Kimika Teorikoa

@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{Nose2025,

title = {Dual Lewis Acid–Base Molecular Cages Facilitate Cooperative N

                    _{2}

                    Activation: Insights from Theory},

author = {Holliness Nose and Fernando Ruipérez},

doi = {10.1002/cphc.202500624},

issn = {1439-7641},

year  = {2025},

date = {2025-11-09},

journal = {ChemPhysChem},

publisher = {Wiley},

abstract = {

                    Activating molecular nitrogen (N

                    2

                    ) under ambient conditions remains a major challenge. Dual Lewis acid–base molecular cages are investigated to cooperatively activate N

                    2

                    using computational chemistry. Cages composed of Lewis acids (LA) and Lewis bases (LB) connected by a linker chain ([LA,LB]

                    C

                    ) are analyzed via binding free energies, interaction and deformation energies, bond lengths, angles, and Wiberg bond indices and charge distributions. Two interaction arrangements emerge: 1) rigid systems with strong LA‐LB dative bonds that deform substantially upon N

                    2

                    binding and do not act as frustrated Lewis pairs (FLPs), and 2) flexible cages with extended LA‐LB separations displaying typical FLP behavior. Borylene donors enable strong, stable N

                    2

                    interactions, particularly in systems

                    6a

                    and

                    7c

                    , whereas Verkade's base is less effective. Structural flexibility and electronic tuning of LA/LB centers are fundamental for efficient activation. Natural bond orbital and quantum theory of atoms in molecules analyses reveal partially covalent electrostatic interactions at the acidic site and covalent interactions at the basic site. These results provide design principles for molecular cages for N

                    2

                    activation.

                  },

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{Berti2025,

title = {Ultra-Low Atomic Diffusion Barrier on Two-Dimensional Materials: The Case of Pt on Epitaxial Graphene},

author = {Andrea Berti and Ramón M. Bergua and Jose M. Mercero and Deborah Perco and Paolo Lacovig and Silvano Lizzit and Elisa Jimenez-Izal and Alessandro Baraldi},

doi = {10.1021/acsnano.5c13305},

issn = {1936-086X},

year  = {2025},

date = {2025-10-14},

urldate = {2025-10-14},

journal = {ACS Nano},

volume = {19},

number = {40},

pages = {35921--35932},

publisher = {American Chemical Society (ACS)},

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{Muelas2025,

title = {\textit{SNUPN}‐Related Muscular Dystrophy: Novel Phenotypic, Pathological and Functional Protein Insights},

author = {Nuria Muelas and Pablo Iruzubieta and Alberto Damborenea and Laura Pérez‐Fernández and Inmaculada Azorín and Juan Carlos Jiménez García and Ana Töpf and Pilar Martí and Lorena Fores‐Toribio and María Manterola and Rosana Blanco‐Mañez and Oihane Pikatza‐Menoio and Sonia Alonso‐Martín and Volker Straub and Aitziber L. Cortajarena and Adolfo López de Munain and David De Sancho and Lorea Blázquez and Juan J. Vilchez},

doi = {10.1002/acn3.70211},

issn = {2328-9503},

year  = {2025},

date = {2025-10-06},

urldate = {2025-10-06},

journal = {Ann Clin Transl Neurol},

publisher = {Wiley},

abstract = {<jats:title>ABSTRACT</jats:title><jats:sec><jats:title>Objective</jats:title><jats:p><jats:italic>SNUPN</jats:italic>‐related muscular dystrophy or LGMDR29 is a new entity that covers from a congenital or childhood onset pure muscular dystrophy to more complex phenotypes combining neurodevelopmental features, cataracts, or spinocerebellar ataxia. So far, 12 different variants have been described. Here we report the first family with <jats:italic>SNUPN</jats:italic>‐related muscular dystrophy presenting an adult‐onset myopathy as well as novel ultrastructural findings.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Clinical evaluation, muscle and brain magnetic resonance imaging (MRI), and muscle histopathological and electron microscopy analysis were conducted. Functional studies including protein modelling and interaction, immunofluorescence and splicing analysis were also performed.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Two siblings carrying two novel deleterious variants in the <jats:italic>SNUPN</jats:italic> gene (p.Arg27Cys and p.Cys174Tyr) showed adult‐onset proximo‐distal and axial muscle weakness with early respiratory involvement. One patient presented with asymptomatic cerebellar atrophy. Muscle MRI identified involvement in the paravertebral, triceps brachii, sartorius and gracilis muscles. The histopathology revealed dystrophic changes and an abnormal pattern of cytoskeletal and myofibrillar proteins, while electron microscopy disclosed the proliferation of granules and vesicles associated with features of nuclear envelope and sarcolemma remodelling. Functional studies showed that <jats:italic>SNUPN</jats:italic> variants impair snurportin‐1 function through reduced binding affinity to importin‐β and impaired folding, leading to disturbed nuclear import of small nuclear ribonucleoproteins and downstream splicing.</jats:p></jats:sec><jats:sec><jats:title>Interpretation</jats:title><jats:p>Our work expands the phenotype of <jats:italic>SNUPN</jats:italic>‐related muscular dystrophy and provides more insights into their pathological profile. We advise <jats:italic>SNUPN</jats:italic> testing in patients with late‐onset proximo‐distal and axial weakness with early respiratory impairment and features reminding inclusion body myositis (IBM). Granular deposits suggestive of biomolecular condensates perturbed cell organelle traffic and membrane homeostasis, opening new avenues to understand the pathomechanisms involved in this novel disease.</jats:p></jats:sec>},

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{Teotonico2025,

title = {Introduction of 9‐Bromo‐9‐Borafluorene Scaffold Into Deep Blue Emitting π‐Conjugated Polymers},

author = {Jacopo Teotonico and Daniele Mantione and Kimberly K. Hollister and Haritz Sardon and Nicholas Ballard and Fernando Ruipérez and Robert J. Gilliard and Fernando Vidal},

doi = {10.1002/pol.20241163},

issn = {2642-4169},

year  = {2025},

date = {2025-09-01},

urldate = {2025-09-01},

journal = {Journal of Polymer Science},

volume = {63},

number = {17},

pages = {3538--3545},

publisher = {Wiley},

abstract = {<jats:title>ABSTRACT</jats:title><jats:p>We report the first successful incorporation of 9‐bromo‐9‐borafluorene into a π‐conjugated co‐polymer consisting of 9,9‐silafluorene and 9,9‐dioctylfluorene units through a SiB exchange reaction. The parent 9,9‐silafluorene copolymer exhibits deep blue fluorescence, with CIE 1931 (0.15, 0.04), a high quantum yield (<jats:italic>Φ</jats:italic> = 93.9%), and excellent thermal stability (<jats:italic>T</jats:italic>

<jats:sub>5d</jats:sub> = 439°C). Density functional theory (DFT) calculations were employed to investigate the optical and electronic properties, revealing the structure of the molecular orbitals that contribute to the HOMO–LUMO bandgap of these conjugated co‐polymers. Additionally, we explored the Lewis acidity of the borafluorene unit and its potential for forming dynamic networks through reversible Lewis pair interactions, using 4,4′‐bipyridine as a model Lewis base. The integration of both silicon and boron into a π‐conjugated polymer backbone offers new opportunities for tuning the optical and electronic properties of materials for potential applications in OLED materials.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Verdugo2025,

title = {Choline–geranate (CAGE) ionic liquids potentiate the anticancer activity of platinum-based drugs},

author = {Marta Costa Verdugo and Giulia Sierri and Laura Hernandez-Fernandez and Elena Formoso and José I. Miranda and Francesco Saverio Sica and Alejandro H. Orrego and Alba González and Elixabete Rezabal and Francesca Re and Luca Salassa},

doi = {10.1039/d5cc02226f},

issn = {1364-548X},

year  = {2025},

date = {2025-08-07},

journal = {Chem. Commun.},

volume = {61},

number = {65},

pages = {12167--12170},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {CAGE IL formulations significantly enhance the potency of platinum-based drugs in glioblastoma cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grabowski2025b,

title = {Molecular Hydrogen as a Proton Donor in HH···F Hydrogen Bonds—BF_{4}^{−}···(H_{2})_{\textit{n}} Clusters},

author = {Sławomir J. Grabowski},

doi = {10.1002/cphc.202500243},

issn = {1439-7641},

year  = {2025},

date = {2025-08-04},

journal = {ChemPhysChem},

volume = {26},

number = {15},

publisher = {Wiley},

abstract = {The MP2/6‐311++G(d,p) calculations are performed to analyze geometric, energetic, and topological parameters of BF4−···(H2)n clusters (n up to 8). These analyses are supported by the Natural Bond Orbitals method and the Quantum Theory in Atoms in Molecules approach. The BF4− anion acts as the Lewis base since its whole molecular surface is characterized by the negative electrostatic potential. The hydrogen molecules in clusters are considered to play the role of Lewis acid ligands. These ligands are located linearly in directions being the elongation of BF bonds if the number of H2 molecules in the cluster does not exceed 4. For the greater clusters (n ≥ 5), all H2 molecules tend to form linear HH···F arrangements, or nearly so. However, the BF···H angles are sometimes far from linearity. The HH···F interactions may be classified as hydrogen bonds; the analysis of such interactions is also performed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lew-Yee_Piris_2025,

title = {Metal-Insulator Transition described by NOFT},

author = {Juan Felipe Huan Lew-Yee and Mario Piris },

url = {https://www.revistacubanadefisica.org/index.php/rcf/article/view/53},

year  = {2025},

date = {2025-07-01},

urldate = {2025-07-01},

journal = {Revista Cubana de Física},

volume = {42},

number = {1},

pages = {30–36},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grabowski2025,

title = {Triel Bonds─Interactions without Borders, Similarly as Hydrogen Bonds},

author = {Sławomir J. Grabowski},

doi = {10.1021/acs.cgd.5c00466},

issn = {1528-7505},

year  = {2025},

date = {2025-06-18},

journal = {Crystal Growth & Design},

volume = {25},

number = {12},

pages = {4539--4552},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yu2025,

title = {Piercing Molecular Graphenes: Precision Synthesis and Photophysics of NBN-Edged Porous Molecular Carbons},

author = {Yang Yu and Asier Izu and José M. Marín Beloqui and Shammi Rana and Kunal S. Mali and Steven De Feyter and David Casanova and Juan Casado and Junzhi Liu},

doi = {10.1021/jacs.5c06175},

issn = {1520-5126},

year  = {2025},

date = {2025-06-11},

journal = {J. Am. Chem. Soc.},

volume = {147},

number = {23},

pages = {20098--20108},

publisher = {American Chemical Society (ACS)},

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}

}

@article{Stevens2025,

title = {Synthesis, characterization and reactivity of a series of alkaline earth and rare earth iminophosphoranomethanide complexes},

author = {Matthew P. Stevens and Yu Liu and Elias Alexopoulos and Shifaa S. A. Xec Daudo and Rebecca R. Hawker and Adam Khan and Luis Lezama and Daniel Reta and Fabrizio Ortu},

doi = {10.1038/s42004-025-01572-5},

issn = {2399-3669},

year  = {2025},

date = {2025-06-05},

journal = {Commun Chem},

volume = {8},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

          <jats:p>There is a great demand from the synthetic community for readily accessible organometallic alkaline earth and rare earth compounds that can be used as synthons for the preparation of new complexes and materials. Here we report the use of the methanide ligand {CH(SiMe<jats:sub>3</jats:sub>)P(Ph)<jats:sub>2</jats:sub> = NSiMe<jats:sub>3</jats:sub>}<jats:sup>–</jats:sup> (NPC-H) in the stabilization of alkaline earth and rare earth organometallics and their potential use as synthetic precursors. <jats:italic>Bis</jats:italic>- and <jats:italic>tris-</jats:italic>methanide complexes were obtained following two methods: (1) deprotonation of the proligand with organometallic precursors; (2) salt elimination reactivity between potassium methanide and metal iodides. All compounds were characterised by multinuclear nuclear magnetic resonance, infra-red spectroscopy, elemental analysis, ultraviolet-visible spectroscopy and single crystal X-ray diffraction. Additionally, selected rare earth methanides were tested as synthetic precursors for the preparation of solvent-free rare earth complexes. Finally, the electronic structures of open-shell divalent rare earth methanides were probed using electron paramagnetic resonance, magnetometry studies and ab initio calculations.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lew-Yee2025b,

title = {Advancing Natural Orbital Functional Calculations through Deep Learning-Inspired Techniques for Large-Scale Strongly Correlated Electron Systems},

author = {Juan Felipe Huan Lew-Yee and Jorge M. del Campo and Mario Piris},

doi = {10.1103/physrevlett.134.206401},

issn = {1079-7114},

year  = {2025},

date = {2025-05-20},

journal = {Phys. Rev. Lett.},

volume = {134},

number = {20},

publisher = {American Physical Society (APS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xu2025,

title = {How many distinct and reliable multireference diagnostics are there?},

author = {Xiang Xu and Luis Soriano-Agueda and Xabier López and Eloy Ramos-Cordoba and Eduard Matito},

doi = {10.1063/5.0250636},

issn = {1089-7690},

year  = {2025},

date = {2025-03-28},

volume = {162},

number = {12},

publisher = {AIP Publishing},

abstract = {Economical multireference (MR) diagnostics are essential for high-throughput computational studies, enabling the rapid and accurate identification of molecules affected by nondynamic correlation within large molecular datasets. Although various MR diagnostics have been proposed, benchmarking studies that help identify the criteria for an effective diagnostic are still scarce. In this article, we examine a wide range of correlation measures to evaluate their potential as MR diagnostics. We identify a small set of valid size-intensive correlation measures based on maximum metrics, exhibiting similar predictive values. Among these, we highlight INDmax, which offers an easy interpretation: it captures the largest deviation of a natural orbital occupancy from the boundary values corresponding to a single-reference wave function. No energy-based correlation measure was found suitable for constructing MR diagnostics. Finally, we demonstrate how average correlation measures, although not suitable as MR diagnostics, can provide a more comprehensive view of electron correlation within the molecule.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lew-Yee2025,

title = {Efficient Energy Measurement of Chemical Systems via One-Particle Reduced Density Matrix: A NOF-VQE Approach for Optimized Sampling},

author = {Juan Felipe Huan Lew-Yee and Mario Piris},

doi = {10.1021/acs.jctc.4c01734},

issn = {1549-9626},

year  = {2025},

date = {2025-03-11},

journal = {J. Chem. Theory Comput.},

volume = {21},

number = {5},

pages = {2402--2413},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gastearena2025,

title = {Exploring N_{2} activation using novel Lewis acid/base pairs: computational insight into frustrated Lewis pair reactivity},

author = {Xuban Gastearena and Jon M. Matxain and Fernando Ruipérez},

doi = {10.1039/d4dt03425b},

issn = {1477-9234},

year  = {2025},

date = {2025-03-04},

journal = {Dalton Trans.},

volume = {54},

number = {10},

pages = {4338--4352},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {Geometrically constrained transition metal-free Lewis acids effectively capture N2 and Lewis bases help activate it through a “push–pull” mechanism. Triptycene-based and phosphine-based FLPs represent the most promising candidates for N2 activation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}