ONIOM scheme

In addition to the studies studied by use and presented above, we will briefly present some examples from other research groups. Due to the flexibility of the ONIOM scheme, it can be used to address many different types of problems in biocatalysis. This is by no means an extensive listing, but it illustrates main types of ONIOM applications to date. 

The theoretical studies were carried out employing the ONIOM scheme developed by Morokuma and collaborators (18). This approach can be of great... 

Abstract Computations utilizing the ONIOM scheme have been used to model key... 

The study of this problem is an example of the usefulness of CS ab initio methods. It is computationally easy to repeat calculations of wavefunction, energy and all the above mentioned properties for MS solutes with an increasing number n of solvent molecules and to determine at what n value the saturation for this effect is reached. Calculations on MS systems show other interesting aspects of the problem. The n S molecules must be inserted in the solvent as a supermolecule. In fact MM descriptions or Hartree QM descriptions (without exchange) have no effect on this correction. The quality of the wavefunction seems not to be important for the correction (it is important, however, for the main calculation of the property) calculations with an ONIOM scheme [26] with the solvent molecules kept at a low HF description gives the same accurate description as the full high level QM calculations [24],... 

The performance of the cluster approach can be improved dramatically if it is combined with the recently developed ONIOM methodology43 which is an n-layered integrated molecular orbital and molecular mechanics approach. A threelayered version of the ONIOM approximation allows a quantum-mechanical study of systems which are normally considered with molecular mechanics methods to be performed. The three-layered total energy expression for the ONIOM scheme is defined as... 

To assess the reliability of the particular ONIOM scheme employed in the analysis of the aldol addition, Ojea and coworkers" considered the difference between the activation energies of the most stable transition structures 136 and 137 in the favored disolvated reaction channel (130 and 131) as a convenient parameter for the -value test proposed by Morokuma" . In this manner the error of the ONIOM(I) and ONIOM(II) extrapolations, with respect to their benchmark calculations at the B3LYP/6-31- -G //HF/6-31G level, were 0.86 and 0.60 kcalmol", respectively. When the geometry optimizations at the ONIOM(II) level were followed by single-point energy evaluations at the B3LYP/6-31-l-G level, the error was reduced to less than 0.10 kcalmoG. ... 

A new hybrid approach that promises to be very useful for the study of chemical reactions and systems containing charged species has been developed by Rega et al.145 It combines the ONIOM scheme with an ADMP approach that is shown to be significantly faster than hybrid BOMD, and because it is an atom centred approach it can treat systems with periodic boundaries and long-ranged interactions. 

In a review article, Hillier and coworkers presented preliminary results for the same reaction, using the slightly smaller Mo(EDT)2(OCHj) model. With the B3LYP method and the LANL2DZ basis set on Mo and 6-31G on the other atoms, they obtained the same reaction barrier as Webster and Hall. However, they also tried to add 478 atoms from the surrounding enzyme, treated by the semiempirical PM3 approach in a QM/QM ONIOM scheme. This reduced the activation barrier by 18 kJ mol". Given the low level of theory applied, these results should be considered with caution. 

Rega et al. [104] have proposed the QM/MM approach ADMP/ONIOM which implements the atom-centred density matrix propagation within the QM/MM ONIOM scheme of Maseras and Morokuma [105]. The ONIOM approach consists of separating the system in parts described at different levels of theory, for example a model part treated at Hartree-Fock or DFT level (QM), embedded in surroundings that will be treated at a molecular mechanics level (MM). The real system is composed of the model system and of the surrounding system, and the ONIOM energy is ... 

Figure 3 Schematics of the three-dimensional extrapolation scheme, IMOMO( G2 ). Use a G2-type method for extrapolation of correlation methods and basis sets, and the ONIOM scheme for extrapolation of the molecular size. The points represented by black circles are actually calculated values, and those represented by shaded circles are extrapolated values...

Table 4 Activation Barriers a. Energies of Reaction (in kcal mol ) and their Errors from the Pure B3LYP Benchmark for the Oxidative Addition of H2 to Pt(P(r-Bu)3)2 Calculated with Various ONIOM Schemes...

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