With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Nucleic acids that store and transfer biological information are polymeric diesters of
phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases …

We present a fast, accurate, and robust approach for determination of free energy profiles
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …

We describe the generalized weighted thermodynamic perturbation (gwTP) method for
estimating the free energy surface of an expensive “high-level” potential energy function …

Metal–organic frameworks (MOFs) have been reported to be versatile catalysts because of
their amenability to modular design and tunability. Recently, a series of zirconium-based …

A-234,[EtO–P (O)(F)–NC (Me)–N (Et) 2], is the suspected A-type nerve agent used in the
Skripal attack on the 4th of March 2018. Studies related to the structure and reactivity of this …

We perform molecular dynamics simulations, based on recent crystallographic data, on the 8–
17 DNAzyme at four states along the reaction pathway to determine the dynamical …

Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand
cleavage through 2′-O-transphosphorylation, provoking the question of whether protein …

We redevelop the variational free energy profile (vFEP) method using a cardinal B-spline
basis to extend the method for analyzing free energy surfaces (FESs) involving three or …

A new approach for performing Particle Mesh Ewald in ab initio quantum
mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis …