Molecular and supramolecular chemistry

Lecturer(s): Christelle YEROMONAHOS, Naoufel HADDOUR
Course ⋅ 12 hTC ⋅ 18 hAutonomy ⋅ 18 h


Metabolites are low molecular weigth species, present in blood, among an abundant background of high molecular weight species. Metabolites are the biomarkers of a large range of pathologies. However their detection, for clinical use, is still a global challenge. Chemical functionalization of porous silicon surfaces, by using specific molecules, could allow the selective trapping of metabolites. Such a trapping could allow to improve the sensitivity of the detection tools, classically used in hospitals (mass spectrometry). Objectives of this course is to study the effects of the physico-chemical properties of molecules (structure, hydrophile-liphophile balance, charges) on the intermolecular interactions. A large part of the course will be based on the use of a molecular simulations software (HyperChem). In order to illustrate the concepts covered, the course is based on the diagnosis of sepsis and the research work carried out in the Chemistry and Nanobiotechnologies team at INL and in Bioelectrochemistry group of Ampère Lab.


Intermolecular interactions, Molecular Dynamics simulations, innovative clinical diagnostic tools


This course will be presented in the form of a case study.

First, the physicochemical properties of single molecules will be presented (structure, hydrophilic hydrophobic balance, charges). Secondly, the physicochemical properties of supramolecular structures will be analyzed from the properties of the single molecules that constitute them by molecular modeling (energy of interactions...). The results of this analysis will be used to design a biomedical analysis tool.

This course is based on the concepts presented in the UE "Physics-Chemistry of Matter". A significant portion of the teaching will be based on the molecular modeling software HyperChem.


  • Presentation of the field of research and work in progress at the INL laboratory.
  • Presentation of high performance computing tools required in this field. Presentation of the resources available at Ecole Centrale Lyon.
  • Training on the modeling tools used in this course:
    • Energy minimization by molecular mechanics methods and applications to the molecules studied.
    • Energy minimization by quantum mechanical methods and applications to the molecules studied.
  • Analysis of the properties of single molecules.
  • Modeling of intermolecular interactions
  • Analysis of experimental data and comparison with modeling results
  • Design of electrochemical and photoelectrochemical biosensors from polymers.

Learning Outcomes

  • C2N1: Define a system and its boundaries, identifie the phenomena involved and propose a simple model. Formulate the hypotheses.
  • C2N3: Characterize the complexity of a system, identifie interactions and sources of uncertainty.
  • C1I1: Carrie out a state of the art and implement creative methods, on a problem open to technical-scientific-economic questions, and formalize the result.


Score = 50% knowledge + 50% know-how Knowledge score = 50% final exam + 50% continuous assessment Know-how score = = 50% final exam + 50% continuous assessment