TABLE 3.
Partial atomic charge and hydrogen bond free energy calculated for six atoms of the residue C1 and eight atoms of the residue G1 of the molecule s-PNA
| Mother atom name and residue | Hydrogen atoms names | Partial atomic charges (e) | Total bond free energy (kT) |
|---|---|---|---|
| N1′ (C1) | HT1 | 0.33 | −7.0 |
| HT2 | 0.33 | ||
| HT3 | 0.33 | ||
| O1′ (C1) | – | −0.51 | −5.1 |
| O2 (C1) | – | −0.49 | −4.8 |
| N3 (C1) | – | −0.66 | −4.4 |
| N4 (C1) | H41 | 0.37 | −3.5 |
| H42 | 0.33 | ||
| O3′ (C1) | – | −0.51 | −3.1 |
| N2 (G1) | H21 | 0.32 | −5.1 |
| H22 | 0.35 | ||
| O3′ (G1) | – | −0.51 | −4.9 |
| N3 (G1) | – | −0.74 | −4.8 |
| O6 (G1) | – | −0.51 | −4.6 |
| N7 (G1) | – | −0.60 | −4.5 |
| O1′ (G1) | – | −0.51 | −4.1 |
| N1′ (G1) | H1′ | 0.31 | −4.1 |
| N1 (G1) | H1 | 0.26 | −3.8 |
| Total ΔG | −63.8 |
The values of the free energy change were calculated using Eq. 4 and the interatomic distance distribution density found in the MD simulation that lasted 250 ns.