Free energy calculation of modified base-pair formation in explicit solvent: A predictive model

Chemical structures of the modified nucleosides. Modified uridine chemical structures: 2-thiouridine (s²U), pseudouridine (Ψ), 5-methylaminomethyluridine (mnm⁵U), 5-methoxy-carbonylmethyluridine (mcm⁵s²U), 5-oxyacetic acid uridine (cmo⁵U), and 5-methylaminomethyl-2-thiouridine (mnm⁵s²U). R represents the ribose sugar attached to the base and 5′-phosphate. The first base demonstrates the standard uracil base numbering and can be applied throughout.