ORGANIC CHEMISTRY OF BIOMOLECULES - PHYSICAL METHODS IN ORGANIC CHEMISTRY AND LABORATORY
Learning outcomes of the course unit
The aim of the course is to give an adequate knowledge of
- properties and reactivity of biologically relevant organic molecules:
carbohydrates, amino acids and peptides, lipids, nucleic acids;
- modification of their structure, synthesis of derivatives and mimics;
- their application in different fields of science.
- a thorough knowledge of the most common advanced 1D and 2D NMR techniques for the structural analysis or organic compounds.
- The student will be able to identify autonomously the structure of an
organic compound through the interpretation of several 1D and 2D NMR spectra.
Organic Chemistry 1 and 2
Course contents summary
Chemico-physical properties and reactivity of carbohydrates, amino acid
and peptides, lipids and nucleic acids.
Modification of their structure and synthesis of corresponding oligomers.
Use as raw material for the production of chemicals.
Noncovalent interaction with molecular and macromolecular species.
Magnetic properties of nuclei: angular momentum and spin angular
momentum. The Vector model. Fundamental concepts of 2D NMR
spectroscopy. Relaxation processes. The Chemical exchange. The
modern NMR spectrometer. Interpretation of 1D e 2D NMR spectra and
determination of the structure of an organic compound.
Laboratory: Synthesis of an organic compound and its structural
characterization through advanced NMR techniques.
Why to synthesize a peptide. Structure and properties of amino acids and peptides. Nitrogen protecting groups: insertion and removal. Possible secondary reactions. Protecting groups of carboxylic and hydroxyl groups. Methods for activation and coupling. Possible racemisation phenomena and mechanisms. Methods of solid phase synthesis. Resins and cleavage conditions.
Carbohydrates. Role of carbohydrates in non metabolic biological processes. Structure, properties, nomenclature. Anomeric effect. Oxidation and reduction reactions. Glycosylation reactions: concept of glycosyl donor and glycosyl acceptor, promoters, protecting groups. Enzymatic synthesis of glycosidic bond. Oligosaccharide and glycoconjugates synthesis on solid phase.
Synthesis of glycosidic clusters and concept of multivalency and glycoside cluster effect. Carbohydrates as renewable raw material for fine chemicals. Nucleic acids Structure and properties. Synthesis. Modified nucleic acids and mimics.
Antigene and antisense strategies. DNA and RNA binders. Nucleic acids as smart material for nanotechnology
Lipids Structure and properties. Autooxidation reactions. Synthesis of complex lipids: some examples. Self-assembly of lipids: double layers, lamellar phases, vesicles, liposomes. Delivery applications. Determination of size and zeta potential by DLS. Investigation through AFM and TEM
Magnetic properties of nuclei: angular momentum and spin angular momentum. Microscopic magnetism. Correlation between magnetism and spin angular momentum.
- NMR Frequencies and Chemical shift. Linewidth and lineshape. Scalar coupling. The basic NMR experiment.
- Energy levels and NMR spectra. The spectrum for one spin. The energy levels for two coupled spins.
- The Vector model. The bulk magnetization. Larmor precession. Detection. Pulses. "On resonance" pulses. The rotating frame. The basic impulse-acquisition sequence. Calibration of pulses. The Spin-Echo experiment. Pulses of various phase. "Off-resonance" effetcs and "soft" pulses. Fourier Transformation and data processing. FID representation.
Peaks linewidth and lineshape. FID manipulation. Zero filling.
- The "Product Operators" formalism. Product operators for one spin. Hamiltonians for spins and delays. Equation of motion. The spin-echo experiments with the product operators formalism. Product operators for two weakly coupled spins.
- Fundamental concepts of 2D NMR spectroscopy. 2D NMR experiments with coherence transfer mediated by J-coupling. COSY and DQF-COSY: pulses sequence and spectra interpretation. Double Quantum NMR Spectroscopy. Heterocorrelated 2D NMR spectroscopy. HMQC, HSQC and HMBC experiments: pulses sequence and spectra interpretation. 2D
TOCSY NMR experiment: pulses sequence and spectra interpretation.
- Relaxation and Nuclear Overhauser Effect (NOE). The origin of the nuclear relaxation phenomenon. Mechanisms of relaxation. Correlation time. Population of the states. Longitudinal relaxation of isolated spins. Dipolar longitudinal relaxation of two spins. Cross-relaxation. Relaxation due to chemical shift anisotropy.
- NOEDif, NOESY and ROESY experiments: pulses sequence and spectra interpretation
- Coherence selection: phase cycling cycle and field gradient pulses.
- The modern NMR spectrometer. Magnet and Probe, Lock Channel, Shim and homogeneity of the magnetic field. RF synthesizer, amplifier and duplexer. Receiver and Quadrature detection. Analogue to digital
convertor (ADC). Limits of digitization.
- 1D NMR spectra acquisition and processing (1H and 13C).
Peptidi e Peptidomimetici, V. Santagada, G. Caliendo, Piccin Nuova
- The Sugar Code. Fundamentals of Glycosciences, Hans-Joachim Gabius
Ed., 2009 Wiley -VCH Verlag, Weinheim
- Carbohydrates in Chemistry and Biology, B. Ernst, G. W. Hart, P. Sinay
Eds., Vol. 1-4, 2000 Wiley -VCH Verlag, Weinheim
- Carbohydrates as Organic Raw Materials, Frieder W. Lichtenthaler Ed.,
VCH Weinheim, 1991
- Introduction to Glycobiology, M. E. Taylor, K. Drickamer Eds., 2006
Oxford University Press
- Bioorganic Chemistry - Carbohydrates, S. M. Hecht, Ed., 1999 Oxford
- The Molecular and Supramolecular Chemistry of Carbohydrates, S.
David Ed., 1997 Oxford University Press
- Bioorganic Chemistry - Nucleic Acids, Sidney M. Hecht, Ed., 1996 Oxford
- Gli Oligonucleotidi Sintetici - Principi e applicazioni, CNR - Progetto
Strategico Nucleotidi Antisenso, UTET Periodici
- DNA Interactions with Polymers and Surfactants, R. S. Dias and B.
Lindman Eds, Wiley Interscience, 2008
- DNA and RNA Binders - From small molecules to drugs, M. Demeunynck,
C. Bailly and W. D. Wilson Eds., Wiley-VCH, 2003
- Articoli di review tratti dalla letteratura sui singoli argomenti
- J. Keeler "Understanding NMR Spectroscopy", 2nd Edition, Wiley, 2010.
- T. D. W. Claridge "High-Resolution NMR Techniques in Organic
Chemistry, 2nd edition, Tetrahedron Organic Chemistry, Vol. 27, Elsevier,
- N. E. Jacobsen "NMR Spectroscopy Explained: Simplified Theory,
Applications and Examples for Organic Chemistry and Structural Biology,
Assessment methods and criteria
Oral examination with exercises on the synthesis of saccharides, peptides
and nucleic acids. The final examination will include a written part in which the candidates
have to assign the structure of a known organic compounds to the
resonances of several 1D and 2D NMR spectra. In the following oral part,
the candidates will be enquired on the theoretical topics discussed during
the first part of the course.