Sunday, September 20th 2020                           


Modelling and Spectroscopy

Detailed topic: Light-(macro)molecules interactions :

Involved people  : Denis Jacquemin (Prof.), Adèle Laurent (CNRS Researcher), Daniel Escudero-Masa (Marie-Curie postdoctoral fellow), Ciro Guido (LUMOMAT postdoctoral fellow), Simon Budzak (Postdoctoral fellow), Gabriel Marchand (postdoctoral fellow), Anouar Belhboub (postdoctoral fellow), Kathy Chen (PhD student), Cloé Azarias (PhD student), Titouan Jaunet-Lahary (PhD student).


General overview

Within this research topic, the aim is to evaluate the electronic properties related to the excited states by not only interpreting the experimental data but also by predicting and optimizing the electronic properties of new compounds. Computational state-of-the-art methods are employed to simulate absorption and emission spectra of compounds in condensed phase or in heterogeneous complex environments (DNA, protein, guest-host …). Theoretical tools allow us to perform this work using diverse approaches going from quantum mechanics (QM) often based on the electronic density (TD-DFT, BSE) or on wavefunction (CIS, CIS(D), CC2, ADC( 2), CASSCF, EOM-CCSD…) to QM/MM hybrid methods combining QM and molecular mechanics (MM). This research theme is divided into three main axes involving (i) dyes, (ii) photochromes and (iii) biological systems.

Some recent reviews:


Axis-1 : Organic dyes

Organic dyes are a family of compounds of major industrial interest, particularly, for their "green" applications. Indeed, all efforts are recently putting to cleantech such as photovoltaic cells. The most scrutinized dyes are those absorbing in the infrared, with a large quantum yield, a high (photo) stability, ... Within this context, the group has the technology to model the absorption and emission spectra of these molecules in condensed phase taking into account the vibronic coupling (within the harmonic approximation). Such a methodology reproduce the experimental spectra and explain their shape. Therefore, variations in the optical spectra (shapes and positions) can be predicted for auxochromic substitutions, pH changes, solvatochromism and acidochromism effects... and new efficient dyes can be suggested to experiments.

Many varieties of dyes were investigated in the group, thus only recents studies are highlighted hereafter. This first axis includes (i) the study of cyanine derivatives (BODIPY, Aza-BODIPY, BORANIL…) being a theoretical challenge, (ii) understanding and characterization of the reactivity of porphyrin derivatives, and more specifically of the azacalixphyrine and (iii) the simulated dye properties exhibiting excited state intramolecular proton transfer (ESIPT). Note that the associated benchmark studies (choice of DFT functional, basic sets, solvent model, methodology...) to define an efficient protocol characterizing the excited states (vibronic spectra, vertical transitions, solvent effects) are in the Methodological Developments theme (Axis-2)

Significant articles:
(i) A.M. Grabarz, et al. , J. Org. Chem. 2016, 81 , 2280–2292.
P. Boulanger et al. , J. Chem. Theory Comput. 2014, 10 , 4548–56 .
S. Chibani et al. , Chem. Sci. 2013, 4 , 1950-63 .

(ii) G. Marchand, et al. , Phys. Chem. Chem. Phys. 2016, 18 , 9608-9615.
G. Marchand et al. , Phys. Chem. Chem. Phys. 2015, 17 , 5290–5297 ,
H. Audi et al. , Chem. Commun. 2014, 50 , 15140-43 .

(iii) Simon Budzak, Denis Jacquemin, J. Phys. Chem.B , 2016, 120 , 6730-6738.
C. Azarias, et al. , Chem. Sci . 2016, 7 , 3763-3774.
K. Benelhadj et al. , Chem. Eur. J. 2014, 20 , 1-16 .
P. Hubin et al. , Phys. Chem. Chem. Phys. 2014, 16 , 25288–95 .


Axis-2 : Photochromes

A photochrome is a molecule which can be present in two forms (closed/open, cis / trans …), the transformation from one form to another is thermally or photochemically induced via the absorption of radiation energy or of distinct wavelengths (UV, visible or infrared). Such a photochromic reaction is reversible between the two molecular states that are characterized by their own electronic properties and, thus, highly different optical properties. Organic photochromes offer undeniable potential for their use in the transmission and storage of a bit of data (0 or 1) using the optical or electronic way. .

Our objectives are (i) to improve photochromic compounds maximizing the linear and non-linear optical properties of the two electronic states, (ii) to evaluate their fatigue resistance through the exploration of the reactivity forming non-photochromic by-products, (iii) to simulate the electronic properties of multi-photochromes (molecular entity containing two or more photochromes) for increasing the amount of stored data (iv) to model the interactions between a (multi-)photochrome(s) and a semiconductor surface (NiO, TiO2, Cu, ...) as well as their electronic properties. Such a work is carried out with (TD-)DFT or multi-reference methods and considered periodic boundary conditions for surface calculations.

Publications de référence :
(i) K. J. Chen et al. , J. Phys Chem C 2014, 118 , 4334-45 .      
T. Jaunet-Lahary et al. , J. Phys Chem C 2014, 18 , 28831-84

(ii) D. Mendive-Tapia et al. , Phys. Chem. Chem. Phys. 2014, 16 , 18463–71

(iii) A. Fihey, D. Jacquemin Chem. Sci. 2015, 6 , 3495-3503
A. Fihey, A. Perrier, W. R. Browne, D. Jacquemin, Chem. Soc. Rev. 2015, 44 , 3719-3759 .     
 B. Lasorne et al. Chem. Sci. 2015 6 , 5695-5702.     
 A. Perrier, F. Maurel, D. Jacquemin Acc. Chem. Res. 2012, 45 , 1173–82 .

(iv) K. J Chen et al. J. Mater. Chem. A 2016, 4 , 2217-2227 .     
K. J. Chen, F. Boucher, D. Jacquemin J. Phys. Chem. C 2015, 119 , 16860-16869 ,.     
K. J. Chen et al. , J. Phys Chem C 2015,
119 , 3684 -3696.    
  A. Fihey, B. Le Guennic, D. Jacquemin, J. Phys. Chem. Lett. 2015, 6 , 3067-3073.


Axis-3: Biological systems

It consists in the modeling of macromolecules that are naturally or artificially fluorescent using complementary approaches, combining docking, molecular modeling, QM/MM and QM/QM' hybrid methods to characterize their spectral properties. These two categories of fluorescent macromolecules are used extensively in the framework of medical imaging but also in biology for the detection of disease or abnormality. Naturally fluorescent macromolecules intrinsically contain a chromophore while artificial ones are modified by site-directed mutagenesis by introducing a molecular probe (or marker) instead of an amino acid into the protein of interest. The spectral changes induced by the presence or absence of a ligand/drug within a macromolecules allow to get a very local information about the position of the ligand.

The objectives of this axis are (i) to extend the color palette of naturally fluorescent proteins by offering new chromophores or new mutations within the photoactive site and (ii) determine the therapeutic protein of interest position a ligand or drug in order to modulate its activity and, in close collaboration with experimental groups.