DFT molecular dynamics and free energy analysis of a charge density wave surface system

This Accepted Manuscript will be available for reuse under a CC BY-NC-ND licence after 24 months of embargo periodThe K/Si(111):B 3×3 surface, with one K atom per 3×3 unit cell, is considered a prototypical case of a surface Mott phase at room temperature. Our Density Functional Theory (DFT) Molecular Dynamics (MD) and free energy calculations show, however, a 23×3 Charge Density Wave (CDW) ground state. Our analysis shows that at room temperature the K atoms easily diffuse along the lines of a honeycomb network on the surface and that the 3×3 phase appears as the result of the dynamical fluctuations between degenerate CDW states. DFT-MD free energy calculations also show a 23×3↔3×3 transition temperature below 90 K. The competing electron-electron and electron-phonon interactions at low temperature are also analyzed; using DFT calculations, we find that the electron-phonon negative-U * is larger than the electron-electron Hubbard U, indicating that the CDW survives at very low temperatureThis work was supported by grant nos. MAT2014-59966-R and MAT2017-88258-R from the Ministerio de Economía, Industria y Competitividad (Spain

Two-step ATP-driven opening of cohesin head.

The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the “head” structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.post-print4709 K

Significance of nuclear quantum effects in hydrogen bonded molecular chains

In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of {\pi}-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to new electronic in-gap states localized at the ends. These findings demonstrate the identification of a new class of isomeric hydrogen bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. We anticipate that this work will open new research directions towards the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling

Generating antiaromaticity in polycyclic conjugated hydrocarbons by thermally selective skeletal rearrangements at interfaces

Antiaromatic polycyclic conjugated hydrocarbons (PCHs) are attractive research targets because of their interesting structural, electronic and magnetic properties. Unlike aromatic compounds, the synthesis of antiaromatic PCHs is challenging because of their high reactivity and lack of stability, which stems from the small energy gap between their highest occupied and lowest unoccupied molecular orbitals. Here we describe a strategy for the introduction of antiaromatic units in PCHs via thermally selective intra- and intermolecular ring-rearrangement reactions of dibromomethylene-functionalized molecular precursors upon sublimation on a hot Au(111) metal surface, not available in solution chemistry. The synthetic value of these reactions is proven by the integration of pentalene segments into acene-based precursors, which undergo intramolecular ring rearrangement, and the formation of π-conjugated ladder polymers, linked through cyclobutadiene connections, due to ring-rearrangement and homocoupling reactions of indenofluorene-based precursors. The reaction products are investigated by scanning tunnelling microscopy and non-contact atomic force microscopy, and mechanistic insights are unveiled by computational studies. [Figure not available: see fulltext.] © 2023, The Author(s), under exclusive licence to Springer Nature Limited.This project has received funding from Comunidad de Madrid (projects QUIMTRONIC-CM (Y2018/NMT-4783) and NanoMagCost (P2018/NMT-4321)), an ERC Consolidator Grant (ELECNANO, 766555), ERC (SyG TOMATTO ERC-2020-951224) and Ministerio de Ciencia, Innovacion y Universidades (projects SpOrQuMat (PGC2018-098613-B-C21), CTQ2017-83531-R, PID2019-108532GB-I00, PID2020-114653RB-I00 and CTQ2016-81911-REDT). We acknowledge the support from the ‘(MAD2D-CM)-UCM’ and the ‘(MAD2D-CM)-IMDEA-Nanociencia’ projects funded by Comunidad de Madrid, by the Recovery, Transformation and Resilience Plan, and by NextGenerationEU from the European Union. IMDEA Nanociencia is appreciative of support from the ‘Severo Ochoa’ Programme for Centers of Excellence in R&D (MINECO, grant nos. SEV-2016-0686 and CEX2020-001039-S). Q.C., D.S.-P. and P.J. acknowledge funding support from the CzechNanoLab Research Infrastructure supported by MEYS CR (LM2023051) and GACR project no. 20-13692X. Computational resources were provided by the e-INFRA CZ project (ID 90140), supported by the Ministry of Education, Youth and Sports of the Czech Republic. A.S.-G. acknowledges funding from the ‘Ministerio de Universidades’ for the ‘Plan de Recuperación, Transformación y Resiliencia’ under Margarita Salas grant agreement CA1/RSUE/2021-00369. J.I.U. acknowledges the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 886314. We acknowledge B. Cirera for fruitful discussions.The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. The Fireball software package is available 458 at: https://github.com/fireball-QMD and PP-SPM software package can be downloaded at: https://github.com/Probe-Particle/ppafm#probe-particle-model.Peer reviewe

Macrociclos funcionales multicomponente ensamblados mediante enlace de hidrógeno

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Física Teórica de la Materia Condensada. Fecha de lectura: 12-05-202

A closed local-orbital unified description of DFT and many-body effects

This is the Accepted Manuscript version of an article accepted for publication in Journal of Physics Condensed Matter. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at https://doi.org/10.1088/1361-648X/ac6eaeDensity functional theory (DFT) is usually formulated in terms of the electron density as a function of position n(r). Here we discuss an alternative formulation of DFT in terms of the orbital occupation numbers {n α } associated with a local-orbital orthonormal basis set {φ α }. First, we discuss how the building blocks of DFT, namely the Hohenberg-Kohn theorems, the Levy-Lieb approach and the Kohn-Sham method, can be adapted for a description in terms of {n α }. In particular, the total energy is now a function of {n α }, E[{n α }], and a Kohn-Sham-like Hamiltonian is derived introducing the effects of the electron-electron interactions via effective potentials, {Vαeff= ∂Eee[{nβ}]/∂ nα} . In a second step we consider the Hartree and exchange energies and discuss how to describe them, in the spirit of a DFT approach, in terms of the orbital occupation numbers. In this contribution special attention is paid to the description of the (intra-atomic) correlation energy and corresponding correlation potentials {V corr,α }. For this purpose, a model system is analyzed in detail, whereby an atomic Hamiltonian interacts with the environment via a simplified model; the use of this model allows us to obtain the correlation energy and potentials (in terms of {n α }) for different cases corresponding to low, intermediate and high electron correlationsThis paper has been written to honor the memory of the great scientist Prof. Enrico Clementi. We thank Pablo Pou, Yannick J Dappe and Pablo Bolcatto for helpful discussions. We acknowledge financial support from the Spanish Ministry of Science and Innovation through Project Nos. MAT2017-88258-R and CEX2018-000805-M (María de Maeztu Program for Units of Excellence in R & D

A local-orbital density functional formalism for a many-body atomic Hamiltonian: Hubbard-Hund's coupling and DFT + U functional

In the conventional DFT + U approach, the mean field solution of the Hubbard Hamiltonian associated with the d or f (iσ) electrons of a transition metal atom is used to define the DFT + U potential acting on the iσ-electrons. In this work, we go beyond that mean field solution by analyzing the correlation energy and potential for a multi-level atom described by a Kanamori Hamiltonian connected to different channels representing the environment. As a first step, we analyze the many-body solution of our model, using a local-orbital density functional formalism that takes as independent variables the orbital occupancies, n iσ , of the atomic orbitals; accordingly, we present the corresponding density functional solution describing the correlation energy and potential as a function of n iσ . Then, we use this analysis to introduce a DFT + U potential extending previous proposals to materials with arbitrarily high correlation. In particular, we find that this potential mainly screens the conventional mean field potential contribution, and also yields new terms associated with the number of atomic electrons. Our results show that the atomic correlation effects enhance the role played by the intra-atomic exchange interaction and favor the formation of magnetic solutionsThis work was funded by Spanish Ministry of Science and Innovation under projects No. MAT2017-88258-R and No. CEX2018-000805-M (María de Maeztu Programme for Units of Excellence in R & D

Medidas preventivas centradas en la interfaz urbano-rural protegen a las comunidades rurales productoras de alimentos del SARS-CoV-2

Introduction: Rural food-producing communities are fundamental for the development of economic activities associated with sustainability and food security. However, despite the importance of rurality in Colombia, preventive strategies continue to be implemented homogeneously, without considering the dynamics of SARS-CoV-2 in rural food-producing communities.Objective: To model real areas in Colombia involving rural and urban populations that have intrinsic SARS-CoV-2 transmission dynamics. Characterize rural-urban interactions by means of a parameter that provides different scenarios and allows us to identify interactions capable of preventing SARS-CoV-2 transmission in rural food-producing communities.Materials and methods: The dynamics of SARS-CoV-2 infection was modeled in five case studies (Boyacá, Caquetá, Cundinamarca, Santander and Sucre) considering urban and rural areas and their interaction (connectivity) in the urban-rural interface. For this purpose, an epidemiological compartmental model considering a classification of individuals according to their economic activity and their epidemiological status was assessed. Results: Preventive measures focused on the urban-rural interface impact the number of deaths in rural areas. Hence, it is possible to assume that the dynamics of the disease in rural areas depend on the constant interaction with infected individuals from urban areas, which occurs due to the food production dynamics in the urban-rural interface. Conclusions: Preventive measures should focus on places of high transmissibility and risk for rural communities, such as the urban-rural interface. This work highlights the importance of national heterogeneous preventive measures and the protection of rural communities from the social and economic impacts of SARS-CoV-2.Introducción. Las comunidades rurales productoras de alimentos son fundamentales para el desarrollo de actividades económicas asociadas a la sostenibilidad y la seguridad alimentaria. Sin embargo, a pesar de la importancia de la ruralidad en Colombia, las estrategias de prevención continúan siendo implementadas homogéneamente, sin considerar la dinámica del SARS-CoV-2 en estas comunidades.Objetivo. Modelar la dinámica del SARS-CoV-2 en poblaciones rurales colombianas. Se quiso caracterizar la interacción rural-urbana mediante un parámetro que proporciona diferentes contextos y permite identificar una interacción rural-urbana capaz de prevenir la transmisión del SARS-CoV-2 en comunidades rurales productoras de alimentos. Materiales y métodos. La dinámica de transmisión del SARS-CoV-2 se modeló en cinco estudios de caso (Boyacá, Caquetá, Cundinamarca, Santander y Sucre) considerando áreas urbanas y rurales, así como su interacción (conectividad) en la interfaz urbanorural. Para ello, se empleó un modelo epidemiológico compartimental que considera una clasificación de los individuos según su actividad económica y su estado epidemiológico. Resultados. Las medidas preventivas enfocadas en la interfaz urbano-rural impactan el número de muertes en áreas rurales. Por lo tanto, es posible asumir que la dinámica de la enfermedad en las áreas rurales depende del contacto constante con los individuos infectados de las áreas urbanas, lo que ocurre debido a la dinámica de los sistemas de producción de alimentos en la interfaz urbano-rural.Conclusiones. Las medidas de prevención deben enfocarse en lugares con gran transmisibilidad y riesgo para las comunidades rurales, como la interfaz urbano-rural. En este trabajo se destaca la importancia de las medidas preventivas heterogéneas y la protección de las comunidades rurales contra los impactos sociales y económicos del SARS-CoV-2

Mulliken-Dipole Population Analysis

Atomic charge is one of the most important concepts in Chemistry. Mulliken population analysis is historically the most important method to calculate atomic charges and is still widely used. One basic hypothesis of this method is the half-and-half partition of the overlap populations, Q(μ, v), into equal charges in orbitals μ and v. This partition preserves the monopole moment of the overlap density but, other than that, is arbitrary. In this work we derive a new population analysis (which we designate Mulliken-Dipole population analysis) based on the conservation of both the monopole moment and the dipole moment along the bond direction. Test calculations show that the Mulliken-Dipole atomic charges are in accord to the chemical intuition; also they are very different from the Mulliken ones, being quite similar to the Hirshfeld atomic charges. Mulliken-Dipole atomic charges are conceptually appealing and very easy to calculate. In a further step, we also show how this Mulliken-Dipole population analysis can be used to derive atomic charges for atomistic simulations that reproduce the total dipole moment of the molecule, yielding at the same time a good description of the local charges and dipole moments for the molecular fragments.<br /