Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 103, Issue 5, Pages 1233-1237Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0510342103
Keywords
ab initio; Hartree-Fock; interaction energy; quantum mechanics; RNA
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Funding
- NCRR NIH HHS [RR 03037, G12 RR003037] Funding Source: Medline
- NIGMS NIH HHS [S06 GM 606654] Funding Source: Medline
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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.
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