Model-Based Evidence Review of Ternary Self-Assembly with MD, MM/GBSA and PCA
Graphical abstract
Summary
Explicit-solvent dynamics, clustering, RDF, contacts, SASA, PCA/FEL and conditional MM/GBSA are combined to review ternary co-assembly and conformational modes. The graphical abstract links aggregation snapshots, structural metrics and conformational distributions across the assembly process. The combined results clarify aggregation paths, key contacts and representative states. The result-focused presentation supports efficient review of the main evidence and research priorities.
Computational results
Computational Results
Figure 1. Compound H (Compound A, green) ∙ Compounds I (EB, orange) and Compounder C (Composed B, red) Conformation distribution of three-membered mixing systems in aqueous solution at different time points in the molecular dynamics (MD) simulation process, showing the overall configuration of the 0 ns,10 ns、 30 ns、 50 ns、 80 ns and 100 ns time systems respectively For clarity of view the hidden water molecules and ions. Below is a local enlarged graph of the 100 ns moment of configuration, in which the yellow void represents the action of hydrogen bonds and the blue void representing the pi-π stacking action.
This figure presents the principal structures and trends in “Computational Results” and connects them to the case-level ranking and result interpretation.
Figure 2. Analysis of the structure and interactions of the Compound H, Compounds I and Compounding C triangles in the 100 ns molecular dynamics (MD) simulation. (A) Systemic RMSD as a whole changes over time; (B) System rotational radius changes overtime; (C) The radial distribution function between the solvent aromatic rings and the center of mass of the solution g (r) is only a statistical molecular pairing; (D) The number of intermolecular hydrogen bonds and π-π roles in the system varies over time. (E) Dissolved interval short-range van der Waals, SR) with static electrical Coulomb, SR interactions can change over time and (F) System solvents and surface area SASAs can change with time.
This figure presents the principal structures and trends in “Computational Results” and connects them to the case-level ranking and result interpretation.
Figure 3. Selective analysis of the components in a triangular system. A) Six molecules are distributed in a radius-to-center distribution function between compound A-Compound A, EB-EB, Compound B-Compund B, Compact A-Eb, and aromatic ring compound B. B) The number of molecularly interpolated atomic contacts between different types of molecules varies over time. C) The equilibrium phase is reduced to the average contact of "each molecule" to eliminate the effects of the different number of components.
This figure presents the principal structures and trends in “Computational Results” and connects them to the case-level ranking and result interpretation.
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| Calculation | ΔG | ΔEvdW | ΔEele | ΔGGB | ΔGsurf |
|---|---|---|---|---|---|
| Compound A vs EB+Compound B | -226.48 ± 1.32 | -462.5 ± 1.5 | -171.5 ± 1.9 | 475.3 ± 2.1 | -67.8 ± 0.2 |
| EB vs Compound A+Compound B | -402.83 ± 2.36 | -729.0 ± 3.2 | -229.4 ± 2.1 | 647.6 ± 2.9 | -92.1 ± 0.3 |
| Compound B vs Compound A+EB | -313.85 ± 1.90 | -506.9 ± 2.5 | -107.3 ± 1.1 | 357.1 ± 1.9 | -56.7 ± 0.2 |
This table consolidates the key comparisons in “Computational Results”, making differences across conditions and candidates directly reviewable.
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