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 → Stereoscopic ↓


Structural analysis


Structural analysis is a fundamental topic within stereochemistry, a branch of organic chemistry. It revolves around the study of the different spatial arrangements of atoms in a molecule. These arrangements arise from rotations around single bonds. The ability of molecules to adopt different shapes, or structures, greatly affects their chemical reactivity and physical properties. Understanding structural analysis is important for understanding molecular behavior and activity.

Principles of conformal analysis

In organic chemistry, molecules containing single bonds can rotate about these bonds. This rotation gives rise to different spatial arrangements called conformations. Some of the conformations of a molecule are more stable due to lower energy, while others are less stable. The basic goal of conformational analysis is to determine these energy differences and understand the factors that affect conformational stability.

A classical example of this is the study of ethane, C_2H_6. Ethane can rotate freely around the carbon-carbon single bond. By observing these rotations, we identify two limiting structures: staggered and eccentric.

Staggered versus eclipsed conformations

What is the difference between the staggered and eclipsed forms of ethane? In the staggered form, the hydrogen atoms attached to one carbon are located between the hydrogen atoms attached to the other carbon. This arrangement minimizes the repulsion between the electron clouds around the hydrogen atoms, making the staggered form lower in energy and more stable.

On the other hand, in the eclipsed configuration the hydrogen atoms are aligned right behind each other, which maximizes the repulsive interactions. This makes the eclipsed configuration higher in energy.

Staggered Eclipse

The energy difference between these structures arises from torsional strain and can be represented in a diagram known as an energy profile diagram.

Energy profile diagram

To visualize the changes in energy as a molecule rotates around a single bond, an energy profile diagram is often used. For ethane, such a diagram plots the potential energy against the dihedral angle, which changes as the bond rotates.

Angle Energy

The minimum points represent staggered structures, while the maximum points represent eclipsed structures. This diagram shows the potential energy changes as a function of the dihedral angle between the groups attached to the carbon atoms.

Factors affecting structural stability

Several factors determine the stability of conformations. These factors include steric hindrance, torsional strain, and the presence of intermolecular interactions such as hydrogen bonds or dipole-dipole interactions.

Static hindrance

Stergic hindrance occurs when atoms or groups are very close to each other, resulting in repulsion forces due to the overlap of electron clouds. This principle becomes especially important in molecules with large substituents. For example, in butane, bulky groups such as methyl groups increase steric hindrance, affecting which structure prevails.

Torsional strain

Torsional strain arises from resistance to rotation about the bonds. It is maximum in eclipsed conformations where the bonds or groups are directly aligned. For example, in propane, the eclipsed conformation has higher torsional strain than the staggered version, which is energetically favourable.

Intermolecular interactions:

Noncovalent interactions within a molecule can stabilize specific structures. For example, intermolecular hydrogen bonding can bind a molecule into a particular structure. Dipole-dipole interactions, especially in polar molecules, can also dictate conformational preferences.

Applications of conformal analysis

Structural analysis offers immense value in a variety of applications ranging from medicinal chemistry to materials science.

Medicinal chemistry

In drug development, it is important to understand the preferred structure of a molecule. Drugs often selectively bind to a receptor site that is complementary to a specific molecular structure. Adjusting the structure of a molecule can have a significant impact on its pharmacological efficacy and specificity.

Biochemical systems

Structural analysis helps to understand the functionality of biochemical molecules such as proteins. Phenotype characteristics of enzymes and proteins often arise from a specific arrangement of their amino acids and the resulting changes in structure.

Polymer chemistry

The physical properties of polymers depend on their conformational properties. Conformational analysis can help design polymers with desired mechanical strengths and elasticities.

Complex molecules: the case of cyclohexane

Larger molecules exhibit more complex conformational behavior. A classic example of this is cyclohexane, C_6H_{12}. Unlike linear molecules, cyclohexane prefers to adopt a contracted ring to reduce strain.

Cyclohexane can exist primarily in two forms: chair and boat. The chair form is more stable and has lower energy because it has less static strain and torsional strain.

Chair structure

In the chair form of cyclohexane, the carbons appear in a bent, zigzag fashion, alternating between two parallel planes. This reduces electron repulsion and strain within the molecule.

Chair structure

Boat structure

The boat shape, while relieving some angular stress, is less preferred because of the static hindrance between the flagpole hydrogen at the bow and stern of the boat. This creates additional static and torsional stress compared to the chair shape.

Boat structure

Understanding the structural preferences of cyclohexane provides insight into its chemistry and impacts the reactivity of its derivatives.

Conclusion

Conformational analysis is an integral part of stereochemistry that enables chemists to understand and predict the spatial arrangement of atoms within a molecule. Its principles are important not only in understanding the stability and reactivity of organic compounds, but also their interactions in biological systems and applications in the physical sciences. Fundamental examples such as ethane and cyclohexane illustrate how slight differences in atom position can have profound effects, guiding further exploration and application.


PHD → 2.2.2


U
username
0%
completed in PHD

← Prev (2.2.1)
Chirality and optical activity
Next (2.2.3) →
Stereoelectronic effects

Comments 



Structural analysis

https://www.chemistryelite.com/phd/2.2.2?ceal=en