Calculations ONIOM

A thorough computational study of this process has been carried out using B3LYP/ONIOM calculations.31 The rate-determining step is found to be the formation of the rhodium hydride intermediate. The barrier for this step is smaller for the minor complex than for the major one. Additional details on this study can be found at ... 

Table 2-2. 1-, 2- and 3-layered ONIOM calculations for the deprotonation energy (in kcal/mol) of NH —CnBuH — CO—NH—CH2 — CO—NH — CHnBu — COO- system using the optimized geometries by the respective methods (Reprinted with permission from Morokuma et al. [11]. Copyright 2006 American Chemical Society.)... 

In these ONIOM calculations we optimized positions of all atoms of amino acids that had at least one atom within 7 A from either iron center. 

Figure 2-6. Real and model system used in ONIOM calculations of the reaction mechanism in isopenicillin N synthase...

Figure 2-8. (A) X-ray structure of GPx dimer, (B) monomer used as die real system in ONIOM calculations, and (C) structure of the active site including two water molecules (Adapted from Prabhakar et al. [27]. Reprinted with permission. Copyright 2004 American Chemical Society.)...

Fig. 31.9 Turnover-limiting transition states for enantioselec-tive hydrogenation derived from DFT calculations, (a) ONIOM calculations, PP=Me-DUPHOS [45]. (b) Full computation on all atoms, PP = Ws-PP with a rigid Et group to simulate Bu [47], Numbers refer to the energy in kcal mol-1 of the states relative to the resting state.

Application of CBS extrapolations to the A5-ketosteroid isomerase-catalyzed conversion of A5-androstene-3,17-dione to the A4 isomer (Fig. 4.10) provides a test case for extensions to enzyme kinetics. This task requires integration of CBS extrapolations into multilayer ONIOM calculations [56, 57] of the steroid and the active site combined with a polarizable continuum model (PCM) treatment of bulk dielectric effects [58-60], The goal is to reliably predict absolute rates of enzyme-catalyzed reactions within an order of magnitude, in order to verify or disprove a proposed mechanism. 

The purpose of ONIOM is to obtain a better balance between accuracy and computational cost. We illustrate this using the 3Wa cluster. The ONIOM calculation with TD-DFT/medium in the low level takes half the computing time as the target, and has excellent results (error compared to target less than 0.05 eV). ONIOM with TD-HF/medium in the low level takes about a tenth of the CPU time relative to the target. The error with this low level is about 0.2 eV, which is much smaller than the error of 1.2 eV in a conventional TD-UF/medium calculation. 

Fig. 10 Partitioning scheme for ONIOM calculations of the "[Rh((R,R)-Me-DuPHOS)]+ +enamide" system...

Fig.6 Schematic representation of the adopted model system of HIV-1 RT binding site and bound a nevirapine [70], b 8-Cl TIBO [71], and c efavirenz [72] in ONIOM calculations...

FIGURE 19.2 Inner and outer layers used for the ONIOM calculations. Left atoms in the inner layer are shown with their atomic symbols and atoms in the outer layer are shown in a stick representation. Right the inner layer is shown with the hydrogen link atoms. 

Fig. 28.7. Models used in the ONIOM calculations. For each model, the numbered carbons denote the high-level atoms and carbon atoms directly connected to them are treated as the hydrogen link atoms in the ONIOM calculations. Oxygen atoms are not shown in the figure and are considered as high-level atoms. The bonds shown in bold represent the high-level system and the remaining bonds drawn with dotted lines are just shown to better locate the high-level system in the nanombe.

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