Paper Citing NAMD - Abstract
Watanabe, Toshio; Inadomi, Yuichi; Umeda, Hiroaki; Fukuzawa, Kaori; Tanaka, Shigenori; Nakano, Tatsuya; Nagashima, Umpei
Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:1328-1337, JUN 2009
Fragment molecular orbital (FMO) and FMO-MO (MOs of the FMO) calculations with three typical fragmentations were performed for DNA molecules with various lengths up to 40 base pairs (bps) to validate the accuracy of the total energy and the interfragment interaction energy (IFIE). The respective accuracies of the FMO energies are 5.8 X 10(-5), 1.3 x 10 (4), and 5.0 x 10(-3) hartree/bp for large, medium, and small fragmentations with HF/STO-3G, all sufficiently satisfying chemical accuracy. Two iterative calculations of the FMO-MO methods gave sufficient accuracy as less than 6.6 x 10(-5) hartree/bp even with small fragmentation. The IFIE validations showed that IFIE, even with small fragmentation, has sufficient accuracy for chemical analyses. Small fragmentation is useful for the interaction analysis, not only for the hydrogen bonding interaction of base pairs but also for the stacking interaction of bases. For analyses of DNA molecules, IFIE analysis with small fragmentation is expected to be a powerful tool. Some frontier MOs of the largest model DNA examined in this study were delocalized over multiple base pairs, which well reflected the conductivity of DNA by a coherent mechanism. Such delocalized MO cannot be obtained in terms of the usual FMO calculation. This is a typical demonstration of the advantages of the FMO-MO calculation. These fundamental data for validation of the total energy and IFIE are expected to promote FMO and FMO-MO applications to biosystems related to DNA molecules.
