Recent Research Developments
|Index of Recent Research News|
December 12, 2005
RNA systems are highly negatively charged
and exhibit strong interactions with solvent and metal ions.
These interactions are sensitive to electronic polarization effects,
and are attenuated by local charge. Semiempirical quantum models
that are most typically used in hybrid quantum mechanical/molecular
mechanical (QM/MM) simulations of RNA catalysis are limited in their
accuracy due to systematically poor treatment of charge-dependent
response properties, in particular polarizability. One method to
increase the reliability of these models would be to increase the size
basis set in the molecular orbital expansion; however, this techniques
would greatly increase the computational cost of the simulations by
orders of magnitude.
Recently, Professor Darrin York and
graduate student Timothy Giese have
developed a method to greatly improve the semiempirical electronic
response properties through a
density-functional expansion method called chemical potential
equalization (CPE). The method does not significantly increase
the computational cost of the calculations, and is therefore a very
attractive alternative to much more expensive ab initio methods. This
development demonstrates a considerable advance in the arsenal of
multi-scale computational models used to study highly charged reactive
systems such as those encountered in RNA catalysis.
The results have recently been published in a JCP article. These results make an important contribution toward the design of next-generation semiempirical quantum models for biological molecules that can be used in linear-scaling electronic structure and QM/MM simulations.
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Next scheduled update: January 2, 2005.
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