title: 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.
authors.affiliation: Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5341, USA.
authors.forename: Lulu
authors.initials: L
authors.lastname: Huang
authors.forename: Lou
authors.initials: L
authors.lastname: Massa
authors.forename: Jerome
authors.initials: J
authors.lastname: Karle
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D012984:Software
chemical_list: D011108:Polymers; D012313:RNA; D012343:RNA, Transfer