. Author manuscript; available in PMC: 2008 Sep 14.

Published in final edited form as: J Am Chem Soc. 2008 Feb 14;130(10):3053–3064. doi: 10.1021/ja076529e

Table 1.

Summary of Simulations Discussed in the Present Work^a

abbreviation	Mg²⁺ ion	state	time (ns)	potential
apo-RS	absent	reactant	12.0	CHARMM
b-RS	bridging	reactant	12.0	CHARMM
c-RS	C-site	reactant	12.0	CHARMM
c-RS⁻	C-site	deprotonation reactant	12.0	CHARMM
b-ETS	bridging	early TS mimic	12.0	CHARMM
b-LTS	bridging	late TS mimic	12.0	CHARMM
c-ETS	C-site	early TS mimic	12.0	CHARMM
c-LTS	C-site	late TS mimic	12.0	CHARMM
b-ETSQM	bridging	early TS	1.0	QM/MM
b-LTSQM	bridging	late TS	1.0	QM/MM

Simulation for the full-length hammerhead differ by their initial placement of the Mg²⁺, protonation state of the 2′OH of C17, and progression along the reaction coordinate. A total of eight 12-ns simulations were performed with the all-atom CHARMM27 nucleic acid force field³², ³³ with extension to reactive intermediate models,³⁰ and two 1-ns simulations using a QM/MM potential using the AM1/d-PhoT Hamiltonian⁴³ for phosphoryl transfer. Initial Mg²⁺ placement was either in the bridging position²⁹(coordinated to the A9 and scissile phosphates) or the “C-site’’ position²⁴ (coordinating the A9 phosphate and N₇ of G10.1)