The Accuracy of Total Energy and Electron Density by FMO method by way of Fragmentation format of Catechine molecule

Abstract

The fragment molecular orbital (FMO) method is one of the approximated molecular orbital (MO) method developed by Kitaura et al. In the FMO method, a target molecule is divided into small fragments and MO calculations are performed for each fragment and fragment pair to obtain the total energy and one-electron properties of entire molecule. Therefore the FMO method makes it possible to calculate the electronic structure for large molecules such as proteins, enzymes and DNAs. In the FMO method, the positions to divide bond in the fragmentaion are very important because they affect the accuracy of the obtained electronic structure. The fragmentation for proteins and DNAs can be performed routinely since the bond-dividing positions for them have been determined experimentally. For chemical species except proteins and DNAs, however, the bond-dividing position has not been revealed, yet, which is the main reason to limit the application of the FMO method. In this study, we inspects the accuracy of total energy and electron density by FMO method by way of fragmentation formats of catechine molecule, which is known of physiologically active substance. The accuracy varies with fragment formats and there is strong correlation between total energy and electron density. There exist some fragmentation formats where total energy differences are less than 10kcal/mol and they give correct electron densities. Therefore we think that there are some appropriate formats besides conventional fragmentation format.=