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Vibrational Spectroscopies: Classical Molecular Dynamics

We develop methodologies for calculating infrared (IR) and vibrational circular dichroism (VCD) spectra of fluxional systems using classical molecular dynamics simulations with polarizable force fields. These spectroscopies are highly sensitive to molecular interactions, particularly hydrogen bonds, and require dynamic approaches that account for anharmonic effects. The tools developed have been applied to solvation studies, such as hydrated sulfate ions in growing water droplets [Clavaguéra2021, Thaunay2018], interactions between phosphates and divalent cations [Puyo-Fourtine2022], and the study of chiral molecules in solution and crystalline phases [LeBarbus-Debus2020].

We combine experimental approaches led by Anne Zehnacker (ISMO, U. Paris-Saclay) with molecular dynamics to interpret VCD spectra of chiral molecules in condensed phases. For example, the calculation of electric and magnetic dipole moments of various molecules has been implemented using the AMOEBA polarizable force field in the Tinker software (thesis by Jessica Bowles [Bowles-Thèse2022, Bowles2024]). The determination of IR and VCD absorption spectra from molecular dynamics trajectories has been implemented and its performance evaluated through comparison with ab initio simulations [Bowles2023b]. Additionally, a method for mode assignment using effective mode analysis has been developed [Bowles2023a]. These advances pave the way for determining the VCD spectra of chemically complex systems in condensed phases. Integration of VCD calculations into Tinker-HP is ongoing with the development team (LCT, Sorbonne U.). Furthermore, in collaboration with experimentalists from IJCLab, the structural and vibrational properties of water-ionic liquid mixtures have been studied using classical molecular dynamics.

These efforts converge into a new theme focusing on understanding the properties of deep eutectic solvents by combining VCD spectroscopy with theoretical approaches (thesis by Emeline Boyer 2023).

Development of a Methodology Using Polarizable Force Fields for Calculating Vibrational Circular Dichroism Spectra in Gas and Condensed Phases, Including Crystalline and Solvated Systems

Collaborations

Anne Zehnacker and Katia Le Barbu-Debus (ISMO, U. Paris-Saclay), Veronika Zinovyeva (IJCLab, U. Paris-Saclay), Elise Duboué-Dijon (LBT/IBPC, Paris), Florent Calvo (LIPhy, U. Grenoble Alpes), Rodolphe Vuilleumier (Laboratoire Pasteur, ENS Paris), Gilles Ohanessian (LCM/IPP, Palaiseau).

Data Analysis

Since 2016, we have been developing the SK-Ana software package for analyzing spectro-kinetic data (transient absorption, fluorescence, etc.) using chemometric methods (SVD, MCR-ALS) and parametric approaches (hybrid Bayesian models). This tool is central to analyzing results from the ELYSE platform [Wang2019, Kaczmarek2020, Denisov2022, Knezevic2023]. Its graphical interface and containerization facilitate experimenters' autonomy in analyzing such signals. SK-Ana has started to be used by other laboratories [Shang2021, Iwamatsu2022] and has recently been adapted for studying photo-induced charge accumulation [CruzNeto2023].