Electronic structure methods ONIOM

The ONIOM method developed by Morokuma and co-workers, a well-defined hybrid method which supports any combination of electronic structure methods (Hartree-Fock, DFT, or semiempirical) and optionally molecular mechanics as well within a single calculation (the important sites within a molecule are treated with the higher accuracy electronic structure method and the remainder of the system is treated with molecular mechanics). 

The concept has been generalized in the ONIOM method to include several layers, for example using high level ab initio (e.g. CCSD(T)) in the central part, lower-level electronic structure theory (e.g. MP2) in an intermediate layer and a force field to treat the outer layer. 

Comparisons between optimized and X-ray structures were once again made by calculating root-mean-square (RMS) deviations. When comparing all heavy atoms in the protein, the total RMS deviation is approximately 1.7 A, irrespective of method for the model system or the ONIOM implementation (mechanical, ONIOM-ME, or electronic embedding, ONIOM-EE). The largest deviations occur for residues in the vicinity of the second monomer. Therefore, adding the second monomer to the model should improve the calculated geometries. 

Fig. 4. Schematic energy profiles for the intramolecular proton transfer of HPMO inside p-CD showing the relative energy of each stationary point in kcal/mol as obtained within the ONIOM method (see text). The dashed line indicates the vertical transition, (a) and (b) correspond, respectively, to the process taking place from El and E2 structures (see Fig. 5). A prime is used to denote the first electronically excited singlet state Si.

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