RNA structural dynamics as captured by molecular simulations: a comprehensive overview
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 …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
[HTML][HTML] Phosphodiester models for cleavage of nucleic acids
S Mikkola, T Lönnberg… - Beilstein journal of organic …, 2018 - beilstein-journals.org
Nucleic acids that store and transfer biological information are polymeric diesters of
phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases …
phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases …
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
A method is presented for the efficient evaluation of long-range electrostatic forces in
combined quantum mechanical and molecular mechanical (QM/MM) calculations of periodic …
combined quantum mechanical and molecular mechanical (QM/MM) calculations of periodic …
Combined QM/MM, machine learning path integral approach to compute free energy profiles and kinetic isotope effects in RNA cleavage reactions
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 …
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …
Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis
Benchmark quantum calculations of proton affinities and gas-phase basicities of molecules
relevant to biochemical processes, particularly acid/base catalysis, are presented and …
relevant to biochemical processes, particularly acid/base catalysis, are presented and …
Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …
Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight
H Lönnberg - Organic & biomolecular chemistry, 2011 - pubs.rsc.org
RNA molecules participate in many fundamental cellular processes either as a carrier of
genetic information or as a catalyst, and hence, RNA has received increasing interest both …
genetic information or as a catalyst, and hence, RNA has received increasing interest both …
Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory. 1. Parameterization
Phosphate chemistry is involved in many key biological processes, yet the underlying
mechanism often remains unclear. For theoretical analysis to effectively complement …
mechanism often remains unclear. For theoretical analysis to effectively complement …
Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer
Benchmark calculations of proton affinities and gas-phase basicities of molecules most
relevant to biological phosphoryl transfer reactions are presented and compared with …
relevant to biological phosphoryl transfer reactions are presented and compared with …
Nucleophilic attack on phosphate diesters: a density functional study of in− line reactivity in dianionic, monoanionic, and neutral systems
A density functional study of the hydrolysis reaction of phosphodiesters with a series of
attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles …
attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles …