You can find below the publication list of all members of the theoretical chemistry group at ENS. For the list of each individual member, please consult their personal webpage from the Members page.
2022 |
Spectroscopic fingerprints of cavity formation and solute insertion as a measure of hydration entropic loss and enthalpic gain Article de journal Simone Pezzotti; Federico Sebastiani; Eliane P van Dam; Sashary Ramos; Valeria Conti Nibali; Gerhard Schwaab; Martina Havenith Angew. Chem. Int. Ed., 134 (29), p. e202203893, 2022. @article{pezzotti_Ang2022, title = {Spectroscopic fingerprints of cavity formation and solute insertion as a measure of hydration entropic loss and enthalpic gain}, author = {Simone Pezzotti and Federico Sebastiani and Eliane P van Dam and Sashary Ramos and Valeria Conti Nibali and Gerhard Schwaab and Martina Havenith}, year = {2022}, date = {2022-01-01}, journal = {Angew. Chem. Int. Ed.}, volume = {134}, number = {29}, pages = {e202203893}, publisher = {Wiley Online Library}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Structure of the photosynthetic Calvin-Benson-Bassham sedoheptulose-1,7-bisphosphatase SBPase from the model microalgaChlamydomonas reinhardtii Article de journal Théo Le Moigne; Martina Santoni; Lucile Jomat; Stéphane D Lemaire; Mirko Zaffagnini; Nicolas Chéron; Julien Henri 2022. @article{Moigne_2022, title = {Structure of the photosynthetic Calvin-Benson-Bassham sedoheptulose-1,7-bisphosphatase SBPase from the model microalgaChlamydomonas reinhardtii}, author = {Th\'{e}o Le Moigne and Martina Santoni and Lucile Jomat and St\'{e}phane D Lemaire and Mirko Zaffagnini and Nicolas Ch\'{e}ron and Julien Henri}, url = {http://dx.doi.org/10.1101/2022.10.28.514230}, doi = {10.1101/2022.10.28.514230}, year = {2022}, date = {2022-01-01}, publisher = {Cold Spring Harbor Laboratory}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Click-Chemistry-Based Biomimetic Ligands Efficiently Capture G-Quadruplexes In Vitro and Help Localize Them at DNA Damage Sites in Human Cells Article de journal Francesco Rota Sperti; Baptiste Dupouy; Jérémie Mitteaux; Angélique Pipier; Marc Pirrotta; Nicolas Chéron; Ibai E Valverde; David Monchaud JACS Au, 2 (7), p. 1588-1595, 2022. @article{doi:10.1021/jacsau.2c00082, title = {Click-Chemistry-Based Biomimetic Ligands Efficiently Capture G-Quadruplexes In Vitro and Help Localize Them at DNA Damage Sites in Human Cells}, author = {Francesco Rota Sperti and Baptiste Dupouy and J\'{e}r\'{e}mie Mitteaux and Ang\'{e}lique Pipier and Marc Pirrotta and Nicolas Ch\'{e}ron and Ibai E Valverde and David Monchaud}, url = {https://doi.org/10.1021/jacsau.2c00082}, doi = {10.1021/jacsau.2c00082}, year = {2022}, date = {2022-01-01}, journal = {JACS Au}, volume = {2}, number = {7}, pages = {1588-1595}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Acids at the Edge: Why Nitric and Formic Acid Dissociations at Air-Water Interfaces Depend on Depth and on Interface Specific Area. Article de journal M de la Puente; R David; A Gomez; D Laage J Am Chem Soc, 144 (23), p. 10524–10529, 2022. @article{delaPuente2022, title = {Acids at the Edge: Why Nitric and Formic Acid Dissociations at Air-Water Interfaces Depend on Depth and on Interface Specific Area.}, author = {M de la Puente and R David and A Gomez and D Laage}, year = {2022}, date = {2022-01-01}, journal = {J Am Chem Soc}, volume = {144}, number = {23}, pages = {10524\textendash10529}, address = {PASTEUR, Department of Chemistry, \'{E}cole Normale Sup\'{e}rieure-PSL, Sorbonne Universit\'{e}, CNRS, Paris 75005, France.}, abstract = {Whether the air-water interface decreases or increases the acidity of simple organic and inorganic acids compared to the bulk is critically important in a broad range of environmental and biochemical processes. However, a consensus has not yet been achieved on this key question. Here we use machine learning-based reactive molecular dynamics simulations to study the dissociation of paradigmatic nitric and formic acids at the air-water interface. We show that the local acidity profile across the interface is determined by changes in acid and conjugate base solvation and that the acidity decreases abruptly over a transition region of a few molecular layers. At the interface, both acids are weaker than in the bulk due to desolvation. In contrast, acidities below the interface reach a plateau and are all the stronger compared to those in the bulk as the surface to volume ratio of the aqueous phase is large, due to the growing impact of the stabilization of the released proton at the surface of the water. These results imply that the measured degree of dissociation sensitively depends on the experimental probing length and system size and suggest a molecular explanation for the contrasting experimental results. The aerosol size dependence of acidity has important consequences for atmospheric chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Whether the air-water interface decreases or increases the acidity of simple organic and inorganic acids compared to the bulk is critically important in a broad range of environmental and biochemical processes. However, a consensus has not yet been achieved on this key question. Here we use machine learning-based reactive molecular dynamics simulations to study the dissociation of paradigmatic nitric and formic acids at the air-water interface. We show that the local acidity profile across the interface is determined by changes in acid and conjugate base solvation and that the acidity decreases abruptly over a transition region of a few molecular layers. At the interface, both acids are weaker than in the bulk due to desolvation. In contrast, acidities below the interface reach a plateau and are all the stronger compared to those in the bulk as the surface to volume ratio of the aqueous phase is large, due to the growing impact of the stabilization of the released proton at the surface of the water. These results imply that the measured degree of dissociation sensitively depends on the experimental probing length and system size and suggest a molecular explanation for the contrasting experimental results. The aerosol size dependence of acidity has important consequences for atmospheric chemistry. |
2021 |
Using Activation Energies to Elucidate Mechanisms of Water Dynamics. Article de journal ZA Piskulich; D Laage; WH Thompson J Phys Chem A, 125 (46), p. 9941–9952, 2021. @article{Piskulich2021b, title = {Using Activation Energies to Elucidate Mechanisms of Water Dynamics.}, author = {ZA Piskulich and D Laage and WH Thompson}, year = {2021}, date = {2021-01-01}, journal = {J Phys Chem A}, volume = {125}, number = {46}, pages = {9941\textendash9952}, address = {Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States. PASTEUR, Department de Chimie, \'{E}cole Normale Sup\'{e}rieure, PSL University, Sorbonne Universit\'{e}, CNRS, Paris 75005, France. Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States.}, abstract = {Recent advances in the calculation of activation energies are shedding new light on the dynamical time scales of liquid water. In this Perspective, we examine how activation energies elucidate the central, but not singular, role of the exchange of hydrogen-bond (H-bond) partners that rearrange the H-bond network of water. The contributions of other motions to dynamical time scales and their associated activation energies are discussed along with one case, vibrational spectral diffusion, where H-bond exchanges are not mechanistically significant. Nascent progress on outstanding challenges, including descriptions of non-Arrhenius effects and activation volumes, are detailed along with some directions for future investigations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent advances in the calculation of activation energies are shedding new light on the dynamical time scales of liquid water. In this Perspective, we examine how activation energies elucidate the central, but not singular, role of the exchange of hydrogen-bond (H-bond) partners that rearrange the H-bond network of water. The contributions of other motions to dynamical time scales and their associated activation energies are discussed along with one case, vibrational spectral diffusion, where H-bond exchanges are not mechanistically significant. Nascent progress on outstanding challenges, including descriptions of non-Arrhenius effects and activation volumes, are detailed along with some directions for future investigations. |
A Model Electron Transfer Reaction in Confined Aqueous Solution. Article de journal JF Olivieri; D Laage; JT Hynes Chemphyschem, 22 (21), p. 2247–2255, 2021. @article{Olivieri2021, title = {A Model Electron Transfer Reaction in Confined Aqueous Solution.}, author = {JF Olivieri and D Laage and JT Hynes}, year = {2021}, date = {2021-01-01}, journal = {Chemphyschem}, volume = {22}, number = {21}, pages = {2247\textendash2255}, address = {PASTEUR, Department of Chemistry, \'{E}cole Normale Sup\'{e}rieure, PSL University, Sorbonne Universit\'{e}, CNRS, 75005, Paris, France. Department of Chemistry, University of Colorado, Boulder, CO 80309, USA.}, abstract = {Liquid water confined within nanometer-sized channels exhibits a strongly reduced local dielectric constant perpendicular to the wall, especially at the interface, and this has been suggested to induce faster electron transfer kinetics at the interface than in the bulk. We study a model electron transfer reaction in aqueous solution confined between graphene sheets with classical molecular dynamics. We show that the solvent reorganization energy is reduced at the interface compared to the bulk, which explains the larger rate constant. However, this facilitated solvent reorganization is due to the partial desolvation by the graphene sheet of the ions involved in the electron transfer and not to a local dielectric constant reduction effect.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Liquid water confined within nanometer-sized channels exhibits a strongly reduced local dielectric constant perpendicular to the wall, especially at the interface, and this has been suggested to induce faster electron transfer kinetics at the interface than in the bulk. We study a model electron transfer reaction in aqueous solution confined between graphene sheets with classical molecular dynamics. We show that the solvent reorganization energy is reduced at the interface compared to the bulk, which explains the larger rate constant. However, this facilitated solvent reorganization is due to the partial desolvation by the graphene sheet of the ions involved in the electron transfer and not to a local dielectric constant reduction effect. |
Confined Water’s Dielectric Constant Reduction Is Due to the Surrounding Low Dielectric Media and Not to Interfacial Molecular Ordering Article de journal Jean-François Olivieri; James T Hynes; Damien Laage J Phys Chem Lett, 12 , p. 4319–4326, 2021. @article{Olivieri2021a, title = {Confined Water’s Dielectric Constant Reduction Is Due to the Surrounding Low Dielectric Media and Not to Interfacial Molecular Ordering}, author = {Jean-Fran\c{c}ois Olivieri and James T Hynes and Damien Laage}, year = {2021}, date = {2021-01-01}, journal = {J Phys Chem Lett}, volume = {12}, pages = {4319\textendash4326}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
On the role of hydrogen-bond exchanges in the spectral diffusion of water Article de journal Zeke A Piskulich; Damien Laage; Ward H Thompson J Chem Phys, 154 (6), p. 064501, 2021. @article{Piskulich2021, title = {On the role of hydrogen-bond exchanges in the spectral diffusion of water}, author = {Zeke A Piskulich and Damien Laage and Ward H Thompson}, year = {2021}, date = {2021-01-01}, journal = {J Chem Phys}, volume = {154}, number = {6}, pages = {064501}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cation enrichment in the ion atmosphere is promoted by local hydration of DNA Article de journal Chun Yu Ma; Simone Pezzotti; Gerhard Schwaab; Magdalena Gebala; Daniel Herschlag; Martina Havenith Phys. Chem. Chem. Phys., 23 (40), p. 23203–23213, 2021. @article{Pezzotti_DNA2021, title = {Cation enrichment in the ion atmosphere is promoted by local hydration of DNA}, author = {Chun Yu Ma and Simone Pezzotti and Gerhard Schwaab and Magdalena Gebala and Daniel Herschlag and Martina Havenith}, year = {2021}, date = {2021-01-01}, journal = {Phys. Chem. Chem. Phys.}, volume = {23}, number = {40}, pages = {23203--23213}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Stripping away ion hydration shells in electrical double-layer formation: Water networks matter Article de journal Serena R Alfarano; Simone Pezzotti; Christopher J Stein; Zhou Lin; Federico Sebastiani; Sarah Funke; Claudius Hoberg; Inga Kolling; Chun Yu Ma; Katja Mauelshagen; others Proc. Natl. Acad. Sci., 118 (47), p. e2108568118, 2021. @article{Alfaranoe2108568118, title = {Stripping away ion hydration shells in electrical double-layer formation: Water networks matter}, author = {Serena R Alfarano and Simone Pezzotti and Christopher J Stein and Zhou Lin and Federico Sebastiani and Sarah Funke and Claudius Hoberg and Inga Kolling and Chun Yu Ma and Katja Mauelshagen and others}, year = {2021}, date = {2021-01-01}, journal = {Proc. Natl. Acad. Sci.}, volume = {118}, number = {47}, pages = {e2108568118}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Molecular fingerprints of hydrophobicity at aqueous interfaces from theory and vibrational spectroscopies Article de journal Simone Pezzotti; Alessandra Serva; Federico Sebastiani; Flavio Siro Brigiano; Daria Ruth Galimberti; Louis Potier; Serena Alfarano; Gerhard Schwaab; Martina Havenith; Marie-Pierre Gaigeot J. Phys. Chem. Lett., 12 (15), p. 3827–3836, 2021. @article{pezzotti2021molecular, title = {Molecular fingerprints of hydrophobicity at aqueous interfaces from theory and vibrational spectroscopies}, author = {Simone Pezzotti and Alessandra Serva and Federico Sebastiani and Flavio Siro Brigiano and Daria Ruth Galimberti and Louis Potier and Serena Alfarano and Gerhard Schwaab and Martina Havenith and Marie-Pierre Gaigeot}, year = {2021}, date = {2021-01-01}, journal = {J. Phys. Chem. Lett.}, volume = {12}, number = {15}, pages = {3827--3836}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction Article de journal Ellen M Adams; Simone Pezzotti; Jonas Ahlers; Maximilian Rüttermann; Maxim Levin; Adi Goldenzweig; Yoav Peleg; Sarel J Fleishman; Irit Sagi; Martina Havenith JACS Au, 1 (7), p. 1076-1085, 2021. @article{Pezzotti_JACSau2021, title = {Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction}, author = {Ellen M Adams and Simone Pezzotti and Jonas Ahlers and Maximilian R\"{u}ttermann and Maxim Levin and Adi Goldenzweig and Yoav Peleg and Sarel J Fleishman and Irit Sagi and Martina Havenith}, doi = {10.1021/jacsau.1c00155}, year = {2021}, date = {2021-01-01}, journal = {JACS Au}, volume = {1}, number = {7}, pages = {1076-1085}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
The key role of solvent in condensation: mapping water in liquid-liquid phase-separated FUS Article de journal Jonas Ahlers; Ellen M Adams; Verian Bader; Simone Pezzotti; Konstanze F Winklhofer; Jörg Tatzelt; Martina Havenith Biophys. J., 120 (7), p. 1266–1275, 2021. @article{Pezzotti_LLPS2021, title = {The key role of solvent in condensation: mapping water in liquid-liquid phase-separated FUS}, author = {Jonas Ahlers and Ellen M Adams and Verian Bader and Simone Pezzotti and Konstanze F Winklhofer and J\"{o}rg Tatzelt and Martina Havenith}, year = {2021}, date = {2021-01-01}, journal = {Biophys. J.}, volume = {120}, number = {7}, pages = {1266--1275}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Size dependence of hydrophobic hydration at electrified gold/water interfaces Article de journal Alessandra Serva; Mathieu Salanne; Martina Havenith; Simone Pezzotti Proc. Natl. Acad. Sci., 118 (15), p. e2023867118, 2021. @article{serva2021size, title = {Size dependence of hydrophobic hydration at electrified gold/water interfaces}, author = {Alessandra Serva and Mathieu Salanne and Martina Havenith and Simone Pezzotti}, year = {2021}, date = {2021-01-01}, journal = {Proc. Natl. Acad. Sci.}, volume = {118}, number = {15}, pages = {e2023867118}, publisher = {National Acad Sciences}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
The role of hydrophobic hydration in the free energy of chemical reactions at the gold/water interface: size and position effects Article de journal Alessandra Serva; Martina Havenith; Simone Pezzotti J. Chem. Phys., 155 (20), p. 204706, 2021. @article{serva2021JCP, title = {The role of hydrophobic hydration in the free energy of chemical reactions at the gold/water interface: size and position effects}, author = {Alessandra Serva and Martina Havenith and Simone Pezzotti}, year = {2021}, date = {2021-01-01}, journal = {J. Chem. Phys.}, volume = {155}, number = {20}, pages = {204706}, publisher = {AIP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells Article de journal Joanna Zell; Katerina Duskova; Leïla Chouh; Madeleine Bossaert; Nicolas Chéron; Anton Granzhan; Sébastien Britton; David Monchaud Nucleic Acids Research, 49 (18), p. 10275-10288, 2021, ISSN: 0305-1048. @article{10.1093/nar/gkab796, title = {Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells}, author = {Joanna Zell and Katerina Duskova and Le\"{i}la Chouh and Madeleine Bossaert and Nicolas Ch\'{e}ron and Anton Granzhan and S\'{e}bastien Britton and David Monchaud}, url = {https://doi.org/10.1093/nar/gkab796}, doi = {10.1093/nar/gkab796}, issn = {0305-1048}, year = {2021}, date = {2021-01-01}, journal = {Nucleic Acids Research}, volume = {49}, number = {18}, pages = {10275-10288}, abstract = {DNA is intrinsically dynamic and folds transiently into alternative higher-order structures such as G-quadruplexes (G4s) and three-way DNA junctions (TWJs). G4s and TWJs can be stabilised by small molecules (ligands) that have high chemotherapeutic potential, either as standalone DNA damaging agents or combined in synthetic lethality strategies. While previous approaches have claimed to use ligands that specifically target either G4s or TWJs, we report here on a new approach in which ligands targeting both TWJs and G4s in vitro demonstrate cellular effects distinct from that of G4 ligands, and attributable to TWJ targeting. The DNA binding modes of these new, dual TWJ-/G4-ligands were studied by a panel of in vitro methods and theoretical simulations, and their cellular properties by extensive cell-based assays. We show here that cytotoxic activity of TWJ-/G4-ligands is mitigated by the DNA damage response (DDR) and DNA topoisomerase 2 (TOP2), making them different from typical G4-ligands, and implying a pivotal role of TWJs in cells. We designed and used a clickable ligand, TrisNP-α, to provide unique insights into the TWJ landscape in cells and its modulation upon co-treatments. This wealth of data was exploited to design an efficient synthetic lethality strategy combining dual ligands with clinically relevant DDR inhibitors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } DNA is intrinsically dynamic and folds transiently into alternative higher-order structures such as G-quadruplexes (G4s) and three-way DNA junctions (TWJs). G4s and TWJs can be stabilised by small molecules (ligands) that have high chemotherapeutic potential, either as standalone DNA damaging agents or combined in synthetic lethality strategies. While previous approaches have claimed to use ligands that specifically target either G4s or TWJs, we report here on a new approach in which ligands targeting both TWJs and G4s in vitro demonstrate cellular effects distinct from that of G4 ligands, and attributable to TWJ targeting. The DNA binding modes of these new, dual TWJ-/G4-ligands were studied by a panel of in vitro methods and theoretical simulations, and their cellular properties by extensive cell-based assays. We show here that cytotoxic activity of TWJ-/G4-ligands is mitigated by the DNA damage response (DDR) and DNA topoisomerase 2 (TOP2), making them different from typical G4-ligands, and implying a pivotal role of TWJs in cells. We designed and used a clickable ligand, TrisNP-α, to provide unique insights into the TWJ landscape in cells and its modulation upon co-treatments. This wealth of data was exploited to design an efficient synthetic lethality strategy combining dual ligands with clinically relevant DDR inhibitors. |
2020 |
Wrapping Up Hydrophobic Hydration: Locality Matters Article de journal V Conti Nibali; S Pezzotti; F Sebastiani; D R Galimberti; G Schwaab; M Heyden; M -P Gaigeot; M Havenith J. Phys. Chem. Lett., 11 (12), p. 4809-4816, 2020. @article{Pezzotti_JPCL2020, title = {Wrapping Up Hydrophobic Hydration: Locality Matters}, author = {V Conti Nibali and S Pezzotti and F Sebastiani and D R Galimberti and G Schwaab and M Heyden and M -P Gaigeot and M Havenith}, doi = {10.1021/acs.jpclett.0c00846}, year = {2020}, date = {2020-01-01}, journal = {J. Phys. Chem. Lett.}, volume = {11}, number = {12}, pages = {4809-4816}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Protein Preferential Solvation in Water:Glycerol Mixtures Article de journal Nicolas Chéron; Margaux Naepels; Eva Pluhařová; Damien Laage The Journal of Physical Chemistry B, 124 (8), p. 1424-1437, 2020. @article{doi:10.1021/acs.jpcb.9b11190, title = {Protein Preferential Solvation in Water:Glycerol Mixtures}, author = {Nicolas Ch\'{e}ron and Margaux Naepels and Eva Pluha\v{r}ov\'{a} and Damien Laage}, url = {https://doi.org/10.1021/acs.jpcb.9b11190}, doi = {10.1021/acs.jpcb.9b11190}, year = {2020}, date = {2020-01-01}, journal = {The Journal of Physical Chemistry B}, volume = {124}, number = {8}, pages = {1424-1437}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Activation energies and the extended jump model: How temperature affects reorientation and hydrogen-bond exchange dynamics in water Article de journal Zeke A Piskulich; Damien Laage; Ward H Thompson J Chem Phys, 153 (7), p. 074110, 2020. @article{Piskulich2020a, title = {Activation energies and the extended jump model: How temperature affects reorientation and hydrogen-bond exchange dynamics in water}, author = {Zeke A Piskulich and Damien Laage and Ward H Thompson}, year = {2020}, date = {2020-01-01}, journal = {J Chem Phys}, volume = {153}, number = {7}, pages = {074110}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes Article de journal Irene Maffucci; Damien Laage; Guillaume Stirnemann; Fabio Sterpone Phys Chem Chem Phys, 22 (33), p. 18361–18373, 2020. @article{Maffucci2020, title = {Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes}, author = {Irene Maffucci and Damien Laage and Guillaume Stirnemann and Fabio Sterpone}, year = {2020}, date = {2020-01-01}, journal = {Phys Chem Chem Phys}, volume = {22}, number = {33}, pages = {18361\textendash18373}, abstract = {A key aspect of life’s evolution on Earth is the adaptation of proteins to be stable and work in a very wide range of temperature conditions. A detailed understanding of the associated molecular mechanisms would also help to design enzymes optimized for biotechnological …}, keywords = {}, pubstate = {published}, tppubtype = {article} } A key aspect of life’s evolution on Earth is the adaptation of proteins to be stable and work in a very wide range of temperature conditions. A detailed understanding of the associated molecular mechanisms would also help to design enzymes optimized for biotechnological … |
Water dynamics at electrified graphene interfaces: a jump model perspective Article de journal Yiwei Zhang; Guillaume Stirnemann; James T Hynes; Damien Laage Phys Chem Chem Phys, 22 , p. 10581 – 10591, 2020. @article{Zhang2020a, title = {Water dynamics at electrified graphene interfaces: a jump model perspective}, author = {Yiwei Zhang and Guillaume Stirnemann and James T Hynes and Damien Laage}, year = {2020}, date = {2020-01-01}, journal = {Phys Chem Chem Phys}, volume = {22}, pages = {10581 \textendash 10591}, abstract = {Changes in water reorientation dynamics at electrified graphene interfaces arise from the interfaces’ impact on water hydrogen-bond exchanges; the asymmetric behavior with electrode potential sign is quantitatively described by an extended jump model.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Changes in water reorientation dynamics at electrified graphene interfaces arise from the interfaces’ impact on water hydrogen-bond exchanges; the asymmetric behavior with electrode potential sign is quantitatively described by an extended jump model. |
Water Structure, Dynamics, and Sum-Frequency Generation Spectra at Electrified Graphene Interfaces Article de journal Yiwei Zhang; Hilton B de Aguiar; James T Hynes; Damien Laage J Phys Chem Lett, 11 , p. 624–631, 2020. @article{Zhang2020b, title = {Water Structure, Dynamics, and Sum-Frequency Generation Spectra at Electrified Graphene Interfaces}, author = {Yiwei Zhang and Hilton B de Aguiar and James T Hynes and Damien Laage}, year = {2020}, date = {2020-01-01}, journal = {J Phys Chem Lett}, volume = {11}, pages = {624\textendash631}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
An Isolated Water Droplet in the Aqueous Solution of a Supramolecular Tetrahedral Cage Article de journal Federico Sebastiani; Trandon A Bender; Simone Pezzotti; Wan-Lu Li; Gerhard Schwaab; Robert G Bergman; Kenneth N Raymond; Dean F Toste; Teresa Head-Gordon; Martina Havenith Proc. Natl. Acad. Sci., 117 (52), p. 32954–32961, 2020. @article{sebastiani2020isolated, title = {An Isolated Water Droplet in the Aqueous Solution of a Supramolecular Tetrahedral Cage}, author = {Federico Sebastiani and Trandon A Bender and Simone Pezzotti and Wan-Lu Li and Gerhard Schwaab and Robert G Bergman and Kenneth N Raymond and Dean F Toste and Teresa {Head-Gordon} and Martina Havenith}, doi = {10.1073/pnas.2012545117}, year = {2020}, date = {2020-01-01}, journal = {Proc. Natl. Acad. Sci.}, volume = {117}, number = {52}, pages = {32954--32961}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2019 |
Ions Control Interfacial Water Structure and Dynamics at Silica Surfaces Article de journal Aashish Tuladhar; Shalaka Dewan; Simone Pezzotti; Flavio Siro Brigiano; Fabrizio Creazzo; Marie-Pierre Gaigeot; and Eric Borguet J. Am. Chem. Soc., 142 , p. 6991-7000, 2019. @article{Pezzotti_ions_ordering2019, title = {Ions Control Interfacial Water Structure and Dynamics at Silica Surfaces}, author = {Aashish Tuladhar and Shalaka Dewan and Simone Pezzotti and Flavio Siro Brigiano and Fabrizio Creazzo and Marie-Pierre Gaigeot and and Eric Borguet}, year = {2019}, date = {2019-01-01}, journal = {J. Am. Chem. Soc.}, volume = {142}, pages = {6991-7000}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Molecular hydrophobicity at a macroscopically hydrophilic surface Article de journal Jenée D Cyran; Michael A Donovan; Doris Vollmer; Flavio Siro Brigiano; Simone Pezzotti; Daria R Galimberti; Marie-Pierre Gaigeot; Mischa Bonn; Ellen H G Backus Proc. Natl. Acad. Sci., 116 (5), p. 1520-1525, 2019. @article{Pezzotti_PNAS2019, title = {Molecular hydrophobicity at a macroscopically hydrophilic surface}, author = {Jen\'{e}e D Cyran and Michael A Donovan and Doris Vollmer and Flavio Siro Brigiano and Simone Pezzotti and Daria R Galimberti and Marie-Pierre Gaigeot and Mischa Bonn and Ellen H G Backus}, doi = {10.1073/pnas.1819000116}, year = {2019}, date = {2019-01-01}, journal = {Proc. Natl. Acad. Sci.}, volume = {116}, number = {5}, pages = {1520-1525}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Solvent effects on the vibrational spectrum of 3-hydroxyflavone Article de journal A P Seitsonen; A Idrissi; S Protti; A Mezzetti Journal of Molecular Liquids, 275 , p. 723–728, 2019. @article{Seitsonen:2019, title = {Solvent effects on the vibrational spectrum of 3-hydroxyflavone}, author = {A P Seitsonen and A Idrissi and S Protti and A Mezzetti}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057841646&doi=10.1016%2fj.molliq.2018.11.020&partnerID=40&md5=21ae25517ffabf644cd8eb8d94d34435}, doi = {10.1016/j.molliq.2018.11.020}, year = {2019}, date = {2019-01-01}, journal = {Journal of Molecular Liquids}, volume = {275}, pages = {723--728}, abstract = {3-hydroxyflavone (3HF) is a widely studied molecule that acts as a simplified prototype of biological, more complex flavonoids. Its solvation mechanism is still under investigation. Here we report a joint experimental and simulation study of the vibrational properties of 3HF in gas phase and in simple liquids tetrachloromethane, chloroform and acetonitrile using infra-red (IR) and Raman spectroscopies. We find reasonably good agreement between the static and molecular dynamics simulations employing density functional theory at the level of generalised gradient approximation (GGA) and hybrid functionals, but the agreement with the experimental spectra is only reasonable in the case of the IR spectroscopy and relatively poor in the case of Raman spectroscopy. The results can, however, be used as a starting point for discussing the solvation behaviour of the flavonoids. © 2018}, keywords = {}, pubstate = {published}, tppubtype = {article} } 3-hydroxyflavone (3HF) is a widely studied molecule that acts as a simplified prototype of biological, more complex flavonoids. Its solvation mechanism is still under investigation. Here we report a joint experimental and simulation study of the vibrational properties of 3HF in gas phase and in simple liquids tetrachloromethane, chloroform and acetonitrile using infra-red (IR) and Raman spectroscopies. We find reasonably good agreement between the static and molecular dynamics simulations employing density functional theory at the level of generalised gradient approximation (GGA) and hybrid functionals, but the agreement with the experimental spectra is only reasonable in the case of the IR spectroscopy and relatively poor in the case of Raman spectroscopy. The results can, however, be used as a starting point for discussing the solvation behaviour of the flavonoids. © 2018 |
Deconvolution of BIL-SFG and DL-SFG spectroscopic signals reveals order/disorder of water at the elusive aqueous silica interface Article de journal Simone Pezzotti; Daria Ruth Galimberti; Marie-Pierre Gaigeot Phys. Chem. Chem. Phys., 21 , p. 22188-22202" doi ="10.1039/C9CP02766A, 2019. @article{Pezzotti_PCCP2019, title = {Deconvolution of BIL-SFG and DL-SFG spectroscopic signals reveals order/disorder of water at the elusive aqueous silica interface}, author = {Simone Pezzotti and Daria Ruth Galimberti and Marie-Pierre Gaigeot}, year = {2019}, date = {2019-01-01}, journal = {Phys. Chem. Chem. Phys.}, volume = {21}, pages = {22188-22202" doi ="10.1039/C9CP02766A}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Benzimidazoles as Metal-Free and Recyclable Hydrides for CO2 Reduction to Formate Article de journal C -H Lim; S Ilic; A Alherz; B T Worrell; S S Bacon; J T Hynes; K D Glusac; C B Musgrave Journal of the American Chemical Society, 141 (1), p. 272–280, 2019. @article{Lim:2019, title = {Benzimidazoles as Metal-Free and Recyclable Hydrides for CO2 Reduction to Formate}, author = {C -H Lim and S Ilic and A Alherz and B T Worrell and S S Bacon and J T Hynes and K D Glusac and C B Musgrave}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058544348&doi=10.1021%2fjacs.8b09653&partnerID=40&md5=538b0ec89a42c986b6e46df1217fc701}, doi = {10.1021/jacs.8b09653}, year = {2019}, date = {2019-01-01}, journal = {Journal of the American Chemical Society}, volume = {141}, number = {1}, pages = {272--280}, abstract = {We report a novel metal-free chemical reduction of CO2 by a recyclable benzimidazole-based organo-hydride, whose choice was guided by quantum chemical calculations. Notably, benzimidazole-based hydride donors rival the hydride-donating abilities of noble-metal-based hydrides such as [Ru(tpy)(bpy)H]+ and [Pt(depe)2H]+. Chemical CO2 reduction to the formate anion (HCOO-) was carried out in the absence of biological enzymes, a sacrificial Lewis acid, or a base to activate the substrate or reductant. 13CO2 experiments confirmed the formation of H13COO- by CO2 reduction with the formate product characterized by 1H NMR and 13C NMR spectroscopy and ESI-MS. The highest formate yield of 66% was obtained in the presence of potassium tetrafluoroborate under mild conditions. The likely role of exogenous salt additives in this reaction is to stabilize and shift the equilibrium toward the ionic products. After CO2 reduction, the benzimidazole-based hydride donor was quantitatively oxidized to its aromatic benzimidazolium cation, establishing its recyclability. In addition, we electrochemically reduced the benzimidazolium cation to its organo-hydride form in quantitative yield, demonstrating its potential for electrocatalytic CO2 reduction. These results serve as a proof of concept for the electrocatalytic reduction of CO2 by sustainable, recyclable, and metal-free organo-hydrides. © 2018 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report a novel metal-free chemical reduction of CO2 by a recyclable benzimidazole-based organo-hydride, whose choice was guided by quantum chemical calculations. Notably, benzimidazole-based hydride donors rival the hydride-donating abilities of noble-metal-based hydrides such as [Ru(tpy)(bpy)H]+ and [Pt(depe)2H]+. Chemical CO2 reduction to the formate anion (HCOO-) was carried out in the absence of biological enzymes, a sacrificial Lewis acid, or a base to activate the substrate or reductant. 13CO2 experiments confirmed the formation of H13COO- by CO2 reduction with the formate product characterized by 1H NMR and 13C NMR spectroscopy and ESI-MS. The highest formate yield of 66% was obtained in the presence of potassium tetrafluoroborate under mild conditions. The likely role of exogenous salt additives in this reaction is to stabilize and shift the equilibrium toward the ionic products. After CO2 reduction, the benzimidazole-based hydride donor was quantitatively oxidized to its aromatic benzimidazolium cation, establishing its recyclability. In addition, we electrochemically reduced the benzimidazolium cation to its organo-hydride form in quantitative yield, demonstrating its potential for electrocatalytic CO2 reduction. These results serve as a proof of concept for the electrocatalytic reduction of CO2 by sustainable, recyclable, and metal-free organo-hydrides. © 2018 American Chemical Society. |
Circular dichroism and angular deviation in x-ray absorption spectra of Dy2ScN@ C80 single-molecule magnets on h-BN/Rh(111) Article de journal T Greber; A P Seitsonen; A Hemmi; J Dreiser; R Stania; F Matsui; M Muntwiler; A A Popov; R Westerström Physical Review Materials, 3 (1), 2019. @article{Greber:2019, title = {Circular dichroism and angular deviation in x-ray absorption spectra of Dy2ScN@ C80 single-molecule magnets on h-BN/Rh(111)}, author = {T Greber and A P Seitsonen and A Hemmi and J Dreiser and R Stania and F Matsui and M Muntwiler and A A Popov and R Westerstr\"{o}m}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060612538&doi=10.1103%2fPhysRevMaterials.3.014409&partnerID=40&md5=b74a780f93dca9f124b95bcec5c689dc}, doi = {10.1103/PhysRevMaterials.3.014409}, year = {2019}, date = {2019-01-01}, journal = {Physical Review Materials}, volume = {3}, number = {1}, abstract = {Endohedral fullerenes, such as Dy2ScN@C80, are single-molecule magnets with long relaxation times of their magnetization. An open and anisotropic 4f electron shell in the lanthanides (here Dy) imposes a magnetic moment that maintains its orientation at liquid-helium temperatures for macroscopic times. If these molecules shall be used as single-bit information storage elements or for quantum operations, the orientation of the endohedral units and the orientation of the magnetic moments has to be controlled. X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (XMCD) - with variation of the angle of x-ray incidence - allows for the detection of these two structural elements. We present XMCD data of Dy2ScN@C80 on an h-BN/Rh(111) nanomesh that display at 2 K a large hysteresis with a coercive field of 0.4 T. The angular dependence of the XAS data at the Dy M5 edge indicates partial ordering of the endohedral units. In order to quantify anisotropic orientation we introduce the "deviation" D as an operational quantity that measures differences between two spectra. © 2019 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Endohedral fullerenes, such as Dy2ScN@C80, are single-molecule magnets with long relaxation times of their magnetization. An open and anisotropic 4f electron shell in the lanthanides (here Dy) imposes a magnetic moment that maintains its orientation at liquid-helium temperatures for macroscopic times. If these molecules shall be used as single-bit information storage elements or for quantum operations, the orientation of the endohedral units and the orientation of the magnetic moments has to be controlled. X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (XMCD) - with variation of the angle of x-ray incidence - allows for the detection of these two structural elements. We present XMCD data of Dy2ScN@C80 on an h-BN/Rh(111) nanomesh that display at 2 K a large hysteresis with a coercive field of 0.4 T. The angular dependence of the XAS data at the Dy M5 edge indicates partial ordering of the endohedral units. In order to quantify anisotropic orientation we introduce the "deviation" D as an operational quantity that measures differences between two spectra. © 2019 American Physical Society. |
Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions. Article de journal D Laage; G Stirnemann J Phys Chem B, 123 (15), p. 3312–3324, 2019. @article{Laage2019, title = {Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions.}, author = {D Laage and G Stirnemann}, year = {2019}, date = {2019-01-01}, journal = {J Phys Chem B}, volume = {123}, number = {15}, pages = {3312\textendash3324}, address = {PASTEUR, D\'{e}partement de chimie, \'{E}cole normale sup\'{e}rieure, PSL University, Sorbonne Universit\'{e}, CNRS, 75005 Paris, France. CNRS Laboratoire de Biochimie Th\'{e}orique, Institut de Biologie Physico-Chimique, PSL University, Sorbonne Paris Cit\'{e}, 13 rue Pierre et Marie Curie, 75005 Paris, France.}, abstract = {Aqueous ionic solutions are ubiquitous in chemistry and in biology. Experiments show that ions affect water dynamics, but a full understanding of several questions remains needed: why some salts accelerate water dynamics while others slow it down, why the effect of a given salt can be concentration-dependent, whether the effect of ions is rather local or more global. Numerical simulations are particularly suited to disentangle these different effects, but current force fields suffer from limitations and often lead to a poor description of dynamics in several aqueous salt solutions. Here, we develop an improved classical force field for the description of alkali halides that yields dynamics in excellent agreement with experimental measurements for water reorientational and translational dynamics. These simulations are analyzed with an extended jump model, which allows to compare the effects of ions on local hydrogen-bond exchange dynamics and on more global properties like viscosity. Our results unambiguously show that the ion-induced changes in water dynamics are usually mostly due to a local effect on the hydrogen-bond exchange dynamics; in contrast, the change in viscosity leads to a smaller effect, which governs the retardation only for a minority of salts and at high concentrations. We finally show how the respective importance of these two effects can be directly determined from experimental measurements alone, thus providing guidelines for the selection of an electrolyte with specific dynamical properties.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aqueous ionic solutions are ubiquitous in chemistry and in biology. Experiments show that ions affect water dynamics, but a full understanding of several questions remains needed: why some salts accelerate water dynamics while others slow it down, why the effect of a given salt can be concentration-dependent, whether the effect of ions is rather local or more global. Numerical simulations are particularly suited to disentangle these different effects, but current force fields suffer from limitations and often lead to a poor description of dynamics in several aqueous salt solutions. Here, we develop an improved classical force field for the description of alkali halides that yields dynamics in excellent agreement with experimental measurements for water reorientational and translational dynamics. These simulations are analyzed with an extended jump model, which allows to compare the effects of ions on local hydrogen-bond exchange dynamics and on more global properties like viscosity. Our results unambiguously show that the ion-induced changes in water dynamics are usually mostly due to a local effect on the hydrogen-bond exchange dynamics; in contrast, the change in viscosity leads to a smaller effect, which governs the retardation only for a minority of salts and at high concentrations. We finally show how the respective importance of these two effects can be directly determined from experimental measurements alone, thus providing guidelines for the selection of an electrolyte with specific dynamical properties. |