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66. Nuria Anguita-Ortiz and Juan J. Nogueira.

The Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNaV 1.5 Channel.

Submitted, 2024.

Preprint: 10.26434/chemrxiv-2024-dzkc1

65. Mateo Julian Mateo Rayo Alape, Carla Bandeira, Giovana Bonano, Juan J. Nogueira, and Herculano Martinho.

Vibrational Analysis of Hepcidin-25 Hormone: Perspectives for Hyperinflammation Diagnosis.

Submitted, 2024.

64. Henar Mateo-delaFuente Juan J. Nogueira.

OLUFF: a Novel Set of Ground and Excited State Force Field Parameters of the Emitting Oxiluciferin Species.

Submitted, 2024.

Preprint:

63. Vito F. Palmisano, Claudio Agnorelli, Shirin Faraji, Juan J. Nogueira.

Computational Design of an Improved Photoswitchable Psychedelics Based on Light Absorption, Membrane Permeation and Protein Binding.

Submitted, 2024.

Preprint: 10.26434/chemrxiv-2024-ljkf8-v2

62. Lucía López-Pacios, Juan J. Nogueira, and Lara Martinez-Fernandez.

Computational characterization of the DAD photoisomerization: Functionalization, protonation and solvation effects.

Submitted, 2024.

Preprint: 10.26434/chemrxiv-2024-067sp

61. Jesús Lucia Tamudo, Rubén López-Sánchez, Juan J. Nogueira, and Sergio Díaz-Tendero.

Effect of Weak Intermolecular Interactions on the Ionization of Benzene Derivatives Dimers.

Journal of Chemical Physics, 2024, accepted.

Preprint: 10.26434/chemrxiv-2024-6mx5c

60. Marta Dudek, Lucía López-Pacios, Nasim Sabouri, Juan J. Nogueira, Lara Martinez-Fernandez, and Marco Deiana.

Harnessing Light for G-Quadruplex Modulation: Dual Isomeric Effects of an Ortho-Fluoroazobenzene Derivative

The Journal of Physical Chemistry Letters, 2024, 15, 9757–9765. DOI: 10.1021/acs.jpclett.4c02285

59. Marta Dudek, Lucía López-Pacios, Nasim Sabouri, Juan J. Nogueira, Lara Martinez-Fernandez and Marco Deiana.

A Rationally Designed Azobenzene Photoswitch for DNA G-Quadruplex Regulation in Live Cells.

Angewandte Chemie International Edition, 2024, e202413000. DOI: 10.1002/anie.202413000

58. Nuria Anguita-Ortiz, Andrea Lombardi, Noelia Faginas-Lago and Juan J. Nogueira.

Insights into Ion Conduction Mechanisms through the ORF3a Channel by Computational Modelling.

Computational Science and Its Applications - ICCSA 2024 Workshops, 402-414. DOI: 10.1007/978-3-031-65329-2_27​

57. Felix Egun , Laura Rego , Ana Martinez , Douglas Garratt , Gustavo Cárdenas , Juan J. Nogueira , Jacob Lee , Kaixiang Zhao , Ru-Pan Wang , David Ayuso , Jonathan Barnard , Sandra Beauvarlet , Philip Bucksbaum , David Cesar , Ryan Coffee , Joseph Duris , Leszek Frasinski , Nils Huse , Katarzyna Kowalczyk , Kirk Larsen , Mary Matthews , Shaul Mukamel , Jordan O'Neal , Thomas Penfold , Emily Thierstein , John Tisch , James Turner , Josh Vogwell , Nora Berrah , Taran Driver , Ming-Fu Lin , Georgi Dakovski , Stefan Moeller , James Cryan , Agostino Marinelli , Antonio Picón , Jonathan Marangos.

Attosecond Impulsive Stimulated X-ray Raman Scattering in Liquid Water. 

Science Advances, 2024, 10, eadp0841. DOI: 10.1126/sciadv.adp0841

56. Jesús Lucia Tamudo, Juan J. Nogueira, and Sergio Díaz-Tendero.

Charge Transfer Mechanism in Guanine-based Self-Assembled Monolayers on a Gold Surface.

Langmuir, 2024, 40, 15129–15139. DOI: 10.1021/acs.langmuir.4c01512

Preprint: 10.26434/chemrxiv-2023-jmslr

55. Jesús Lucia Tamudo, Sergio Díaz-Tendero, and Juan J. Nogueira.

Modelling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches.

Journal of Chemical Information and Modeling, 2024, 64, 4802–4810. DOI: 10.1021/acs.jcim.4c00528

Preprint: 10.26434/chemrxiv-2024-sxxg3

54. Vito F. Palmisano, Nuria Anguita-Ortiz, Shirin Faraji and Juan J. Nogueira.

Voltage Gated Ion Channels: Structure, Pharmacology and Photopharmacology.

ChemPhysChem 2024, e202400162.

Preprint 2023: 10.26434/chemrxiv-2022-q2603 

53. Vito F. Palmisano, Claudio Agnorelli, Andrea Fagiolini, David Erritzoe, David Nutt, Shirin Faraji, and Juan J. Nogueira.

Membrane Permeation of Psychedelic Tryptamines by Dynamic Simulations. 

Biochemistry, 2024, 63, 419-428. DOI: 10.1021/acs.biochem.3c00598

Preprint: 10.26434/chemrxiv-2023-0jwg5

52. Jesús Lucia Tamudo, Manuel Alcamí, Sergio Díaz-Tendero, and Juan J. Nogueira.

One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA.

Biochemistry 2023, 62, 3312-3322. DOI: 10.1021/acs.biochem.3c00324

Preprint: 10.26434/chemrxiv-2023-csvcp

51. Vito F. Palmisano, Claudio Agnorelli, David Erritzoe, Andrea Fagiolini, Shirin Faraji, and Juan J. Nogueira.

Characterization of the Binding Poses of Classical and Photoswitchable Psychedelics Interacting with 5-HT2AR.

Preprint 2023: 10.26434/chemrxiv-2023-0jwg5

50. Julia Arnanz, Fernando Romeo-Gella, Juan J. Nogueira, and Inés Corral.

In Silico Investigation of the Photoisomerization Mechanism of Push-Push Azoderivatives

Dyes and Pigments 2023, 219, 111555. DOI: 10.1016/j.dyepig.2023.111555

Preprint: 10.26434/chemrxiv-2023-2c6bb

49. Henar Mateo-delaFuente, Davide Avagliano, Marco Garavelli, and Juan J. Nogueira.

The Protein Environment Restricts the Intramolecular Charge Transfer Character of the Luciferine/Luciferase Complex

Physical Chemistry Chemical Physics 2023, 25, 16507-16519. DOI: 10.1039/D3CP01387A.

Preprint: 10.26434/chemrxiv-2023-88slr 

48. Lorena Ruano, Marcos Mandado, and Juan J. Nogueira.

Automatic Characterization of Drug/Amino Acid Interactions by Energy Decomposition Analysis

Theoretical Chemistry Accounts 2023, 142, 55. DOI: 10.1007/s00214-023-02997-8

Preprint: 10.21203/rs.3.rs-2674723/v1

47. Jesús Lucia Tamudo, Sergio Díaz-Tendero, and Juan J. Nogueira.

Intramolecular and Intermolecular Hole Delocalization Rules the Reducer Character of Isolated Nucleobases and Homogeneous Single-Stranded DNA.

Physical Chemistry Chemical Physics, 2023, 25, 14578-14589. DOI: 10.1039/D3CP00884C.

Preprint: 10.26434/chemrxiv-2023-l1n1p

46.Vito F. Palmisano, Shirin Faraji, and Juan J. Nogueira.

Effect of Stacking Interactions on Charge Transfer States in Photoswitches Interacting with Ion Channels.

Physical Chemistry Chemical Physics, 2023, 25, 8331-8335. DOI: 10.1039/D2CP05678J. 

Preprint: 10.26434/chemrxiv-2022-gkwnf

45. Jesús Lucia Tamudo, Juan J. Nogueira and Sergio Díaz-Tendero.

An Efficient Multilayer Approach to Model DNA-Based Nano-Biosensors.

The Journal of Physical Chemsitry C 2023, 127, 1513-1525. DOI: 10.1021/acs.jpcb.2c07225.

Preprint: 10.26434/chemrxiv-2022-d8w78

44. Álvaro Pérez-Barcia, Gustavo Cárdenas, Juan J. Nogueira and Marcos Mandado.

Effect of the QM Size, Basis Set and Polarisation on QM/MM Energy Decomposition Analysis.

Journal of Chemical Information and Modeling 2023, 63, 882-897. DOI: 10.1021/acs.jcim.2c01184.

Preprint: 10.26434/chemrxiv-2022-8686w

43.Raúl Alvarado, Gustavo Cárdenas, Juan J. Nogueira, Nicolás Ramos-Berdullas, and Marcos Mandado.

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis.

Membranes 2023, 13, 28. DOI: 10.3390/membranes13010028.

Preprint: 10.20944/preprints202211.0283.v1

42. Gustavo Cárdenas, Jesús Lucia-Tamudo, Henar Mateo-delaFuente, Vito F. Palmisano, Nuria Anguita-Ortiz, Lorena Ruano, Álvaro Pérez-Barcia, Sergio Díaz-Tendero, Marcos Mandado, and Juan J. Nogueira.

MoBioTools: A Toolkit to Setup QM/MM Calculations.

Journal of Computational Chemistry, 2023, 44, 516–533. DOI: 10.1002/jcc.27018.

Preprint: 10.26434/chemrxiv-2022-cncp2

MoBioTools Github

41. Jesús Lucia-Tamudo, Gustavo Cárdenas, Nuria Anguita-Ortiz, Sergio Díaz-Tendero and Juan J. Nogueira.

Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches.

Journal of Chemical Information and Modeling 2022, 62, 3365–3380. DOI: 10.1021/acs.jcim.2c00234.

Preprint: 10.26434/chemrxiv-2022-629k2

40. Juan J. Nogueira.

New Challenges for Photopharmacology and Computational Modelling.

Trends in Biochemical Sciences, 2022, 47, 822–823. DOI: 10.1016/j.tibs.2022.05.003.

39. P. Bernát Szabó, Francesc Sabanés Zariquiey, and Juan J. Nogueira.

Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations.

Journal of Chemical Information and Modeling 2021, 61, 5508–5523. DOI: 10.1021/acs.jcim.1c00924.

Preprint: 10.33774/chemrxiv-2021-0dwfq 

38. Gustavo Cárdenas,  Álvaro Pérez-Barcia, Marcos Mandado, and Juan J. Nogueira.

Characterization of Cisplatin/Membrane Interactions by QM/MM Energy Decomposition Analysis.

Physical Chemistry Chemical Physics, 2021, 23, 20533-20540. DOI: 10.1039/D1CP03382D.

Preprint: 10.33774/chemrxiv-2021-45h42-v3

37. Gustavo Cárdenas, Ivan Trentin, Ludwig Schwiedrzik, David Hernández-Castillo, Grace A. Lowe, Julian Kund, Christine Kranz, Sarah Klinger, Robert Stach, Boris Mizaikoff, Philipp Marquetand, Juan J. Nogueira, Carsten Streb, and Leticia González.

Activation by Oxidation and Ligand Exchange in a Molecular Manganese Vanadium Oxide Water Oxidation Catalyst.

Chemical Science, 2021, 12, 12918-12927. DOI: 10.1039/D1SC03239A.

Preprint: 10.33774/chemrxiv-2021-7w62s

36. Lorena Ruano, Gustavo Cárdenas, and Juan J. Nogueira.

The Permeation Mechanism of Cisplatin through a Dioleoylphosphocholine Bilayer. 

ChemPhysChem, 2021, 22, 1251-1261, DOI: 10.1002/cphc.202100059

Preprint: 10.26434/chemrxiv.12917957.v2

35. Vito F. Palmisano, Carlos Gómez-Rodellar, Hannah Pollak, Gustavo Cárdenas, Ben Corry, Shirin Faraji, and Juan J. Nogueira.

Binding of Azobenzene and p-Diaminoazobenzene to the Human Voltage-Gated Sodium Channel NaV1.4.

Physical Chemistry Chemical Physics, 2021, 23, 3552-3564, DOI: 10.1039/D0CP06140A.

Preprint: 10.26434/chemrxiv.13311692.v1

34. Gustavo Cárdenas and Juan J. Nogueira.

Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States.

Molecules, 2020, 25, 5927, DOI: 10.3390/molecules25245927

Preprint: 10.20944/preprints202011.0047.v1

33. Gustavo Cárdenas and Juan J. Nogueira.

An Algorithm to Correct for the CASSCF Active Space in Multiscale QM/MM Calculations Based on Geometry Ensembles.

International Journal of Quantum Chemistry, 2020, 121, e26533, DOI: 10.1002/qua.26533

Preprint: 10.26434/chemrxiv.12917930.v1

32. Lea M. Ibele, Pedro A. Sánchez-Murcia, Sebastian Mai, Juan J. Nogueira, and Leticia González.

Excimers Intermediates en Route to Long-Lived Charge Transfer States in Single-Stranded Adenine DNA Revealed by Nonadiabatic Dynamics. 

The Journal of Physical Chemistry Letters 2020, 11, 7483-7488, DOI: 10.1021/acs.jpclett.0c02193

31. Pedro A. Sánchez-Murcia, Juan J. Nogueira, Felix Plasser, and Leticia González.

Orbital-Free Photophysical Descriptors to Predict Directional Excitations in Metal-Based Photosensitizers.

Chemical Science 2020, 11, 7685-7693, DOI: 10.1039/D0SC01684E

30. Maria S. Legina, Juan J. Nogueira, Wolfgang Kandioller, Michael A. Jakupec, Leticia González, and Bernhard K. Keppler

Biological Evaluation of Novel Thiomaltol-Based Organometallic Complexes as Topoisomerase IIα Inhibitors.

Journal of Biological Inorganic Chemistry 2020, 25, 451-465, DOI: 10.1007/s00775-020-01775-2.

29. Isolde Sandler, Juan J. Nogueira, and Leticia González.

Solvent Reorganization Triggers Photo-induced Solvated Electron Generation in Solvated Phenol.

Physical Chemistry Chemical Physics 2019, 21, 14261-14269, DOI: 10.1039/C8CP06656F.

28. J. Patrick Zobel, Juan J. Nogueira, and Leticia González.

Finite-Temperature Wigner Phase-Space Sampling and Temperature Effects on the Excited-State Dynamics of 2-Nitronaphthalene.

Physical Chemistry Chemical Physics 2019, 21, 13906-13915, DOI: 10.1039/C8CP03273D.

27. Martina De Vetta, Omar Baig, Dorika Steen, Juan J. Nogueira, Leticia González.

Assessing Configurational Sampling in the QM/MM Calculation of Temoporfin Absorption Spectrum and Triplet Density of States.

Molecules 2018, 23, 2932. DOI: 10.3390/molecules23112932.

26. Juan J. Nogueira, Sven Rossbach, Christian Ochsenfeld, and Leticia González.

Effect of DNA Environment on Electronically Excited States of Methylene Blue Evaluated by a Three-Layered QM/QM/MM ONIOM Scheme.

Journal of Chemical Theory and Computation 2018, 14, 4298–4308. DOI: 10.1021/acs.jctc.8b00185. 

25. Martina De Vetta, Leticia González, and Juan J. Nogueira.

Hydrogen Bonding Regulates the Stability of Liposome-encapsulated Chlorin Photosensitizers.

ChemistryOpen 2018, 7, 475-483. DOI: 10.1002/open.201800050.

24. J. Patrick Zobel, Moritz Heindl, Juan J. Nogueira, and Leticia González.

Vibrational Sampling and Solvent Effects on the Electronic Structure of the Absorption Spectrum of 2-Nitronaphthalene.

Journal of Chemical Theory and Computation 2018, 14, 3205–3217. DOI: 10.1021/acs.jctc.8b00198. 

23. J. Patrick Zobel, Juan J. Nogueira, and Leticia González.

The Mechanism of Ultrafast Intersystem Crossing in 2-Nitronaphthalene.

Chemistry – A European Journal 2018, 24, 5379-5387. DOI: 10.1002/chem.201705854.

22. Juan J. Nogueira and Leticia González.

Computational Photophysics in the Presence of an Environment.

Annual Reviews of Physical Chemistry 2018, 69, 473-497. DOI: 10.1146/annurev-physchem-050317-021013.

21. Martina De Vetta, Maximilam F. S. J. Menger, Juan J. Nogueira, and Leticia González.

Solvent Effects on Electronically Excited States: QM/Continuum vs QM/Explicit Models.

The Journal of Physical Chemistry B 2018, 122, 2975-2984. DOI: 10.1021/acs.jpcb.7b12560. Special Issue “Manuel Yáñez and Otilia Mó Festschrift”.

20. P. Sánchez-Murcia, Juan J. Nogueira, and L. González.

Exciton Localization on Ru-based Photosensitizers Induced by Binding to Lipid Membranes.

The Journal of Physical Chemistry Letters 2018, 9, 683-688. DOI: 10.1021/acs.jpclett.7b03357.

19. C. Rauer, Juan J. Nogueira, P. Marquetand, and Leticia González.

Stepwise Photosensitized Thymine Dimerization Mediated by an Exciton Intermediate.

Monatshefte für Chemie - Chemical Monthly 2018, 149, 1-9. DOI: 10.1007/s00706-017-2108-4.

18. Juan J. Nogueira, Felix Plasser, and Leticia González.

Electronic Delocalization, Charge Transfer and Hypochromism in the UV Absorption Spectrum of Polyadenine Unravelled by Multiscale Computations and Quantitative Wavefunction Analysis.

Chemical Science 2017, 8, 5682-5691. DOI: 10.1039/C7SC01600J.

17. Juan J. Nogueira, Alice Corani, Amal El Nahhas, Alessandro Pezzella, Marco d'Ischia, Leticia González, and Villy Sundström.

Sequential Proton-Coupled Electron Transfer Mediates Excited State Deactivation of a Eumelanin Building Block.

The Journal of Physical Chemistry Letters 2017, 8, 1004-1008. DOI: 10.1021/acs.jpclett.6b03012.

16. Juan J. Nogueira, Maximiliam Meixner, Marius Bittermann, and Leticia González

Impact of Lipid Environment on Photodamage Activation of Methylene Blue.

ChemPhotoChem 2017, 1, 178-182. DOI: 10.1002/cptc.201600062.

15. Joanna Czapla-Masztafiak, Juan J. Nogueira, Ewelina Lipiec, Wojciech M. Kwiatek, Bayden R. Wood, Glen B. Deacon, Yves Kayser, Daniel L. A. Fernandes, Mariia V. Pavliuk, Jakub Szlachetko, Leticia González, and Jacinto Sá.

Direct Determination of Metal Complexes Interaction with DNA by Atomic Telemetry and Multiscale Molecular Dynamics.

The Journal of Physical Chemistry Letters 2017, 8, 805-811. DOI: 10.1021/acs.jpclett.7b00070. Spotlighted by the editor.

14. J. Patrick Zobel, Juan J. Nogueira, and Leticia González.

The IPEA Dilemma in CASPT2.

Chemical Science 2017, 8, 1482 – 1499. DOI: 10.1039/C6SC03759C.

13. Philipp Marquetand, Juan J. Nogueira, Sebastian Mai, Felix Plasser, and Leticia González.

Challenges in Simulating Light-Induced Processes in DNA.

Molecules 2017, 22, 49. DOI: 10.3390/molecules22010049.

Special Issue: Experimental and Computational Photochemistry of Bioorganic Molecules.

12. Clemens Rauer, Juan J. Nogueira, Philipp Marquetand, and Leticia González.

Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics.

Journal of the American Chemical Society 2016, 138, 15911-15916. DOI: 10.1021/jacs.6b06701. Front cover.

11. J. Patrick Zobel, Juan J. Nogueira, and Leticia González.

Quenching of Charge Transfer in Nitrobenzene Induced by Vibrational Motion.

The Journal of Physical Chemistry Letters 2015, 6, 3006-3011. DOI: 10.1021/acs.jpclett.5b00990.

10. Juan J. Nogueira, Markus Oppel, and Leticia González.

Enhancing Intersystem Crossing in Phenotiazinium Dyes by Intercalation into DNA.

Angewandte Chemie International Edition 2015, 54, 4375-4378. DOI: 10.1002/anie.201411456.

9. Juan J. Nogueira, Yang Wang, Fernando Martin, Manuel Alcami, David R. Glowacki, Dmitrii V. Shalashilin, Emanuele Paci, Antonio Fernandez-Ramos, William L. Hase, Emilio Martínez-Núñez, and Saulo A. Vazquez.

Unraveling the Factors that Control Soft Landing of Small Silyl Ions on Fluorinated Self-Assembled Monolayers.

The Journal of Physical Chemistry C 2014, 118, 10159-10169. DOI: 10.1021/jp501841a.

8. Juan J. Nogueira and Leticia González.

Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences.

Biochemistry 2014, 53, 2391-2412. DOI: 10.1021/bi500068z.

7. Juan J. Nogueira, William L. Hase, and Emilio Martínez-Núñez.

Understanding Energy Transfer in Gas-Surface Collisions from Gas-Phase Models.

The Journal of Physical Chemistry C 2014, 118, 2609-2621. DOI: 10.1021/jp4117134.

6. Manuel Monge-Palacios, Juan J. Nogueira and Emilio Martínez-Núñez.

Energy Transfer and Thermal Accommodation in Ozone Scattering from a Perfluorinated Self-Assembled Monolayer.

The Journal of Physical Chemistry C 2012, 116, 25454-25464. DOI: 10.1021/jp309733w.

5. Juan J. Nogueira, Antonio Sánchez-Coronilla, Jorge M.C. Marques, William L. Hase, Emilio Martínez-Núñez, and Saulo A. Vázquez.

Intermolecular Potentials for Simulations of Collisions of SiNCS+ and (CH3)2SiNCS+ Ions with Fluorinated Self-Assembled Monolayers.

Chemical Physics. 2012, 399, 193-204. DOI: 10.1016/j.chemphys.2011.02.014. Special Issue in honour to Gerardo Delgado Barrio.

4. Juan J. Nogueira, Zahra Homayoon, Saulo A. Vázquez, and Emilio Martínez-Núñez.

Chemical Dynamics Study of NO Scattering from a Perfluorinated Self-Assembled Monolayer.

The Journal of Physical Chemistry C 2011, 115, 23817-23830. DOI: 10.1021/jp206034c.

3. Juan J. Nogueira, S. A. Vázquez, U. Lourderaj, W. L. Hase, and E. Martínez-Núñez.

Chemical Dynamics Simulations CO2 in the Ground and First Excited Bend States Colliding with a Perfluorinated Self-Assembled Monolayer.

The Journal of Physical Chemistry C 2010, 114, 18455-18464. DOI: 10.1021/jp103511g.

2. Juan J. Nogueira, Emilio Martínez-Núñez, and Saulo A. Vázquez.

Improved United-Atom Models for Perfluorinated Self-Assembled Monolayers.

The Journal of Physical Chemistry C 2008, 113, 3300-3312. DOI: 10.1021/jp809929f.

1. Juan J. Nogueira, Saulo A. Vázquez, Oleg A. Mazyar, William L. Hase, Bradford G. Perkins, David J. Nesbitt, and Emilio Martínez-Núñez.

Dynamics of CO2 Scattering off a Perfluorinated Self-Assembled Monolayer. Influence of the Incident Collision Energy, Mass Effects, and Use of Different Surface Models.

The Journal of Physical Chemistry A 2008, 113, 3850-3865. DOI: 10.1021/jp809756f. Special Issue in honour to George C. Schatz.

Book Chapters

1. Juan J. Nogueira and Ben Corry

Ion Channel Permeation and Selectivity.

In The Oxford Handbook of Neuronal Ion Channels. Edited by Arin Bhattacharjee. Oxford University Press, 2019. DOI:10.1093/oxfordhb/9780190669164.013.22

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