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 ↓


Geometrical isomerism


In the study of organic chemistry, stereochemistry is an important branch that explores the spatial arrangement of atoms within molecules. A fascinating phenomenon within stereochemistry is "geometric isomerism." This concept, also known as "cis-trans isomerism" or "E-Z isomerism," deals with the orientation of parts of a molecule relative to one another. This type of symmetry occurs when molecules have limited rotation around certain bonds, such as double bonds or rings.

Basic concept of geometrical isomerism

Geometrical isomerism arises when different atoms or groups are bonded to carbon atoms that are joined by a rigid structure such as a double bond (C=C) or a ring. In alkenes, due to the double bond, there is restricted rotation, which leads to different spatial arrangements of the substituent groups. These different arrangements cannot be easily interchanged without breaking the pi bonds of the double bond.

To better understand geometric isomerism, consider two main arrangements:

  1. Cis-isomer: When two similar or identical groups are on the same side of the double bond or ring.
  2. Trans-isomer: When two similar or identical groups are on opposite sides of a double bond or ring.

Example

Ethene derivative

Let's look at a simple example involving ethylene derivatives:

 HH  / C = C /  XX

Here, X represents the substituent groups attached to the carbon atoms.

In the cis-isomer:

 HH  / C = C /  XX

In the trans-isomer:

 XH  / C = C /  HX

Real-world example: 2-butene

cis-2-butene
 H CH 3  / C = C /  CH 3 H
trans-2-butene
 CH 3 H  / C = C /  H CH 3

Conditions for geometrical isomerism

For a compound to show geometrical isomerism it must satisfy the following conditions:

  • The molecule must contain a double bond or a ring restricting rotation of the parts about the bond.
  • Each carbon atom in the double bond or part of the ring must have two different substituents.

Visual representation and plane symmetry

Geometric isomers are often depicted in a plane, using symmetry to distinguish between isomers. In many cases, we use a plane to divide the molecule into two parts:

 ------ Plane ----- CH 3 H  / C -- C /  H CH 3

EZ Notation

When more complex substituents are involved, the cis-trans terminology becomes less useful. Therefore, a more general system called EZ notation is used. The rules for determining E and Z isomers are based on the Cahn-Ingold-Prelog priority rules.

How to specify the EZ designation?

To assign EZ notation to a given isomer:

  1. Identify and prioritize the substituent on each carbon of the double bond. Higher atomic numbers are given higher priority.
  2. If the priority groups on each carbon are on the same side, it is the Z-isomer (from the German word "zusammen", meaning together).
  3. If the priority groups on each carbon are in opposite directions, it is the E-isomer (from the German word "entgegen", meaning opposite).

Example

Consider this compound:

 Cl H  / C = C /  CH 3 Br

For the given structure:

  1. Compare the atomic numbers of Cl and H. Cl has higher atomic number, so it gets higher priority.
  2. Compare the atomic number of CH3 vs Br. Br has a higher atomic number, so it gets higher priority.
  3. The priority groups (Cl and Br) are in opposite directions; therefore, it is an E-isomer.

Understanding structural differences

Some molecules show different boiling and melting points and solubilities due to differences in their geometrical isomers:

Boiling point

Consider the cis and trans isomers of 2-butene. cis-2-butene typically shows a slightly higher boiling point than trans-2-butene due to the polar nature of cis configuration, which enables stronger London dispersion forces.

Melting point

In contrast, trans isomers pack better in the solid state, often resulting in higher melting points than cis isomers.

Solubility

Differences in geometry also affect solubility. For example, the polarity present in cis isomers can cause them to have greater solubility in polar solvents than trans isomers.

Importance of geometrical isomerism

Geometric isomerism is important because different isomers display different chemical and physical properties, which affect how they interact with other substances. This has important implications in biology, materials science, and pharmacology:

  • Pharmacology: The activity of a drug may depend on the isomeric form, which contributes to the intended therapeutic outcome.
  • Physics: Physical properties such as strength, ductility, and colour can be affected by geometric configuration.
  • Biological processes: Enzymatic reactions can select specific isomers for binding, which determine metabolic pathways.

Challenges and considerations

Understanding and working with geometric symmetry presents challenges due to the complexity of multi-substituted systems. Specifying the correct EZ notation requires familiarity with precedence rules and spatial orientation, which can sometimes require higher dimensional understanding beyond simple plane representations.

Complex molecules and further studies

Complex molecules such as natural products, polymers, and advanced synthetic compounds can exhibit multiple isomerism characteristics. New methods continue to be explored to isolate these properties and use them to design molecules with desired characteristics.

For graduate students and researchers, a thorough understanding of geometric isomerism provides an essential foundation to further explore the fascinating world of stereochemistry and its wide applications in scientific advancement.


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Geometrical isomerism

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