METODI FISICI IN CHIMICA BIOORGANICA

The course aims to provide students with a solid theoretical and practical knowledge in the use of IR, UV-Vis and NMR spectroscopic techniques, with particular attention to the analysis of proteins, polymers and complex materials. Through lectures and laboratory experiences, students will acquire the skills needed to interpret and analyze complex spectra, understanding the structural and functional information that can be obtained from each technique.

During the course, students will learn to use infrared spectroscopy for the study of the secondary structure of proteins and for advanced applications such as the analysis of pharmaceutical materials, microplastics and coatings. UV-Vis spectroscopy will allow to characterize the thermal stability of proteins and to interpret the nature of chromophores in organic compounds, while NMR spectroscopy will be used to investigate the dynamics and structure of macromolecules, including proteins and polymers, through multidimensional experiments.

At the end of the course, students will be able to apply spectroscopic techniques to solve complex problems in the chemical and biochemical fields, developing a critical ability in the interpretation of experimental data and in the recognition of molecular structures. They will also be able to use advanced approaches such as saturation difference NMR spectroscopy to study ligand-protein interactions and the investigation of biochemical mechanisms.

Attendance according to the rules of the CdS in CTF http://www.dsf.unict.it/corsi/lm-13_ctf/regolamento-didattico

IR

IR Spectroscopy Review from the Physical Methods in Organic Chemistry Course.

Infrared spectroscopy of proteins. Absorption of infrared light. Information that can be derived from the infrared spectrum. Infrared spectrometers. Sampling techniques. Time-resolved infrared spectroscopy. The absorption of amino acid side chains. The absorption of the protein backbone. Overview of protein studies. Studying protein function with reaction-induced infrared difference spectroscopy. Interpretation of difference spectra. Reaction-induced infrared difference spectroscopy—selected examples.

Introduction to Infrared (IR) Microscopy-spectroscopy. Analysis of Foreign Materials. Analysis of Paints and Coatings. Evaluation of Rubber Products. Evaluation of Some Physical Properties of Polymers. Component Distribution Analysis of Foods. Applications of IR Microscopy in Pharmaceuticals and Medicine. Analysis of Microplastics.

Lab Experience: Protein secondary structure elucidation using FTIR spectroscopy

Uv-Vis

The Nature of Electronic Excitations. The Origin of UV Band Structure. Principles of Absorption Spectroscopy. Instrumentation. Presentation of Spectra. Solvents. What Is a Chromophore? The Effect of Conjugation. The Effect of Conjugation on Alkenes. The Woodward–Fieser Rules for Dienes. Carbonyl Compounds; Enones. Woodward’s Rules for Enones. a,b-Unsaturated Aldehydes, Acids, and Esters. Aromatic Compounds. Model Compound Studies. Visible Spectra: Color in Compounds. What to Look for in an Ultraviolet Spectrum: A Practical Guide. Pharmaceutical and Bio-Sciences Applications

Lab Experience: Characterization of Protein Thermal Stability Using UV-Vis Spectroscopy

NMR

NMR Spectroscopy Review from the Physical Methods in Organic Chemistry Course.

Relaxation. Spin-Lattice Relaxation of 13C Nuclei (T1). Relaxation Mechanisms. Experimental Determination of T1. Relationships between T1 and Chemical Structure. Influence of Protons in CH, CH2 and CH3 Groups. Influence of Molecular Size. Segmental Mobilities. Anisotropy of the Molecular Mobility. Suppression of the Water Signal. Spin-Spin Relaxation (T2). Relaxation Mechanisms. Experimental Determination of T2 ; the Spin-Echo Experiment. Line-widths of NMR Signals.

One-Dimensional NMR Experiments using Complex Pulse Sequences. Basic Techniques Using Pulse Sequences and Pulsed Field Gradients. The Effect of the Pulse on the Longitudinal Magnetization (Mz). The Effect of the Pulse on the Transverse Magnetization Components (Mx·, My·). The Effect of Pulsed Field Gradients on the Transverse Magnetization. The ]-Modulated Spin-Echo Experiment. The Pulsed Gradient Spin-Echo Experiment. Signal Enhancement by Polarization Transfer. The SPI Experimeny. The INEPT Experiment. The Reverse INEPT Experiment with Proton Detection. The DEPT Experiment. The Selective TOCSY Experiment. The One-Dimensional INADEQUATE Experiment.

The Nuclear Overhauser Effect. Theoretical Background. The Two-Spin System. Enhancement Factors. Multi-Spin Systems. From the One-Dimensional to the Two-Dimensional Experiments, NOESY and ROESY. Experimental Aspects.

Dynamic NMR Spectroscopy (DNMR). Quantitative Calculations. Complete Line-shape Analysis. The Coalescence Temperature Tc and the Corresponding Rate Constant kc. Activation Parameters. The Arrhenius Activation Energy EA. The Free Enthalpy of Activation DG. Estimating the Limits of Error. Rate Constants in Reactions with Intermediate Stages. Intermolecular Exchange Processes. Applications. Rotation about CC Single Bonds. C( sp3)-C( sp3) Bonds. C(sp2 )-C(sp3) Bonds. C(sp2 )-C(sp2) Bonds. Rotation about a Partial Double Bond. Inversion at Nitrogen and Phosphorus Atoms. Ring Inversion. Valence Tautomerism. Keto-Enol Tautomerism. Intermolecular Proton Exchange. Reactions and Equilibration Processes.

Macromolecules. Synthetic Polymers. The Tacticity of Polymers. Polymerization of Dienes. Copolymers. Solid-State NMR Spectroscopy of Polymers. Bio polymers. Peptides and Proteins. Sequence Analysis. The Three-Dimensional Structure of Proteins. Polynucleotides. Oligosaccharides and Polysaccharides.

STD NMR. The STD NMR Experiment. Theoretical Concepts. STD NMR Pulse Sequences. Experimental Considerations. Practical Example. Ligand Screening Practical Example. Ligand Epitope Mapping Practical Example. Determination of the Dissociation Constant (Kd) Practical Example. DEEP-STD NMR Practical Example.

NMR Spectroscopy in Biochemistry and Medicine. Introduction. Elucidating Reaction Pathways in Biochemistry. Syntheses using Singly 13C-Labeled Precursors. Low Levels of 13C Enrichment. High Levels of 13C Enrichment. Syntheses using Doubly 13C-Labeled Precursors. High-Resolution in vivo NMR Spectroscopy. 31P NMR Experiments. 1H and 13C NMR Experiments. Magnetic Resonance Tomography. Basic Principles and Experimental Considerations. Applications. Magnetic Resonance Tomography. Magnetic Resonance Spectroscopy, 1H MRS.

1. Horst Friebolin - Basic One and Two-Dimensional N MR Spectroscopy - Wiley
   
2. G. M. Lampman, D. L. Pavia, G. S. Kriz, And J. R. Vyvyan - Introduction to Spectroscopy Fifth edition - CENGAGE Learning.