In-depth Hirschfeld Surface Analysis, Interaction Energy, Molecular Docking, and DFT Investigations of Electronic Properties of 2,4-dimethyl-1-nitrobenzene

Year 2024, Volume: 11 Issue: 2, 491 - 508

Youcef Megrouss Yahıaouı Salem Boukabcha Nourdine Mansour Azayez Sid Ahmed Kaas Abdelkader Chouaıh Mokhtaria Drıssı

https://doi.org/10.18596/jotcsa.1259444

Abstract

Quantum-chemical calculations, molecular docking, and Hirshfeld surface analysis of a structure of 2,4-dimethyl-1-nitrobenzene constitute the main aspects of this work. The crystal structure of the title compound which is liquid at room temperature, was obtained by in situ cryo crystallization The crystal packing is stabilized by C5–H5…O2 and C7–H7C…N1 intermolecular hydrogen bonds. The analysis of the obtained results of the density functional theory calculations is in good agreement with the experimental data. The analysis of global chemical reactivity descriptors shows that the compound exhibits more stability and less reactivity at high polar media. Hirshfeld surface and 2D-fingerprint plots analysis shows that the H…H, O…H/H…O, C…C, and C…H/H…C contacts are the significant contributors stabilizing the crystal structure of 2,4-dimethyl-1-nitrobenzene. The RDG-NCI analysis of the molecule was performed to determine the non-covalent interactions present within the molecule. In addition, the compound under investigation presents a biological activity when it is docked into the protein (PDB ID: 4Y0S) with the binding energy system of -6.6 kcal/mol.

Keywords

molecular docking, Hirschfeld surface analysis, DFT, RDG, interaction energy, ELF, LOL analysis

References

• 1. Minasyan YV, Degtyarenko AI, Кosmacheva KD, Plekhovich SD, Zelentsov SV. Effect of Acceptor and Donor Substituents in The ortho, meta, and para Positions in the Nitrobenzene Molecule on the Reaction of Interaction with Ethylene. Multidisciplinary Digital Publishing Institute Proceedings. 2018;9(1):50. Available from: <URL>
• 2. Program NT. Report on carcinogens, 2011. National Toxicology Program, US Department of Health and Human Services, Washington, DC. 2011.
• 3. Services UDoHaH. Hazardous substances data bank (HSDB, online database). National Toxicology Information Program, National Library of Medicine, Bethesda, MD. 1993. Available from: <URL>
• 4. Atsdr U. Agency for toxic substances and disease registry. Case Studies in environmental medicine http://www atsdr cdc gov/HEC/CSEM/csem html. 1997.
• 5. Arora PK, Sasikala C, Ramana CV. Degradation of chlorinated nitroaromatic compounds. Applied microbiology and biotechnology. 2012;93:2265-77. Available from: <URL>
• 6. Tas DO, Pavlostathis SG. Occurrence, toxicity, and biotransformation of pentachloronitrobenzene and chloroanilines. Critical Reviews in Environmental Science and Technology. 2014;44(5):473-518. Available from: <URL>
• 7. Zhang J, Mitchell LA, Parrish DA, Shreeve JnM. Enforced layer-by-layer stacking of energetic salts towards high-performance insensitive energetic materials. Journal of the American Chemical Society. 2015;137(33):10532-5. Available from: <URL>
• 8. Cardenuto MH, Champagne B. The first hyperpolarizability of nitrobenzene in benzene solutions: investigation of the effects of electron correlation within the sequential QM/MM approach. Physical Chemistry Chemical Physics. 2015;17(36):23634-42. Available from: <URL>
• 9. Soto J, Algarra M. Electronic structure of nitrobenzene: A benchmark example of the accuracy of the multi-state CASPT2 theory. The Journal of Physical Chemistry A. 2021;125(43):9431-7. Available from: <URL>
• 10. Millán R, Soriano MD, Cerdá Moreno C, Boronat M, Concepción P. Combined spectroscopic and computational study of nitrobenzene activation on non-noble metals-based mono-and bimetallic catalysts. Nanomaterials. 2021;11(8):2037. Available from: <URL>
• 11. Boubegra N, Megrouss Y, Boukabcha N, Chouaih A, Hamzaoui F. The electrostatic properties of 1, 2-dimethyl-3-nitrobenzene compound: ab initio calculation and X-ray charge density analysis. Rasayan Journal of Chemistry. 2016;9(4). Available from: <URL>
• 12. Kumar MS, Vibhanjali M, Tripathi P, Adil KM. Quantum Chemical Descriptors Based QSTR Study of Nitrobenzene Derivatives against Tetrahymena Pyriformis. Research Journal of Chemical Sciences. ISSN.2231:606X. Available from: <URL>
• 13. Krishnakumar S, Das AK, Singh PJ, Shastri A, Rajasekhar B. Experimental and computational studies on the electronic excited states of nitrobenzene. Journal of Quantitative Spectroscopy and Radiative Transfer. 2016;184:89-99. Available from: <URL>
• 14. Seshadri S, Padmavathy M. Structure, characterization and DFT studies of 1, 2-Dichloro-4-fluoro-5-Nitrobenzene. 2018. Available from: <URL>
• 15. Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical review B. 1988;37(2):785. Available from: <URL>
• 16. Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Physical review A. 1988;38(6):3098. Available from: <URL>
• 17. Caricato M, Frisch MJ, Hiscocks J. Gaussian 09: IOps Reference: Gaussian Wallingford, CT, USA; 2009. Available from: <URL>
• 18. Turner M, McKinnon J, Wolff S, Grimwood D, Spackman P, Jayatilaka D, et al. CrystalExplorer (Version 17.5). University of Western Australia. 2017.
• 19. Lu T, Chen F. Multiwfn: A multifunctional wavefunction analyzer. Journal of computational chemistry. 2012;33(5):580-92. Available from: <URL>
• 20. Kanmazalp SD, Macit M, Dege N. Hirshfeld surface, crystal structure and spectroscopic characterization of (E)-4-(diethylamino)-2-((4-phenoxyphenylimino) methyl) phenol with DFT studies. Journal of Molecular Structure. 2019;1179:181-91. Available from: <URL>
• 21. Kansız S, Dege N. Synthesis, crystallographic structure, DFT calculations and Hirshfeld surface analysis of a fumarate bridged Co (II) coordination polymer. Journal of Molecular Structure. 2018;1173:42-51. Available from: <URL>
• 22. Turner MJ, Grabowsky S, Jayatilaka D, Spackman MA. Accurate and efficient model energies for exploring intermolecular interactions in molecular crystals. The journal of physical chemistry letters. 2014;5(24):4249-55. Available from: <URL>
• 23. Bader R. A quantum theory. Clarendon: Oxford, UK. 1990.
• 24. Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W. Revealing noncovalent interactions. Journal of the American Chemical Society. 2010;132(18):6498-506. Available from: <URL>
• 25. Aouad MR, Messali M, Rezki N, Said MA, Lentz D, Zubaydi L, et al. Hydrophobic pocket docking, double-proton prototropic tautomerism in contradiction to single-proton transfer in thione⇔ thiol Schiff base with triazole-thione moiety: Green synthesis, XRD and DFT-analysis. Journal of Molecular Structure. 2019;1180:455-61. Available from: <URL>
• 26. Agarwal P, Bee S, Gupta A, Tandon P, Rastogi V, Mishra S, et al. Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2, 6-dichlorobenzonitrile. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2014;121:464-82. Available from: <URL>
• 27. Jacobsen H. Localized-orbital locator (LOL) profiles of chemical bonding. Canadian Journal of Chemistry. 2008;86(7):695-702. Available from: <URL>
• 28. Silvi B, Savin A. Classification of chemical bonds based on topological analysis of electron localization functions. Nature. 1994;371(6499):683-6. Available from: <URL>
• 29. Jensen F. Introduction to computational chemistry: John wiley & sons; 2017.
• 30. Cohen HD, Roothaan C. Electric dipole polarizability of atoms by the Hartree—Fock method. I. Theory for closed‐shell systems. The Journal of chemical physics. 1965;43(10):S34-S9. Available from: <URL>
• 31. Demirtaş G, Dege N, İçbudak H, Yurdakul Ö, Büyükgüngör O. Experimental and DFT Studies on Poly [di-μ 3-acesulfamato-O, O: O′; O′: O, O-di-μ-acesulfamato-O, O; N-di-μ-aqua-dicalcium (II)] Complex. Journal of Inorganic and Organometallic Polymers and Materials. 2012;22:671-9. Available from: <URL>
• 32. Evecen M, Tanak H, Tinmaz F, Dege N, İlhan İÖ. Experimental (XRD, IR and NMR) and theoretical investigations on 1-(2-nitrobenzoyl) 3, 5-bis (4-methoxyphenyl)-4, 5-dihydro-1H-pyrazole. Journal of Molecular Structure. 2016;1126:117-26. Available from: <URL>
• 33. Aihara J-i. Reduced HOMO− LUMO gap as an index of kinetic stability for polycyclic aromatic hydrocarbons. The Journal of Physical Chemistry A. 1999;103(37):7487-95. Available from: <URL>
• 34. Fuentealba P, Parr RG. Higher‐order derivatives in density‐functional theory, especially the hardness derivative∂ η/∂ N. The Journal of chemical physics. 1991;94(8):5559-64. Available from: <URL>
• 35. Mulliken RS. A new electroaffinity scale; together with data on valence states and on valence ionization potentials and electron affinities. The Journal of Chemical Physics. 1934;2(11):782-93. Available from: <URL>
• 36. Pearson RG. Hard and soft acids and bases. Journal of the American Chemical society. 1963;85(22):3533-9. Available from: <URL>
• 37. Pearson RG. Absolute electronegativity and hardness correlated with molecular orbital theory. Proceedings of the National Academy of Sciences. 1986;83(22):8440-1. Available from: <URL>
• 38. Chattaraj PK, Roy DR. Update 1 of: electrophilicity index. Chemical reviews. 2007;107(9):PR46-PR74. Available from: <URL>
• 39. Ayers PW, Parr RG. Beyond electronegativity and local hardness: Higher-order equalization criteria for determination of a ground-state electron density. The Journal of chemical physics. 2008;129(5). Available from: <URL>
• 40. Demircioğlu Z, Kaştaş ÇA, Büyükgüngör O. Theoretical analysis (NBO, NPA, Mulliken Population Method) and molecular orbital studies (hardness, chemical potential, electrophilicity and Fukui function analysis) of (E)-2-((4-hydroxy-2-methylphenylimino) methyl)-3-methoxyphenol. Journal of Molecular structure. 2015;1091:183-95. Available from: <URL>
• 41. Lee C, Yang W, Parr RG. Local softness and chemical reactivity in the molecules CO, SCN− and H2CO. Journal of Molecular Structure: Theochem. 1988;163:305-13. Available from: <URL>
• 42. Chattaraj PK, Maiti B, Sarkar U. Philicity: a unified treatment of chemical reactivity and selectivity. The Journal of Physical Chemistry A. 2003;107(25):4973-5. Available from: <URL>
• 43. Filimonov D, Lagunin A, Gloriozova T, Rudik A, Druzhilovskii D, Pogodin P, et al. Prediction of the biological activity spectra of organic compounds using the PASS online web resource. Chemistry of Heterocyclic Compounds. 2014;50:444-57. Available from: <URL>
• 44. Thomas R, Hossain M, Mary YS, Resmi K, Armaković S, Armaković SJ, et al. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations. Journal of Molecular Structure. 2018;1158:156-75. Available from: <URL>
• 45. Loch JI, Bonarek P, Polit A , Jablonski M, Czub M, Ye X, Lewinski, K. Goat beta-lactoglobulin complex with pramocaine (GLG-PRM) PDB May 25, 2020. Available from: <URL>
• 46. Sawyer L, Kontopidis G. The core lipocalin, bovine β-lactoglobulin. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology. 2000;1482(1-2):136-48. Available from: <URL>
• 47. Flower DR. The lipocalin protein family: structure and function. Biochemical journal. 1996;318(1):1-14. Available from: <URL>
• 48. Richter A, Eggenstein E, Skerra A. Anticalins: exploiting a non-Ig scaffold with hypervariable loops for the engineering of binding proteins. FEBS letters. 2014;588(2):213-8. Available from: <URL>
• 49. Gilbreth RN, Koide S. Structural insights for engineering binding proteins based on non-antibody scaffolds. Current opinion in structural biology. 2012;22(4):413-20. Available from: <URL>
• 50. Loch JI, Bonarek P, Polit A, Jabłoński M, Czub M, Ye X, et al. β-Lactoglobulin interactions with local anaesthetic drugs–Crystallographic and calorimetric studies. International journal of biological macromolecules. 2015;80:87-94. Available from: <URL>
• 51. Li H, Wang H-Y, Kang S, Silverman RB, Poulos TL. Electrostatic control of isoform selective inhibitor binding in nitric oxide synthase. Biochemistry. 2016;55(26):3702-7. Available from: <URL>
• 52. Mumit MA, Pal TK, Alam MA, Islam MA-A-A-A, Paul S, Sheikh MC. DFT studies on vibrational and electronic spectra, HOMO–LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2, 4, 5-trimethoxyphenylmethylene) hydrazinecarbodithioate. Journal of molecular structure. 2020;1220:128715. Available from: <URL>
• 53. Guerroudj AR, Boukabcha N, Benmohammed A, Dege N, Belkafouf NEH, Khelloul N, et al. Synthesis, crystal structure, vibrational spectral investigation, intermolecular interactions, chemical reactivity, NLO properties and molecular docking analysis on (E)-N-(4-nitrobenzylidene)-3-chlorobenzenamine: A combined experimental and theoretical study. Journal of Molecular Structure. 2021;1240:130589. Available from: <URL>