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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
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Ysa��as J. Alvarado Joanna Baricelli Jos�� Caldera-Luzardo N��stor Cubill��n Gladys Ferrer-Amado Yovani Marrero-Ponce Victoria Mancilla Miguel A. Rocafull Jos�� Ojeda-Andara Luz E. Thomas Joan Vera-Villalobos Miguel Morales-Toyo 《Journal of solution chemistry》2011,40(1):26-39
The solubilities in water (W) and in 3 mol?L?1 aqueous acetonitrile at 298.15 K of thiophene-2-, furan-2- and pyrrole-2-carboxaldehyde phenylhydrazone along with their nitro and 2,4-dinitro derivatives, referred to as PCT, PCF, PCP, NPCT, NPCF, NPCP, DPCT, DPCF and DPCP, respectively, are reported. The standard Gibbs energy of transfer from W to solvent mixtures ( $\Delta G^{\mathrm{transf}}_{\mathrm{W-mix}}$ ) was estimated for each solute. The results indicate that the transfer process for all systems is a spontaneous process. Calculations under the scaled-particle theory suggest that the work of cavity creation (????G c), which is associated with the transfer of the phenylhydrazone from W to mix, dominates the magnitude of $\mathrm {\Delta} G^{\mathrm{transf}}_{\mathrm{W-mix}}$ . UV spectroscopic measurements suggest that these compounds bind calf thymus(CT)-DNA via intercalation mode in a buffer?C3 mol?L?1 acetonitrile solution. The binding constant (K b) depends on the nitro-substitution on the phenyl moiety and the electronegativity of the heteroatom in the heterocyclic ring. The corresponding Gibbs energy of binding ( $\Delta G_{\mathrm{DNA-B}}^{0}$ ) of phenylhydrazone derivatives to CT-DNA shows a marked dependence with ????G c. The anticancer activity on human breast cancer cell lines MDA-231, MDA-435 and HT-29 human colon adenocarcinoma cell line was evaluated for the compounds NPCT, NPCF, DPCT and PCT. 相似文献
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Ysaías J. Alvarado Néstor Cubillán María G. Leal Paola H. Labarca Elba Michelena Yovani Marrero Ponce 《Journal of solution chemistry》2007,36(9):1139-1155
The values of electronic polarizability of quinoline and isoquinoline in extremely diluted liquid solution are reported in this paper. These were obtained by means of three new strategies based on UV-visible-NIR spectroscopy, the Kramers-Krönig relations, high precision densitometry and high exactitude refractometry, which are called here Arakawa’s Approximation (AA), Optical Substractive Approximation (OSA) and Optical Differential Approximation (ODA). In general the static electronic polarizability values of solute molecules obtained by ODA and OSA are in excellent agreement with the reported theoretical values at the Density Functional Theory (DFT) level and the Atom monopole-dipole model, but strong discrepancies were observed with the experimental values previously reported for quinoline and isoquinoline using refractometric and electro-optic methods. These differences were interpreted and analyzed in terms of dielectric intermolecular forces, resonant and pre-resonant effects. The AA method is shown to fail in predicting the polarizability of the quinoline and isoquinoline molecules. 相似文献
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Cañizares-Carmenate Yudith Mena-Ulecia Karel MacLeod Carey Desmond Perera-Sardiña Yunier Hernández-Rodríguez Erix W. Marrero-Ponce Yovani Torrens Francisco Castillo-Garit Juan A. 《Molecular diversity》2022,26(3):1383-1397
Molecular Diversity - With the advancement of combinatorial chemistry and big data, drug repositioning has boomed. In this sense, machine learning and artificial intelligence techniques offer a... 相似文献