Linked-atom procedure

It is interesting to compare the possibilities and errors of different hybrid QM/MM schemes. The careful examination and comparison of link atom and LSCF techniques was performed in Ref. [128] using the CHARMM force field [114] and the AMI method [143] as a quantum chemical procedure. In the case of the link atom procedure two options were used QQ - the link atom does not interact with the MM subsystem and HQ - link atom interacts with all MM atoms. The main conclusion of this consideration is that the LSCF and the link atom schemes are of similar quality. The error in the proton affinity determination induced by these schemes is several kcal/mol. It is noteworthy that all the schemes work rather badly in description of conformational properties of n-butane. The large charge on the MM atoms in the proximity of the QM subsystem (especially on the boundary atom) cause significant errors in the proton affinity estimates for all methods (especially, in the case of the LSCF approach where the error can be of tens of kcal/mol). This is not surprising since the stability and transferability of intrabond one- and two-electron density matrix elements Eq. (19) is broken here. It proves that the simple electrostatic model is not well appropriate for these schemes and that a detailed analysis of the... 

Linked-Atom-Least-Squares Procedure. Molecular models having... 

The Linked-Atom Least-Squares (LALS) procedure (44) was used to generate molecular models of cellotetraose. The glucose residues were kept in the standard Cj conformation all bond angles cmd bond lengths were fixed at standard values (43). The constrained model of the crystal structure was optimized against both X-ray data and non-covalent interatomic interactions, as described by Smith and Arnott (44). 

For many molecular systems that are of interest in chemistry and biochemistry, one can partition the QM/MM system by cutting chemical bonds linking the QM and MM parts and then saturate the dangling bonds at the boundary of QM region by the so-called link atoms [41,43,44]. This procedure and the similar ones can be justified because of the presence of well-defined and localized chemical bonds in such molecular systems. Unfortunately, for metallic materials, the procedure is no longer valid owing to the delocalized nature of metallic bonding it becomes impractical to cut and saturate bonds. In fact, the very concept of... 

Writing electron dot diagrams for molecules or ions containing only two atoms is relatively easy. When several atoms are to be represented as being linked together by means of covalent bonds, the following procedure may be used to determine precisely the total number of electrons which must be... 

---