Monthly Archives: September 2014

Sunlight functions in life

Lot of events in the body are due to a photochemical reaction according to the nature:

  • The key step in this process is the isomerization of the 11-cis retinal into the 11-trans retinal according to the sunlight. This isomerization actives an ionic  flux which actives receptors in the retina permitting  the process of eyesight.
  • An other function is for the “jaundice infant”. When hemoglobin is gradiented it converts into bilisturine in the liver. However, infants haven’t a mature liver and this bilisturine goes directly in the blood giving this yellow color. This dangerous impact is treated with light. The babies are exposed under light because the irradiation allows the isomerization of the cis bilisturine which is insoluble in trans-bilisturine which is soluble and eliminated by urinary system.
  • Everybody know vitamin D, which have a function about the bone structure.This vitamin comes from the exposure to sunlight. Consequently, lot of people lake of vitamin D in winters or in cold countries.

Molecular Tectonics by Pr Wais Hosseini

Molecular Tectonics : From Tectons Tectons to Networks.

An ensemble of Disordered Inert Construvtion Units (non-informed) and an ensemble of active construction units (informed) Tectons form accordinf to Periodic Patterns a perdiodic Architecture. There are several paramaters:

  1. Low probability in the absence of external intervention
  2. External intervention sequential construction process
  3. Self assembly: a sequential building process

A tecton is a building block and by interactions, they form together the sequential construction process.

As in Dynamic combinatorial chemistry, the building blocks form several different assembly, the best recognition is for the Energy minima of the assembly. For each energy level, there are different thermodynamic energies, consequently, the best assembly is for the lower energy system.

What is Molecular Network

Thanks to Pr Hosseini , ” Molecular networks in the crystalline phase are infinite periodic molecular assemblies formed under self-assembly conditions between self-complementary or complementary tectons. These size architectures may be regarded as hypermolecules formed by supramolecular synthesis based on reversible inter-tectons interactions. Molecular tectonics is based on molecular recongnition, events and their iteration leading to translational symmetry”

It’s concerned with the design and description of periodic architecture called molecular networks

Molecular level deals with individual modules: tectons, recognition and association periodicity.

DFT Calculation

DFT Calculation is a very useful skill to determinate deferent parameters into a molecule:

Molecular structures

Bond lengths are accurate to within 1-2%

Vibrational frequencies

Within 5-10% accuracy

Atomization energies


Desired accuracy for hybrid functionals

Ionization and affinity energies

Average error around 0.2 eV for hybrid functionals

But, we have to take into account the limitations of DFT :

The Band gap is a problem, and an overbidding (LSDA calculations usually give too large cohesive energies or too high bulk moduli.


Makoto Fujita, University of Tokyo

The lecture of Makoto Fujita was wonderful, this man is really clever, and sweet.

During his first lecture is has spoken about the structure and the function on the Nanoscale:

His work is based with molecular self assembly based on coordination chemistry. With that, he has explained us the combinaison of transition metal’s quire planer with pyridine bridging ligands which gives rise to a quantitative self assembly of nano sized, discrete organic frameworks.

Many examples were cited:

  • Square molecules (JACS 1990)
  • Linked-ring molecules (Nature 1994 and 1999)
  • Cages (Nature 1995)
  • Tubes (JACS 2004)
  • Capsules (Nature 1999)

He focused on the cavity-directed reaction and property control of organic molecules: one of the most important features of 3D host.

Moreover, this powerful is applied to the bottom-up construction of discrete, well defined nano-scale stuctures.

Third day of the Summer School

Today it was the lecture of Jean-Pierre Sauvage. I’ve already written about his work in molecular machines.


But do you know what Catenanes are?


They were the first molecule whose structures couldn’t be described with the standard properties. Reported by Frisch and Wasserman, they synthesis a molecule consisting of two interlocked rings and they called them (2)-catenane. The two rings in the linked .
Catenane structure are the same in terms of atoms, bonds. If we give a direction to these catenanes they became chiral.
“The archetype of topologically non trivial compounds” catena mean chain .
To synthesis the catenanes there is a template methods. The pioneers of this synthesis are Fraser Stoddart and co-worker who have contributed a lot with the pi – pi stacking and H bonds in 1989.
Following by Chris Hunter , Fritz Vögtle in 1992 with the H Bonding.
Makoto Fujita showed the kinetic aspect labile bonds between Pd and Nitrogen atoms and hydrophobic interactions in 1994.
Until the works of JP Sauvage with lot of co workers who work about these and improve them.



Second day of the summer school, very great!

The second day of the “Summer school “was still a great event.

The first part presented by Harry Anderson, Department of Chemistry, University of Oxford.

Fist lecture: An introduction to molecular Wires

It’s amazing to see the mediate charge transport in very huge complex. He always works about porphyrins adding lot of groups around the pyrrole compounds.

Second lecture: Template-Directed synthesis of porphyrin nanorings 

He showed in his second lecture, the amazingly supramolecular control and the coordination of a metal center leading to full possibilities for a template-directed synthesis. The template has a crucial function giving the shape to the final complex. An assembly of pi conjugated nanorings lead to nanotubes. 

The second part was presented by Thomas ward, University of Basel

He explained that an artificial metalloenzyme results from the incorporation of a catalycally competent organometallic moiety within a host protein.

The last lecture, was presented by Jaume Veciana,  CSIC and CIBER-BBN, Bellaterra.

He showed us the impact of nanotechnology field in medicine and drugs. It’s very useful to take into account the advantages of nanotechnology, nanoparticules which permit the administration of drugs which can’t be without them. We saw for example, a polymeric nanoparticles very efficient to bind antibiotic and cross over the membrane and are able to destruct bacteria,…

Also, the widely used of CO2, a green component, to organic solvents. It allows the preparation of nanoparticles with application in nanomedicine.



Jean Marie Lehn (Nobel Prize) and I

First day of the challenge in supramolecular chemistry

Jean-Marie Lehn ( during: 3h)

Perspectives in chemistry: From Molecular to Supramolecular Chemistry towards Adapatative Chemistry

 Chemistry is the science of structure and transformation of non living and living matter. He showed us the complexity of the matter, the wide range of very powerful procedures for mastering the organisation of the matter and how more complicated molecules are build.

Supramolecular chemistry is a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity.

These features define the dynamic combinatorial chemistry DCC, on both, molecular and supramolecular chemistry.

EPR Spectroscopy

  EPR, Electron Paramagnetic Resonance, is a spectroscopic technique only for species which have an unpaired number of electrons: ParaMagnetic compounds.

Sometime, the name for this analyze is also ESR: Electron Spin Resonance.

These include many transitions metal ions, free radicals, etc.

As a result EPR crossed several skills: chemistry, physics, biology, materials science, medical science and others.

What kind of information gives an EPR spectroscopy? 

Only EPR spectroscopy is able to detects unpaired electrons and the presence of free radicals. Moreover, EPR has the unique power to identify the detected ParaMagnetic species. The sample we want analyze can be solid as a powder or liquide.

This magnetic resonance technique is very similar to the NMR Spectroscopy, used for species which have a pair number of electrons: DiaMagnetic compounds.

But, EPR doesn’t measure the nuclear transition in the sample as in NMR but detects the transition of unpaired electrons in an applied magnetic field. Effectively, when we submit an external magnetic field B, it creates two distincts energy levels for the unpaired electrons : the α level: Ms= +1/2 and the β level: Ms= -1/2, allowing to measure them as they are driven between the two levels. (look at the schema above)

In order for the transition to occur, the lower β and upper α states have to be exactly matched by the microwave frequency.