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}

}

@article{Silva-Brea2025,

title = {Designing mimosine-containing peptides as efficient metal chelators: Insights from molecular dynamics and quantum calculations},

author = {D. Silva-Brea and J. Aduriz-Arrizabalaga and D. De Sancho and X. Lopez},

doi = {10.1016/j.jinorgbio.2024.112807},

issn = {0162-0134},

year  = {2025},

date = {2025-03-03},

urldate = {2025-03-03},

journal = {Journal of Inorganic Biochemistry},

volume = {264},

pages = {112807},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zubeltzu2025,

title = {Redefining the dielectric response of nanoconfined liquids: Insights from water},

author = {Jon Zubeltzu and Fernando Bresme and Matthew Dawber and Marivi Fernandez-Serra and Emilio Artacho},

doi = {10.1103/qp52-s5d5},

issn = {2643-1564},

year  = {2025},

date = {2025-03-03},

urldate = {2025-03-03},

journal = {Phys. Rev. Research},

volume = {7},

number = {4},

publisher = {American Physical Society (APS)},

abstract = {<jats:p>

                    Recent experiments show that the relative dielectric constant

                    <a:math xmlns:a="http://www.w3.org/1998/Math/MathML">

                      <a:mi>ε</a:mi>

                    </a:math>

                    of water confined to a film of nanometric thickness reaches a strikingly low value of 2.1, barely above the bulk's 1.8 value for the purely electronic response. We argue that

                    <b:math xmlns:b="http://www.w3.org/1998/Math/MathML">

                      <b:mi>ε</b:mi>

                    </b:math>

                    is not a well-defined measure for dielectric properties at subnanometer scales due to the ambiguous definition of confinement width. Instead, we propose the 2D polarizability

                    <c:math xmlns:c="http://www.w3.org/1998/Math/MathML">

                      <c:msub>

                        <c:mi>α</c:mi>

                        <c:mo>⊥</c:mo>

                      </c:msub>

                    </c:math>

                    as the appropriate, well-defined response function whose magnitude can be directly obtained from both measurements and computations. Once the appropriate description is used, understanding the interplay between electronic and ionic contributions becomes critical, contrary to what is widely assumed. This highlights the importance of electronic degrees of freedom in interpreting the dielectric response of polar fluids under nanoconfinement conditions, as revealed by molecular dynamics simulations.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gastearena2025b,

title = {Computational Analysis of the Lewis Acid-Catalyzed Zwitterionic Ring-Expansion Polymerization (ZREP) of Monosubstituted Ethylene Oxide},

author = {Xuban Gastearena and Fabienne Barroso-Bujans and Fernando Ruipérez and Jon M. Matxain},

doi = {10.1021/acs.joc.4c02264},

issn = {1520-6904},

year  = {2025},

date = {2025-02-21},

journal = {J. Org. Chem.},

volume = {90},

number = {7},

pages = {2592--2601},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lanuza2025b,

title = {How can polyoxometalates have phosphodiesterase Activity? Unravelling the catalytic effect of heptamolybdate in the hydrolysis of phosphodiester models},

author = {Jose Lanuza and Ángel Sanchez-Gonzalez and Xabier Lopez and Adria Gil},

doi = {10.1016/j.inoche.2025.113908},

issn = {1387-7003},

year  = {2025},

date = {2025-02-04},

journal = {Inorganic Chemistry Communications},

volume = {174},

number = {174},

pages = {113908},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grande‐Aztazi2024,

title = {The Aromaticity of Osmapentalenes Derivatives – An Analysis Based on Electron‐Delocalization Indices},

author = {Rafael Grande‐Aztazi and Eduard Matito and Jesus M. Ugalde and Jose M. Mercero},

doi = {10.1002/cphc.202400713},

issn = {1439-7641},

year  = {2025},

date = {2025-02-01},

journal = {ChemPhysChem},

volume = {26},

number = {3},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>A systematic investigation of the aromatic features of the electronic structures of a family of recently synthesized osmapentalene derivatives has been carried by means of indices derived from the calculated one‐electron density matrix of the corresponding geometry optimized compounds, and complemented by the analysis of the valence molecular orbitals and the delocalized bonding units emerging from the adaptive natural density partitioning method. The calculated delocalization indices between consecutive atom pairs, and normalized multicenter indices are very suggestive of the aromatic character of the equatorial fused carbon rings (except triangular ones) for all the members of the family. Since the electron‐delocalization based indices allow precise quantification of the aromaticity, differences of the aromatic character among the various members have also been highlighted, and have been found to be consistent with the magnetic based criteria indices reported earlier. Finally, the valence molecular orbitals along with the delocalized bonding units of the adaptive natural density partitioning indicate that the aromaticity of these compounds is sustained by either 10 or 14 <jats:italic>π</jats:italic> electrons, which satisfy the Hückel aromatic electron counting rule.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gastearena2024,

title = {Unveiling the electronic origin of lanthanide based Metal Organic Framework with ideal spin filtering capacity},

author = {Xuban Gastearena and Jesus M. Ugalde and German E. Pieslinger and Eider San Sebastian and Elisa Jimenez-Izal},

doi = {10.1038/s42005-024-01651-4},

issn = {2399-3650},

year  = {2024},

date = {2024-12-00},

journal = {Commun Phys},

volume = {7},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractRecently, a three dimensional metal-organic framework (MOF) based on Dy(III) and the L-tartrate ligand was experimentally shown to exhibit a spin polarization (SP) power of 100% at room temperature. The material’s spin filtering ability was ascribed to the chiral-induced spin selectivity (CISS) effect. In this work, we computationally characterize the electronic structure of this MOF, revealing that the high SP of the material is linked to the asymmetric arrangement, around the Fermi level, of the alpha- and beta-spin electron states arising from the 4f-states of the lanthanide Dy atom, which results in two different conduction channels (band gaps) for each spin state. Based on the understanding gathered in this work, we propose that the substitution of the hydroxyl groups of the ligand by mercaptan groups should boost the electrical conductivity, while retaining the spin filtering power of the material.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mattioni2024,

title = {Vibronic effects on the quantum tunnelling of magnetisation in Kramers single-molecule magnets},

author = {Andrea Mattioni and Jakob K. Staab and William J. A. Blackmore and Daniel Reta and Jake Iles-Smith and Ahsan Nazir and Nicholas F. Chilton},

doi = {10.1038/s41467-023-44486-3},

issn = {2041-1723},

year  = {2024},

date = {2024-12-00},

journal = {Nat Commun},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractSingle-molecule magnets are among the most promising platforms for achieving molecular-scale data storage and processing. Their magnetisation dynamics are determined by the interplay between electronic and vibrational degrees of freedom, which can couple coherently, leading to complex vibronic dynamics. Building on an ab initio description of the electronic and vibrational Hamiltonians, we formulate a non-perturbative vibronic model of the low-energy magnetic degrees of freedom in monometallic single-molecule magnets. Describing their low-temperature magnetism in terms of magnetic polarons, we are able to quantify the vibronic contribution to the quantum tunnelling of the magnetisation, a process that is commonly assumed to be independent of spin-phonon coupling. We find that the formation of magnetic polarons lowers the tunnelling probability in both amorphous and crystalline systems by stabilising the low-lying spin states. This work, thus, shows that spin-phonon coupling subtly influences magnetic relaxation in single-molecule magnets even at extremely low temperatures where no vibrational excitations are present.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Piris2024b,

title = {Time-Resolved Chemical Bonding Structure Evolution by Direct-Dynamics Chemical Simulations},

author = {Mario Piris and Xabier Lopez and Jesus M. Ugalde},

doi = {10.1021/acs.jpclett.4c03010},

issn = {1948-7185},

year  = {2024},

date = {2024-11-28},

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

pages = {12138--12143},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zubeltzu2024,

title = {Structural insights into carboxylic-acid based DES across H-bond donor ratios: impact of CL&Pol refinement},

author = {Jon Zubeltzu and Elixabete Rezabal},

doi = {10.1039/d4cp03233k},

issn = {1463-9084},

year  = {2024},

date = {2024-11-07},

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

volume = {26},

number = {43},

pages = {27486--27497},

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

abstract = {Improved force field parameters refine H-bond network and long-range structure in carboxylic-acid-based deep eutectic solvents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ugartemendia2024c,

title = {Boosting synergistic effects between PtGe nanoalloys and 2D materials for PEMFC applications},

author = {Andoni Ugartemendia and Ramón M. Bergua and Jose M. Mercero and Elisa Jimenez-Izal},

doi = {10.1016/j.ijhydene.2024.09.279},

issn = {0360-3199},

year  = {2024},

date = {2024-11-01},

journal = {International Journal of Hydrogen Energy},

volume = {89},

pages = {233--253},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lobato2024,

title = {Prediction of long-term creep modulus of thermoplastics using brief tests and interpretable machine learning},

author = {Héctor Lobato and Carlos Cernuda and Kepa Zulueta and Aitor Arriaga and Jon M. Matxain and Aizeti Burgoa},

doi = {10.1016/j.ijsolstr.2024.113014},

issn = {0020-7683},

year  = {2024},

date = {2024-11-00},

journal = {International Journal of Solids and Structures},

volume = {304},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bergua2024,

title = {PdTi alloys as an excellent catalyst for semi-hydrogenation reactions},

author = {Ramon M. Bergua and Theodoros Pavloudis and Andoni Ugartemendia and Richard E. Palmer and Elisa Jimenez-Izal},

doi = {10.1016/j.apsusc.2024.160798},

issn = {0169-4332},

year  = {2024},

date = {2024-11-00},

journal = {Applied Surface Science},

volume = {672},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Piris2024,

title = {Exploring the potential of natural orbital functionals},

author = {Mario Piris},

doi = {10.1039/d4sc05810k},

issn = {2041-6539},

year  = {2024},

date = {2024-10-30},

journal = {Chem. Sci.},

volume = {15},

number = {42},

pages = {17284--17291},

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

abstract = {In recent years, Natural Orbital Functional (NOF) theory has gained importance in quantum chemistry, effectively addressing a major challenge: providing accurate and balanced descriptions of systems with strong electronic correlation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{David2024,

title = {Promoting exchange coupling in (Cp^{iPr_{5}})_{2}Gd_{2}X_{3} complexes},

author = {Grégoire David and Boris Le Guennic and Daniel Reta},

doi = {10.1039/d4cc03025g},

issn = {1364-548X},

year  = {2024},

date = {2024-10-15},

journal = {Chem. Commun.},

volume = {60},

number = {83},

pages = {11988--11991},

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

abstract = {The impact of structural and chemical modifications on magnetic exchange couplings in mixed-valence gadolinium-based (CpiPr5)2Gd2I3 compounds is investigated by means of the DFT-based decomposition method.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hink2024,

title = {Mixed Stereochemistry Macrocycle Acts as a Helix-Stabilizing Peptide N-Cap},

author = {Fabian Hink and Julen Aduriz-Arrizabalaga and Xabier Lopez and Hiroaki Suga and David De Sancho and Joseph M. Rogers},

doi = {10.1021/jacs.4c05378},

issn = {1520-5126},

year  = {2024},

date = {2024-09-04},

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

volume = {146},

number = {35},

pages = {24348--24357},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MóranPlata2024,

title = {Alloxazine-Based Ligands and Their Ruthenium Complexes as NADH Oxidation Catalysts and G4 Binders},

author = {Maria Jesus Móran Plata and Laura Marretta and Lander Gaztelumendi and German E. Pieslinger and Romina R. Carballo and Elixabete Rezabal and Giampaolo Barone and Virginia Martínez-Martínez and Alessio Terenzi and Luca Salassa},

doi = {10.1021/acs.inorgchem.4c02314},

issn = {1520-510X},

year  = {2024},

date = {2024-09-02},

journal = {Inorg. Chem.},

volume = {63},

number = {35},

pages = {16362--16373},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Iruzubieta2024,

title = {Biallelic variants in \textit{SNUPN} cause a limb girdle muscular dystrophy with myofibrillar-like features},

author = {Pablo Iruzubieta and Alberto Damborenea and Mihaela Ioghen and Simon Bajew and Roberto Fernandez-Torrón and Ana Töpf and Álvaro Herrero-Reiriz and Diana Epure and Katharina Vill and Aurelio Hernández-Laín and María Manterola and Mikel Azkargorta and Oihane Pikatza-Menoio and Laura Pérez-Fernandez and Mikel García-Puga and Gisela Gaina and Alexandra Bastian and Ioana Streata and Maggie C Walter and Wolfgang Müller-Felber and Simone Thiele and Saioa Moragón and Nerea Bastida-Lertxundi and Aitziber López-Cortajarena and Felix Elortza and Gorka Gereñu and Sonia Alonso-Martin and Volker Straub and David de Sancho and Raluca Teleanu and Adolfo López de Munain and Lorea Blázquez},

doi = {10.1093/brain/awae046},

issn = {1460-2156},

year  = {2024},

date = {2024-08-01},

volume = {147},

number = {8},

pages = {2867--2883},

publisher = {Oxford University Press (OUP)},

abstract = {Abstract

               Alterations in RNA-splicing are a molecular hallmark of several neurological diseases, including muscular dystrophies, where mutations in genes involved in RNA metabolism or characterized by alterations in RNA splicing have been described. Here, we present five patients from two unrelated families with a limb-girdle muscular dystrophy (LGMD) phenotype carrying a biallelic variant in SNUPN gene.

               Snurportin-1, the protein encoded by SNUPN, plays an important role in the nuclear transport of small nuclear ribonucleoproteins (snRNPs), essential components of the spliceosome. We combine deep phenotyping, including clinical features, histopathology and muscle MRI, with functional studies in patient-derived cells and muscle biopsies to demonstrate that variants in SNUPN are the cause of a new type of LGMD according to current definition. Moreover, an in vivo model in Drosophila melanogaster further supports the relevance of Snurportin-1 in muscle.

               SNUPN patients show a similar phenotype characterized by proximal weakness starting in childhood, restrictive respiratory dysfunction and prominent contractures, although inter-individual variability in terms of severity even in individuals from the same family was found. Muscle biopsy showed myofibrillar-like features consisting of myotilin deposits and Z-disc disorganization. MRI showed predominant impairment of paravertebral, vasti, sartorius, gracilis, peroneal and medial gastrocnemius muscles. Conservation and structural analyses of Snurportin-1 p.Ile309Ser variant suggest an effect in nuclear-cytosol snRNP trafficking. In patient-derived fibroblasts and muscle, cytoplasmic accumulation of snRNP components is observed, while total expression of Snurportin-1 and snRNPs remains unchanged, which demonstrates a functional impact of SNUPN variant in snRNP metabolism. Furthermore, RNA-splicing analysis in patients’ muscle showed widespread splicing deregulation, in particular in genes relevant for muscle development and splicing factors that participate in the early steps of spliceosome assembly.

               In conclusion, we report that SNUPN variants are a new cause of limb girdle muscular dystrophy with specific clinical, histopathological and imaging features, supporting SNUPN as a new gene to be included in genetic testing of myopathies. These results further support the relevance of splicing-related proteins in muscle disorders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alghrably2024,

title = {Metabolites from Marine Macroorganisms of the Red Sea Acting as Promoters or Inhibitors of Amylin Aggregation},

author = {Mawadda Alghrably and Mohamed A. Tammam and Aikaterini Koutsaviti and Vassilios Roussis and Xabier Lopez and Giulia Bennici and Abeer Sharfalddin and Hanan Almahasheer and Carlos M. Duarte and Abdul-Hamid Emwas and Efstathia Ioannou and Mariusz Jaremko},

doi = {10.3390/biom14080951},

issn = {2218-273X},

year  = {2024},

date = {2024-08-00},

journal = {Biomolecules},

volume = {14},

number = {8},

publisher = {MDPI AG},

abstract = {Amylin is part of the endocrine pancreatic system that contributes to glycemic control, regulating blood glucose levels. However, human amylin has a high tendency to aggregate, forming isolated amylin deposits that are observed in patients with type 2 diabetes mellitus. In search of new inhibitors of amylin aggregation, we undertook the chemical analyses of five marine macroorganisms encountered in high populations in the Red Sea and selected a panel of 10 metabolites belonging to different chemical classes to evaluate their ability to inhibit the formation of amyloid deposits in the human amylin peptide. The thioflavin T assay was used to examine the kinetics of amyloid aggregation, and atomic force microscopy was employed to conduct a thorough morphological examination of the formed fibrils. The potential ability of these compounds to interact with the backbone of peptides and compete with β-sheet formation was analyzed by quantum calculations, and the interactions with the amylin peptide were computationally examined using molecular docking. Despite their structural similarity, it could be observed that the hydrophobic and hydrogen bond interactions of pyrrolidinones 9 and 10 with the protein sheets result in one case in a stable aggregation, while in the other, they cause distortion from aggregation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fernandez‐Calvo2024,

title = {The strongest protein binder is surprisingly labile},

author = {Alba Fernandez‐Calvo and Antonio Reifs and Laura Saa and Aitziber L. Cortajarena and David De Sancho and Raul Perez‐Jimenez},

doi = {10.1002/pro.5030},

issn = {1469-896X},

year  = {2024},

date = {2024-07-00},

journal = {Protein Science},

volume = {33},

number = {7},

publisher = {Wiley},

abstract = {AbstractBacterial adhesins are cell‐surface proteins that anchor to the cell wall of the host. The first stage of infection involves the specific attachment to fibrinogen (Fg), a protein found in human blood. This attachment allows bacteria to colonize tissues causing diseases such as endocarditis. The study of this family of proteins is hence essential to develop new strategies to fight bacterial infections. In the case of the Gram‐positive bacterium Staphylococcus aureus, there exists a class of adhesins known as microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Here, we focus on one of them, the clumping factor A (ClfA), which has been found to bind Fg through the dock‐lock‐latch mechanism. Interestingly, it has recently been discovered that MSCRAMM proteins employ a catch‐bond to withstand forces exceeding 2 nN, making this type of interaction as mechanically strong as a covalent bond. However, it is not known whether this strength is an evolved feature characteristic of the bacterial protein or is typical only of the interaction with its partner. Here, we combine single‐molecule force spectroscopy, biophysical binding assays, and molecular simulations to study the intrinsic mechanical strength of ClfA. We find that despite the extremely high forces required to break its interactions with Fg, ClfA is not by itself particularly strong. Integrating the results from both theory and experiments we dissect contributions to the mechanical stability of this protein.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Elizalde2024,

title = {Tuning Reprocessing Temperature of Aliphatic Polyurethane Networks by Alkoxyamine Selection},

author = {Fermin Elizalde and Vincent Pertici and Robert Aguirresarobe and Marta Ximenis and Giulia Vozzolo and Luis Lezama and Fernando Ruipérez and Didier Gigmes and Haritz Sardon},

doi = {10.1021/acsapm.4c00840},

issn = {2637-6105},

year  = {2024},

date = {2024-06-28},

journal = {ACS Appl. Polym. Mater.},

volume = {6},

number = {12},

pages = {7057--7065},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Franco2024,

title = {Softmax parameterization of the occupation numbers for natural orbital functionals based on electron pairing approaches},

author = {Lizeth Franco and Iván A. Bonfil-Rivera and Juan Felipe Huan Lew-Yee and Mario Piris and Jorge M. del Campo and Rodrigo A. Vargas-Hernández},

doi = {10.1063/5.0213719},

issn = {1089-7690},

year  = {2024},

date = {2024-06-28},

volume = {160},

number = {24},

publisher = {AIP Publishing},

abstract = {Within the framework of natural orbital functional theory, having a convenient representation of the occupation numbers and orbitals becomes critical for the computational performance of the calculations. Recognizing this, we propose an innovative parametrization of the occupation numbers that takes advantage of the electron-pairing approach used in Piris natural orbital functionals through the adoption of the softmax function, a pivotal component in modern deep-learning models. Our approach not only ensures adherence to the N-representability of the first-order reduced density matrix (1RDM) but also significantly enhances the computational efficiency of 1RDM functional theory calculations. The effectiveness of this alternative parameterization approach was assessed using the W4-17-MR molecular set, which demonstrated faster and more robust convergence compared to previous implementations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ugartemendia2024d,

title = {Doping Efects on Ethane/Ethylene Dehydrogenation Catalyzed by Pt_{2}X Nanoclusters},

author = {Andoni Ugartemendia and José M. Mercero and Elisa Jimenez‐Izal and Abel de Cózar},

doi = {10.1002/cphc.202400095},

issn = {1439-7641},

year  = {2024},

date = {2024-06-17},

journal = {ChemPhysChem},

volume = {25},

number = {12},

publisher = {Wiley},

abstract = {AbstractThe catalytic dehydrogenation of light alkanes is key to transform low‐cost hydrocarbons to high value‐added chemicals. Although Pt is extremely efficient at catalyzing this reaction, it suffers from coke formation that deactivates the catalyst. Dopants such as Sn are widely used to increase the stability and lifetime of Pt. In this work, the dehydrogenation reaction of ethane catalyzed by Pt3 and Pt2X (X=Si, Ge, Sn, P and Al) nanocatalysts has been studied computationally by means of density functional calculations. Our results show how the presence of dopants in the nanocluster structure affects its electronic properties and catalytic activity. Exploration of the potential energy surfaces show that non–doped catalyst Pt3 present low selectivity towards ethylene formation, where acetylene resulting from double dehydrogenation reaction will be obtained as a side product (in agreement with the experimental evidence). On the contrary, the inclusion of Si, Ge, Sn, P or Al as dopant agents implies a selectivity enhancement, where acetylene formation is not energetically favoured. These results demonstrate the effectiveness of such dopant elements for the design of Pt–based catalysts on ethane dehydrogenation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pagnacco2024,

title = {Zwitterionic ring expansion polymerization of \textit{tert}‐butyl glycidyl ether with B(C_{6}F_{5})_{3} towards the generation of cyclic chains},

author = {Carlo Andrea Pagnacco and Xuban Gastearena and Estibaliz González de San Román and Jon M. Matxain and Fabienne Barroso‐Bujans},

doi = {10.1002/pol.20240112},

issn = {2642-4169},

year  = {2024},

date = {2024-06-15},

journal = {Journal of Polymer Science},

volume = {62},

number = {12},

pages = {2704--2715},

publisher = {Wiley},

abstract = {AbstractThe synthesis of cyclic polymers via zwitterionic ring expansion polymerization is limited to a few number of monomer and catalyst pairs. Herein we report the synthesis of cyclic poly(tert‐butyl glycidyl ether) through the polymerization of tert‐butyl glycidyl ether (tBGE) with B(C6F5)3 in different reaction conditions that include different solvents, monomer to initiator ratio, monomer concentration and temperature. We found that bimodal molecular weight distribution is formed in almost all reaction conditions caused by cyclization of short chains. Subsequent chain elongation leads to the formation of cycles of higher molecular weight, particularly in cyclohexane and under bulk conditions. The formation of non‐cyclic byproducts is common in all the systems investigated. Low molecular weight cyclic chains (Mn = 0.7 kDa, Ð = 1.1) of high topological purity were successfully isolated by preparative gel permeation chromatography. By using a click scavenging protocol, the non‐cyclic byproducts were eliminated from the high molecular weight fraction (Mn = 3 kDa, Ð = 1.3) generating pure cyclic chains. Mechanistic investigation using density functional theory calculations was performed on the formation of zwitterionic intermediates and the transfer reaction to the monomer, which notably affects chain growth by the attack of the glycidyl oxygen of the monomer on the growing chain.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grabowski2024,

title = {Hydrogen bond types which do not fit accepted definitions},

author = {Sławomir J. Grabowski},

doi = {10.1039/d4cc01769b},

issn = {1364-548X},

year  = {2024},

date = {2024-06-13},

journal = {Chem. Commun.},

volume = {60},

number = {49},

pages = {6239--6255},

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

abstract = {There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Montero-Cabrera2024,

title = {Alternative CNDOL Fockians for fast and accurate description of molecular exciton properties},

author = {Luis A. Montero-Cabrera and Ana L. Montero-Alejo and Alan Aspuru-Guzik and José M. García de la Vega and Mario Piris and Lourdes A. Díaz-Fernández and Yoana Pérez-Badell and Alberto Guerra-Barroso and Javier E. Alfonso-Ramos and Javier Rodríguez and María E. Fuentes and Carlos M. de Armas},

doi = {10.1063/5.0208809},

issn = {1089-7690},

year  = {2024},

date = {2024-06-07},

volume = {160},

number = {21},

publisher = {AIP Publishing},

abstract = {CNDOL is an a priori, approximate Fockian for molecular wave functions. In this study, we employ several modes of singly excited configuration interaction (CIS) to model molecular excitation properties by using four combinations of the one electron operator terms. Those options are compared to the experimental and theoretical data for a carefully selected set of molecules. The resulting excitons are represented by CIS wave functions that encompass all valence electrons in the system for each excited state energy. The Coulomb–exchange term associated to the calculated excitation energies is rationalized to evaluate theoretical exciton binding energies. This property is shown to be useful for discriminating the charge donation ability of molecular and supermolecular systems. Multielectronic 3D maps of exciton formal charges are showcased, demonstrating the applicability of these approximate wave functions for modeling properties of large molecules and clusters at nanoscales. This modeling proves useful in designing molecular photovoltaic devices. Our methodology holds potential applications in systematic evaluations of such systems and the development of fundamental artificial intelligence databases for predicting related properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mitxelena2024,

title = {Assessing the global natural orbital functional approximation on model systems with strong correlation},

author = {Ion Mitxelena and Mario Piris},

doi = {10.1063/5.0207325},

issn = {1089-7690},

year  = {2024},

date = {2024-05-28},

volume = {160},

number = {20},

publisher = {AIP Publishing},

abstract = {In the past decade, natural orbital functional (NOF) approximations have emerged as prominent tools for characterizing electron correlation. Despite their effectiveness, these approaches, which rely on natural orbitals and their associated occupation numbers, often require hybridization with other methods to fully account for all correlation effects. Recently, a global NOF (GNOF) has been proposed [Piris, Phys. Rev. Lett. 127, 233001 (2021)] to comprehensively address both dynamic and static correlations. This study evaluates the performance of GNOF on strongly correlated model systems, including comparisons with highly accurate Full Configuration Interaction calculations for hydrogen atom clusters in one, two, and three dimensions. Additionally, the investigation extends to a BeH2 reaction, involving the insertion of a beryllium atom into a hydrogen molecule along a C2v pathway. According to the results obtained using GNOF, consistent behavior is observed across various correlation regions, encompassing a range of occupations and orbital schemes. Furthermore, distinctive features are identified when varying the dimensionality of the system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Iturralde2024,

title = {Artificial Spores as Multi‐Functional Biocatalysts to Perform Biosynthetic Cascades},

author = {Maialen Iturralde and Magdalena Ripoll and Desiré di Silvio and Marta Gallego and Daniel A. Grajales‐Hernández and Xabier López and Lorena Betancor and Fernando López‐Gallego},

doi = {10.1002/adfm.202406097},

issn = {1616-3028},

year  = {2024},

date = {2024-05-25},

journal = {Adv Funct Materials},

publisher = {Wiley},

abstract = {AbstractCells exhibit diverse structural formations such as biofilms and spores, enabling them to acquire novel functionalities. Many of these structures display biomacromolecules, including enzymes, tethered to cell walls to support various extracellular processes. Alternatively, encapsulating single cells with polymer coatings offers a strategy that circumvents the need for genetic engineering while imparting artificial functionalities to cells. Here, a universal method is presented for encapsulating single gram‐negative microbes with polymeric coatings based on the ancestral gall ink formed by tannic acid‐iron complexes. As a result, synthetic spores are achieved that selectively bind His‐tagged enzymes through the formation of unprecedented galloyl/imidazole‐Fe2+ complexes via ligand substitution demonstrated by density functional theory. These synthetic spores with a thickness of 41.5 ± 4.2 nm and a stiffness of 6.0 ± 3.5 GPa serve as biocatalytic materials for the one‐pot oxidative amination of diols into amino alcohols, facilitated by the cooperative catalysis between intracellular endogenous or recombinant oxidoreductases, and an extracellular transaminase from Pseudomonas fluorescens displayed at the spore surface. These spores maintain their performance in three consecutive batch cycles. Integrating isolated enzymes onto the surface of engineered microbes coated with polymers offers novel opportunities for synthetic biology, advancing the efficiency of biosynthetic cascades in solid‐state environments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Salvador2024,

title = {APOST-3D: Chemical concepts from wavefunction analysis},

author = {P. Salvador and E. Ramos-Cordoba and M. Montilla and L. Pujal and M. Gimferrer},

doi = {10.1063/5.0206187},

issn = {1089-7690},

year  = {2024},

date = {2024-05-07},

volume = {160},

number = {17},

publisher = {AIP Publishing},

abstract = {Open-source APOST-3D software features a large number of wavefunction analysis tools developed over the past 20 years, aiming at connecting classical chemical concepts with the electronic structure of molecules. APOST-3D relies on the identification of the atom in the molecule (AIM), and several analysis tools are implemented in the most general way so that they can be used in combination with any chosen AIM. Several Hilbert-space and real-space (fuzzy atom) AIM definitions are implemented. In general, global quantities are decomposed into one- and two-center terms, which can also be further grouped into fragment contributions. Real-space AIM methods involve numerical integrations, which are particularly costly for energy decomposition schemes. The current version of APOST-3D features several strategies to minimize numerical error and improve task parallelization. In addition to conventional population analysis of the density and other scalar fields, APOST-3D implements different schemes for oxidation state assignment (effective oxidation state and oxidation states localized orbitals), molecular energy decomposition schemes, and local spin analysis. The APOST-3D platform offers a user-friendly interface and a comprehensive suite of state-of-the-art tools to bridge the gap between theory and experiment, representing a valuable resource for both seasoned computational chemists and researchers with a focus on experimental work. We provide an overview of the code structure and its capabilities, together with illustrative examples.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barrios2024,

title = {Modulated spin dynamics of [Co_{2}] coordination helicates \textit{via} differential strand composition},

author = {Leoní A. Barrios and Nuria Capó and Hanae Boulehjour and Daniel Reta and Inés Tejedor and Olivier Roubeau and Guillem Aromí},

doi = {10.1039/d4dt00629a},

issn = {1477-9234},

year  = {2024},

date = {2024-04-30},

journal = {Dalton Trans.},

volume = {53},

number = {17},

pages = {7611--7618},

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

abstract = {A family of bis-pyrazolylpyridine ligands represents a versatile entry into [Co2] triple-stranded helicates encapsulating various anionic guests, enabling to study the effects of different factors on the mechanisms of magnetic relaxation of their individual Co(ii) centers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}