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31.
César R. García-Jacas Yovani Marrero-Ponce Ricardo Vivas-Reyes José Suárez-Lezcano Felix Martinez-Rios Julio E. Terán Longendri Aguilera-Mendoza 《Journal of computational chemistry》2020,41(12):1209-1227
Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications. 相似文献
32.
Jennifer Paola Hernández Mancera Francisco Núñez-Zarur Soledad Gutiérrez-Oliva Alejandro Toro-Labbé Ricardo Vivas-Reyes 《Journal of computational chemistry》2020,41(23):2022-2032
Quantum chemical calculations were used to study the mechanism of Diels-Alder reactions involving chiral anthracenes as dienes and a series of dienophiles. The reaction force analysis was employed to obtain a detailed scrutiny of the reaction mechanisms, it has been found that thermodynamics and kinetics of the reactions are quite consistent: the lower the activation energy, the lower the reaction energy, thus following the Bell-Evans-Polanyi principle. It has been found that activation energies are mostly due to structural rearrangements that in most cases represented more than 70% of the activation energy. Electronic activity mostly due to changes in σ and π bonding were revealed by the reaction electronic flux (REF), this property helps identify whether changes on σ or π bonding drive the reaction. Additionally, new global indexes describing the behavior of the electronic activity were introduced and then used to classify the reactions in terms of the spontaneity of their electronic activity. Local natural bond order electronic population analysis was used to check consistency with global REF through the characterization of specific changes in the electronic density that might be responsible for the activity already detected by the REF. Results show that reactions involving acetoxy lactones are driven by spontaneous electronic activity coming from bond forming/strengthening processes; in the case of maleic anhydrides and maleimides it appears that both spontaneous and non-spontaneous electronic activity are quite active in driving the reactions. 相似文献
33.
Dr. Ricardo Pérez de Tudela Prof. Dominik Marx 《Chemistry (Weinheim an der Bergstrasse, Germany)》2020,26(52):11955-11959
Acid dissociation, and thus liberation of excess protons in small water droplets, impacts on diverse fields such as interstellar, atmospheric or environmental chemistry. At cryogenic temperatures below 1 K, it is now well established that as few as four water molecules suffice to dissociate the generic strong acid HCl, yet temperature-driven recombination sets in simply upon heating that cluster. Here, the fundamental question is posed of how many more water molecules are required to stabilize a hydrated excess proton at room temperature. Ab initio path integral simulations disclose that not five, but six water molecules are needed at 300 K to allow for HCl dissociation independently from nuclear quantum effects. In order to provide the molecular underpinnings of these observations, the classical and quantum free energy profiles were decomposed along the dissociation coordinate in terms of the corresponding internal energy and entropy profiles. What decides in the end about acid dissociation, and thus ion pair formation, in a specific microsolvated water cluster at room temperature is found to be a fierce competition between classical configurational entropy and internal energy, where the former stabilizes the undissociated state whereas the latter favors dissociation. It is expected that these are generic findings with broad implications on acid–base chemistry depending on temperature in small water assemblies. 相似文献
34.
35.
Shantanu Mishra Doreen Beyer Kristjan Eimre Ricardo Ortiz Joaquín Fernndez‐Rossier Reinhard Berger Oliver Grning Carlo A. Pignedoli Roman Fasel Xinliang Feng Pascal Ruffieux 《Angewandte Chemie (International ed. in English)》2020,59(29):12041-12047
Triangular zigzag nanographenes, such as triangulene and its π‐extended homologues, have received widespread attention as organic nanomagnets for molecular spintronics, and may serve as building blocks for high‐spin networks with long‐range magnetic order, which are of immense fundamental and technological relevance. As a first step towards these lines, we present the on‐surface synthesis and a proof‐of‐principle experimental study of magnetism in covalently bonded triangulene dimers. On‐surface reactions of rationally designed precursor molecules on Au(111) lead to the selective formation of triangulene dimers in which the triangulene units are either directly connected through their minority sublattice atoms, or are separated via a 1,4‐phenylene spacer. The chemical structures of the dimers have been characterized by bond‐resolved scanning tunneling microscopy. Scanning tunneling spectroscopy and inelastic electron tunneling spectroscopy measurements reveal collective singlet–triplet spin excitations in the dimers, demonstrating efficient intertriangulene magnetic coupling. 相似文献
36.
37.
Ariel G. De Candia Matias Molnar Leonardo D. Slep Ricardo Baggio 《Acta Crystallographica. Section C, Structural Chemistry》2012,68(5):m121-m126
Although it has not proved possible to crystallize the newly prepared cyclam–methylimidazole ligand 1‐[(1‐methyl‐1H‐imidazol‐2‐yl)methyl]‐1,4,8,11‐tetraazacyclotetradecane (LIm1), the trans and cis isomers of an NiII complex, namely trans‐aqua{1‐[(1‐methyl‐1H‐imidazol‐2‐yl)methyl]‐1,4,8,11‐tetraazacyclotetradecane}nickel(II) bis(perchlorate) monohydrate, [Ni(C15H30N6)(H2O)](ClO4)2·H2O, (1), and cis‐aqua{1‐[(1‐methyl‐1H‐imidazol‐2‐yl)methyl]‐1,4,8,11‐tetraazacyclotetradecane}nickel(II) bis(perchlorate), [Ni(C15H30N6)(H2O)](ClO4)2, (2), have been prepared and structurally characterized. At different stages of the crystallization and thermal treatment from which (1) and (2) were obtained, a further two compounds were isolated in crystalline form and their structures also analysed, namely trans‐{1‐[(1‐methyl‐1H‐imidazol‐2‐yl)methyl]‐1,4,8,11‐tetraazacyclotetradecane}(perchlorato)nickel(II) perchlorate, [Ni(ClO4)(C15H30N6)]ClO4, (3), and cis‐{1,8‐bis[(1‐methyl‐1H‐imidazol‐2‐yl)methyl]‐1,4,8,11‐tetraazacyclotetradecane}nickel(II) bis(perchlorate) 0.24‐hydrate, [Ni(C20H36N6)](ClO4)2·0.24H2O, (4); the 1,8‐bis[(1‐methyl‐1H‐imidazol‐2‐yl)methyl]‐1,4,8,11‐tetraazacyclotetradecane ligand is a minor side product, probably formed in trace amounts in the synthesis of LIm1. The configurations of the cyclam macrocycles in the complexes have been analysed and the structures are compared with analogues from the literature. 相似文献
38.
Félix Freire Dr. Enrique Lallana Emilio Quiñoá Prof. Dr. Ricardo Riguera Prof. Dr. 《Chemistry (Weinheim an der Bergstrasse, Germany)》2009,15(44):11963-11975
The conformational compositions of the tris(α‐methoxy‐α‐phenylacetic acid) ester derivatives of 1,2,3‐prim,sec,sec‐triols are presented. These conformations have been determined by theoretical and experimental data (i.e., energy‐ and chemical‐shift calculations, circular dichroism (CD) experiments, coupling‐constant analysis, enantioselective deuteration experiments, and low‐temperature NMR spectroscopic studies). A detailed analysis of the anisotropic effects due to the most significant conformers in the 1H NMR spectra supported the correlation between the 1H NMR spectra (ΔδRS value of H(3′) and |Δ(ΔδRS)| parameters) and the absolute configuration of the substrate. The study also allows the identification of the pro‐R and pro‐S methylene protons from their vicinal coupling constants and relative chemical shifts. 相似文献
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40.
Ray L. Frost Yunfei Xi Ricardo Scholz Fernanda M. Belotti 《Transition Metal Chemistry》2012,37(8):777-782
In this research, we have used vibrational spectroscopy to study the phosphate mineral kosnarite KZr2(PO4)3. Interest in this mineral rests with the ability of zirconium phosphates (ZP) to lock in radioactive elements. ZP have the capacity to concentrate and immobilize the actinide fraction of radioactive phases in homogeneous zirconium phosphate phases. The Raman spectrum of kosnarite is characterized by a very intense band at 1,026?cm?1 assigned to the symmetric stretching vibration of the PO4 3? ??1 symmetric stretching vibration. The series of bands at 561, 595 and 638?cm?1 are assigned to the ??4 out-of-plane bending modes of the PO4 3? units. The intense band at 437?cm?1 with other bands of lower wavenumber at 387, 405 and 421?cm?1 is assigned to the ??2 in-plane bending modes of the PO4 3? units. The number of bands in the antisymmetric stretching region supports the concept that the symmetry of the phosphate anion in the kosnarite structure is preserved. The width of the infrared spectral profile and its complexity in contrast to the well-resolved Raman spectrum show that the pegmatitic phosphates are better studied with Raman spectroscopy. 相似文献