Kimika Teorikoa

@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{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{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 = {General Biochemistry, General Chemistry, General Physics and Astronomy, Genetics and Molecular Biology, Multidisciplinary},

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 = {2024-11-00},

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{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}

}