Graduate
  1. Physical Chemistry  1.1. Thermodynamics  1.1.1. Laws of Thermodynamics  1.1.2. Enthalpy and heat capacity  1.1.3. Entropy and free energy  1.1.4. Phase Equilibrium  1.1.5. Statistical thermodynamics  1.1.6. Thermodynamic cycle  1.1.7. Fugacity and activity  1.2. Quantum Chemistry  1.2.1. Principles of quantum mechanics  1.2.2. Schrödinger Equation  1.2.3. Particle in a box  1.2.4. Operators and eigenvalues  1.2.5. Atomic orbitals  1.2.6. Molecular orbital theory  1.2.7. Perturbation theory  1.2.8. Valence bond theory  1.2.9. Hybridization and chemical bonding  1.3. Chemical kinetics  1.3.1. Rate laws and reaction mechanisms  1.3.2. Collision theory  1.3.3. Transition state theory  1.3.4. Enzyme Kinetics  1.3.5. Chain Reactions and Polymerization  1.3.6. Photochemical reactions  1.4. Statistical mechanics  1.4.1. Partitioning functions  1.4.2. Molecular distribution functions  1.4.3. Boltzmann Distribution  1.4.4. Bose–Einstein and Fermi–Dirac statistics  1.5. Spectroscopy  1.5.1. Rotational Spectroscopy  1.5.2. Vibrational Spectroscopy  1.5.3. Electronic Spectroscopy  1.5.4. Nuclear magnetic resonance spectroscopy  1.5.5. Mass Spectrometry  1.5.6. Raman Spectroscopy  1.5.7. Electron paramagnetic resonance spectroscopy  1.6. Surface and colloidal chemistry  1.6.1. Absorption isotherm  1.6.2. Surface tension and wetting  1.6.3. Colloidal Stability  1.6.4. Catalysis  1.6.5. Emulsions and micelles  1.7. Electrochemistry  1.7.1. Nernst equation  1.7.2. Electrochemical cells  1.7.3. Conductivity and mobility  1.7.4. War  1.7.5. Fuel cells  1.7.6. Electrolysis
  2. Organic chemistry  2.1. Reaction mechanism  2.1.1. Nucleophilic substitution reactions  2.1.2. Electrophilic addition reactions  2.1.3. Elimination reactions  2.1.4. Rearrangement reactions  2.1.5. Radical reactions  2.1.6. Pericyclic reactions  2.2. Spectroscopy and structural determination  2.2.1. UV-Vis Spectroscopy  2.2.2. IR Spectroscopy  2.2.3. NMR Spectroscopy  2.2.4. Mass Spectrometry  2.2.5. X-ray crystallography  2.3. Stereoscopic  2.3.1. Chirality and optical activity  2.3.2. Structural analysis  2.3.3. Geometrical isomerism  2.3.4. Dynamic Stereochemistry  2.4. Organometallic Chemistry  2.4.1. Organolithium and organomagnesium reagents  2.4.2. Palladium-catalyzed cross-coupling reactions  2.4.3. Transition Metal Complexes  2.4.4. Metal–carbon bond  2.5. Polymer chemistry  2.5.1. Polymerization mechanism  2.5.2. Polymer Characteristics  2.5.3. Biodegradable Polymer  2.5.4. Conducting polymer  2.5.5. Supramolecular polymers  2.6. Medicinal chemistry  2.6.1. Drug design and development  2.6.2. Pharmacokinetics and pharmacodynamics  2.6.3. Structure-activity relationships  2.6.4. Molecular docking and drug screening
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Crystal field theory  3.1.2. Ligand field theory  3.1.3. Spectrochemical Series  3.1.4. Chelation and stability  3.2. Organometallic Chemistry  3.2.1. Metal Carbonyls  3.2.2. Catalysis by organometallic complexes  3.2.3. Metallocenes  3.3. Bio-inorganic chemistry  3.3.1. Metalloproteins and enzymes  3.3.2. The role of metals in biological systems  3.3.3. Metal ion transport and storage  3.4. Solid state chemistry  3.4.1. Crystal Structures  3.4.2. Band theory of solids  3.4.3. Superconductors  3.4.4. Defects in the crystal  3.5. Lanthanides and Actinides  3.5.1. Electronic configuration in lanthanides and actinides  3.5.2. Coordination chemistry of the lanthanides  3.5.3. Magnetic Properties of Lanthanides
  4. Analytical chemistry  4.1. Chromatography  4.1.1. Gas Chromatography  4.1.2. High Performance Liquid Chromatography  4.1.3. Thin Layer Chromatography  4.2. Spectroscopic Techniques  4.2.1. Atomic absorption spectroscopy  4.2.2. X-ray diffraction  4.2.3. Inductively coupled plasma spectroscopy  4.3. Electroanalytical methods  4.3.1. Potentiometry  4.3.2. Voltammetry  4.3.3. Colometry  4.4. Mass Spectrometry  4.4.1. Ionization Technique  4.4.2. Fragmentation Pattern  4.5. Chemometrics  4.5.1. Multidisciplinary analysis  4.5.2. Machine Learning in Chemistry
  5. Theoretical and Computational Chemistry  5.1. Molecular dynamics simulation  5.1.1. Force fields and energy minimization  5.1.2. Monte Carlo simulation in molecular dynamics simulations  5.2. Quantum chemical methods  5.2.1. Hartree–Fock theory  5.2.2. Density functional theory  5.2.3. Semi-empirical methods  5.3. Computational drug design  5.3.1. Molecular Docking  5.3.2. QSAR Modeling  5.3.3. Virtual Screening
  6. Biochemistry  6.1. Enzyme Kinetics  6.1.1. Michaelis-Menten kinetics  6.1.2. Inhibition mechanism  6.2. Metabolism and Bioenergetics  6.2.1. Glycolysis  6.2.2. Citric acid cycle  6.2.3. Electron transport chain  6.3. molecular Biology  6.3.1. DNA replication and repair  6.3.2. Protein synthesis  6.3.3. Gene Regulation  6.4. Structural Biochemistry  6.4.1. Protein Folding  6.4.2. Membrane Biophysics
  7. Environmental Chemistry  7.1. Atmospheric Chemistry  7.1.1. Greenhouse gases  7.1.2. Ozone depletion  7.1.3. Air pollutants and smoke  7.2. Water Chemistry  7.2.1. pH and water hardness  7.2.2. Wastewater treatment  7.2.3. Aquatic Chemistry  7.3. Soil Chemistry  7.3.1. Heavy metal contamination  7.3.2. Soil pH and Buffering  7.3.3. Nutrient cycling  7.4. Toxicology and Chemical Safety  7.4.1. Toxicokinetics  7.4.2. Risk Assessment in Toxicology and Chemical Safety in Environmental Chemistry  7.4.3. Effects of pollutants on the environment

Graduate → Organic chemistry ↓


Stereoscopic


Stereochemistry is an important and fascinating branch of chemistry that studies the three-dimensional arrangement of atoms within molecules. It investigates how these arrangements affect the properties and reactions of chemical compounds, providing invaluable information about the behavior of molecules in biological systems and synthetic processes.

Basic concepts of stereochemistry

At its core, stereochemistry focuses on the spatial arrangement of atoms. Understanding stereochemistry begins with understanding isomerism. Isomers are molecules with the same molecular formula but different structures or arrangements of atoms. Specifically, stereochemistry deals with stereoisomers, which differ only in their spatial arrangement.

Types of stereoisomers

Stereoisomers can be divided into two categories:

  1. Enantiomers: These are non-superimposed mirror images of each other. An everyday analogy could be the relationship between a person's left and right hand. Even though they reflect each other, they cannot be perfectly aligned or superimposed on each other.
  2. Diastereomers: These are not mirror images and generally have different physical properties. These include any stereomeric pair that is not considered an enantiomer.

To right

The mainstay of stereochemistry is the concept of chirality. A molecule is considered chiral if it has a non-superimposed mirror image. Such molecules lack an internal plane of symmetry.

Chirality in organic molecules

Chirality arises primarily from the presence of a chiral center, which is typically a carbon atom bonded to four different groups. The spatial arrangement of molecules affects how they react and interact with other chiral entities, leading to profound implications in pharmaceuticals, where one enantiomer may be therapeutic, while another may be harmful.

C*HXYR

In the above example, carbon (*) acts as the chiral center, bonded to four different groups, X, Y, R, and H. This configuration leads to two non-superimposable forms, often resulting in enantiomers.

Visualization of chirality

Left Hand Right hand

The diagram above represents the left and right handed enantiomers. Notice how they are mirrored but cannot align or superimpose exactly.

Assigning configurations: R/S system

To express the absolute configuration at the chiral center, organic chemists adopt the R/S nomenclature system. This method assigns priority to each substituent attached to the chiral center based on its atomic number.

  1. Order the substituents according to decreasing atomic number; the one with higher atomic number is given higher priority.
  2. Position the molecule so that the group with the lowest priority is far away (usually at the back).
  3. If the sequence is clockwise, the configuration is R (rectus); if counterclockwise, it is S (sinister).

Cis-trans isomerism

Cis-trans isomerism is another stereochemistry aspect, primarily associated with double bonds or rings where rotation is restricted.

Cis-trans in alkynes

Take the case of a simple alkene:

CH3CH=CHCH3

Here, the arrangement around the double bond can be as follows:

  • Cis: Similar groups/atoms located on the same side.
  • Trans: Same groups/atoms in opposite directions.
CH3 H H CH3

Although this is a simplified model, it emphasizes spatial nature, and contributes significantly to properties such as boiling point, density, and biological activity.

Naming and representation

Naming systems or naming conventions play an important role in stereochemistry, ensuring clarity and precision in chemical communication.

For complex systems the cis–trans descriptor is combined with additional stereochemical descriptors:

  • E/Z nomenclature: It is used when there are multiple types of substituents around a double bond.
    • Assign priority by CIP (Cahn–Ingold–Prelog) rules.
    • If the top-priority groups on each carbon are on the same side, use Z (zusammen, together).
    • If the top priority groups are in the opposite direction, use E (entgegen, opposite).

Explain further with an example:

CH3CH=C(C6H5)CH3

Apply the CIP rules to identify whether phenyl (C6H5) takes precedence over other groups because of higher atomic number or multiple bond considerations.

Stereochemistry in biological molecules

The effects of stereochemistry are pervasive in biological systems, as many biological molecules, including proteins, carbohydrates, nucleic acids, and hormones, are naturally chiral.

Proteins and enzymes

Proteins are built from amino acids, most of which are chiral, usually in the L-configuration. The spatial configuration of amino acids determines both protein folding and function.

Sugar

Sugars or carbohydrates display stereochemistry dominantly at each chiral carbon within their structure. For example, glucose is a ubiquitous sugar with multiple chiral centers:

C6H12O6 - D-glucose

The specific spatial arrangement of D-glucose makes it compatible with metabolizing enzymes, demonstrating the biological importance of stereochemistry.

Stereochemistry in drug design

The pharmaceutical industry benefits greatly from understanding stereochemistry. Enantiomers can have very different biological effects. A classic case concerns thalidomide, which was initially sold as a sedative. While one enantiomer provided therapeutic relief, the other led to severe birth defects.

Enantiomeric purity

Enantiomeric purity or the predominance of one enantiomer in a preparation may be important to ensure. Methods such as chiral chromatography help achieve this.

Stereoselective reactions

Reactions can be designed to selectively favor the formation of specific stereoisomers. Terms associated with these processes include:

  • Stereospecific reaction: A reaction in which the stereochemistry of the reactants determines the stereochemistry of the products.
  • Stereoselective reaction: preferential formation of a particular stereoisomer when multiple stereoisomers are possible.

An example of this is the Sharpless epoxidation, a method that produces epoxides with excellent enantioselectivity, highlighting both academic and practical importance.

Conclusion

Stereochemistry is a vast and complex subject that is essential to understanding molecular properties, reactions, and applications. Its importance extends from basic research to the depths of biological mechanisms and pharmaceuticals, underscoring its significance across a variety of disciplines and industries. Mastering stereochemistry requires not only an understanding of the theoretical frameworks but also an appreciation of its practical implications and applications.


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Stereoscopic

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