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NMR Spectroscopy and Molecular Design

Course code

ΝΜD 102

Type of course


Level of course

Postgraduate (MSc)

Year of study




ECTS credits


Name of lecturer(s)

Prof. J. Matsoukas, Prof. G. Spyroulias, Assoc. Prof. Tsivgoulis, Assoc. Prof. T. Tselios

Learning outcomes

At the end of this course the student should be able to

1.Present the 2D NMR techniques, 1Η-1Η /13C/15Ν, and their importance on identification and conformational analysis of biologically active molecules and to analyze homo & hetero- nuclear 2D NMR spectra.
2.Present methods for exploring the Conformational Space of potential bioactive molecules.
3.Apply methods for exploring the Conformational Space of potential bioactive molecules.
4.Apply Energy Minimization Methods for exploring the Potential Energy Surface.
5.Present and apply principles of Rational Drug Design based on Receptor-Ligand interactions and using NMR constraints.
6.Apply, based on SAR studies, the appropriate functional groups for modification of Peptides to Peptidomimetics.


At the end of the course the student will have further developed the following skills/competences

1.Ability to demonstrate knowledge and understanding of essential facts, concepts, principles and theories related to 2D NMR, 1Η-1Η /13C/15Ν, and Molecular Modeling and to perform assignment of signal resonances in 2D NMR spectra.
2.Ability to apply such knowledge and understanding to the solution of Spectroscopy and Rational Design issues.
3.Ability to adopt and apply different methodologies on Molecular Modelling techniques.
4.NMR and Molecular Modeling skills needed for continuing professional development.
5.Ability to interact with others on inter or multidisciplinary NMR and Molecular modeling problems.


There are no prerequisite courses. It is however recommended that students should have at least a basic knowledge of NMR spectroscopy and Organic Chemistry.

Course contents

1.Principles of NMR and Organology
Fourier Transform (FT) and Continuous Wave (CW) NMR, Organology data, T1 and T2 relaxation time. Inversion Recovery experiment.
2.13C Spectroscopy-Principles
Principles, Chemical Shift 13C, “Spins Echo” method, ΑPT και DEPT techniques, Examples.
3.2D NMR
Principles, Hetero nuclei coupling, Hetero nuclei 1D NMR, 2D spectrum theory, Types of 2D spectrums: COSY, TOCSY, RELAY, COLOC, INADEQUATE, Examples. Analysis of 2D homo- & hetero- nuclear NMR spectra.
4.Nuclear Overhauser Effect (NOE)
Principles, Effect explanation, NOE and nuclei distance, ΝΟΕ and rotation time Tc (Correlation Time).
5.Molecular Modeling
Basic Principles, Molecular Graphics, Conformations of Proteins-Peptides, Molecular Surfaces, Potential Energy Surfaces, Computer Simulation Methods-Molecular Mechanics, Energy Minimization and Related Methods for Exploring the Energy Surface -Examples
6.Methods for Exploring Conformational Space
Monte Carlo method, Molecular Dynamics-Constraint Dynamics methods, Grid Scan method, Boltzmann Jump method, Examples
7.Rational Drug Design based on Receptor-Ligand interactions
Definition of Pharmacophores, Active Site of Receptors, Molecular Docking, Homology Modeling-Validation
8.Rational Drug Design using NOESY and  ROESY constraints.
9.Structure Activity Relationship (SAR) studies in order to identified pharmacophores for the rational design of “mimetics”.
10.Rational design of Peptidomimetics: Principles and Examples

Recommended reading

1.«NMR: Principles and Applications in Medicine, Pharmaceutical Chemistry, Biochemistry, Food Chemistry», I. Matsoukas, T. Mavromoustakos Parisianoss, Athens, 1th Ed., 2005, ISBN: 960-88751-5-3 (A textbook in Greek language).
2.«An Introduction to Medicinal Chemistry» Graham L. Patrick, 3rd Ed., 2005. ISBN: 0-19-927500-9.
3.«Spectrometric Identification of Organic Compounds» Robert M. Silverstein, Francis X. webster, David Kiemle, 7th Ed., 2005, ISBN: 978-0-471-39362-7.
4.«Molecular Modelling Principles and Applications» Andrew R. Leach, 1995, ISBN: 0-582-38210-6.
5.«NMR and Molecular Modelling» Related notes to the Lectures, Assis. Prof. T. Tselios

Teaching and learning methods

Lectures using slides for overhead projector and/or power-point presentations and appropriate software (Molecular Conceptor II). Problem-solving seminars for NMR and Molecular Modeling-Design. Collaborative problem-solving work by the students working in teams of two.

Assessment and grading methods

1.An assay comprising off a presentation of a subject referred to Molecular Modeling and Rational Drug Design (groups of two students, 50% of the final mark)
2.Written examination (50% of the final mark)

Greek grading scale: 1 to 10. Minimum passing grade: 5.

Grades £3 correspond to ECTS grade F.

Grade 4 corresponds to ECTS grade FX.

For the passing grades the following correspondence normally holds:

5 « E, 6 « D, 7 « C, 8 « B and ³9 « A

Language of instruction

Greek. Instruction may be given in English if foreign students attend the course.