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.
2025 |
Why Proton Grotthuss Diffusion Slows down at the Air-Water Interface while Water Diffusion Accelerates. Article de journal Miguel de la Puente; Axel Gomez; Damien Laage J Phys Chem Lett, 16 (10), p. 2645–2653, 2025. @article{, title = {Why Proton Grotthuss Diffusion Slows down at the Air-Water Interface while Water Diffusion Accelerates.}, author = {Miguel de la Puente and Axel Gomez and Damien Laage}, year = {2025}, date = {2025-01-01}, journal = {J Phys Chem Lett}, volume = {16}, number = {10}, pages = {2645\textendash2653}, address = {Laboratory CPCV, Department of Chemistry, \'{E}cole Normale Sup\'{e}rieure, PSL University, Sorbonne Universit\'{e}, CNRS, 75005 Paris, France.}, abstract = {Excess proton diffusion at aqueous interfaces is crucial for applications including electrocatalysis, aerosol chemistry, and biological energy conversion. While interfaces have been proposed as pathways for channeling protons, proton diffusion at interfaces remains far less understood than in the bulk. Here we focus on the air-water interface and use density functional theory-based deep potential molecular dynamics simulations to reveal the contrasting interface’s impacts: excess proton diffusion slows down compared to the bulk, while water diffusion accelerates. This contrast stems from reduced hydrogen-bond coordination at the interface, which facilitates water diffusion and transient unstable proton rattling but impedes the stable proton hops central to Grotthuss diffusion. As a result, at the interface, excess protons and water molecules diffuse at comparable rates, in stark departure from bulk behavior. This mechanistic insight delineates distinct limiting regimes for bulk-enhanced interfacial proton diffusion, with important implications for interfacial chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Excess proton diffusion at aqueous interfaces is crucial for applications including electrocatalysis, aerosol chemistry, and biological energy conversion. While interfaces have been proposed as pathways for channeling protons, proton diffusion at interfaces remains far less understood than in the bulk. Here we focus on the air-water interface and use density functional theory-based deep potential molecular dynamics simulations to reveal the contrasting interface’s impacts: excess proton diffusion slows down compared to the bulk, while water diffusion accelerates. This contrast stems from reduced hydrogen-bond coordination at the interface, which facilitates water diffusion and transient unstable proton rattling but impedes the stable proton hops central to Grotthuss diffusion. As a result, at the interface, excess protons and water molecules diffuse at comparable rates, in stark departure from bulk behavior. This mechanistic insight delineates distinct limiting regimes for bulk-enhanced interfacial proton diffusion, with important implications for interfacial chemistry. |
Molecular dynamics simulations for enzymatic hydride- transfer reactions: Defining environmental reaction coordinates to capture transition state diversity Article de journal R García-Meseguer; E Duboué-Dijon; S Marti; Javier J Ruiz-Pernia; D Laage; I Tuñón; J T Hynes J Chem Phys, 162 , p. 124118, 2025. @article{, title = {Molecular dynamics simulations for enzymatic hydride- transfer reactions: Defining environmental reaction coordinates to capture transition state diversity}, author = {R Garc\'{i}a-Meseguer and E Dubou\'{e}-Dijon and S Marti and Javier J Ruiz-Pernia and D Laage and I Tu\~{n}\'{o}n and J T Hynes}, year = {2025}, date = {2025-01-01}, journal = {J Chem Phys}, volume = {162}, pages = {124118}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials. Article de journal R David; M de la Puente; A Gomez; O Anton; G Stirnemann; D Laage Digit Discov, 4 (1), p. 54–72, 2025. @article{, title = {ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials.}, author = {R David and M de la Puente and A Gomez and O Anton and G Stirnemann and D Laage}, year = {2025}, date = {2025-01-01}, journal = {Digit Discov}, volume = {4}, number = {1}, pages = {54\textendash72}, address = {PASTEUR, D\'{e}partement de Chimie, \'{E}cole Normale Sup\'{e}rieure, PSL University, Sorbonne Universit\'{e}, CNRS 75005 Paris France rolf.david@ens.psl.eu guillaume.stirnemann@ens.psl.eu damien.laage@ens.psl.eu.}, abstract = {The emergence of artificial intelligence is profoundly impacting computational chemistry, particularly through machine-learning interatomic potentials (MLIPs). Unlike traditional potential energy surface representations, MLIPs overcome the conventional computational scaling limitations by offering an effective combination of accuracy and efficiency for calculating atomic energies and forces to be used in molecular simulations. These MLIPs have significantly enhanced molecular simulations across various applications, including large-scale simulations of materials, interfaces, chemical reactions, and beyond. Despite these advances, the construction of training datasets-a critical component for the accuracy of MLIPs-has not received proportional attention, especially in the context of chemical reactivity, which depends on rare barrier-crossing events that are not easily included in the datasets. Here we address this gap by introducing ArcaNN, a comprehensive framework designed for generating training datasets for reactive MLIPs. ArcaNN employs a concurrent learning approach combined with advanced sampling techniques to ensure an accurate representation of high-energy geometries. The framework integrates automated processes for iterative training, exploration, new configuration selection, and energy and force labeling, all while ensuring reproducibility and documentation. We demonstrate ArcaNN’s capabilities through two paradigm reactions: a nucleophilic substitution and a Diels-Alder reaction. These examples showcase its effectiveness, the uniformly low error of the resulting MLIP everywhere along the chemical reaction coordinate, and its potential for broad applications in reactive molecular dynamics. Finally, we provide guidelines for assessing the quality of MLIPs in reactive systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The emergence of artificial intelligence is profoundly impacting computational chemistry, particularly through machine-learning interatomic potentials (MLIPs). Unlike traditional potential energy surface representations, MLIPs overcome the conventional computational scaling limitations by offering an effective combination of accuracy and efficiency for calculating atomic energies and forces to be used in molecular simulations. These MLIPs have significantly enhanced molecular simulations across various applications, including large-scale simulations of materials, interfaces, chemical reactions, and beyond. Despite these advances, the construction of training datasets-a critical component for the accuracy of MLIPs-has not received proportional attention, especially in the context of chemical reactivity, which depends on rare barrier-crossing events that are not easily included in the datasets. Here we address this gap by introducing ArcaNN, a comprehensive framework designed for generating training datasets for reactive MLIPs. ArcaNN employs a concurrent learning approach combined with advanced sampling techniques to ensure an accurate representation of high-energy geometries. The framework integrates automated processes for iterative training, exploration, new configuration selection, and energy and force labeling, all while ensuring reproducibility and documentation. We demonstrate ArcaNN’s capabilities through two paradigm reactions: a nucleophilic substitution and a Diels-Alder reaction. These examples showcase its effectiveness, the uniformly low error of the resulting MLIP everywhere along the chemical reaction coordinate, and its potential for broad applications in reactive molecular dynamics. Finally, we provide guidelines for assessing the quality of MLIPs in reactive systems. |
2024 |
Structural Optimization of Azacryptands for Targeting Three-Way DNA Junctions Article de journal Angélique Pipier; Titouan Chetot; Apollonia Kalamatianou; Nicolas Martin; Maëlle Caroff; Sébastien Britton; Nicolas Chéron; Lukáš Trantírek; Anton Granzhan; David Monchaud Angewandte Chemie International Edition, n/a (n/a), p. e202409780, 2024. @article{https://doi.org/10.1002/anie.202409780, title = {Structural Optimization of Azacryptands for Targeting Three-Way DNA Junctions}, author = {Ang\'{e}lique Pipier and Titouan Chetot and Apollonia Kalamatianou and Nicolas Martin and Ma\"{e}lle Caroff and S\'{e}bastien Britton and Nicolas Ch\'{e}ron and Luk\'{a}\v{s} Trant\'{i}rek and Anton Granzhan and David Monchaud}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202409780}, doi = {https://doi.org/10.1002/anie.202409780}, year = {2024}, date = {2024-06-14}, journal = {Angewandte Chemie International Edition}, volume = {n/a}, number = {n/a}, pages = {e202409780}, abstract = {Transient melting of the duplex-DNA (B-DNA) during DNA transactions allows repeated sequences to fold into non-B DNA structures, including DNA junctions and G-quadruplexes. These noncanonical structures can act as impediments to DNA polymerase progression along the duplex, thereby triggering DNA damage and ultimately jeopardizing genomic stability. Their stabilization by ad hoc ligands is currently being explored as a putative anticancer strategy since it might represent an efficient way to inflict toxic DNA damage specifically to rapidly dividing cancer cells. The relevance of this strategy is only emerging for three-way DNA junctions (TWJs) and, to date, no molecule has been recognized as a reference TWJ ligand, featuring both high affinity and selectivity. Herein, we characterize such reference ligands through a combination of in vitro techniques comprising affinity and selectivity assays (competitive FRET-melting and TWJ Screen assays), functional tests (qPCR and Taq stop assays), and structural analyses (molecular dynamics and NMR investigations). We identify novel azacryptands TrisNP-amphi and TrisNP-ana as the most promising ligands, interacting with TWJs with high affinity and selectivity. These ligands represent new molecular tools to investigate the cellular roles of TWJs and explore how they can be exploited in innovative anticancer therapies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Transient melting of the duplex-DNA (B-DNA) during DNA transactions allows repeated sequences to fold into non-B DNA structures, including DNA junctions and G-quadruplexes. These noncanonical structures can act as impediments to DNA polymerase progression along the duplex, thereby triggering DNA damage and ultimately jeopardizing genomic stability. Their stabilization by ad hoc ligands is currently being explored as a putative anticancer strategy since it might represent an efficient way to inflict toxic DNA damage specifically to rapidly dividing cancer cells. The relevance of this strategy is only emerging for three-way DNA junctions (TWJs) and, to date, no molecule has been recognized as a reference TWJ ligand, featuring both high affinity and selectivity. Herein, we characterize such reference ligands through a combination of in vitro techniques comprising affinity and selectivity assays (competitive FRET-melting and TWJ Screen assays), functional tests (qPCR and Taq stop assays), and structural analyses (molecular dynamics and NMR investigations). We identify novel azacryptands TrisNP-amphi and TrisNP-ana as the most promising ligands, interacting with TWJs with high affinity and selectivity. These ligands represent new molecular tools to investigate the cellular roles of TWJs and explore how they can be exploited in innovative anticancer therapies. |
Competing reaction mechanisms of peptide bond formation in water revealed by deep potential molecular dynamics and path sampling Article de journal Rolf David; Iñaki Tuñón; Damien Laage J Am Chem Soc, 2024. @article{David2024, title = {Competing reaction mechanisms of peptide bond formation in water revealed by deep potential molecular dynamics and path sampling}, author = {Rolf David and I\~{n}aki Tu\~{n}\'{o}n and Damien Laage}, year = {2024}, date = {2024-01-01}, journal = {J Am Chem Soc}, abstract = {… the presence of two competing distinct mechanisms for peptide … both reaction pathways, via a general base catalysis mechanism … This result contrasts with the conventional mechanism …}, keywords = {}, pubstate = {published}, tppubtype = {article} } … the presence of two competing distinct mechanisms for peptide … both reaction pathways, via a general base catalysis mechanism … This result contrasts with the conventional mechanism … |
Neural-network-based molecular dynamics simulations reveal that proton transport in water is doubly gated by sequential hydrogen-bond exchange Article de journal Axel Gomez; Ward H Thompson; Damien Laage Nature Chem, 16 , p. 1838, 2024. @article{, title = {Neural-network-based molecular dynamics simulations reveal that proton transport in water is doubly gated by sequential hydrogen-bond exchange}, author = {Axel Gomez and Ward H Thompson and Damien Laage}, year = {2024}, date = {2024-01-01}, journal = {Nature Chem}, volume = {16}, pages = {1838}, abstract = {… calculations and neural-network-based molecular dynamics simulations that account for … proton transport mechanism. Our simulations reveal an equilibrium between two stable proton-…}, keywords = {}, pubstate = {published}, tppubtype = {article} } … calculations and neural-network-based molecular dynamics simulations that account for … proton transport mechanism. Our simulations reveal an equilibrium between two stable proton-… |
Are changes in antibiotic prophylaxis recommendations responsible for an increased risk of cefazolin allergy? Article de journal Nicolas Chéron; Luc de Chaisemartin; Simon Aubert; Felix Laborier; Philippe Montravers; Catherine Neukirch; Aurélie Gouel-Chéron Anaesthesia Critical Care & Pain Medicine, 43 (2), p. 101349, 2024, ISSN: 2352-5568. @article{CHERON2024101349, title = {Are changes in antibiotic prophylaxis recommendations responsible for an increased risk of cefazolin allergy?}, author = {Nicolas Ch\'{e}ron and Luc de Chaisemartin and Simon Aubert and Felix Laborier and Philippe Montravers and Catherine Neukirch and Aur\'{e}lie Gouel-Ch\'{e}ron}, url = {https://www.sciencedirect.com/science/article/pii/S2352556824000079}, doi = {https://doi.org/10.1016/j.accpm.2024.101349}, issn = {2352-5568}, year = {2024}, date = {2024-01-01}, journal = {Anaesthesia Critical Care & Pain Medicine}, volume = {43}, number = {2}, pages = {101349}, abstract = {Background The first line of prevention of surgical site infection relies on the timely administration of antibiotic prophylaxis. First- and second-generation cephalosporins are the most recommended antibiotics in elective surgery. The incidence of cefazolin allergy has increased worldwide over the years. The sensitization mechanism of cefazolin is currently unknown, and data supporting cross-reactivity between penicillins and cephalosporins are lacking. Sensitization could occur through previous exposure either to cefazolin or to structurally related chemical agents. The objective of this study was to evaluate sensitization agents towards cefazolin. Methods The OpenBabel chemoinformatics toolbox was used to search for similarities between cefazolin and other molecules in an extensive drug database. Using the pholcodine-rocuronium similarity score as a threshold, we selected drugs with the most similar structure to that of cefazolin. Exposure to those drugs and cefazolin was assessed in a cohort of patients with skin test-proven cefazolin allergy at a specialized allergy centre via a self-administered anonymous questionnaire. Results Using the pholcodine-rocuronium similarity score as a threshold (score≥0.7), 42 molecules were found to be similar to cefazolin (all cephalosporins). Only 8 were marketed in France. None of the 14 cefazolin-allergic patients who answered the questionnaire (65% female, median age 56 years) reported exposure to any identified antibiotics. In contrast, 11 (78%) had at least one previous surgery requiring cefazolin before the index case. Conclusion Direct previous cefazolin exposure was identified in 78% of cefazolin-allergic patients. Cefazolin started to take a central place in antibiotic prophylaxis after 2010, when cefamandole usage decreased drastically. Changes in antibiotic prophylaxis over the past 14 years in France could have been the turning point for the increased incidence of cefazolin allergy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background The first line of prevention of surgical site infection relies on the timely administration of antibiotic prophylaxis. First- and second-generation cephalosporins are the most recommended antibiotics in elective surgery. The incidence of cefazolin allergy has increased worldwide over the years. The sensitization mechanism of cefazolin is currently unknown, and data supporting cross-reactivity between penicillins and cephalosporins are lacking. Sensitization could occur through previous exposure either to cefazolin or to structurally related chemical agents. The objective of this study was to evaluate sensitization agents towards cefazolin. Methods The OpenBabel chemoinformatics toolbox was used to search for similarities between cefazolin and other molecules in an extensive drug database. Using the pholcodine-rocuronium similarity score as a threshold, we selected drugs with the most similar structure to that of cefazolin. Exposure to those drugs and cefazolin was assessed in a cohort of patients with skin test-proven cefazolin allergy at a specialized allergy centre via a self-administered anonymous questionnaire. Results Using the pholcodine-rocuronium similarity score as a threshold (score≥0.7), 42 molecules were found to be similar to cefazolin (all cephalosporins). Only 8 were marketed in France. None of the 14 cefazolin-allergic patients who answered the questionnaire (65% female, median age 56 years) reported exposure to any identified antibiotics. In contrast, 11 (78%) had at least one previous surgery requiring cefazolin before the index case. Conclusion Direct previous cefazolin exposure was identified in 78% of cefazolin-allergic patients. Cefazolin started to take a central place in antibiotic prophylaxis after 2010, when cefamandole usage decreased drastically. Changes in antibiotic prophylaxis over the past 14 years in France could have been the turning point for the increased incidence of cefazolin allergy. |
Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase Article de journal Nicolas Chéron Journal of Chemical Information and Modeling, 64 (8), p. 3375-3385, 2024, (PMID: 38533570). @article{doi:10.1021/acs.jcim.3c01830, title = {Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase}, author = {Nicolas Ch\'{e}ron}, url = {https://doi.org/10.1021/acs.jcim.3c01830}, doi = {10.1021/acs.jcim.3c01830}, year = {2024}, date = {2024-01-01}, journal = {Journal of Chemical Information and Modeling}, volume = {64}, number = {8}, pages = {3375-3385}, note = {PMID: 38533570}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tuning Acid–Base Chemistry at an Electrified Gold/Water Interface Article de journal Steffen Murke; Wanlin Chen; Simone Pezzotti; Martina Havenith J. Am. Chem. Soc., 146 (18), p. 12423-12430, 2024. @article{TuningAcidBase_JACS, title = {Tuning Acid\textendashBase Chemistry at an Electrified Gold/Water Interface}, author = {Steffen Murke and Wanlin Chen and Simone Pezzotti and Martina Havenith}, doi = {10.1021/jacs.3c13633}, year = {2024}, date = {2024-01-01}, journal = {J. Am. Chem. Soc.}, volume = {146}, number = {18}, pages = {12423-12430}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
SOS: Shape, orientation, and size tune solvation in electrocatalysis Article de journal Alessandra Serva; Simone Pezzotti J. Chem. Phys., 160 (9), 2024. @article{serva2024sos, title = {SOS: Shape, orientation, and size tune solvation in electrocatalysis}, author = {Alessandra Serva and Simone Pezzotti}, year = {2024}, date = {2024-01-01}, journal = {J. Chem. Phys.}, volume = {160}, number = {9}, publisher = {AIP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hydration water drives the self-assembly of guanosine monophosphate Article de journal Yu Heng Tao; Simon Schulke; Gerhard Schwaab; Gareth L Nealon; Simone Pezzotti; Stuart I Hodgetts; Alan R Harvey; Martina Havenith; Vincent P Wallace Biophys. J., 123 (8), p. 931–939, 2024. @article{tao2024hydration, title = {Hydration water drives the self-assembly of guanosine monophosphate}, author = {Yu Heng Tao and Simon Schulke and Gerhard Schwaab and Gareth L Nealon and Simone Pezzotti and Stuart I Hodgetts and Alan R Harvey and Martina Havenith and Vincent P Wallace}, year = {2024}, date = {2024-01-01}, journal = {Biophys. J.}, volume = {123}, number = {8}, pages = {931--939}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Neural network potentials for exploring condensed phase chemical reactivity Article de journal Axel Gomez; Miguel de la Puente; Rolf David; Damien Laage Comptes Rendus. Chimie, 27 (S5), p. 1–17, 2024. @article{, title = {Neural network potentials for exploring condensed phase chemical reactivity}, author = {Axel Gomez and Miguel de la Puente and Rolf David and Damien Laage}, year = {2024}, date = {2024-01-01}, journal = {Comptes Rendus. Chimie}, volume = {27}, number = {S5}, pages = {1\textendash17}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Activation and friction in enzymatic loop opening and closing dynamics Article de journal Kirill Zinovjev; Paul Guénon; Carlos A Ramos-Guzmán; Javier J Ruiz-Pernía; Damien Laage; Iñaki Tuñón Nat Commun, 15 , p. 2490, 2024. @article{Zinovjev2024, title = {Activation and friction in enzymatic loop opening and closing dynamics}, author = {Kirill Zinovjev and Paul Gu\'{e}non and Carlos A Ramos-Guzm\'{a}n and Javier J Ruiz-Pern\'{i}a and Damien Laage and I\~{n}aki Tu\~{n}\'{o}n}, year = {2024}, date = {2024-01-01}, journal = {Nat Commun}, volume = {15}, pages = {2490}, abstract = {… loop opening and closing is strongly activated. It is governed by torsional rearrangement around a single loop …, which can dynamically trap the loop. Considering both torsional barrier …}, keywords = {}, pubstate = {published}, tppubtype = {article} } … loop opening and closing is strongly activated. It is governed by torsional rearrangement around a single loop …, which can dynamically trap the loop. Considering both torsional barrier … |
Solid-liquid interfaces: Atomic-scale structure and dynamics Article de journal Angela Stelson; Damien Laage; Kathleen Schwarz; Ravishankar Sundararaman J Appl Phys, 135 (16), p. 160401, 2024. @article{Stelson2024, title = {Solid-liquid interfaces: Atomic-scale structure and dynamics}, author = {Angela Stelson and Damien Laage and Kathleen Schwarz and Ravishankar Sundararaman}, year = {2024}, date = {2024-01-01}, journal = {J Appl Phys}, volume = {135}, number = {16}, pages = {160401}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
A Structure-Dynamics Relationship Enables Prediction of the Water Hydrogen Bond Exchange Activation Energy from Experimental Data Article de journal Zeke A Piskulich; Damien Laage; Ward H Thompson Chem Sci, 2024. @article{, title = {A Structure-Dynamics Relationship Enables Prediction of the Water Hydrogen Bond Exchange Activation Energy from Experimental Data}, author = {Zeke A Piskulich and Damien Laage and Ward H Thompson}, year = {2024}, date = {2024-01-01}, journal = {Chem Sci}, abstract = {It has long been understood that the structural features of water are determined by hydrogen bonding (H-bonding) and that the exchange of, or between, H-bond partners underlies many of.}, keywords = {}, pubstate = {published}, tppubtype = {article} } It has long been understood that the structural features of water are determined by hydrogen bonding (H-bonding) and that the exchange of, or between, H-bond partners underlies many of. |
Neural Network-Based Sum-Frequency Generation Spectra of Pure and Acidified Water Interfaces with Air Article de journal M de la Puente; A Gomez; D Laage J Phys Chem Lett, 15 , p. 3096–3102, 2024. @article{delaPuente2024, title = {Neural Network-Based Sum-Frequency Generation Spectra of Pure and Acidified Water Interfaces with Air}, author = {M de la Puente and A Gomez and D Laage}, year = {2024}, date = {2024-01-01}, journal = {J Phys Chem Lett}, volume = {15}, pages = {3096\textendash3102}, abstract = {J. Phys. Chem. Lett. 0.0:3096-3102}, keywords = {}, pubstate = {published}, tppubtype = {article} } J. Phys. Chem. Lett. 0.0:3096-3102 |
Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences. Article de journal E Frezza; D Laage; E Duboué-Dijon J Phys Chem Lett, p. 4351–4358, 2024. @article{Frezza2024, title = {Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences.}, author = {E Frezza and D Laage and E Dubou\'{e}-Dijon}, year = {2024}, date = {2024-01-01}, journal = {J Phys Chem Lett}, pages = {4351\textendash4358}, address = {Universit\'{e} Paris Cit\'{e}, CNRS, CiTCoM, Paris 75006, France. PASTEUR, Department of Chemistry, \'{E}cole Normale Sup\'{e}rieure-PSL, Sorbonne Universit\'{e}, CNRS, Paris 75005, France. Universit\'{e} Paris Cit\'{e}, CNRS, Laboratoire de Biochimie Th\'{e}orique, 13 rue Pierre et Marie Curie, Paris 75005, France.}, abstract = {Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms O|R| and O|S| in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA O|R| sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to O|R|, due to the different phosphate orientations in A-form double helical RNA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms O|R| and O|S| in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA O|R| sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to O|R|, due to the different phosphate orientations in A-form double helical RNA. |
Impact of interfacial curvature on molecular properties of aqueous interfaces Article de journal M de la Puente; D Laage J Chem Phys, 160 , p. 234504, 2024. @article{delaPuente2024a, title = {Impact of interfacial curvature on molecular properties of aqueous interfaces}, author = {M de la Puente and D Laage}, year = {2024}, date = {2024-01-01}, journal = {J Chem Phys}, volume = {160}, pages = {234504}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2023 |
Real-time measure of solvation free energy changes upon liquid-liquid phase separation of $alpha$-elastin Article de journal Benedikt König; Simone Pezzotti; Sashary Ramos; Gerhard Schwaab; Martina Havenith Biophys. J. doi = https://doi.org/10.1016/j.bpj.2023.07.023, 2023. @article{konig2023LLPS, title = {Real-time measure of solvation free energy changes upon liquid-liquid phase separation of $alpha$-elastin}, author = {Benedikt K\"{o}nig and Simone Pezzotti and Sashary Ramos and Gerhard Schwaab and Martina Havenith}, year = {2023}, date = {2023-01-01}, journal = {Biophys. J. doi = https://doi.org/10.1016/j.bpj.2023.07.023}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
How the Acidity of Water Droplets and Films Is Controlled by the Air–Water Interface Article de journal Miguel de la Puente; Damien Laage J Am Chem Soc, 145 , p. 25186–25194, 2023. @article{delaPuente2023, title = {How the Acidity of Water Droplets and Films Is Controlled by the Air\textendashWater Interface}, author = {Miguel de la Puente and Damien Laage}, year = {2023}, date = {2023-01-01}, journal = {J Am Chem Soc}, volume = {145}, pages = {25186\textendash25194}, abstract = {Acidity is a key determinant of chemical reactivity in atmospheric aqueous aerosols and water microdroplets used for catalysis. However, many fundamental questions about these …}, keywords = {}, pubstate = {published}, tppubtype = {article} } Acidity is a key determinant of chemical reactivity in atmospheric aqueous aerosols and water microdroplets used for catalysis. However, many fundamental questions about these … |
Local solvation structures govern the mixing thermodynamics of glycerol--water solutions Article de journal Debasish Das Mahanta; Dennis Robinson Brown; Simone Pezzotti; Songi Han; Gerhard Schwaab; Scott M Shell; Martina Havenith Chem.Sci., 14 (26), p. 7381–7392, 2023. @article{debasish2023Glycerol, title = {Local solvation structures govern the mixing thermodynamics of glycerol--water solutions}, author = {Debasish Das Mahanta and Dennis Robinson Brown and Simone Pezzotti and Songi Han and Gerhard Schwaab and Scott M Shell and Martina Havenith}, year = {2023}, date = {2023-01-01}, journal = {Chem.Sci.}, volume = {14}, number = {26}, pages = {7381--7392}, publisher = {Royal Society of Chemistry}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hydration makes a difference! How to tune protein complexes between liquid-liquid and liquid-solid phase separation. Article de journal Sashary Ramos; Janine Kamps; Simone Pezzotti; Konstanze Winklhofer; Jorg Tatzelt; Martina Havenith Phys. Chem. Chem. Phys., 2023. @article{ramos2023hydration, title = {Hydration makes a difference! How to tune protein complexes between liquid-liquid and liquid-solid phase separation.}, author = {Sashary Ramos and Janine Kamps and Simone Pezzotti and Konstanze Winklhofer and Jorg Tatzelt and Martina Havenith}, doi = {10.1039/D3CP03299J}, year = {2023}, date = {2023-01-01}, journal = {Phys. Chem. Chem. Phys.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dielectric response of confined water films from a classical density functional theory perspective Article de journal Daniel Borgis; Damien Laage; Luc Belloni; Guillaume Jeanmairet Chem Sci, 14 (40), p. 11141–11150, 2023. @article{Borgis2023, title = {Dielectric response of confined water films from a classical density functional theory perspective}, author = {Daniel Borgis and Damien Laage and Luc Belloni and Guillaume Jeanmairet}, year = {2023}, date = {2023-01-01}, journal = {Chem Sci}, volume = {14}, number = {40}, pages = {11141\textendash11150}, abstract = {Classical density functional theory confirms and explains the low dielectric constants measured for nanoscale slits containing a high dielectric constant liquid.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Classical density functional theory confirms and explains the low dielectric constants measured for nanoscale slits containing a high dielectric constant liquid. |
On the trail of molecular hydrophilicity and hydrophobicity at aqueous interfaces Article de journal Wanlin Chen; Stephanie E Sanders; Burak Ozdamar; Dorian Louaas; Flavio Siro Brigiano; Simone Pezzotti; Poul B Petersen; Marie-Pierre Gaigeot J. Phys. Chem. Lett., 14 (5), p. 1301–1309, 2023. @article{chen2023trail, title = {On the trail of molecular hydrophilicity and hydrophobicity at aqueous interfaces}, author = {Wanlin Chen and Stephanie E Sanders and Burak Ozdamar and Dorian Louaas and Flavio Siro Brigiano and Simone Pezzotti and Poul B Petersen and Marie-Pierre Gaigeot}, year = {2023}, date = {2023-01-01}, journal = {J. Phys. Chem. Lett.}, volume = {14}, number = {5}, pages = {1301--1309}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Liquid--Liquid Phase Separation? Ask the Water! Article de journal Simone Pezzotti; Benedikt König; Sashary Ramos; Gerhard Schwaab; Martina Havenith J. Phys. Chem. Lett., 14 (6), p. 1556–1563, 2023. @article{pezzotti2023LLPS, title = {Liquid--Liquid Phase Separation? Ask the Water!}, author = {Simone Pezzotti and Benedikt K\"{o}nig and Sashary Ramos and Gerhard Schwaab and Martina Havenith}, year = {2023}, date = {2023-01-01}, journal = {J. Phys. Chem. Lett.}, volume = {14}, number = {6}, pages = {1556--1563}, publisher = {ACS Publications}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2022 |
Explicit models of motions to understand protein side-chain dynamics Article de journal Nicolas Bolik-Coulon; Olivier Languin-Cattoën; Diego Carnevale; Milan Zachrdla; Damien Laage; Fabio Sterpone; Guillaume Stirnemann; Fabien Ferrage Physical Review Letters, 129 , p. 203001, 2022. @article{Bolik-Coulon2022b, title = {Explicit models of motions to understand protein side-chain dynamics}, author = {Nicolas Bolik-Coulon and Olivier Languin-Catto\"{e}n and Diego Carnevale and Milan Zachrdla and Damien Laage and Fabio Sterpone and Guillaume Stirnemann and Fabien Ferrage }, url = {https://doi.org/10.1103/PhysRevLett.129.203001 }, doi = {10.1103/PhysRevLett.129.203001 }, year = {2022}, date = {2022-11-10}, journal = {Physical Review Letters}, volume = {129 }, pages = {203001}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
The soft breeze of the cation atmosphere around DNA Article de journal Fabien Ferrage; Damien Laage Biophysical Journal, 121 , p. 3307, 2022. @article{Ferrage2022, title = {The soft breeze of the cation atmosphere around DNA}, author = {Fabien Ferrage and Damien Laage }, url = {https://doi.org/10.1016/j.bpj.2022.08.003 }, doi = {10.1016/j.bpj.2022.08.003 }, year = {2022}, date = {2022-09-20}, journal = {Biophysical Journal}, volume = {121}, pages = {3307}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
On water reorientation dynamics in cation hydration shells Article de journal Eva Pluhařová; Guillaume Stirnemann; Damien Laage J Mol Liq, 363 , p. 119886, 2022. @article{, title = {On water reorientation dynamics in cation hydration shells}, author = {Eva Pluha\v{r}ov\'{a} and Guillaume Stirnemann and Damien Laage}, year = {2022}, date = {2022-01-01}, journal = {J Mol Liq}, volume = {363}, pages = {119886}, 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} } |
Explicit models of motions to understand protein side-chain dynamics Article de journal Nicolas Bolik-Coulon; Olivier Languin-Cattoën; Diego Carnevale; Milan Zachrdla; Damien Laage; Fabio Sterpone; Guillaume Stirnemann; Fabien Ferrage Phys Rev Lett, 129 , p. 203001, 2022. @article{, title = {Explicit models of motions to understand protein side-chain dynamics}, author = {Nicolas Bolik-Coulon and Olivier Languin-Catto\"{e}n and Diego Carnevale and Milan Zachrdla and Damien Laage and Fabio Sterpone and Guillaume Stirnemann and Fabien Ferrage}, year = {2022}, date = {2022-01-01}, journal = {Phys Rev Lett}, volume = {129}, pages = {203001}, abstract = {Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy. |