Modern phasing methods may be subdivided into: (a) ab initio approaches, which include direct methods, Patterson techniques, charge flipping, and VLD (vive la difference). These approaches do not use (but, suitably modified, some of them can) any prior information on the molecular geometry. (b) non-ab initio methods. In this category, we include molecular replacement (MR), isomorphous derivatives (SIR-MIR) and anomalous dispersion (SAD-MAD) approaches. MR exploits information on the molecular geometry (i.e. the target molecule is known to be similar to that present in another previously solved structure), SIR-MIR uses the supplementary information contained in the experimental data from one or more isomorphous structures, and SAD-MAD exploits anomalous dispersion effects (we will see that such effects simulate isomorphism). It is immediately clear that classification into ab initio and non-ab initio categories may be questionable, because it hides substantial diversities in the prior information. For example, SAD-MAD, unlike SIR-MIR, may use the native protein data only, and no prior information on the molecular geometry is necessary; apparently, this may be considered to belong to the ab initio category. MR does not use supplementary experimental data, and therefore seems not to be similar to SAD-MAD and SIR-MIR. The latter two techniques are often referred to as experimental phasing approaches, but also this appellation is questionable; indeed, the experiment does not provide phases, these are derived by treating the experimental data, as in any other phasing approach. The above considerations suggest that a more precise, even if conventional, definition for ab initio methods is necessary; in this book, they are identified as those techniques which do not use the molecular geometry as prior information and exploit only native data, without anomalous dispersion effects. We have seen in Section 12.8 that some approaches use low-level prior information, not specific to the current structure, but valid for a large range of compounds (e.g. the coordination of some heavy atoms and corresponding bond angles and distances). Also such procedures may be considered as ab initio approaches; to this category we add ARCIMBOLDO, which combines the ‘trivial’ information that a protein consists of smaller molecular fragments of known geometry (among which are α-helices) with MR. ARCIMBOLDO is summarized in Section 13.9.
Electronic structure predictions in Bi-O-S systems
