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Quantum Chemical Calculations (Ab Initio & DFT), Hirshfeld Surface Analysis, Crystal Structure and Molecular Docking Study of 2-Chloro-4-(4-fluoro-phenyl)-6-isopropyl-pyrimidine-5-carboxylic Acid Methyl Ester

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Abstract

Pyrimidine derivatives are well-known nitrogen containing heterocyclic compound which play an important role in medicinal and pharmaceutical applications. The synthesized compound, 2-chloro-4-(4-fluoro-phenyl)-6-isopropyl-pyrimidine-5-carboxylic acid methyl ester has been confirmed by single crystal X-ray diffraction studies. Title compound crystallizes in monoclinic space group P21/c with a = 8.5272(11) Å, b = 17.774(2) Å, c = 10.2732(14) Å, β = 111.005(2)° and Z = 4. The number of weak but significant C–H···O, C–H···N, C–F···π and π–π interactions take part, in the stability of the crystal packing and also the quantitative contributions of these interactions towards the crystal packing are investigated by Hirshfeld surface analysis. A static disorders have been observed in isopropyl substituent group of atoms C20 and C21 due to anisotropic thermal motion. Ab-initio and Density Functional Theory (DFT) calculations have been carried out for the title molecule using RHF/6-311G and B3LYP/6-311G basis set respectively without polarization function, predicting the optimized geometry which can well reproduce structural parameters. Mullikan charge distributions conforms the role of specific atom especially the donor/acceptor groups in the intermolecular interactions. In the present study, the neutral chlorine Cl (Mullikan charge is 0.0038 and 0.0256 by RHF and B3LYP respectively) does not take part in intermolecular interaction, whereas fluorine F (Mullikan charge is −0.4358 and −0.3319 by RHF and B3LYP respectively) took active part in intermolecular interactions. The calculated HOMO and LUMO energies show that charge transfer occur in the molecule. To investigate the effect of different substituted groups on molecular conformation and hence on its pharmacology, the title compound redesigned with different halogens replacing fluorine of fluoro-phenyl ring and docked with human estrogen receptor (2IOK) and attempted to predict the best drug.

Graphical Abstract

The molecular structure of 2-chloro-4-(4-fluro-phenyl)-6-isopropyl-pyrimidine-5-carboxylic acid methyl ester has been determine, weak but significant interactions like C–H···O, C–H···F and π–π are involved in the stability of the structure and the quantitative contributions of these interactions towards the crystal packing are investigated by Hirshfeld surface analysis.

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Acknowledgments

We are thankful to CSMCRI, Bhavnagar, India for collecting intensity data of the crystal using Smart Apex –II CCD diffractometer.

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Authors and Affiliations

  1. Bhavan’s Shri I. L. Pandya Arts–Science and Smt. J. M. Shah Commerce College, Dakor, Gujarat, India

    Sahaj A. Gandhi

  2. Department of Physics, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India

    Urmila H. Patel

  3. Gujarat Arts and Science College, Ahmedabad, Gujarat, India

    Rajesh D. Modh

  4. Department of Chemistry, Saurashtra University, Rajkot, Gujarat, India

    Yogesh Naliyapara

  5. Department of Chemistry, Shree M. & N. Virani Science College, Rajkot, Gujarat, India

    Anil S. Patel

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  1. Sahaj A. Gandhi
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Correspondence to Sahaj A. Gandhi.

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Gandhi, S.A., Patel, U.H., Modh, R.D. et al. Quantum Chemical Calculations (Ab Initio & DFT), Hirshfeld Surface Analysis, Crystal Structure and Molecular Docking Study of 2-Chloro-4-(4-fluoro-phenyl)-6-isopropyl-pyrimidine-5-carboxylic Acid Methyl Ester. J Chem Crystallogr 46, 387–398 (2016). https://doi.org/10.1007/s10870-016-0668-5

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  • DOI: https://doi.org/10.1007/s10870-016-0668-5

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