AddRemove: A new link model for use in QM/MM studies

The division of a system under study in a quantum mechanical (QM) and a classical system in QM/MM molecular mechanical calculations is sometimes very natural, but a problem arises in the case of bonds crossing the QM/MM boundary. A new link model that uses a capping (link) atom to satisfy the valences of the quantum chemical system is presented, with the position of the capping atom depending on the positions of the real atoms involved in the link bond. Using this method no degrees of freedom for the capping atom are introduced. Moreover, the introduction of this artificial atom is corrected for by subtracting the classical MM interactions with the real QM system it would have if it were a classical atom. That is, the capping atoms are added and removed. The new model has been tested on three amino acid residues and shows a clear improvement over other link models (as represented by the Integrated Molecular Orbital and Molecular Model (IMOMM)/ADF implementation). The average absolute deviation for the C-alpha-C-beta bond distance, as obtained when comparing the full QM and QM/MM results, is around 0.75 pm. The IMOMM model predicts distances for the C-alpha-C-backbone and C-alpha-N-backbone bonds, with an average absolute deviation of 2.3-2.8 and 5.3-5.5 pm, respectively; this is an increase by a factor of 3.1-4.0 and 7.1-7.3 compared with the C-alpha-C-beta bond. For the new AddRemove model, the average absolute deviations are 1.0-1.2 and 0.6-0.9 pm, respectively, for the C-alpha-C-backbone and C-alpha-N-backbone bonds; compared with the C.-C. bond, this indicates only a slight change, with a factor of 1.3-1.6 and 0.8-1.2, respectively. The new AddRemove model therefore performs much better and is shown to be a substantial improvement over the IMOMM model. (C) 2002 Wiley Periodicals, Inc.