European Journal of Chemistry 2022, 13(2), 135-144 | doi: https://doi.org/10.5155/eurjchem.13.2.135-144.2225 | Get rights and content

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Synthesis, X-ray crystal structure, DFT, Hirshfeld surfaces, energy frameworks, and molecular docking analysis of a bicyclic ortho-aminocarbonitrile derivative


Ruchika Sharma (1) orcid , Sandeep Ashok Sankpal (2) orcid , Pradeep Jangonda Patil (3) orcid , Saminathan Murugavel (4) orcid , Sonachalam Sundramoorthy (5) orcid , Rajni Kant (6,*) orcid

(1) Chemical Crystallography Laboratory, Department of Physics, University of Jammu, Jammu Tawi-180006, India
(2) Department of Chemistry, Shivaji University, Kolhapur, Maharashtra-416004, India
(3) Department of Chemistry, Shivaji University, Kolhapur, Maharashtra-416004, India
(4) Department of Physics, Thanthai Periyar Government Institute of Technology, Vellore-632002, Tamil Nadu, India
(5) Department of Physics, Agni College of Technology OMR, Thalambur, Chennai-600130, Tamil Nadu, India
(6) Chemical Crystallography Laboratory, Department of Physics, University of Jammu, Jammu Tawi-180006, India
(*) Corresponding Author

Received: 21 Jan 2022 | Revised: 19 Feb 2022 | Accepted: 20 Feb 2022 | Published: 30 Jun 2022 | Issue Date: June 2022

Abstract


2-Amino-4-(2, 5-dimethoxyphenyl)-4a,5,6,7-tetrahydronaphthalene-1,3,3(4H)-tricarbonitrile has been synthesized and characterized by conventional spectroscopic techniques (FT-IR and 1H NMR) and the three-dimensional structure elucidated by single crystal X-ray diffraction studies (SC-XRD). It exists in monoclinic crystal system with space group P21/c and lattice parameters: a = 14.641(13) Å, b = 8.653(4) Å, c = 16.609(10) Å, β = 116.34(3)°, and Z = 4. In the crystal packing, molecules are connected through N-H···O and N-H···N intermolecular and intramolecular C-H···O interactions. The N1-H11···N2 interaction results in the formation of a dimer corresponding to R22(12) graph-set motif. The molecular structure has been theoretically optimized by using density functional theory (DFT) with the basis set B3LYP/6-311G (d,p). The optimized bond geometry shows consistency with the SC-XRD data. Besides this, the molecular electrostatic potential (MEP), Mulliken charges, and frontier molecular orbital analysis have been described. The dnorm, shape index, curvedness, crystal voids, 2D fingerprint (FP) plots, and 3D energy frameworks using Hirshfeld surface (HS) studies have also been computed and investigated. The molecular docking studies for 2-amino-4-(2, 5-dimethoxyphenyl)-4a,5,6,7-tetrahydronaphthalene-1,3,3(4H)-tricarbonitrile with DNA gyrase/lanosterol 14α-demethylase suggest that the compound may act as an active antimicrobial drug.


Keywords


Hirshfeld surface; Molecular docking; X-ray crystallography; 3D energy framework; Density functional theory; Molecular electrostatic potential

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DOI: 10.5155/eurjchem.13.2.135-144.2225

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Funding information


The University of Jammu for funding under the RUSA-2.0 project of the Government of India

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How to cite


Sharma, R.; Sankpal, S.; Patil, P.; Murugavel, S.; Sundramoorthy, S.; Kant, R. Eur. J. Chem. 2022, 13(2), 135-144. doi:10.5155/eurjchem.13.2.135-144.2225
Sharma, R.; Sankpal, S.; Patil, P.; Murugavel, S.; Sundramoorthy, S.; Kant, R. Synthesis, X-ray crystal structure, DFT, Hirshfeld surfaces, energy frameworks, and molecular docking analysis of a bicyclic ortho-aminocarbonitrile derivative. Eur. J. Chem. 2022, 13(2), 135-144. doi:10.5155/eurjchem.13.2.135-144.2225
Sharma, R., Sankpal, S., Patil, P., Murugavel, S., Sundramoorthy, S., & Kant, R. (2022). Synthesis, X-ray crystal structure, DFT, Hirshfeld surfaces, energy frameworks, and molecular docking analysis of a bicyclic ortho-aminocarbonitrile derivative. European Journal of Chemistry, 13(2), 135-144. doi:10.5155/eurjchem.13.2.135-144.2225
Sharma, Ruchika, Sandeep Ashok Sankpal, Pradeep Jangonda Patil, Saminathan Murugavel, Sonachalam Sundramoorthy, & Rajni Kant. "Synthesis, X-ray crystal structure, DFT, Hirshfeld surfaces, energy frameworks, and molecular docking analysis of a bicyclic ortho-aminocarbonitrile derivative." European Journal of Chemistry [Online], 13.2 (2022): 135-144. Web. 19 Aug. 2022
Sharma, Ruchika, Sankpal, Sandeep, Patil, Pradeep, Murugavel, Saminathan, Sundramoorthy, Sonachalam, AND Kant, Rajni. "Synthesis, X-ray crystal structure, DFT, Hirshfeld surfaces, energy frameworks, and molecular docking analysis of a bicyclic ortho-aminocarbonitrile derivative" European Journal of Chemistry [Online], Volume 13 Number 2 (30 June 2022)

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