Élise Duboué-Dijon – Publications

Journal Articles

  1. N.L. Le Nguyen, O. Tichacek, P. Jungwirth, H. Martinez-Seara, P.E. Mason, E. Duboué-Dijon, Ion pairing in aqueous tetramethylammonium--acetate solutions by neutron scattering and molecular dynamics simulations, 2024, ChemRXiv preprint doi: 10.26434/chemrxiv-2024-b804r

  2. J. Puyo-Fourtine, L. Kantin, M. Andelkovic, C. Tisné, E. Frezza, I. Tunon, E. Duboué-Dijon, Molecular mechanism of rRNA maturation by M5: interplay between conformational flexibility and reactivity, 2024, ChemRXiv preprint doi: 10.26434/chemrxiv-2024-l454b

  3. S. Forget, M. Juillé, E. Duboué-Dijon, G. Stirnemann, Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme, 2024, J. Chem. Theory Comput. 20, 6263-6277 [preprint][data]

  4. E. Frezza, D. Laage, E. Duboué-Dijon*, Molecular origin of distinct hydration dynamics in double helical DNA and RNA sequences, 2024, J. Phys. Chem. Lett., 15, 4351-4358 [preprint] [data]

  5. P. Mason, T. Martinek, B. Fábián, M. Vazdar, P. Jungwirth, O. Tichacek, E. Duboué-Dijon, H. Martinez-Seara, Hydration of biologically relevant tetramethylammonium cation by neutron scattering and molecular dynamics, 2024, Phys. Chem. Chem. Phys., 26, 3208-3218  [postprint]

  6. J. Puyo, M. Juillé, J. Hénin, C. Clavaguéra, E. Duboué-Dijon*, A consistent picture of phosphate--divalent cation binding from models with implicit and explicit electronic polarization, 2022, J. Phys. Chem. B, 126, 4022-4034. [postprint] [data]

  7. E. Duboué-Dijon*, J. Hénin*, Building intuition for binding free energy calculations: bound state definition, restraints, and symmetry. J. Chem. Phys. 2021, 154, 204101 [postprint]

  8. D. Mendes de Oliveira, S.R. Zukowski, V. Palivec, J. Hénin, H. Martinez Seara, D. Ben Amotz, P. Jungwirth, E. Duboué-Dijon*, Binding of Divalent Cations to Aqueous Acetate: Molecular Simulations Guided by Raman Spectroscopy.  Phys. Chem. Chem. Phys., 2020, 22, 24014-24027 [postprint][data]

  9. E. Duboué-Dijon*, M. Javanainen, P. Delcroix, P. Jungwirth*, H. Martinez-Seara*, A practical guide to biologically-relevant molecular simulations with charge scaling for electronic polarization, J. Chem. Phys., 2020, 153, 050901 [open access]

  10. P.E. Mason, P. Jungwirth, E. Duboué-Dijon*, Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics. J. Phys. Chem. Lett, 2019, 10, 3254-3259 [data] [postprint]

  11. K. Brezina, E. Duboué-Dijon, V. Palivec, J. Jiracek, T. Krizek, C.M. Viola, T.R. Ganderton, A.M. Brzozowski and P. Jungwirth, Can arginine inhibit insulin aggregation? A combined protein crystallography, capillary electrophoresis and molecular simulations study. J. Phys. Chem. B, 2018, 122, 10069-10076 [postprint]

  12. E. Duboué-Dijon, P. Delcroix, H; Martinez-Seara, J. Hladilkova, P. Coufal, T. Krizek and P. Jungwirth, Binding of divalent cations to insulin: Capillary electrophoresis and molecular simulations, J. Phys. Chem. B, 2018, 122, 5640-5648 [open access]

  13. T. Martinek, E. Duboué-Dijon, S. Timr, P.E. Mason, K. Baxova, H.E. Fischer, B. Schmidt, E. Pluharova and P. Jungwirth, Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering.  J. Chem. Phys., 2018, 122, 10069-10076 [open access]

  14. G. Stirnemann, E. Duboué-Dijon, D. Laage, Ab initio simulations of water dynamics in aqueous TMAO solutions: temperature and concentration effects. J. Phys. Chem. B, 2017, 121, 11189-11197 [postprint]

  15. E. Duboué-Dijon*, P.E. Mason, H.E. Fischer, P. Jungwirth*, Hydration and ion pairing in aqueous Mg2+ and Zn2+ solutions: force field description aided by neutron scattering experiments and ab initio molecular dynamics simulations. J. Phys. Chem. B, 2017, 122, 3296-3306 [postprint]

  16. E. Duboué-Dijon, E. Pluharova, D. Domin, K. Sen, A.C. Fogarty, N. Chéron, D. Laage, Coupled valence-bond state molecular dynamics description of an enzyme-catalyzed reaction in a non-aqueous organic solvent. J. Phys. Chem. B, 2017, 12, 7027-7041 [postprint]

  17. E. Duboué-Dijon*, P.E. Mason, H.E. Fischer, P. Jungwirth, Changes in the hydration structure of imidazole upon protonation: Neutron scattering and molecular simulations. J. Chem. Phys., 2017, 146, 185102 [postprint]

  18. E. Duboué-Dijon, A.C. Fogarty, J.T. Hynes, D. Laage, Dynamical disorder in the DNA hydration shell, J. Am. Chem. Soc., 2016, 138, 7610-7620

  19. E. Duboué-Dijon, D. Laage, Characterization of the local structure in liquid water by various order parameters. J. Phys. Chem. B, 2015, 119, 8406-8418 [open access]

  20. E. Duboué-Dijon, D. Laage, Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J. Chem. Phys. 2014, 141, 22D529

  21. A.C. Fogarty, E. Duboué-Dijon, D. Laage, W.T. Thompson, Origins of the non-exponential reorientation dynamics of nanoconfined water. J. Chem. Phys., 2014, 141, 18C523

  22. E. Duboué-Dijon, A.C. Fogarty, D. Laage, Temperature dependence of hydrophobic hydration dynamics: from retardation to acceleration. J. Phys. Chem. B., 2014, 118, 1574-1583

  23. A.C. Fogarty, E. Duboué-Dijon, F. Sterpone, J.T. Hynes, D. Laage, Biomolecular hydration dynamics: a jump model perspective. Chem. Soc. Rev., 2013, 42, 5672-5683 [postprint]