Density-functional B3LYP

In the ONIOM(QM MM) scheme as described in Section 2.2, the protein is divided into two subsystems. The QM region (or model system ) contains the active-site selection and is treated by quantum mechanics (here most commonly the density functional B3LYP [31-34]). The MM region (referred to as the real system ) is treated with an empirical force field (here most commonly Amber 96 [35]). The real system contains the surrounding protein (or selected parts of it) and some solvent molecules. To analyze the effects of the protein on the catalytic reactions, we have in general compared the results from ONIOM QM MM models with active-site QM-only calculations. Such comparisons make it possible to isolate catalytic effects originating from e.g. the metal center itself from effects of the surrounding protein matrix. 

The calculations were performed in three steps. For each structure considered, a geometry optimization was performed using the hybrid density functional B3LYP method (21). For open shell systems unrestricted DFT was used. In this first step, a standard valence double zeta basis set (the lacvp basis set) was used. Since models including also second shell amino acid residues were used, a full geometry optimization is not possible. The second shell residues would then move in unrealistic ways. For this reason, one atom of each amino acid residue was frozen from the X-ray structure. This procedure has been found to work very well in previous studies (22,23). It might be thought that this... 

Density functional B3LYP calculation performed on [H2N(CH2)3]2SnF2 isomers of the model compound showed that the all-trans isomer is energetically preferred. However, the LUMO of the cis isomer is of lower energy than the LUMO of the former, which suggests that the fluoride attack at tin in solution leading to hexacoordinate anionic species (Section IX.B) can take place at the cis isomer971b. 

Since these interactions only rarely are discussed, we list t5q>ical results from their work in Table 4. It is seen that fairly large basis sets are needed in order to obtain results that can be considered close to converged. Moreover, the density-functional B3LYP method yields larger absolute values than does the Hartree-Fock method. Finally, the repulsion contribution amounts to only some 10-20% of the dispersion contribution. 

The structure and energy properties of the thiazole/C302 1 1 complex have been investigated in solid argon matrices using ab initio HF, MP2, and density functional B3LYP calculations at the 6-31G"" level <2001JST(560)197>. 

The electron affinities of a series of substituted quinones have been calculated using the hybrid Hartree Fock/density functional B3LYP method with a 6-311G(3d,p) basis set. The precision and accuracy plot for the Ea obtained from... 

---