Rational Design of Non-Covalent Imprinted Polymers Based on the Combination of Molecular Dynamics Simulation and Quantum Mechanics Calculations
<p>Schematic of the steps involved in a typical molecular dynamics simulation for a pre-polymerisation mixture illustrated for a system based on a functional monomer (AM) and 2,4-D in chloroform: (<b>A</b>) Components added to the design. (<b>B</b>) A 5 ns production phase and the pre-polymerisation mixture after equilibration. (<b>C</b>) Statistical analysis results of the different pre-polymerisation mixtures produced.</p> "> Figure 2
<p>Atoms studied using radial distribution functions (RDFs).</p> "> Figure 3
<p>Optimised geometry of complexes; the ab initio mechanical quantum computation was based on Density Function Theory<tt> (</tt>DFT) at the Becke 3-parameter-Lee-Yang-Parr (B3LYP) level with 6-311+G** basis set.</p> "> Figure 4
<p>MESP-mapped molecular vdW surfaces of the complexes.</p> "> Figure 5
<p>Configurations of the last frames of imprinting systems P1–P3 using DMSO as the solvent. (2,4-D molecules (red); 4-VP molecules (black); TFMAA molecules (green); AM molecules (cyan); DMSO molecules (tan)).</p> "> Figure 6
<p>RDFs displaying probabilities of obtaining the atomic densities of the functional monomers at various separation distances from the 2,4-D functional groups in the imprinting systems P1–P3.</p> "> Figure 7
<p>Conformations of the last frames of the imprinting systems P4–P8 with chloroform as the solvent. (DMAEMA molecules (black); 2,4-D molecules (red); 4-VP molecules (black); AM molecules (cyan); TFMAA molecules (green); MAA molecules (green); chloroform (grey)).</p> "> Figure 8
<p>RDFs displaying probabilities of obtaining the atomic densities of the functional monomers for various separation distances from the 2,4-D functional groups in the imprinting systems P4–P8.</p> "> Figure 9
<p>Number of H–H bonds produced between the functional monomers and 2,4-D in the imprinting systems P4–P8 with chloroform as the solvent.</p> "> Figure 10
<p>Conformations of the last frame of the imprinting systems P8–P10. (2,4-D molecules (red); AM molecules (cyan); chloroform molecules (grey)).</p> "> Figure 11
<p>Number of H–H bonds produced between functional monomers and 2,4-D in the imprinting systems P8–P10.</p> ">
Abstract
:1. Introduction
2. Computational Details
2.1. QM Calculations for Characterising Template–Monomer Complexes
2.2. MD Simulations for the Characterisation of the Types and Strengths of All Pre-Polymerization Interactions
3. Results
3.1. QM Calculations for Characterising Template–Monomer Complexes
3.2. MD Simulations for Characterising the Types and Strengths of All Pre-Polymerisation Interactions
3.2.1. Validity of the Force Field and Thermostat
3.2.2. Imprinting Systems Utilising DMSO as the Solvent
3.2.3. Imprinting Systems Using Chloroform as the Solvent
3.2.4. Effect of the Ratio of the Template to Functional Monomer
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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System | Template | Functional Monomer | Solvent | Pord. (ns) |
---|---|---|---|---|
P1 | 2,4-D (30) | 4-VP (90) | DMSO (5597) | 5 |
P2 | 2,4-D (30) | TFMAA (90) | DMSO (5597) | 5 |
P3 | 2,4-D (30) | AM (90) | DMSO (5597) | 5 |
P4 | 2,4-D (30) | 4-VP (90) | Chloroform (5597) | 5 |
P5 | 2,4-D (30) | DMAEMA (90) | Chloroform (5597) | 5 |
P6 | 2,4-D (30) | MAA (90) | Chloroform (5597) | 5 |
P7 | 2,4-D (30) | TFMAA (90) | Chloroform (5597) | 5 |
P8 | 2,4-D (30) | AM (90) | Chloroform (5597) | 20 |
P9 | 2,4-D (30) | AM (120) | Chloroform (5597) | 20 |
P10 | 2,4-D (30) | AM (150) | Chloroform (5597) | 20 |
Complexes | ΔE (kcal mol−1) | ΔE (kJ mol−1) |
---|---|---|
2,4-D-MAA | −15.22735846 | −63.6808128 |
2,4-D-4-VP | −13.99844915 | −58.5415141 |
2,4-D-TFMAA | −15.06473297 | −63.000713 |
2,4-D-DMAEMA | −9.400457481 | −39.3127132 |
2,4-D-AM | −14.78296843 | −61.8223738 |
AM-AM | −11.44639108 | −47.8688072 |
2,4-D-2,4-D | −14.95939287 | −62.5601807 |
TFMAA-TFMAA | −15.44972291 | −64.6107412 |
MAA-MAA | −15.31651508 | −64.0536657 |
Complexes | ΔE (kcal mol−1) | ΔE (kJ mol−1) |
---|---|---|
2,4-D-4-VP | −13.28510834 | −55.5583229 |
2,4-D-TFMAA | −13.83121146 | −57.8421261 |
2,4-D-AM | −13.43036435 | −56.1657835 |
Molecule | Simulation Value (GAFF) | Actual Value | Error (GAFF) |
---|---|---|---|
EGDMA | 1.05966 | 1.051 | 0.82% |
4-VP | 0.974502 | 0.9800 | 0.56% |
Chloroform | 1.50788 | 1.4840 | 1.58% |
DMAEMA | 0.968347 | 0.933 | 3.65% |
2,4-D | 1.524 | 1.563 | 2.50% |
DMSO | 1.10964 | 1.1 | 0.87% |
MAA | 1.020 | 1.015 | 0.49% |
TFMAA | 1.267 | 1.326 | 4.45% |
AM | 1.089 | 1.122 | 2.94% |
Functional Monomers | Electrostatic Interactions (Eelec) | vdW Interaction (EvdW) | Total Nonbonded Interaction (Etotal) |
---|---|---|---|
4-VP | −6.05165 | −64.0863 | −70.13795 |
TFMAA | −10.4431 | −61.7837 | −72.2268 |
AM | −52.1894 | −33.9448 | −86.1342 |
Functional Monomers | Electrostatic Interactions (Eelec) | vdW Interaction (EvdW) | Total Nonbonded Interaction (Etotal) |
---|---|---|---|
4-VP | −67.6674 | −63.1676 | −130.835 |
DMAEMA | −157.803 | −98.5257 | −256.3287 |
TFMAA | −896.046 | −25.2375 | −921.2835 |
MAA | −966.629 | 14.0713 | −952.5577 |
AM | −1208.74 | −12.9599 | −1221.6999 |
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Yu, X.; Mo, J.; Yan, M.; Xin, J.; Cao, X.; Wu, J.; Wan, J. Rational Design of Non-Covalent Imprinted Polymers Based on the Combination of Molecular Dynamics Simulation and Quantum Mechanics Calculations. Polymers 2024, 16, 2257. https://doi.org/10.3390/polym16162257
Yu X, Mo J, Yan M, Xin J, Cao X, Wu J, Wan J. Rational Design of Non-Covalent Imprinted Polymers Based on the Combination of Molecular Dynamics Simulation and Quantum Mechanics Calculations. Polymers. 2024; 16(16):2257. https://doi.org/10.3390/polym16162257
Chicago/Turabian StyleYu, Xue, Jiangyang Mo, Mengxia Yan, Jianhui Xin, Xuejun Cao, Jiawen Wu, and Junfen Wan. 2024. "Rational Design of Non-Covalent Imprinted Polymers Based on the Combination of Molecular Dynamics Simulation and Quantum Mechanics Calculations" Polymers 16, no. 16: 2257. https://doi.org/10.3390/polym16162257