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 → Physical Chemistry ↓


Spectroscopy and molecular structure


Introduction

Spectroscopy is a scientific technique that uses the interaction of light with matter to study the properties of various substances. It is a major aspect of physical chemistry and helps in understanding the molecular structure and dynamics of molecules. The basic idea behind spectroscopy is based on the absorption, emission or scattering of electromagnetic radiation by atoms or molecules.

Fundamentals of spectroscopy

Spectroscopy is based on the principle that atoms and molecules can absorb or emit electromagnetic radiation of specific wavelengths. These interactions depend on the energy levels of the electrons within the atoms. When atoms or molecules absorb light, the electrons are excited from a lower energy level to a higher energy level. Conversely, when they emit light, they move from a higher energy level to a lower energy level.

Electromagnetic radiation

To understand the concept of spectroscopy it is important to understand electromagnetic radiation. Electromagnetic radiation consists of waves, which are characterized by their wavelength, frequency and energy. The relationship between these properties can be described by the following equations:

c = λν

where c is the speed of light, λ is the wavelength, and ν is the frequency.

The energy of radiation is given by:

E = hν

where h is the Planck constant.

Energy levels in atoms and molecules

In both atoms and molecules, energy levels are quantized, meaning they are limited to certain discrete values. These energy levels are obtained from solutions of Schrödinger's equation and determine how atoms and molecules interact with electromagnetic radiation.

Types of spectroscopy

Infrared (IR) spectroscopy

Infrared spectroscopy deals with the infrared region of the electromagnetic spectrum (wavelengths longer than visible light but shorter than microwaves). It provides information about the vibrations of atoms in a molecule, and therefore, can be used to identify functional groups within a molecule.

Consider a simple diatomic molecule (AB). This molecule has vibration modes that can be described as follows:

AB <==> AB (vibrating bond)

In the IR spectrum, vibrational modes are observed based on the absorption of infrared light.

Ultraviolet-visible (UV-Vis) spectroscopy

UV-Vis spectroscopy involves the absorption of ultraviolet or visible light by electrons in a molecule, which causes electronic transitions between different energy levels. This type of spectroscopy is particularly useful for studying conjugated systems and electronic transitions in metals and complexes.

Example: The UV-Vis spectrum of benzene shows absorption bands due to π → π* transitions of its conjugated pi-electron system.

Nuclear magnetic resonance (NMR) spectroscopy

NMR spectroscopy is a powerful tool for elucidating the structure of organic compounds. It is based on the interaction of atomic nuclei with external magnetic fields and radiofrequency radiation. The most common nuclei studied in NMR are 1H and 13C.

Example: The 1H NMR spectrum provides information about the number and environment of hydrogen atoms, such as chemical shifts, splitting patterns, and coupling constants.

Mass spectrometry

Although not a form of spectroscopy in the traditional sense, mass spectrometry is often used in conjunction with spectroscopic techniques. This involves ionizing chemical compounds to produce charged molecules and measuring their mass-to-charge ratio. This information helps determine the molecular weight and structure of a compound.

Molecular structure determination

Spectroscopy is integral in determining molecular structures. Each type of spectroscopy provides different pieces of the puzzle, helping scientists infer the complete structure of a molecule. Let's look at how these techniques help identify and confirm molecular structures.

IR spectroscopy and functional groups

IR spectroscopy is particularly effective for identifying functional groups within a molecule. Each functional group has a specific absorption range:

  • Alcohols (OH stretch): 3200-3600 cm -1
  • Carbonyl (C=O stretch): 1700-1750 cm -1
  • Alkenes (C=C stretching): 1600-1680 cm -1

NMR spectroscopy and structural elucidation

NMR spectroscopy provides extensive information about the local environment of a nucleus (e.g., H +, 13C). Chemical shifts indicate the electronic environment, while multiplicity gives information about the number of neighboring atoms. Pairing patterns define the spatial alignment of atoms within a molecule.

UV-Vis spectroscopy and conjugated systems

UV-Vis spectroscopy is optimal for investigating conjugated systems such as aromatics. By examining the wavelength and intensity of the absorption bands, one can estimate the extent of conjugation and electron transitions in the compound.

Complementary techniques: mass spectrometry

Mass spectrometry provides molecular mass information, which complements spectral data obtained from other techniques. Fragmentation patterns within the mass spectrum help elucidate structure by revealing how a molecule breaks down into its components.

Visualization of spectra

Absorption bands

The above view shows a hypothetical absorption band in the IR spectrum. This band corresponds to a particular vibration mode of a functional group in the sample molecule.

Applications in research and industry

Spectroscopy is not limited to academic research but also extends to diverse industrial applications such as pharmaceuticals for drug characterization, environmental monitoring for pollutant detection, and materials science for structure analysis.

Advancements and future directions

Recent advances in spectroscopy have allowed for increased sensitivity and precision. Techniques such as time-resolved or ultrafast spectroscopy enable scientists to study molecular dynamics and reactions in real time. Additionally, the integration of machine learning and AI into spectral analysis promises to revolutionize the way spectroscopic data is interpreted.

Conclusion

Spectroscopy is an important tool in the field of chemistry and beyond. Its ability to reveal molecular structure and dynamics has paved the way for many scientific advances. As the technique develops, spectroscopy will continue to expand its scope, providing deeper insights into the molecular world.


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Spectroscopy and molecular structure

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