Malays. J. Anal. Sci. Volume 30 Number 4 (2026): 1779

 

Research Article

 

Modelling metal-organic framework pesticides delivery system using computer simulations

 

Mohd Hairudin Haryadi1, Nur Hana Faujan1,3 and Muhammad Alif Mohammad Latif1,2,3*

 

1Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia

2Nanomaterials Synthesis and Characterization Laboratory, Institute of Nanoscience and Nanotechnology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia

3Centre for Foundation Studies in Science of Universiti Putra Malaysia, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia

 

*Corresponding author: aliflatif@upm.edu.my

 

Received: 12 November 2025; Revised: 26 May 2026; Accepted: 24 June 2026; Published: 30 August 2026

 

Abstract

The pesticide delivery system is a promising technique that can improve efficiency, reduce environmental impact, and enable controlled release of pesticides. Cyclodextrin Metal-Organic Framework (CD-MOF-1) is a suitable candidate for enhancing pesticide encapsulation and release due to its biocompatibility and porous structure. This study employed computer simulations to analyse the encapsulation and adsorption behaviour of four pesticides: Avermectin (AVM), Dazomet (DAZ), Mancozeb (MAN), and Hexaconazole (HEX). A combination of Density Functional Theory (DFT), Molecular Dynamics (MD), and Grand Canonical Monte Carlo (GCMC) simulations was used to assess their electronic properties, structural stability, diffusion, and adsorption behaviour. Simulation results showed that MAN exhibited the most favourable dynamic delivery system properties, with the smallest HOMO-LUMO gap of 4.37 eV, the highest adsorption capacity, and the highest diffusion coefficient of 3.88 × 10-8 cm2/s. In contrast, DAZ showed the lowest root-mean-square deviation (RMSD) of 0.07 nm, indicating excellent structural stability. HEX showed intermediate delivery behaviour with a diffusion coefficient of 1.92 × 10-8 cm2/s. AVM showed the highest binding energy of 422.4 kJ/mol and the lowest diffusion coefficient of 2.99 × 10-10 cm2/s, making it more suitable for prolonged storage. These findings demonstrate the versatility of CD-MOF-1 as a pesticide delivery system and highlight its potential for sustainable agricultural applications.

 

Keywords: Adsorption, cyclodextrin-MOF, encapsulation, pesticide delivery, computer simulation

 


References

1.        Holleman, C. (2024). The State of Food Security and Nutrition in the World 2024 – Financing to end hunger, food insecurity and malnutrition in all its forms. FAO; IFAD; UNICEF; WFP; WHO.

2.        Navarro, D., & Gennari, P. (2023). Tracking progress on food and agriculture-related SDG indicators 2023. FAO.

3.        Mall, D., Larsen, A., & Martin, E. (2018). Investigating the (mis)match between natural pest control knowledge and the intensity of pesticide use. Insects, 9(1), 2.

4.        Camara, M. C., Campos, E. V. R., Monteiro, R. A., Do Espirito Santo Pereira, A., De Freitas Proença, P. L., & Fraceto, L. F. (2019). Development of stimuli-responsive nano-based pesticides: emerging opportunities for agriculture. Journal of Nanobiotechnology, 17(1), 100.

5.        Neri-Badang, M. C., & Chakraborty, S. (2019). Carbohydrate polymers as controlled release devices for pesticides. Journal of Carbohydrate Chemistry, 38(1), 67–85.

6.        Du, L., Liao, S., Khatib, H. A., Stoddart, J. F., & Zink, J. I. (2009). Controlled-access hollow mechanized silica nanocontainers. Journal of the American Chemical Society, 131(42), 15136–15142.

7.        Flaherty, R. J., Nshime, B., DeLaMarre, M., DeJong, S., Scott, P., & Lantz, A. W. (2013). Cyclodextrins as complexation and extraction agents for pesticides from contaminated soil. Chemosphere, 91(7), 912–920.

8.        Kaziem, Amir. E., Gao, Y., Zhang, Y., Qin, X., Xiao, Y., Zhang, Y., You, H., Li, J., & He, S. (2018). α-Amylase triggered carriers based on cyclodextrin anchored hollow mesoporous silica for enhancing insecticidal activity of avermectin against Plutella xylostella. Journal of Hazardous Materials, 359, 213–221.

9.        Zhang, X., Liu, J., Hou, W., Tong, J., Ren, L., Sun, G., & Sun, Y. (2016). Preparation and properties of pesticide/cyclodextrin complex intercalated into ZnAl-layered double hydroxide. Industrial & Engineering Chemistry Research, 55(6), 1550–1558.

10.     Smaldone, R. A., Forgan, R. S., Furukawa, H., Gassensmith, J. J., Slawin, A. M. Z., Yaghi, O. M., & Stoddart, J. F. (2010). Metal–organic frameworks from edible natural products. Angewandte Chemie International Edition, 49(46), 8630–8634.

11.     Zhou, W., Wu, H., Hartman, M. R., & Yildirim, T. (2007). Hydrogen and methane adsorption in metal−organic frameworks: A high-pressure volumetric study. The Journal of Physical Chemistry C, 111(44), 16131–16137.

12.     Liang, K., Ricco, R., Doherty, C. M., Styles, M. J., Bell, S., Kirby, N., Mudie, S., Haylock, D., Hill, A. J., Doonan, C. J., & Falcaro, P. (2015). Biomimetic mineralization of metal-organic frameworks as protective coatings for biomacromolecules. Nature Communications, 6(1), 7240.

13.     Tuan Kob@Yaakub, T. N. A., Abdul Rahman, M. B., Felipe, G., & Mohammad Latif, M. A. (2024). Synthesis and modelling of functionalized UiO-66 metal-organic frameworks for gas adsorption. Malaysian Journal of Analytical Sciences, 28(3), 489–499.

14.     Rajkumar, T., Kukkar, D., Kim, K.-H., Sohn, J. R., & Deep, A. (2019). Cyclodextrin-metal–organic framework (CD-MOF): From synthesis to applications. Journal of Industrial and Engineering Chemistry, 72, 50–66.

15.     Huang, Z., & Lee, H. K. (2015). Micro-solid-phase extraction of organochlorine pesticides using porous metal-organic framework MIL-101 as sorbent. Journal of Chromatography A, 1401, 9–16.

16.     Vikrant, K., Tsang, D. C. W., Raza, N., Giri, B. S., Kukkar, D., & Kim, K.-H. (2018). Potential utility of metal–organic framework-based platform for sensing pesticides. ACS Applied Materials & Interfaces, 10(10), 8797–8817.

17.     Yang, Q., Wang, J., Zhang, W., Liu, F., Yue, X., Liu, Y., Yang, M., Li, Z., & Wang, J. (2017). Interface engineering of metal organic framework on graphene oxide with enhanced adsorption capacity for organophosphorus pesticide. Chemical Engineering Journal, 313, 19–26.

18.     Liu, C., Wang, P., Liu, X., Yi, X., Zhou, Z., & Liu, D. (2019). Multifunctional β-cyclodextrin MOF-derived porous carbon as efficient herbicides adsorbent and potassium fertilizer. ACS Sustainable Chemistry & Engineering, 7(17), 14479–14489.

19.     Liu, G., Li, L., Xu, D., Huang, X., Xu, X., Zheng, S., Zhang, Y., & Lin, H. (2017). Metal–organic framework preparation using magnetic graphene oxide–β-cyclodextrin for neonicotinoid pesticide adsorption and removal. Carbohydrate Polymers, 175, 584–591.

20.     Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2023). PubChem 2023 update. Nucleic Acids Research, 51(D1), D1373–D1380.

21.     Groom, C. R., Bruno, I. J., Lightfoot, M. P., & Ward, S. C. (2016). The Cambridge Structural Database. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 72(2), 171–179.

22.     Makkar, P., & Ghosh, N. N. (2021). A review on the use of DFT for the prediction of the properties of nanomaterials. RSC Advances, 11(45), 27897–27924.

23.     Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A. V., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ortiz, J. V., Izmaylov, A. F., Sonnenberg, J. L., Williams-Young, D., Ding, F., Lipparini, F., Egidi, F., Goings, J., Peng, B., Petrone, A., Henderson, T., Ranasinghe, D., Zakrzewski, V. G., Gao, J., Rega, N., Zheng, G., Liang, W., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Throssell, K., Montgomery, J. A., Jr., Peralta, J. E., Ogliaro, F., Bearpark, M. J., Heyd, J. J., Brothers, E. N., Kudin, K. N., Staroverov, V. N., Keith, T. A., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A. P., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Millam, J. M., Klene, M., Adamo, C., Cammi, R., Ochterski, J. W., Martin, R. L., Morokuma, K., Farkas, O., Foresman, J. B., & Fox, D. J. (2016). Gaussian˜16 Revision C.01.

24.     Breneman, C. M., & Wiberg, K. B. (1990). Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. Journal of Computational Chemistry, 11(3), 361–373.

25.     Martínez, L., Andrade, R., Birgin, E. G., & Martínez, J. M. (2009). PACKMOL : A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13), 2157–2164.

26.     Lindahl, Abraham, Hess, & Spoel, V. D. (2021). GROMACS 2021.1 Source code (Version 2021.1) [Computer software]. Zenodo.

27.     Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., & Skiff, W. M. (1992). UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. Journal of the American Chemical Society, 114(25), 10024–10035.

28.     Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960.

29.     Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation, 4(1), 116–122.

30.     Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593.

31.     Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101.

32.     Rühle, V. (2008). Pressure coupling/barostats. Journal Club, 2008, 1–5.

33.     Allen, M. P., & Tildesley, D. J. (2017). Computer Simulation of Liquids (2nd edition). Oxford University Press.

34.     Frenkel, D., & Smit, B. (2002). Understanding molecular simulation: From algorithms to applications. Elsevier Science.

35.     Dubbeldam, D., Calero, S., Ellis, D. E., & Snurr, R. Q. (2016). RASPA: Molecular simulation software for adsorption and diffusion in flexible nanoporous materials. Molecular Simulation, 42(2), 81–101.

36.     Walton, K. S., & Snurr, R. Q. (2017). Applicability of the BET method for determining surface areas of microporous metal-organic frameworks. Journal of the American Chemical Society, 129(27), 8552–8556.

37.     Hartlieb, K. J., Ferris, D. P., Holcroft, J. M., Kandela, I., Stern, C. L., Nassar, M. S., Botros, Y. Y., & Stoddart, J. F. (2017). Encapsulation of ibuprofen in CD-MOF and related bioavailability studies. Molecular Pharmaceutics, 14(5), 1831–1839.

38.     Rosen, A. S., Fung, V., Huck, P., O’Donnell, C. T., Horton, M. K., Truhlar, D. G., Persson, K. A., Notestein, J. M., & Snurr, R. Q. (2022). High-throughput predictions of metal–organic framework electronic properties: Theoretical challenges, graph neural networks, and data exploration. NPJ Computational Materials, 8(1), 1–10.

39.     Mancuso, J. L., Mroz, A. M., Le, K. N., & Hendon, C. H. (2020). Electronic structure modeling of metal–organic frameworks. Chemical Reviews, 120(16), 8641–8715.

40.     Huang, Y., Rong, C., Zhang, R., & Liu, S. (2017). Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory. Journal of Molecular Modeling, 23, 3715.

41.     Poddar, A., Conesa, J. J., Liang, K., Dhakal, S., Reineck, P., Bryant, G., Pereiro, E., Ricco, R., Amenitsch, H., Doonan, C., Mulet, X., Doherty, C. M., Falcaro, P., & Shukla, R. (2019). Encapsulation, visualization and expression of genes with biomimetically mineralized zeolitic imidazolate framework-8 (ZIF-8). Small (Weinheim an Der Bergstrasse, Germany), 15(36), e1902268.

42.     Zybaylo, O., Shekhah, O., Wang, H., Tafipolsky, M., Schmid, R., Johannsmann, D., & Wöll, C. (2010). A novel method to measure diffusion coefficients in porous metal–organic frameworks. Physical Chemistry Chemical Physics, 12(28), 8093–8098.

43.     Li, Z., Sun, Y., Pan, X., Gao, T., He, T., Chen, C., Zhang, B., Fu, X., & Huang, Q. (2022). Controlled release of thymol by cyclodextrin metal-organic frameworks for preservation of cherry tomatoes. Foods, 11(23), 3818.

44.     Sun, Q., Sheng, J., & Yang, R. (2021). Encapsulation of curcumin in CD-MOFs: promoting its incorporation into water-based products and consumption. Food & Function, 12(21), 10795–10805.

45.     Zhang, T., Svensson, P. H. W., Brumboiu, I. E., Lanzilotto, V., Grazioli, C., Guarnaccio, A., Johansson, F. O. L., Beranová, K., Coreno, M., de Simone, M., Floreano, L., Cossaro, A., Brena, B., & Puglia, C. (2022). Clarifying the adsorption of triphenylamine on Au(111): Filling the HOMO–LUMO gap. The Journal of Physical Chemistry C, 126(3), 1635–1643.