M1 Chemistry - International Track - ERASMUS Mundus

none

Content

French courses: Developing the four language skills in order to be able to communicate with the French: oral and written understanding and oral and written expressions; practical aspects of language in the multimedia room semi self-guided.

Aims

Language Course: The student will acquire the basic knowledge in the national language and a glimpse at national culture and heritage of the hosting country.

Elementary Linear Algebra, and Undergraduate Physical Chemistry

Content

Chapter 1: Fundamental concepts

• Domain of quantum mechanics : “microscopic word”
• Properties of electromagnetic waves
• Wave-particle duality : de Broglie’s wave for a free particle
• Double slit experiment
• Wave function,
• Time dependent and time independent Schrödinger equations
• Superposition of states
• Postulates of quantum mechanics

Chapter 2: Quantization

• Quantization in an infinite well (1D, 2D and 3D)
• Tunnelling effects
• Finite 1D well
• Double well

Chapter 3: Molecular vibrations

• Born-Oppenheimer approximation
• Separation of the center of mass in a two-body problem
• Harmonic oscillators
• Vibration of a diatomic molecules
• Vibrational normal modes
• Franck-Condon principle

Chapter 4: Rotations and Hydrogenic atoms

• Particle on a sphere
• Rigid diatomic rotor
• Angular

Chapter 5: Electronic structure of molecules and nanoparticles

• Molecular Hamiltonian
• Born-Oppenheimer approximation
• Linear combination of atomic orbitals
• Orthogonal and nonorthogonal basis sets, minimal basis set
• Molecule orbitals : sigma/pi, overlap
• Molecular orbital energies, Koopman theorem
• HOMO-LUMO gap
• Mulliken charge, ionisation energy, electronegativity, electron affinity
• Molecular Orbital diagram, Walsh correlation diagram
• Extended Hückel Theory
• Introduction to Tight-Binding Density Functional Theory

Aims

The course introduces the fundamentals of quantum mechanics and applies the timedependent and time independent Schrödinger equations to analytically solvable systems. The free electron confined in a box potential, the hydrogen atom, the rotational and vibrational motions of diatomic molecules are treated in detail. Important concepts related to electronic structure are introduced. Approximate methods such as extended Hückel theory and tight-binding density functional theory are applied to study the structure and reactivity of molecules and nanoparticles.

Theoretical courses, tutorials and practicals.

Atomistics.
Knowledge on the fundamental reactions on the following topics:
Alkanes, Alkenes, Alkynes and aromatics, Haloganated compounds, alcohols, aldehydes and ketones

Content

• Part I: inorganic chemistry: Definition of metal complexes, d orbitals description, crystal field theory, Molecular orbitals theory,  Angular Overlap Model. Important  parameters affecting the d block. Basics on reactivity.
• Part II: organic chemistry: Structure and reactivity of aromatic compounds, Reactivities of carbonyls, carboxyls, amines and phosphorus compounds.

Aims

Transition metal complexes are at the heart of all biological processes that support life and are crucial in the development of new technologies for a sustainable world. Research in this field spans from synthesis, spectroscopic characterization, electronic description, surface science, electrochemical and photochemical processes. This course aims at providing the students with a solid basis in coordination chemistry and related areas with the defining goals to address energetic and environmental challenges facing our societies.

Theoretical courses, tutorials and practicals.

Recommended Books

• Keynotes in Organic Chemistry, 2nd Edition, Andrew F. Parsons, 2013, ISBN: 978-1-119-99914-0 (http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1119999146.html)
• Organic Chemistry Demystified, Daniel R. Bloch, 2006 (http://www.goodreads.com/book/show/749253.Organic_Chemistry_Demystified
• An Introduction to inorganic chemistry / Keith F. Purcell, John C. Kotz, Philadelphia : Saunders College

Fundamentals of Kinetics (reaction order, rate constant, Arrhenius law,…)
Solution Chemistry (acid-base, redox, precipitation, complexation,…)
Basics of Chemical Thermodynamics (enthalpy, entropy, Gibbs free energy, equilibrium constant,…)

Reaction kinetics

• Relation between rates and mechanisms of chemical reactions
• Collision theory of reaction rates
• Activated complex theory
• Reactions in solution
• Introduction to photochemistry

- Redox reactions and Electrochemistry

• Fundamentals of electron transfer
• Cyclic and linear sweep voltammetry
• Thermodynamics and kinetics of electron transfer
• Electron transfer in biological systems

Laboratory training

• Laser Induced Fluorescence of I2 gas
• Study of molecules by Flash photolysis method
• Influence of the ionic strength on the solubility of a salt
• Cyclic voltammetry of a reversible system
• Mediated redox enzyme electrochemistry

Reaction kinetics in gas and solution: experimental and theoretical approaches. Thermodynamics and kinetics of electron transfers : applications to biological systems

Theoretical courses, tutorials and practicals.

Physical Chemistry, P.W. Atkins, J. De Paula, Ed. Oxford University press
Chemical kinetics and dynamics, J. I. Steinfeld, J. S. Franscisco, W. L. Hase, Ed. Prentice Hall, Englewood Cliffs, New Jersey

None

Biophysics and microscopies for the life sciences

• Optical microscopy: Fluorescence and fluorescent probes for biology, setups for microscopy, super-resolved microscopy techniques, applications to quantitative analysis of molecular behaviors in live cells
• Introduction to Atomic Force Microscopy: Atomic Force Microscopy (AFM): Theory and application of AFM. From cells to single molecule studies (Living cells imaging, DNA imaging, biopolymer elasticity).

This course is an introduction to several concepts of Biophysics organized by a multidisciplinary team composed of physico-chemist, physicists and cell biologists. It will focus on microscopies and their application to biology.

Theoretical courses, tutorials and practicals

Practical courses

• Visualization of cell’s cytoskeleton: The aim of the course is to use the immunofluorescence technique to stain components of the cell (actin filaments, tubulins and microtubules) on fixed cells.
• Bioinformatics: The aim of this course is to learn how to use the PDB website and to visualize protein structures in 3D with VMD.
• Atomic force microscopy: This practical course will teach to student how to use an AFM (imaging and force curve analysis) to study fixed and dried cells (bacteria or eukaryotic cells).
• Spectroscopic analysis of the isomerization of a GFP chromophore: The aim of this practical course is to analyze the molecular events happening in a cyan fluorescent protein upon a pH jump from 7 to 5.
• Data analysis of microscopy data [3h ON, ½ classe] Students will analyze time-resolved recordings of biological parameters. They will use in-situ calibration data to quantify cellular concentrations.

Activities in small groups, research related tutorials and hands-on will help to develop critical faculties of the students.

Basics on quantum mechanics (hamiltonien, states of a system)
Basics on classical mechanics (motion of solid bodies)
Description of a photon (as a particle, as an electromagnetic wave)

This teaching unit deals with 4 of the main standard spectroscopic techniques: Mass spectrometry, IR and UV spectroscopies and NMR. Mass Spectrometry: 
Introduction to Mass spectrometry and instrument components (gas phase ion source and mass analyzers).
Interpretation of electron impact fragmentation mass spectra of organic molecules.
Structural and sequence information obtained from tandem mass spectrometry.
 Optical spectroscopies & Photophysical processes
When molecules and light meet
Electronic transitions – UV-visible and fluorescence
Rovibrational spectroscopy – IR spectroscopy.  NMR: Nuclear Magnetic Resonance (NMR) spectroscopy. Introduction and presentation  of the concepts allowing for molecular structure determination, for composition analysis of mixtures, access to dynamics  selected systems, applications to the life science area, and development on NMR equipment.

To gain an overview on the standard methods of optical spectroscopy (IR, UV-vis, fluo, NMR): associated spectral ranges, probed molecular properties, applications in analytical chemistry.
To understand the fundamental photochemical processes.
To gain knowledge about the chemical analysis of compounds using mass spectrometry

Theoretical courses, tutorials and 4 practicals. Mass spectrometry study on gas-phase protonated peptides 
Fluorimetry: Polyatomic molecules in condensed phase 
Infrared spectroscopy: Rotation vibration spectra of CO and HCl 
Nuclear Magnetic Resonance

Students are asked to participate interactively and prepare the exercises that will be proposed.

Content

One-week winter school organized at the end of the first semester at U.Porto and AMU (rotating locations).

In this school, students will get an introduction to different aspects of computational data science as it can be applied to chemical and material sciences.

Guest researchers from both the academic and non-academic sectors working in the domain of Artificial Intelligence will also present their current research.

Mathematical algorithms for data treatments, computational approaches, and programming methods and tools (i.e.Python, hand machine/deep learning techniques) will be introduced and applied to several problems to solve, such as searching for new molecules, medicines, and materials more eco-friendly and more sustainable, and prediction of properties of complex substances that have yet to be synthesized.

Introduction to sustainable development
Life Cycle Assessment (LCA) - eco-design
Chemical waste management/recycling and the circular economy
Renewable and bio-based chemistry
Environmental regulations/standards in chemistry
Environmental performance assessment/certification

•    Educate yourself on the concepts of sustainable development
•    Identify the major environmental regulatory regimes
•    Highlight the role of chemistry: its contributions, challenges, and potential for action
•    Develop critical thinking on environmental and societal issues

6 video modules in French with English subtitles to watch online, followed by a test to obtain certification in the form of a digital badge.

Identify key sustainable development issues to learn about responsible practices