Bio-KT Lab Publications

@article{Lew-Yee2026b,

title = {A Python-Based Module for Exploring Machine Learning-Inspired Optimization Algorithms Using Quantum Chemistry},

author = {Juan Felipe Huan Lew-Yee and Elixabete Rezabal and Xabier Lopez and Mario Piris and Jose M. Mercero},

doi = {10.1021/acs.jchemed.5c01470},

issn = {1938-1328},

year  = {2026},

date = {2026-07-14},

urldate = {2026-07-14},

journal = {J. Chem. Educ.},

volume = {103},

number = {7},

pages = {3929--3937},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jiménez-García2026b,

title = {MartiniSurf: Automated Simulations of Surface-Immobilized Biomolecular Systems with Martini},

author = {Juan Carlos Jiménez-García and Fernando López-Gallego and Xabier López and David De Sancho},

doi = {10.1021/acs.jcim.6c00953},

issn = {1549-960X},

year  = {2026},

date = {2026-06-16},

urldate = {2026-06-16},

journal = {J. Chem. Inf. Model.},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Luna2026b,

title = {Solvent switch strategy to facilitate the downstream process of chemical recycling of plastics},

author = {Emelin Luna and Ion Olazabal and Tobias de Somer and Pieter Nachtergaele and Xabier Lopez and Marta Ximenis and Steven de Meester and Haritz Sardon},

doi = {10.1016/j.resconrec.2025.108686},

issn = {0921-3449},

year  = {2026},

date = {2026-02-23},

journal = {Resources, Conservation and Recycling},

volume = {226},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jiménez-García2026,

title = {Mechanistic Determinants of Oriented Enzyme Immobilization from Martini Simulations},

author = {Juan Carlos Jiménez-García and Nicoll Zeballos and Fernando López-Gallego and Xabier López and David De Sancho},

doi = {10.1021/acs.jpclett.5c03753},

issn = {1948-7185},

year  = {2026},

date = {2026-02-19},

urldate = {2026-02-19},

journal = {J. Phys. Chem. Lett.},

volume = {17},

number = {7},

pages = {2094--2102},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Guimarães2025,

title = {Computational Analysis of a Next-Generation Platinum-Based Chemotherapies that Induce DNA Double-Strand Breaks},

author = {Amanda R. Guimarães and Óscar R. Ballesteros and Iván Rivilla and Irene Olaizola and Mikel Odriozola-Gimeno and Abel de Cózar and David de Sancho and Xabier Lopez and Jesus M. Banales and Fernando P. Cossío},

doi = {10.1021/acs.jcim.5c01654},

issn = {1549-960X},

year  = {2026},

date = {2026-01-12},

urldate = {2026-01-12},

journal = {J. Chem. Inf. Model.},

volume = {66},

number = {1},

pages = {668--683},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DeSancho2025,

title = {Crossover in aromatic amino acid interaction strength between tyrosine and phenylalanine in biomolecular condensates},

author = {David De Sancho and Xabier Lopez},

doi = {10.7554/elife.104950},

issn = {2050-084X},

year  = {2025},

date = {2025-12-04},

urldate = {2025-12-04},

journal = {ELIFE},

volume = {14},

number = {RP104950},

publisher = {eLife Sciences Publications, Ltd},

abstract = {<jats:p>Biomolecular condensates often form through the self-assembly of disordered proteins with low-complexity sequences. In these polypeptides, the aromatic amino acids phenylalanine and tyrosine act as key ‘sticker’ residues, driving the cohesion of dense phases. Recent studies on condensates suggest a hierarchy in sticker strength, with tyrosine being more adhesive than phenylalanine. This hierarchy aligns with experimental data on amino acids solubilities and potentials of mean force derived from atomistic simulations. However, it contradicts conventional chemical intuition based on hydrophobicity scales and pairwise contact statistics from experimental structures of proteins, which suggest that phenylalanine should be the stronger sticker. In this work, we use molecular dynamics simulations and quantum chemistry calculations to resolve this apparent discrepancy. Using simple model peptides and side-chain analogues, we demonstrate that the experimentally observed hierarchy arises from the lower free energy of transfer of tyrosine into the condensate, mediated by both stronger protein-protein interactions and solvation effects in the condensate environment. Notably, as the dielectric constant of the media surrounding the stickers approaches that of an apolar solvent, the trend reverses, and phenylalanine becomes the stronger sticker. These findings highlight the role of the chemical environment in modulating protein-protein interactions, providing a clear explanation for the crossover in sticker strength between tyrosine and phenylalanine in different media.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Olaizola2025,

title = {New platinum derivatives selectively cause double-strand DNA breaks and death in naïve and cisplatin-resistant cholangiocarcinomas},

author = {Irene Olaizola and Mikel Odriozola-Gimeno and Paula Olaizola and Francisco J. Caballero-Camino and Noelia Pastor-Toyos and Mireia Tena-Garitaonaindia and Ainhoa Lapitz and Beatriz Val and Amanda R. Guimaraes and Maitane Asensio and Maider Huici-Izagirre and Colin Rae and David de Sancho and Xabier Lopez and Pedro M. Rodrigues and Elisa Herraez and Oscar Briz and Laura Izquierdo-Sanchez and Aitziber Eleta-Lopez and Alexander M. Bittner and Ana Martinez-Amesti and Teresa Miranda and Sumera I. Ilyas and Chiara Braconi and Maria J. Perugorria and Luis Bujanda and Iván Rivilla and Jose J.G. Marin and Fernando P. Cossío and Jesus M. Banales},

doi = {10.1016/j.jhep.2025.04.034},

issn = {0168-8278},

year  = {2025},

date = {2025-11-04},

journal = {Journal of Hepatology},

volume = {83},

number = {5},

pages = {1077--1091},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Urriolabeitia2025,

title = {Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT},

author = {Asier Urriolabeitia and Julia Contreras-García and David De Sancho and Xabier López},

doi = {10.1021/acs.jcim.5c01501},

issn = {1549-960X},

year  = {2025},

date = {2025-10-13},

urldate = {2025-10-13},

journal = {J. Chem. Inf. Model.},

volume = {65},

number = {19},

pages = {10613--10623},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ludeña2025,

title = {Toward a formulation of a CISS theory with the inclusion of two-particle relativistic effects, electron–phonon coupling, and electron–electron correlation. An application to NMR-based chiral discrimination},

author = {Eduardo V. Ludeña and Jesus M. Ugalde and Xabier Lopez and Louis-S. Bouchard and Vladimiro Mujica},

doi = {10.1063/5.0272982},

issn = {1089-7690},

year  = {2025},

date = {2025-09-28},

urldate = {2025-09-28},

volume = {163},

number = {12},

publisher = {AIP Publishing},

abstract = {<jats:p>The current status of the theoretical foundations of the Chiral-Induced Spin Selectivity (CISS) effect has substantially improved from its original one-electron formulation. However, there is a need to improve the inclusion of electron–vibrational interaction, the exchange and correlation effects arising from electron–electron interactions, and non-Born–Oppenheimer coupling to enhance the predictive power of the theory and its agreement with experiments. In an attempt to overcome these difficulties, we advance in the present work a microscopic quantum mechanical treatment of CISS based on the relativistic Breit–Pauli many-particle Hamiltonian. In particular, we determine in this context the effect that including non-Born–Oppenheimer components arising in a Taylor expansion of the electron–nuclear potential has on the spin–orbit coupling term of this Hamiltonian. We also consider in this framework the electron–electron exchange and correlation effects and propose some practical approximations based on non-relativistic approaches. Finally, we extend the application of the Breit–Pauli Hamiltonian to describe nuclear–nuclear spin interactions and discuss the possibility of explaining enantiomeric selectivity in cross-polarization nuclear magnetic resonance experiments.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Balahoju2025,

title = {Radical Formation by Direct Single Electron Transfer between Nitrobenzene and Anionic Organo Bases},

author = {Shivaprasad Achary Balahoju and Nicholus Bhattacharjee and Luis Lezama and Xabier Lopez and Pablo Salcedo-Abraira and Antonio Rodríguez-Diéguez and Daniel Reta},

doi = {10.1021/acsomega.5c02989},

issn = {2470-1343},

year  = {2025},

date = {2025-06-10},

journal = {ACS Omega},

volume = {10},

number = {22},

pages = {23798--23807},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}