Blanc SIMI 8 - Blanc - SIMI 8 - Chimie du solide, colloïdes, physicochimie

Understanding Nonlinear Vibrational spectroscopic probes of Energy Intermolecular transfer in Liquids – unveil

How does water protect DNA from heat ?

The structure of DNA is fragile and could be irremediably destroyed by an excess of energy. In connection with spectroscopy experiments, our theoretical study aims at elucidating at the molecular level through which channels an excess of heat is dissipated by DNA.

Understanding the intermolecular vibrational energy transfer in solution

The first goal of the project is fundamental and aims at understanding at the molecular level which factors govern the energy exchange between molecules in a liquid and how this is appears in modern non-linear vibrational spectroscopy techniques. The second goal is to apply this new understanding to the cooling of DNA and to determine the pathways followed by energy.

This project requires to develop a new theoretical framework in order to describe the energy transfer between the vibrations of different molecules in solution. This new approach will be applied to the interpretation of multidimensional spectra obtained by modern nonlinear vibrational spectroscopy.

We have shown that a water molecule whose vibration is excited goes very rapidly (in less than 100 fs) from a quantum character where two states are superimposed like Schrödinger’s cat simultaneously dead and alive, to a classical character closer to our daily experience where the molecule is either excited or not excited. We have also characterized the arrangement of water molecules around a DNA double helix. With our simulations, we have provided a molecular interpretation to some recent ultrafast infrared spectroscopy experiments. These results pave the way to construct a new theoretical framework describing vibrational energy transfers between DNA and water.

The new theoretical framework that we have constructed shows that several commonly employed hypothesis in the description of vibrational energy transfer in solution are not valid. Our new model will provide an improved understanding of vibrational energy transfers in solution. These energy exchanges play a crucial role for chemical ractions and biochemical processes.

This project has so far led to the elaboration of six articles (incl. 1 already published). The results have been presented in six invited communications in international conferences, in 6 seminars in foreign universities, and in 5 other conferences. This project has stimulated new collaborations with renowned groups in Germany and in the United States.

A collaborative theoretical and computational chemistry research program to explore and understand approaches for probing vibrational energy transfer (VET) via nonlinear spectroscopy is proposed. The primary focus will be on exploring techniques for elucidating solvation structure and dynamics using solute–solvent intermolecular VET as a signature. This framework will be applied to investigate the mechanisms of heat dissipation from DNA and show what nonlinear infrared spectra reveal about DNA hydration structure and dynamics. At a molecular scale, the flow of vibrational energy can no longer be described by a simple heat conduction picture, and the pathways followed by the energy depend critically on the molecular architecture and on the vibrational couplings between the modes. Identifying these pathways reveals which chemical groups are close enough to be coupled, and therefore provides valuable structural information, especially for complex molecules such as solvated DNA. Such experimental investigations have recently become possible with the advent of modern nonlinear spectroscopy techniques such as two-dimensional infrared (2D IR) photon-echo spectroscopy. While 2D IR spectroscopy has been successfully used to study processes such as hydrogen-bond dynamics or protein structural relaxation, investigators have only recently begun to consider how it can be used to probe intermolecular VET. As in 2D NMR, 2D IR spectra reveal energy transport, but with a sub-picosecond time resolution. Interpreting the multidimensional spectral patterns is challenging and requires an advanced theoretical framework since in both cases the nonlinear vibrational spectra differ significantly from those predicted by simplistic modeling. The proposed research will bridge this gap. In particular, theoretical approaches will be developed for 1) testing approximations frequently invoked in modeling intermolecular VET, including the dipole-dipole coupling approximation and decoherence effects, 2) predicting 2D IR spectra for systems with solute-solvent VET, 3) deriving mechanistic understanding from 2D IR measurements, i.e., understanding how different VET mechanisms are manifested in such nonlinear spectroscopic measurements. This new methodology will be applied to the heat dissipation mechanism in hydrated DNA. DNA vibrational cooling is a key step in the DNA excess energy dissipation process. The efficient transfer of the excess vibrational energy to the surrounding water is crucial to avoid thermal denaturation of the fragile hydrogen-bonded double strand structure. However, this mechanism remains poorly understood. Understanding the VET to the solvent will connect the very recently obtained experimental 2D IR spectra with a molecular-scale description of DNA hydration structure and dynamics. A privileged collaboration with the group who has measured the first 2D IR spectra of DNA has also been established. The results of this project will be especially beneficial to investigations of VET phenomena in liquids and at liquid interfaces. It will be possible to use such an improved description for the interpretation of a new generation of experiments probing in full depth the microscopic structure and dynamics of a broad range of biomolecular systems in aqueous environments, ranging from DNA to proteins or membranes. The insight gained in the understanding of DNA vibrational cooling will benefit all the studies aiming at improving the DNA protection vis-a-vis an excess energy. Understanding the key factors governing the vibrational energy dissipation pathways and rates will provide insight for designing DNA thermal protection strategies.

Project coordinator

Monsieur Damien LAAGE (ECOLE NORMALE SUPERIEURE) – damien.laage@ens.fr

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.

Partner

ENS / Pasteur ECOLE NORMALE SUPERIEURE

Help of the ANR 222,560 euros
Beginning and duration of the scientific project: December 2011 - 36 Months

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