To provide a more quantitative overview of the structural arrangements and interactions formed between the activated dinucleotides and the templating strand, we carried out additional global analyses of the trajectories. Consequently, we evaluated the percentage of Watson-Crick base pairing interactions, the conformations of the sugar rings within the activated dinucleotide and the terminal nucleotide of the primer as well as the distance between its associated 3 ′oxygen and the phosphorus atom of the adjacent nucleotide. As explained below, these structural parameters are of particular importance for the rate and fidelity of nonenzymatic RNA template copying. We first focused on the population (in %) of WC base pairing interactions near the dinucleotide binding site, with the focus on the two activated nucleotides and their partners within the templating strand. The NH• • • N hydrogen bond distance in such interactions was estimated to 2.02 Å, while NH• • • O bonds were shown to reach up to 2.17 Å . Given that crystal structures are affected by crystal packing effects and do not account for the oscillation of hydrogen bonding contacts we applied slightly more relaxed thresholds of 2.2 Å for NH• • • N distances and 2.5 Å for NH• • • O distances, to identify frames containing WC interactions for the two nucleotide pairs. In the case when all of the necessary hydrogen bonding distances were below these thresholds, given structure was counted towards the population of WC base pairing interactions. Otherwise the WC interaction was treated as absent. This analysis illustrated in Fig. demonstrates that the GpAIpG dinucleotide achieved the highest overall percentages, with 89.0% for adjacent nucleobase and 81.9% for terminal nucleobase. Similarly, the adjacent nucleotides of CpAIpC, CpAIpG and GpAIpC dinucleotides exhibited a comparably high population of the WC base pairing interactions, namely, 76.7%, 82.8% and 82.5%, respectively. However, despite the fact that the nucleobases of these three dinucleotides are involved in three WC hydrogen bonding interactions, the terminal nucleotides exhibited much lower degree of WC base pairing (24 -31%) than in the case of the parent GpAIpG system. This indicates that proper binding of the imidazole-bridged dinucleotide intermediate is in fact supported by stacking interactions. The highest degrees of stacking can be generally achieved for dinucleotides cotaining only purine nucleobases, while we showed that in the presence of pyrimidine nucleobases the dinucleotides tend to fold into O-stacked and often G-stacked structures.