Learning outcomes

The students are introduced to advanced concepts and methods of theoretical chemistry and finally to computer modeling and simulations, including links with various computer algorithms. A key aspect of the course is to allow students to understand the role of the input parameters necessary for the calculations. Some specific issues that are treated in the course are the determination of molecular and bulk properties, of molecular reactivities, as well as aspects of electron correlation.

Goals

The students are introduced to advanced concepts and methods of theoretical chemistry and finally to computer modeling and simulations, including links with various computer algorithms. A key aspect of the course is to allow students to understand the role of the input parameters necessary for the calculations. Some specific issues that are treated in the course are the determination of molecular and bulk properties, of molecular reactivities, as well as aspects of electron correlation.

Content

Y. Olivier

Part I :

1. Representations of molecular structures

2. Interaction energy and force fields

3. Potential Energy Surface Sampling

a. Monte Carlo

b. Molecular Dynamics

c. Simulated annealing

d. Entropy and free energy

4. "Soft Computing"

a. Genetic algorithms

b. Artificial neural networks

5. "Comparative modelling"

a. Molecular similarity

b. QSAR

c. Molecular alignments

 

B. Champagne

Density functional theory

1. Introduction and densities within wavefunctionapproaches

2. The Thomas-Fermi model

3. The Hohenberg and Kohn theorems

4. The Kohn-Sham approach

  4.A. Kohn-Sham equation

  4.B. XC functionals and their performance for determining geometries, vibrational spectra, optical properties, interaction energies

  4.C. Self-Interaction

  4.D. Conceptual DFT

Time-Dependent Density functional theory

  5.A. TDDFT equations

  5.B. Approximate TDDFT schemes

  5.C. GW and BSE methods

  5.D. Simulating UV/vis absorption and CD spectra

 

Table of contents

Y. Olivier

Part I :

1. Representations of molecular structures

2. Interaction energy and force fields

3. Introduction to geometry optimization methods

Part II :

1. Introduction to statistical mechanics simulations

a. Background theory (reminder)

b. Monte Carlo

c. Molecular Dynamics

d. Simulated annealing

e. Entropy and free energy

2. "Soft Computing"

a. Genetic algorithms

b. Artificial neural networks

3. "Comparative modelling"

a. Molecular similarity

b. QSAR

c. Molecular alignments

 

B. Champagne

Density functional theory

1. Introduction and densities within wavefunctionapproaches

2. The Thomas-Fermi model

3. The Hohenberg and Kohn theorems

4. The Kohn-Sham approach

  4.A. Kohn-Sham equation

  4.B. XC functionals and their performance for determining geometries, vibrational spectra, optical properties, interaction energies

  4.C. Self-Interaction

  4.D. Conceptual DFT

Time-Dependent Density functional theory

  5.A. TDDFT equations

  5.B. Approximate TDDFT schemes

  5.C. GW and BSE methods

  5.D. Simulating UV/vis absorption and CD spectra

 

Assessment method

For the quantum chemistry part, 

1°) 1/3 for an oral presentation (10 minutes, 10 slides Max) at the end of the semester about a critical reading of a scientific publication on DFT/TDDFT

2°) 2/3 for the written exam on the essential aspects of DFT and TDDFT, followed by a oral discussion (Questions will be asked on the methodological DFT and TDDFT aspects).

 

 
 
For the Molecular Modeling part, the evaluation can consist of a written exam, followed by an oral one, covering all chapters.
The evaluation also covers the content of the pratical labs, their presentation, calculations, and the behavior of the student during the labs. Students are not excused from practical lab works when the practical exam grade is < 10/20, and/or the theoretical exam is not presented.
 
 
 

Sources, references and any support material

A. Szabo and N.S. Ostlund, Modern Quantum Chemistry (MacMillan, New York), (1982). R.G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules, (Oxford University Press, Oxford, 1989). R. McWeeny, Methods of Molecular Quantum Mechanics, (Academic, San Diego, 1992). W. Koch and M.C. Holthausen, A Chemist's Guide to Density Functional Theory, (Wiley-VCH, Weinheim, 2001).

A. Leach Molecular Modelling: Principles and Applications 2nd Edition (Pearson Education (US))

 

 

Language of instruction

Anglais
Training Study programme Block Credits Mandatory
Master de spécialisation en nanotechnologie Standard 0 6
Master 120 en sciences chimiques, à finalité spécialisée en chimie en entreprise Standard 0 6
Master 120 en sciences physiques, à finalité spécialisée en physique du vivant Standard 0 6
Master 60 en sciences physiques Standard 0 6
Master 120 en sciences chimiques, à finalité didactique Standard 0 6
Master 60 in Chemistry Standard 0 6
Master 120 en sciences physiques, à finalité spécialisée en physique et data Standard 0 6
Master 60 en sciences chimiques Standard 0 6
Master 120 en sciences physiques, à finalité didactique Standard 0 6
Master 120 en sciences physiques, à finalité approfondie Standard 0 6
Master 120 en sciences chimiques, à finalité approfondie Standard 0 6
Master 120 en sciences physiques, à finalité spécialisée en physique du vivant Standard 1 6
Master 120 en sciences chimiques, à finalité spécialisée en chimie en entreprise Standard 1 6
Master 60 en sciences physiques Standard 1 6
Master 120 en sciences chimiques, à finalité didactique Standard 1 6
Master 120 en sciences physiques, à finalité spécialisée en physique et data Standard 1 6
Master 60 in Chemistry Standard 1 6
Master 60 en sciences chimiques Standard 1 6
Master 120 en sciences physiques, à finalité didactique Standard 1 6
Master 120 en sciences physiques, à finalité approfondie Standard 1 6
Master 120 en sciences chimiques, à finalité approfondie Standard 1 6
Master de spécialisation en nanotechnologie Standard 1 6
Master 120 en sciences physiques, à finalité spécialisée en physique du vivant Standard 2 6
Master 120 en sciences physiques, à finalité spécialisée en physique et data Standard 2 6
Master 120 en sciences physiques, à finalité didactique Standard 2 6
Master 120 en sciences physiques, à finalité approfondie Standard 2 6