CE29 - Chimie : analyse, théorie, modélisation

Ultrafast Reactivity of Biomolecules under Irradiation – RUBI

We use the tools of computational chemistry like DFT (Density Functional Theory) and hybrid DFT/MM (Molecular Mechanics) schemes

- Evidence of non-additive effect for energy deposition in molecules by ionizing rays, due to the presence ot environment molecules. This effect could be introduced in predictive models.
-Implementatopn of an hybrid FTB/MM scheme inthe deMon-Nano softare. Thi module will be available to the community by the end of 2021

We continue our research program as defined in the submitted proposal. One is to continue the developement of DFTB/MMpol scheme with polarizable force field. The othe one is to investigate iradition of peptides/oligonucleotides and models of interstellar ices.

1. First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation by Karwan Ali Omar, Karim Hasnaoui and Aurélien de la Lande. Annual Reviews of Physical Chemistry. 2021 72, 20.1–20.21. DOI: doi.org/10.1146/annurev-physchem-101419-013639
1. Femtosecond Responses of Hydrated DNA Irradiated by Ionizing Rays, Focus on the Sugar-Phosphate Part by Aurélien de la Lande. Theoretical Chemistry Accounts. 2021 140, 77. DOI: doi.org/10.1007/s00214-021-02778-1

Submission summary

In-depth knowledge of the consequences of interaction of biomolecules with ionizing radiations is of fundamental importance for progress in medicine, radiotherapy and radioprotection as well as for addressing the panspermia hypothesis. The physicochemical events taking place during the first picoseconds after irradiation have so far escaped the scrutiny of researchers. Yet the plethora of vibrationally hot, electronically excited and highly reactive species formed upon irradiation is likely to trigger rich and non-conventional chemistry. For complex biostructures such as DNA or proteins irradiation could undergo currently unknown chemical damages with dramatic consequences for health. In the field of astrochemistry, ionizing radiations could have played a crucial role. The bombardment of the early Earth by comets that have captured organic rich interstellar icy grains is thought to have provided the molecular precursors at the origin of life on Earth. Such an assumption depends on the survival of these precursor under cosmic irradiations.
We will thus explore the early steps of radiation induced damages on biomolecules from first-principles atomistic simulations. RUBI will result in innovative simulation techniques available for the community and is expected to have a great impact on the fundamental understanding of the early steps following matter irradiation, a hot topic in many different research fields. The chemical physics following irradiation of matter produces a plethora of extremely aggressive and unstable chemical species that may directly damage molecules. The reactivity within the ultrafast (<ps) time domain is a terra incognita that we will explore in RUBI relying on computational approaches that go beyond the current state-of-the-art. We will conduct for the first time first principles simulations of irradiation of complex biostructures (oligonucleotides, peptides, DNA, proteins, DNA/protein complexes) and of prebotic molecules embedded in interstellar ices. We will explore the ultrafast responses covering time domains ranging from the attosecond to the nanosecond. Simulations rooted on Time-Dependent Density Functional Theory will permit to describe collision of biological matter by high energy charged particles. We will decipher the microscopic mechanisms responsible for ionization of biomolecules, of ultrafast charge migration, energy relaxation and dissipation, all taking place on the femtosecond time scale. Ab initio molecular dynamics simulations will unravel the chemical reactivity of the primary species produced by irradiation on the biomolecules. Important chemical events such as DNA strand breaking, or peptide bond cleavages in proteins are the type of process we expect to observe in such simulations. The role played by cosmic irradiation in the chemical processing of prebiotic molecules trapped in ices will also be investigated. We will work with hybrid polarizable Quantum Mechanics/Molecular Mechanics schemes. To go further, we will implement original tools based on Density Functional Theory Tight Binding. <br />RUBI will have tremendous impact on our understanding of the molecular mechanisms involved in irradiation of biological matter. This is fundamental knowledge that is needed to prevent healthy tissues damages, or on the contrary to target malignant cells specifically in radiotherapies. It may also provide unprecedented hints about the possible origin of prebiotic molecules on Earth. The data produced in RUBI will also be of high value for researcher developing/using Monte-Carlo track structure codes. Once properly tested the new simulations algorithms will be merged to the public versions of the codes deMon2k and deMonNano, which are open-source programs, free for academics usage.

Project coordination


The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


ICGM Institut de chimie moléculaire et des matériaux - Institut Charles Gerhardt Montpellier
CINVESTAV Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional / Département de chimie

Help of the ANR 421,677 euros
Beginning and duration of the scientific project: December 2019 - 48 Months

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