The Kernel Energy Method: Application to a tRNA

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 o...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2006-01, Vol.103 (5), p.1233-1237
Main Authors: Huang, Lulu, Massa, Lou, Karle, Jerome
Format: Article
Language:English
Subjects:
Approximation
Atoms
Base Sequence
Biochemistry
Biological Sciences
Crystal structure
Crystallography, X-Ray
DNA
Hydrogen
Hydrogen Bonding
Hydrogen bonds
Models, Chemical
Models, Molecular
Models, Statistical
Models, Theoretical
Molecular Conformation
Molecular Sequence Data
Molecules
Nucleic Acid Conformation
Nucleic acids
Polymers - chemistry
Quantum theory
Ribonucleic acid
RNA
RNA - chemistry
RNA, Transfer - chemistry
Saccharomyces cerevisiae - metabolism
Software
Transfer RNA
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0510342103