A Five-Coordinate Copper(II) Complex Constructed from Sterically Hindered 4-Chlorobenzoate and Benzimidazole: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT, Docking Studies and Antibacterial Activity
Abstract
:1. Introduction
2. Experimental
2.1. Materials and Physical Measurements
2.2. Crystallographic Analysis
2.3. Hirshfeld Surface Analysis
2.4. DFT Calculation
2.5. Molecular Docking Method
2.6. Antimicrobial Test
2.7. Synthesis
Synthesis of Cu(BZDH)2(4Clbz)2 (1)
3. Result and Discussion
3.1. Synthesis
3.2. Structural Description
3.3. Infrared Spectra
3.4. The UV Spectrum of the Complex
3.5. Hirshfeld Surfaces Analysis
3.6. Structural Analysis
3.6.1. Frontier Molecular Orbitals (FMOs) Analysis
3.6.2. Molecular Electrostatic Potential Analysis
3.6.3. Reactivity Parameters
- Ionization potential (I) = −EHOMO;
- Electron affinity (A) = −ELUMO;
- Chemical hardness (η) = (I − A)/2;
- Chemical potential (μ) = −(I + A)/2;
- Softness (S) = ½η;
- Electronegativity (χ) = (I + A)/2;
- Electrophilicity index (ω) = μ2 /2η.
3.7. Molecular Docking Studies
3.8. Antibacterial Test
4. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Parameters | 1 |
---|---|
Empirical formula | C28H20Cl2CuN4O4 |
Formula weight | 610.93 |
Temperature (K) | 100(3) |
Wavelength (Å) | 0.71073 |
Crystal system | Monoclinic |
Space group | P21/c |
a (Å) | 14.5042(3) |
b (Å) | 13.2293(2) |
c (Å) | 13.6286(2) |
α (º) | 90 |
β (º) | 104.816(2) |
γ(º) | 90 |
Volume (Å3) | 2528.12(8) |
Z | 4 |
Density (Mg/m3) | 1.605 |
Absorp. coeff. (mm−1) | 1.120 |
F(000) | 1244 |
Crystal size (mm3) | 0.35 × 0.25 × 0.15 |
Theta range for data collection | 2.4, 25.0 |
Index ranges | −1 7≤ h ≤ 17; −15 ≤ k ≤ 15; −16 ≤ l ≤ 16 |
Reflection collected | 71647 |
Independent reflections | 4469 [R(int) = 0.055] |
Goodness of fit on F2 | 1.13 |
Final R indices [I > 2sigma(I)] | 0.0361 |
R indices (all data) | 0.0427 |
Largest diff. peak and hole (eÅ−3) | 1.12 and −0.42 |
Atoms | 1 Bond Length (Å) |
Cu-O1 | 1.9873(18) |
Cu-O2 | 2.440(2) |
Cu-O3 | 1.9406(18) |
Cu-N1 | 2.015(2) |
Cu-N3 | 2.004(2) |
Atoms | 1 Bond Angle (º) |
O1-Cu-O2 | 58.89(7) |
O1-Cu-O3 | 167.73(7) |
O1-Cu-N1 | 91.40(8) |
O1-Cu-N3 | 89.00(8) |
O2-Cu-O3 | 108.84(7) |
O2-Cu-N1 | 96.30(8) |
O2-Cu-N3 | 96.85(8) |
O3-Cu-N1 | 90.41(9) |
O3-Cu-N3 | 92.40(8) |
N1-Cu-N3 | 164.87(9) |
Compound | D–H…A | d(D–H) | d(H…A) | d(D…A) | <(DHA) |
---|---|---|---|---|---|
1 | N2-H1…O4#I | 0.79(4) | 2.32(4) | 3.041(3) | 153(3) |
N4-H2…O4#II | 0.83(4) | 2.03(4) | 2.813(3) | 160(3) | |
C16-H16-O1 | 0.95 | 2.32 | 2.991(3) | 128 | |
C21-H21-O2#III | 0.95 | 2.30 | 2.969(4) | 127 |
Complex | I (eV) | A (eV) | η (eV) | μ (eV) | S (eV) | χ (eV) | ω (eV) |
---|---|---|---|---|---|---|---|
1 | 6.655 | 1.387 | 2.633 | −4.0214 | 0.18985 | 4.02140 | 3.07026 |
Complexes | Molecular Docking | |
---|---|---|
“Kb”/M−1 | ∆G/KJmol−1 | |
Complex 1 | 4.09 × 104 | −26.31 |
Benzimidazole | 9.54 × 102 | −17.00 |
4-Chlorobenzoic acid | 1.94 × 103 | −18.75 |
Test Organisms Compounds | Inhibition Zone Diameter (mm) (± Standard Deviation) Data Are Stated as Average Standard Deviation (N = 3) | |||
---|---|---|---|---|
S. aureus (G−) | K. pneumoniae (G+) | A. baumannii (G+) | P. aeruginosa (G+) | |
BZDH | 12.2 ± 1.3 | 0 | 9.5 ± 1.1 | 0 |
1 | 20.4 ± 0.8 | 0 | 11.0 ± 1.2 | 17.3 ± 0.3 |
Ofloxacin | 18.2 ± 0.9 | 0 | 18.0 ± 1.3 | 0 |
Amoxicillin/Clavulanate | 0 | 0 | 20.6 ± 1.2 | 0 |
Ceftazidime | 0 | 0 | 14.3 ± 1.2 | 0 |
Cefuroxime | 0 | 0 | 14.1 ± 0.2 | 0 |
Gentamicin | 12.0 ± 1.1 | 16.3 ± 1.2 | 18.5 ± 0.6 | 11 ± 0.9 |
Nitrofurantoin | NA | 25.1 ± 0.2 | 23.2 ± 1.1 | 0 |
Ciprofloxacin | NA | 18.3 ± 0.7 | 20.7 ± 1.1 | 0 |
Ampicillin | NA | 0 | 16.5 ± 0.4 | 0 |
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Ajibola, A.A.; Perveen, F.; Jan, K.; Anibijuwon, I.I.; Shaibu, S.E.; Sieroń, L.; Maniukiewicz, W. A Five-Coordinate Copper(II) Complex Constructed from Sterically Hindered 4-Chlorobenzoate and Benzimidazole: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT, Docking Studies and Antibacterial Activity. Crystals 2020, 10, 991. https://doi.org/10.3390/cryst10110991
Ajibola AA, Perveen F, Jan K, Anibijuwon II, Shaibu SE, Sieroń L, Maniukiewicz W. A Five-Coordinate Copper(II) Complex Constructed from Sterically Hindered 4-Chlorobenzoate and Benzimidazole: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT, Docking Studies and Antibacterial Activity. Crystals. 2020; 10(11):991. https://doi.org/10.3390/cryst10110991
Chicago/Turabian StyleAjibola, Abiodun A., Fouzia Perveen, Kalsoom Jan, Ibikunle I. Anibijuwon, Solomon E. Shaibu, Lesław Sieroń, and Waldemar Maniukiewicz. 2020. "A Five-Coordinate Copper(II) Complex Constructed from Sterically Hindered 4-Chlorobenzoate and Benzimidazole: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT, Docking Studies and Antibacterial Activity" Crystals 10, no. 11: 991. https://doi.org/10.3390/cryst10110991
APA StyleAjibola, A. A., Perveen, F., Jan, K., Anibijuwon, I. I., Shaibu, S. E., Sieroń, L., & Maniukiewicz, W. (2020). A Five-Coordinate Copper(II) Complex Constructed from Sterically Hindered 4-Chlorobenzoate and Benzimidazole: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT, Docking Studies and Antibacterial Activity. Crystals, 10(11), 991. https://doi.org/10.3390/cryst10110991