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Metal ions play a central, functional, and structural role in many molecular structures, from small catalysts to metal-organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parameterization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parameterization of supramolecular structures. Metallicious has been tested on diverse systems including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters accurately reproduce the reference properties obtained from quantum calculations and crystal structures. Molecular dynamics simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with nonbonded and cationic dummy models. Overall, metallicious facilitates the atomistic modeling of supramolecular systems, key for understanding their dynamic properties and host-guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious).
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In the southeastern region of Brazil, ticks of the species Rhipicephalus (B.) microplus are constantly present on cattle throughout the year. This is due to climatic conditions that favor the biology of these ticks and resistance to the acaricides in use that has developed. The aim of this study was to evaluate the efficacy of the fungus Purpureocillium lilacinum (IBCB 130) in powdered form, applied via a drone, from the bioFUNGUS spray dispenser (NCB Sistemas Embarcados Ltda), onto pasture for controlling these ticks. This experiment was conducted at Aptaregional, Regional Research and Development Unit of Pindamonhangaba, São Paulo, Brazil. To evaluate the efficacy of treatment, two groups were formed (treated and control), each with ten calves of the Girolando breed, which were kept in two separate paddocks in which the main grass species was Brachiaria decumbens. The treated paddock received seven monthly applications (November-May) of the fungus Purpureocillium lilacinum (5â¯g de P. lilacinum in 200â¯g of wheat flour). The control paddock did not receive any treatment. Tick counts performed on the animals every two weeks showed that, over the entire period, the treatment had a mean efficacy of 48.59â¯%. The months of December and January presented the highest efficacy rates, of 63.50â¯% and 83.87â¯%, respectively.
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Introduction: Active surveillance (AS) is increasingly recognized as an appropriate strategy for selected patients with papillary thyroid microcarcinomas (PTMC). However, some factors, including physician-related ones, hinder its widespread adoption. Methods: To explore the prevailing barriers and the impact of information on attitudes towards AS implementation, we developed a questionnaire that was completed before and after reading a simple information leaflet by 317 doctors working in different work environments. This leaflet provides information about the overdiagnosis of PTMC, the concept of AS, results of early studies, and main advantages and disadvantages of AS. Results: We observed a greater resistance to AS among male physicians who were more likely to maintain the initial recommendation for surgery or referral to a head and neck surgeon than female physicians (77 % vs. 46 %, p = 0.01), regardless of their medical specialty. Fear of disease progression and of the patient losing follow-up were the main concerns. Reading the educational material significantly increased the number of physicians who endorsed AS as an initial approach to PTMC without risk factors from 14 % to 34 % (p < 0,001). This change in attitude was even more significant when doctors were confronted with a case of PTMC in an elderly patient. Gender, medical specialty, age range and academic environment were the factors that were determinants on the influence of the informative leaflet on the decision-making. The leaflet also increased the number of doctors who considered themselves capable of dealing with this patient profile; however, 17 % declared that the place where they worked would not be able to meet the need for periodic assessments and necessary examinations. This was particularly true for the 20 % of the professionals working in rural areas. Conclusion: A simple educational leaflet with basic information presented via social media increased the number of Brazilian physicians who endorsed AS for PTMC management and proved to be a facilitating tool for understanding and accepting it. Our results suggest that this method can be easily extended to larger population.
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Metal ions are irreplaceable in many areas of chemistry, including (bio)catalysis, self-assembly and charge transfer processes. Yet, modelling their structural and dynamic properties in diverse chemical environments remains challenging for both force fields and ab initio methods. Here, we introduce a strategy to train machine learning potentials (MLPs) using MACE, an equivariant message-passing neural network, for metal-ligand complexes in explicit solvents. We explore the structure and ligand exchange dynamics of Mg2+ in water and Pd2+ in acetonitrile as two illustrative model systems. The trained potentials accurately reproduce equilibrium structures of the complexes in solution, including different coordination numbers and geometries. Furthermore, the MLPs can model structural changes between metal ions and ligands in the first coordination shell, and reproduce the free energy barriers for the corresponding ligand exchange. The strategy presented here provides a computationally efficient approach to model metal ions in solution, paving the way for modelling larger and more diverse metal complexes relevant to biomolecules and supramolecular assemblies.
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Extended π-systems often form supramolecular aggregates, drastically changing their optical and electronic properties. However, aggregation processes can be difficult to characterize or predict. Here, we show that butadiyne-linked 8- and 12-porphyrin nanorings form stable and well-defined bimolecular aggregates with remarkably sharp NMR spectra, despite their dynamic structures and high molecular weights (12.7 to 26.0 kDa). Pyridine breaks up the aggregates into their constituent rings, which are in slow exchange with the aggregates on the NMR time scale. All the aggregates have the same general two-layer sandwich structure, as deduced from NMR spectroscopy experiments, including 1H DOSY, 1H-1H COSY, TOCSY, NOESY, and 1H-13C HSQC. This structure was confirmed by analysis of residual dipolar couplings from 13C-coupled 1H-13C HSQC experiments on one of the 12-ring aggregates. Variable-temperature NMR spectroscopy revealed an internal ring-on-ring rotation process by which two π-π stacked conformers interconvert via a staggered conformation. A slower dynamic process, involving rotation of individual porphyrin units, was also detected by exchange spectroscopy in the 8-ring aggregates, implying partial disaggregation and reassociation. Molecular dynamics simulations indicate that the 8-ring aggregates are bowl-shaped and highly fluxional, compared to the 12-ring aggregates, which are cylindrical. This work demonstrates that large π-systems can form surprisingly well-defined aggregates and may inspire the design of other noncovalent assemblies.
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Solvent effects influence all stages of the chemical processes, modulating the stability of intermediates and transition states, as well as altering reaction rates and product ratios. However, accurately modelling these effects remains challenging. Here, we present a general strategy for generating reactive machine learning potentials to model chemical processes in solution. Our approach combines active learning with descriptor-based selectors and automation, enabling the construction of data-efficient training sets that span the relevant chemical and conformational space. We apply this strategy to investigate a Diels-Alder reaction in water and methanol. The generated machine learning potentials enable us to obtain reaction rates that are in agreement with experimental data and analyse the influence of these solvents on the reaction mechanism. Our strategy offers an efficient approach to the routine modelling of chemical reactions in solution, opening up avenues for studying complex chemical processes in an efficient manner.
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Cage catalysis continues to create significant interest, yet catalyst function remains poorly understood. Herein, we report mechanistic insights into coordination-cage-catalyzed Michael addition using kinetic and computational methods. The study has been enabled by the detection of identifiable catalyst intermediates, which allow the evolution of different cage species to be monitored and modeled alongside reactants and products. The investigations show that the overall acceleration results from two distinct effects. First, the cage reaction shows a thousand-fold increase in the rate constant for the turnover-limiting C-C bond-forming step compared to a reference state. Computational modeling and experimental analysis of activation parameters indicate that this stems from a significant reduction in entropy, suggesting substrate coencapsulation. Second, the cage markedly acidifies the bound pronucleophile, shifting this equilibrium by up to 6 orders of magnitude. The combination of these two factors results in accelerations up to 109 relative to bulk-phase reference reactions. We also show that the catalyst can fundamentally alter the reaction mechanism, leading to intermediates and products that are not observable outside of the cage. Collectively, the results show that cage catalysis can proceed with very high activity and unique selectivity by harnessing a series of individually weak noncovalent interactions.
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The release of strain energy is a fundamental driving force for organic reactions. However, absolute strain energy alone is an insufficient predictor of reactivity, evidenced by the similar ring strain but disparate reactivity of cyclopropanes and cyclobutanes. In this work, we demonstrate that electronic delocalization is a key factor that operates alongside strain release to boost, or even dominate, reactivity. This delocalization principle extends across a wide range of molecules containing three-membered rings such as epoxides, aziridines, and propellanes and also applies to strain-driven cycloaddition reactions. Our findings lead to a "rule of thumb" for the accurate prediction of activation barriers in such systems, which can be easily applied to reactions involving many of the strained building blocks commonly encountered in organic synthesis, medicinal chemistry, polymer science, and bioconjugation. Given the significance of electronic delocalization in organic chemistry, for example in aromatic π-systems and hyperconjugation, we anticipate that this concept will serve as a versatile tool to understand and predict organic reactivity.
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Organic(porous) and metal-organic cages are promising biomimetic platforms with diverse applications spanning recognition, sensing, and catalysis. The key to the emergence of these functions is the presence of well-defined inner cavities capable of binding a wide range of guest molecules and modulating their properties. However, despite the myriad cage architectures currently available, the rational design of structurally diverse and functional cages with specific host-guest properties remains challenging. Efficiently predicting such properties is critical for accelerating the discovery of novel functional cages. Herein, we introduce CageCavityCalc (C3), a Python-based tool for calculating the cavity size of molecular cages. The code is available on GitHub at https://github.com/VicenteMartiCentelles/CageCavityCalc. C3 utilizes a novel algorithm that enables the rapid calculation of cavity sizes for a wide range of molecular structures and porous systems. Moreover, C3 facilitates easy visualization of the computed cavity size alongside hydrophobic and electrostatic potentials, providing insights into host-guest interactions within the cage. Furthermore, the calculated cavity can be visualized using widely available visualization software, such as PyMol, VMD, or ChimeraX. To enhance user accessibility, a PyMol plugin has been created, allowing nonspecialists to use this tool without requiring computer programming expertise. We anticipate that the deployment of this computational tool will significantly streamline cage cavity calculations, thereby accelerating the discovery of functional cages.
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Programas Informáticos , Modelos Moleculares , Algoritmos , Porosidad , Conformación MolecularRESUMEN
Bridged bicycloalkanes such as bicyclo[1.1.1]pentanes (BCPs) and bicyclo[3.1.1]heptanes (BCHeps) are important motifs in contemporary drug design due to their potential to act as bioisosteres of disubstituted benzene rings, often resulting in compounds with improved physicochemical and pharmacokinetic properties. Access to such motifs with proximal nitrogen atoms (i.e. α-amino/amido bicycloalkanes) is highly desirable for drug discovery applications, but their synthesis is challenging. Here we report an approach to α-amino BCPs and BCHeps through the visible-light enabled addition of α-amino radicals to the interbridgehead C-C bonds of [1.1.1] and [3.1.1]propellane respectively. The reaction proceeds under exceptionally mild conditions and displays broad substrate scope, providing access to an array of medicinally-relevant BCP and BCHep products. Experimental and computational mechanistic studies provide evidence for a radical chain pathway which depends critically on the stability of the α-amino radical, as well as effective catalyst turnover.
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Small ruminants (sheep and goats) constantly suffer from endoparasitoses caused by gastrointestinal nematodes. Among these, the species Haemonchus contortus (Rudolphi, 1803) is considered to be the one of greatest importance within sheep farming. This nematode is difficult to control due to its resistance to most commercial anthelmintics. The aim of the present study was to assess the potential of macrochelid mites as macrobiological agents for controlling endoparasitoses of sheep caused by the nematode, H. contortus. For this, novel in vitro methodology was used, in which assessments were made not only of the predatory ability but also the population growth of mite species (Macrocheles merdarius, Macrocheles robustulus and Holostaspella bifoliata) when offered larvae of the nematode, H. contortus. The predatory ability of the mites, M. merdarius and H. bifoliata were efficient regarding their predatory ability against H. contortus nematode larvae. The mite, M. merdarius exhibited the highest predation rate with mean distribution values for the treated group of 18656 ± 10091 and for the control group of 1178 ± 712 (P < 0.0001). The species, H. bifoliata presented the highest population growth rate, with a percentage acarid recovery rate of 263% in relation to the number added initially. The data from this in vitro predation experiment suggest that, M. merdarius and H. bifoliata showed promise as macrobiological agents for controlling gastrointestinal endoparasitoses of sheep caused by the nematode, H. contortus given that both species reduced the population of this helminth by more 70% and the number of mites recovered was three times greater than the number added.
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Hemoncosis , Ácaros , Control Biológico de Vectores , Enfermedades de las Ovejas , Haemonchus , Hemoncosis/prevención & control , Ácaros/fisiología , Larva , Conducta Predatoria , Control Biológico de Vectores/normas , Crecimiento Demográfico , Femenino , Animales , Ovinos , Enfermedades de las Ovejas/parasitología , Enfermedades de las Ovejas/prevención & control , Heces/parasitología , Especificidad de la Especie , Técnicas In VitroRESUMEN
Objetivo: Identificar, nas produções científicas, as repercussões ocorridas nos serviços de hospitalização pediátrica decorrentes da pandemia da Coronavirus Disease 2019 (covid-19). Métodos: Revisão Integrativa da Literatura, realizada entre os anos de 2019 e 2021 nas seguintes bases de dados SCIELO, LILACS, SCOPUS, CINAHL, MEDLINE e COCHRANE. Resultados: Dos 1.424 estudos encontrados, 25 foram selecionados para leitura na íntegra, resultando em uma amostra final de 14 estudos incluídos na revisão. Foram constituídas categorias para representar os temas recorrentes: declínio de atendimentos nos serviços de emergência pediátrica; adaptações dos serviços pediátricos no controle e prevenção da covid-19; e hospitalização pediátrica e necessidades em saúde das crianças. Conclusão: Os achados intensificaram necessidade de reavaliação sobre o cuidado prestado no período de hospitalização pediátrica pelos gestores em saúde, além da assistência prestada as crianças durante este período, principalmente no que tange ao cuidado integral a essa clientela. (AU)
Objective: To identify, in scientific production, the repercussions that occurred in pediatric hospitalization services resulting from the Coronavirus Disease 2019 pandemic (covid-19). Methods: Integrative Literature Review, carried out between april and june 2021 in the following databases SCIELO, LILACS, SCOPUS, CINAHL, MEDLINE and COCHRANE. Results: Of the 1,424 studies found, 25 were selected for full reading, resulting in a final sample of 14 studies included in the review. Categories were created to represent the recurrent themes: decline in pediatric emergency services; adaptations of pediatric services in the control and prevention of covid-19; and pediatric hospitalization and children's health needs. Conclusion: The findings intensified the need for reassessment of the care provided during the period of pediatric hospitalization by health managers, in addition to the care provided to children during this period, especially with regard to comprehensive care for this clientele. (AU)
Objetivo: Identificar, en la producción científica, las repercusiones ocurridas en los servicios de hospitalización pediátrica producto de la pandemia de Enfermedad por Coronavirus 2019 (covid-19). Métodos: Revisión Integrativa de Literatura, realizada entre abril y junio de 2021 en las siguientes bases de datos SCIELO, LILACS, SCOPUS, CINAHL, MEDLINE y COCHRANE. Resultados: De los 1,424 estudios encontrados, 25 fueron seleccionados para lectura completa, lo que resultó en una muestra final de 14 estudios incluidos en la revisión. Se crearon categorías para representar los temas recurrentes: disminución de los servicios de emergencia pediátrica; adaptaciones de los servicios pediátricos en el control y prevención de covid-19; y hospitalización pediátrica y necesidades de salud infantil. Conclusión: Los hallazgos intensificaron la necesidad de reevaluar la atención brindada durante el período de hospitalización pediátrica por parte de los administradores de salud, además de la atención brindada a los niños durante este período, especialmente en lo que respecta a la atención integral a esta clientela. (AU)
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COVID-19 , Pediatría , Servicios de Salud del Niño , Salud Infantil , HospitalizaciónRESUMEN
Artificial ion transport systems have emerged as an important class of compounds that promise applications in chemotherapeutics as anticancer agents or to treat channelopathies. Stimulus-responsive systems that offer spatiotemporally controlled activity for targeted applications remain rare. Here we utilize dynamic hydrogen bonding interactions of a 4,6-dihydroxy-isophthalamide core to generate a modular platform enabling access to stimuli-responsive ion transporters that can be activated in response to a wide variety of external stimuli, including light, redox, and enzymes, with excellent OFF-ON activation profiles. Alkylation of the two free hydroxyl groups with stimulus-responsive moieties locks the amide bonds through intramolecular hydrogen bonding and hence makes them unavailable for anion binding and transport. Triggering using a particular stimulus to cleave both cages reverses the hydrogen bonding arrangement, to generate a highly preorganized anion binding cavity for efficient transmembrane transport. Integration of two cages that are responsive to orthogonal stimuli enables multi-stimuli activation, where both stimuli are required to trigger transport in an AND logic process. Importantly, the strategy provides a facile method to post-functionalize the highly active transporter core with a variety of stimulus-responsive moieties for targeted activation with multiple triggers.
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Enlace de Hidrógeno , Aniones/química , Ionóforos/química , Oxidación-Reducción , Estructura Molecular , Transporte IónicoRESUMEN
The media and even the specialized literature report that the ultraviolet (UV) protection for sunglasses is critical, on the grounds that sunglasses can have a counter effect if the lenses do not provide adequate UV protection. They reason that the primary and natural mechanism is that the pupil of the eye contracts to attenuate radiation and protect the inner eye under sun exposure. Therefore, if dark lenses do not provide appropriate UV protection, there is an increased UV incidence in the inner eye due to pupil dilation, which enhances the adverse effects and impacts the ocular tissues more severely than in situations without UV protection. However, no existing literature properly quantified or supported this argument. In this work, the influx of solar UV throughout the pupil of the eye was calculated in two situations: when a person wear sunglasses and when he/she does not. In both situations, the pupil dilation and the field of view (squint) were considered with their dependence on the brightness of the ambient, calculated by modeling the solar irradiation. Finally, it was assessed whether sunglasses with poor UV protection actually increase the UV influx throughout the dilated pupil compared to the non-dilated pupil. A set of 214 sunglasses lenses were tested and the results show that pupil dilation does not play an important role in the UV influx throughout the pupil. It was observed that the FOV is the main player, surpassing the pupil size contribution by up to 314.3%, disproving the common explanation. Because of the major role of the FOV, our results show that sunglasses with UV-A protection below 86% may have a slight potential to increase hazards to the eye compared to not wearing sunglasses at all. These results can have direct impact on sunglasses standards regarding the UV protection linked to the category of the lenses.
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Luz Solar , Rayos Ultravioleta , Femenino , Humanos , Rayos Ultravioleta/efectos adversos , Dilatación , Procedimientos Quirúrgicos Oftalmológicos , AnteojosRESUMEN
The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, so releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG↓X motif in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.
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Prediction of the outcome of ring opening of small organic rings under cationic conditions can be challenging due to the intermediacy of nonclassical carbocations. For example, the solvolysis of cyclobutyl or cyclopropylmethyl derivatives generates up to four products on nucleophilic capture or elimination via cyclopropylcarbinyl and bicyclobutonium ions. Here, we show that such reaction outcomes can be controlled by subtle changes to the structure of nonclassical carbocation. Using bicyclo[1.1.0]butanes as cation precursors, the regio- and stereochemistry of ring opening is shown to depend on the degree and nature of the substituents on the cationic intermediates. Reaction outcomes are rationalized using computational models, resulting in a flowchart to predict product formation from a given cation precursor.
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Strained macrocycles display interesting properties, such as conformational rigidity, often resulting in enhanced π-conjugation or enhanced affinity for non-covalent guest binding, yet they can be difficult to synthesize. Here we use computational modeling to design a template to direct the formation of an 18-porphyrin nanoring with direct meso-meso bonds between the porphyrin units. Coupling of a linear 18-porphyrin oligomer in the presence of this template gives the target nanoring, together with an unexpected 36-porphyrin ring by-product. Scanning tunneling microscopy (STM) revealed the elliptical conformations and flexibility of these nanorings on a Au(111) surface.
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Although the overall prognosis for differentiated thyroid cancer (DTC) is excellent, a subset of patients will experience disease recurrence or may not respond to standard treatments. In recent years, DTC management has become more personalized in order to enhance treatment efficacy and avoid unnecessary interventions.In this context, major guidelines recommend post-surgery staging to assess the risk of disease persistence, recurrence, and mortality. Consequently, risk stratification becomes pivotal in determining the necessity of postoperative adjuvant therapy, which may include radioiodine therapy (RIT), the degree of TSH suppression, additional imaging studies, and the frequency of follow-up.However, the intermediate risk of recurrence is a highly heterogeneous category that encompasses various risk criteria, often combined, resulting in varying degrees of aggressiveness and a recurrence risk ranging from 5 to 20%. Furthermore, there is not enough long-term prognosis data for these patients. Unlike low- and high-risk DTC, the available literature is contradictory, and there is no consensus regarding adjuvant therapy.We aim to provide an overview of intermediate-risk differentiated thyroid cancer, focusing on criteria to consider when deciding on adjuvant therapy in the current context of personalized approach, including molecular analysis to enhance the accuracy of patient management.
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Radioisótopos de Yodo , Neoplasias de la Tiroides , Humanos , Tiroidectomía , Resultado del TratamientoRESUMEN
Resumo: A partir de uma perspectiva decolonial, o objetivo da pesquisa foi compreender os lugares do negro na Psicanálise atualmente. Para isto, foram realizadas 13 entrevistas semiestruturadas com psicólogas e psicanalistas negras com prática clínica. A partir de análise categorial-temática, identificamos quatro categorias: escolha da Psicanálise, articulações entre Psicanálise e relações raciais, descobrindo-se negra e a cor da Psicanálise e das (não) psicanalistas. Diante do reconhecimento das limitações da Psicanálise, foi a experiência vivida do negro o motor de deslocamento ontológico que viabilizou desobediências epistêmicas configuradas na articulação da Psicanálise com teorias sociais. Este resultado evidencia o entrelaçamento da colonialidade do saber e do ser na matriz colonial do poder e enfatiza a desobediência ontológica como via fundamental para práticas psis antirracistas.
Resumen: Desde una perspectiva decolonial, el objetivo de la investigación fue comprender los lugares de las personas negras en el Psicoanálisis hoy. Para ello, se realizaron 13 entrevistas semiestructuradas a psicólogas y psicoanalistas negras con práctica clínica. A partir de un análisis categorial-temático identificamos cuatro categorías: elección del Psicoanálisis, articulaciones entre Psicoanálisis y relaciones raciales, descubrirse negra y el color del Psicoanálisis y de las (no) psicoanalistas. Dado el reconocimiento de las limitaciones del Psicoanálisis, fue la experiencia vivida por las personas negras el motor del desplazamiento ontológico que permitió la desobediencia epistémica configurada en la articulación del Psicoanálisis con las teorías sociales. Este resultado resalta el entrelazamiento de la colonialidad del conocimiento y el estar en la matriz colonial de poder y enfatiza la desobediencia ontológica como un camino fundamental hacia las prácticas psi antirracistas.
Abstract: From a decolonial perspective, the aim of the research was to understand the places of black people in Psychoanalysis today. For this, 13 semi-structured interviews were carried out with black psychologists and psychoanalysts with clinical practice. From a categorical-thematic analysis, we identified four categories: choosing Psychoanalysis, articulating Psychoanalysis and racial relations, discovering oneself as black and the color of Psychoanalysis and of (non) psychoanalysts. Given the recognition of Psychoanalysis's constraints, it was the lived experience of black people that was the engine of ontological displacement that enabled epistemic disobedience configured in the articulation of Psychoanalysis with social theories. This result highlights the intertwining of the coloniality of knowledge and being in the colonial matrix of power, emphasizing ontological disobedience as a fundamental path to anti-racist psychological practices.