Fragment molecular orbital method

Fukuzawa K, Mochizuki Y, Tanaka S, Kitaura K, Nakano T. Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 2006 110 16102-10. 

Fedorov DG, Ishida T, Uebayasi M, Kitaura K (2007) The fragment molecular orbital method... 

Nagata, T, Fedorov, D. G., Kitaura, K., Gordon, M. S. [2009]. A Combined Effective Fragment Potential-Fragment Molecular Orbital Method. 1. The Energy Expression and Initial Applications, J. Chem. Phys., 131, 024101. 

Steinmann, C., Fedorov, D. G., Jensen, J. H. (2010], Effective Fragment Molecular Orbital Metliod A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods,/. Phys. Chem. A, 114,8705-8712. 

Pruitt, S. R., Steinmann, C., Jensen, J. H., Gordon, M. S. (2013]. Fully Integrated Effective Fragment Molecular Orbital Method, /. Chem. Theory Comp., 9, 2235-2249. 

Another acronym for this approach is FO (frontier orbital) theory. The acronym FMO is also used for the fragment molecular orbital method. See, for example, Fedorov, D. G. Kitaura, K. J. Phys. Chem. A 2007, 111, 6904. 

Fujimoto H, KogaN, Fukui K (1981) Coupled fragment molecular orbital method for interacting systems. J Am Chem Soc 103(25) 7452-7457... 

Fragment Molecular Orbital Method An Approximate Computational Method for Large Molecules. 

Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method. 

Fedorov, D. G., 8c Kitaura, K. (2007). Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. The Journal of Physical Chemistry A, 111, 6904-6914. 

Kistler KA, Matsika S (2009) Solvatochromic shifts of uracil and cytosine using a combined multireference configuration interaction/molecular dynamics approach and the fragment molecular orbital method. J Phys Chem A 113 12396-12403... 

Kitaura, K., Ikeo, E., Asada, T, Nakano, T, Uebayasi, M. Fragment molecular orbital method an approximate computational method for large molecules. Chem. Phys. Lett. 313, 701-706... 

Reactions in solution have been analyzed computationally using the QM/ MM method. Although the QM/MM method can treat chemical events in solution at a reasonable computational expense, it has the inherent limitation that nucleophilic participation by solvent molecules cannot be treated by the classical MM scheme. Thus, a full QM method is required to describe the hydrolysis mechanism of CH3 substrates. The fragment molecular orbital (FMO)-MD scheme,144 146 which treats the whole system in a full QM fashion, makes it possible to deal with solution reaction dynamics with a reasonable number of solvent molecules explicitly with the accuracy of the given QM level. 

The overall catalytic mechanism of Rubisco is depicted in Figure 25. After the enzyme is activated by formation of carbamate at Lys-191 the first, and sometimes the rate-limiting, step is enolisation which is followed by carboxylation or oxygenation. The reaction mechanism has been studied by Tapia and co-workers by molecular orbital methods (Andres et al., 1992 1993 Tapia and Andres, 1992 Tapia et al., 1994a). However, their calculations considered only the reacting fragments in the gas phase and therefore could not be used to deduce the catalytic effect of the enzyme. 

The orbitals of methane, CH4, and those of the related fragments CH3, CH2, and CH can be described using the molecular orbital method, as we have done for all the systems studied so far in this book. But the valence-bond approach, introduced by L. Pauling, can also be used this is perhaps the simplest way to establish an initial relationship between the electronic structures of organic and inorganic fragments. 

An important development related to the MCPs was the introduction of the model core potentials to the fragment molecular orbital (FMO) calculations [115]. The FMO/MCP method allows to carry out quantum mechanical calculations for large scale systems containing heavy metal atoms. 

This review concentrates on the fundamentals of supermolecule model chemistries for clusters of atoms/molecules held together by weak chemical forces. The principles behind the appropriate selection of theoretical method and basis set for a particular class of weak noncovalent interactions provide the foundation for understanding more complex computational schemes that might require the user to specify more than just a method and/or basis set, such as highly efficient fragmentation schemes [e.g., the effective fragment potential (EFP) method, " the fragment molecular orbital (FMO) method, the... 

Assuming that the semiempirical molecular orbital methods, such as MNDO, AMI, or PM3, should be preferable to fragmental approaches for log P calculations, Bodor and co-workers proposed an alternative method based on quantum mechanically calculated parameters,Their best model, which uses 18 independent variables (Table 11 and Eq. [27]), is the basis of a computerized version called BLOGP. 

A unique feature of the program is its ability to carry out all-electron calculations based on the Fragment Molecular Orbital (FMO) method (Fedorov and Kitaura 2007, 2009). 

Under the circumstances, a number of theoretical methods have been already developed to improve the QM/MM-MD method, e.g., the modification of the semi-empirical QM Hamiltonians [7, 52-54], the optimization of the QM/MM empirical parameters [10] and the replacement of the empirical repulsion potential functions [55]. However, these methods need the numerical values of some reasonable reference quantities to optimize the parameters for some specific molecular systems. Moreover, it is usually hard to obtain the reference experimental or computational ones in solution. It is, therefore, reasonable and plausible as a second best strategy that the closer MM solvent molecules around the QM solute should be included into the QM region to avoid the serious problems in the boundary between QM and MM regions. This is because the most serious problem is originating in the quantum-mechanical behaviors. On the basis of such strategy, we have developed the number-adaptive multiscale (NAM) QM/MM-MD [56, 57] and the QM/MM-MD method combined with the fragment molecular orbital (FMO) one, i.e., FMO-QM/MM-MD method [20]. 

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