Table 2.
Selected quantities (SD in brackets) calculated for the relevant conformations along the LFEPs of IMI•DNA (between IMI and tract d[5′-CGTTGGC-3′]2, top) and DST•DNA (between DST and tract d[5′-CGATTAGC-3′]2, bottom)
| IMI•DNA | Min 1 | TS 1-2 | TS 1-3 | Min 2 | Min 3 | TS 3-4 |
|---|---|---|---|---|---|---|
| Coulomb | −8.4 (2.5) | −7.3 (2.4) | −4.8 (3.0) | −7.9 (2.4) | −2.9 (2.3) | −2.3 (1.3) |
| Van der Waals2 | −38.1 (3.4) | −37.7 (4.9) | −22.2 (3.5) | −38.0 (4.3) | −19.4 (2.4) | −6.2 (2.2) |
| # H-bonds | 0.9 (0.6) | 0.7 (0.5) | 0.5 (0.8) | 0.7 (0.5) | 0.2 (0.7) | 0.0 (0.2) |
| TΔShyd | 4.7 (9.8) | 4.7 (9.8) | 4.7 (9.8) | 4.7 (9.1) | 2.5 (9.8) | 0.2 (9.1) |
| ΔGhyd | −5.0 (10.5) | −5.0 (10.5) | −3.4 (10.5) | −5.0 (9.7) | −2.6 (10.5) | −0.2 (9.7) |
| # H2OIMI | 9.0 (1.7) | 9.1 (1.6) | 11.0 (2.3) | 8.8 (1.7) | 12.4 (2.2) | 13.4 (2.4) |
| # H2Od[5′- CGTTGGC -3′]2 | 6.6 (1.3) | 6.7 (1.1) | 7.2 (1.1) | 6.7 (1.2) | 8.9 (1.2) | 10.6 (1.0) |
| DST•DNA | Min 1 | TS 1-2 | Min 2 | TS 2-3 | Min 3 | TS 3-4 |
| Coulomb | −35.4 (5.3) | −20.6 (2.8) | −23.5 (5.6) | −20.8 (3.7) | −13.9 (5.2) | −18.2 (1.2) |
| Van der Waals2 | −75.3 (4.6) | −59.5 (4.5) | −56.1 (2.4) | −21.1 (4.0) | −12.2 (2.3) | −0.9 (2.1) |
| # H-bonds | 3.9 (1.0) | 1.7 (0.8) | 1.7 (0.8) | 1.5 (0.7) | 1.5 (0.7) | 1.0 (0.2) |
| TΔShyd | 13.1 (9.1) | 11.6 (10.6) | 9.4 (8.3) | 5.3 (11.3) | 3.3 (9.8) | 0.5 (5.4) |
| ΔGhyd | −13.9 (9.7) | −12.3 (11.3) | −9.9 (8.9) | −5.8 (12.1) | −3.4 (10.5) | −0.5 (6.3) |
| # H2ODST | 11.4 (1.9) | 16.4 (1.9) | 18.0 (1.5) | 18.9 (3.2) | 19.8 (2.5) | 22.3 (3.7) |
| # H2Od[5′-CGATTAGC-3′]2 | 5.4 (0.8) | 8.9 (1.6) | 12.5 (0.7) | 10.7 (1.1) | 12.5 (1.1) | 15.3 (1.3) |
The Coulomb and van der Waals energies are reported in Kilocalories per mole (the values of Coulomb and van der Waals interaction energies in ‘Out’ are respectively 0.1 and 0.4 kcal/mol in IMI•DNA, and 0.1, 0.1 kcal/mol in DST•DNA). These are very approximate values and they are reported here only for qualitative comparisons. The hydration entropies (times the temperature) and hydration free energies are calculated as in ref. (102) and referred to the unbound system (i.e. to the sum of the same quantities extracted from simulations of free-standing duplexes and free ligands in solution). The number of intermolecular H-bonds and the number of waters within the first hydration shells of the ligand and of DNA tracts d[5′-CGTTGGC-3′]2 (IMI) or d[5′-CGATTAGC-3′]2 (DST) are also reported.