Table 3.
Parameter | Protonated Methyl Ribose |
Deprotonated Methyl Ribose |
Phosphorane Methyl Ribose |
2′,3′-cyclic Methyl Ribose |
---|---|---|---|---|
Rmin/2O2′ | 1.77 | 1.75 | 1.76 | 1.77 |
∊ O2′ | −0.1521 | −0.3236 | −0.2378 | −0.1521 |
L-J parameters for the deprotonated ribose phosphate were fit to the water binding coordination distance (1.713 Å) and the water binding coordination energy (18.4 kcal/mol) with TIP3P water (See Table 4 as well). L-J parameters for axial phosphorane oxygens (bond order ≈ 0.5) were determined by averaging between the protonated (bond order ≈ 0.0) and 2′,3′-cyclic (bond order ≈ 1.0) structures.