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Vargas R, Garza J, Martínez A, Ibarra IA. Computational tools to study non-covalent interactions and confinement effects in chemical systems. Chem Commun (Camb) 2024; 60:3008-3018. [PMID: 38376468 DOI: 10.1039/d3cc06347j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Confinement is a very common phenomenon in chemistry, for example, when molecules are located inside cavities. In these conditions, the electronic structure of atoms and molecules is modified. These changes could be mapped through the interaction with other molecules since non-covalent interactions between molecules are also influenced by confinement. In this work we address both topics, non-covalent interactions, and confined systems, using quantum chemistry tools with new software, emphasizing the importance of analyzing both fields simultaneously.
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Affiliation(s)
- Rubicelia Vargas
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa. C.P. 09340, Ciudad de México, Mexico.
| | - Jorge Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa. C.P. 09340, Ciudad de México, Mexico.
| | - Ana Martínez
- Departamento de Materiales de Baja Dimensionalidad. Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Ciudad Universitaria S.N., Coyoacán 04510, Ciudad de México, Mexico
- On sabatical at Museo Nacional de Ciencias Naturales, CSIC, Spain
| | - Ilich A Ibarra
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa. C.P. 09340, Ciudad de México, Mexico.
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS). Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Ciudad Universitaria S.N., Coyoacán 04510, Ciudad de México, Mexico
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Jevremović A, Stanojković A, Arsenijević D, Arsenijević A, Arzumanyan G, Mamatkulov K, Petrović J, Nedić Vasiljević B, Bajuk-Bogdanović D, Milojević-Rakić M. Mitigating toxicity of acetamiprid removal techniques - Fe modified zeolites in focus. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129226. [PMID: 35739746 DOI: 10.1016/j.jhazmat.2022.129226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/11/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
All remediation pathways in aqueous solutions come down to three dominant ones - physical, chemical, and combinations thereof. Materials proposed for adsorption and oxidative degradation can induce positive or negative effects on cells compared to the pollutants themselves. Present research deals with the effects different methods for pesticide remediation have and how they impact cytotoxicity. With this particular intention, Fe-modified zeolites (obtained via citrate/oxalate complexes) of three zeotypes (MFI, BEA and FAU) were prepared and tested as adsorbents and Fenton catalysts for the removal of the acetamiprid pesticide. The materials are characterized by AFM, FTIR spectroscopy and ICP-OES. A different effect of the zeolite framework and modification route was found among the samples, which leads to pronounced adsorption (FAU), efficient Fenton degradation (MFI) or synergistic effect of both mechanisms (BEA). The cytotoxic effects of acetamiprid in the presence of zeolites, in pristine and modified forms, were tested on the MRC-5 human fibroblast cell line. A complete survey of the toxicity effect behind different pesticide removal methods is presented. Since neither adsorption nor catalytic degradation is the best option for pesticide removal, the focus is shifted to a combination of these methods, which proved to be optimal for pesticide toxicity reduction.
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Affiliation(s)
- Anka Jevremović
- University of Belgrade Faculty of Physical Chemistry, 11000 Belgrade, Serbia.
| | - Ana Stanojković
- University of Belgrade Faculty of Physical Chemistry, 11000 Belgrade, Serbia
| | - Dragana Arsenijević
- University of Kragujevac Faculty of Medical Sciences, Department of Pharmacy and Center for Molecular Medicine and Stem Cells Research, 34000 Kragujevac, Serbia
| | - Aleksandar Arsenijević
- University of Kragujevac Faculty of Medical Sciences, Department of Pharmacy and Center for Molecular Medicine and Stem Cells Research, 34000 Kragujevac, Serbia
| | - Grigory Arzumanyan
- Joint Institute for Nuclear Research, Laboratory of Neutron Physics, Sector of Raman Spectroscopy Centre Nanobiophotonics, Dubna, Russia
| | - Kahramon Mamatkulov
- Joint Institute for Nuclear Research, Laboratory of Neutron Physics, Sector of Raman Spectroscopy Centre Nanobiophotonics, Dubna, Russia
| | - Jelena Petrović
- University of Belgrade "VINČA" Institute of Nuclear Sciences National Institute of the Republic of Serbia, Department of Physical Chemistry, Mike Petrovića Alasa, 11000 Belgrade, Serbia
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Zhu X, Hu CT, Erriah B, Vogt-Maranto L, Yang J, Yang Y, Qiu M, Fellah N, Tuckerman ME, Ward MD, Kahr B. Imidacloprid Crystal Polymorphs for Disease Vector Control and Pollinator Protection. J Am Chem Soc 2021; 143:17144-17152. [PMID: 34634905 DOI: 10.1021/jacs.1c07610] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Imidacloprid, the world's leading insecticide, has been approved recently for controlling infectious disease vectors; yet, in agricultural settings, it has been implicated in the frightening decline of pollinators. This argues for strategies that sharply reduce the environmental impact of imidacloprid. When used as a contact insecticide, the effectiveness of imidacloprid relies on physical contact between its crystal surfaces and insect tarsi. Herein, seven new imidacloprid crystal polymorphs are reported, adding to two known forms. Anticipating that insect uptake of imidacloprid molecules would depend on the respective free energies of crystal polymorph surfaces, measurements of insect knockdown times for the metastable crystal forms were as much as nine times faster acting than the commercial form against Aedes, Anopheles, and Culex mosquitoes as well as Drosophila (fruit flies). These results suggest that replacement of commercially available imidacloprid crystals (a.k.a. Form I) in space-spraying with any one of three new polymorphs, Forms IV, VI, IX, would suppress vector-borne disease transmission while reducing environmental exposure and harm to nontarget organisms.
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Affiliation(s)
- Xiaolong Zhu
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Chunhua T Hu
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Bryan Erriah
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Leslie Vogt-Maranto
- Department of Chemistry, New York University, New York, New York 10003 United States
| | - Jingxiang Yang
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Yongfan Yang
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Mengdi Qiu
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Noalle Fellah
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Mark E Tuckerman
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
- NYU-ECNU Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
| | - Michael D Ward
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
| | - Bart Kahr
- Department of Chemistry and Molecular Design Institute, New York University, New York, New York 10003 United States
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Palomino-Asencio L, Ramírez-Torres A, Avelar J, Garza J, García-Hernández E. Functionalized graphene pieces to trap the insecticide imidacloprid: a theoretical analysis. J Mol Model 2019; 25:117. [DOI: 10.1007/s00894-019-4016-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/29/2019] [Indexed: 11/24/2022]
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Badillo-Ramírez I, Landeros-Rivera B, de la O-Cuevas E, Vargas R, Garza J, Saniger JM. Interaction of 5-S-cysteinyl-dopamine with graphene oxide: an experimental and theoretical study for the detection of a Parkinson's disease biomarker. NEW J CHEM 2019. [DOI: 10.1039/c9nj03781k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spectroscopic and theoretical analysis in the adsorption of 5-S-Cys-DA over GO for the development of platform biosensors with Raman spectroscopy.
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Affiliation(s)
- Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología
- Universidad Nacional Autónoma de México
- Circuito Exterior S/N
- Ciudad Universitaria
- Ciudad de México
| | - Bruno Landeros-Rivera
- División de Ciencias Básicas e Ingeniería
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | | | - Rubicelia Vargas
- División de Ciencias Básicas e Ingeniería
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | - Jorge Garza
- División de Ciencias Básicas e Ingeniería
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología
- Universidad Nacional Autónoma de México
- Circuito Exterior S/N
- Ciudad Universitaria
- Ciudad de México
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Zaragoza IP, Soriano-Agueda LA, Hernández-Esparza R, Vargas R, Garza J. Analyzing ZnO clusters through the density-functional theory. J Mol Model 2018; 24:164. [PMID: 29909582 DOI: 10.1007/s00894-018-3691-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Abstract
The potential energy surface of Zn n O n clusters (n = 2, 4, 6, 8) has been explored by using a simulated annealing method. For n = 2, 4, and 6, the CCSD(T)/TZP method was used as the reference, and from here it is shown that the M06-2X/TZP method gives the lowest deviations over PBE, PBE0, B3LYP, M06, and MP2 methods. Thus, with the M06-2X method we predict isomers of Zn n O n clusters, which coincide with some isomers reported previously. By using the atoms in molecules analysis, possible contacts between Zn and O atoms were found for all structures studied in this article. The bond paths involved in several clusters suggest that Zn n O n clusters can be obtained from the zincite (ZnO crystal), such an observation was confirmed for clusters with n = 2 - 9,18 and 20. The structure with n = 23 was obtained by the procedure presented here, from crystal information, which could be important to confirm experimental data delivered for n = 18 and 23.
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Affiliation(s)
- Irineo-Pedro Zaragoza
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México Campus Instituto Tecnológico de Tlalnepantla, Av. Mario Colín S/N, La Comunidad, Tlalnepantla de Baz, C.P. 54070, Estado de México, México
| | - Luis-Antonio Soriano-Agueda
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, Ciudad de México, México
| | - Raymundo Hernández-Esparza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, Ciudad de México, México
| | - Rubicelia Vargas
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, Ciudad de México, México
| | - Jorge Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, Ciudad de México, México.
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