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Navarro-López DE, Perfecto-Avalos Y, Zavala A, de Luna MA, Sanchez-Martinez A, Ceballos-Sanchez O, Tiwari N, López-Mena ER, Sanchez-Ante G. Unraveling the Complex Interactions: Machine Learning Approaches to Predict Bacterial Survival against ZnO and Lanthanum-Doped ZnO Nanoparticles. Antibiotics (Basel) 2024; 13:220. [PMID: 38534655 DOI: 10.3390/antibiotics13030220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The rise in antibiotic-resistant bacteria is a global health challenge. Due to their unique properties, metal oxide nanoparticles show promise in addressing this issue. However, optimizing these properties requires a deep understanding of complex interactions. This study incorporated data-driven machine learning to predict bacterial survival against lanthanum-doped ZnO nanoparticles. The effect of incorporation of lanthanum ions on ZnO was analyzed. Even with high lanthanum concentration, no significant variations in structural, morphological, and optical properties were observed. The antibacterial activity of La-doped ZnO nanoparticles against Gram-positive and Gram-negative bacteria was qualitatively and quantitatively evaluated. Nanoparticles induce 60%, 95%, and 55% bacterial death against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, respectively. Algorithms such as Multilayer Perceptron, K-Nearest Neighbors, Gradient Boosting, and Extremely Random Trees were used to predict the bacterial survival percentage. Extremely Random Trees performed the best among these models with 95.08% accuracy. A feature relevance analysis extracted the most significant attributes to predict the bacterial survival percentage. Lanthanum content and particle size were irrelevant, despite what can be assumed. This approach offers a promising avenue for developing effective and tailored strategies to reduce the time and cost of developing antimicrobial nanoparticles.
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Affiliation(s)
- Diego E Navarro-López
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Gral Ramón Corona No. 2514, Colonia Nuevo México, Zapopan 45121, Jalisco, Mexico
| | - Yocanxóchitl Perfecto-Avalos
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Gral Ramón Corona No. 2514, Colonia Nuevo México, Zapopan 45121, Jalisco, Mexico
| | - Araceli Zavala
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Gral Ramón Corona No. 2514, Colonia Nuevo México, Zapopan 45121, Jalisco, Mexico
| | - Marco A de Luna
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Gral Ramón Corona No. 2514, Colonia Nuevo México, Zapopan 45121, Jalisco, Mexico
| | - Araceli Sanchez-Martinez
- Departamento de Ingenieria de Proyectos, Centro Universitario de Ciencias Exactas e Ingenierias (CUCEI), Universidad de Guadalajara, Av. José Guadalupe Zuno # 48, Industrial Los Belenes, Zapopan 45157, Jalisco, Mexico
| | - Oscar Ceballos-Sanchez
- Departamento de Ingenieria de Proyectos, Centro Universitario de Ciencias Exactas e Ingenierias (CUCEI), Universidad de Guadalajara, Av. José Guadalupe Zuno # 48, Industrial Los Belenes, Zapopan 45157, Jalisco, Mexico
| | - Naveen Tiwari
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela, Rúa Jenaro de La Fuente S/N, 15782 Santiago de Compostela, Spain
| | - Edgar R López-Mena
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Gral Ramón Corona No. 2514, Colonia Nuevo México, Zapopan 45121, Jalisco, Mexico
| | - Gildardo Sanchez-Ante
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Gral Ramón Corona No. 2514, Colonia Nuevo México, Zapopan 45121, Jalisco, Mexico
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Winter MJ. Chemdex: quantification and distributions of valence numbers, oxidation numbers, coordination numbers, electron numbers, and covalent bond classes for the elements. Dalton Trans 2024; 53:493-511. [PMID: 38087991 DOI: 10.1039/d3dt03738j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The paper introduces Chemdex, a freely accessible web-based database of over 70 000 compounds characterised by crystallography from across the periodic table. Its software calculates for an atom of interest within each compound classifications including valence number, oxidation number, coordination number, electron number, several covalent bond classifications, and the attached atom set. Users may explore distributions of these classifications by percentages and heat map displays for individual elements or sets of elements, or in several cases for one classification plotted against a second. These properties often display clear periodicity. Based upon distributions across the periodic table of valence numbers, electron numbers, coordination numbers, and attached atom data suggestions are made regarding the placement of hydrogen in the periodic table, membership of group 3 in the periodic table, locations of the early actinoids in the periodic table, and assignments of certain elements as metalloids.
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Affiliation(s)
- Mark J Winter
- Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, UK.
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Dubova M, Goldstone RL. Carving joints into nature: reengineering scientific concepts in light of concept-laden evidence. Trends Cogn Sci 2023; 27:656-670. [PMID: 37173157 DOI: 10.1016/j.tics.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
A new wave of proposals suggests that scientists must reassess scientific concepts in light of accumulated evidence. However, reengineering scientific concepts in light of data is challenging because scientific concepts affect the evidence itself in multiple ways. Among other possible influences, concepts (i) prime scientists to overemphasize within-concept similarities and between-concept differences; (ii) lead scientists to measure conceptually relevant dimensions more accurately; (iii) serve as units of scientific experimentation, communication, and theory-building; and (iv) affect the phenomena themselves. When looking for improved ways to carve nature at its joints, scholars must take the concept-laden nature of evidence into account to avoid entering a vicious circle of concept-evidence mutual substantiation.
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Affiliation(s)
- Marina Dubova
- Cognitive Science Program, Indiana University, 1101 E. 10th Street, Bloomington, IN 47405, USA.
| | - Robert L Goldstone
- Cognitive Science Program, Indiana University, 1101 E. 10th Street, Bloomington, IN 47405, USA; Department of Psychological and Brain Sciences, Indiana University, 1101 E. 10th Street, Bloomington, IN 47405, USA
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Neve F. Chemistry of superheavy transition metals. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2084394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Francesco Neve
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata di Rende (CS), Italy
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Chan L, Cotton SA, Dickson J, W. G. Platt A, Raithby PR, Schiffers S, Tait A, Warren JE. Structural diversity in the series of lanthanide complexes [Ln(Ph3PO)n(NCS)3] (n = 3, 4). Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cotton SA, Raithby PR, Schiffers S, Teat SJ, Warren JE. The Synthesis and Structure of a Scandium Nitrate Hydroxy-Bridged Dimeric Complex Supported by Bipyridyl Ligands. Molecules 2022; 27:molecules27062024. [PMID: 35335383 PMCID: PMC8954743 DOI: 10.3390/molecules27062024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 11/16/2022] Open
Abstract
The current discussion on whether scandium, yttrium and lanthanum should represent Group 3 in the Periodic Table or whether lutetium should replace lanthanum in the group has prompted us to further explore the structural chemistry of the Group 3 elements and compare the coordination numbers and coordination geometries adopted. The steric and electronic properties of the coordinated ligands have a major influence on the structures adopted. We report the synthesis and crystal structure determination of an unusual dinuclear scandium complex [(bipy)(NO3)2Sc(µ-OH)2Sc(NO3)2(bipy)] obtained by the reaction of hydrated scandium nitrate with 2,2'-bipyridyl (bipy) in either ethanol or nitromethane. The crystal structure of the complex shows that the scandium centers are eight coordinate, and the structure obtained contrasts with related complexes found in the lanthanide series [Ln(bipy)2(NO3)3] and [Ln(phen)2(NO3)3] (phen = phenanthroline) and in [M(terpy)(NO3)3] (M = Sc, Er-Lu), where these complexes are all mononuclear.
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Affiliation(s)
- Simon A. Cotton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Correspondence:
| | - Paul R. Raithby
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; (P.R.R.); (S.S.)
| | - Stephanie Schiffers
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; (P.R.R.); (S.S.)
| | - Simon J. Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - John E. Warren
- Department of Mechanical, Aerospace & Civil Engineering, University of Manchester, Manchester M1 3BB, UK;
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Cotton SA, Harrowfield JM. On the singularity of scandium. NEW J CHEM 2022. [DOI: 10.1039/d2nj00117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonding interactions of the [Sc2(OH)2(OH2)10]4+ dimer containing 7-coordinate Sc(iii).
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Affiliation(s)
- Simon A. Cotton
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
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