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Beheshti A, Pourbasheer E, Ganjali MR. Density function theory calculation to study the oxidation potential of electron-donating compounds; affirming the oxidation mechanism by NICS calculations. J Mol Model 2023; 29:32. [PMID: 36609766 DOI: 10.1007/s00894-022-05431-1] [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: 02/16/2022] [Accepted: 12/18/2022] [Indexed: 01/09/2023]
Abstract
The manuscript describes a method for understanding the correlation of structural features and first oxidation potentials [Formula: see text] of electron-donating compounds (EDCs) with tetrathiafulvalene (TTF), dithiadiazafulvalenes (DTDAF), and tetraazafulvalene (TAF) frameworks. The density functional theory (DFT) procedure at B3LYP (6-31 + g(d)) was used for geometric optimization, given the large dimensions of the molecules studied, and their high structural similarity. First of all, the correlation between the oxidation potential and the highest occupied molecular orbital (HOMO) energy level as an effective quantum chemical descriptor was examined. Then, nucleus-independent chemical shifts (NICSs) calculation was applied to affirm the oxidation mechanism and interpret the effect of replacing the sulfur atoms by nitrogen, on the oxidation process. Finally, a more comprehensive investigation of structural features that affect the oxidation potential, topological, geometrical, constitutional, as well as, electrostatic, charged partial surface area, quantum-chemical, molecular orbital, and thermodynamic descriptors was calculated. A predictive model was developed based on the genetic algorithm multivariate linear regression (GA-MLR). There was an outstanding agreement between the theoretical and the experimental values obtained for the first oxidation potentials of the test set (Q2Ext = 0.981).
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Affiliation(s)
- Abolghasem Beheshti
- Department of Chemistry, Payame Noor University (PNU), P.O. Box, 19395-3697, Tehran, Iran.
| | - Eslam Pourbasheer
- Department of Chemistry, Faculty of Science, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran.,National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Toropova AP. Medicinal Chemistry and Computational Chemistry: Mutual Influence and Harmonization. Mini Rev Med Chem 2020; 20:1320-1321. [PMID: 32600227 DOI: 10.2174/138955752014200626163614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche Mario Negri IRCCS Via Mario Negri 2, 20156 Milano, Italy
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Oyarzo J, Bosque R, Toro P, Silva CP, Arancibia R, Font-Bardía M, Artigas V, Calvis C, Messeguer R, Klahn AH, López C. A novel type of organometallic 2-R-2,4-dihydro-1H-3,1-benzoxazine with R = [M(η5-C5H4)(CO)3] (M = Re or Mn) units. Experimental and computational studies of the effect of substituent R on ring-chain tautomerism. Dalton Trans 2019; 48:1023-1039. [DOI: 10.1039/c8dt03265c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Novel 2-cyrhetrenyl and cymantrenyl-2,4-dihydro-1H-3,1-benzoxazines.
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Toropov AA, Toropova AP, Benfenati E, Nicolotti O, Carotti A, Nesmerak K, Veselinović AM, Veselinović JB, Duchowicz PR, Bacelo D, Castro EA, Rasulev BF, Leszczynska D, Leszczynski J. QSPR/QSAR Analyses by Means of the CORAL Software. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In this chapter, the methodology of building up quantitative structure—property/activity relationships (QSPRs/QSARs)—by means of the CORAL software is described. The Monte Carlo method is the basis of this approach. Simplified Molecular Input-Line Entry System (SMILES) is used as the representation of the molecular structure. The conversion of SMILES into the molecular graph is available for QSPR/QSAR analysis using the CORAL software. The model for an endpoint is a mathematical function of the correlation weights for various features of the molecular structure. Hybrid models that are based on features extracted from both SMILES and a graph also can be built up by the CORAL software. The conceptually new ideas collected and revealed through the CORAL software are: (1) any QSPR/QSAR model is a random event; and (2) optimal descriptor can be a translator of eclectic information into an endpoint prediction.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pablo R. Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
| | | | - Eduardo A. Castro
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
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Nesměrák K, Toropov AA, Toropova AP. Model for electrochemical parameters for 4-(benzylsulfanyl)pyridines calculated from the molecular structure. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Worachartcheewan A, Prachayasittikul V, Toropova AP, Toropov AA, Nantasenamat C. Large-scale structure-activity relationship study of hepatitis C virus NS5B polymerase inhibition using SMILES-based descriptors. Mol Divers 2015; 19:955-64. [DOI: 10.1007/s11030-015-9614-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Toropov AA, Toropova AP, Benfenati E, Nicolotti O, Carotti A, Nesmerak K, Veselinović AM, Veselinović JB, Duchowicz PR, Bacelo D, Castro EA, Rasulev BF, Leszczynska D, Leszczynski J. QSPR/QSAR Analyses by Means of the CORAL Software. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS IN DRUG DESIGN, PREDICTIVE TOXICOLOGY, AND RISK ASSESSMENT 2015. [DOI: 10.4018/978-1-4666-8136-1.ch015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter, the methodology of building up quantitative structure—property/activity relationships (QSPRs/QSARs)—by means of the CORAL software is described. The Monte Carlo method is the basis of this approach. Simplified Molecular Input-Line Entry System (SMILES) is used as the representation of the molecular structure. The conversion of SMILES into the molecular graph is available for QSPR/QSAR analysis using the CORAL software. The model for an endpoint is a mathematical function of the correlation weights for various features of the molecular structure. Hybrid models that are based on features extracted from both SMILES and a graph also can be built up by the CORAL software. The conceptually new ideas collected and revealed through the CORAL software are: (1) any QSPR/QSAR model is a random event; and (2) optimal descriptor can be a translator of eclectic information into an endpoint prediction.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pablo R. Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
| | | | - Eduardo A. Castro
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Argentina
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SMILES-based quantitative structure–property relationships for half-wave potential of N-benzylsalicylthioamides. Eur J Med Chem 2013; 67:111-4. [DOI: 10.1016/j.ejmech.2013.05.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 01/17/2023]
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Nesmerak K, Toropov AA, Toropova AP. SMILES-based quantitative structure–retention relationships for RP HPLC of 1-phenyl-5-benzylsulfanyltetrazoles. Struct Chem 2013. [DOI: 10.1007/s11224-013-0293-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gajewicz A, Rasulev B, Dinadayalane TC, Urbaszek P, Puzyn T, Leszczynska D, Leszczynski J. Advancing risk assessment of engineered nanomaterials: application of computational approaches. Adv Drug Deliv Rev 2012; 64:1663-93. [PMID: 22664229 DOI: 10.1016/j.addr.2012.05.014] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/20/2012] [Accepted: 05/25/2012] [Indexed: 02/06/2023]
Abstract
Nanotechnology that develops novel materials at size of 100nm or less has become one of the most promising areas of human endeavor. Because of their intrinsic properties, nanoparticles are commonly employed in electronics, photovoltaic, catalysis, environmental and space engineering, cosmetic industry and - finally - in medicine and pharmacy. In that sense, nanotechnology creates great opportunities for the progress of modern medicine. However, recent studies have shown evident toxicity of some nanoparticles to living organisms (toxicity), and their potentially negative impact on environmental ecosystems (ecotoxicity). Lack of available data and low adequacy of experimental protocols prevent comprehensive risk assessment. The purpose of this review is to present the current state of knowledge related to the risks of the engineered nanoparticles and to assess the potential of efficient expansion and development of new approaches, which are offered by application of theoretical and computational methods, applicable for evaluation of nanomaterials.
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Affiliation(s)
- Agnieszka Gajewicz
- Laboratory of Environmental Chemometrics, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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SMILES-based QSPR model for half-wave potentials of 1-phenyl-5-benzyl-sulfanyltetrazoles using CORAL. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.04.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
AbstractCORAL (‘CORrelation And Logic’) is freeware available on the Internet www.insilico.eu/coral The aim of this program is to establish a correlation between an endpoint and descriptors calculated with a simplified molecular input line entry system (SMILES). Three models calculated by CORAL for toxicity towards rat (-pLD50) of inorganic substances (three random splits) have shown that CORAL could be a good tool to model this endpoint. The average statistical characteristics for the CORAL models are the following: n=38, r2=0.8461, q2=0.8298, s=0.273, F=198 (subtraining set); n=37, r2=0.8144, s=0.322, F=154 (calibration set); and n=10, r2=0.8004, Rm (test)2 =0.7815, s=0.240, F=32 (validation set).
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Nesměrák K, Doležal R, Hudská V, Bártl J, Štícha M, Waisser K. Quantitative Structure-Electrochemistry Relationship of 1-Phenyl-5-benzyl-sulfanyltetrazoles and Their Electrooxidation as a Metabolic Model. ELECTROANAL 2010. [DOI: 10.1002/elan.201000092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Comparison of conventional artificial neural network and wavelet neural network in modeling the half-wave potential of aldehydes and ketones. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2009.11.083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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QSPR study for the prediction of half-wave potentials of benzoxazines by heuristic method and radial basis function neural network. OPEN CHEM 2009. [DOI: 10.2478/s11532-009-0033-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe half-wave potential (E1/2) is an important electrochemical property of organic compounds. In this work, a quantitative structure-property relationship (QSPR) analysis has been conducted on the half-wave reduction potential (E1/2) of 40 substituted benzoxazines by means of both a heuristic method (HM) and a non-linear radial basis function neural network (RBFNN) modeling method. The statistical parameters provided by the HM model (R2 =0.946; F=152.576; RMSCV=0.0141) and the RBFNN model (R2=0.982; F=1034.171 and RMS =0.0209) indicated satisfactory stability and predictive ability. The obtained models showed that benzoxazines with larger Min valency of a S atom (MVSA), lower Relative number of H atom (RNHA) and Min n-n repulsion for a C-H bond (MnnRCHB) and Minimal Electrophilic Reactivity Index for a C atom (MERICA) can be more easily reduced. This QSPR approach can contribute to a better understanding of structural factors of the organic compounds that contribute to the E1/2, and can be useful in predicting the E1/2 of other compounds.
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Beheshti A, Riahi S, Ganjali MR. Quantitative structure–property relationship study on first reduction and oxidation potentials of donor-substituted phenylquinolinylethynes and phenylisoquinolinylethynes: Quantum chemical investigation. Electrochim Acta 2009. [DOI: 10.1016/j.electacta.2009.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hemmateenejad B, Yazdani M. QSPR models for half-wave reduction potential of steroids: A comparative study between feature selection and feature extraction from subsets of or entire set of descriptors. Anal Chim Acta 2009; 634:27-35. [DOI: 10.1016/j.aca.2008.11.062] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 11/26/2008] [Accepted: 11/27/2008] [Indexed: 11/25/2022]
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Toropov AA, Rasulev BF, Leszczynski J. QSAR modeling of acute toxicity by balance of correlations. Bioorg Med Chem 2008; 16:5999-6008. [DOI: 10.1016/j.bmc.2008.04.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2007] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
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Toropov AA, Rasulev BF, Leszczynska D, Leszczynski J. Additive SMILES based optimal descriptors: QSPR modeling of fullerene C60 solubility in organic solvents. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.07.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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QSPR study on solubility of fullerene C60 in organic solvents using optimal descriptors calculated with SMILES. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.04.094] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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