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QSAR Studies on Nitrobenzene Derivatives using Hyperpolarizability and Conductor like Screening model as Molecular Descriptors

Yıl 2022, Cilt: 9 Sayı: 3, 953 - 968, 31.08.2022
https://doi.org/10.18596/jotcsa.1083840

Öz

Quantitative structure-activity relationship (QSAR) models were useful in understanding how chemical structure relates to the toxicology of chemicals. In the present study, we report quantum molecular descriptors using conductor like screening model (COs) area, the linear polarizability, first and second order hyperpolarizability for modelling the toxicology of the nitro substituent on the benzene ring. All the molecular descriptors were performed using semi-empirical PM6 approaches. The QSAR model was developed using stepwise multiple linear regression. We found that the stable QSAR modelling of toxicology benzene derivatives used second order hyper-polarizability and COs area, which satisfied the statistical measures. The second order hyperpolarizability shows the best QSAR model. We also discovered that the nitrobenzene derivative’s substitutional functional group has a significant effect on the quantum molecular descriptors, which reflect the QSAR model.

Teşekkür

The authors would like to thank Dr James J. P. Stewart from MOPAC Inc. for his permission to use the MOPAC software, and UiTM’s Department of Infostructure for the MiniTab software usage permission. Additionally, the authors wish to express gratitude to Universiti Teknologi MARA for financial assistance.

Kaynakça

  • 1. Ayub R, Raheel A. High-Value Chemicals from Electrocatalytic Depolymerization of Lignin: Challenges and Opportunities. IJMS. 2022 Mar 29;23(7):3767.
  • 2. Hagiopol C. Chapter 3: The tree fractionation: the extraction of natural polyphenols. CHENG K, Hagiopol C, editors. S.l.: ELSEVIER; 2021. 33–84 p. ISBN: 978-0-12-822205-8.
  • 3. Manickam P, Vijay D. Chapter 2 - Chemical hazards in textiles. In: Muthu S, editor. Chemical Management in Textiles and Fashion. Woodhead Publishing; 2021. p. 19–52.
  • 4. Oladele JO, Oyeleke OM, Akindolie BO, Olowookere BD, Oladele OT. Vernonia amygdalina Leaf Extract Abates Oxidative Hepatic Damage and Inflammation Associated with Nitrobenzene in Rats. Jordan Journal of Biological Sciences. 2021;14(3):463–9.
  • 5. Siqueira Soldaini Oliveira R, Borges I. Correlation Between Molecular Charge Properties and Impact Sensitivity of Explosives: Nitrobenzene Derivatives. Prop, Explos, Pyrotech. 2021 Feb;46(2):309–21.
  • 6. Xavier JA, Silva TL, Torres-Santos EC, de Vasconcelos CC, Boane A, dos Santos RA, et al. Unveiling the relevance of the redox character of nitroaromatic and nitroheteroaromatic compounds as potential medicines. Current Opinion in Electrochemistry. 2021 Oct;29:100740.
  • 7. Adhikari C, Mishra B kumar. Quantitative Structure-Activity Relationships of Aquatic Narcosis: A Review. CAD. 2018 Mar 21;14(1):7–28.
  • 8. Kadam VV, Balakrishnan RM, Ponnan Ettiyappan J, Thomas NS, D Souza SA, Parappan S. Sensing of p-nitrophenol in aqueous solution using zinc oxide quantum dots coated with APTES. Environmental Nanotechnology, Monitoring & Management. 2021 Dec;16:100474.
  • 9. Nepali K, Lee HY, Liou JP. Nitro-Group-Containing Drugs. J Med Chem. 2019 Mar 28;62(6):2851–93.
  • 10. Ji Z, Ji Y, Ding R, Lin L, Li B, Zhang X. DNA-templated silver nanoclusters as an efficient catalyst for reduction of nitrobenzene derivatives: a systematic study. Nanotechnology. 2021 Feb 19;32(19):195705.
  • 11. Rajak SK, others. QSAR study in terms of conceptual density functional theory based descriptors in predicting toxicity of nitrobenzenes towards Tetrahymena pyriformis. Indian Journal of Chemical Technology (IJCT). 2022;28(4):467–72.
  • 12. Bilal M, Bagheri AR, Bhatt P, Chen S. Environmental occurrence, toxicity concerns, and remediation of recalcitrant nitroaromatic compounds. Journal of Environmental Management. 2021 Aug;291:112685.
  • 13. Shaker B, Ahmad S, Lee J, Jung C, Na D. In silico methods and tools for drug discovery. Computers in Biology and Medicine. 2021 Oct;137:104851.
  • 14. Wang L, Ding J, Pan L, Cao D, Jiang H, Ding X. Quantum chemical descriptors in quantitative structure–activity relationship models and their applications. Chemometrics and Intelligent Laboratory Systems. 2021 Oct;217:104384.
  • 15. Dahmani R, Manachou M, Belaidi S, Chtita S, Boughdiri S. Structural characterization and QSAR modeling of 1,2,4-triazole derivatives as α-glucosidase inhibitors. New J Chem. 2021;45(3):1253–61.
  • 16. Alias AN, Zabidi ZM, Zakaria NA, Mahmud ZS, Ali R. Biological Activity Relationship of Cyclic and Noncyclic Alkanes Using Quantum Molecular Descriptors. OJAppS. 2021;11(08):966–84.
  • 17. Karelson M, Lobanov VS, Katritzky AR. Quantum-Chemical Descriptors in QSAR/QSPR Studies. Chem Rev. 1996 Jan 1;96(3):1027–44.
  • 18. Wady A, Khalid M, Alotaibi M, Ahmed Y. Synthesis, characterization, DFT calculations, and catalytic epoxidation of two oxovanadium(IV) Schiff base complexes. Journal of the Turkish Chemical Society Section A: Chemistry. 2022 Jan 17;9(1):163–208.
  • 19. Yunusa U, Umar U, Idriss S, Ibrahim A, Abdullahi T. Experimental and DFT Computational Insights on the Adsorption of Selected Pharmaceuticals of Emerging Concern from Water Systems onto Magnetically Modified Biochar. Journal of the Turkish Chemical Society Section A: Chemistry. 2021 Nov 11;8(4):1179–96.
  • 20. Gieseking RLM. A new release of MOPAC incorporating the INDO /S semiempirical model with CI excited states. J Comput Chem. 2021 Feb 15;42(5):365–78.
  • 21. Wang S, Zhang X, Gui B, Xu X, Su L, Zhao YH, et al. Comparison of modes of action between fish, cell and mitochondrial toxicity based on toxicity correlation, excess toxicity and QSAR for class-based compounds. Toxicology. 2022 Mar;470:153155.
  • 22. Andini S, Araya-Cloutier C, Lay B, Vreeke G, Hageman J, Vincken JP. QSAR-based physicochemical properties of isothiocyanate antimicrobials against gram-negative and gram-positive bacteria. LWT. 2021 Jun;144:111222.
  • 23. Kurtz HA, Stewart JJP, Dieter KM. Calculation of the nonlinear optical properties of molecules. J Comput Chem. 1990 Jan;11(1):82–7.
  • 24. Klamt A. The COSMO and COSMO‐RS solvation models. WIREs Comput Mol Sci. 2011 Sep;1(5):699–709.
  • 25. Hostaš J, Řezáč J, Hobza P. On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions. Chemical Physics Letters. 2013 May;568–569:161–6.
  • 26. Stewart J. MOPAC2016. Colorado Springs, CO; 2016.
  • 27. Fatemi MH, Malekzadeh H. Prediction of Log(IGC 50 ) −1 for Benzene Derivatives to Ciliate Tetrahymena pyriformis from Their Molecular Descriptors. BCSJ. 2010 Mar 15;83(3):233–45.
  • 28. Osaghi B, Safa F. QSPR study on the boiling points of aliphatic esters using the atom-type-based AI topological indices. Rev Roum Chim. 2019;64(2):183–9.
  • 29. Mustapha A, Shallangwa G, Ibrahim MT, Bello AU, Ebuka DA, Uzairu A, et al. QSAR studies on some C14-urea tetrandrine compounds as potent anti-cancer against Leukemia cell line (K562). Journal of the Turkish Chemical Society, Section A: Chemistry. 2018 Dec 25;5(3):1391–402.
  • 30. Majumdar S, Basak SC. Editorial: Beware of Naïve q2, use True q2: Some Comments on QSAR Model Building and Cross Validation. CAD. 2018 Mar 21;14(1):5–6.
  • 31. Rakhimbekova A, Akhmetshin TN, Minibaeva GI, Nugmanov RI, Gimadiev TR, Madzhidov TI, et al. Cross-validation strategies in QSPR modelling of chemical reactions. SAR and QSAR in Environmental Research. 2021 Mar 4;32(3):207–19.
  • 32. Toma C, Manganaro A, Raitano G, Marzo M, Gadaleta D, Baderna D, et al. QSAR Models for Human Carcinogenicity: An Assessment Based on Oral and Inhalation Slope Factors. Molecules. 2020 Dec 29;26(1):127.
  • 33. Baumann D, Baumann K. Reliable estimation of prediction errors for QSAR models under model uncertainty using double cross-validation. J Cheminform. 2014 Dec;6(1):47.
  • 34. Veerasamy R, Rajak H, Jain A, Sivadasan S, Varghese CP, Agrawal RK. Validation of QSAR models-strategies and importance. Int J Drug Des Discov. 2011;3:511–9.
  • 35. Goel H, Yu W, Ustach VD, Aytenfisu AH, Sun D, MacKerell AD. Impact of electronic polarizability on protein-functional group interactions. Phys Chem Chem Phys. 2020;22(13):6848–60.
  • 36. Tandon H, Ranjan P, Chakraborty T, Suhag V. Polarizability: a promising descriptor to study chemical–biological interactions. Mol Divers. 2021 Feb;25(1):249–62.
  • 37. Zhu T, Chen W, Singh RP, Cui Y. Versatile in silico modeling of partition coefficients of organic compounds in polydimethylsiloxane using linear and nonlinear methods. Journal of Hazardous Materials. 2020 Nov;399:123012.
  • 38. Zyss J. Hyperpolarizabilities of substituted conjugated molecules. II. Substituent effects and respective σ–π contributions. The Journal of Chemical Physics. 1979 Apr;70(7):3341–9. .
Yıl 2022, Cilt: 9 Sayı: 3, 953 - 968, 31.08.2022
https://doi.org/10.18596/jotcsa.1083840

Öz

Kaynakça

  • 1. Ayub R, Raheel A. High-Value Chemicals from Electrocatalytic Depolymerization of Lignin: Challenges and Opportunities. IJMS. 2022 Mar 29;23(7):3767.
  • 2. Hagiopol C. Chapter 3: The tree fractionation: the extraction of natural polyphenols. CHENG K, Hagiopol C, editors. S.l.: ELSEVIER; 2021. 33–84 p. ISBN: 978-0-12-822205-8.
  • 3. Manickam P, Vijay D. Chapter 2 - Chemical hazards in textiles. In: Muthu S, editor. Chemical Management in Textiles and Fashion. Woodhead Publishing; 2021. p. 19–52.
  • 4. Oladele JO, Oyeleke OM, Akindolie BO, Olowookere BD, Oladele OT. Vernonia amygdalina Leaf Extract Abates Oxidative Hepatic Damage and Inflammation Associated with Nitrobenzene in Rats. Jordan Journal of Biological Sciences. 2021;14(3):463–9.
  • 5. Siqueira Soldaini Oliveira R, Borges I. Correlation Between Molecular Charge Properties and Impact Sensitivity of Explosives: Nitrobenzene Derivatives. Prop, Explos, Pyrotech. 2021 Feb;46(2):309–21.
  • 6. Xavier JA, Silva TL, Torres-Santos EC, de Vasconcelos CC, Boane A, dos Santos RA, et al. Unveiling the relevance of the redox character of nitroaromatic and nitroheteroaromatic compounds as potential medicines. Current Opinion in Electrochemistry. 2021 Oct;29:100740.
  • 7. Adhikari C, Mishra B kumar. Quantitative Structure-Activity Relationships of Aquatic Narcosis: A Review. CAD. 2018 Mar 21;14(1):7–28.
  • 8. Kadam VV, Balakrishnan RM, Ponnan Ettiyappan J, Thomas NS, D Souza SA, Parappan S. Sensing of p-nitrophenol in aqueous solution using zinc oxide quantum dots coated with APTES. Environmental Nanotechnology, Monitoring & Management. 2021 Dec;16:100474.
  • 9. Nepali K, Lee HY, Liou JP. Nitro-Group-Containing Drugs. J Med Chem. 2019 Mar 28;62(6):2851–93.
  • 10. Ji Z, Ji Y, Ding R, Lin L, Li B, Zhang X. DNA-templated silver nanoclusters as an efficient catalyst for reduction of nitrobenzene derivatives: a systematic study. Nanotechnology. 2021 Feb 19;32(19):195705.
  • 11. Rajak SK, others. QSAR study in terms of conceptual density functional theory based descriptors in predicting toxicity of nitrobenzenes towards Tetrahymena pyriformis. Indian Journal of Chemical Technology (IJCT). 2022;28(4):467–72.
  • 12. Bilal M, Bagheri AR, Bhatt P, Chen S. Environmental occurrence, toxicity concerns, and remediation of recalcitrant nitroaromatic compounds. Journal of Environmental Management. 2021 Aug;291:112685.
  • 13. Shaker B, Ahmad S, Lee J, Jung C, Na D. In silico methods and tools for drug discovery. Computers in Biology and Medicine. 2021 Oct;137:104851.
  • 14. Wang L, Ding J, Pan L, Cao D, Jiang H, Ding X. Quantum chemical descriptors in quantitative structure–activity relationship models and their applications. Chemometrics and Intelligent Laboratory Systems. 2021 Oct;217:104384.
  • 15. Dahmani R, Manachou M, Belaidi S, Chtita S, Boughdiri S. Structural characterization and QSAR modeling of 1,2,4-triazole derivatives as α-glucosidase inhibitors. New J Chem. 2021;45(3):1253–61.
  • 16. Alias AN, Zabidi ZM, Zakaria NA, Mahmud ZS, Ali R. Biological Activity Relationship of Cyclic and Noncyclic Alkanes Using Quantum Molecular Descriptors. OJAppS. 2021;11(08):966–84.
  • 17. Karelson M, Lobanov VS, Katritzky AR. Quantum-Chemical Descriptors in QSAR/QSPR Studies. Chem Rev. 1996 Jan 1;96(3):1027–44.
  • 18. Wady A, Khalid M, Alotaibi M, Ahmed Y. Synthesis, characterization, DFT calculations, and catalytic epoxidation of two oxovanadium(IV) Schiff base complexes. Journal of the Turkish Chemical Society Section A: Chemistry. 2022 Jan 17;9(1):163–208.
  • 19. Yunusa U, Umar U, Idriss S, Ibrahim A, Abdullahi T. Experimental and DFT Computational Insights on the Adsorption of Selected Pharmaceuticals of Emerging Concern from Water Systems onto Magnetically Modified Biochar. Journal of the Turkish Chemical Society Section A: Chemistry. 2021 Nov 11;8(4):1179–96.
  • 20. Gieseking RLM. A new release of MOPAC incorporating the INDO /S semiempirical model with CI excited states. J Comput Chem. 2021 Feb 15;42(5):365–78.
  • 21. Wang S, Zhang X, Gui B, Xu X, Su L, Zhao YH, et al. Comparison of modes of action between fish, cell and mitochondrial toxicity based on toxicity correlation, excess toxicity and QSAR for class-based compounds. Toxicology. 2022 Mar;470:153155.
  • 22. Andini S, Araya-Cloutier C, Lay B, Vreeke G, Hageman J, Vincken JP. QSAR-based physicochemical properties of isothiocyanate antimicrobials against gram-negative and gram-positive bacteria. LWT. 2021 Jun;144:111222.
  • 23. Kurtz HA, Stewart JJP, Dieter KM. Calculation of the nonlinear optical properties of molecules. J Comput Chem. 1990 Jan;11(1):82–7.
  • 24. Klamt A. The COSMO and COSMO‐RS solvation models. WIREs Comput Mol Sci. 2011 Sep;1(5):699–709.
  • 25. Hostaš J, Řezáč J, Hobza P. On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions. Chemical Physics Letters. 2013 May;568–569:161–6.
  • 26. Stewart J. MOPAC2016. Colorado Springs, CO; 2016.
  • 27. Fatemi MH, Malekzadeh H. Prediction of Log(IGC 50 ) −1 for Benzene Derivatives to Ciliate Tetrahymena pyriformis from Their Molecular Descriptors. BCSJ. 2010 Mar 15;83(3):233–45.
  • 28. Osaghi B, Safa F. QSPR study on the boiling points of aliphatic esters using the atom-type-based AI topological indices. Rev Roum Chim. 2019;64(2):183–9.
  • 29. Mustapha A, Shallangwa G, Ibrahim MT, Bello AU, Ebuka DA, Uzairu A, et al. QSAR studies on some C14-urea tetrandrine compounds as potent anti-cancer against Leukemia cell line (K562). Journal of the Turkish Chemical Society, Section A: Chemistry. 2018 Dec 25;5(3):1391–402.
  • 30. Majumdar S, Basak SC. Editorial: Beware of Naïve q2, use True q2: Some Comments on QSAR Model Building and Cross Validation. CAD. 2018 Mar 21;14(1):5–6.
  • 31. Rakhimbekova A, Akhmetshin TN, Minibaeva GI, Nugmanov RI, Gimadiev TR, Madzhidov TI, et al. Cross-validation strategies in QSPR modelling of chemical reactions. SAR and QSAR in Environmental Research. 2021 Mar 4;32(3):207–19.
  • 32. Toma C, Manganaro A, Raitano G, Marzo M, Gadaleta D, Baderna D, et al. QSAR Models for Human Carcinogenicity: An Assessment Based on Oral and Inhalation Slope Factors. Molecules. 2020 Dec 29;26(1):127.
  • 33. Baumann D, Baumann K. Reliable estimation of prediction errors for QSAR models under model uncertainty using double cross-validation. J Cheminform. 2014 Dec;6(1):47.
  • 34. Veerasamy R, Rajak H, Jain A, Sivadasan S, Varghese CP, Agrawal RK. Validation of QSAR models-strategies and importance. Int J Drug Des Discov. 2011;3:511–9.
  • 35. Goel H, Yu W, Ustach VD, Aytenfisu AH, Sun D, MacKerell AD. Impact of electronic polarizability on protein-functional group interactions. Phys Chem Chem Phys. 2020;22(13):6848–60.
  • 36. Tandon H, Ranjan P, Chakraborty T, Suhag V. Polarizability: a promising descriptor to study chemical–biological interactions. Mol Divers. 2021 Feb;25(1):249–62.
  • 37. Zhu T, Chen W, Singh RP, Cui Y. Versatile in silico modeling of partition coefficients of organic compounds in polydimethylsiloxane using linear and nonlinear methods. Journal of Hazardous Materials. 2020 Nov;399:123012.
  • 38. Zyss J. Hyperpolarizabilities of substituted conjugated molecules. II. Substituent effects and respective σ–π contributions. The Journal of Chemical Physics. 1979 Apr;70(7):3341–9. .
Toplam 38 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Fiziksel Kimya
Bölüm Makaleler
Yazarlar

Ahmad Nazib Alias 0000-0001-9263-8092

Zubainun Mohamed Zabidi Bu kişi benim 0000-0001-5927-7037

Yayımlanma Tarihi 31 Ağustos 2022
Gönderilme Tarihi 7 Mart 2022
Kabul Tarihi 12 Haziran 2022
Yayımlandığı Sayı Yıl 2022 Cilt: 9 Sayı: 3

Kaynak Göster

Vancouver Nazib Alias A, Mohamed Zabidi Z. QSAR Studies on Nitrobenzene Derivatives using Hyperpolarizability and Conductor like Screening model as Molecular Descriptors. JOTCSA. 2022;9(3):953-68.