscopic world, molecular machines work on the nanoscale.

Types of molecular machines

Many types of molecular machines have been developed. Here are some examples:

  • Rotaxanes: These are made up of a ring trapped on a molecular axis, where the ring can rotate along the axis. The structure prevents the ring from coming apart, converting external energy into mechanical motion.
  • Catenanes: These contain two or more interlocked rings that can rotate relative to each other. A sample chemical representation: 
    [R1]>[R2]
  • Molecular motors: These molecules undergo rotation or directional motion when energy is applied. An example of this is the light-driven unidirectional rotation of rotaxanes.
  • Switching devices: Some molecules can toggle between states depending on external stimuli such as light, pH or electrochemical signals. Their ability to change states enables them to perform specific actions.

Examples of molecular machines

1. Molecular motor

A simple linear molecular motor moves after being exposed to light. The structure of the motor is similar to a set of gears. Once the light hits the molecule, it absorbs energy and induces the necessary geometric changes, resulting in motion.

2. Rotaxane

Rotaxanes are molecular machines that consist of a "wheel" or ring stuck in a "spindle." The synthesis of rotaxanes often involves threading a molecular ring on a spindle in the presence of specially designed end groups, or "stoppers," which prevent the ring from sliding.

Stoppers at each end ensure that the ring remains stationary, allowing it to slide along the axis when energy is added. Rotaxanes have been used to create molecular elevators, muscles, and machines that move objects.

Applications of molecular machines

The development of molecular machines has brought promising results in various fields. These can be applied in drug delivery, material science, nanotechnology and information storage. Some of these applications are as follows:

  • Drug delivery: Molecular machines can carry drugs to specific target areas in the human body. Once they reach the target site, they can release drug molecules in response to specific stimuli.
  • Nanotechnology: Molecular machines are essential to the advancement of nanotechnology by providing solutions for creating nanoscale devices. They can help control the motion of parts within these devices.
  • Data storage: The demand for data storage is increasing every year around the world. Molecular machines can provide new ways of storing information by turning nanoscale switches on and off.

Challenges in the development of molecular machines

Despite their potential, the development of molecular machines faces several challenges:

  • Energy efficiency: An important challenge is to find ways to efficiently convert chemical or light energy into mechanical work at the molecular level.
  • Precision control: Designing systems that can precisely control the function of these machines remains an ambitious challenge.
  • Scalability: Translating the complexity of molecular machines into practical applications requires technologies that can be scaled up for large-scale production.

Conclusion

Molecular machines represent the convergence of chemistry and technological innovation. They operate at the nanoscale but hold enormous potential to revolutionize technology and medicine. As researchers make progress in understanding and harnessing these machines, they could profoundly impact humanity's ability to interact with and manipulate materials at the smallest scales.

The field is still new, and there is much to be discovered. The exploration of molecular machines in supramolecular chemistry represents a frontier with rich potential for creativity and innovation in solving some of the world's most important scientific challenges.


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Molecular Machines

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