Methods of Structural Analysis

Code:

Q2013

Acronym:

Q2013

Level:

200

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2016/2017 - 2S

Active?	Yes
Web Page:	https://moodle.up.pt/course/view.php?id=2354
Responsible unit:	Department of Chemistry and Biochemistry
Course/CS Responsible:	Bachelor in Chemistry

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
L:BQ	2	Official Study Plan	3	-	6	56	162
L:Q	50	study plan from 2016/17	2	-	6	56	162
			3

Teaching language

Suitable for English-speaking students

Objectives

The aim of this course is to provide the theoretical and practical skills necessary to use spectroscopic techniques to study the chemical structure of molecular compounds.

Learning outcomes and competences

After completing this course, the students should:

• Know how to interpret changes in ultraviolet-visible spectra, identifying the type of electronic transition responsible. Know how to apply Woodward-Fieser and Fieser-Kuhn rules to estimate the wavelength of maximum absorption of organic compounds. To know to predict the effect of substituents in UV/vis spectra.
• Know how to interpret FTIR spectra of small molecules, based on the identification of typical vibration frequencies for specific groups. Identify the spectral regions corresponding to functional groups and fingerprint. Know how to interpret and predict the effect of substituents, hydrogen bonding, etc. in the typical frequencies of functional groups.
• Know how to obtain structural information from 1H NMR spectra of small molecules, by analyses of chemical shift and coupling pattern. Identify chemically equivalent atoms in a molecular structure and predict the 1H NMR spectrum based on that structure. Know how to interpret 13C NMR spectra of small molecules, including DEPT. Know how to interpret "D NMR spectra of COSY and HETCOR.
• Know how to obtain structural information using mass spectrometry, including recognising typical fragmentation patterns.
• Know how to use fluorescence to obtain information on location and molecular environment, using techniques of fluorescence quenching, half-life, quantum yield, anisotropy and resonance energy transfer measurements.

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

The students should have attended, and preferably completed successfully, the following courses  Química I, Química II, Laboratório de Química I, Laboratório de Química II, Tratamento de Resultados em Química, Química Orgânica, Laboratório de Química Orgânica, Química Inorgânica e Laboratório de Química Inorgânica, or equivalent units.

Program

1. Ultraviolet-visible spectroscopy

Interaction between matter and light; absorption bands; relaxation mechanisms; atomic and molecular spectra. Spectrophotometers and how to measure UV/vis spectra. Lambert-Beer law and limitations. Energy levels of molecules; Franck-Condon principle; Intensity of absorption bands and selection rules. Energy diagrams of molecular orbitals to interpret electronic spectra; types of transitions in organic compounds; bathochromic and hypsochromic shift; hyperchromic and hypochromic shift; effect of multiple chromophores; effect of conjugation of double bonds; effect of substituents; application of  Woodward-Fieser and Fieser-Kuhn rules; effect of solvent and pH; spectra of complexes of transition metals; types of transitions and intensity; how to obtain information about metal complexes from UV/vis spectra.

 

1. Infrared spectroscopy

 

Introduction. Mechanism and absorption modes. Relation between bonding properties and absorption. Factors that determine the intensity and position of absorption bands. Fourier transform. Instrumentation. Sample preparation. Detection of functional groups. Structural analysis and identification, Applications and interpretation of spectra.

 

1. Nuclear Magnetic Resonance (NMR).

 Introduction. Spectroscopic transitions and electromagnetic spectrum. Nuclear spin and nuclear magnetic moment. Mechanism of energy absorption (resonance). Population of nuclear spin states. Energy gap between nuclear spin states: interdependence of magnetic field and resonance frequency. Active nuclei in NMR. Chemical shift. Magnetic anisotropy. Magnetic equivalence. Effects of substituents on protection/deprotection. Spin-spin coupling. Coupling constant. Integration. Instrumentation and sample preparation. Deuterated solvents and solvent effect. 1st order spectra and 2nd order spectra. Typical chemical shifts in 1H NMR. 13C NMR spectra. Characteristic chemical shifts. Carbon-hydrogen coupling. Decoupled 13C spectra. Off-resonance decoupling. Factors that affect the chemical shift. DEPT sequences. Unidimensional (1D) and bidimensional (2D) spectra. Applications and interpretation of spectra.

• Mass spectrometry

Introduction. Ionization methods. Mass analysers and detectors. Instrumentation. Ion analysis. Isotopic abundance. Molecular ion, base ion and isotopic patterns. Electronic impact mass spectrometry and chemical ionization. Types of characteristic fragmentation and structural analysis. Molecular weight and molecular formula determination. Applications and interpretation of spectra.

 

1. Fluorescence spectroscopy

Jablonski diagram; singlet and triplet states; Stokes shift; Half-life and quantum yield. Relation between fluorescence intensity and concentration of fluorophore. Fluorescence quenching and Stern-Volmer equation. Fluorescence anisotropy. Resonance energy transfer. Time-resolved fluorescence. Applications.

Mandatory literature

Silverstein, Robert M.; Spectrometric identification of organic compounds. ISBN: 0-471-09070-0
Pavia, Donald L.; Introduction to spectroscopy. ISBN: 0-7216-7119-5

Teaching methods and learning activities

In the theoretical classes the main principles of each technique are presented and discussed, using experimental examples for a better understanding. In the problem solving classes, case studies are discussed relative to the interpretation of experimental data based on spectroscopic techniques. In addition, the students have three lab projects on UV/vis spectroscopy, FTIR and fluorescence spectroscopy.

Software

Jmol
ChemDraw
Excel

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Exame	80,00
Trabalho laboratorial	20,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Elaboração de relatório/dissertação/tese	6,00
Frequência das aulas	50,00
Trabalho laboratorial	6,00
Total:	62,00

Eligibility for exams

Have a positive grade in at least 2 out of the 3 laboratory projects, including report.

Calculation formula of final grade

Evaluation involves two componentes: one exam and the grade corresponding to the lab classes. The final grade is calculated as:

Final grade = 0,80 x exam grade + 0,20 lab grade

Students may choose to do the exam of the "época normal" in two parts, the first one during the semester, and the second in the day of the exam.

Examinations or Special Assignments

N.A.

Internship work/project

N.A.

Special assessment (TE, DA, ...)

Students that prove that cannot attend the lab classes should do a final laboratory exam.

Classification improvement

The students may try to improve their final evaluation by repeating the final exam, within 1 year of having successfully completed the course.  The laboratory evaluation cannot be repeated.