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Journal of Chemical Crystallography

, Volume 46, Issue 8–9, pp 371–386 | Cite as

Analysis of Intermolecular Interactions in 2,3,5 Trisubstituted Pyrazoles Derivatives: Insights into Crystal Structures, Gaussian B3LYP/6-311G (d,p), PIXELC and Hirshfeld Surface

  • Gayathri Purushothaman
  • Vijay ThiruvenkatamEmail author
Original Paper

Abstract

Two derivatives of pyrazole have been synthesized with one of the systematic substitutions made on the ortho position of the phenyl ring attached to the pyrazole moiety and characterised via single crystal X-ray diffraction. The nature of the molecules appear as planar with the hydrogen bonding features analysed quantitatively. The derivatives are geometrically optimized and studied for its molecular confirmation at the B3LYP/6-311G (d,p). The structure overlay, molecular packing and intermolecular hydrogen bonding are studied quantitatively using Hirshfeld surface and 2D fingerprint plots. In both the compounds, packing of the molecules is derived via strong O–H···N and weak C–H···O, C–H···π interactions stabilizing the packing. Further, the structure overlay between the experimental structures and the geometrically optimized structures along with frequency analysis at the quantum chemical level shows the deviation in the central pyrazole moiety and the substituted phenyl ring with the RMSD value of 0.5051 and 0.6305 Å respectively. The lattice energy is calculated for both the compounds using PIXELC module in Coulomb–London–Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions.

Graphical Abstract

Keywords

Molecular confirmation B3LYP/6-311G (d,p) PIXELC Hirshfeld surface 2D fingerprint Lattice energy 

Supplementary material

10870_2016_667_MOESM1_ESM.doc (27 kb)
Supplementary material 1 (DOC 26 kb)

References

  1. 1.
    Nauduri D, Reddy GB (1998) Antibacterials and antimycotics: part 1: synthesis and activity of 2-pyrazoline derivatives. Chem Pharm Bull (Tokyo) 46(8):1254–1260CrossRefGoogle Scholar
  2. 2.
    Azarifar D, Shaebanzadeh M (2002) Synthesis and characterization of new 3,5-dinaphthyl substituted 2-pyrazolines and study of their antimicrobial activity. Molecules 7(12):885–895CrossRefGoogle Scholar
  3. 3.
    Kuroda T, Suzuki F, Tamura T, Ohmori K, Hosoe H (1992) A novel synthesis and potent antiinflammatory activity of 4-hydroxy-2(1H)-oxo-1-phenyl-1,8-naphthyridine-3-carboxamides. J Med Chem 35:1130–1136CrossRefGoogle Scholar
  4. 4.
    Zhang C-Y, Liu X-H, Wang B-L, Wang S-H, Li Z-M (2010) Synthesis and antifungal activities of new pyrazole derivatives via 1,3-dipolar cycloaddition reaction. Chem Biol Drug Des 75(5):489–493CrossRefGoogle Scholar
  5. 5.
    Ochi T, Jobo-Magari K, Yonezawa A, Matsumori K, Fujii T (1999) Anti-inflammatory and analgesic effects of a novel pyrazole derivative. Eur J Pharmacol 365(2–3):259–266CrossRefGoogle Scholar
  6. 6.
    Chen K, Kuo SC, Hsieh MC, Mauger A, Lin CM, Hamel E, Lee KH (1997) Antitumor agents. 178. Synthesis and biological evaluation of substituted 2-aryl-1,8-naphthyridin-4(1H)-ones as antitumor agents that inhibit tubulin polymerization. J Med Chem 40(97):3049–3056CrossRefGoogle Scholar
  7. 7.
    Bilgin AA, Palaska E, Sunal R (1993) Studies on the synthesis and antidepressant activity of some 1-thiocarbamoyl-3,5-diphenyl-2-pyrazolines. Arzneimittelforschung 43(10):1041–1044Google Scholar
  8. 8.
    Cetin A, Cansiz A, Digrak M (2003) 3-Aryl-5-furylpyrazolines and their biological activities. Heteroat Chem 14(4):345–347CrossRefGoogle Scholar
  9. 9.
    Wu H, Feng JT, Lin KC, Zhang X (2012) Synthesis and herbicidal activity of substituted pyrazole isothiocyanates. Molecules 17:12187–12196CrossRefGoogle Scholar
  10. 10.
    Hashioka S, McLarnon JG, Ryu JK, Youssef AM, Abd-El-Aziz AS, Neeland EG, Klegeris A (2011) Pyrazole compound 2-MBAPA as a novel inhibitor of microglial activation and neurotoxicity in vitro and in vivo. J Alzheimers Dis 27(3):531–541Google Scholar
  11. 11.
    Malla Reddy V, Ravinder Reddy K (2010) Synthesis and antimicrobial activity of some novel 4-(1H-benz[d]imidazol-2yl)-1,3-thiazol-2-amines. Chem Pharm Bull (Tokyo) 58(7):953–956CrossRefGoogle Scholar
  12. 12.
    Govindaraju M, Mylarappa BN, Ajay Kumar K (2013) Synthesis of novel pyrazole derivatives and their efficacy as antimicrobial agents”. Int J Pharm Pharm Sci 5(4):734–737Google Scholar
  13. 13.
    Desiraju GR (1997) Designer crystals: intermolecular interactions, network structures and supramolecular synthons. Chem Commun 16:1475–1482CrossRefGoogle Scholar
  14. 14.
    Gautam STD (1999) The weak hydrogen bond in structural chemistry and biology. Oxford University Press/International Union of Crystallography, OxfordGoogle Scholar
  15. 15.
    Desiraju GR (2005) C–H···O and other weak hydrogen bonds. From crystal engineering to virtual screening. Chem Commun 24:2995–3001CrossRefGoogle Scholar
  16. 16.
    Nangia A, Desiraju GR (1999) Pseudopolymorphism: occurrences of hydrogen bonding organic solvents in molecular crystals. Chem Commun 7:605–606CrossRefGoogle Scholar
  17. 17.
    Munshi P, Row TNG (2005) Exploring the lower limit in hydrogen bonds: analysis of weak C−H···O and C−H···π interactions in substituted coumarins from charge density analysis. J Phys Chem A 109:659–672CrossRefGoogle Scholar
  18. 18.
    Shukla R, Shripanavar C, Chopra D, Sg B (2015) Quantitative analysis of intermolecular interactions in the crystal structure of 4-(2-(ethoxymethyl) phenyl)-1Hpyrazol-3-ol. Struct Chem Crystallogr Commun 1(1):1–8Google Scholar
  19. 19.
    Spackman MA, Jayatilaka D (2009) Hirshfeld surface analysis. CrystEngComm 11(1):19–32CrossRefGoogle Scholar
  20. 20.
    Montiel S (2015) Crystal structure and hirshfeld surface analysis of 1,2-bis((2-(bromomethyl)phenyl)thio)ethane and two polymorphs of 1,2-bis((2-((pyridin-2-ylthio)methyl)phenyl)thio)ethane. Mod Chem Appl 03(02):1–7CrossRefGoogle Scholar
  21. 21.
    Panini P, Mohan TP, Gangwar U, Sankolli R, Chopra D (2013) Quantitative crystal structure analysis of 1,3,4-thiadiazole derivatives. CrystEngComm 15(22):4549CrossRefGoogle Scholar
  22. 22.
    Spackman MA, McKinnon JJ (2002) Fingerprinting intermolecular interactions in molecular crystals. CrystEngComm 4(66):378CrossRefGoogle Scholar
  23. 23.
    Wolff D, Grimwood DJ, McKinnon JJ, Turner MJ, Jayatilaka MA, Spackman MA (2012) CrystalExplorer (Version 3.1). University of Western Australia, CrawleyGoogle Scholar
  24. 24.
    McKinnon JJ, Spackman MA, Mitchell AS (2004) Novel tools for visualizing and exploring intermolecular interactions in molecular crystals. Acta Crystallogr B 60(6):627–668CrossRefGoogle Scholar
  25. 25.
    Wood PA, Francis D, Marshall WG, Moggach SA, Parsons S, Pidcock E, Rohl AL (2008) A study of the high-pressure polymorphs of L-serine using ab initio structures and PIXEL calculations. CrystEngComm 10:1154–1166CrossRefGoogle Scholar
  26. 26.
    Vologzhanina AV, Korlyukov AA, Avdeeva VV, Polyakova IN, Malinina EA, Kuznetsov NT (2013) Theoretical QTAIM, ELI-D, and hirshfeld surface analysis of the Cu-(H)B interaction in [Cu2(bipy)2B10H10]. J Phys Chem A 117:13138CrossRefGoogle Scholar
  27. 27.
    Narayan B, Saraswat D, Tiwari M, Kumar A (2010) Synthesis and antimalarial evaluation of 1,3,5-trisubstituted pyrazolines. Eur J Med Chem 45(2):430–438CrossRefGoogle Scholar
  28. 28.
    Macrae CF, Bruno IJ, Chisholm JA, Edgington PR, McCabe P, Pidcock E, Rodriguez-Monge L, Taylor R, van de Streek J, Wood PA (2008) Mercury CSD 2.0 new features for the visualization and investigation of crystal structures. J Appl Crystallogr 41(2):466–470CrossRefGoogle Scholar
  29. 29.
    Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64(1):112–122CrossRefGoogle Scholar
  30. 30.
    Farrugia LJ (2012) WinGX and ORTEP for Windows: an update. J Appl Crystallogr 45(4):849–854CrossRefGoogle Scholar
  31. 31.
    Farrugia LJ (1999) WinGX suite for small-molecule single-crystal crystallography. J Appl Crystallogr 32:837–838CrossRefGoogle Scholar
  32. 32.
    Farrugia LJ (1997) ORTEP-3 for Windows—a version of ORTEP-III with a graphical user interface (GUI). J Appl Crystallogr 30(5):565CrossRefGoogle Scholar
  33. 33.
    Spek AL (2009) Structure validation in chemical crystallography. Acta Crystallogr D 65(2):148–155CrossRefGoogle Scholar
  34. 34.
    Watkin DM, Pearce L, Prout CK (1993) CAMERON—a molecular graphics package. University of Oxford, OxfordGoogle Scholar
  35. 35.
    Spackman MA, McKinnon JJ, Jayatilaka D (2008) Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm 10(4):377–388Google Scholar
  36. 36.
    Jayatilaka D, Grimwood DJ, Lee A, Lemay A, Russel AJ, Taylor C, Wolff SK, Cassam-Chenai P, Whitton A (2005) TONTO—a system for computational chemistry. The University of Western Australia, NedlandsGoogle Scholar
  37. 37.
    Negarestani A, Hashemi SM, Naseri F, Namvaran M, Mohammad S, Montazeri H (1976) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98(7):1976Google Scholar
  38. 38.
    Tokay N, Seferoğlu Z, Öğretir C, Ertan N (2008) Quantum chemical studies on the structures of some heterocyclic azo disperse dyes. ARKIVOC 15:9–20Google Scholar
  39. 39.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M (2009) Gaussian Inc., Wallingford CTGoogle Scholar
  40. 40.
  41. 41.
    Gavezzotti A (2011) Liquids and method. New J Chem 35:1360–1368CrossRefGoogle Scholar
  42. 42.
    Elahi A, Kant R (2014) Quantitative analysis of weak intermolecular interactions in coumarin-3-carboxylate derivatives. Eur Chem Bull 3(7):619–623Google Scholar
  43. 43.
    Gavezzotti A (2011) Efficient computer modeling of organic materials. The atom–atom, Coulomb–London–Pauli (AA-CLP) model for intermolecular electrostatic-polarization, dispersion and repulsion energies. New J Chem 35:1360–1368CrossRefGoogle Scholar
  44. 44.
    Allen FH, Groom CR (2014) The Cambridge Structural Database in retrospect and prospect. Angew Chem Int Ed 53:662–671CrossRefGoogle Scholar
  45. 45.
    Samuel Motherwell WD, Allen MFH (2002) Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry. Acta Crystallogr B 58:407–422CrossRefGoogle Scholar
  46. 46.
    Allen FH (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B 58:380–388CrossRefGoogle Scholar
  47. 47.
    Allen FH, Kennard O, Watson DG, Brammer L, Orpen AG (1987) Tables of bond lengths determined by X-Ray and neutron diffraction. J Chem Soc Perkin Trans 2:S1–S19CrossRefGoogle Scholar
  48. 48.
    Cremer D, Pople JA (1975) A General definition of ring puckering coordinates. J Am Chem Soc 97(6):1354–1358CrossRefGoogle Scholar
  49. 49.
    Venkatesan P, Thamotharan S, Ilangovan A, Liang H, Sundius T (2016) Crystal structure, Hirshfeld surfaces and DFT computation of NLO active (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid. Spectrochim Acta A 153:625–636CrossRefGoogle Scholar
  50. 50.
    Soman R, Sujatha S, Arunkumar C (2014) Quantitative crystal structure analysis of fluorinated porphyrins. J Fluorine Chem 163:16–22CrossRefGoogle Scholar
  51. 51.
    Seth SK, Maity GC, Kar T (2011) Structural elucidation, Hirshfeld surface analysis and quantum mechanical study of para-nitro benzylidene methyl arjunolate. J Mol Struct 1000(1–3):120–126CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Biological Engineering and PhysicsIndian Institute of Technology GandhinagarGandhinagarIndia

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