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Adaptive QM/MM (quantum mechanical/molecular mechanical) methods repartition molecules on-the-fly into the QM and MM regions based on a partitioning criterion. A density-based partitioning scheme offers a unique way of carrying out QM and MM assignments on the presence/absence of (non) covalent interactions between non-QM core molecules and the QM core. Here, we present two improvements to promote our density-based adaptive partitioning strategy for adaptive QM/MM calculations. First, bond formation/breaking processes between non-QM core molecules and the QM core are monitored using a density-based descriptor, to define an adaptive QM core region on the fly. Second, the density-based adaptive QM/MM partitioning scheme is made efficient enough for large systems by utilizating an adaptive search region and a Voronoi style-partitioning scheme. The adaptive search region is used to preselect the subset of molecules that may interact strongly enough with the QM core region, and then a density-based interaction calculation is only carried out on this subset. A Voronoi style-partitioning scheme achieves an efficient assignment of the density-based interactions. [ABSTRACT FROM AUTHOR]

An artificial nucleoside surrogate with 1H-imidazo[ 4,5-f][1,10]phenanthroline (P) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal-mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective AgI-mediated base pairs strongly depends on the sequence context. Quantum mechanical/ molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B-DNA duplex. [ABSTRACT FROM AUTHOR]

An artificial nucleoside surrogate with 1H-imidazo[4,5-f][1,10]phenanthroline (P) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal-mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag(I) -mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B-DNA duplex., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)