Computational studies ONIOM method

Despite the availability of fast computers and efficient codes for accurate quantum chemistry calculations, it is not likely in the near future that we will be able to study chemical reactions in proteins taking all the proteins atoms into quantum mechanical calculations. Hybrid methods in which different parts of large molecular systems are treated by different theoretical levels of methods are likely to play a key role in such studies for the coming decade or more. The ONIOM method we have developed is a versatile hybrid method that allows combining different quantum mechanical methods as well as molecular mechanics method in multiple layers, some features of... 

Another way of performing calculations using the cluster model is the use of a hybrid method. It is a theoretical method, which uses different approaches for different parts of the molecular system. The ONIOM method is one of the hybrid methods developed quite recently to facilitate accurate ab initio calculations of large chemical species. The ONIOM method (n-layered integrated molecular orbital and molecular mechanics approach) [29] is a multi-level extrapolation method, in which the studied molecular system is divided into two or more parts or layers. The most important part of the system from the chemical point of view (the inner part, IP) is treated at a high" level of theory (the HL method - a high level of ab initio molecular orbital method) and the rest of the system is described by a computationally less demanding method (the LL method - the lowest ab initio approximation or even semiempirical or molecular mechanic approximations) [30]. 

Although most computational studies of organotin systems employ ECPs, other methods can be used to describe tin. These methods include semi-empirical methods, all-electron relativistic methods, and hybrid energy methods, such as Morokuma s ONIOM method and hybrid quantum mechanical and molecular mechanics methods (QM/MM). 

Morokuma, K., Wang, Q., 8c Vreven, T. (2006). Performance evaluation of the three-layer ONIOM method Case study for a zwitterionic peptide. Journal of Chemical Theory and Computation, 2, 1317-1324. 

Brookes NJ et al (2009) The influence of peripheral ligand bulk on nitrogen activation by three-coordinate molybdenum complexes - a theoretical study using the ONIOM method. J Comput Chem 30 2146-2156... 

To understand the effect of the protein on this modeled reaction mechanism, we selected the first reaction step, H2O2 reduction by a glutathione molecule for further investigations using the ONIOM (QM MM) method [28], The computational setup was similar to the structural study, but the effects of the additional water molecules were added from the active-site model. It is assumed that the reaction coordinate is the same as in the active-site study and no additional reaction pathways were investigated. An important point of the present ONIOM study is the full optimization of QM MM transition states using the novel ONIOM algorithms [9],... 

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],... 

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