in silico
Phase 1: In Silico Validation
- Objective
- To computationally confirm that CB[7] encapsulation can sterically shield the oNB triplet state from O₂ quenching, predict binding modes, and estimate the reduction in k_q before any wet-lab synthesis.
- Estimated cost
- €500-2000
- Estimated duration
- 4-6 weeks
- Success criteria
- Predicted k_q(encapsulated) from MD+Smoluchowski · ≤4×10⁸ M⁻¹·s⁻¹ · (Compute from D_eff and R_eff using k_q = 4πR_eff D_eff N_A)
- Ratio D_eff/D_bulk from PMF · ≤0.10 (10-fold reduction) · (Extract D_eff from umbrella sampling PMF via Smoluchowski-Einstein relation)
- MM-PBSA binding free energy · ≤ -23 kJ/mol · (g_mmpbsa tool on last 50 ns of MD trajectory)
- Go if
- All three success criteria met: predicted k_q(encapsulated) ≤4×10⁸ M⁻¹·s⁻¹, D_eff/D_bulk ≤0.10, and ΔG_binding ≤ -23 kJ/mol.
- No-go if
- Predicted k_q(encapsulated) >6×10⁸ M⁻¹·s⁻¹ OR ΔG_binding > -15 kJ/mol (K_a < 10³ M⁻¹).
- Pivot if
- If binding pose shows oNB group partially exposed (SASA > 50% of free), test alternative cucurbituril homologues (CB[8]) in silico before proceeding.
- Risks
- Force field inaccuracies for oNB group (e.g., missing polarization effects) lead to incorrect binding pose.Probability: mediumMitigation: Cross-validate with semi-empirical PM7 calculations in MOPAC2016; re-run top 3 poses with DFT (B3LYP/6-31G*) optimization.
- Umbrella sampling convergence requires >50 windows; insufficient sampling yields noisy PMF.Probability: mediumMitigation: Use WHAM analysis with 200 bootstrap iterations; extend each window to 2 ns if autocorrelation time >500 ps.
- No suitable CB[7] crystal structure with correct protonation state (neutral at pH 7).Probability: lowMitigation: Use CB[7] from PDB 6Q3Q and manually adjust carbonyl oxygens to neutral form; validate with pKa prediction via Jaguar (Schrödinger).