Structural Analysis


The student should acquire a deep formation on structural analysis of organic compounds, based on UV/Vis, IV, MS and NMR spectral techniques. In the case of NMR, besides the practical aspects on structural analysis, advanced theoretical knowledge shall be transmitted, enabling the student to process 1D and 2D NMR spectra.

General characterization





Responsible teacher

António Gil de Oliveira Santos, Eurico José da Silva Cabrita


Weekly - 4

Total - 63

Teaching language



General knowledge of quantum chemistry, physical chemistry and spectroscopy and organic chemistry.


1. R. M. Silverstein, F. X. Webster, D. J. Kiemle, Spectrometric Identification of Organic Compounds, John Wiley & Sons, Inc.

2. E. De Hoffmann, J. Charette, V. Stroobant , Mass Spectrometry,  Principles and Applications, John Wiley & Sons.

3. T. D. W. Claridge, High-Resolution NMR Techniques in Organic Chemistry, Pergamon (Tetrahedron Organic Chemistry Series, Volume 19).

4. D. A. Skoog, F. James. Holler, T. A. Nieman, Principles of Instrumental Analysis, Saunders College Publishing.

5. E. Pretsch, P. Bühlmann, C. Affolter, R. Martinez, Determinación Estructural de Compuestos Orgánicos, Springer-Verlag Iberica, 2001

Teaching method

Classes use modern multimedia techniques, including 3D animation. Students have access to all necessary equipment, as spectrometers and desktop computers with software for spectral processing and 3D modelling and visualization.

Evaluation method

Overall assessment of the course:

Throughout the semester, students complete three (2) mandatory partial tests with different weigh for the final score: 1st Test (40%) and 2nd Test (60%). The grade (final score) will be the weighted average of the partial test scores summed with the grade correction obtained through class attendance (see bellow, Frequency). Only students who obtain at least 9.50 in the final score will be approved.

Frequency (Exclusion from final examination):

Student attendance to the classes will be accounted to the final score in accordance with the document "Faltas.pdf", available in "Documentação de Apoio/Outros". This system is applicable to all students, independent of the number of inscriptions in the UC. If the penalty due to the student attendance is higher than 10.50 valores (see  document "Faltas.pdf"), the student will be excluded from final examination.

"RECURSO" Examination:

Students with a final score below 9.50 will have access to the exam - Recurso.  This examination will consider all the course syllabus. For these students, the final score will be the sum of the examination grade and the grade of the attendance (see Frequency above). Only students with a final score equal or higher than 9.50 values will be approved.

Subject matter

Infrared spectroscopy. Revision of important theoretical concepts. Spectra interpretation. Characteristic group absorption of organic compounds.

Mass spectrometry. Instrumentation. Ionization and fragmentation. Fragmentation mechanisms. Structure elucidation.

Nuclear magnetic resonance. General theoretical concepts and experimental applications.

Structure elucidation based on UV/Vis, IV, MS and NMR spectra.

NMR of heteroatoms.

Advanced theoretical concepts in uni-dimensional NMR. Presentation of some common pulse sequences. Spectral simulation.

Introduction to bi-dimensional NMR techniques. COSY, NOESY, HMQC. HMBC.

Detailed program

1. Review of general concepts in spectroscopy Ultraviolet / Visible.

2. Review of general concepts in infrared spectroscopy.

3. Introduction to mass spectrometry.



Mass spectra.

Spectra of high and low resolution.

Exact masses.

Molecular ionization and cleavage.

Functional groups.

Fragmentation mechanisms.

Degradations: simple and complex degradations.

4. Nuclear Magnetic Resonance.

4.1 Chemical and physical aspects.

Active nuclei in NMR.

NMR energy transitions.

         Chemical shift
 in 1H NMR.

Chemical shift in 13C NMR.

References for chemical shift.

D scale of chemical shift.

Intensity of signals in NMR.

Spin coupling in 1H and 13C NMR.

Spin systems.

Analysis of  first order spectra

Second order spectra.

Spin decoupling.



Nuclear Overhauser effect (NOE).

Structural analysis on the basis of coupling constants.

4.2 Theoretical aspects of nuclear magnetic resonance.


Larmor frequency.

Coherence of spin.


Radio frequency pulses.

Obtaining the FID.

Fourier transform.



Acquisition time.

Digital resolution and actual resolution.

Quadrature detection.

Phase Cycle.

Spin decoupling.

Experiments using multiple pulses.

4.3 instrumental aspects of nuclear magnetic resonance.

Continuous waves spectrometers

Fourier transform spectrometers



Accumulation of transients.

Signal to noise ratio.

4.4 NMR spectroscopy in two dimensions.

Analysis heteronuclear correlation spectra. HMQC, HMBC.

Homonuclear correlation spectroscopy. COSY.

Contacts through space. NOESY.