Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials and Physical Measurements
2.2. Synthetic Procedures
2.2.1. Synthesis of Intermediates 2a–h
2.2.2. Synthesis of Target Compounds 3a–h
2.3. Crystal Structural Determination
2.4. Insecticidal Activities
2.5. Fungicidal Activities
2.6. Theoretical Calculations
2.7. Homology Modeling
2.8. Molecular Docking
3. Results and Discussion
3.1. Synthesis and Spectroscopic Properties
3.2. Crystal Structure
3.3. Quantum Chemistry Calculations of the Geometry and Electronic Structure
3.4. Molecular-Docking Stimulation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Compound | 3c |
---|---|
CCDC No. | 1878063 |
Empirical formula | C11H14N2O |
Formula weight | 190.24 |
Temperature/K | 100.00(10) |
Crystal system | monoclinic |
Space group | C2/c |
a/[Å] | 37.331(3) |
b/[Å] | 5.5684(3) |
c/[Å] | 9.3753(7) |
α/° | 90 |
β/° | 91.350(6) |
γ/° | 90 |
Volume/Å3 | 1948.4(2) |
Z | 8 |
Dc g/cm3 | 1.297 |
μ/mm−1 | 0.085 |
F(000) | 816.0 |
Crystal size/mm3 | 0.13 × 0.11 × 0.09 |
Radiation | MoKα (λ = 0.71073) |
2Θ range for data collection/° | 4.366 to 58.916 |
Index ranges | −41 ≤ h ≤ 49, −7 ≤ k ≤ 7, −9 ≤ l ≤ 12 |
Reflections collected | 7305 |
Independent reflections | 2377 [Rint = 0.0286, Rsigma = 0.0311] |
Data/restraints/parameters | 2377/0/128 |
Goodness-of-fit on F2 | 1.044 |
Final R indexes [I > = 2σ (I)] | R1 = 0.0469, wR2 = 0.1192 |
Final R indexes [all data] | R1 = 0.0542, wR2 = 0.1255 |
Largest diff. peak/hole/e Å−3 | 0.26/−0.42 |
Bond | d [Å] | Bond | d [Å] |
---|---|---|---|
O(1)–C(9) | 1.232(2) | N(1)–C(7) | 1.467(2) |
N(1)–C(9) | 1.384(2) | N(2)–C(8) | 1.454(2) |
N(1)–C(1) | 1.408(2) | C(1)–C(2) | 1.404(2) |
C(1)–C(6) | 1.399(2) | C(4)–C(5) | 1.392(2) |
C(2)–C(3) | 1.386(2) | C(3)–C(4) | 1.394(2) |
Angle | (°) | Angle | (°) |
C(9)–N(1)–C(1) | 126.9(1) | N(2)–C(9)–N(1) | 108.2(1) |
C(9)–N(1)–C(7) | 110.6(1) | C(2)–C(1)–N(1) | 122.6(1) |
C(1)–N(1)–C(7) | 121.3(1) | C(6)–C(1)–N(1) | 119.0(1) |
C(9)–N(2)–C(8) | 112.9(1) | N(1)–C(7)–C(8) | 103.3(1) |
O(1)–C(9)–N(1) | 126.0(1) | C(5)–C(4)–C(3) | 117.0(1) |
O(1)–C(9)–N(2) | 125.8(1) | N(2)–C(8)–C(7) | 102.0(1) |
D–H···A | d(D–H)/(Å) | d(H···A)/(Å) | d(D···A)/(Å) | <(DHA)/(°) |
---|---|---|---|---|
N(2)–H(2)···O(1) #1 | 0.86 | 2.08 | 2.885(2) | 155 |
C(8)–H(8B)···O(1) #2 | 0.97 | 2.56 | 3.358(2) | 139 |
C(2)–H(2A)···O(1) | 0.93 | 2.26 | 2.871(2) | 123 |
Compd. | Mortality (%) 600 mg/L | Inhibitory Rate (%) 50 mg/L | ΔE Value (ev) | |||
---|---|---|---|---|---|---|
P. xylostella | P. capsici | P. sojae | P. litchi | P. infestans | ||
3a | 0 | 77.5 | 71.1 | 38.2 | 82.1 | 0.2065 |
3b | 16.7 | 71.3 | 53.7 | 27.7 | 55.1 | 0.2010 |
3c | 20.0 | 59.6 | 26.2 | 4.9 | 49.2 | 0.1996 |
3d | 40.0 | 93.7 | 84.5 | 46.5 | 85.9 | 0.1894 |
3e | 13.3 | 60.7 | 37.3 | 19.9 | 61.6 | 0.1894 |
3f | 86.7 | 59.6 | 30.9 | 8.8 | 39.7 | 0.1946 |
3g | 30.0 | 64.1 | 34.0 | 5.4 | 40.4 | 0.1993 |
3h | 60.0 | 90.9 | 83.2 | 49.2 | 89.6 | 0.1965 |
DPMF | 23.0 | - | - | - | - | 0.2007 |
cyazofamid | - | 100 | 100 | 95 | 100 | 0.1701 |
Compound | Docking Score | Mortality (%) |
---|---|---|
3a | −8.162 | 0 |
3b | −7.314 | 16.7 |
3c | −7.350 | 20.0 |
3d | −7.713 | 40.0 |
3e | −7.231 | 13.3 |
3f | −7.576 | 86.7 |
3g | −7.763 | 30.0 |
3h | −7.912 | 60.0 |
DPMF | −6.214 | 23.0 |
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Deng, X.; Jin, C.; Xie, Y.; Gao, J.; Zhou, X. Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives. Crystals 2020, 10, 713. https://doi.org/10.3390/cryst10080713
Deng X, Jin C, Xie Y, Gao J, Zhou X. Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives. Crystals. 2020; 10(8):713. https://doi.org/10.3390/cryst10080713
Chicago/Turabian StyleDeng, Xile, Can Jin, Yong Xie, Junbo Gao, and Xiaomao Zhou. 2020. "Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives" Crystals 10, no. 8: 713. https://doi.org/10.3390/cryst10080713
APA StyleDeng, X., Jin, C., Xie, Y., Gao, J., & Zhou, X. (2020). Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives. Crystals, 10(8), 713. https://doi.org/10.3390/cryst10080713