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A Pyranopyrimidine Derivative: Synthesis, Characterization, Hirshfeld Surface Analysis and Computational Investigation

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Abstract

A pyranopyrimidine derivative named as 10-amino-7-(2,4-diamino-6-oxidopyrimidin-1-ium-5-yl)-7H-benzo[7,8]chromeno[2,3-d]pyrimidin-9-ium-8-olate dimethylformamide acetic acid hydrate (ADCP) is synthesized by the reaction of 2-hydroxy-1-naphthaldehyde and 2,6-diaminopyrimidin-4-ol in the presence of ethanol and dimethylformamide. The synthesized compound is characterized by single crystal X-ray diffraction technique. The molecule exists as a doubly zwitterion ion and the supramolecular assembly is stabilized by N–H⋯N, N–H⋯O and O–H⋯N bonding interactions. These intermolecular interactions are further investigated and justified by Hirshfeld Surface Analysis. Void analysis is carried out in order to check the response of the crystal to an applied stress. Quantum chemical calculations are carried out at B3LYP/6-31G(d,p) electron density model for finding the interaction energies between molecular pairs.

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REFERENCES

  1. L. Weber, K. Illgen, and M. Almstetter. Discovery of new multi component reactions with combinatorial methods. Synlett, 1999, 1999(3), 366-374. https://doi.org/10.1055/s-1999-2612

    Article  Google Scholar 

  2. I. Ugi, A. Dömling, and W. Hörl. Multicomponent reactions in organic chemistry. Endeavour, 1994, 18(3), 115-122. https://doi.org/10.1016/s0160-9327(05)80086-9

    Article  CAS  Google Scholar 

  3. G. H. Posner. Multicomponent one-pot annulations forming 3 to 6 bonds. Chem. Rev., 1986, 86(5), 831-844. https://doi.org/10.1021/cr00075a007

    Article  CAS  Google Scholar 

  4. A. R. Bhat, A. H. Shalla, and R. S. Dongre. Synthesis of new annulated pyrano[2,3-d]pyrimidine derivatives using organo catalyst (DABCO) in aqueous media. J. Saudi Chem. Soc., 2017, 21, S305-S310. https://doi.org/10.1016/j.jscs.2014.03.008

    Article  CAS  Google Scholar 

  5. J. Yu and H. Wang. Green synthesis of pyrano[2,3-d]-pyrimidine derivatives in ionic liquids. Synth. Commun., 2005, 35(24), 3133-3140. https://doi.org/10.1080/00397910500282661

    Article  CAS  Google Scholar 

  6. S. Balalaie, S. Abdolmohammadi, H. R. Bijanzadeh, and A. M. Amani. Diammonium hydrogen phosphate as a versatile and efficient catalyst for the one-pot synthesis of pyrano[2,3-d]pyrimidinone derivatives in aqueous media. Mol. Divers., 2008, 12(2), 85-91. https://doi.org/10.1007/s11030-008-9079-7

    Article  CAS  PubMed  Google Scholar 

  7. M. M. Heravi, A. Ghods, F. Derikvand, K. Bakhtiari, and F. F. Bamoharram. H14[NaP5W30O110] catalyzed one-pot three-component synthesis of dihydropyrano[2,3-c]pyrazole and pyrano[2,3-d]pyrimidine derivatives. J. Iran. Chem. Soc., 2010, 7(3), 615-620. https://doi.org/10.1007/bf03246049

    Article  CAS  Google Scholar 

  8. M. Bararjanian, S. Balalaie, B. Movassag, and A. M. Amani. One-pot synthesis of pyrano[2,3-d]pyrimidinone derivatives catalyzed by L-proline in aqueous media. J. Iran. Chem. Soc., 2009, 6(2), 436-442. https://doi.org/10.1007/bf03245854

    Article  CAS  Google Scholar 

  9. M. M. Heravi, A. Ghods, K. Bakhtiari, and F. Derikvand. Zn[(L)proline]2: An efficient catalyst for the synthesis of biologically active pyrano[2,3-d]pyrimidine derivatives. Synth. Commun., 2010, 40(13), 1927-1931. https://doi.org/10.1080/00397910903174390

    Article  CAS  Google Scholar 

  10. A. A. Shestopalov, L. A. Rodinovskaya, A. M. Shestopalov, and V. P. Litvinov. One-step synthesis of substituted 4,8-dihydropyrano[3,2-b]pyran-4-ones. Russ. Chem. Bull., 2004, 53(3), 724/725. https://doi.org/10.1023/b:rucb.0000035666.05686.89

    Article  CAS  Google Scholar 

  11. G. M. Ziarani, S. Faramarzi, S. Asadi, A. Badiei, R. Bazl, and M. Amanlou. Three-component synthesis of pyrano[2,3-d]-pyrimidine dione derivatives facilitated by sulfonic acid nanoporous silica (SBA-Pr-SO3H) and their docking and urease inhibitory activity. Daru, J. Pharm. Sci., 2013, 21(1), 3. https://doi.org/10.1186/2008-2231-21-3

    Article  CAS  Google Scholar 

  12. H. H. Zoorob, M. Abou Elzahab, M. Abdel-Mogib, M. A. Ismail, and M. Abdel-Hamid. 1,3-Dimethylpyrimidoheterocycles as antibacterial agents. Arzneimittelforschung, 1997, 47(8), 958-962.

  13. A. Mobinikhaledi, N. Foroughifar, and M. A. Bodaghi Fard. Eco-friendly and efficient synthesis of pyrano[2,3-d] pyrimidinone and tetrahydrobenzo[b]pyran derivatives in water. Synth. React. Inorg., Met. Nano-Met. Chem., 2010, 40(3), 179-185. https://doi.org/10.1080/15533171003629121

    Article  CAS  Google Scholar 

  14. D. Heber, C. Heers, and U. Ravens. Positive inotropic activity of 5-amino-6-cyano-1,3-dimethyl-1,2,3,4-tetrahydropyrido [2,3-d] pyrimidine-2,4-dione in cardiac muscle from guinea-pig and man. Part 6: Compounds with positive inotropic activity. Pharmazie, 1993, 48(7), 537-541.

  15. E. M. Grivsky, S. Lee, C. W. Sigel, D. S. Duch, and C. A. Nichol. Synthesis and antitumor activity of 2,4-diamino-6-(2,5-dimethoxybenzyl)-5-methylpyrido[2,3-d]pyrimidine. J. Med. Chem., 1980, 23(3), 327-329. https://doi.org/10.1021/jm00177a025

    Article  CAS  PubMed  Google Scholar 

  16. J. Davoll, J. Clarke, and E. F. Elslager. Antimalarial substances. 26. Folate antagonists. 4. Antimalarial and antimetabolite effects of 2,4-diamino-6-[(benzyl)amino]pyrido[2,3-d]pyrimidines. J. Med. Chem., 1972, 15(8), 837-839. https://doi.org/10.1021/jm00278a009

    Article  CAS  PubMed  Google Scholar 

  17. A. H. Shamroukh, M. E. A. Zaki, E. M. H. Morsy, F. M. Abdel-Motti, and F. M. E. Abdel-Megeid. Synthesis of pyrazolo[4′,3′:5,6]pyrano[2,3-d]pyrimidine derivatives for antiviral evaluation. Arch. Pharm., 2007, 340(5), 236-243. https://doi.org/10.1002/ardp.200700005

    Article  CAS  PubMed  Google Scholar 

  18. L. R. Bennett, C. J. Blankley, R. W. Fleming, R. D. Smith, and D. K. Tessman. Antihypertensive activity of 6-arylpyrido[2,3-d]pyrimidin-7-amine derivatives. J. Med. Chem., 1981, 24(4), 382-389. https://doi.org/10.1021/jm00136a006

    Article  CAS  PubMed  Google Scholar 

  19. E. De Clercq. Potential of bromovinyldeoxyuridine in anticancer chemotherapy. Anticancer Res., 1986, 6(4), 549-556.

  20. K. S. Jain, N. Arya, N. N. Inamdar, P. B. Auti, S. A. Unawane, H. H. Puranik, M. S. Sanap, A. D. Inamke, V. J. Mahale, C. S. Prajapati, and C. J. Shishoo. The chemistry and bio-medicinal significance of pyrimidines & condensed pyrimidines. Curr. Top. Med. Chem., 2016, 16(28), 3133-3174. https://doi.org/10.2174/1568026616666160609100410

    Article  CAS  Google Scholar 

  21. G. M. Sheldrick. SHELXT - Integrated space-group and crystal-structure determination. Acta Crystallogr., Sect. A: Found. Adv., 2015, 71(1), 3-8. https://doi.org/10.1107/s2053273314026370

    Article  Google Scholar 

  22. G. M. Sheldrick. Crystal structure refinement with SHELXL. Acta Crystallogr., Sect. C: Struct. Chem., 2015, 71(1), 3-8. https://doi.org/10.1107/s2053229614024218

    Article  Google Scholar 

  23. A. L. Spek. Structure validation in chemical crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr., 2009, 65(2), 148-155. https://doi.org/10.1107/s090744490804362x

    Article  CAS  Google Scholar 

  24. L. J. Farrugia. WinGX and ORTEP for Windows: an update. J. Appl. Crystallogr., 2012, 45(4), 849-854. https://doi.org/10.1107/s0021889812029111

    Article  CAS  Google Scholar 

  25. J. Bernstein, R. E. Davis, L. Shimoni, and N.-L. Chang. Patterns in hydrogen bonding: functionality and graph set analysis in crystals. Angew. Chem., Int. Ed. Engl., 1995, 34(15), 1555-1573. https://doi.org/10.1002/anie.199515551

    Article  CAS  Google Scholar 

  26. P. R. Spackman, M. J. Turner, J. J. McKinnon, S. K. Wolff, D. J. Grimwood, D. Jayatilaka, and M. A. Spackman. CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. J. Appl. Crystallogr., 2021, 54(3), 1006-1011. https://doi.org/10.1107/s1600576721002910

    Article  CAS  Google Scholar 

  27. M. A. Spackman and D. Jayatilaka. Hirshfeld surface analysis. CrystEngComm, 2009, 11(1), 19-32. https://doi.org/10.1039/b818330a

    Article  CAS  Google Scholar 

  28. O. Simsek, M. Ashfaq, M. N. Tahir, S. Ozturk, and E. Agar. Synthesis and charaterizations of the Schiff base derived from 2-hydroxy-5-nitrobenzaldehyde alongwith Hirshfeld surface analysis and computational study. JStruct. Chem., 2023, 64(5), 942-953. https://doi.org/10.1134/s0022476623050128

    Article  CAS  Google Scholar 

  29. S. L. Rubab, A. R. Raza, B. Nisar, M. Ashfaq, Y. Altaf, R. Hussain, N. Sajjad, M. S. Akram, M. N. Tahir, M. A. Shaheen, M. F. ur Rehman, and H. M. Ali. Synthesis, crystal structure, DFT calculations, Hirshfeld surface analysis and in silico drug-target profiling of (R)-2-(2-(1,3-dioxoisoindolin-2-yl)propanamido)benzoic acid methyl ester. Molecules, 2023, 28(11), 4375. https://doi.org/10.3390/molecules28114375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. J. J. McKinnon, D. Jayatilaka, and M. A. Spackman. Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chem. Commun., 2007, (37), 3814. https://doi.org/10.1039/b704980c

    Article  Google Scholar 

  31. S. A. Al-Jibori, G. H. H. Al-Jibori, M. Ashfaq, T. Khalil, M. Laguna, C. Wagner, M. N. Tahir, and A. S. M. Al-Janabi. Synthesis, characterization, crystal structure, Hirshfeld surface analysis of Cd(II)-1, 2-benzisothiazol-3(2H)-one complexes. J. Mol. Struct., 2023, 1289, 135803. https://doi.org/10.1016/j.molstruc.2023.135803

    Article  CAS  Google Scholar 

  32. M. Haroon, M. W. Baig, T. Akhtar, M. N. Tahir, and M. Ashfaq. Relativistic two-component time dependent density functional studies and Hirshfeld surface analysis of halogenated arylidenehydrazinylthiazole derivatives. J. Mol. Struct., 2023, 1287, 135692. https://doi.org/10.1016/j.molstruc.2023.135692

    Article  CAS  Google Scholar 

  33. M. J. Turner, J. J. McKinnon, D. Jayatilaka, and M. A. Spackman. Visualisation and characterisation of voids in crystalline materials. CrystEngComm, 2011, 13(6), 1804-1813. https://doi.org/10.1039/c0ce00683a

    Article  CAS  Google Scholar 

  34. A. S. Faihan, R. H. AlShammari, M. Ashfaq, S. Muhammad, S. A. Al-Jibori, M. N. Tahir, M. R. Hatshan, A. S. Al-Janabi, and S. M. Al-Moayid. Synthesis, spectroscopic, crystallographic, quantum and molecular docking investigations of cis-4,5-diphenylimidazolidine-2-thione. J. Mol. Struct., 2023, 1286, 135633. https://doi.org/10.1016/j.molstruc.2023.135633

    Article  CAS  Google Scholar 

  35. M. N. Tahir, A. Ali, M. Khalid, M. Ashfaq, M. Naveed, S. Murtaza, I. Shafiq, M. A. Asghar, R. Orfali, and S. Perveen. Efficient synthesis of imine-carboxylic acid functionalized compounds: Single crystal, Hirshfeld surface and quantum chemical exploration. Molecules, 2023, 28(7), 2967. https://doi.org/10.3390/molecules28072967

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. M. J. Turner, S. Grabowsky, D. Jayatilaka, and M. A. Spackman. Accurate and efficient model energies for exploring intermolecular interactions in molecular crystals. J. Phys. Chem. Lett., 2014, 5(24), 4249-4255. https://doi.org/10.1021/jz502271c

    Article  CAS  PubMed  Google Scholar 

  37. A. Ali, Z. U. Din, M. Ibrahim, M. Ashfaq, S. Muhammad, D. Gull, M. N. Tahir, E. Rodrigues-Filho, A. G. Al-Sehemi, and M. Suleman. Acid catalyzed one-pot approach towards the synthesis of curcuminoid systems: unsymmetrical diarylidene cycloalkanones, exploration of their single crystals, optical and nonlinear optical properties. RSC Adv., 2023, 13(7), 4476-4494. https://doi.org/10.1039/d2ra07681k

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. A. Ali, M. Ashfaq, Z. U. Din, M. Ibrahim, M. Khalid, M. A. Assiri, A. Riaz, M. N. Tahir, E. Rodrigues-Filho, M. Imran, and A. Kuznetsov. Synthesis, structural, and intriguing electronic properties of symmetrical bis-aryl-α,β-unsaturated ketone derivatives. ACS Omega, 2022, 7(43), 39294-39309. https://doi.org/10.1021/acsomega.2c05441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to H. A. Shad, M. Haroon or M. Ashfaq.

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Text © The Author(s), 2023, published in Zhurnal Strukturnoi Khimii, 2023, Vol. 64, No. 11, 118603.https://doi.org/10.26902/JSC_id118603

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Tahir, M.N., Shad, H.A., Haroon, M. et al. A Pyranopyrimidine Derivative: Synthesis, Characterization, Hirshfeld Surface Analysis and Computational Investigation. J Struct Chem 64, 2200–2212 (2023). https://doi.org/10.1134/S0022476623110173

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