QCRNA 1.0: a database of quantum calculations for RNA catalysis.
This work outlines a new on-line database of quantum calculations for RNA catalysis (QCRNA) available via the worldwide web at http://theory.chem.umn.edu/QCRNA. The database contains high-level density functional calculations for a large range of molecules, complexes and chemical mechanisms important to phosphoryl transfer reactions and RNA catalysis. Calculations are performed using a strict, consistent protocol such that a wealth of cross-comparisons can be made to elucidate meaningful trends in biological phosphate reactivity. Currently, around 2000 molecules have been collected in varying charge states in the gas phase and in solution. Solvation was treated with both the PCM and COSMO continuum solvation models. The data can be used to study important trends in reactivity of biological phosphates, or used as benchmark data for the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations.
Giese
Timothy J
TJ
Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA.
Gregersen
Brent A
BA
Liu
Yun
Y
Nam
Kwangho
K
Mayaan
Evelyn
E
Moser
Adam
A
Range
Kevin
K
Faza
Olalla Nieto
ON
Lopez
Carlos Silva
CS
de Lera
Angel Rodriguez
AR
Schaftenaar
Gijs
G
Lopez
Xabier
X
Lee
Tai-Sung
TS
Karypis
George
G
York
Darrin M
DM
D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D011789:Quantum Theory; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity; D013816:Thermodynamics
D016337:RNA, Catalytic