QUÍMICA TEÓRICA Y COMPUTACIONAL
Cap de grup: Ramon Crehuet
El Grupo de Química Teórica y Computacional (CTCG) estudia el comportamiento y las propiedades de las moléculas para comprender su reactvidad, su dinámica y sus interacciones. Usamos tanto métodos de la Química Cuántica como de Modelización Molecular.
- Reacciones de oxidación con un papel importante en química atmosférica y del medio ambiente, así como en sistemas biológicos.
- Dinámica de proteínas, con especial interés en Proteínas Intrínsecamente Desordenadas y catálisis enzimática.
Personal científico
Ramon Crehuet
Científico Titular
ramon.crehuet@iqac.csic.es
Sergi Vela
Científico Titular
sergi.vela@iqac.csic.es
Francesco Colizzi
Científico Titular
francesco.colizzi@iqac.csic.es
Eloy Ramos
Científico Titular
eloy.ramos@iqac.csic.es
Ramon Guixa-Gonzalez
Científico Titular
ramon.guixa@iqac.csic.es
Personal laboratorio
Albert Ortega Bartolome
Investigador Predoctoral
albert.ortega@iqac.csic.es
Oriol Barcenas Lopez
Investigador Predoctoral
Berta Bori Bru
Investigadora Predoctoral
berta.bori@iqac.csic.es
- Generic residue numbering of the GAIN domain of adhesion GPCRs
Seufert, Florian,Pérez-Hernández, Guillermo, Pándy-Szekeres, Gáspár, Guixà-González, Ramon, Langenhan, Tobias, Gloriam, David E., Hildebrand, Peter W.
Nature Communications, 16(1),246, 2025 - Leveraging Cryptic Ligand Envelopes through Enhanced Molecular Simulations
Colizzi, F.
J. Phys. Chem. Lett. 2025, 16, 2, 443–453 - Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation
Valentín Iglesias, Jarosław Chilimoniuk, Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura, Michał Burdukiewicz
Computational and Structural Biotechnology Journal, Volume 23, December 2024, Pages 4011-4018 - Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity
Mateusz Zalewski, Valentin Iglesias, Oriol Bárcenas, Salvador Ventura, Sebastian Kmiecik
Protein Science, Volume 33, Issue 10, October 2024. Article number e5180 - Automated prediction of ground state spin for transition metal complexes
Yuri Cho, Ruben Laplaza, Sergi Vela and Clémence Corminboeuf
Digital Discovery, 2024,3, 1638-1647 - Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor
Hossein Batebi, Guillermo Pérez-Hernández, Sabrina N. Rahman, Baoliang Lan, Antje Kamprad, Mingyu Shi, David Speck, Johanna K. S. Tiemann, Ramon Guixà-González, Franziska Reinhardt, Peter F. Stadler, Makaía M. Papasergi-Scott, Georgios Skiniotis, Patrick Scheerer, Brian K. Kobilka, Jesper M. Mathiesen, Xiangyu Liu & Peter W. Hildebrand
Nature Structural & Molecular Biology volume 31, pages1692–1701 (2024) - Triplet State Radical Chemistry: Significance of the Reaction of 3SO2 with HCOOH and HNO3
Josep M. Anglada, Marilia T. C. Martins-Costa, Joseph S. Francisco and Manuel F. Ruiz-López
J. Am. Chem. Soc. 2024
- APOST-3D: Chemical concepts from wavefunction analysis
Pedro Salvador, Eloy Ramos-Cordoba, Marc Montilla, Leila Puja, and Martí Gimferrer
J. Chem. Phys. 160, 172502 (2024)
- Spurious Oscillations Caused by Density Functional Appproximations: Who is to blame, Exchange or Correlation?
Sebastian P. Sitkiewicz, Rubén R. Ferradás, Eloy Ramos-Cordoba, Robert Zaleśny, Eduard Matito, and Josep M. Luis
J. Chem. Theory Comput., 20, 8, 3144-3153, (2024)
- Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs
Johan G. Olsen, Andreas Prestel, Noah Kassem, Sebastian S. Broendum 1, Hossain Mohammad Shamim, Signe Simonsen, Martin Grysbæk, Josefine Mortensen, Louise Lund Rytkjær, Gitte W. Haxholm, Riccardo Marabini, Christian Holmberg, Antony M. Carr, Ramon Crehuet, Olaf Nielsen and Birthe B. Kragelund
Nucleic Acids Research, Volume 52, Issue 4, 2, 2024
- Carving out a Glycoside Hydrolase Active Site for Incorporation into a New Protein Scaffold Using Deep Network Hallucination
Anders Lønstrup Hansen, Frederik Friis Theisen, Ramon Crehuet, Enrique Marcos, Nushin Aghajari and Martin Willemoës
ACS Synth. Biol. 2024
- Controlling the Diradical Character of Thiele Like Compounds
Josep M. Anglada, Jordi Poater, Ibério de P. R. Moreira and Josep Maria Bofill
J. Org. Chem. 2023,
- The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity
Carlos A. Elena-Real, Amin Sagar, Annika Urbanek, Matija Popovic, Anna Morató, Alejandro Estaña, Aurélie Fournet, Christine Doucet, Xamuel L. Lund, Zhen-Dan Shi, Luca Costa, Aurélien Thureau, Frédéric Allemand, Rolf E. Swenson, Pierre-Emmanuel Milhiet, Ramon Crehuet, Alessandro Barducci, Juan Cortés, Davy Sinnaeve, Nathalie Sibille & Pau Bernadó
Nature Structural & Molecular Biology, 30, 309–320, 2023
- Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing
Kerry Blair, Muhammad Tehseen, Vlad-Stefan Raducanu, Taha Shahid, Claudia Lancey, Fahad Rashid, Ramon Crehuet, Samir M. Hamdan & Alfredo De Biasio
Nature Communications | ( 2022) 13:7833
- Fast Sulfate Formation Initiated by the Spin-Forbidden Excitation of SO2 at the Air–Water Interface
Chu Gong, Xu Yuan, Dong Xing, Dongmei Zhang, Marilia T. C. Martins-Costa, Josep M. Anglada, Manuel F. Ruiz-López, Joseph S. Francisco, and Xinxing Zhang
J. Am. Chem. Soc. 2022
- A glutamine-based single α-helix scaffold to target globular proteins
Albert Escobedo, Jonathan Piccirillo, Juan Aranda, Tammo Diercks, Borja Mateos, Carla Garcia-Cabau, Macarena Sánchez-Navarro, Busra Topal, Mateusz Biesaga Lasse Staby, Birthe B. Kragelund, Jesús García, Oscar Millet, Modesto Orozco, Murray Coles, Ramon Crehuet & Xavier Salvatella
Nat Commun 13, 7073, 2022
- Photosensitization mechanisms at the air–water interface of aqueous aerosols
Marilia T. C. Martins-Costa, Josep M. Anglada, Joseph S. Franciscoc and Manuel F. Ruiz-López
Chem. Sci., 2022, Advance Article
- Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation
Nicolai Tidemand Johansen, Marta Bonaccorsi, Tone Bengtsen, Andreas Haahr Larsen, Frederik Grønbæk Tidemand, Martin Cramer Pedersen, Pie Huda, Jens Berndtsson, Tamim Darwish
eLife 2022;11:e71887
- Mg2+dependent conformational equilibria in CorA and an integrated view on transport regulation
Johansen, N.T., Bonaccorsi, M., Bengtsen, T., Larsen, A.H., Tidemand, F.G., Pedersen, M.C., Huda, P., Berndtsson, J., Darwish, T., Yepuri, N.R., Martel, A., Pomorski, T.G., Bertarello, A., Sansom, M., Rapp, M., Crehuet, R., Schubeis, T., Lindorff-Larsen, K., Pintacuda, G., Arleth, L.
eLife, 11, art. no. e71887, 2022
- Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties
Giulio Tesei, Thea K. Schulze, Ramon Crehuet and Kresten Lindorff-Larsen
Proceedings of the National Academy of Sciences Nov 2021, 118 (44) e2111696118; DOI: 10.1073/pnas.2111696118
- Identification of a Catalytic Nucleophile-Activating Network in the endo-α-N-Acetylgalactosaminidase of Family GH101
Hansen, A.Lø., Koivisto, J.M., Simonsen, S., Dong, Z., Crehuet, R., Hansen, D.K., Willemoës, M.
Biochemistry, 60 (45), pp. 3398-3407. 2021
- Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA
Claudia Lancey, Muhammad Tehseen, Souvika Bakshi, Matthew Percival, Masateru Takahashi, Mohamed A. Sobhy, Vlad S. Raducanu , Kerry Blair, Frederick W. Muskett, Timothy J. Ragan, Ramon Crehuet, Samir M. Hamdan & Alfredo De Biasio
Nat Commun 12, 6095, 2021
- Tight electrostatic regulation of the OH production rate from the photolysis of hydrogen peroxide adsorbed on surfaces
Manuel F. Ruiz-López, Marilia T. C. Martins-Costa, Joseph S. Francisco, and Josep M. Anglada
PNAS, 118 (30) e2106117118, 2021
- DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
Tesei, G., Martins, J.M., Kunze, M.B.A., Wang, Y., Crehuet, R., Lindorff-Larsen, K.
PLoS Computational Biology, 17 (1), art. no. e1008551, 2021
- Reactivity of Undissociated Molecular Nitric Acid at the Air–Water Interface
Josep M. Anglada, Marilia T. C. Martins-Costa, Joseph S. Francisco and Manuel F. Ruiz-López
J. Am. Chem. Soc, 143, 1, 453–462,2021
- Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
Agustí Emperador, Ramon Crehuet and Elvira Guàrdia
Polymers 2021, 13(2), 176
- The Aqueous Surface as an Efficient Transient Stop for the Reactivity of Gaseous NO2 in Liquid Water
Marilia T. C. Martins-Costa, Josep M. Anglada, Joseph S. Francisco, and Manuel F. Ruiz-López
Journal of the American Chemical Society, 142 (50), pp. 20937-20941. 2020 - Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design
Sorokina, M., M. C. Teixeira, J., Barrera-Vilarmau, S., Paschke, R., Papasotiriou, I., Rodrigues, J.P.G.L.M., Kastritis, P.L.
Scientific Data, 7 (1), art. no. 309, 2020
- Photoinduced Oxidation Reactions at the Air–Water Interface
Josep M. Anglada, Marilia T. C. Martins-Costa, Joseph S. Francisco and Manuel F. Ruiz-López
J. Am. Chem. Soc.142 (38), pp. 16140-16155, 2020
- Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins
Ahmed, M.C., Crehuet, R., Lindorff-Larsen, K.
Methods in molecular biology (Clifton, N.J.), 2141, pp. 429-445. 2020
- Two-step reaction mechanism reveals new antioxidant capability of cysteine disulfides against hydroxyl radical attack
Ramon Crehuet, Josep M. Anglada, Joseph S. Francisco, and Yu Xia
PNAS (2020)
- Molecular reactions at aqueous interfaces
Manuel F. Ruiz-Lopez , Joseph S. Francisco, Marilia T. C. Martins-Costa and Josep M. Anglada
Nat Rev Chem (2020).
- A New Mechanism of Acid Rain Generation from HOSO at the Air–Water Interface
Manuel F. Ruiz-López, Marilia T. C. Martins-Costa, Josep M. Anglada, Joseph S. Francisco
J. Am. Chem. Soc.2019
- Bayesian-maximum-entropy reweighting of IDP ensembles based on NMR chemical shifts
Crehuet, R., Buigues, P.J., Salvatella, X., Lindorff-Larsen, K.
Entropy, 21 (9), art. no. 898, 2020.
- Photochemistry of HOSO radical in the gas phase
Trabelsi, T., Anglada, J.M., Ruiz-López, M.F., Francisco, J.S.
Journal of Chemical Physics, 151 (11), art. no. 111103, 2019 .
- Formation of a stable biradical triplet state cation versus a closed shell singlet state cation by oxidation of adducts of 3,6-dimethoxycarbazole and polychlorotriphenylmethyl radicals
Paola Ballesteros, Alba Cuadrado, Alejandra Gilabert, Lluís Fajarí, Ignasi Sirés, Enric Brillas, Maria Pilar Almajano, Dolores Velasco, Josep M. Anglada and Luis Juliá
Phys. Chem. Chem. Phys., 2019, Advance Article
- Theoretical Investigation of the Photoexcited NO2 + H2O reaction at the Air‐Water interface and Its Atmospheric Implications
Marilia T. C. Martins-Costa, Josep M. Anglada, Joseph S. Francisco, Manuel Ruiz-Lopez
Chem. Eur. J. 10.1002/chem.201902769
- Atmospheric Spectroscopy and Photochemistry at Environmental Water Interfaces
J. Zhong, M. Kumar, J.M. Anglada, M.T.C. Martins-Costa, M.F. Ruiz-Lopez, X.C. Zeng, and Joseph S. Francisco
Annual Review of Physical Chemistry, Vol. 70:45-69 2019
- Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor
Albert Escobedo, Busra Topal, Micha B. A. Kunze, Juan Aranda, Giulio Chiesa, Daniele Mungianu, Ganeko Bernardo-Seisdedos, Bahareh Eftekharzadeh, Margarida Gairí, Roberta Pierattelli, Isabella C. Felli, Tammo Diercks, Oscar Millet, Jesús García, Modesto Orozco, Ramon Crehuet, Kresten Lindorff-Larsen & Xavier Salvatella
NATURE COMMUNICATIONS| (2019) 10:2
- Triplet state promoted reaction of SO2 with H2O by competition between proton coupled electron transfer (pcet) and hydrogen atom transfer (hat) processes
Josep M. Anglada, Marilia T. C. Martins-Costa, Joseph S. Francisco and Manuel F. Ruiz-López
Phys. Chem. Chem. Phys., 2019, 21, 9779
- The gas phase oxidation of HCOOH by Cl and NH2 radicals. Proton coupled electron transfer versus hydrogen atom transfer
Josep M Anglada, Ramon Crehuet, Albert Solé
Molecular Physics,2018
- p15PAF binding to PCNA modulates the DNA sliding surface
De March, M., Barrera-Vilarmau, S., Crespan, E., Mentegari, E., Merino, N., Gonzalez-Magaña, A., Romano-Moreno, M., Maga, G., Crehuet, R., Onesti, S., Blanco, F.J., De Biasio, A.
Nucleic acids research, 46 (18), pp. 9816-9828. 2018
- Tropospheric oxidation of methyl hydrotrioxide (CH3OOOH) by hydroxyl radica
Josep M. Anglada and Albert Sole
Phys.Chem.Chem.Phys., 2018, 20, 27406
- Photochemistry of SO2 at the Air–Water Interface: A Source of OH and HOSO Radicals
Marilia T. C. Martins-Costa, Josep M. Anglada, Joseph S. Francisco, Manuel F. Ruiz-López
Am. Chem. Soc., 2018, 140 (39), pp 12341–12344
- Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study
Alagia, A., Jorge, A.F., Aviñó, A., Cova, T.F.G.G., Crehuet, R., Grijalvo, S., Pais, A.A.C.C., Eritja, R.
Chemical Science 2018, 9 (8), pp. 2074-2086.
- Reactivity of Hydropersulfides toward the Hydroxyl Radical Unraveled: Disulfide Bond Cleavage, Hydrogen Atom Transfer, and Proton-Coupled Electron Transfer.
Anglada, J.M., Crehuet, R., Adhikari, S., Francisco, J.S., Xia, Y.
Phys Chem Chem Phys 2018, 20 (7), 4793-4804 .
- Structural Basis of Human PCNA Sliding on DNA
De March, M.; Merino, N.; Barrera-Vilarmau, S.; Crehuet, R.; Onesti, S.; Blanco, F. J.; De Biasio, A.
Nat. Commun. 2017, 8, 13935.
- The Atmospheric Oxidation of CH
3 OOH by the OH Radical: The Effect of Water VaporAnglada, J. M.; Crehuet, R.; Martins-Costa, M.; Francisco, J. S.; Ruiz-López, M.
Phys. Chem. Chem. Phys. 2017, 19 (19).
- Impact of cloud water droplets on OH production rate from peroxide photolysis
M.T. C. Martins-Costa, J. M. Anglada, J. S. Francisco and Manuel F. Ruiz-López.
Phys Chem. Chem. Phys.2017, 19, 31621-31627.
- Disentangling Polydispersity in the PCNA-P15PAFComplex, a Disordered, Transient and Multivalent Macromolecular Assembly.
Cordeiro, T. N.; Chen, P.-C.; De Biasio, A.; Sibille, N.; Blanco, F. J.; Hub, J. S.; Crehuet, R.; Bernadó, P.
Nucleic Acids Res. 2017, 45 (3).
- The Stability of α-Hydroperoxyalkyl Radicals.
Anglada, J. M.; Crehuet, R.; Francisco, J. S.
Chem. - A Eur. J. 2016, 22 (50).
- Impact of the water dimer on the atmospheric reactivity of carbonyl oxides.
J.M. Anglada, and A.Solé.
PhysChemChemPhys. 2016, 18, 17698-17712.
- Synthesis, Functional Assays, Electrophysiological Activity and Field Tests of Pheromone Antagonists of the Tomato Leafminer Tuta Absoluta.
Dominguez, A.; Puigmartí, M.; Bosch, M. P.; Rosell, G.; Crehuet, R.; Ortiz, A.; Quero, C.; Guerrero, A.
- Agric. Food Chem. 2016.
- Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.
Kanaan, N.; Crehuet, R.; Imhof, P.
- Phys. Chem. B 2015, 119 (38), 12365–12380.
- Enzymatic Minimum Free Energy Path Calculations Using Swarms of Trajectories.
Sanchez-Martinez, M.; Field, M.; Crehuet, R.
J.Phys. Chem. B 2015, 119 (3).
- Interconnection of Reactive Oxygen Species Chemistry across the Interfaces of Atmospheric, Environmental, and Biological Processes.
Josep M. Anglada, Marilia Martins-Costa, Joseph S. Francisco, and Manuel F. Ruiz-López.
Acc. Chem. Res., 2015, 48, 575-583.
- Spectroscopic signatures of ozone at the air-water interface and photochemistry implications.
J.M. Anglada, M. Martins-Costa, M.F. Ruiz-López, J.S. Francisco.
Proc. Natl. Acad. Sci.., 2014, 111, 11618-11693.
- Mechanistic Studies on the Intramolecular Cyclization of O-Tosyl Phytosphingosines to Jaspines.
Crehuet, R.; Mormeneo, D.; Anglada, J. M.; Delgado, A.
Nat. Prod. Commun. 2014, 9 (8), 1087–1090.
- Spectroscopic signatures of ozone at the air-water interface and photochemistry implications.
J.M. Anglada, M. Martins-Costa, M.F. Ruiz-López, J.S. Francisco.
Proc. Natl. Acad. Sci.., 2014, 111, 11618-11693.
- Unexpected Reactivity of Amidogen Radical in the Gas Phase Degradation of Nitric Acid
Josep M Anglada, Santiago Olivella, Albert Solé.
J. Am. Chem. Soc., 2014, 136, 6834-6837.
