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.
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. |
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. |
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} } |
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 … |
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 … |
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} } |
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. |
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 |
2023 |
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. |
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 … |
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} } |
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} } |
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} } |
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} } |
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} } |
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. |
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} } |
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} } |
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} } |
Unexpectedly High Capacitance of the Metal Nanoparticle/Water Interface: Molecular-Level Insights into the Electrical Double Layer Article de journal Mahnaz Azimzadeh Sani; Nicholas G Pavlopoulos; Simone Pezzotti; Alessandra Serva; Paolo Cignoni; Julia Linnemann; Mathieu Salanne; Marie-Pierre Gaigeot; Kristina Tschulik Angew. Chem., Int. Ed., 134 (5), p. e202112679, 2022. @article{azimzadeh2022unexpectedly, title = {Unexpectedly High Capacitance of the Metal Nanoparticle/Water Interface: Molecular-Level Insights into the Electrical Double Layer}, author = {Mahnaz Azimzadeh Sani and Nicholas G Pavlopoulos and Simone Pezzotti and Alessandra Serva and Paolo Cignoni and Julia Linnemann and Mathieu Salanne and Marie-Pierre Gaigeot and Kristina Tschulik}, year = {2022}, date = {2022-01-01}, journal = {Angew. Chem., Int. Ed.}, volume = {134}, number = {5}, pages = {e202112679}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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} } |
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. |