Table 4.

Tuning of the gHBfix potential for base pairing and its effects on the folding of r(gcGAGAgc) TL. Populations (in %) of two major conformations, i.e., the native state (with properly folded stem and loop) and all states with folded A-form stem (independent of the loop conformation), are displayed for each gHBfix combination at the reference REST2 replica (T = 298 K). See Figure S7 for the examples of most populated clusters from REST2 simulations.^a

(–NH…N–) interaction bias (kcal/mol)	(–NH…O–) interaction bias (kcal/mol)
	$\left(\begin{array}{c}\text{NH}\dots \text{O}\\ +0.0\end{array}\right)$	$\left(\begin{array}{c}\text{NH}\dots \text{O}\\ +0.5\end{array}\right)$	$\left(\begin{array}{c}\text{NH}\dots \text{O}\\ +1.0\end{array}\right)$
$\left(\begin{array}{c}\text{NH}\dots \text{N}\\ +1.0\end{array}\right)$	20.0/33.2b	40.3/72.1	0.0/5.6
$\left(\begin{array}{c}\text{NH}\dots \text{N}\\ +0.5\end{array}\right)$	5.1/6.9	9.1/26.4	22.1/53.6
$\left(\begin{array}{c}\text{NH}\dots \text{N}\\ +0.0\end{array}\right)$	0.0/0.0c	0.0/3.9	0.0/29.1

^aCluster analysis performed for the last 7 μs from the 10-μs-long trajectory at 298 K; the $\text{gHBfix}\left(\begin{array}{c}2-\text{OH}\dots \text{nbO}/\text{bO}\\ -0.5\end{array}\right)$ potential applied in all simulations.

^bThe numbers before and after “/” report population of native state with all signature interactions and all states with folded A-form stem, respectively. The first population is thus inherently included in the second.

^cREST2 simulation with the $\text{gHBfix}\left(\begin{array}{c}2-\text{OH}\dots \text{nbO}/\text{bO}\\ -0.5\end{array}\right)$ potential affecting only SPh interactions.