PHYSICAL METHODS IN ORGANIC CHEMISTRY

The course aims to provide students with the theoretical and practical bases to interpret the IR, NMR and Mass spectra of organic compounds. The course provides all the necessary tools for the interpretation of spectra and the recognition of unknown organic structures. During the lessons, the student acquires the skills necessary for the recognition of organic functions, the quantification of the atoms present in an organic molecule and the connectivity between them. The student becomes able to apply spectroscopy to the recognition of compounds of organic nature with development of critical ability in spectroscopic analysis.

Three modules: infrared spectroscopy, mass spectrometry and nuclear magnetic resonance spectroscopy.

IR spectroscopy

The electromagnetic radiation. Fundamental characteristics of electromagnetic radiation. Infrared (IR) radiation. The IR spectrum. IR absorption. The wave number. Transmittance (T) and Absorbance (A). Molecular vibrations. The degrees of freedom. Theoretical number of fundamental vibrations. Hooke's law. IR absorption regions in accordance with Hooke's law. C-H stretching calculation. Coupled interactions. Fermi resonance and overtone. Hydrogen bond in IR. The instrumentation. Fourier transform. Dispersion spectrophotometer and Fourier transform (FTIR). Sample preparation. Reflectance methods - Attenuated total reflectance (ATR). IR measurement (FT-IR). IR measurement (ATR FT-IR). Interpretation of spectra. IR of chemical classes: Linear Alkanes, Alkanes with branched chains, Cyclic Alkanes, Alkenes, Linear non-conjugated Alkenes, Cyclic and cumulative Alkenes, Conjugated Alkenes, Alkynes, Aromatic hydrocarbons, Alcohols and phenols, Ketones, Conjugated ketones, b-diketones, cyclic ketones, aldehydes, carboxylic acids, esters and lactones, amides and lactams, amines. Quantitative IR spectroscopy. Raman spectroscopy. Stokes and anti-Stokes lines. Raman spectroscopy - Selection rules. Raman spectroscopy - applications. IR spectra report.

Mass spectrometry

Characteristics of a typical mass spectrometer. High vs. low resolution. Methods of ionization. Electronic impact (EI), Chemical ionization (CI). Ionization methods by desorption: Ionization by bombardment with fast atoms, Ionization by laser desorption (MALDI). Desorption vs. EI-CI. Evaporative Ionization Methods: Thermospray Mass Spectrometry, Electrospray Mass Spectrometry (ESI or ES). ES and EI mass spectra of lactose. ES mass spectra of the VGSE peptide. Mass Analyzers. Mass analyzers: magnetic sector, Mass analyzers: time-of-flight (TOF), Mass analyzers: quadrupole (QMF), Mass analyzers: ion trap (3D QIT). MS-MS mass tandem. HPLC-DAD-APCI-MS / MS. Detectors: Destructive Detector. Recognition of the molecular ion peak. Common fragmentations. Nitrogen rule. Low resolution molecular ion. Isotopic peaks and exact masses. High resolution molecular ion. Hydrogen deficiency index. Main fragmentation reactions of organic compounds. a cleavage. Relative abundance of ionic fragments generated by a cleavage. Benzyl and allyl cleavage. Splitting of "not activated" bonds. Retro Diels-Alder reaction (RDA). McLafferty transposition. Onio reaction. Elimination of CO. Mass spectra of some chemical classes: Hydrocarbons, Alcohols, Ethers, Ketones, Aldehydes, Carboxylic acids, Esters, Amines, Nitriles, Nitro compounds, Sulfur compounds, Halogenated compounds. Halogenated Compounds - Simulated profile of M, M + 2, M + 4, Isotopic peaks. Elementary composition: binomial approach. Elementary composition: grid approach. Calculate the isotope pattern for molecules such as: Cl₂Br, Br₂, SBr₂, SiClBr, Cl₃ etc. Mass spectra report.

NMR spectroscopy

Magnetic properties of nuclei. Quantum number of spins. Excitation of nuclei with spin ½. Larmor frequency. Magnetization vector. Longitudinal spin relaxation. Transverse spin relaxation. Instrumentation. Choice of solvent and sample preparation. Sensitivity of NMR experiments. Chemical shift and spin-spin coupling. Shielded and unshielded protons. Tetramethylsilane (TMS) as a reference compound. Chemical shift. Electronegativity and Chemical shift. Diamagnetic anisotropy. Acetylene. Acetaldehyde alkenes. and aromatic compounds. Electronic effects and chemical shifting: a, b-unsaturated ketones, substituted vinyl ether, aniline, nitrobenzene. General regions of proton chemical shifts in organic molecules. Spin coupling. Rule of n + 1 (2nI + 1). Pascal's triangle. Spin coupling - ethyl cleavage model. Spin coupling - the coupling constant. Relationship between the Chemical shift and the spin coupling constant. first order multiplet. First order complex multiplet. Loosely coupled system. Strongly coupled system. One-bond coupling (¹J). Geminal couplings (²J). H-C-H angle in geminal coupling. Spin coupling - ³J. Bond angle and ³J. Karplus relationship. Long-range couplings. ⁴J allyl coupling. ⁴J propargyl coupling. ⁴J homoalllic coupling. ⁴J homopropargyl coupling. ⁴J coupling W. Pople's notation, chemically equivalent protons. Magnetically equivalent protons. Homotypic protons. Enantiotopic protons. Diastereotopic protons. Diastereotopic hydrogens: ethyl 3-hydroxybutanoate. Protons on heteroatoms. Exchangeable protons. Coupling of protons with ¹⁹F. Coupling of protons with D (²H). Coupling of protons with ³¹P and ²⁹S. Coupling of protons with ¹³C. ¹H NMR of some chemical classes: Alkanes, Alkenes, Aromatic compounds, Alkynes, Alkyl halides, Alcohols, Ethers, Amines, Nitriles, Aldehydes, Ketones, Esters, Carboxylic acids, Amides, Nitroalkanes. Selective spin decoupling: double resonance. Nuclear overhauser effect (NOE). Cross-polarization: origin of the NOE. NOE for difference (NOE difference). NOESY (Nuclear Overhauser Enhancement SpectroscopY). Report of ¹H and ¹³C NMR spectra. ¹³C NMR Aspects that differ from ¹H NMR, ¹H decoupling techniques. Comparison between the ¹H and ¹³C NMR chemical displacement scales. T₁ relaxation. “Inversion-recovery” method for T₁ measurement. NOE and spin coupling ¹³C-¹H. Controlled proton decoupling. Values of ¹J-CH coupling constants. Values of ²J-CH coupling constants. Coupling constants with other nuclei: ¹⁹F, ³¹P and D. Solvents in ¹³C NMR. ¹³C quantitative NMR. Reverse controlled proton decoupling. Chemical equivalence for ¹³C NMR. ¹³C not equivalent. Monosubstituted aromatic rings. Disubstituted aromatic rings. ATP and DEPT. The magnetization vector M during the ATP experiment in methine, methylene, methyl and quaternary carbons. DEPT 90 and DEPT 135 interpretation. ¹³C chemical shifts for main classes of organic compounds. Additive shift parameters in linear and branched aliphatic hydrocarbons, alkenes and aromatic compounds. 2D NMR spectroscopy: COSY, HETCOR, HSQC, HMBC, TOCSY, NOESY, ROESY, INADEGUATE.

1. R. M. Silverstein, F. x. Webster, D. J. Kiemle- Identificazione Spettrometrica di Composti Organici Terza edizione - Casa Editrice Ambrosiana.
2. G. M. Lampman, D. L. Pavia, G. S. Kriz, And J. R. Vyvyan - Introduction to Spectroscopy Fifth edition- CENGAGE Learning.
3. M. Hesse, H. Meier, B. Zeeh - Metodi Spettroscopici nella Chimica Organica Seconda edizione – EdiSES.
4. A. Randazzo - Guide to NMR Spectral Interpretation - Loghia.