Undergraduate
  1. General chemistry  1.1. Introduction to Chemistry  1.2. Atomic Structure  1.2.1. Subatomic particles  1.2.2. Atomic Model  1.2.3. Quantum numbers  1.2.4. Electron Configuration  1.2.5. Periodic trends  1.2.6. Isotopes and their applications  1.3. Chemical bond  1.3.1. Ionic bond  1.3.2. Covalent bonds  1.3.3. Metal Bond  1.3.4. Hybridization  1.3.5. Molecular geometry and VSEPR theory  1.3.6. Bond polarity and dipole moment  1.4. Stoichiometry  1.4.1. Mole concept  1.4.2. Empirical and molecular formula  1.4.3. Limiting reactant and excess reactant  1.4.4. Percent Yield and Purity  1.4.5. Dilution calculation  1.5. States of matter  1.5.1. Gas Laws  1.5.2. Matter and Intermolecular Forces  1.5.3. Solid and Crystal Structures  1.5.4. Phase diagram  1.5.5. Plasma and supercritical fluid  1.6. Chemical reactions  1.6.1. Types of Chemical Reactions  1.6.2. Balancing Chemical Equations  1.6.3. Thermochemical reactions  1.6.4. Reaction energy profiles  1.7. Solutions and Mixtures  1.7.1. Concentration units  1.7.2. Syndrome properties  1.7.3. Solubility and Solubility Rules  1.7.4. Henry's Law and Raoult's Law  1.7.5. Partition coefficient  1.8. Chemical equilibrium  1.8.1. Law of mass action  1.8.2. Le Chatelier's principle  1.8.3. Reaction quotient  1.8.4. To use this online calculator for Equilibrium Constant, enter Equilibrium Constant (Eq.) and hit the calculate button. Here is how the Equilibrium Constant calculation can be explained with given input values -> 0.05 = 0.05/0.  1.8.5. Acid-base balance  1.9. Acids and bases  1.9.1. Arrhenius, Brønsted–Lowry, and Lewis definitions  1.9.2. pH and pOH  1.9.3. Acid-base titration  1.9.4. Buffer Solution  1.9.5. Acid-base indicator  1.9.6. Polyprotic Acids and Bases  1.10. Electrochemistry  1.10.1. redox reactions  1.10.2. Galvanic and Electrolytic Cells  1.10.3. Nernst equation  1.10.4. Electrolysis  1.10.5. Faraday's laws of electrolysis  1.11. Thermodynamics  1.11.1. Laws of Thermodynamics  1.11.2. Enthalpy, entropy and Gibbs free energy  1.11.3. Spontaneity of reactions  1.11.4. Thermodynamic cycles (Hess's law, Carnot cycle)  1.12. Kinetics  1.12.1. Rate law and reaction order  1.12.2. Activation Energy and Catalyst  1.12.3. Collision theory  1.12.4. Reaction mechanism  1.12.5. Transition state theory
  2. Organic chemistry  2.1. Structure and relationships  2.1.1. Hybridisation in Carbon Compounds  2.1.2. Resonance and aromatization  2.1.3. Molecular orbitals  2.1.4. Inductive and mesomeric effects  2.2. Hydrocarbons  2.2.1. Hydrocarbons  2.2.2. Alkene  2.2.3. Alkynes  2.2.4. Aromatic compounds  2.2.5. Cycloalkanes and Conformation  2.3. Functional Group  2.3.1. Alcohols and phenols  2.3.2. Ethers and epoxides  2.3.3. Aldehyde and ketone  2.3.4. Carboxylic acids and derivatives  2.3.5. Amin  2.3.6. Esters and amides  2.3.7. Thiols and sulfides  2.4. Stereoscopic  2.4.1. Isomerism in Stereochemistry  2.4.2. Chirality and optical activity  2.4.3. Structural analysis  2.4.4. Diastereomers and Enantiomers  2.5.1. Substitution reactions  2.5.2. Elimination reactions  2.5.3. Addition reactions  2.5.4. Radical reactions  2.5.5. Rearrangement reactions  2.5.6. Pericyclic Reactions  2.6. Spectroscopy and structural analysis  2.6.1. Infrared Spectroscopy  2.6.2. Nuclear magnetic resonance spectroscopy  2.6.3. Mass Spectrometry  2.6.4. UV-visible spectroscopy  2.6.5. X-ray crystallography  2.7. Polymer chemistry  2.7.1. Addition and Condensation Polymers  2.7.2. Polymerization mechanism  2.7.3. Biodegradable Polymer  2.7.4. Conducting and smart polymers
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Ligands and coordination compounds  3.1.2. Crystal field theory  3.1.3. Molecular Orbital Theory in Coordination Compounds  3.1.4. Jahn–Taylor distortion  3.2. Main Group Chemistry  3.2.1. Alkali and alkaline earth metals  3.2.2. Halogens and Noble Gases  3.2.3. Transition metals and their complexes  3.2.4. Lanthanides and Actinides  3.3. Solid state chemistry  3.3.1. Crystal lattices and unit cells  3.3.2. Defects in solids  3.3.3. Electrical and magnetic properties  3.3.4. Superconductivity  3.4. Bio-inorganic chemistry  3.4.1. Metal ions in biology  3.4.2. Enzymatic reactions with metals  3.4.3. Metal poisoning and detoxification  3.4.4. Metalloproteins and Metalloenzymes
  4. Physical chemistry  4.1. Quantum Chemistry  4.1.1. Wave–particle duality  4.1.2. Schrödinger Equation  4.1.3. Quantum Numbers and Orbitals  4.1.4. Atomic and molecular spectroscopy  4.2. Statistical mechanics  4.2.1. Maxwell–Boltzmann distribution  4.2.2. Partitioning functions  4.2.3. Bose–Einstein and Fermi–Dirac statistics  4.3. Chemical thermodynamics  4.3.1. Gibbs Free Energy  4.3.2. Phase transition  4.3.3. Thermodynamic efficiency  4.4. Surface chemistry  4.4.1. Absorption and Catalysis  4.4.2. Colloids and Emulsions
  5. Analytical Chemistry  5.1. Classical methods  5.1.1. Gravimetric Analysis  5.1.2. titrimeter  5.2. Instrumental methods  5.2.1. Chromatography  5.2.2. Spectroscopy  5.2.3. Electroanalytical methods  5.2.4. X-ray diffraction
  6. Industrial Chemistry  6.1. Petrochemistry  6.2. Chemical engineering principles  6.3. Green Chemistry  6.4. Pharmaceuticals and Drug Synthesis
  7. Biochemistry  7.1. Carbohydrates  7.2. Proteins and enzymes  7.3. Lipids and membranes  7.4. Nucleic acids  7.5. Metabolism and Bioenergetics  7.6. Enzyme kinetics and mechanism

Undergraduate → Organic chemistry → Stereoscopic ↓


Structural analysis


Structural analysis is an important concept in stereochemistry, particularly in the field of organic chemistry. It involves studying the different spatial arrangements of atoms in a molecule that arise from rotation around single bonds. These different arrangements, or conformations, can have significant effects on the physical and chemical properties of molecules. This analysis is important because it helps us understand the behavior of molecules in different environments, the stereochemical pathways they prefer, and their chemical reactivity. Before moving on to more complex molecules, the simplest type of structural analysis can be explained using ethane as a model.

Basic concepts

Before delving deeper into conformational analysis, it is necessary to understand some basic concepts:

  • Conformation: Conformation is a specific arrangement of atoms in a molecule that can be changed into other arrangements by rotation about single bonds.
  • Dihedral angle: The angle between two intersecting planes, which, in the context of conformational analysis, is usually between atoms or groups bonded to adjacent carbon atoms.

Conformational isomers of ethane

Ethane, C_2H_6, is the simplest molecule to study in conformational analysis. The molecule can rotate freely around the carbon-carbon single bond, forming different conformations.

        HH
         ,
          CC
         ,
        HH

In ethane, the two most important conformations are the staggered and eclipsed conformations:

Staggered conformation

In the staggered conformation, the hydrogen atoms on one carbon are located at the maximum distance from the hydrogen atoms on the adjacent carbon. This conformation is energetically favourable because it minimises the repulsive electron-electron interactions between the hydrogen atoms.

Assumed structure

In the eclipsed form, the hydrogen atoms on one carbon line up directly with the hydrogen atoms on the opposite carbon. This results in increased repulsion between the electron clouds, making the eclipsed form higher in energy and less stable than the staggered forms.

Potential energy diagram

The potential energy diagram can be used to show the energy changes that occur when ethane rotates around a carbon-carbon bond. As a model describes the conformational changes in ethane from staggered to eclipsed and back, the diagram resembles a wave:

    energy __ __
                  ,
                  ,
    |_____________|_________|__________ dihedral angle
      0° (60° - staggered) 120° 180° (240° - staggered) 300° 360°

The diagram shows a minimum at the staggered structures and a maximum at the eclipsed structures. The energy difference between these structures is typically small, but significant enough to affect chemical reactivity and properties.

Conformational analysis of butane (C4H10)

Butane is another molecule that is often used to illustrate conformational analysis. It is more complex than ethane because of the presence of an additional carbon-carbon bond. Consider the rotation about the central single bond (the C2-C3 bond):

        HH
         ,
          CC
         ,
        C–C
         ,
          HH

Anti and gauche simulation

The two most important forms of butane are the anti and gauche forms:

Anti: The anti conformation occurs when the two methyl groups on adjacent carbon atoms are 180 degrees apart. This is the chair conformation with the lowest energy.

Gauche: The gauche conformation occurs when the methyl groups are 60 degrees apart. This conformation is higher in energy than the anti one due to steric repulsion between the two methyl groups.

Energy profile of butane

The energy profile of the rotation of butane about the central bond can be represented similarly to that of ethane, but with additional peaks and valleys.

    energy ______
              ,
            ,
    ,
     0° 60° Gauche 120° 180° Anti 240° 300° Gauche 360°

In this profile, the anti conformation is the lowest energy state, while the eclipsed conformation associated with the methyl groups is the highest.

Molecular flexibility and reactivity

Structural analysis of molecules such as ethane and butane highlights how rotation around single bonds can lead to different spatial arrangements. This flexibility is a fundamental feature of organic molecules and affects their reactivity and interactions with other molecules. For example:

  • Enzyme selectivity: Many enzymes are selective toward specific structures of substrates, recognizing only particular spatial arrangements that precisely fit their active site.
  • Reaction pathways: Some structures may be more reactive than others, making it easier to react along that specific pathway.

Conformational analysis in cyclohexane

Cyclohexane provides a unique example of conformational analysis. It does not exhibit simple rotations around single bonds due to its ring structure, but it can adopt different structures depending on the ring puckering. The most stable structure is the chair structure. Here is an example:

       HH
        ,
         CC
        ,
       CC
      ,
     h---h h---h

Chair, boat and bent boat shapes

  • Chair conformation: In the chair conformation, the carbon atoms are ordered such that steric hindrance is minimized.
  • Boat structure: The boat structure has some assumed interactions and static stresses.
  • Folded boat conformation: An intermediate conformation between the chair and boat conformation, with less stretch than the pure boat conformation.

Equatorial and axial positions: In the chair conformation, the substituents on the cyclohexane ring can occupy either the equatorial or axial positions. The equatorial positions are generally more stable due to less steric hindrance.

Importance of conformal analysis

Structure analysis is important for a deeper understanding of organic chemistry. It provides insight into how molecules behave under different conditions and how they take on different shapes and forms. This knowledge is applicable to:

  • Molecular design: By understanding preferred conformations, chemists can design molecules with specific properties for use in pharmaceuticals, materials, and industries.
  • Prediction of reaction outcomes: Reaction mechanisms can be better understood and predicted by studying how the structure of the reactants affects their reactivity.
  • Stereochemistry: The stereochemical outcomes of reactions can be significantly affected by conformational preferences, facilitating the synthesis of molecules with desired stereochemistry.

Through careful analogical analysis, chemists can become skilled at predicting and controlling the behavior of molecules, ultimately leading to innovations in a variety of scientific disciplines.


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Chirality and optical activity
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Diastereomers and Enantiomers

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Structural analysis

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