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a) CHARMM27 standard and modified nucleotide residues: b) A standard CHARMM27 ribonucleotide analog (no base) with the 2′ position protonated; c) 2′ deprotonated ribose phosphate (i.e., activated at the 2′ position); d) ribose phosphorane (i.e., intermediate/transition state model); 2′,3′-cyclic ribose phosphate (i.e., transesterification product). Color coding of atoms is as follows: carbon=turquoise, oxygen=red, phosphorous=brown, hydrogen=white.
