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The Kernel Energy Method: application to a tRNA.

ABSTRACT: The Kernel Energy Method (KEM) may be used to calculate quantum mechanical molecular energy by the use of several model chemistries. Simplification is obtained by mathematically breaking a large molecule into smaller parts, called kernels. The full molecule is reassembled from calculations carried out on the kernels. KEM is as yet untested for RNA, and such a test is the purpose here. The basic kernel for RNA is a nucleotide that in general may differ from those of DNA. RNA is a single strand rather than the double helix of DNA. KEM energy has been calculated for a tRNA, whose crystal structure is known, and which contains 2,565 atoms. The energy is calculated to be E = -108,995.1668 (a.u.), in the Hartree-Fock approximation, using a limited basis. Interaction energies are found to be consistent with the hydrogen-bonding scheme previously found. In this paper, the range of biochemical molecules, susceptible of quantum studies by means of the KEM, have been broadened to include RNA.

SUBMITTER: Huang L

PROVIDER: S-EPMC1360573 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature

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The Kernel Energy Method: application to a tRNA.

Huang Lulu L Massa Lou L Karle Jerome J

Proceedings of the National Academy of Sciences of the United States of America 20060123 5

The Kernel Energy Method (KEM) may be used to calculate quantum mechanical molecular energy by the use of several model chemistries. Simplification is obtained by mathematically breaking a large molecule into smaller parts, called kernels. The full molecule is reassembled from calculations carried out on the kernels. KEM is as yet untested for RNA, and such a test is the purpose here. The basic kernel for RNA is a nucleotide that in general may differ from those of DNA. RNA is a single strand ra ...[more]

PMID: 16432197

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The Kernel Energy Method: application to a tRNA.

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The Kernel Energy Method: application to a tRNA.

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