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Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems

English title Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems
Applicant Meuwly Markus
Number 169079
Funding scheme Project funding
Research institution Physikalische Chemie Departement Chemie Universität Basel
Institution of higher education University of Basel - BS
Main discipline Physical Chemistry
Start/End 01.10.2016 - 30.09.2019
Approved amount 400'000.00
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Keywords (7)

Reactive Dynamics; QM/MM Simulations; Protein-Ligand Interactions; Computational Vibrational Spectroscopy; Multipolar Force Fields; Force Fields; Molecular Dynamics

Lay Summary (German)

Lead
The goal of this project is to understand intermolecular interactionsand the role of dynamics in chemical reactions relevant to chemistryand biology by using computer simulations. Intermolecular interactionscontrol all molecular processes starting at the association of twoatoms to form a diatomic molecule up to cellular phenomena inorganisms involving protein folding and protein association. For amolecular understanding of such phenomena the accurate description ofintermolecular interactions is the single most important task.
Lay summary

 
Da viele Prozesse in chemischen oder biologischen Systemen auf
vergleichsweise langen Zeitskalen (Sekunden) verglichen mit
molekularen Zeitskalen (Picosekunden) stattfinden und/oder die
relevanten räumlichen Dimensionen (Nano- bis Mikrometer) viel größer
als molekulare Längenskalen (Angström) sind, muessen geeignete Modelle
für intermolekulare Wechselwirkungen entwickelt werden. Sorgfältig
entwickelte Rechenmodelle, welche auf Vergleichen mit experimentellen
Daten beruhen, koennen über die atomistischen Details in chemischen
Reaktionen Auskunft geben. Diese Verfahren gehören zu den wichtigsten
Prozessen für lebende Organismen, wie beispielsweise den
Metabolismus. Ihr Verständnis hängt entscheidend von einer genauen
Beschreibung der intermolekularen Wechselwirkungen zwischen den
beteiligten Molekülen und der Kerndynamik ab. Für dieses Projekt
entwickeln wir numerische Methoden und Rechenstrategien um die
Energetik und Dynamik chemischer Reaktionen in komplexen Systemen zu
verstehen. Typische Anwendungen dieser Methoden sind die
Infrarotspektroskopie kleiner Molekuele in Protein, welche darueber
Auskunft geben kann, an welchen Orten das Probenmolekuel bindet. Diese
Information ist fuer die Entwicklung von pharmakologischen Wirkstoffen
von besonderer Bedeutung. Mit einer Kombination von verbesserten
Kraftfeldern und quantenchemischen Rechnungen untersuchen wir
chemische Reaktionen wie beispielsweise Proton-gekoppelter
Wasserstoff-Transfer, Ligand-Bindung an Proteine. Systeme Von
besonderem Interesse sind Myoglobin (zuständig für die Speicherung und
den Transport von Sauerstoff) und truncated Hämoglobin-N, welches bei
der Entgiftung von Bakterien beteiligt ist. Ein großer Teil der Arbeit
wird mit in Zusammenarbeit mit experimentellen Partnern in der Schweiz
und im Ausland durchgefuehrt.

Direct link to Lay Summary Last update: 02.10.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
Effect of Single-Point Mutations on Nitric Oxide Rebinding and the Thermodynamic Stability of Myoglobin
Diamantis Polydefkis, El Hage Krystel, Meuwly Markus (2019), Effect of Single-Point Mutations on Nitric Oxide Rebinding and the Thermodynamic Stability of Myoglobin, in J Phys Chem B, 123(9), 1961-1972.
Exhaustive state-to-state cross sections for reactive molecular collisions from importance sampling simulation and a neural network representation
Koner Debasish, Unke Oliver T., Boe Kyle, Bemish Raymond J., Meuwly Markus (2019), Exhaustive state-to-state cross sections for reactive molecular collisions from importance sampling simulation and a neural network representation, in J Chem Phys, 150(21), 211101.
Long-range versus short-range effects in cold molecular ion-neutral collisions
Doerfler Alexander D., Eberle Pascal, Koner Debasish, Tomza Michal, Meuwly Markus, Willitsch Stefan (2019), Long-range versus short-range effects in cold molecular ion-neutral collisions, in Nat. Comm., 10, 5429.
Molecular Determinants for Rate Acceleration in the Claisen Rearrangement Reaction
Brickel Sebastian, Meuwly Markus (2019), Molecular Determinants for Rate Acceleration in the Claisen Rearrangement Reaction, in J Phys Chem B, 123(2), 448-456.
Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk
Xu Zhen-Hao, Meuwly Markus (2019), Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk, in J Phys Chem B, 123(46), 9846-9861.
Near dissociation states for H$_2^+$–He on MRCI and FCI potential energy surfaces
Koner Debasish, San Vicente Veliz Juan Carlos, van der Avoird Ad, Meuwly Markus (2019), Near dissociation states for H$_2^+$–He on MRCI and FCI potential energy surfaces, in PCCP, in print, in print.
O-2 formation in cold environments
Pezzella Marco, Meuwly Markus (2019), O-2 formation in cold environments, in J Phys Chem B, 21(11), 6247-6255.
PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges
Unke Oliver T., Meuwly Markus (2019), PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges, in J Comp Theo Chem, 15(6), 3678-3693.
Probing the Differential Dynamics of the Monomeric and Dimeric Insulin from Amide-I IR Spectroscopy
Desmond Jasmine L., Koner Debasish, Meuwly Markus (2019), Probing the Differential Dynamics of the Monomeric and Dimeric Insulin from Amide-I IR Spectroscopy, in J Phys Chem B, 123(30), 6588-6598.
Reactive atomistic simulations of Diels-Alder reactions: The importance of molecular rotations
Rivero Uxia, Unke Oliver T., Meuwly Markus, Willitsch Stefan (2019), Reactive atomistic simulations of Diels-Alder reactions: The importance of molecular rotations, in J Chem Phys, 151(10), 104301.
Reactive molecular dynamics for the [Cl–CH3–Br]− reaction in the gas phase and in solution: a comparative study using empirical and neural network force fields
Brickel Sebastian, Das Akshaya Kumar, Unke Oliver Thorsten, Turan Haydar Taylan, Meuwly Markus (2019), Reactive molecular dynamics for the [Cl–CH3–Br]− reaction in the gas phase and in solution: a comparative study using empirical and neural network force fields, in Elec. Struc., 1, 024002.
Reactive molecular dynamics: From small molecules to proteins
Meuwly Markus (2019), Reactive molecular dynamics: From small molecules to proteins, in WIREs, 9(1), e1386.
Response to comment on `Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
El Hage Krystel, Hedin Florent, Gupta Prashant K., Meuwly Markus, Karplus Martin (2019), Response to comment on `Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size', in ELIFE, 8, e45318.
Sampling reactive regions in phase space by following the minimum dynamic path
Unke Oliver T., Brickel Sebastian, Meuwly Markus (2019), Sampling reactive regions in phase space by following the minimum dynamic path, in J Chem Phys, 150(7), 074107.
Vibrational Spectroscopy of N-3(-) in the Gas and Condensed Phase
Salehi Seyedeh Maryam, Koner Debasish, Meuwly Markus (2019), Vibrational Spectroscopy of N-3(-) in the Gas and Condensed Phase, in J Phys Chem B, 123(15), 3282-3290.
A reactive, scalable, and transferable model for molecular energies from a neural network approach based on local information
Unke Oliver T., Meuwly Markus (2018), A reactive, scalable, and transferable model for molecular energies from a neural network approach based on local information, in J Chem Phys, 148(24), 241708.
An efficient water force field calibrated against intermolecular THz and Raman spectra
Sidler David, Meuwly Markus, Hamm Peter (2018), An efficient water force field calibrated against intermolecular THz and Raman spectra, in J Chem Phys, 148(24), 244504.
Free energy simulations for protein ligand binding and stability
El Hage Krystel, Mondal Padmabati, Meuwly Markus (2018), Free energy simulations for protein ligand binding and stability, in Mol. Sim., 44(13-14, SI), 1044-1061.
From in silica to in silico: retention thermodynamics at solid-liquid interfaces
El Hage Krystel, Bemish Raymond J., Meuwly Markus (2018), From in silica to in silico: retention thermodynamics at solid-liquid interfaces, in J Phys Chem Lett, 20(27), 18610-18622.
Implications of short time scale dynamics on long time processes (vol 4, 061507, 2017)
El Hage Krystel, Brickel Sebastian, Hermelin Sylvain, Gaulier Geoffrey, Schmidt Cedric, Bonacina Luigi, van Keulen Siri C., Bhattacharyya Swarnendu, Chergui Majed, Hamm Peter, Rothlisberger Ursula, Wolf Jean-Pierre, Meuwly Markus (2018), Implications of short time scale dynamics on long time processes (vol 4, 061507, 2017), in Struct. Dyn., 5(1), 019901.
Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated HemoglobinN
Das Akshaya Kumar, Meuwly Markus (2018), Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated HemoglobinN, in Angew., 57(13), 3509-3513.
Molecular Oxygen Formation in Interstellar Ices Does Not Require Tunneling
Pezzella Marco, Unke Oliver T., Meuwly Markus (2018), Molecular Oxygen Formation in Interstellar Ices Does Not Require Tunneling, in J Phys Chem Lett, 9(8), 1822-1826.
Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions
Schmid Maurus H., Das Akshaya Kumar, Landis Clark R., Meuwly Markus (2018), Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions, in J Comp Theo Chem, 14(7), 3565-3578.
Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase
Mondal Padmabati, Meuwly Markus (2018), Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase, in Sci. Rep., 8, 5281.
The C(P-3) + NO(X-2 Pi) -> O(P-3) + CN(X-2 Sigma(+)), N(D-2)/N(S-4) + CO(X-1 Sigma(+)) reaction: Rates, branching ratios, and final states from 15 K to 20 000 K
Koner Debasish, Bemish Raymond J., Meuwly Markus (2018), The C(P-3) + NO(X-2 Pi) -> O(P-3) + CN(X-2 Sigma(+)), N(D-2)/N(S-4) + CO(X-1 Sigma(+)) reaction: Rates, branching ratios, and final states from 15 K to 20 000 K, in J Chem Phys, 149(9), 094305.
The Role of Water in the Stability of Wild-type and Mutant Insulin Dimers
Raghunathan Shampa, El Hage Krystel, Desmond Jasmine L., Zhang Lixian, Meuwly Markus (2018), The Role of Water in the Stability of Wild-type and Mutant Insulin Dimers, in J Phys Chem B, 122(28), 7038-7048.
Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size
El Hage Krystel, Hedin Florent, Gupta Prashant K., Meuwly Markus, Karplus Martin (2018), Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size, in ELIFE, 7, e35560.
A computational study of the Diels-Alder reactions between 2,3-dibromo-1,3-butadiene and maleic anhydride
Rivero Uxia, Meuwly Markus, Willitsch Stefan (2017), A computational study of the Diels-Alder reactions between 2,3-dibromo-1,3-butadiene and maleic anhydride, in Chem Phys Lett, 683, 598-605.
A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations (vol 56, pg 1479, 2016)
Hedin Florent, El Hage Krystel, Meuwly Markus (2017), A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations (vol 56, pg 1479, 2016), in JCIM, 57(1), 102-103.
Charge migration and charge transfer in molecular systems
Worner Hans Jakob, Arrell Christopher A., Banerji Natalie, Cannizzo Andrea, Chergui Majed, Das Akshaya K., Hamm Peter, Keller Ursula, Kraus Peter M., Liberatore Elisa, Lopez-Tarifa Pablo, Lucchini Matteo, Meuwly Markus, Milne Chris, Moser Jacques-E., Rothlisberger Ursula, Smolentsev Grigory, Teuscher Joel, van Bokhoven Jeroen A., Wenger Oliver (2017), Charge migration and charge transfer in molecular systems, in Struct. Dyn., 4(6), 061508.
Communication: Vibrational relaxation of CO((1)Sigma) in collision with Ar(S-1) at temperatures relevant to the hypersonic flight regime
Denis-Alpizar Otoniel, Bemish Raymond J., Meuwly Markus (2017), Communication: Vibrational relaxation of CO((1)Sigma) in collision with Ar(S-1) at temperatures relevant to the hypersonic flight regime, in J Chem Phys, 146(11), 111102.
Hydration Control Through Intramolecular Degrees of Freedom: Molecular Dynamics of {[}Cu(11)(Imidazole)(4)]}
Das Akshaya K., Meuwly Markus (2017), Hydration Control Through Intramolecular Degrees of Freedom: Molecular Dynamics of {[}Cu(11)(Imidazole)(4)]}, in J Phys Chem B, 121(38), 9024-9031.
Implications of short time scale dynamics on long time processes
El Hage Krystel, Brickel Sebastian, Hermelin Sylvain, Gaulier Geoffrey, Schmidt Cedric, Bonacina Luigi, van Keulen Siri C., Bhattacharyya Swarnendu, Chergui Majed, Hamm Peter, Rothlisberger Ursula, Wolf Jean-Pierre, Meuwly Markus (2017), Implications of short time scale dynamics on long time processes, in Struct. Dyn., 4(6), 019901.
Kinetic isotope effects and how to describe them
Karandashev Konstantin, Xu Zhen-Hao, Meuwly Markus, Vanicek Jiri, Richardson Jeremy O. (2017), Kinetic isotope effects and how to describe them, in Struct. Dyn., 4(6), 061501.
Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
Diamantis Polydefkis, Unke Oliver T., Meuwly Markus (2017), Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N, in PLoS, 13(3), e1005450.
Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics
Unke Oliver T., Devereux Mike, Meuwly Markus (2017), Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics, in J Chem Phys, 147(16), 161712.
Molecular Mechanisms Underlying Solute Retention at Heterogeneous Interfaces
El Hage Krystel, Gupta Prashant Kumar, Bemish Raymond, Meuwly Markus (2017), Molecular Mechanisms Underlying Solute Retention at Heterogeneous Interfaces, in J Phys Chem Lett, 8(18), 4600-4607.
Nonadiabatic effects in electronic and nuclear dynamics
Bircher Martin P., Liberatore Elisa, Browning Nicholas J., Brickel Sebastian, Hofmann Cornelia, Patoz Aurelien, Unke Oliver T., Zimmermann Tomas, Chergui Majed, Hamm Peter, Keller Ursula, Meuwly Markus, Woerner Hans-Jakob, Vanicek Jiri, Rothlisberger Ursula (2017), Nonadiabatic effects in electronic and nuclear dynamics, in Struct. Dyn., 4(6), 061510.
Non-Standard Protein Engineering at the Boundary of Molecular Mechanics and Quantum Chemistry: Halogen-Based Design of Insulin Analogs
Weiss Michael A., Phillips Nelson F., Ismail-Beigi Faramarz, Pandyarajan Vijay, Yang Yanwu, Chen Yen-Shan, Wickramasinghe Nalinda, Smith Brian, Menting John G., Lawrence Michael C., El-Hage Krystel, Meuwly Markus (2017), Non-Standard Protein Engineering at the Boundary of Molecular Mechanics and Quantum Chemistry: Halogen-Based Design of Insulin Analogs, in J biol chem, 112(3, 1), 53-53.
OH-Stretching Overtone Induced Dynamics in HSO3F from Reactive Molecular Dynamics Simulations
Brickel Sebastian, Meuwly Markus (2017), OH-Stretching Overtone Induced Dynamics in HSO3F from Reactive Molecular Dynamics Simulations, in J Phys Chem A, 121(27), 5079-5087.
Perspective: THz-driven nuclear dynamics from solids to molecules
Hamm Peter, Meuwly Markus, Johnson Steve L., Beaud Paul, Staub Urs (2017), Perspective: THz-driven nuclear dynamics from solids to molecules, in Struct. Dyn., 4(6), 061601.
Quantum and quasiclassical trajectory studies of rotational relaxation in Ar-N-2(+) collisions
Denis-Alpizar Otoniel, Unke Oliver T., Bemish Raymond J., Meuwly Markus (2017), Quantum and quasiclassical trajectory studies of rotational relaxation in Ar-N-2(+) collisions, in J Chem Phys, 19(41), 27945-27951.
Reactive collisions for NO((II)-I-2) + N(S-4) at temperatures relevant to the hypersonic flight regime
Denis-Alpizar Otoniel, Bemish Raymond J., Meuwly Markus (2017), Reactive collisions for NO((II)-I-2) + N(S-4) at temperatures relevant to the hypersonic flight regime, in PCCP, 19(3), 2392-2401.
Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces
Unke Oliver T., Meuwly Markus (2017), Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces, in JCIM, 57(8), 1923-1931.
Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches
Antipov Sergey V., Bhattacharyya Swarnendu, El Hage Krystel, Xu Zhen-Hao, Meuwly Markus, Rothlisberger Ursula, Vanicek Jiri (2017), Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches, in Struct. Dyn., 4(6), 061509.
Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate
Xu Zhen-Hao, Meuwly Markus (2017), Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate, in J Phys Chem A, 121(29), 5389-5398.
Vibrational Stark spectroscopy for assessing ligand-binding strengths in a protein
Mondal Padmabati, Meuwly Markus (2017), Vibrational Stark spectroscopy for assessing ligand-binding strengths in a protein, in PCCP, 19(24), 16131-16143.

Datasets

Solvated protein fragments data set

Author Unke, Oliver; Meuwly, Markus
Persistent Identifier (PID) 10.5281/zenodo.2605372
Repository Zenodo


Collaboration

Group / person Country
Types of collaboration
Prof. Q. Cui, University of Madison/WI United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. H. Kjaergaard Denmark (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Prof. M. A. Johnson United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Prof. P. Hamm, University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
CECAM Workshop Talk given at a conference Electrostatics from Multipoles to neural networks 12.12.2019 Lausanne, Switzerland Meuwly Markus;
Seminar Individual talk Insights into Chemical Reactivity from Empirical and Neural Network-Learned Reactive Force Fields 03.12.2019 Bristol, Great Britain and Northern Ireland Meuwly Markus;
Seminar Individual talk Reactive Molecular Dynamics for Biological Applications 10.12.2018 Cambridge, Botson, United States of America Koner Debasish; Brickel Sebastian; Das Akshaya Kumar; Meuwly Markus; Pezzella Marco; Xu Zhen-Hao;
Seminar Talk given at a conference Quantitative Atomistic Simulations: Insights into Reaction Mechanisms and Biological Rearrangements 08.12.2018 Sydney, Australia Meuwly Markus;
Computational Chemistry meets Artificial Intelligence, Talk given at a conference From Physics-based Force Fields to Machine Learning Molecular Interactions 06.12.2018 Lausanne, Switzerland Koner Debasish; Salehi Seyedeh Maryam; Brickel Sebastian; Meuwly Markus;
WATOC Talk given at a conference uantitative Atomistic Simulations for Chemical and Biological Applications 08.12.2017 Munich, Germany Meuwly Markus; Brickel Sebastian;
Computational Vibrational Dynamics Talk given at a conference Vibrational Dynamics 07.12.2017 Telluride, United States of America Pezzella Marco; Das Akshaya Kumar; Brickel Sebastian; Xu Zhen-Hao; Meuwly Markus;
Seminar Individual talk Accurate Force Fields for Biochemical Applications: Structural Dynamics of Myoglobin and Insulin 02.12.2017 Uppsala, Sweden Brickel Sebastian; Meuwly Markus;


Associated projects

Number Title Start Funding scheme
132406 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2010 Project funding
188724 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2019 Project funding
149439 Intermolecular Interactions and the Role of Dynamics for Chemical Reactions in Complex Systems 01.10.2013 Project funding
125760 NCCR MUST: Molecular Ultrafast Science and Technology (phase I) 01.07.2010 National Centres of Competence in Research (NCCRs)

Abstract

The goal of this project is to develop, implement and applycomputational strategies to characterize, understand and predictproperties of complex systems at a molecular level. To this end,computational techniques including multipolar (MTP) force fields,adiabatic reactive molecular dynamics (ARMD) simulations, andmolecular mechanics with proton transfer (MMPT) are used and furtherdeveloped. Multipolar force fields will be extended to routinespectroscopic applications such as 1- and 2-dimensional infraredspectroscopies. This will be applied to spectroscopic probes,primarily nitriles (-CN), which are sensitive environmental probes forprotein interiors. Fluctuating MTPs will be used to study the 1d- and2d-IR spectroscopy of-CN-containing inhibitors in human aldosereductase (hALR2) and benzonitrile in Lysozyme. Multiplesurface-ARMD will be combined with the fewest switching surfacehopping (FSSH) methodology for investigating nonadiabatic effects inchemical dynamics. This will considerably extend the range ofapplicability for MS-ARMD. Initial applications concernphotodissociation and recombination of ICN in solution and O2formation in amorphous ice at low temperatures. In a next step, thestructural and solvent dynamics upon oxidation from Cu(I) to Cu(II) incopper-phenanthroline complexes will be investigated. Also, standardARMD simulations will be used to study multiple-ligand dynamics in theactive site of truncated Hemoglobin N which is responsible fordenitrification. Molecular mechanics with proton transfer will becombined with multi state-ARMD to investigate proton transfer in thecondensed phase on extended time scales. Computationally efficientevaluation of accurate energy functions is particularly important whenusing it for multidimensional spectroscopy which typically requiresextensive conformational sampling to converge the frequency frequencycorrelation function. The developments will allow atomisticallyrefined simulations of the recently recorded 2d-IR spectrum of theexcess proton in liquid water. The present proposal involves tworesearch themes: reactive simulations in the condensed phase andcomputational vibrational spectroscopy which both require accuraterepresentations of the intermolecular interactions.
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