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Machine learning interatomic potentials (MLIPs) are one of the main techniques in the materials science toolbox, able to bridge ab initio accuracy with the computational efficiency of classical force fields. This allows simulations ranging from atoms, molecules, and biosystems, to solid and bulk materials, surfaces, nanomaterials, and their interfaces and complex interactions. A recent class of advanced MLIPs, which use equivariant representations and deep graph neural networks, is known as universal models. These models are proposed as foundation models suitable for any system, covering most elements from the periodic table. Current universal MLIPs (UIPs) have been trained with the largest consistent data set available nowadays. However, these are composed mostly of bulk materials' DFT calculations. In this article, we assess the universality of all openly available UIPs, namely MACE, CHGNet, and M3GNet, in a representative task of generalization: calculation of surface energies. We find that the out-of-the-box foundation models have significant shortcomings in this task, with errors correlated to the total energy of surface simulations, having an out-of-domain distance from the training data set. Our results show that while UIPs are an efficient starting point for fine-tuning specialized models, we envision the potential of increasing the coverage of the materials space toward universal training data sets for MLIPs.
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In this experimental-theoretical study, the effect of furan on Ziegler-Natta catalyst productivity, melt flow index (MFI), and mechanical properties of polypropylene were investigated. Through the analysis of the global and local reactivity of the reagents, it was determined that the furan acts as an electron donor. In contrast, the titanium of the ZN catalyst acts as an electron acceptor. It is postulated that this difference in reactivity could lead to forming a furan-titanium complex, which blocks the catalyst's active sites and reduces its efficiency for propylene polymerization. Theoretical results showed a high adsorption affinity of furan to the active site of the Ti catalyst, indicating that furan tends to bind strongly to the catalyst, thus blocking the active sites and decreasing the availability for propylene polymerization. The experimental data revealed that the presence of furan significantly reduced the productivity of the ZN catalyst by 10, 20, and 41% for concentrations of 6, 12.23, and 25.03 ppm furan, respectively. In addition, a proportional relationship was observed between the furan concentration and the MFI melt index of the polymer, where the higher the furan concentration, the higher the MFI. Likewise, the presence of furan negatively affected the mechanical properties of polypropylene, especially the impact Izod value, with percentage decreases of 9, 18, and 22% for concentrations of 6, 12.23, and 25.03 ppm furan, respectively.
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This research study examined how the use of dimethylformamide (DMF) as an inhibitor affects the propylene polymerization process when using a Ziegler-Natta catalyst. Several experiments were carried out using TiCl4/MgCl2 as a catalyst, aluminum trialkyl as a cocatalyst, and different amounts of DMF. Then, we analyzed how DMF influences other aspects of the process, such as catalyst activity, molecular weight, and the number of branches in the polymer chains obtained, using experimental and computational methods. The results revealed that as the DMF/Ti ratio increases, the catalyst activity decreases. From a concentration of 5.11 ppm of DMF, a decrease in catalyst activity was observed, ranging from 45 TM/Kg to 44 TM/Kg. When the DMF concentration was increased to 40.23 ppm, the catalyst activity decreased to 43 TM/Kg, and with 75.32 ppm, it dropped even further to 39 TM/Kg. The highest concentration of DMF evaluated, 89.92 ppm, resulted in a catalyst productivity of 36.5 TM/Kg and lost productivity of 22%. In addition, significant changes in the polymer's melt flow index (MFI) were noted as the DMF concentration increased. When 89.92 ppm of DMF was added, the MFI loss was 75%, indicating a higher flowability of the polymer. In this study, it was found that dimethylformamide (DMF) exhibits a strong affinity for the titanium center of a Ziegler-Natta (ZN) catalyst, with an adsorption energy (Ead) of approximately -46.157 kcal/mol, indicating a robust interaction. This affinity is significantly higher compared to propylene, which has an Ead of approximately -5.2 kcal/mol. The study also revealed that the energy gap between the highest occupied molecular orbital (HOMO) of DMF and the lowest unoccupied molecular orbital (SOMO) of the Ziegler-Natta (ZN) catalyst is energetically favorable, with a value of approximately 0.311 eV.
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Psychoactive natural products are potent serotonergic agonists capable of modulating brain functions such as memory and cognition. These substances have shown therapeutic potential for treating various mental disorders. The fact that N,N-dimethyltryptamine (DMT) is produced endogenously in several plants and animals, including humans, makes it particularly attractive. As an amino acid-derived alkaloid, the DMT biosynthetic pathway is part of the L-tryptophan biochemical cascade and can be divided into the decarboxylation by an aromatic L-amino acid decarboxylase (AADC) for tryptamine formation and the subsequent double-methylation by the indolethylamine-N-methyltransferase (INMT) through the cofactor S-adenosyl-L-methionine (SAM), a methyl donor. Unlike the decarboxylation mechanism of L-tryptophan, the molecular details of the double methylation of tryptamine have not been elucidated. Therefore, we propose an in silico model using molecular dynamics (MD), non-covalent interaction index (NCI) and density functional theory (DFT) calculations with the ONIOM QM:MM B3LYP/6-31+G(d,p):MM/UFF level of theory. Based on the obtained energetic data, the potential energy surface (PES) indicates an SN2 mechanism profile, with the second methylation energy barrier being the rate-limiting step with δG=60kJâmol-1 larger than the previous methylation, following the NCI analysis showing more repulsive interactions for the second transition state. In addition, the hybridization information of each reaction step provides geometric details about the double-methylation.
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N,N-Dimetiltriptamina , Triptofano , Humanos , Animais , Triptaminas , AminoácidosRESUMO
Cancer is one of the leading causes of human death worldwide, being one of the most serious problems faced by mankind. For the diagnosis, Magnetic Resonance Imaging (MRI), through effective contrast agents (Cas), has greatly helped in the diagnosis at the initial stages. However, it is necessary to include new compounds more effective and selective for cancer diagnosis. The complexes with Mn2+, Cu2+ and Zn2+ have received great attention due to their applications as CAs for MRI. Those materials can shorten the T2 and T2* transverse relaxation times. Thus, the representative structures for hyperfine coupling constants (HFCCs) were selected from docking results by frequency of occupancy calculations. From the Multivariate Analysis to obtain the PCA graphs in the choice of a representative conformations. it is possible to notice that the variable energy does not present a high correlation with the other variables, and structural factors, such as the spatial positions of the metal atoms, seem to be important in the reactivity of the complexes. Structural factors, such as the spatial positions of the metal atoms, seem to be important in the reactivity of the complexes. Theoretical findings suggest that the compounds are capable of increasing the Aiso values of the water molecules, but the complex [Zn(H2O)(NNO)] shows a greater influence, being more sensitive to the Electron paramagnetic resonance parameters than the complexes [CuCl(H2O)NNO] and [MnCl2(H2O)(NNO)] with the explicit solvent and the enzyme. MRI contrast agents have generated various problems due to their high toxicity. In this perspective, this compound may be a promising alternative for transporting the CAs into diseased tissue.Communicated by Ramaswamy H. Sarma.
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Meios de Contraste , Complexos de Coordenação , Humanos , Meios de Contraste/química , Manganês/química , Imageamento por Ressonância Magnética , Metais , Zinco/química , Complexos de Coordenação/químicaRESUMO
Only a limited number of multinucleating ligands can stably maintain multinuclear metal structures in aqueous solutions. In this study, a water-soluble dinucleating ligand, 2,6-bis{[N-(carboxylatomethyl)-N-methyl-amino]methyl}-4-methylphenolate ((sym-cmp)3-), was prepared and its copper(II) complexes were structurally characterized. Using the single-crystal X-ray diffraction method, their dimer-of-dimers type defect cubane tetranuclear copper(II) structures were characterized for [Cu4(sym-cmp)2Cl2(H2O)2] and [Cu4(sym-cmp)2(CH3O)2(CH3OH)2]. In the complexes, each copper(II) ion has a five-coordinate square-pyramidal coordination geometry. The coordination bond character was confirmed by the density functional theory (DFT) calculation on the basis of the crystal structure, whereby we found the bonding and anti-bonding molecular orbitals. From the cryomagnetic measurement and the magnetic analysis, overall antiferromagnetic interaction was observed, and this magnetic behavior is also explained by the DFT result. Judging from the molar conductance and the electronic spectra, the bridging chlorido ligand dissociates in water, but the dinuclear copper(II) structure was found to be maintained in an aqueous solution. In conclusion, the tetranuclear copper(II) structures were crystallographically characterized, and the dinuclear copper(II) structures were found to be stabilized even in an aqueous solution.
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We have previously synthesized and characterized the chrysin coordination complex with the oxidovanadium(IV) cation (VIVO(chrys)2) and characterized in ethanolic solution and in solid state. Because suitable single crystals for X-ray diffraction determinations could not be obtained, in the present work, we elucidate the geometrical parameters of this complex by computational methodologies. The optimization and vibrational investigation were carried out both in ethanolic solution and in gas phase. The computational results support the experimentally proposed geometries of the VIVO(chrys)2 complex, thus leading to the conclusion that the complex exists as conformers with trans-octahedral geometry in ethanolic solution and as conformers with cis-octahedral geometry in the solid state. The complex also exists as conformers with trans-octahedral geometry in aqueous media. The active species formed after dissolution in DMSO showed anticancer and antimetastatic behavior in human lung cell line A549 with moderate binding (Kaca. 105 M-1) to bovine serum albumin (BSA). The interaction through hydrogen bonding and van der Waals forces resulted in a spontaneous process. Site marker competitive experiments showed binding sites for chrysin mainly located in site II (subdomain IIIA) and in site I (subdomain IIIA) for the complex. FT-IR spectral measurements showed evidences of the alterations of protein secondary structure in the presence of chrysin and VIVO(chrys)2.
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Antineoplásicos/farmacologia , Movimento Celular/efeitos dos fármacos , Complexos de Coordenação/farmacologia , Flavonoides/farmacologia , Soroalbumina Bovina/metabolismo , Compostos de Vanádio/farmacologia , Células A549 , Animais , Antineoplásicos/química , Antineoplásicos/metabolismo , Sítios de Ligação , Bovinos , Sobrevivência Celular/efeitos dos fármacos , Complexos de Coordenação/química , Complexos de Coordenação/metabolismo , Flavonoides/química , Flavonoides/metabolismo , Humanos , Estrutura Molecular , Ligação Proteica , Conformação Proteica/efeitos dos fármacos , Espécies Reativas de Oxigênio/metabolismo , Soroalbumina Bovina/química , Compostos de Vanádio/química , Compostos de Vanádio/metabolismoRESUMO
The potential of nitrones (N-oxides) as therapeutic antioxidants is due to their ability to counteract oxidative stress, mainly attributed to their action as radical scavengers toward C- and O-centered radicals. Among them, nitrones from the amidinoquinoxaline series resulted in interesting derivatives, due to the ease with which it is possible to introduce proper substituents within their structure in order to modulate their lipophilicity. The goal is to obtain lipophilic antioxidants that are able to interact with cell membranes and, at the same time, enough hydrophilic to neutralize those radicals present in a water compartment. In this work, the antioxidant efficacy of a series of amidinoquinoxaline nitrones has been evaluated regarding the oxidation of 2-deoxyribose and lipid peroxidation. The results have been rationalized on the basis of the different possible mechanisms involved, depending on some of their properties, such as lipophilicity, the ability to scavenge free radicals, and to undergo single electron transfer (SET) reactions.
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BACKGROUND: Redox active metal cations, such as Cu2 +, have been related to induce amyloid plaques formation and oxidative stress, which are two of the key events in the development of Alzheimer's disease (AD) and others metal promoted neurodegenerative diseases. In these oxidative events, standard reduction potential (SRP) is an important property especially relevant in the reactive oxygen species formation. OBJECTIVE: The SRP is not usually considered for the selection of drug candidates in anti-AD treatments. In this work, we present a computational protocol for the selection of multifunctional ligands with suitable metal chelating, pharmacokinetics, and redox properties. METHODS: The filtering process is based on quantum chemical calculations and the use of in silico tools. Calculations of SRP were performed by using the M06-2X density functional and the isodesmic approach. Then, a virtual screening technique (VS) was used for similar structure search. RESULTS: Protocol application allowed the assessment of chelating, drug likeness, and redox properties of copper ligands. Those molecules showing the best features were selected as molecular scaffolds for a VS procedure in order to obtain related compounds. After applying this process, we present a list of candidates with suitable properties to prevent the redox reactions mediated by copper(II) ion. CONCLUSION: The protocol incorporates SRP in the filtering stage and can be effectively used to obtain a set of potential drug candidates for AD treatments.