Doing Charges Right: Modelling Ion-Controlled Biological Processes with the Correct Toolbox

Project Information

Q-SCALING

Grant agreement ID: 101095957

DOI

10.3030/101095957

EC signature date 8 June 2023

Start date 1 October 2023

End date 30 September 2028

Funded under

• European Research Council (ERC)

Total cost

€ 2 499 115,00

EU contribution

€ 2 499 115,00

Coordinated by

USTAV ORGANICKE CHEMIE A BIOCHEMIE, AV CR, V.V.I.
Czechia

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (12)

Ion pairing in aqueous tetramethylammonium–acetate solutions by neutron scattering and molecular dynamics simulations

Author(s): Ngoc Lan Le Nguyen, Ondrej Tichacek, Pavel Jungwirth, Hector Martinez-Seara, Philip E. Mason, Elise Duboué-Dijon
Published in: Physical Chemistry Chemical Physics, 2025, ISSN 1463-9076
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.1039/D4CP04312J

Hydration of biologically relevant tetramethylammonium cation by neutron scattering and molecular dynamics

Author(s): Philip E. Mason, Tomas Martinek, Balázs Fábián, Mario Vazdar, Pavel Jungwirth, Ondrej Tichacek, Elise Duboué-Dijon, Hector Martinez-Seara
Published in: Physical Chemistry Chemical Physics, Issue 26, 2024, ISSN 1463-9076
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.1039/D3CP05449G

Nonaqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations

Author(s): Vojtech Kostal, Pavel Jungwirth, Hector Martinez-Seara
Published in: The Journal of Physical Chemistry Letters, Issue 14, 2023, ISSN 1948-7185
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPCLETT.3C02231

From the outer ear to the nerve: A complete computer model of the peripheral auditory system

Author(s): Ondrej Tichacek, Pavel Mistrík, Pavel Jungwirth
Published in: Hearing Research, Issue 440, 2024, ISSN 0378-5955
Publisher: Elsevier BV
DOI: 10.1016/J.HEARES.2023.108900

Cation−π Interactions in Biomolecular Contexts by Neutron Scattering and Molecular Dynamics: A Case Study of the Tetramethylammonium Cation

Author(s): Matej Cervenka, Brennon L. Shanks, Philip E. Mason, Pavel Jungwirth
Published in: The Journal of Physical Chemistry B, Issue 129, 2025, ISSN 1520-6106
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPCB.5C02001

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

Author(s): Ricky Nencini, Carmelo Tempra, Denys Biriukov, Miguel Riopedre-Fernandez, Victor Cruces Chamorro, Jakub Polák, Philip E. Mason, Daniel Ondo, Jan Heyda, O. H. Samuli Ollila, Pavel Jungwirth, Matti Javanainen, Hector Martinez-Seara
Published in: Journal of Chemical Theory and Computation, Issue 20, 2024, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.4C00743

Charge Scaling Force Field for Biologically Relevant Ions Utilizing a Global Optimization Method

Author(s): Shujie Fan, Philip E. Mason, Victor Cruces Chamorro, Brennon L. Shanks, Hector Martinez-Seara, Pavel Jungwirth
Published in: Journal of Chemical Theory and Computation, Issue 21, 2025, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.5C00873

NMR-Derived Salt Bridges in Insulin Analogue: Resolving Artifactual Overbinding in Molecular Dynamics via Charge Scaling

Author(s): Ngoc Lan Le Nguyen, Jiří Žák, Pavel Jungwirth, Martin Lepšík
Published in: The Journal of Physical Chemistry Letters, Issue 16, 2025, ISSN 1948-7185
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPCLETT.5C01786

Building Water Models Compatible with Charge Scaling Molecular Dynamics

Author(s): Victor Cruces Chamorro, Pavel Jungwirth, Hector Martinez-Seara
Published in: The Journal of Physical Chemistry Letters, Issue 15, 2024, ISSN 1948-7185
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPCLETT.4C00344

Rapid flipping between electrolyte and metallic states in ammonia solutions of alkali metals

Author(s): Marco Vitek, Igor Rončević, Ondrej Marsalek, H. Christian Schewe, Pavel Jungwirth
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-59071-Z

Hydration numbers of biologically relevant divalent metal cations from <i>ab initio</i> molecular dynamics and continuum solvation methods

Author(s): Tadeáš Kalvoda, Tomas Martinek, Pavel Jungwirth, Lubomír Rulíšek
Published in: The Journal of Chemical Physics, Issue 160, 2024, ISSN 0021-9606
Publisher: AIP Publishing
DOI: 10.1063/5.0192024

Stability and Reactivity of Aromatic Radical Anions in Solution with Relevance to Birch Reduction

Author(s): Tatiana Nemirovich, Brandon Young, Krystof Brezina, Philip E. Mason, Robert Seidel, Dominik Stemer, Bernd Winter, Pavel Jungwirth, Stephen E. Bradforth, H. Christian Schewe
Published in: Journal of the American Chemical Society, Issue 146, 2024, ISSN 0002-7863
Publisher: American Chemical Society (ACS)
DOI: 10.1021/JACS.3C11655