ANR-PRC ULTRArchae (2022-2025)

Ultrafast structural dynamics
of Archaerhodopsin–3 in its fluorescent state

Partner: Nicolas Ferré

Archaerhodopsin-3 (AR-3), a photo-activated proton pump from Halorubrum sodomense, is the progenitor of an entire class of genetically encoded fluorescent membrane voltage indicators (GEVI). Like in other microbial rhodopsins, absorption of visible light triggers in AR-3 the retinal chromophore reversible photoisomerization which leads to the existence of several intermediates with lifetimes covering the sub-picosecond to millisecond time scale. At variance with other 1-photon-based fluorescent rhodopsins, wild-type AR-3 fluorescence is taking place after 3-photon absorption. The underlying molecular mechanism is still unknown, motivating the present investigation.

Using advanced methods of ultrafast electronic and vibrational spectroscopy and state-of-the-art quantum chemistry methods, combined with time-resolved X-ray crystallography, the ULTRArchae consortium will provide for the first time a detailed mechanistic understanding of the structure-function relationship leading to unusual fluorescence properties in AR-3 and its variants.


On the quest of a biological compass: magnetic field effects on the cryptochrome protein

Principal Investigator: Miquel Huix-Rotllant

Certain migratory animals orient during their long-distance migrations by perceiving the terrestrial magnetic field. The exact molecular origin of such a sense is still unknown. Recently, the cryptochrome protein has been proposed as responsible for such a “biological compass”. The photochemical mechanism would be based on the radical pair creation in donor-acceptor complexes: after light absorption, an electron transfer occurs between one flavin and the tryptophans forming the active site of cryptochrome, generating in this way a localized radical pair. Such a radical pair would undergo a coherent dynamics of populations of singlet and triplet excited states.

Theoretical models have shown that such dynamics can be affected by low-intensity external magnetic fields, supposing that the excited states have specific magnetic and dynamical properties: long-lived radical pairs, different singlet and triplet reactivity, anisotropic hyperfine coupling, etc. To this point, there is no proof that such a mechanism can exist in a biological medium. We propose to develop a multi-scale quantum dynamical model with the objective of determining the effect of magnetic fields on the activity of the cryptochrome protein. This model is based on analytic effective Hamiltonians, which contain the information of magnetic, electronic, and vibrational properties of the excited states of the protein. Such Hamiltonians will be used subsequently to propagate wavepackets in real-time under the action of external magnetic fields.

The project will give the first proof of whether the cryptochrome protein can be considered as a biological compass. Furthermore, the results can constitute the first direct proof of the effect of a low-intensity magnetic field on the mechanism of a photochemical reaction taking place in a biological medium


Multiple trajectories towards excited states

Partner: Miquel Huix-Rotllant

Multicross aims at understanding transition metal photophysics to a new level of detail thanks to a joint experimental and theoretical research program spanning three laboratories and two countries. Ultrafast optical spectroscopy and X-ray techniques will be pushed to time resolutions approaching 10 fs.

Quantum models will be used to solve time-dependent Schrodinger equation to follow the photoinduced wavepacket motion and dispersion along different excited state trajectories that will be controlled by different pump laser pulses. Because the same physical model will be able to explain the different experimental findings, the outcomes will be little biased and the resulting representations can be used to clarify the mechanisms behind the unexpected properties of ultrafast intersystem crossing of transition metal compounds.

ERC AdG SubNano (2019-2024)

Computational Photochemistry in the Long Timescale

Principal investigator: Mario Barbatti

The goal of SubNano is to massively speed up dynamics simulations of photoexcited molecules to address sub-nanosecond phenomena (that is, one thousand times above the current simulation limits).

Such methods will allow exploring phenomena, like vibrational relaxation, fluorescence, slow internal conversion, intersystem crossing, which have been left aside by computational chemistry, too focused on ultrafast processes.

The sub-ns methodology will be employed to investigate the long timescale nonadiabatic dynamics of photoinduced processes in nucleic acids, including DNA photostabilization via excitonic processes, biological fluorescent markers, and DNA pyrimidine-dimer repair.

FetOpen BoostCrop (2019-2022)

Boosting Crop Growth using Natural Product and Synthesis Enabled Solar Harvesting

Work package manager: Mario Barbatti

BoostCrop is an EU funded research project that has a long term vision to develop a highly efficient, environmentally friendly, and affordable foliar spray for crop growth enhancement and thus sustainable food security. See our plan for further details.

Our team combines the expertise of 6 participant universities with 13 university-based lead investigators, one government institute with one section leader, one SME with two group leaders and encompasses the 3 major disciplines of Chemistry, Physics, Biology.

ANR- shapeNread (2019-2023)

Conformational design for high throughput MS/MS reading of digital polymers

Partners: Anouk Siri / Didier Siri

The shapeNread project aims at optimizing the tridimensional structure of encoded synthetic polymers to allow their high throughput sequencing by coupling tandem mass spectrometry with ion mobility spectrometry. Synthesis of these polymers will allow binary information to be contained in blocks, each labeled with a specific tag to enable their distinction in terms of mass and conformation. To do so, tags will be conceived by molecular modeling based on their propensity to provide different collision cross sections for all blocks. Once released in a first activation stage, block-containing fragments could hence be separated by ion mobility and further be individually sequenced after a second activation stage. Such a structural design would allow high throughput reading of molecularly encoded information (at least one decabyte per chain) by MS/MS-IMS-MS/MS. Appropriate development of the MS-DECODER software will enable automated data analysis.

A*Midex- PYRENEX (2019-2022)

Pyrene as Universal Building Block for the Design of π-Conjugation and Topology in Organic Electronics: from Chains to Ribbons and Helices

Partners: Anouk Siri / Didier Siri

Pyrene is a remarkable chromophore in view of its excited-state properties and the dependence of its fluorescence upon the environment. Transition to pyrene oligomers and polymers, the key concept of this joint proposal, opens important questions as to the delocalization of excitons and the mechanisms of energy transfer between the subunits. Such features will sensitively depend upon the way in which the pyrene moieties are connected. This is why we target both linear and ribbon structures, with direct aryl-aryl couplings or with additional sulfide bridges, thereby even including extended p-systems with helicity (chirality). It is innovative to combine sulfur and pyrene chemistry, in order to create new building blocks, which will themselves serve to create conjugated 2D or 3D geometrical objects of various topologies. This project will also tackle the relation between topology and opto-electronic properties, for opening up a new direction and future perspectives in materials science and in polyaromatic chemistry.