Table 4.
N3–H3 bond and interatomic distances (in Å) | ||||||
N3–H3 | H3/OP2 | N3/OP2 | ||||
Methoda | MM | QM/MM | MM | QM/MM | MM | QM/MM |
System | ||||||
2n0j_wt | 1.011 | 1.034 | 1.86 | 1.84 | 2.86 | 2.87 |
2n0j_wt_K+ | 1.010 | 1.036 | 1.78 | 1.75 | 2.76 | 2.77 |
2n0j_C14+ | 1.010 | 1.047 | 1.78 | 1.65 | 2.73 | 2.66 |
Methoda | MM | QM | ||||
System | ||||||
Uracil base (reference) | 1.004 | 1.017 | ||||
Cytosine+ base (reference) | 1.003 | 1.017 |
aMethod used to perform the optimization: MM—molecular mechanics (bsc0χOL3); QM—TPSS-D3; QM/MM—TPSS-D3 in the QM part of the system and bsc0χOL3 in the MM part of the system. The reference MM and QM optimizations of isolated bases were performed in continuum solvent as implemented in AMBER (40,74) and in COSMO model (75), respectively. All other calculations (QM/MM and MM of the complete NSR) were performed in explicit SPC/E solvent.